title: 103022-001-047_R1.fastq_MouseLiver_65_HFD.30mgpkg.Volixibat

city: Zeist

first: Lars

last: Verschuren

address: Utrechtseweg 48

department: Microbiology and Systems Biology

institute: TNO

data_processing:
Clustering and DNA sequencing were performed by GenomeScan BV (Leiden, Netherlands) using a NextSeq 500 sequencer (Illumina, San Diego, California, USA) with a single-read 75-cycle sequencing protocol with at least 15 million reads per sample.
Fastq files of the same sample (from mutiple sequence runs an/or lanes) were merged to 1 fastq-file/sample.
Reads of the fastq files were aligned to the mouse reference genome (GRCm38p4) using the Star2.5 alignment algorithm. The default mismatch rate of 2% was used (3 mismatches in a read of 150 bases). The alignment files (BAM files) were sorted and indexed with the Samtools v0.1.18 package.
Htseq-count 0.6.1p1 was used to count the read mapping frequency/gene (transcript region) resulting in count.files.
Genome_build: Genome Reference Consortium Human Build 38 patch release 7 (GRCh38.p7)
Supplementary_files_format_and_content: The count files contain the # reads mapped per gene (not normalized per sample).

source_name: mouse liver

growth_protocol: Male Ldlr-/-.Leiden mice were characterized and compared to human pathophysiology previously (Morrison et al., Hepatology Communications, 2018; Morrison et al., Frontiers Physiology, 2018) and were bred by TNO Metabolic Health Research at facilities of InnoSer Laboratories (Leiden, The Netherlands).Mice were housed in Makrolon® cages (two to four mice per cage) at approximately 21oC, with a 12-hour daily light cycle and relative humidity of 50–60%. The mice were supplied with food and tap water ad libitum, and were fed either standard chow (Ssniff R/MH, Soest, Germany) ¬or a NASH-inducing HFD (containing 45 kcal% fat from lard, 35 kcal% from carbohydrates, primarily sucrose and 20%kcal from protein; D12451, Research Diets, New Brunswick, NJ) as described previously.[41] The mice were sacrificed by carbon dioxide asphyxiation.   All experiments were performed in concordance with the Netherlands law on animal experiments, and were approved by an independent committee on animal care and experimentation (Dierexperimentencommissie Zeist, Netherlands; approval number 3682/TNO-130), in a facility accredited by the Association for Assessment and Accreditation of Laboratory Animal Care.

extract_protocol:
The mice were sacrificed at week 24 and the livers were isolated for histological evaluation of NASH parameters (as described above) [40] and lipid analysis. White adipose tissue depots were also collected and weighed. Gene expression analysis was carried out on liver tissue from eight mice in each group, selected as being representative of the group based on mean values of NASH parameters. All analyses were performed blindly.
Total RNA from 8 animals per group was extracted from snap-frozen liver tissue using the Ambion RNAqueous total RNA isolation kit (Thermo Fisher Scientific, Inc.). The RNA concentration was measured using a NanoDrop 1000 spectrophotometer (Isogen Life Science, De Meern, Netherlands). RNA quality was assessed using the 2100 Bioanalyzer (Agilent Technologies, Amstelveen, Netherlands). Samples were prepared in accordance with the manufacturer’s protocol using the NEBNext Ultra Directional RNA Library Prep Kit for Illumina (New England Biolabs, Ipswich, Massachusetts, USA). mRNA was isolated from total RNA using the NEBNext Poly(A) mRNA magnetic isolation module (New England Biolabs). cDNA synthesis was performed and used for ligation with the sequencing adapters and polymerase chain reaction (PCR) amplification of the resulting product. The quality and yield of the PCR products were consistent with the expected size distribution (300–800 base pairs). The sequences were directly aligned with the mouse reference genome (GRCm38p4) using the Star2.5 algorithm with default settings.
NEBNext Ultra Directional RNA Library Prep Kit for Illumina (New England Biolabs, Ipswich, Massachusetts, USA)

treatment_protocol: Mice (N = 75, between 16-18 weeks old) were matched by body weight and plasma cholesterol, triglyceride, and blood glucose levels were divided into five study groups, and maintained on either a chow diet (n = 10), a HFD (n = 20), or a HFD supplemented with volixibat 5, 15, or 30 mg/kg (n = 15 in each dose group) for 24 weeks.

tag: subject

tag: sampling time after initiation intervention=treatment=diet

tag: treatment

tag: tissue

value: liver


title: DC10 ex vivo, biological rep 1

status: Public on Jun 07 2019

type: SRA

city: Milano

first: Silvia

last: Gregori

state: Non-US/Canada

address: via olgettina , 58

country: Italy

institute: San Raffaele Telethon Institute for Gene Therapy (SR-TIGET),  IRCCS San Raffaele Scientific Institute.

description:
024B_DC10exVivo
ex vivo isolated DC-10

library_source: transcriptomic

data_processing:
Raw RNA sequences were trimmed using Skewer and then aligned against the human reference genome GRChv38 using STAR v2.5.3a with '--quantMode GeneCounts' option.
DESeq2 was used for calling transcripts to determine the total counts per gene and to calculate differential gene expression between samples and clustering.
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text files include absolute reads count per gene for each Sample

molecule: total RNA

organism: Homo sapiens

source_name: peripheral blood CD14+CD16+CD141+CD163+ cells from healthy donor

extract_protocol:
RNA was isolated using RNeasy Micro or RNA MiRNeasy Kit (QIAGEN, CA, USA) and 10 ng of total or poly-adenylated RNA was converted to cDNA by random primers amplification.
The library was constructed and amplified from cDNA using the Nextera DNA Library Prep Kit with unique dual adaptors (Illumina, NY USA).

treatment_protocol: Cells were washed with PBS and frozen as dried pellet

tag: selection

value: FACS-isolation based on positivity for CD14 CD16 CD141 and CD163 markers

tag: culture conditions

value: no in vitro culture


title: 103022-001-039_R1.fastq_MouseLiver_72_HFD.30mgpkg.Volixibat

country: Netherlands

organism: Mus musculus


title: 103022-001-040_R1.fastq_MouseLiver_74_HFD.30mgpkg.Volixibat


title: 103022-001-038_R1.fastq_MouseLiver_71_HFD.30mgpkg.Volixibat


title: 103022-001-035_R1.fastq_MouseLiver_66_HFD.30mgpkg.Volixibat


title: 103022-001-034_R1.fastq_MouseLiver_64_HFD.30mgpkg.Volixibat


title: WT_1_t4_rep3

city: Rehovot

first: Noa

last: Bossel Ben-Moshe

address: Hertzl Street

country: Israel

institute: Weizmann

data_processing:
The cel-seq pipeline (https://github.com/yanailab/CEL-Seq-pipeline) was used for sample demultiplexing, alignment to the genome (GRCh38), and gene counting.
Data was normalized to a library size factor. Factors were calculated by dividing the total number of reads from each sample to the median of the total number of reads across all samples.
Data was transformed to log2 scale, and minimal expression threshold was set to 2.
The three replicates of each sample were averaged, except for 3 samples we excluded due to low coverage (<100K exonic reads), and therefore for 3 samples (TLR10#1 t=4h, TLR10#2 t=0 and WT#3 t=0), only 2 replicates were averaged.
Genome_build: GRCh38
Supplementary_files_format_and_content: [*rep*txt]  the processed normalized gene count table of each replicate
[data_matrix.txt]  the average expression levels of each sample (from 3 replicates)

source_name: PBMCs

growth_protocol: Venous blood was drawn from the cubital vein of volunteers and PBMCS were isolated as described in Li et al. 2016. The cells were counted and frozen until used. A day before experiment, the cells where defrosted, suspended in medium (RPMI 1640 with L- Glutamine supplemented with 10% heat inactivated fetal bovine serum and 1mM sodium pyruvate) and plated on untreated plates. A day after, the cells were collected from the dish. To avoid cell lost, the dish was washed with medium and the remaining cells were added to the collected cells. The cells were then manually counted with trypan blue and normalized so the same amount of cells was used for each individual (1-5*10^5 cells per replicate, depends on the amount of live cells in the least concentrated sample).

extract_protocol:
At the indicated time points after infection the cells were washed with PBS, then suspended with RLT buffer (from RNeasy Mini Kit, Qiagen) + 1% β-mercaptoethanol and kept in -80°c until further extraction. RNA was then extracted with RNeasy Mini Kit (Qiagen).
RNA-seq libraries were prepared according to Cel-seq libraries protocol (Hashimshony, T. et al Genome Biology 2016) with a minor modification: the starting material was purified bulk RNA.

treatment_protocol: Salmonella strain used in this study was derived from the wild-type strain SL1344 containing GFP (pFPV25.1; Addgene). Cultures of Salmonella were grown in Luria-Bertani (LB) medium at 37°c for 16 hours and used for PBMCs infection at MOI 25 for the exposed cells, and PBS was added to the naive samples. After 30 min of internalization, the cells were washed and suspended with media containing 50 ug/ml gentamicin to eliminate Salmonella that were not internalized. The cells were incubated for the time indicated in each experiment at 37°c in 5% CO2 in non-treated cell culture plates.

tag: genotype

value: WT

tag: individual (ind name)

tag: infection

value: Salmonella enterica serovar Typhimurium

tag: time (post-infection)

value: 4 hr

tag: cell type

value: PBMCs

tag: replicate


title: 103022-001-037_R1.fastq_MouseLiver_70_HFD.30mgpkg.Volixibat


title: 103022-001-036_R1.fastq_MouseLiver_68_HFD.30mgpkg.Volixibat


title: 103022-001-031_R1.fastq_MouseLiver_58_HFD.15mgpkg.Volixibat


title: 103022-001-029_R1.fastq_MouseLiver_53_HFD.15mgpkg.Volixibat


title: 103022-001-032_R1.fastq_MouseLiver_60_HFD.15mgpkg.Volixibat


title: 103022-001-030_R1.fastq_MouseLiver_56_HFD.15mgpkg.Volixibat


title: 103022-001-028_R1.fastq_MouseLiver_52_HFD.15mgpkg.Volixibat


title: 103022-001-027_R1.fastq_MouseLiver_50_HFD.15mgpkg.Volixibat


title: 103022-001-023_R1.fastq_MouseLiver_43_HFD.5mgpkg.Volixibat


title: 103022-001-025_R1.fastq_MouseLiver_46_HFD.15mgpkg.Volixibat


title: 103022-001-022_R1.fastq_MouseLiver_41_HFD.5mgpkg.Volixibat


title: 103022-001-024_R1.fastq_MouseLiver_45_HFD.5mgpkg.Volixibat


title: 103022-001-020_R1.fastq_MouseLiver_38_HFD.5mgpkg.Volixibat


title: 103022-001-021_R1.fastq_MouseLiver_39_HFD.5mgpkg.Volixibat


title: 103022-001-019_R1.fastq_MouseLiver_36_HFD.5mgpkg.Volixibat


title: 103022-001-018_R1.fastq_MouseLiver_34_HFD.5mgpkg.Volixibat


title: 103022-001-017_R1.fastq_MouseLiver_32_HFD.5mgpkg.Volixibat


title: 103022-001-014_R1.fastq_MouseLiver_24_HFD

value: HFD


title: 103022-001-016_R1.fastq_MouseLiver_30_HFD


title: 103022-001-015_R1.fastq_MouseLiver_28_HFD


title: 103022-001-012_R1.fastq_MouseLiver_19_HFD


title: 103022-001-011_R1.fastq_MouseLiver_16_HFD


title: 103022-001-010_R1.fastq_MouseLiver_13_HFD


title: 103022-001-007_R1.fastq_MouseLiver_9_Chow

value: Chow


title: 103022-001-013_R1.fastq_MouseLiver_22_HFD


title: 103022-001-006_R1.fastq_MouseLiver_8_Chow


title: 103022-001-003_R1.fastq_MouseLiver_4_Chow


title: 103022-001-004_R1.fastq_MouseLiver_6_Chow


title: 103022-001-008_R1.fastq_MouseLiver_10_Chow


title: 103022-001-009_R1.fastq_MouseLiver_11_HFD


title: 103022-001-005_R1.fastq_MouseLiver_7_Chow


title: 103022-001-026_R1.fastq_MouseLiver_48_HFD.15mgpkg.Volixibat


title: 103022-001-001_R1.fastq_MouseLiver_2_Chow


title: INPUT_H3K4me3_Ankrd31ko_1

city: Montpellier cedex 5

first: Julie

middle: A. J.

last: Clement

address: 141, rue de la Cardonille

department: IGH

country: France

institute: CNRS

description: Input DNA for the ChIP-seq of the Ankrd31KO mouse, replicate 1

library_source: genomic

data_processing:
Base-calling was performed  using CASAVA
ChIPseq reads were aligned to the mm10 genome using Bowtie2 (for H3K4me3) or BWA and its modified algorithm proposed in Khil et al., 2012  (for DMC1). The mouse mm10 genome was redindexed after removing the chrY part of the pseudoautosomal region to avoid multimapping over this homologous region.
Reads that were unmapped or duplicated were filtered out in each experiment.
Peaks were called using MACS2
IDR method was used to deal with replicates for H3K4me3 and DMC1 peaks. Final peaksets were built from merged replicates, according to the IDR method.
Genome_build: mm10
Supplementary_files_format_and_content: bigwig were built from merged replicates after alignment step for DMC1 and H3K4me3 experiments.bigwig for each replicates are also provided for DMC1 experiment.

molecule: genomic DNA

source_name: Mouse testis

extract_protocol:
Cell suspension was prepared by filtering homogenized tissue, then lysed.Lysates were sonicated and chromatin complexes were isolated with appropriate antibody.
Standard library construction was performed with the Illumina Trueseq protocol (Illumina, IP-202-9001DOC). For DMC1 experiment, an additional step of kinetic enrichment was performed as described in Khil et al. 2012.
ChIP-seq for H3K4me3 CHIPseq experiment ; SSDS method described in Khil et al. 2012 for DMC1 ChIPseq

tag: strain

value: Ankrd31 tm1Atot

tag: Sex

value: male

value: whole-testis

tag: age

value: 13 days post-partum

tag: chip antibody

value: none (input)


title: INPUT_H3K4me3_Ankrd31ko_2

description: Input DNA for the ChIP-seq of the Ankrd31KO mouse, replicate 2


title: INPUT_H3K4me3_Ankrd31wt_2

description: Input DNA for the ChIP-seq of the B6 mouse, replicate 2


title: 103022-001-002_R1.fastq_MouseLiver_3_Chow


title: CHIP_H3K4me3_Ankrd31ko_2

description: H3K4me3 ChIP-seq of the Ankrd31KO mouse, replicate 2

value: Abcam, rabbit polyclonal antibody anti-H3K4me3, ab8580


title: INPUT_H3K4me3_Ankrd31wt_1

description: Input DNA for the ChIP-seq of the B6 mouse, replicate 1


title: CHIP_H3K4me3_Ankrd31ko_1

description: H3K4me3 ChIP-seq of the Ankrd31KO mouse, replicate 1


title: CHIP_H3K4me3_Ankrd31wt_2

description: H3K4me3 ChIP-seq of the B6 mouse, replicate 2


title: ESC_HIRAKO2_RNA-seq_rep1

city: Dallas

first: Laura

last: Banaszynski

state: TX

address: 5323 Harry Hines Blvd

department: Green Center for Reproductive Biology Sciences

country: USA

institute: UT Southwestern Medical Center

data_processing:
The RNA-seq reads were aligned to the mm10 mouse reference genome using TopHat aligner.
Mapped reads were further converted to “bigWig” files counting reads in non-overlapping 200-bp windows across the genome using BEDTools for presentation as genome browser tracks  (Quinlan et al, 2010).
The seqeunce length was 34 for R1 and 34 for R2 for paired-end data.
Genome_build: mm10
Supplementary_files_format_and_content: bigWig

molecule: polyA RNA

source_name: Embryonic stem cells

growth_protocol: ESCs were cultured under standard conditions (KO-DMEM, 2 mM Glutamax, 15% ES grade fetal bovine serum, 0.1 mM 2-mercaptoethanol, and leukemia inhibitory factor (LIF)). For early passages, cells were maintained on an irradiated feeder layer. To remove feeders, cells were passaged at least two passages off of feeders onto gelatin-coated plates.

extract_protocol:
RNA was extracted using a Qiagen RNeasy kit.
Libraries were constructed according to the Illumina Tru-seq protocol.

tag: genotype/variation

value: Hira KO


title: ESC_HIRAWT2_RNA-seq_rep1 (ctrl for HIRA KO2)


title: ESC_HIRAWT2_RNA-seq_rep2 (ctrl for HIRA KO2)


title: ESC_HIRAKO2_RNA-seq_rep2


title: ESC_HIRAKO1_RNA-seq_rep2


title: ESC_HIRAWT1_RNA-seq_rep1 (ctrl for HIRA KO1)


title: ESC_H33WT_H3K27ac_AuroraBi

data_processing:
The ChIP-seq reads were aligned to the mm10 mouse reference genome using the Bowtie software package (Langmead et al, 2009) .
Mapped reads were further converted to “bigWig” files counting reads in non-overlapping 200-bp windows across the genome using BEDTools for presentation as genome browser tracks  (Quinlan et al, 2010).
The seqeunce length was 33 for R1 and 33 for R2 for paired-end data.
Genome_build: mm10
Supplementary_files_format_and_content: bigWig

extract_protocol:
Native ChIP was performed as described (Goldberg et al. 2010). Briefly, ESCs were harvested and treated with Mnase, resulting in a population consisting mainly of mono- to trinucleosomes. Crosslinking ChIP was performed as described (Goldberg et al. 2010). Briefly, cell were harvested and crosslinked in 1% PFA. Chromatin was then sheared to 200-700 bp. For both procedures, chromatin was isolated and used for ChIP according to standard procedures.
Libraries were constructed according to the Illumina Tru-seq protocol.

treatment_protocol: mESCs were cultured for 2 days, then the media was replace with fresh media containing DMSO, 10 uM SB 218078 (Chk1 inhibitor) or 10 uM ZM 447439 (Aurora B inhibitor) for 4hs.

tag: strain/background

value: wild type

value: H3K27ac (39133, Active Motif)

tag: ChIP

value: native

value: mESCs were treated with 10 uM ZM 447439 (Aurora B inhibitor) for 4hs


title: ESC_HIRAWT1_RNA-seq_rep2 (ctrl for HIRA KO1)

value: WT


title: ESC_H33WT_H3K27ac_Chk1i

tag: treatment

value: mESCs were treated with 10 uM SB 218078 (Chk1 inhibitor) for 4hs


title: ESC_H33WT_H33S31P_Chk1i


title: ESC_H33WT_H3K27ac_DMSO (ctrl for Chk1i/AuroraBi)

value: mESCs were treated with DMSO for 4hs


title: ESC_H33WT_H33S31P_DMSO (ctrl for Chk1i)


title: ESC_H33WT_H33S31P


title: ESC_H33KO_H3K18ac

value: H3.3 KO


title: ESC_H33WT_H3K18ac (ctrl for H33 KO)


title: EB_H33KO_ATAC

data_processing:
The ATAC-seq reads were aligned to the mm10 mouse reference genome using the BWA aligner (Li and Durbin, 2010) .
Mapped reads were further converted to “bigWig” files counting reads in non-overlapping 200-bp windows across the genome using BEDTools for presentation as genome browser tracks  (Quinlan et al, 2010).
The seqeunce length was 33 for R1 and 33 for R2 for paired-end data.
Genome_build: mm10
Supplementary_files_format_and_content: bigWig

source_name: embryonic stem cells

extract_protocol:
Samples were prepared according to the Illumina Nextera protocol
Libraries were constructed according to the Illumina Nextera protocol.

treatment_protocol: To form embryoid bodies, mESCs were dissociated into single cell suspension, resuspended in differentiation medium (DMEM, 15% FBS, 1x MEM-NEAA, 1x Penicillin-Streptomycin, 50 μM β-mercaptoethanol) and seeded in hanging drops. After day 3 the embryoid bodies were transferred in differentiation medium to low attachment dishes in a shaking incubator and analyzed at day 4.

tag: genotype/variaton

value: embryoid bodies


title: EB_H33KO_RNA-seq_rep1

description:
PolyA RNA
Embryoid Bodies differentiation for 4 days.

data_processing:
The RNA-seq reads were aligned to the mm10 mouse reference genome using TopHat aligner.
Mapped reads were further converted to “bigWig” files counting reads in non-overlapping 200-bp windows across the genome using BEDTools for presentation as genome browser tracks (Quinlan et al., 2010).
The sequence length was 34 for R1 and 34 for R2 for paired-end data.
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: bigWig

source_name: Embryoid Bodies

extract_protocol:
RNA was extracted using a Qiagen RNeasy kit.
Libraries were constructed according to the Illumina TruSeq protocol.

treatment_protocol: To form embryoid bodies, mESCs were dissociated into single cell suspension, resuspended in differentiation medium (DMEM, 15% FBS, 1x MEM-NEAA, 1x Penicillin-Streptomycin, 50 μM β-mercaptoethanol) and seeded in hanging drops. After day 3, the embryoid bodies were transferred in differentiation medium to low attachment dishes in a shaking incubator and analyzed at day 4.

value: Embryoid Bodies


title: EB_H33KO_RNA-seq_rep2


title: EB_H33WT_ATAC (ctrl for H33 KO)


title: CHIP_H3K4me3_Ankrd31wt_1

description: H3K4me3 ChIP-seq of the B6 mouse, replicate 1

tag: tissue


title: EB_H33WT_RNA-seq_rep2 (ctl for H3.3 KO)


title: ESC_H33WT_RNA-seq_rep1 (ctl for H3.3 KO)

description: PolyA RNA

value: Embryonic stem cells


title: ESC_H33KO_RNA-seq_rep2

description: PolyA RNA


title: ESC_H33WT_RNA-seq_rep2 (ctl for H3.3 KO)

description: PolyA RNA


title: EB_H33WT_RNA-seq_rep1 (ctl for H3.3 KO)


title: ESC_H33KO_RNA-seq_rep1

description: PolyA RNA


title: ESC_DAXXKO_Input_H33

data_processing:
The ChIP-seq reads were aligned to the mm10 mouse reference genome using the Bowtie software package (Langmead et al., 2009).
Mapped reads were further converted to “bigWig” files counting reads in non-overlapping 200-bp windows across the genome using BEDTools for presentation as genome browser tracks (Quinlan et al., 2010).
The sequence length was 33 for R1 and 33 for R2 for paired-end data.
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: bigWig

extract_protocol:
Native ChIP was performed as described (Goldberg et al. 2010). Briefly, ESCs were harvested and treated with MNase, resulting in a population consisting mainly of mono- to trinucleosomes. Crosslinking ChIP was performed as described (Goldberg et al. 2010). Briefly, cells were harvested and crosslinked in 1% PFA. Chromatin was then sheared to 200-700 bp. For both procedures, chromatin was isolated and used for ChIP according to standard procedures.
Libraries were constructed according to the Illumina TruSeq protocol.

value: DAXX KO

tag: chip type

value: crosslink


title: ESC_HIRAKO1_RNA-seq_rep1


title: ESC_ATRXDAXXWT_Input_H33 (ctrl for ATRX & DAXX KO)


title: ESC_ATRXKO_Input_H33

value: ATRX KO


title: ESC_H33KO_Input_p300


title: ESC_ATRXDAXXWT_H33 (ctrl for ATRX & DAXX KO)


title: ESC_DAXXKO_H33


title: ESC_H33WT_Input_p300 (ctrl for H33 KO)


title: ESC_H33WT_p300 (ctrl for H33 KO)

value: p300 (sc-584, Santa Cruz)


title: ESC_ATRXKO_H33


title: EB_H33KO_H33_H3K27ac

description: Embryoid Bodies differentiation for 4 days.


title: EB_H33KO_S31E_H3K27ac


title: EB_H33KO_H32_H3K27ac


title: EB_H33KO_H3K27ac


title: EB_H33WT_H3K27ac (ctrl for addback)


title: EB_H33KO_S31A_H3K27ac


title: EB_H33KO_Input


title: EB_H33WT_Input (ctrl for H33 KO)


title: EB_H33KO_H3K27ac_rep2


title: EB_H33KO_H3K27ac_rep1


title: ESC_HIRAKO2_Input

value: HIRA KO


title: ESC_HIRAWT2_Input (ctrl for HIRA KO4)


title: ESC_HIRAWT2_H3K27ac (ctrl for HIRA KO4)


title: ESC_HIRAKO2_H3K27ac


title: EB_H33WT_H3K27ac_rep2 (ctrl for H33 KO)


title: ESC_DAXXKO_Input


title: ESC_ATRXDAXXWT_Input (ctrl for ATRX & DAXX KO)


title: ESC_ATRXKO_Input


title: ESC_H33KO_p300


title: ESC_ATRXKO_H3K27ac


title: ESC_DAXXKO_H3K27ac


title: ESC_HIRAKO_Input


title: ESC_HIRAKO_H3K27ac


title: ESC_H33KO_H3K122ac


title: ESC_HIRAWT_H3K27ac (ctrl for HIRA KO)


title: ESC_H33KO_H3K4me1_rep2

value: H3K4me1 (ab8895, Abcam)


title: ESC_H33WT_H3K122ac (ctrl for H33 KO)


title: ESC_H33WT_H3K64ac (ctrl for H33 KO)

value: H3K64ac (ABE1057, Millipore)


title: ESC_H33WT_H3K4me1_rep2 (ctrl for H33 KO)


title: EB_H33WT_H3K27ac_rep1 (ctrl for H33 KO)

value: H3K27ac (39133, Active Motif)


title: ESC_H33KO_H3K64ac

value: native


title: ESC_H33WT_H3K4me1_rep1 (ctrl for H33 KO)


title: ESC_H33KO_H3K4me1_rep1


title: ESC_H33WT_H3K27ac_mAb (ctrl for H33 KO)

value: H3K27ac (39685, Active Motif)


title: ESC_H33KO_H3K27ac_pAb


title: ESC_H33WT_H3K27ac_pAb (ctrl for H33 KO)

value: WT


title: ESC_H33KO_H3K27ac_mAb


title: ESC_H33WT_Input (ctrl for H33 KO)


title: ESC_H33KO_Input


title: ESC_H33WT_ATAC (ctl for H3.3 KO)

data_processing:
The ATAC-seq reads were aligned to the mm10 mouse reference genome using the BWA aligner (Li and Durbin, 2010).
Mapped reads were further converted to “bigWig” files counting reads in non-overlapping 200-bp windows across the genome using BEDTools for presentation as genome browser tracks (Quinlan et al., 2010).
The sequence length was 33 for R1 and 33 for R2 for paired-end data.
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: bigWig

extract_protocol:
Samples were prepared according to the Illumina Nextera protocol.
Libraries were constructed according to the Illumina Nextera protocol.


title: ESC_ATRXDAXXWT_H3K27ac (ctrl for ATRX & DAXX KO)


title: ESC_HIRAWT_Input (ctrl for HIRA KO)


title: ESC_HIRAKO1_ATAC

value: Hira KO


title: ESC_HIRAWT_ATAC (ctl for HIRA KO1)


title: WT_2_t4_rep1

tag: genotype

value: Salmonella enterica serovar Typhimurium

value: 4 hr

value: PBMCs


title: WT_3_t0_rep1

tag: individual (ind name)

value: control

value: 0 hr


title: GF gBT-I rep2

city: Clayton

first: Moshe

last: Olshansky

state: Vic

address: 19 Innovation Walk (Bldg 76)

department: Microbiology

country: Australia

institute: Monash University

description:
counts.txt
GF_2

data_processing:
Basecalls performed using CASAVA
Paired end reads were aligned to mm10 genome using tophat with –b2-very-sensitive and default options otherwise.
Only pairs where both reads had a MapQ >= 10 were kept and duplicates were removed using MarkDuplicates from picard tools.
Reads were assigned to gene by featureCounts from subread bioconductor R package using RefSeq annotation
Genes which did not have at least 3 counts in every file of at least one condition were removed from further analysis
Differential expression analysis was done using edgeR bioconductor package with batch effect. Genes with adjusted p-value of less than 0.05 and |logFC| > 1 were deemed Differentially Expressed.
Genome_build: mm10
Supplementary_files_format_and_content: tab delimited file containing the raw counts where rows are genes and columns are samples

source_name: gBT-I

growth_protocol: total splenocytes from tg gBT-I SPF mice were activated with gB498-505 peptide and LPS in vitro and split and provided with IL-1 on d2 and d3. Activated gBT-I were transferred into SPF and GF mice on d4 intravenously.

extract_protocol:
splenic gBT-I were enriched and sorted on d7 post transfer and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: in vitro activated tg CD8+ T cells, d7 post transfer

tag: donor strain

value: gBT-I tg

tag: recipient strain

value: GF C57BL/6

value: spleen


title: gBT-I Ctrl rep1

description:
counts.csv
BR1

data_processing:
Basecalls performed using CASAVA
Paired end reads were aligned to mm10 genome using tophat with –b2-very-sensitive and default options otherwise.
Only pairs where both reads had a MapQ >= 10 were kept and duplicates were removed using MarkDuplicates from picard tools.
Reads were assigned to gene by featureCounts from subread bioconductor R package using RefSeq annotation
Genes which did not have at least 5 counts in every file of at least one condition were removed from further analysis
Differential expression analysis was done using edgeR bioconductor package with batch (mouse) effect. Genes with adjusted p-value of less than 0.05 and |logFC| > 1 were deemed Differentially Expressed.
Genome_build: mm10
Supplementary_files_format_and_content: CSV file containing raw counts. Rows are genes and columns are samples.

growth_protocol: total splenocytes from tg gBT-I SPF mice were activated with gB498-505 peptide and LPS in vitro and split and provided with IL-2 on d2,  d3, d4, and d5. Cells were harvested on d6 post activation.

extract_protocol:
in vitro activated gBT-I were harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: cell type

value: tg CD8+ T cells

tag: activation

value: in vitro activation, d6


title: GF gBT-I rep1

description:
counts.txt
GF_1


title: gBT-I + Butyrate rep2

description:
counts.csv
BR4

value: in vitro activation, butyrate treatment starting d3, d6

tag: strain


title: gBT-I Ctrl rep3

description:
counts.csv
BR5


title: gBT-I + Butyrate rep1

description:
counts.csv
BR2


title: gBT-I Ctrl rep2

description:
counts.csv
BR3


title: SPF gBT-I rep1

description:
counts.txt
B6_1

value: SPF C57BL/6


title: pHL8042/EM1084-3_seed

city: Pullman

first: Li

last: Tian

state: WA

address: Clark hall, IBC, Washington State University

department: IBC

institute: Washington State University

description:
RNA sequencing
Expression File-Tudor-SN mutant vs WT

data_processing:
RNA-seq reads were trimmed and mapped to the rice genome database (http://rice.plantbiology.msu.edu/index.shtml) using the CLC genomics workbench (Qiagen)
Genome_build: mapped to rice genome database (http://rice.plantbiology.msu.edu/index.shtml)
Supplementary_files_format_and_content: Excel file, including information of Total counts, RPKM, TPM and CPM

organism: Oryza sativa

source_name: Rice developing seeds

growth_protocol: Wild type, mutant lines and transgenic were grown in walk-in growth chambers with a diurnal cycle of 12 h light/12 h dark at 27oC.

extract_protocol:
Total RNA samples of wild type, EM1084 and pHL8042/EM1084 were extracted from the dehulled 10-14 days old developing seeds using Plant RNA Reagent (Invitrogen, www.invitrogen.com)
RNA-seq libraries were constructed using a ScriptSeqTM v2 RNA-Seq Library Preparation Kit (Illumina) following the manufacturer's instructions

value: Seed

tag: Stage

value: 10-14 days after flowering

value: WT-OsTSN complemented transgenic of EM1084


title: pHL8042/EM1084-2_seed


title: pHL8042/EM1084-1_seed


title: EM1084-3_seed

value: Tudor-SN mutant E503K


title: ESC_H33KO_ATAC

value: H3.3 KO

value: Embryonic stem cells


title: EM1084-1_seed


title: EM1084-2_seed


title: gBT-I + Butyrate rep3

description:
counts.csv
BR6


title: CHIP_DMC1_Ankrd31ko_1

description: DMC1-SSDS of the Ankrd31KO mouse, replicate 1

value: Ankrd31 tm1Atot

tag: Sex

value: male

value: whole-testis

tag: age

value: adult

value: Santa Cruz, goat polyclonal anti-DMC1, C-20, lot #D2215


title: CHIP_DMC1_Ankrd31wt_2

description: DMC1-SSDS of the B6 mouse, replicate 2

tag: chip antibody


title: WT-1_seed

value: wild type


title: WT-2_seed


title: CHIP_DMC1_Ankrd31ko_2

description: DMC1-SSDS of the Ankrd31KO mouse, replicate 2


title: CHIP_DMC1_Ankrd31wt_1

description: DMC1-SSDS of the B6 mouse, replicate 1


title: WT-3_seed


title: Input DNA

city: Bethesda

first: Kevin

last: Brick

state: MD

address: 5/205 Memorial Drive

department: GBB

institute: NIDDK

description: PWD wild-type; Input DNA

data_processing:
H3K4me3 ChIP-Seq data were aligned to the reference mm10 genome using bwa 0.7.12 (Li 2013). H3K4me3 ChIP-Seq data were aligned to the reference mm10 genome using bwa 0.7.12 (Li 2013). Aligned BAM files were converted to BED files with bedtools (Quinlan and Hall 2010) and duplicate reads were discarded. NCIS (Liang and Keleş 2012) was used to determine the background correction ratio (rBG). MACS 2.1.0.20150731 (Zhang et al. 2008) was used with the following arguments to call peaks: --ratio {rBG} -g mm --bw 1000 --keep-dup all --slocal 5000 -t {ChIP bed file} -c {input bed file}.
genome build: mm10
processed data files format and content: For each SSDS experiment, the associated BAM file contains all paired end ssDNA reads identified for that sample. Custom BAM tags describe properties of each read pair used for ssDNA detection: it : ITR length uh : microhomology length os : microhomology offset mm : # mismatches DSB hotspots are provided in bedgraph format for each DMC1 SSDS sample. Background corrected hotspot strength is listed in the fourth column. A bedgraph file is provided for H3K4me3 ChIP-Seq peaks. This contains the mm10 coordinates of each H3K4me3 peak. Column 4 is peak strength.

source_name: Testis

extract_protocol:
For H3K4me3 ChIP-Seq, nuclei were isolated from cells using hypotonic lysis. Chromatin was fragmented by MNase digestion. After high speed spin soluble chromatin was removed and used for ChIP.
For H3K4me3 ChIP-Seq, libraries were prepared for sequencing using Bio Scientific's NEXTflex ChIP-Seq Kit (protocol version V11.11) without size selection. Amplification of the libraries was done with 20 µL ligation product, 16 ul water, 12 µL NEXTflex ChIP PCR master mix, 2 µL NEXTflex ChIP primer mix and 14-18 cycles of PCR.

value: PWD/Ph

value: 13-15 days post-partum

value: wild-type

tag: antibody

tag: sequencing technique

value: ChIP-Seq


title: H3K4me3 ChIP-seq wt

description: PWD wild-type; H3K4me3 ChIP-Seq

value: Millipore/EMD 07-473


title: B6_wt_DMC1 SSDS

description: B6 wild-type DMC1 SSDS

data_processing: For DMC1-SSDS samples, samples were aligned to the mm10 reference genome, peak calling was performed, and hotspot strength was calculated as described in (Brick et al. 2018).

extract_protocol:
For DMC1 SSDS, testicular samples were obtained frozen and were directly thawed in 1% paraformaldehyde and gently dissociated. Genomic DNA for whole genome sequencing was extracted from the testicular samples before fixation with the DNeasy Blood and Tissue kit (Qiagen).
DMC1 ChIP was performed as described previously (Smagulova et al., 2011; Khil et al., 2012; Brick et al., 2012) with minor modifications.  Sequencing libraries for anti-DMC1 were prepared following the method described in (Khil et al., 2012).
Single Stranded DNA Sequencing (SSDS)

value: Adult

value: Testis

value: Anti-DMC1 Santa Cruz (C-20, sc 8973)

value: ChIP-Single Stranded DNA Sequencing (SSDS)


title: PWD Prdm9ko DMC1 SSDS (B)

description: PWD Prdm9 knockout; DMC1 SSDS; Sample B

data_processing:
For DMC1-SSDS samples, samples were aligned to the mm10 reference genome, peak calling was performed, and hotspot strength was calculated as described in (Brick et al. 2018).
genome build: mm10
processed data files format and content: For each SSDS experiment, the associated BAM file contains all paired end ssDNA reads identified for that sample. Custom BAM tags describe properties of each read pair used for ssDNA detection: it : ITR length uh : microhomology length os : microhomology offset mm : # mismatches DSB hotspots are provided in bedgraph format for each DMC1 SSDS sample. Background corrected hotspot strength is listed in the fourth column. A bedgraph file is provided for H3K4me3 ChIP-Seq peaks. This contains the mm10 coordinates of each H3K4me3 peak. Column 4 is peak strength.

extract_protocol:
For DMC1 SSDS, testicular samples were obtained frozen and were directly thawed in 1% paraformaldehyde and gently dissociated. Genomic DNA for whole genome sequencing was extracted from the testicular samples before fixation with the DNeasy Blood and Tissue kit (Qiagen). DMC1 ChIP was performed as described previously (Khil et al., 2012; Brick et al., 2018) with minor modifications.
Sequencing libraries for anti-DMC1 were prepared following the method described in (Khil et al., 2012).

value: Prdm9-/- (tm1Ymat/tm1Ymat)


title: SPF gBT-I rep2

description:
counts.txt
B6_2

value: in vitro activated tg CD8+ T cells, d7 post transfer

value: gBT-I tg

value: SPF C57BL/6

value: spleen


title: B6xPWD F7 Prdm9ko DMC1 SSDS (A)

description: B6 x PWD F7 Prdm9 knockout; DMC1 SSDS; Sample A

value: C57Bl/6J x C57Bl/6J F7


title: B6 Prdm9ko DMC1 SSDS (A)

description: B6 Prdm9 knockout; DMC1 SSDS; Sample A


title: D3_Neg_CD3

city: Los Angeles

first: Feiyang

last: Ma

state: CA

address: 610, Charles Young Dr East, TLSB 3000C

department: Molecular Biology Institute

institute: UCLA

data_processing:
RNA-Seq reads were aligned to human genome GRCh38.89 by STAR 2.5.3a. The read counts for each gene were used to make the expression matrix.
Supplementary_files_format_and_content: raw_counts.txt

source_name: T cell

growth_protocol: PBMCs were obtained from the whole blood of healthy donors and memory CD4+ T cells were obtained using an EasySep kit (StemCell Inc.). The cells were grown in RPMI 1640 with 10% fetal calf serum, penicillin (50 U/ml), streptomycin (50 µg/ml), sodium pyruvate (1 mM), and recombinant human IL-2 (1 nM) at a density of 5 x 10^6 cells/ml overnight. The cells were subsequntly stained with antibodies and sorted as CCR6+CD161+CCR4+CXCR3-IL-1RI+ and CCR6+CD161+CCR4+CXCR3-IL-1RI- cells.

extract_protocol:
Cell pellets were harvested and treated with RLT buffer and RNA isolated with Qiagen Rneasy Micro kit following the standard protocol.
Libraries were constructed using Illumina TruSeq Stranded Total RNA Sample Prep kit  following the standard protocol.

treatment_protocol: The sorted IL-1RI+ and IL-1RI- Th17 cells were treated with 100 ng/ml IL-1β, 5 ul/ml Immunocult human T cell activator (StemCell Inc.), or media alone for 9 hours.

tag: individual

value: IL-1RI- Th17 cells

tag: agent


title: B6 Prdm9ko DMC1 SSDS (B)

description: B6 Prdm9 knockout; DMC1 SSDS; Sample A


title: D3_Neg_Media

value: Media


title: D2_Neg_IL1B


title: B6xPWD F7 Prdm9ko DMC1 SSDS (B)

description: B6 x PWD F7 Prdm9 knockout; DMC1 SSDS; Sample B


title: D3_Pos_CD3

value: IL-1RI+ Th17 cells


title: PWD_wt_DMC1 SSDS

description: PWD wild-type DMC1 SSDS

value: PWD/Ph

tag: tissue


title: D2_Neg_Media


title: D2_Neg_CD3


title: D2_Pos_IL1B


title: D2_Pos_Media


title: D1_Pos_IL1B


title: D1_Neg_IL1B


title: D1_Neg_Media


title: D1_Neg_CD3


title: L154425T

city: Seoul

first: Chang Ohk

last: Sung

address: Song-Pa gu,Pung-nap dong

department: Pathology

country: South Korea

institute: Asan Medical Center

description:
HCC-IS
gene expression

data_processing:
Sequenced reads were removed low quality and adapter sequence before analysis. Then th raw RNA-seq data were analyzed using TCGA RNAseq RSEMv2 pipeline.
Mapping by MapSplice v2.2.1 and gene expression estimation after filtering by RSEM v1.3.0, and fixed upper quartile normaliztion for gene expression.
Genome_build: GRCh37
Supplementary_files_format_and_content: tab-delimited text file include column head with sample name, and row name with gene symbol, and upper quartile normalized log2 values for each sample.

source_name: liver cancer

growth_protocol: freezing liquid nitrogen

extract_protocol:
RNA was extracted using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit v2 was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using Illumina protocols.

treatment_protocol: fresh frozen tissue

value: liver


title: D1_Pos_CD3


title: PWD Prdm9ko DMC1 SSDS (A)

description: PWD Prdm9 knockout; DMC1 SSDS; Sample A


title: L154722T

description:
HCC-IS
gene expression


title: D1_Pos_Media


title: L136315T

description:
HCC-IS
gene expression


title: L143704T

description:
HCC-IS
gene expression


title: L130019T

description:
HCC-IS
gene expression


title: D3_Neg_IL1B


title: L113488T

description:
HCC-IS
gene expression


title: D3_Pos_IL1B


title: D2_Pos_CD3


title: D3_Pos_Media


title: L135441T

description:
HCC-IS
gene expression


title: H112288T

description:
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title: H112290T

description:
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title: H112665T

description:
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description:
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description:
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description:
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C-HCC
gene expression


title: H080503T

description:
C-HCC
gene expression


title: H061840T

description:
C-HCC
gene expression


title: H110773T

description:
C-HCC
gene expression


title: H092093T

description:
C-HCC
gene expression


title: H050329T

description:
HCC-IS
gene expression


title: H060236T

description:
C-HCC
gene expression


title: H110146T

description:
C-HCC
gene expression


title: H093650T

description:
C-HCC
gene expression


title: H091730T

description:
C-HCC
gene expression


title: H060638T

description:
C-HCC
gene expression


title: H093295T

description:
C-HCC
gene expression


title: H050420T

description:
C-HCC
gene expression


title: H060776T

description:
C-HCC
gene expression


title: H091547T

description:
C-HCC
gene expression


title: H093032T

description:
C-HCC
gene expression


title: H072999T

description:
HCC-IS
gene expression


title: H081665T

description:
C-HCC
gene expression


title: H072012T

description:
C-HCC
gene expression


title: H080411T

description:
C-HCC
gene expression


title: H072511T

description:
C-HCC
gene expression


title: H050350T

description:
C-HCC
gene expression


title: H072056T

description:
C-HCC
gene expression


title: H072103T

description:
C-HCC
gene expression


title: H072849T

description:
C-HCC
gene expression


title: H104529T

description:
C-HCC
gene expression


title: H071904T

description:
C-HCC
gene expression


title: H060264T

description:
C-HCC
gene expression


title: H071380T

description:
C-HCC
gene expression


title: H110362T

description:
C-HCC
gene expression


title: H093528T

description:
C-HCC
gene expression


title: H104572T

description:
C-HCC
gene expression


title: H093002T

description:
C-HCC
gene expression


title: H060272T

description:
C-HCC
gene expression


title: H091225T

description:
C-HCC
gene expression


title: H060566T

description:
C-HCC
gene expression


title: H091616T

description:
C-HCC
gene expression


title: H093609T

description:
C-HCC
gene expression


title: H060664T

description:
C-HCC
gene expression


title: Responders to Sertralin+Celecoxib Treatment [SAMPLE 82]

type: RNA

city: Rotterdam

first: Hemmo

middle: A

last: Drexhage

state: Zuid-Holland

address: Dr Molewaterplein 40

department: Immunology

institute: ErasmusMC

description: Test

data_processing:
The software included in the Excel program to create the delta CT and normalized values as given.
Matrix normalized worksheet reports normalized signal (against housekeeping gene ABL1).
2^-dCT (normalized, linearized values)

label: FAM

source_name: Monocytes

label_protocol: 1 ug RNA was converted into cDNA using the High Capacity cDNA synthesis kit (Applied Biosystems)

extract_protocol: Total RNA was extracted using QIAgen Rneasy Mini kit

tag: group


title: Responders to Sertralin+Celecoxib Treatment [SAMPLE 80]

description: Test


title: Responders to Sertralin+Celecoxib Treatment [SAMPLE 79]

description: Test


title: Responders to Sertralin+Celecoxib Treatment [SAMPLE 77]

description: Test


title: Responders to Sertralin+Celecoxib Treatment [SAMPLE 78]

description: Test


title: Responders to Sertralin+Celecoxib Treatment [SAMPLE 75]

description: Test


title: Responders to Sertralin+Celecoxib Treatment [SAMPLE 73]

description: Test


title: Responders to Sertralin+Celecoxib Treatment [SAMPLE 74]

description: Test


title: Responders to Sertralin+Celecoxib Treatment [SAMPLE 72]

description: Test


title: Responders to Sertralin+Celecoxib Treatment [SAMPLE 70]

description: Test


title: Responders to Sertralin+Celecoxib Treatment [SAMPLE 71]

description: Test


title: H060670T

description:
C-HCC
gene expression


title: Responders to Sertralin+Celecoxib Treatment [SAMPLE 69]

description: Test


title: Responders to Sertralin+Celecoxib Treatment [SAMPLE 66]

description: Test


title: Responders to Sertralin+Celecoxib Treatment [SAMPLE 67]

description: Test


title: Responders to Sertralin+Celecoxib Treatment [SAMPLE 64]

description: Test


title: Responders to Sertralin+Celecoxib Treatment [SAMPLE 63]

description: Test


title: Responders to Sertralin Treatment [SAMPLE 60]

description: Test

value: Responders to Sertralin Treatment


title: Responders to Sertralin Treatment [SAMPLE 61]

description: Test


title: Responders to Sertralin Treatment [SAMPLE 58]

description: Test


title: Young cMSC4_J101112

city: Toulouse

first: Victorine

last: Douin-Echinard

state: 1 avenue du Pr Jean Poulhès

address: Institut Fédératif de Recherche Bio-Médicale de Toulouse (IFR-BMT), Building L4, Room 106

institute: INSERM

hyb_protocol: 600 ng of Cy3-labelled cRNA (specific activity >6 pmol Cy3/µg cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 25 µl containing 10x Agilent fragmentation buffer and 25x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 25 µl of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to SurePrint G3 Mouse GE v2 microarray (8X60K, Design 074809  enclosed in Agilent SureHyb-enabled hybridization chambers for 17 hours at 65°C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed sequentially in Wash buffer 1 (Agilent Technologies, 1 min) and Wash buffer 2 (Agilent Technologies, 37°C, 1 min).

scan_protocol: Slides were scanned immediately after washing on a Agilent G2505C Microarray Scanner with Agilent Scan Control A.8.5.1 software

data_processing: The scanned images were analyzed with Feature Extraction Software 10.10.1.1 (Agilent) using default parameters (protocol GE1_1010_Sep10 and Grid: 074809_D_F_20150624). All subsequent data analyses were done under R (www.r-project.org) using packages of Bioconductor (www.bioconductor.org). Raw data (median of pixels intensity) were imported into R using the read.maimages function from the limma package. Data were then stored in an ExpressionSet object and normalized by the quantile method using the normalize.quantiles function from the preprocessCore R library. Replicated probes on the array (identical ProbeName) were resolved by taking the median normalized signal of each set of replicated probes. The resulting matrix has 33363rows each corresponding to a unique ProbeName (provided as data Matrix).

source_name: cardiac mesenchymal stromal cell_young

label_protocol: For each sample, Cyanine-3 (Cy3) labeled cRNA was prepared from 200 ng of total RNA using the One-Color Quick Amp Labeling kit (Agilent) according to the manufacturer's instructions, followed by Agencourt RNAClean XP (Agencourt Bioscience Corporation, Beverly, Massachusetts) purification. Dye incorporation and cRNA yield were checked with the Nanodrop ND2000 spectrophotometer (Thermo Scientific).

growth_protocol: Cardiac stroma was obtained by enzymatic digestion of ventricles. After antibody and viaibility dye staining, cardiac MSC were cell sorted by flow cytometry (INFLUX Cytometry facility Inserm U1048) from young or old C57BL/6 mice, centrifugated, resuspended in lysis buffer and stored overnight at -80°C.

extract_protocol: RNA was extracted using the Promega kit ReliaPrep RNA cell miniprep system with DNAse treatment. RNA was quantified using X-pose and quality was monitored with RNA fragment analyser (GetTQ Inserm U1048).

value: male

value: 5 months

value: heart

value: cardiac mesenchymal stromal cell


title: Old cMSC4_V1011

source_name: cardiac mesenchymal stromal cell_old

value: 20 months


title: Young cMSC3_J789


title: Old cMSC3_V789


title: Young cMSC5_J123


title: Responders to Sertralin Treatment [SAMPLE 55]

description: Test


title: Responders to Sertralin Treatment [SAMPLE 52]

description: Test


title: Responders to Sertralin Treatment [SAMPLE 53]

description: Test


title: Young cMSC2_J456


title: Old cMSC2_V456


title: Responders to Sertralin Treatment [SAMPLE 51]

description: Test


title: Old cMSC1_V123


title: Responders to Sertralin Treatment [SAMPLE 50]

description: Test


title: Non-Responder to Sertralin Treatment [SAMPLE 49]

description: Test

value: Non-Responder to Sertralin Treatment


title: Non-Responder to Sertralin Treatment [SAMPLE 45]

description: Test


title: Non-Responder to Sertralin Treatment [SAMPLE 46]

description: Test


title: Non-Responder to Sertralin Treatment [SAMPLE 44]

description: Test


title: Responders to Sertralin Treatment [SAMPLE 57]

description: Test


title: Healthy Controls [Sertraline study] [SAMPLE 42]

description: Control

value: Healthy Controls


title: Non-Responder to Sertralin Treatment [SAMPLE 43]

description: Test


title: Healthy Controls [Sertraline study] [SAMPLE 41]

description: Control


title: Responders to Sertralin Treatment [SAMPLE 62]

description: Test


title: Responders to Sertralin Treatment [SAMPLE 59]

description: Test


title: Responders to Sertralin Treatment [SAMPLE 54]

description: Test


title: Non-Responder to Sertralin Treatment [SAMPLE 47]

description: Test


title: Healthy Controls [Sertraline study] [SAMPLE 37]

description: Control


title: Responders to Sertralin Treatment [SAMPLE 56]

description: Test


title: Healthy Controls [Sertraline study] [SAMPLE 38]

description: Control


title: Healthy Controls [Sertraline study] [SAMPLE 36]

description: Control


title: Healthy Controls [Sertraline study] [SAMPLE 35]

description: Control


title: Healthy Controls [Sertraline study] [SAMPLE 33]

description: Control


title: Healthy Controls [Sertraline study] [SAMPLE 34]

description: Control


title: Healthy Controls [Sertraline study] [SAMPLE 30]

description: Control


title: Healthy Controls [Sertraline study] [SAMPLE 28]

description: Control


title: Healthy Controls [Sertraline study] [SAMPLE 32]

description: Control


title: Healthy Controls [Sertraline study] [SAMPLE 29]

description: Control


title: Healthy Controls [Sertraline study] [SAMPLE 31]

description: Control


title: Healthy Controls [Sertraline study] [SAMPLE 26]

description: Control


title: Healthy Controls [Sertraline study] [SAMPLE 27]

description: Control


title: Healthy Controls [Sertraline study] [SAMPLE 20]

description: Control


title: Healthy Controls [Sertraline study] [SAMPLE 22]

description: Control


title: Healthy Controls [Sertraline study] [SAMPLE 24]

description: Control


title: Healthy Controls [Sertraline study] [SAMPLE 19]

description: Control


title: Healthy Controls [Sertraline study] [SAMPLE 21]

description: Control


title: Healthy Controls [Sertraline study] [SAMPLE 23]

description: Control


title: Healthy Controls [Sertraline study] [SAMPLE 18]

description: Control


title: Healthy Controls [Sertraline study] [SAMPLE 40]

description: Control


title: Healthy Controls [Sertraline study] [SAMPLE 15]

description: Control


title: Healthy Controls [Sertraline study] [SAMPLE 14]

description: Control


title: Healthy Controls [Sertraline study] [SAMPLE 16]

description: Control


title: Healthy Controls [Sertraline study] [SAMPLE 17]

description: Control


title: Healthy Controls [Sertraline study] [SAMPLE 12]

description: Control


title: Healthy Controls [Sertraline study] [SAMPLE 11]

description: Control


title: Healthy Controls [Sertraline study] [SAMPLE 10]

description: Control


title: Healthy Controls [Sertraline study] [SAMPLE 39]

description: Control


title: Healthy Controls [Sertraline study] [SAMPLE 9]

description: Control


title: Healthy Controls [Sertraline study] [SAMPLE 7]

description: Control


title: Healthy Controls [Sertraline study] [SAMPLE 8]

description: Control


title: Healthy Controls [Sertraline study] [SAMPLE 5]

description: Control


title: Healthy Controls [Sertraline study] [SAMPLE 6]

description: Control


title: Healthy Controls [Sertraline study] [SAMPLE 1]

description: Control


title: Healthy Controls [Sertraline study] [SAMPLE 25]

description: Control


title: Healthy Controls [Sertraline study] [SAMPLE 3]

description: Control


title: Healthy Controls [Sertraline study] [SAMPLE 4]

description: Control


title: Healthy Controls [Sertraline study] [SAMPLE 2]

description: Control


title: Responders to Venlafaxine Treatment [SAMPLE 44]

description: Test

data_processing:
The software included in the Excel program to create the delta CT and normalized values as given.
Matrix normalized worksheet reports normalized signal (against housekeeping gene ABL1).
dCT (normalized values)

value: Responders to Venlafaxine Treatment


title: Responders to Venlafaxine Treatment [SAMPLE 41]

description: Test


title: 838

city: Taipei

first: Kuei-Pin

last: Chung

address: No 7, Chung-Shan South Rd

department: Laboratory Medicine

country: Taiwan

institute: National Taiwan University Hospital

data_processing:
Illumia bcl2fastq 2.19 was used for base calling.
RNA reads were aligned and mapped to the mm9 mouse reference genome by TopHat2 (version 2.0.11)
Transcriptome reconstruction was performed by Cufflinks (version 2.1.1), and the abundance of transcripts was measured with Cufflinks in Fragments Per Kilobase of exon model per Million mapped reads (FPKM)
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each sample

source_name: Mfn2 knockout_AT2_Bleomycin

extract_protocol:
RNA was extracted using TRIzol reagent (Invitrogen), and was purified by the RNeasy Plus Mini Kit (Qiagen), together with DNA digestion with the RNA free DNase set (Qiagen).
TruSeq Stranded mRNA Library Preparation kit (Illumina), according to manufacturer’s instructions

tag: strain background

tag: genotype/variation

value: Mfn2 knockout

value: lung

value: Alveolar type 2 (AT2) cells

tag: treatment

value: Bleomycin

tag: time point

value: 5 days after administration


title: Responders to Venlafaxine Treatment [SAMPLE 39]

description: Test


title: 837

tag: cell type


title: Non-Responder to Venlafaxine Treatment [SAMPLE 31]

description: Test

value: Non-Responder to Venlafaxine Treatment


title: Healthy Controls [Sertraline study] [SAMPLE 13]

description: Control


title: Non-Responder to Venlafaxine Treatment [SAMPLE 32]

description: Test


title: 839

source_name: Mfn2 knockout_AT2_PBS

value: PBS


title: 835


title: Non-Responder to Venlafaxine Treatment [SAMPLE 30]

description: Test


title: 829

source_name: MFN1 knockout_AT2_Bleomycin

value: MFN1 knockout


title: 822


title: Non-Responder to Venlafaxine Treatment [SAMPLE 27]

description: Test


title: 845


title: Non-Responder to Venlafaxine Treatment [SAMPLE 26]

description: Test


title: Non-Responder to Venlafaxine Treatment [SAMPLE 28]

description: Test


title: Non-Responder to Venlafaxine Treatment [SAMPLE 25]

description: Test


title: 819


title: 842


title: 821

source_name: MFN1 knockout_AT2_PBS


title: Non-Responder to Venlafaxine Treatment [SAMPLE 24]

description: Test


title: 831


title: Responders to Venlafaxine Treatment [SAMPLE 36]

description: Test


title: Non-Responder to Venlafaxine Treatment [SAMPLE 23]

description: Test


title: Responders to Venlafaxine Treatment [SAMPLE 38]

description: Test


title: 817


title: 813


title: Healthy Controls [Venlafaxine study][SAMPLE 20]

description: Control


title: 832


title: Healthy Controls [Venlafaxine study][SAMPLE 21]

description: Control


title: Healthy Controls [Venlafaxine study][SAMPLE 19]

description: Control


title: 809


title: Healthy Controls [Venlafaxine study][SAMPLE 18]

description: Control


title: 808


title: 802


title: Healthy Controls [Venlafaxine study][SAMPLE 17]

description: Control


title: 801


title: 814


title: 812


title: Healthy Controls [Venlafaxine study][SAMPLE 16]

description: Control


title: 823


title: Healthy Controls [Venlafaxine study][SAMPLE 15]

description: Control


title: 810


title: Healthy Controls [Venlafaxine study][SAMPLE 14]

description: Control


title: Healthy Controls [Venlafaxine study][SAMPLE 22]

description: Control


title: Healthy Controls [Venlafaxine study][SAMPLE 13]

description: Control


title: 806


title: 804


title: Healthy Controls [Venlafaxine study][SAMPLE 12]

description: Control


title: DKO_12-3

source_name: MFN1/2 double knockout_AT2

value: MFN1/2 double knockout

value: 12 weeks after tamoxifen injection


title: Healthy Controls [Venlafaxine study][SAMPLE 11]

description: Control


title: DKO_12-2


title: Healthy Controls [Venlafaxine study][SAMPLE 10]

description: Control


title: iDC, biological rep3

description: immature DC

hyb_protocol: Following fragmentation, biotinylated cRNA probe (25 ng/uL in 100 uL hybridizationconcktail) were hybridized for 17 hr at 45C on GeneChip Human 1.0 ST array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450 (protocol FS450_0007).

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner 3000 7G.

data_processing: The data were analyzed with R and Bioconductor.

label: biotin

source_name: cultured monocytes from peripheral blood of healthy donor

label_protocol: Biotinylated cRNA probes were synthesized using the GeneChip Whole Transcript Sense Target Labeling Assay Kit (Affymetrix) following the manufacturer's instructions.

growth_protocol: Monocytes were cultured for 7 days with GM-CSF/IL-4

extract_protocol: RNA from iDC, mDC, DC-10 and DC-10+LPS cells  was extracted with RNeasy Mini kit (Qiagen, Hilden, Germany) according to manufacturer™ instructions.

treatment_protocol: Cells were haversted, washed with PBS and frozen as dried pellet

tag: differentiation protocol

value: 7 days with GM-CSF/IL-4


title: DKO_12-1


title: iDC, biological rep2

description: immature DC


title: iDC, biological rep1

description: immature DC


title: iDC, biological rep4

description: immature DC


title: DC10+LPS, biological rep4

description:
DC10_LPS_4
LPS-activated DC-10

extract_protocol: RNA from mDC, DC-10 and DC-10+LPS cells  was extracted with RNeasy Mini kit (Qiagen, Hilden, Germany) according to manufacturer™ instructions.

value: IL-10 addition + LPS maturation at day 5


title: CON_12-3


title: CON_12-2


title: B6_wt_H3K4me3 ChIP-seq

description: B6 wild-type; H3K4me3 ChIP-Seq

growth_protocol: Crude isolation of germ cells was conducted from male mice at 12 days post-partum (dpp). For detailed protocol see publication

extract_protocol:
Nuclei were isolated from cells using hypotonic lysis. Chromatin was fragmented by Mnase digestion. After high speed spin soluble chromatin was removed and used for ChIP
Libraries were prepared for sequencing using Bioo Scientific's NEXTflex ChIP-Seq Kit (protocol version V11.11) without size selection. Amplification of the libraries was done with 20 µL ligation product, 16 ul water, 12 µL NEXTflex ChIP PCR master mix, 2 µL NEXTflex ChIP primer mix and 14-18 cycles of PCR.

tag: strain

value: PWD/Ph

value: 12 days post partum

tag: genotype

value: wild-type

value: Testis

value: Millipore/EMD 07-473

value: ChIP-Seq


title: DC10+LPS, biological rep3

description:
DC10_LPS_3
LPS-activated DC-10


title: B6_wt_Input

description: B6 wild-type; Input DNA


title: DC10, biological rep1

description:
DC10_1
DC-10

value: IL-10 addition


title: Healthy Controls [Venlafaxine study][SAMPLE 9]

description: Control

value: Healthy Controls


title: DC10+LPS, biological rep2

description:
DC10_LPS_2
LPS-activated DC-10


title: DC10, biological rep3

description:
DC10_3
DC-10


title: DC10, biological rep2

description:
DC10_2
DC-10


title: mDC, biological rep3

description:
mDC_3
LPS-activated DC

value: LPS maturation at day 5


title: mDC, biological rep2

description:
mDC_2
LPS-activated DC


title: DC10, biological rep4

description:
DC10_4
DC-10


title: DC10+LPS, biological rep1

description:
DC10_LPS_1
LPS-activated DC-10


title: mDC, biological rep1

description:
mDC_1
LPS-activated DC


title: Spaceflight, 8 days old, Sku6 Rep4

city: Gainesville

first: Robert

middle: J.

last: Ferl

state: Florida

address: 1301 Fifield Hall PO Box 110690

department: Horticultural Sciences

institute: University of Florida

description:
FLT_8d_Sku6_to_GC_8d_Sku6
FLT_4d_Sku6_to_FLT_8d_Sku6
FLT_8d_Sku6_to_FLT_8d_Col-0

data_processing:
The data analysis was performed at the ICBR bioinformatics core, University of Florida. Input fastq files were trimmed to remove the adapters and low-quality bases using trimmomatic (version 0.36) with the following parameters: LEADING:3, TRAILING:3, SLIDINGWINDOW:4:15, MINLEN:50. Quality control on the trimmed reads was performed using FastQC version 0.11.2. Reads were aligned to the Col-0 TAIR10 genome using the STAR aligner (version 2.5.1b), and duplicate reads due to PCR artifacts were removed using the Picard MarkDuplicates tool. In total, 502 million reads were aligned to the transcriptome.
Expression quantification and differential gene expression analysis were performed using cufflinks and cuffdiff respectively (version 2.2.1) with default parameters. The cuffdiff output files were parsed with custom scripts to generate the final annotated tables of differentially expressed genes.

organism: Arabidopsis thaliana

source_name: solid 0.5x MS media plates; grown in spaceflight, 8 days old plant harvested into KFT containing RNAlater fixative

growth_protocol: The laboratory preparations and launch conditions:  Dry, sterilized Arabidopsis seeds were planted aseptically on the surface of 10-cm2 solid media plates comprised of 0.5% Phytagel/0.5× MS media, and then immediately wrapped in light-tight black cloth (Duvetyne, SeattleFabrics.com) and transported to KSC (Kennedy Space Center), FL, USA. The wrapped plates were stored at temperatures between 4 and 10 °C until launch within a cold stowage bag nominally at 4 °C. The seeds remained dormant until removed from cold stowage and exposed to light at the initiation of the experiment on the ISS (International Space Station).   Plant growth on the ISS and ISSES: The APEX03-2 experiment plates were grown in the Vegetable Production System (VPS/Veggie) hardware on the Columbus Module of the ISS. The 10-cm2 Petri plates were housed perpendicular (“vertical”) to the overhead LED lighting of the VPS. Plants received between 100–135 μmoles/m2/s PAR inside the VPS. Four and eight days after germination was initiated by unwrapping the plates and exposing them to light in the VPS. The ground control plates were grown inside the VPS ground unit within the ISSES (International Space Station Environment Simulator) chamber at KSC with the 48-h delay. The ISSES chamber replicated the temperature, CO2 levels and lighting that had been experienced by the spaceflight plants in the previous 48 h.

extract_protocol:
Sample preparation for transcriptomics:Seedlings stored in RNAlater were recovered from -80°C freezer. Each tube containing the seedlings was allowed to thaw in the fridge overnight. After completely thawing the samples to room temperature, the seedlings were observed under the microscope. Roots of the preserved seedlings from the spaceflight and ground control harvests were dissected and the rest of the seedlings were saved in RNAlater and stored back to -80°C freezer.For 4 day old roots 5-8 roots were combined to serve as one biological replica. For 8 day old roots 2-3 roots were used to form one biological replica. In each case the four biological replicas were used for the transcriptomic analysis. Total RNA extraction: Total RNA was extracted using Qiashredder and RNAeasy™ kits from QIAGEN (QIAGEN Sciences, MD, USA) according to the manufacturer’s instructions. Residual DNA was removed by performing an on-column digestion using an RNase Free DNase (QIAGEN GmbH, Hilden, Germany). Integrity of the RNA was evaluated using the Agilent 2100 BioAnalyzer (Agilent Technologies, Santa Clara, CA, USA).
Library preparation: RNASeq Libraries Preparation using SMART-Seq V4 ultra low input RNA kit for sequencing combined with Illumina Nextera DNA Sample Preparation Kit  Ten ng of total RNA was used for cDNA library construction using CloneTech SMART-Seq V4 ultra low input RNA kit for sequencing (Clontech Laboratories, Inc, cat#: 634890) according to manufacturer's protocol. Briefly, 1st strand cDNA was primed by the SMART-Seq v4 oligonucleotide and then base-pairs with these additional nucleotides, creating an extended template. The reverse transcriptase then switches templates and continues transcribing to the end of the oligonucleotide, resulting full-length cDNA that contains an anchor sequence that serves as a universal priming site for second strand synthesis. cDNA was amplified with primer II A for 8 PCR cycles. Then Illumina sequencing libraries were generated with 150 pg of cDNA using Illumina Nextera DNA Sample Preparation Kit (Cat#: FC-131-1024) according to manufacturer’s instructions. Briefly, 150 pg of cDNA was fragmented by tagementation reaction and then adapter sequences added onto template cDNA by PCR amplification. Libraries were quantitated by Bioanalyzer and qPCR (Kapa Biosystems, catalog number: KK4824). Finally, the libraries were pooled equal molar concentration and sequenced by Illumina 2X75 NextSeq 500.
Illumina sequencing:Sequencing experiments were performed at the Interdisciplinary Center for Biotechnology Research (ICBR) gene expression and sequencing core, University of Florida.  In preparation for sequencing, barcoded libraries were sized on the bioanalyzer, quantitated by QUBIT and qPCR (Kapa Biosystems, catalog number: KK4824). Individual samples were pooled equimolarly at 4 nM. This working pool was used as input in the NextSeq500 instrument sample preparation protocol (Illumina, Part # 15048776, Rev A). Typically, a 1.3 pM library concentration resulted in optimum clustering density in our instrument (i.e., ~200,000 clusters per mm2). Samples were sequenced on 5 flowcells (5 NextSeq 500 runs), using a 2x75 cycles (paired-end) configuration. A typical sequencing run in the NextSeq500 produced 750-800 million paired-end read with a Q30>=85%. For RNA seq, around 40 million reads provided sufficient depth for transcriptome analysis.

treatment_protocol: On Orbit Operations and harvest: At four or for the second experimental set at eight days, seedlings were harvested by an astronaut into KFT (Kennedy Fixation Tube) containing RNAlater solutions. Once the plants were placed in the KFTs, the KFT was actuated with RNAlater to preserve the sample. At 24 hours post-harvest, KFTs were then transferred to MELFI freezer. Following Dragon Capsule splashdown in the Pacific Ocean, the KFTs transferred to the Cold Stowage charter plane at the Long Beach Airport, placed into an insulated shipper with dry ice, and flown to Johnson Space Center (JSC). The KFTs were then transferred via FedEx ground to the Kennedy Space Center. The KFTs were removed from dry ice and transferred to a -80°C freezer. The PIs retrieved the plant samples from the KFTs and transferred the samples back to the University of Florida.  The harvested material was used to compare the transcriptomes of each genotype. The patterns of gene expression was compared between treatments (spaceflight versus ground control) within each genotype of same age or between two ages within same genotype and within same treatment.

tag: cultivar

tag: material type

value: Roots

tag: organism part

value: whole root of the 8 days old seedling

value: 8 days old plants, light grown

tag: biosource type

value: RNAlater fixed_sample


title: CON_12-1

value: lung

value: Alveolar type 2 (AT2) cells


title: Spaceflight, 8 days old, Sku6 Rep3

tag: age


title: Healthy Controls [Venlafaxine study][SAMPLE 7]

description: Control


title: Spaceflight, 8 days old, Sku6 Rep2


title: Healthy Controls [Venlafaxine study][SAMPLE 6]

description: Control


title: Spaceflight, 8 days old, Sku6 Rep1


title: mDC, biological rep4

description:
mDC_4
LPS-activated DC


title: Healthy Controls [Venlafaxine study][SAMPLE 5]

description: Control


title: Healthy Controls [Venlafaxine study][SAMPLE 8]

description: Control


title: Ground Control, 8 days old, Sku6 Rep2

description:
FLT_8d_Sku6_to_GC_8d_Sku6
GC_4d_Sku6_to_GC_8d_Sku6
GC_8d_Sku6_to_GC_8d_Col-0

source_name: solid 0.5x MS media plates; grown on the ground, 8 days old plant harvested into KFT containing RNAlater fixative


title: Healthy Controls [Venlafaxine study][SAMPLE 4]

description: Control


title: Ground Control, 8 days old, Sku6 Rep1


title: Healthy Controls [Venlafaxine study][SAMPLE 2]

description: Control


title: Spaceflight, 8 days old, Col0 Rep4

description:
FLT_8d_Col-0_to_GC_8d_Col-0
FLT_4d_Col-0_to_FLT_8d_Col-0
FLT_8d_Sku6_to_FLT_8d_Col-0


title: Healthy Controls [Venlafaxine study][SAMPLE 3]

description: Control


title: Ground Control, 8 days old, Sku6 Rep4


title: Healthy Controls [Venlafaxine study][SAMPLE 1]

description: Control


title: 24 hr RelA Mutant Liver, biological rep 3

city: Boston

first: Boston University

last: Microarray and Sequencing Resource

state: MA

address: 72 East Concord Street, E631

department: Microarray and Sequencing Resource

institute: Boston University

description: Gene expression data from KO liver from a F mouse at timepoint 24.

hyb_protocol: The labeled, fragmented DNA was hybridized to the Affymetrix Mouse Gene 2.0 ST Array for 18 hours in a GeneChip Hybridization oven 640 at 45oC with rotation (60 rpm). The hybridized samples were washed and stained using an Affymetrix fluidics station 450.

scan_protocol: After staining, microarrays were immediately scanned using an Affymetrix GeneArray Scanner 3000 7G Plus.

data_processing: Raw Affymetrix CEL files were normalized to produce Entrez Gene-identifier-specific expression values using the implementation of the Robust Multiarray Average (RMA) in the affy Bioconductor package (version 1.36.1), using R version 2.15.1 and the Brainarray mogene20stmmentrezgcdf R package (version 17.0.0).

source_name: liver

label_protocol: Biotin labeling was performed using the WT Plus reagent kit (Affymetrix, Santa Clara, CA) according to the manufacturer's protocol.

growth_protocol: Mice were housed in a specific pathogen free facility with access to food and water ad libitum on a twelve-hour light/dark cycle. Experiments were carried out on 6-12 week old mice.

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions (Life Technologies). RNA was further purified using the the Qiagen RNEasy kit with the optional DNAse treatment.

treatment_protocol: Mice were administered 10^6 CFU of Streptococcus pneumoniae (serotype 3) by tail-vein injection.

tag: Sex

value: F

value: KO

tag: infection

value: Streptococcus pneumoniae (serotype 3)

tag: time

value: 24 hr

value: liver


title: Spaceflight, 8 days old, Col0 Rep3


title: Ground Control, 8 days old, Sku6 Rep3


title: Ground Control, 8 days old, Col0 Rep4

description:
FLT_8d_Col-0_to_GC_8d_Col-0
GC_4d_Col-0_to_GC_8d_Col-0
GC_8d_Sku6_to_GC_8d_Col-0


title: Spaceflight, 8 days old, Col0 Rep1


title: 24 hr RelA Mutant Liver, biological rep 2

description: Gene expression data from KO liver from a M mouse at timepoint 24.

value: M

tag: tissue


title: Ground Control, 8 days old, Col0 Rep3


title: Spaceflight, 4 days old, Sku6 Rep4

description:
FLT_4d_Sku6_to_GC_4d_Sku6
FLT_4d_Sku6_to_FLT_8d_Sku6
FLT_4d_Sku6_to_FLT_4d_Col-0

source_name: solid 0.5x MS media plates; grown in spaceflight, 4 days old plant harvested into KFT containing RNAlater fixative

value: whole root of the 4 days old seedling

value: 4 days old plants, light grown


title: Spaceflight, 4 days old, Sku6 Rep3


title: Ground Control, 8 days old, Col0 Rep1


title: Spaceflight, 8 days old, Col0 Rep2


title: Responders to Imipramin Treatment [SAMPLE 50]

description: Test

tag: group

value: Responders to Imipramin Treatment


title: Spaceflight, 4 days old, Sku6 Rep2


title: Responders to Imipramin Treatment [SAMPLE 48]

description: Test


title: Ground Control, 8 days old, Col0 Rep2


title: Spaceflight, 4 days old, Sku6 Rep1


title: Responders to Imipramin Treatment [SAMPLE 47]

description: Test


title: 24 hr RelA Mutant Liver, biological rep 1


title: Ground Control, 4 days old, Sku6 Rep4

description:
FLT_4d_Sku6_to_GC_4d_Sku6
GC_4d_Sku6_to_GC_8d_Sku6
GC_4d_Sku6_to_GC_4d_Col-0

source_name: solid 0.5x MS media plates; grown on the ground, 4 days old plant harvested into KFT containing RNAlater fixative


title: 24 hr Control Liver, biological rep 2

description: Gene expression data from WT liver from a F mouse at timepoint 24.

value: WT


title: 24 hr Control Liver, biological rep 3


title: Ground Control, 4 days old, Sku6 Rep2


title: Ground Control, 4 days old, Sku6 Rep3


title: Responders to Imipramin Treatment [SAMPLE 44]

description: Test


title: Responders to Imipramin Treatment [SAMPLE 49]

description: Test


title: Responders to Imipramin Treatment [SAMPLE 46]

description: Test


title: Spaceflight, 4 days old, Col0 Rep4

description:
FLT_4d_Col-0_to_FLT_8d_Col-0
FLT_4d_Col-0_to_GC_4d_Col-0
FLT_4d_Sku6_to_FLT_4d_Col-0


title: Spaceflight, 4 days old, Col0 Rep1


title: Spaceflight, 4 days old, Col0 Rep2


title: Responders to Imipramin Treatment [SAMPLE 45]

description: Test


title: Ground Control, 4 days old, Col0 Rep4

description:
FLT_4d_Col-0_to_GC_4d_Col-0
GC_4d_Col-0_to_GC_8d_Col-0
GC_4d_Sku6_to_GC_4d_Col-0


title: 24 hr Control Liver, biological rep 4

description: Gene expression data from WT liver from a M mouse at timepoint 24.


title: 24 hr Control Liver, biological rep 1


title: Ground Control, 4 days old, Col0 Rep3


title: 24 hr Control Liver, biological rep 5


title: 6 hr RelA Mutant Liver, biological rep 3

description: Gene expression data from KO liver from a M mouse at timepoint 6.

value: 6 hr


title: Non-Responder to Imipramin Treatment [SAMPLE 43]

description: Test

value: Non-Responder to Imipramin Treatment


title: Ground Control, 4 days old, Sku6 Rep1

value: Roots


title: Ground Control, 4 days old, Col0 Rep2


title: 6 hr RelA Mutant Liver, biological rep 1

description: Gene expression data from KO liver from a F mouse at timepoint 6.


title: 6 hr Control Liver, biological rep 4

description: Gene expression data from WT liver from a F mouse at timepoint 6.


title: 6 hr RelA Mutant Liver, biological rep 2


title: 6 hr RelA Mutant Liver, biological rep 4


title: Ground Control, 4 days old, Col0 Rep1


title: 6 hr Control Liver, biological rep 3

description: Gene expression data from WT liver from a M mouse at timepoint 6.


title: Spaceflight, 4 days old, Col0 Rep3


title: Mut_Input_R3_P1_m6a

city: Chicago

first: David

last: Pincus

state: IL

institute: University of Chicago

data_processing:
Library strategy: m6A-seq
bases called by Illumina software
aligned to sacCer3 by tophat2
gene counts using feature counts
Genome_build: saccer3

organism: Saccharomyces cerevisiae

source_name: 5h meiotic yeast cells

extract_protocol:
m6a-seq, RNA-seq
Illumina tru-seq

tag: type

value: input


title: Non-Responder to Imipramin Treatment [SAMPLE 42]

description: Test


title: Mut_IP_R3_P1_m6a

value: IP


title: Mut_Input_R1_P1_m6a


title: Mut_Input_R2_P1_m6a


title: Non-Responder to Imipramin Treatment [SAMPLE 41]

description: Test


title: Non-Responder to Imipramin Treatment [SAMPLE 39]

description: Test


title: Non-Responder to Imipramin Treatment [SAMPLE 40]

description: Test


title: Mut_IP_R1_P1_m6a


title: 6 hr Control Liver, biological rep 2


title: WT_IP_R3_P1_m6a


title: WT_Input_R3_P1_m6a


title: Non-Responder to Imipramin Treatment [SAMPLE 38]

description: Test


title: WT_IP_R2_P1_m6a


title: WT_Input_R2_P1_m6a


title: Non-Responder to Imipramin Treatment [SAMPLE 37]

description: Test


title: WT_IP_R1_P1_m6a


title: WT_Input_R1_P1_m6a


title: 0 hr RelA Mutant Liver, biological rep 2

description: Gene expression data from KO liver from a M mouse at timepoint 0.

value: control

value: 0 hr


title: 0 hr RelA Mutant Liver, biological rep 3


title: Mut_IP_R2_P2m6a


title: 0 hr Control Liver, biological rep 4

description: Gene expression data from WT liver from a M mouse at timepoint 0.


title: 0 hr RelA Mutant Liver, biological rep 1


title: Non-Responder to Imipramin Treatment [SAMPLE 35]

description: Test


title: ime4-cat input 2

data_processing:
bases called by Illumina software
aligned to sacCer3 by tophat2
gene counts using feature counts
Genome_build: saccer3


title: ime4-cat input 1


title: rme1-10 input 3


title: ime4-cat input 3


title: Non-Responder to Imipramin Treatment [SAMPLE 34]

description: Test


title: rme1-10 input 1


title: 6 hr Control Liver, biological rep 1

value: F


title: rme1-10 input 2


title: Non-Responder to Imipramin Treatment [SAMPLE 33]

description: Test


title: WT input 2


title: WT input 3


title: WT input 1


title: Non-Responder to Imipramin Treatment [SAMPLE 32]

description: Test


title: 0 hr Control Liver, biological rep 3

description: Gene expression data from WT liver from a F mouse at timepoint 0.


title: ime4-cat polysome 3


title: Non-Responder to Imipramin Treatment [SAMPLE 36]

description: Test


title: Non-Responder to Imipramin Treatment [SAMPLE 31]

description: Test


title: ime4-cat polysome 2


title: 0 hr Control Liver, biological rep 1


title: 0 hr Control Liver, biological rep 2


title: ime4-cat polysome 1


title: rme1-10 polysome 3


title: HEY cells transfected with si-ZEB1-WNT5A-rep2

city: Atlanta

first: Mengnan

last: Zhang

state: Georgia

address: 315 Ferst Drive

department: School of Biological Sciences

institute: Georgia Institute of Technology

description: mRNA expression data of HEY cells transfected with si-ZEB1 and si-WNT5A

hyb_protocol: Chips were hybridized to platform GPL570 platform using Affymetrix HWS KIT and FS450_0004 Protocol.

scan_protocol: Scan on 7G Affymetrix GeneChip scanner.

data_processing: The data were analyzed with Robust Multi-Array Average (RMA) using Affymetrix default analysis.

label_protocol: Total RNA was amplified with Applause 3'-Amplification KIT (NuGen) and labeled with Encor Biotin Module (NuGen).

growth_protocol: The HEY cell line was kindly provided by Gordon Mills, Department of Molecular Therapeutics, University of Texas, MD Anderson Cancer Center. Cells were cultured in RPMI 1640 (Mediatech, Manassas, VA) supplemented with 10% FBS (Fetal Bovine Serum; Atlanta Biologicals, Lawrenceville, GA) and 1% antibiotic-antimycotic solution (Mediatech-Cellgro, Manassas, VA).

extract_protocol: Total RNA was extracted from cells using the RNeasy Mini Kit (RNeasy, Qiagen, Germantown, MD).

treatment_protocol: 1 × 105 cells were seeded per well in 6-well plates. For miRNA transfection, cells at exponential phase of growth were transfected with 33 nM Pre-miR miRNA Precursors (Life Technologies, Carlsbad, CA) using Lipofectamine 2000 (Life Technologies, Carlsbad, CA). Pre-miR miRNA Precursor Negative was used as negative control. For siRNA transfection, cells at exponential phase of growth were transfected with 33 nM Silencer Select (Life Technologies, Carlsbad, CA) using Lipofectamine 2000 (Life Technologies, Carlsbad, CA). Silencer Select Negative Control siRNA was used as a negative control. Cells were allowed to grow for 48 hours before RNA extraction.

value: HEY cells

tag: transfection

value: si-ZEB1 and si-WNT5A


title: Non-Responder to Imipramin Treatment [SAMPLE 30]

description: Test


title: HEY cells transfected with si-ZEB1-WNT5A-rep1

source_name: mRNA expression data of HEY cells transfected with si-ZEB1 and si-WNT5A


title: rme1-10 polysome 2


title: rme1-10 polysome 1


title: HEY cells transfected with si-WNT5A-rep2

description: mRNA expression data of HEY cells transfected with si-WNT5A


title: Non-Responder to Imipramin Treatment [SAMPLE 28]

description: Test


title: Non-Responder to Imipramin Treatment [SAMPLE 29]

description: Test


title: WT polysome 3


title: WT polysome 2


title: WT polysome 1


title: Non-Responder to Imipramin Treatment [SAMPLE 26]

description: Test


title: Non-Responder to Imipramin Treatment [SAMPLE 27]

description: Test


title: HEY cells transfected with si-WNT5A-rep1

source_name: mRNA expression data of HEY cells transfected with si-WNT5A


title: Healthy Controls [Imipramine study][SAMPLE 25]

description: Control

source_name: Monocytes

value: Healthy Controls


title: Healthy Controls [Imipramine study][SAMPLE 24]

description: Control


title: HEY cells transfected with si-ZEB1-rep2

description: mRNA expression data of HEY cells transfected with si-ZEB1


title: HEY cells transfected with si-NC-rep2

description: mRNA expression data of HEY cells transfected with si-NC

value: si-NC


title: Healthy Controls [Imipramine study][SAMPLE 22]

description: Control


title: Healthy Controls [Imipramine study][SAMPLE 21]

description: Control


title: Healthy Controls [Imipramine study][SAMPLE 20]

description: Control


title: Healthy Controls [Imipramine study][SAMPLE 23]

description: Control


title: HEY cells transfected with si-ZEB1-rep1

source_name: mRNA expression data of HEY cells transfected with si-ZEB1


title: Healthy Controls [Imipramine study][SAMPLE 19]

description: Control


title: HEY cells transfected with miR-205-rep3

description: mRNA expression data of HEY cells transfected with miR-205


title: HEY cells transfected with si-NC-rep1

source_name: mRNA expression data of HEY cells transfected with si-NC


title: HEY cells transfected with miR-200b-rep3

description: mRNA expression data of HEY cells transfected with miR-200b


title: HEY cells transfected with miR-205-rep2

source_name: mRNA expression data of HEY cells transfected with miR-205


title: HEY cells transfected with miR-200b-rep2

source_name: mRNA expression data of HEY cells transfected with miR-200b


title: HEY cells transfected with miR-200b-rep1


title: Healthy Controls [Imipramine study][SAMPLE 18]

description: Control


title: HEY cells transfected with miR-205-rep1


title: Healthy Controls [Imipramine study][SAMPLE 17]

description: Control


title: HEY cells transfected with miR-141-rep3

description: mRNA expression data of HEY cells transfected with miR-141


title: HEY cells transfected with miR-141-rep2

source_name: mRNA expression data of HEY cells transfected with miR-141


title: HEY cells transfected with miR-141-rep1


title: Healthy Controls [Imipramine study][SAMPLE 16]

description: Control


title: HEY cells transfected with miR-NC-rep3

description: mRNA expression data of HEY cells transfected with miR-NC

value: miR-NC


title: Healthy Controls [Imipramine study][SAMPLE 15]

description: Control


title: HEY cells transfected with miR-NC-rep2

source_name: mRNA expression data of HEY cells transfected with miR-NC


title: Healthy Controls [Imipramine study][SAMPLE 14]

description: Control


title: HCT116-DKO

city: Camden

first: Jaroslav

last: Jelinek

state: NJ

address: 403 Haddon Avenue

department: Research Labs

institute: Coriell Institute for Medical Research

data_processing:
Illumina HiSeq2500 single end sequencing
tophat2 --sensitive alignment of the paired end reads to hg19, generating one a BAM file
RPKM was calculated using RSeQC package using RPKM_count.py script.
For comparing RPKM values between cell lines count values were first  normalized using quantile normalization.
Genome_build: hg19
Supplementary_files_format_and_content: The processed file is in a tab-delimited txt format. RPKMs and normalized RPKMs are shown.

growth_protocol: HCT116 and HCT116-DKO cell lines were cultured in McCoy's 5a medium with 10% fetal bovine serum.

extract_protocol:
RNA was isolated using Rneasy Mini Kit (Qiagen).
Strand-specific RNA libraries were generated from 1 μg of RNA using TruSeq stranded total RNA with Ribo-Zero Gold (Illumina).

treatment_protocol: Cells were harvested in the exponential growth phase.

tag: cell line

value: colorectal carcinoma with genetic knockouts of both DNA methyltransferases DNMT1 (-/-) and DNMT3b (-/-)

tag: gender

value: male


title: HEY cells transfected with miR-NC-rep1

tag: cell type


title: blood_control_38

type: genomic

city: Wuerzburg

first: Tobias

last: Mueller

address: Am Hubland

country: Germany

institute: University of Wuerzburg

description: control

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

scan_protocol: Arrays were imaged using the Illumina iScan

data_processing: Beta values normalized by quantile normalization method as implemented in the minfi package

label: Cy5 and Cy3

source_name: blood

label_protocol: Standard Illumina Protocol

tag: disease state


title: blood_patient WRN_38

description: patient with WRN mutation

extract_protocol: Illumina Infinium MethylationEPIC BeadChip using standard Illumina protocol

value: classical Werner syndrome


title: blood_control_32

description: control


title: HCT116

value: colorectal carcinoma


title: Healthy Controls [Imipramine study][SAMPLE 13]

description: Control


title: blood_patient WRN_43-2

description: patient with WRN mutation


title: blood_control_22

description: control


title: blood_control_45-1

description: control


title: blood_control_59

description: control


title: blood_patient WRN_59

description: patient with WRN mutation

value: female


title: blood_control_36 2

description: control


title: Healthy Controls [Imipramine study][SAMPLE 12]

description: Control


title: blood_control_43-2

description: control


title: blood_patient WRN_22

description: patient with WRN mutation


title: blood_patient WRN_36

description: patient with WRN mutation


title: blood_control_37-3

description: control


title: blood_patient WRN_32

description: patient with WRN mutation


title: Healthy Controls [Imipramine study][SAMPLE 11]

description: Control


title: SOM RNA-seq rep2

city: New Haven

first: Valerie

last: Reinke

state: CT

address: 333 Cedar St

department: Genetics

institute: Yale University School of Medicine

description:
RNA-seq for glp-1(q224) soma control
SOM_RNA-seq_rep2.bigwig

data_processing:
ChIP-seq:  The raw paired-end ChIP and corresponding input sequencing fastq reads were mapped to ce10 genome by mapping with Bowtie2 (v2.3.2) with default parameters.
ChIP-seq: Wig files were generated by a custom script (https://github.com/guifengwei/glib/blob/master/bam2wig.py),
ChIP-seq:  Peaks were called by MACS2 (v2.1.1)  with the key parameter (-q 0.001 --nomodel --extsize 150).
RNA-seq: The raw paired-end RNA-seq fastq reads were first mapped to rRNA build by bowtie2 (v2.1.0)
RNA-seq:  The remaining unmapped reads were further aligned to ce10 genome by HISAT2 (v2.0.4) with the mode suppressing the unpaired reads
RNA-seq:  The gene annotation was downloaded from UCSC Genome Browser, filtered to remove transcripts <50 nt, then was employed to estimate gene expression and call differential gene expression by Cuffdiff program [20] (v2.2.1) under the default parameters between VC2010 and glp-1(q224) strains.
Genome_build: ce10
Supplementary_files_format_and_content: wig or BigWig files were generated as an output

organism: Caenorhabditis elegans

source_name: glp-1(q224) young adult animals

extract_protocol: Growth:  glp-1(q224) animals were cultured to starvation on NGM plates at 15°C. L1 worms were floated and plated on one 15-cm NGM plate. Worms were cultured at 15°C for four days until gravid. Adult worms were bleached and embryos were incubated with shaking at 15°C for 36-42 hours. 15K L1s were plated to one peptone enriched plate and cultured at 25°C for 46-48 hours until adult stage. Extraction: Worms were harvested by washing with M9 3x and were incubated with shaking for 30–45 minutes in M9 buffer. Worms were centifuged at 3100 rpm for 2 minutes. Supernatant was removed and 500 µL TRIzol was added to the worm pellet.  Total RNA isolation was performed with standard TRIzol RNA extraction. Total RNA was then treated with DNA-free rDNase I and cleaned up using RNeasy Mini Kit. rRNA was depleted by Ribo-Zero rRNA Removal Kit. Library construction:  The Yale Center for Genome Analysis (YCGA) prepared libraries for each sample using the Kapa Biosystems reagents.

tag: developmental stage

value: young adult (YA)

value: Soma

tag: chipped factor

value: none - RNA-seq

tag: antibody

tag: strain


title: blood_patient WRN_37-3

description: patient with WRN mutation


title: SOM RNA-seq rep1

description:
RNA-seq for glp-1(q224) soma control
SOM_RNA-seq_rep1.bigwig


title: Healthy Controls [Imipramine study][SAMPLE 10]

description: Control


title: blood_patient WRN_37-2

description: patient with WRN mutation


title: blood_patient WRN_31

description: patient with WRN mutation


title: blood_control_43-1

description: control


title: IGN RNA-seq rep2

description:
RNA-seq for isolated germ nuclei
IGN_RNA-seq_rep2.bigwig

source_name: Isolated germ nuclei from VC2010 wild type young adult animals

extract_protocol: Growth:  Worms were grown to starvation on NGM plates. Starved L1s were floated on peptone-enriched plates, and grown gravid at 20˚C. Gravid adults were bleached and synchronized by L1 starvation.  L1s were plated to enriched plates and grown until the young adult stage. Extraction: Animals for nuclei isolation were collected from six enriched plates (~0.3 million) per RNA-seq experiment. Young adult animals were harvested at 54-56 hours after plating synchronized L1s when most of the animals had 4-10 embryos. Worms were collected into one 50 mL conical tube and spun at 3100 rpm for 2 minutes and then washed 3x in M9. Worms were incubated for 30–45 minutes in M9 buffer with shaking after the third M9 wash to reduce intestinal bacteria. Then germ nuclei isolation was performed. 500 µL TRIzol was added to the nuclei pellet.  Total RNA isolation was performed with standard TRIzol RNA extraction. Total RNA was then treated with DNA-free rDNase I and cleaned up using RNeasy Mini Kit. rRNA was depleted by Ribo-Zero rRNA Removal Kit. Library construction:  The Yale Center for Genome Analysis (YCGA) prepared libraries for each sample using the Kapa Biosystems reagents.

value: Isolated germ nuclei


title: blood_control_37-2

description: control

value: control


title: blood_patient WRN_43-1

description: patient with WRN mutation


title: IGN RNA-seq rep1

description:
RNA-seq for isolated germ nuclei
IGN_RNA-seq_rep1.bigwig


title: blood_patient WRN_45-1

description: patient with WRN mutation


title: Healthy Controls [Imipramine study][SAMPLE 7]

description: Control