title: Exp. Blastocyst 112515_04 SPIA

city: East Lansing

first: Uros

last: Midic

state: MI

address: 474 S. Shaw Lane

department: Animal Sciences

institute: Michigan State University

data_processing:
Illumina Real Time Analysis (RTA) v1.18.64 (SPIA libraries) & v2.7.6 (SoLo libraries)
Hisat2  to the Ensembl rhesus monkey genome (Mmul build v8.1.0, genome annotation relase-91)
Removing "ExAmp" duplicates with distance threshold 2500 using in-house developed Python code
DESeq2 comparisons between groups of libraries
Genome_build: Mmul 8.1.0 (Macaca Mulatta)
Supplementary_files_format_and_content: raw counts

organism: Macaca mulatta

source_name: Expanded Blastocyst

growth_protocol: Females were observed daily for signs of vaginal bleeding and the first day of menses was assigned cycle day 1. Beginning on cycle day 1–4 recombinant human FSH (r-hFSH: Organon, West Orange, NJ) was administered (37.5 IU) twice daily, intramuscularly for 7 days total. To obtain in vivo matured (VVM) oocytes, females were given recombinant hCG (1000 IU Ovidrel; Serono, Rockland, MA) on treatment day 8 in addition to the FSH treatment outlined above. COCs were removed at 28 – 30 h following hCG by ultrasound-guided aspiration. Oocytes were retrieved from aspirates. In vivo matured oocytes were rinsed and transferred into TL-PVA medium (37°C) under oil and inseminated according to standard procedure for IVF of rhesus macaque oocytes; this is Day 0 of embryo culture. Semen was collected from male macaques that had been trained for this procedure. Sperm were washed from seminal plasma and resuspended in TL-BSA medium. The next morning (Day 1), oocytes were transferred into 70 μl drops of chemically-defined, protein-free hamster embryo culture medium 9 (HECM-9) without or with relaxin (see below) under oil (37°C) and incubated at 37°C in a humidified atmosphere of 5% CO2, 10% O2 and 85% N2 for 48 hours. At approximately 60 hours post insemination non-cleaved oocytes were again assessed for developmental status. Non-cleaved oocytes exhibiting a polar body and all embryos were classified as having matured to metaphase II of meiosis (MII). Embryos were transferred into 70 μl drops of HECM-9 medium with 5% bovine calf serum (Gemini Bioproducts, West Sacramento, CA) with or without relaxin under mineral oil and incubated as described above. Embryos were transferred to fresh medium every other day until fixed on day 8 post insemination. Beginning on Day 5, embryos were observed with a Nikkon SMZ-2B microscope (Melville, NY) housed in a temperature-controlled isolette daily at 0700 and 1700 hrs for developmental stage.

extract_protocol:
All cumulus cells were removed by repeatedly pipetting oocytes with a narrow-gauge pipette that was just slightly larger than the oocytes while observing oocytes with a stereomicroscope. Using the PicoPureTM RNA Extraction kit, total RNA was isolated from each sample following the manufacturer protocol, including a DNAse digestion (RNase-Free DNase Set; Qiagen, Hilden, Germany) to remove any contaminating DNA.
SPIA libraries: 100 ng of each RNA sample was processed with the Ovation RNA-Seq System v2 using Ribo-SPIATM Technology (NuGen, San Carlos, CA).  After this initial processing, a Covaris-2 sonicator was used to mechanically fragment the cDNA to an average of 300 bp. This was then followed by a brief S1 nuclease digestion as previously described (Head et al., 2011).  After bead purification, the cDNA was processed through the Ovation Ultralow DR Multiplex Systems 1-16 (NuGen) for end repair, adaptor ligation and final library amplification.
SoLo libraries: cDNA libraries were produced with Nugen Ovation SoLo RNA-Seq(NuGEN, San Carlos, CA). After bead purification, the cDNA was processed: end repair, adaptor ligation and first round library amplification and purification. Then 20 ng of each library was used for the remainder of library preparation, which included use of InDA-C primers for rRNA depletion, as well as 2nd round library amplification and purification steps. SoLo Custom R1 primer was used instead of a standard Illumina R1 sequencing primer for the sequencing of the libraries.

value: embryo

tag: developmental stage

value: Expanded Blastocyst

tag: library processing kit

value: SPIA


title: PCa92

status: Public on Jan 31 2019

type: RNA

city: Biella

first: Paola

last: Ostano

address: via Malta 3

country: Italy

institute: Fondazione Edo ed Elvo Tempia

hyb_protocol: Samples were hybridized on oligonucleotide glass arrays with sequences representing probes for 2006 human miRs from miRbase v19 (Human miR Microarray Version 19, Agilent Technologies).

scan_protocol: After 20 hours, slides were washed and scanned using an Agilent G2505C dual-laser microarray scanner.

data_processing: Images obtained were analysed using Feature Extraction software version 10.7 and txt files with raw or semi-processed data (by the GeneView tool of Feature Extraction) were given as output.  Raw data were loaded into R and processed using the limma package for microarray analysis.  Background correction and between array normalization were carried out using the normexp method, with an offset = 20, and the quantile method, respectively. Normalized log2 Intensities of replicated probes were then averaged.

molecule: total RNA

organism: Homo sapiens

source_name: plasma

label_protocol: Briefly, 4ul of totRNA were dephosphorylated and denaturated; then a ligation and labeling step with Cy3 was performed

extract_protocol: Extraction was performed using miRNEasy serum/plasma kit from Qiagen. A carrier (bacteriophage MS2 from Roche Diagnostic) was added, together with cel-miR-39-3p mimic.

tag: class

value: Prostate Cancer

tag: psa

tag: gs


title: IFA_BL_4h_3

city: London

first: Deniz

last: Cizmeci

address: Imperial College London

country: United Kingdom

institute: Imperial College London

description:
m.blood.IFA.04.3
Gene expression in blood 4hrs after injection with IFA.

hyb_protocol: Quantity and labeling efficiency were verified before hybridization to whole-genome 8×60 k mouse expression arrays (Agilent design ID 028005).

scan_protocol: Scanned at 5 μm using an Agilent scanner.

data_processing:
Image analysis and data extraction were performed with Agilent's Feature Extraction software (version 11.5) to generate the raw expression data.
Microarray data were pre-processed and normalised using R package limma. The raw data were first background corrected using the normexp method. Background corrected signals were quantile normalised between arrays.

label: not provided

organism: Mus musculus

source_name: Peripheral Blood, 4hr, IFA, replicate 3

label_protocol: Gene expression data were generated from high-quality RNA samples on an Agilent microarray platform (Agilent Technologies). RNA was labeled with a Low Input Quick Amp Labeling Kit (Agilent Technologies) according to the manufacturer’s instructions.

extract_protocol:
Tissue Samples - Small pieces of tissue (3mm x 3mm x 3mm) were harvested and flash frozen in liquid nitrogen. Total RNA isolation including the miRNA species was performed using the miRNeasy mini kit (Qiagen, UK), as described in the standard protocol for purification of microRNA and total RNA from tissues and cells. Briefly, 700 µL QIAzol lysis reagent was added to the tissue sample, and disrupted and homogenized using a tissueruptor probe. Homogenate was incubated at room temperature (15–25°C) for 5 min before addition of 140 µL chloroform and vigorous shaking for 15 s. After incubation at room temperature for 2–3 min the homogenate was centrifuged for 15 min at 12,000 x g at 4°C. The upper aqueous phase was then transferred to a new collection tube (350 µL). 1.5 volumes (525 µL) of 100% ethanol was added and mixed thoroughly by pipetting then all sample was transferred into an RNeasy® Mini column, the sample being pulled through the column by vacuum manifold. The sample on the column was washed using 700 µL Buffer RWT, followed by 2 washes using 500 µL Buffer RPE. The RNeasy Mini column was then placed into a new 2 mL collection tube and centrifuged at full speed for 1 min to completely dry the membrane. The RNeasy Mini column was then transferred to a new 1.5 mL collection tube and 30 µL RNase-free water was directly pipetted onto the column membrane, then centrifuged for 1 min at ≥8000 x g to elute. Purified RNA was stored at -80°C until required for microarray hybridisation.
Blood Samples - 100 µL of peripheral blood harvested from the mouse tail was collected directly into an RNAprotect Animal Blood Tube and the tubes incubated at room temperature (15–25°C) for 2 hours. The blood tubes were then flash frozen in liquid nitrogen for storage. RNA isolation was performed as described in the kit protocol for purification of Total RNA, including miRNA, from RNAprotect stabilized animal blood tubes (100 µL). Briefly, completely thawed tubes were first centrifuged for 3 min at 5000 x g, then the supernatant removed by careful pipetting. The pellet was resuspended in 1 mL of RNase-free water and transferred to a clean RNase-free 2 mL tube. The pellet was completely resuspended in the water, centrifuged for 3 min at 5000 x g and the supernatant carefully removed by pipetting. The pellet was then dissolved in 240 µL Buffer RSB before addition of 200 µL Buffer RBT and 20 µL proteinase K enzyme solution. The tube was vortexed for 5 s then incubated at 55°C for 10 min in a shaking incubator at 1200 rpm. After incubation the sample was added into a Qiashredder spin column and centrifuged for 3 min at 10,000 x g. The supernatant was then transferred to a clean tube and 690 µL 100% ethanol added, mixed thoroughly by pipetting then all sample was transferred into an RNeasy Mini column, the sample being pulled through the column by vacuum manifold. The sample on the column was washed using 350 µL Buffer RWT, followed by addition of 80 µL DNase I solution (in Buffer RDD) and incubation at room temperature for 15 min. After DNase 1 treatment the column was washed with a further 350 µL of RWT followed by 2 washes using 500 µL Buffer RPE and a final wash with 500 µL 80% RNase-free ethanol. The RNeasy Mini column was then placed into a new 2 mL collection tube and centrifuged at full speed for 1 min to completely dry the membrane. The column was then transferred to a new 1.5 mL collection tube and 30 µL RNase-free REB buffer was directly pipetted onto the column membrane, then centrifuged for 1 min at ≥8000 x g to elute. Purified RNA was stored at -80°C until required for microarray hybridisation.

treatment_protocol: 6- to 8-week-old female CB6F1 mice were purchased from Charles River. Animals received a single injection in their right hind leg quadricep muscle and were then culled at specific intervals after the vaccination, either 4, 8, 24, 48, 72 or 168 Hrs. A control group that did not receive a vaccination was culled and tissues harvested. A further control group was employed that received a single saline injection in the right hind leg quadriceps muscle and were culled at the same intervals as the animals that received an active formulation. When each animal was culled the injected muscle site and the iliac lymph nodes that drain the hind leg quadriceps muscles were harvested and flash frozen in liquid nitrogen. Peripheral blood, sampled from the mouse tail vein immediately before humane euthanasia was collected (100 µL) in RNAprotect animal blood tubes (Qiagen, UK). Groups of mice (n = 5 per group per timepoint) received 1/10th of the human dose in 50 µL of one of the following licensed vaccines: Pentavac SD (Diphtheria, Tetanus, Pertussis (Whole Cell), Hepatitis B (rDNA) and Haemophilus Type b Conjugate Vaccine); Agrippal (Trivalent Flu Subunits – H3N2, H1N1 and Influenza B); Fluad (Trivalent Flu Subunits – H3N2, H1N1 and Influenza B + MF59® (oil-in-water emulsion)); Engerix B (Recombinant Hepatitis B) and either Poly I:C (Sigma, UK – P0913: 50 µL of a 1 mg/mL solution), LPS (Invivogen, UK – LPS-EB Ultrapure: 50 µL of a 0.5 mg/mL solution), IFA (Seppic, France – Montanide ISA 51 VG: 50 µL of a 1:1 mixture of IFA and Saline) or Saline alone (Sigma, UK – 50 µL).

tag: strain/background

tag: gender

value: Female

tag: tissue

value: PBMC

tag: treatment

value: IFA

tag: timepoint

tag: animal replicate


title: BPH127

value: Benign Prostatic Hyperplasia


title: C57Bl6-PPARgKO_Thiomac_ChIP_ATF3_Veh

type: SRA

city: La Jolla

first: Jenhan

last: Tao

state: CA

address: 9500 Gilman Drive, Mail code 0651

department: Cellular and Molecular Medicine

country: USA

institute: UC San Diego

library_source: genomic

data_processing:
Reads from each ChIP-seq sample were aligned to the mm10 build of the mouse genome using bowtie2 (with default parameters).
Sam files were converted to tag directories with HOMER
Peaks were called with HOMER with the findPeaks command using the corresponding input file and the parameters -L 0 -C 0 -fdr 0.9
HOMER peak scores from peak files corresponding to replicate experiments were used as input for IDR; peaks with IDR < 0.05 were retained
Genome_build: mm10
Supplementary_files_format_and_content: tab delimited file giving the genomic coordinates of putative binding site for each ChIP target. The "count" column indicates the HOMER peak score

molecule: genomic DNA

source_name: mouse thioglycollate elicited macrophage cells

growth_protocol: TGEMs were grown for 3 days in 10%FBS, 1%Penicillin Streptomycin, DMEM

extract_protocol:
Protein A and G Dynabeads 50/50 mix from Invitrogen are sued for ChIP (10001D, 10003D). IP mix consists of 20ul beads/2ug antibody per 2 million cell ChIP. For preparation, beads were washed with 0.5%BSA-PBS (BSA: , then incubate beads-antibody with 0.5%BSA-PBS for at least 1h on rotator (4oC). Wash 2X with 0.5%BSA-PBS, then resuspend in dilution buffer. Double Crosslinking for ChIP. Media was decanted from cells in 10 cm plates, wash once briefly with PBS (RT). Disuccinimidyl glutarate (Pierce Cat # 20593)  (diluted in DMSO at 200mM)/PBS (RT) was used for 10 min. Then Formaldehyde was added to a final concentration of 1% for an additional 10 min. Reaction was quenched with 1:10 Tris pH 7.4 on ice. Cells were collected and washed twice with cold PBS, spinning at 1000 rcf for 5 min. Nuclei Isolation and Sonication. Resuspend cell pellets in 1 ml of Nuclei Isolation Buffer (50 mM Tris-Ph 8.0, 60 mM KCl, 0.5% NP40) + PI and incubate on ice for 10 minutes. Centrifuge 2,000 g for 3 minutes at 4º C. Resuspend nuclei in 200 ul of fresh Lysis Buffer (0.5% SDS, 10 mM EDTA, 0.5 mM EGTA, 50 mM Tris-HCl (ph8))+ PI. Sonication. Nuclei were then sonicated (10 million cells) for 25 minutes in a Biorupter (settings= 30 seconds=On, 30 seconds=Off, Medium) using thin wall tubes (Diagenode Cat# C30010010). After sonication spin max speed for 10 minute at 4C.  ChIP set up. Sonicated DNA was diluted 5X with 800 Dilution Buffer (1% Triton, 2mM EDTA, 150 mM NaCl, 20 mM Tris-HCl (ph8), 1X Protease Inhibitors).  An aliquot is removed for input samples (5%).  Samples ON at 4º C while rotating. Washing. ChIP are washed 1X with TSE I (20mM Tris-HCl pH7.4, 150mM NaCl, 0.1%SDS, 1% Triton X-100, 2mM EDTA), 2X with TSE III (10mM Tris-HCl pH7.4, 250mM LiCl, 1%IGEPAL, 1%Deoxycholate, 1mM EDTA), 1X with TE+0.1%TritonX-100, transfer to new tube and then wash another time with TE+0.1%TritonX-100.   Elution. Elute with 200 uL Elution Buffer (1% SDS, 10mM Tris pH7.5) for 20 minutes at RT, shaking on the vortex or a nutator or rotator.  De-crosslinking. Add 10 uL of 5 M NaCl and incubate ON at 65º C (or at least 8 hours).  Clean up samples using Zymo ChIP DNA Clean & Concentrator. Elute in 100uL. Take 40uL and proceed to library prep protocol.
dsDNA End Repair. We mixed 40uL of DNA from ChIP or RNA protocols with 2.9uL of H2O, 0.5uL 1% Tween-20, 5uL 10X T4 ligase buffer (Enzymatics cat# L6030-HC-L), 1uL dNTP mix (10 mM  Affymetrix 77119), 0.3 uL T4 DNA pol (Enzymatics P7080L), 0.3uL T4 PNK (Enzymatics Y9040L), 0.06uL Klenow (Enzymatics P7060L) and incubated for 30min at 20°C. 1uL of Seradyn “3 EDAC” SpeedBeads (Thermo 6515-2105-050250) in 93 μL 20% PEG8000/2.5 M NaCl (13% final) was added and incubated for 10 min. Bead clean-up. Beads were collected on a magnet and washed 2X with 80% ethanol. Beads were air-dried for 10 min and then eluted in 15uL ddH2O. dA-Tailing. DNA was mixed with 10.8uL ddH2O, 0.3uL 1% Tween-20, 3uL Blue Buffer (Enzymatics cat# B0110L), 0.6uL dATP (10mM Tech 10216-018), 0.3uL Klenow 3’- 5’ Exo (Enzymatics P7010-LC-L) and incubated for 30min at 37°C. 55.8uL 20% PEG8000/2.5 M NaCl (13% final) was added an incubated for 10 min. Then bead clean up was done. Beads were eluted in 14uL. Y-Shape Adapter Ligation. Sample was mixed with 0.5uL of a BIOO barcode adapter (BIOO Scientific cat# 514104), 15uL Rapid Ligation Buffer (Enzymatics cat@ L603-LC-L), 0.33uL 1% Tween-20 and 0.5uL T4 DNA ligase  HC (Enzymatics L6030-HC-L) and incubated for 15 min at RT.  7 μL of 20% PEG8000/2.5 M NaCl was added and incubated for 10min at RT. Bead clean up was performed and beads were eluted in 21uL. 10uL was then used for PCR amplification (14 cycles) with IGA and IGB primers (AATGATACGGCGACCACCGA, CAAGCAGAAGACGGCATACGA).

treatment_protocol: Veh (PBS) or KLA were added directly to the media

tag: Sex

value: male

value: Veh

tag: genotype

value: PPARgKO

tag: antigen target

tag: library prep

value: ChIP


title: PCa74


title: BPH128


title: Exp. Blastocyst 112515_03 SPIA

library_source: transcriptomic


title: Exp. Blastocyst 112415_04 SPIA


title: ENG_BL_4h_5

description:
m.blood.Engerix.04.5
Gene expression in blood 4hrs after injection with Engerix B.

source_name: Peripheral Blood, 4hr, Engerix B, replicate 5

value: Engerix B


title: BPH114


title: ENG_BL_4h_2

description:
m.blood.Engerix.04.2
Gene expression in blood 4hrs after injection with Engerix B.

source_name: Peripheral Blood, 4hr, Engerix B, replicate 2


title: IFA_BL_4h_1

description:
m.blood.IFA.04.1
Gene expression in blood 4hrs after injection with IFA.

source_name: Peripheral Blood, 4hr, IFA, replicate 1


title: ENG_BL_4h_3

description:
m.blood.Engerix.04.3
Gene expression in blood 4hrs after injection with Engerix B.

source_name: Peripheral Blood, 4hr, Engerix B, replicate 3


title: Norm351

value: Healthy Donor


title: TriFLU-MF59_MU_0h_5

description:
m.muscle.TriFluMF59.00.5
Gene expression baseline at time 0 in muscle before injection with Fluad.

source_name: Muscle, 0hr, Fluad, replicate 5

value: muscle

value: Fluad


title: IFA_BL_4h_2

description:
m.blood.IFA.04.2
Gene expression in blood 4hrs after injection with IFA.

source_name: Peripheral Blood, 4hr, IFA, replicate 2


title: Exp. Blastocyst 112415_03 SPIA


title: Exp. Blastocyst 112415_02 SPIA


title: ENG_BL_4h_4

description:
m.blood.Engerix.04.4
Gene expression in blood 4hrs after injection with Engerix B.

source_name: Peripheral Blood, 4hr, Engerix B, replicate 4


title: PCa87


title: ENG_BL_4h_1

description:
m.blood.Engerix.04.1
Gene expression in blood 4hrs after injection with Engerix B.

source_name: Peripheral Blood, 4hr, Engerix B, replicate 1


title: TriFLU-MF59_MU_0h_4

description:
m.muscle.TriFluMF59.00.4
Gene expression baseline at time 0 in muscle before injection with Fluad.

source_name: Muscle, 0hr, Fluad, replicate 4


title: PCa83


title: TriFLU-MF59_MU_0h_1

description:
m.muscle.TriFluMF59.00.1
Gene expression baseline at time 0 in muscle before injection with Fluad.

source_name: Muscle, 0hr, Fluad, replicate 1


title: PCa77


title: Exp. Blastocyst 111715_05 SPIA


title: PCa75


title: TriFLU_MU_0h_5

description:
m.muscle.TriFlu.00.5
Gene expression baseline at time 0 in muscle before injection with Agrippal.

source_name: Muscle, 0hr, Agrippal, replicate 5

value: Agrippal


title: Exp. Blastocyst 111715_04 SPIA

value: embryo


title: TriFLU-MF59_MU_0h_2

description:
m.muscle.TriFluMF59.00.2
Gene expression baseline at time 0 in muscle before injection with Fluad.

source_name: Muscle, 0hr, Fluad, replicate 2


title: TriFLU-MF59_MU_0h_3

description:
m.muscle.TriFluMF59.00.3
Gene expression baseline at time 0 in muscle before injection with Fluad.

source_name: Muscle, 0hr, Fluad, replicate 3


title: TriFLU_MU_0h_4

description:
m.muscle.TriFlu.00.4
Gene expression baseline at time 0 in muscle before injection with Agrippal.

source_name: Muscle, 0hr, Agrippal, replicate 4


title: genomic DNA from B8N2

type: genomic

city: Guangzhou

first: Yumei

last: Luo

state: Guangdong

address: 63 Duobao Road

country: China

institute: The Third Affiliated Hospital of Guangzhou Medical University

description: breast tumor sample

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to Illumina HumanMethylation450K BeadChip using standard Illumina protocol

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

data_processing: BeadStudio software v3.2

label: Cy5 and Cy3

label_protocol: Standard Illumina Protocol

extract_protocol: genomic DNA was extracted and purified from breast tumor samples using Qiagen DNeasy Kit according to standard instructions

tag: sample type

value: breast tumor

tag: disease state

value: diseased


title: Exp. Blastocyst 112415_01 SPIA

source_name: Expanded Blastocyst

tag: developmental stage

value: Expanded Blastocyst

value: SPIA


title: genomic DNA from B8N3

description: breast tumor sample

value: Female


title: Exp. Blastocyst 111715_03 SPIA

tag: library processing kit


title: PCa106

source_name: plasma

tag: class

value: Prostate Cancer


title: TriFLU_MU_0h_3

description:
m.muscle.TriFlu.00.3
Gene expression baseline at time 0 in muscle before injection with Agrippal.

source_name: Muscle, 0hr, Agrippal, replicate 3


title: genomic DNA from B7N2

description: breast tumor sample


title: Exp. Blastocyst 111715_01 SPIA


title: BPH81

value: Benign Prostatic Hyperplasia

tag: psa


title: PCa89

tag: gs


title: genomic DNA from B7N3

description: breast tumor sample


title: TriFLU_MU_0h_2

description:
m.muscle.TriFlu.00.2
Gene expression baseline at time 0 in muscle before injection with Agrippal.

source_name: Muscle, 0hr, Agrippal, replicate 2

tag: strain/background


title: genomic DNA from B7N1

description: breast tumor sample

tag: gender


title: genomic DNA from B8N1

description: breast tumor sample


title: TriFLU_MU_0h_1

description:
m.muscle.TriFlu.00.1
Gene expression baseline at time 0 in muscle before injection with Agrippal.

source_name: Muscle, 0hr, Agrippal, replicate 1

tag: tissue


title: genomic DNA from B6N1

description: breast tumor sample


title: Exp. Blastocyst 111715_02 SPIA


title: genomic DNA from B6N3

description: breast tumor sample


title: Exp. Blastocyst 111215_02 SPIA


title: BPH71


title: genomic DNA from B6N2

description: breast tumor sample


title: genomic DNA from B5N3

description: breast tumor sample


title: Norm14


title: genomic DNA from B5N5

description: breast tumor sample


title: Exp. Blastocyst 111215_01 SPIA


title: genomic DNA from B5N2

description: breast tumor sample


title: Del. Blastocyst 112515_02 SPIA

source_name: Delayed Blastocyst

value: Delayed Blastocyst


title: genomic DNA from B5N4

description: breast tumor sample


title: SAL_MU_0h_3

description:
m.muscle.saline.00.3
Gene expression baseline at time 0 in muscle before injection with saline.

source_name: Muscle, 0hr, Saline, replicate 3

tag: treatment

value: saline


title: SAL_MU_0h_4

description:
m.muscle.saline.00.4
Gene expression baseline at time 0 in muscle before injection with saline.

source_name: Muscle, 0hr, Saline, replicate 4

tag: timepoint


title: PCa76


title: genomic DNA from B4N4

description: breast tumor sample


title: Del. Blastocyst 112515_01 SPIA


title: BPH66


title: Morula 022916_03 SPIA

source_name: Morula

value: Morula


title: SAL_MU_0h_2

description:
m.muscle.saline.00.2
Gene expression baseline at time 0 in muscle before injection with saline.

source_name: Muscle, 0hr, Saline, replicate 2

tag: animal replicate


title: SAL_MU_0h_5

description:
m.muscle.saline.00.5
Gene expression baseline at time 0 in muscle before injection with saline.

source_name: Muscle, 0hr, Saline, replicate 5


title: Morula 022916_02 SPIA


title: PCa70


title: SAL_MU_0h_1

description:
m.muscle.saline.00.1
Gene expression baseline at time 0 in muscle before injection with saline.

source_name: Muscle, 0hr, Saline, replicate 1


title: genomic DNA from B4N5

description: breast tumor sample


title: Exp. Blastocyst 111215_03 SPIA


title: Morula 022916_01 SPIA


title: PCa64


title: PCa86


title: genomic DNA from B4N3

description: breast tumor sample


title: PolyIC_MU_0h_5

description:
m.muscle.PolyIC.00.5
Gene expression baseline at time 0 in muscle before injection with Poly I:C.

source_name: Muscle, 0hr, Poly I:C, replicate 5

value: PolyIC


title: Morula 022416_03 SPIA


title: genomic DNA from B4N2

description: breast tumor sample


title: PCa84


title: genomic DNA from B3T6

description: breast tumor sample


title: genomic DNA from B5N1

description: breast tumor sample


title: Morula 022416_02 SPIA


title: BPH63


title: genomic DNA from B4N1

description: breast tumor sample


title: PolyIC_MU_0h_2

description:
m.muscle.PolyIC.00.2
Gene expression baseline at time 0 in muscle before injection with Poly I:C.

source_name: Muscle, 0hr, Poly I:C, replicate 2


title: Morula 021016_04 SPIA


title: Morula 021016_03 SPIA


title: PolyIC_MU_0h_4

description:
m.muscle.PolyIC.00.4
Gene expression baseline at time 0 in muscle before injection with Poly I:C.

source_name: Muscle, 0hr, Poly I:C, replicate 4


title: PCa57


title: Norm1


title: PERT_MU_0h_5

description:
m.muscle.Pertussis.00.5
Gene expression baseline at time 0 in muscle before injection with Pentavac SD.

source_name: Muscle, 0hr, Pentavac SD, replicate 5

value: Pentavac SD


title: PolyIC_MU_0h_1

description:
m.muscle.PolyIC.00.1
Gene expression baseline at time 0 in muscle before injection with Poly I:C.

source_name: Muscle, 0hr, Poly I:C, replicate 1


title: BPH62


title: PolyIC_MU_0h_3

description:
m.muscle.PolyIC.00.3
Gene expression baseline at time 0 in muscle before injection with Poly I:C.

source_name: Muscle, 0hr, Poly I:C, replicate 3


title: Morula 021016_02 SPIA


title: Morula 020816_04 SPIA


title: genomic DNA from B3T5

description: breast tumor sample


title: genomic DNA from B3T4

description: breast tumor sample


title: PERT_MU_0h_4

description:
m.muscle.Pertussis.00.4
Gene expression baseline at time 0 in muscle before injection with Pentavac SD.

source_name: Muscle, 0hr, Pentavac SD, replicate 4


title: BPH49

source_name: plasma


title: PCa24


title: Morula 020816_03 SPIA


title: PERT_MU_0h_3

description:
m.muscle.Pertussis.00.3
Gene expression baseline at time 0 in muscle before injection with Pentavac SD.

source_name: Muscle, 0hr, Pentavac SD, replicate 3


title: BPH54


title: genomic DNA from B3T1

description: breast tumor sample


title: Norm6

value: Healthy Donor


title: genomic DNA from B3T2

description: breast tumor sample


title: genomic DNA from B3T3

description: breast tumor sample


title: PERT_MU_0h_2

description:
m.muscle.Pertussis.00.2
Gene expression baseline at time 0 in muscle before injection with Pentavac SD.

source_name: Muscle, 0hr, Pentavac SD, replicate 2

value: muscle


title: PERT_MU_0h_1

description:
m.muscle.Pertussis.00.1
Gene expression baseline at time 0 in muscle before injection with Pentavac SD.

source_name: Muscle, 0hr, Pentavac SD, replicate 1


title: genomic DNA from B3N4

description: breast tumor sample


title: Pca67


title: 8-cell 112815_02 SPIA

source_name: 8-cell embryo

value: 8-cell embryo


title: 8-cell 112815_01 SPIA


title: genomic DNA from B3N3

description: breast tumor sample


title: Norm12


title: 8-cell 112015_01 SPIA


title: BPH53


title: BPH23


title: LPS_MU_0h_2

description:
m.muscle.LPS.00.2
Gene expression baseline at time 0 in muscle before injection with LPS.

source_name: Muscle, 0hr, LPS, replicate 2

value: LPS


title: 8-cell 020816_10 SPIA

value: embryo


title: 8-cell 112015_02 SPIA


title: genomic DNA from B3N1

description: breast tumor sample

value: breast tumor


title: LPS_MU_0h_4

description:
m.muscle.LPS.00.4
Gene expression baseline at time 0 in muscle before injection with LPS.

source_name: Muscle, 0hr, LPS, replicate 4


title: Morula 020816_02 SPIA

source_name: Morula


title: LPS_MU_0h_3

description:
m.muscle.LPS.00.3
Gene expression baseline at time 0 in muscle before injection with LPS.

source_name: Muscle, 0hr, LPS, replicate 3


title: Pca51


title: 8-cell 020816_09 SPIA


title: Pca60


title: IFA_MU_0h_5

description:
m.muscle.IFA.00.5
Gene expression baseline at time 0 in muscle before injection with IFA.

source_name: Muscle, 0hr, IFA, replicate 5

value: IFA


title: LPS_MU_0h_1

description:
m.muscle.LPS.00.1
Gene expression baseline at time 0 in muscle before injection with LPS.

source_name: Muscle, 0hr, LPS, replicate 1


title: LPS_MU_0h_5

description:
m.muscle.LPS.00.5
Gene expression baseline at time 0 in muscle before injection with LPS.

source_name: Muscle, 0hr, LPS, replicate 5


title: Pca40


title: 8-cell 020816_08 SPIA


title: IFA_MU_0h_4

description:
m.muscle.IFA.00.4
Gene expression baseline at time 0 in muscle before injection with IFA.

source_name: Muscle, 0hr, IFA, replicate 4


title: genomic DNA from B3N2

description: breast tumor sample

value: diseased


title: genomic DNA from B2T6

description: breast tumor sample


title: 8-cell 020816_07 SPIA

value: SPIA


title: genomic DNA from B2T4

description: breast tumor sample

value: Female


title: 8-cell 020816_06 SPIA


title: genomic DNA from B2T5

description: breast tumor sample


title: Pca50

value: Prostate Cancer


title: genomic DNA from B2T3

description: breast tumor sample


title: 8-cell 011516_02 SPIA


title: BPH36

value: Benign Prostatic Hyperplasia


title: BPH32


title: IFA_MU_0h_1

description:
m.muscle.IFA.00.1
Gene expression baseline at time 0 in muscle before injection with IFA.

source_name: Muscle, 0hr, IFA, replicate 1


title: ENG_MU_0h_4

description:
m.muscle.Engerix.00.4
Gene expression baseline at time 0 in muscle before injection with Engerix B.

source_name: Muscle, 0hr, Engerix B, replicate 4

value: Engerix B


title: IFA_MU_0h_3

description:
m.muscle.IFA.00.3
Gene expression baseline at time 0 in muscle before injection with IFA.

source_name: Muscle, 0hr, IFA, replicate 3


title: IFA_MU_0h_2

description:
m.muscle.IFA.00.2
Gene expression baseline at time 0 in muscle before injection with IFA.

source_name: Muscle, 0hr, IFA, replicate 2


title: ENG_MU_0h_5

description:
m.muscle.Engerix.00.5
Gene expression baseline at time 0 in muscle before injection with Engerix B.

source_name: Muscle, 0hr, Engerix B, replicate 5


title: Norm3

source_name: plasma


title: genomic DNA from B1T6

description: breast tumor sample


title: ENG_MU_0h_3

description:
m.muscle.Engerix.00.3
Gene expression baseline at time 0 in muscle before injection with Engerix B.

source_name: Muscle, 0hr, Engerix B, replicate 3


title: Norm4


title: Norm17


title: ENG_MU_0h_2

description:
m.muscle.Engerix.00.2
Gene expression baseline at time 0 in muscle before injection with Engerix B.

source_name: Muscle, 0hr, Engerix B, replicate 2


title: genomic DNA from B1T7

description: breast tumor sample


title: DiPSC_serum_C2

city: Warsaw

first: Marcin

last: Tabaka

address: Kasprzaka 44/52

country: Poland

institute: International Centre for Translational Eye Research

data_processing:
Reads were aligned to the UCSC mm10 transcriptome (using RNA-Seq genome-aligner  STAR), and a matrix of UMI counts was obtained using CELLRANGER from the 10X Genomics pipeline  (v2.0.0) with default parameters
The raw expression matrix was downsampled to 15,000 UMIs per cell. Cells with less than 2000 UMIs per cell in total and all genes that were expressed in less than 50 cells were discarded, leaving 251,203 cells and  19,089 genes for further analysis. The elements of expression matrix were normalized by dividing UMI count by the total UMI counts per cell, multiplied by 10,000 and log-transformed after adding a pseudocount of 1.
Genome_build: mm10
Supplementary_files_format_and_content: txt file contains normalized and log-transformed expression matrix

molecule: polyA RNA

source_name: iPSCs

growth_protocol: For the reprogramming assay, 20,000 low passage MEFs (no greater than 3-4 passages from isolation) were seeded in a 6-well plate. These cells were cultured at 37°C and 5% CO2 in reprogramming medium containing KnockOut DMEM (GIBCO), 10% knockout serum replacement (KSR, GIBCO), 10% fetalbovine serum (FBS, GIBCO), 1% GlutaMAX (Invitrogen), 1% nonessential amino acids (NEAA, Invitrogen), 0.055 mM 2-mercaptoethanol (Sigma), 1% penicillin-streptomycin (Invitrogen) and 1,000 U/ml leukemia inhibitory factor (LIF, Millipore). Day 0 medium was supplemented with 2g/mL doxycycline Phase-1(Dox) to induce the polycistronic OKSM expression cassette. Medium was refreshed every other day. At day 8, doxycycline was withdrawn, and cells were transferred to either serum-free 2i medium containing 3 M CHIR99021, 1 M PD0325901, and LIF (Phase-2(2i)) (25) or maintained in reprogramming medium (Phase-2(serum)). Fresh medium was added every other day until the final time point on day 16. Oct4-EGFP positive iPSC colonies should start to appear on day 10, indicative of successful reprogramming of the endogenous Oct4 locus.

extract_protocol:
We collected a total of 250,000 cells over a period of 18 days in two different culture conditions. Cells were also collected from established iPSCs cell lines reprogrammed from the same MEFs, maintained either in Phase-2(2i) conditions or in Phase-2(serum) medium. For all time points, selected wells were trypsinized for 5 mins followed by inactivation of trypsin by addition of MEF medium. Cells were subsequently spun down and washed with 1X PBS supplemented with 0.1% bovine serum albumin. The cells were then passed through a 40 micron filter to remove cell debris and large clumps. Cell count was determined using Neubauer chamber hemocytometer to a final concentration of 1000 cells/ul.
Single-cell RNA-Seq libraries were generated from each time point using the 10X Genomics Chromium Controller Instrument (10X Genomics, Pleasanton, CA) and ChromiumTM Single Cell 3’ Reagent Kits v2  according to manufacturer’s instructions. Reverse transcription and sample indexing was performed using the C1000 Touch Thermal cycler with 96-Deep Well Reaction Module. Briefly, the suspended cells were loaded on a Chromium controller Single-Cell Instrument to first generate single-cell Gel Bead-In-Emulsions (GEMs). After breaking the GEMs, the barcoded cDNA was then purified and amplified. The amplified barcoded cDNA was fragmented, A-tailed and ligated with adaptors. Finally, PCR amplification was performed to enable sample indexing and enrichment of the 3’ RNA-Seq libraries. The final libraries were quantified using Thermo Fisher Qubit dsDNA HS Assay kit (Q32851) and the fragment size distribution of the libraries were determined using the Agilent 2100 BioAnalyzer High Sensitivity DNA kit (5067-4626). Pooled libraries were then sequenced using Illumina Sequencing By Synthesis (SBS) chemistry.

tag: cell types

value: iPSCs (OKSM)

tag: strain


title: genomic DNA from B2T1

description: breast tumor sample


title: DiPSC_serum_C1


title: genomic DNA from B2T2

description: breast tumor sample


title: Norm16


title: genomic DNA from B2N3

description: breast tumor sample


title: genomic DNA from B2N2

description: breast tumor sample


title: DiPSC_2i_C2


title: BPH59


title: BPH42


title: Norm2


title: genomic DNA from B1T5

description: breast tumor sample


title: genomic DNA from B2N1

description: breast tumor sample


title: DiPSC_2i_C1


title: D18_serum_C2

source_name: 2nd MEFs

value: 2nd MEFs (OKSM)


title: BPH43


title: genomic DNA from B1T4

description: breast tumor sample


title: D18_serum_C1


title: TriFLU-MF59_MLN_0h_4

description:
m.MLN.TriFluMF59.00.4
Gene expression baseline at time 0 in lymph nodes before injection with Fluad.

source_name: draining medial iliac lymph nodes (MLN), 0hr, Fluad, replicate 4

value: draining medial iliac lymph nodes (MLN)

value: Fluad


title: PCa65


title: PCa37


title: D18_2i_C2


title: TriFLU-MF59_MLN_0h_3

description:
m.MLN.TriFluMF59.00.3
Gene expression baseline at time 0 in lymph nodes before injection with Fluad.

source_name: draining medial iliac lymph nodes (MLN), 0hr, Fluad, replicate 3


title: TriFLU-MF59_MLN_0h_1

description:
m.MLN.TriFluMF59.00.1
Gene expression baseline at time 0 in lymph nodes before injection with Fluad.

source_name: draining medial iliac lymph nodes (MLN), 0hr, Fluad, replicate 1


title: PCa68


title: TriFLU_MLN_0h_5

description:
m.MLN.TriFlu.00.5
Gene expression baseline at time 0 in lymph nodes before injection with Agrippal.

source_name: draining medial iliac lymph nodes (MLN), 0hr, Agrippal, replicate 5

value: Agrippal


title: TriFLU-MF59_MLN_0h_5

description:
m.MLN.TriFluMF59.00.5
Gene expression baseline at time 0 in lymph nodes before injection with Fluad.

source_name: draining medial iliac lymph nodes (MLN), 0hr, Fluad, replicate 5


title: genomic DNA from B1T2

description: breast tumor sample


title: D18_2i_C1


title: ENG_MU_0h_1

description:
m.muscle.Engerix.00.1
Gene expression baseline at time 0 in muscle before injection with Engerix B.

source_name: Muscle, 0hr, Engerix B, replicate 1

value: muscle


title: genomic DNA from B1T3

description: breast tumor sample


title: TriFLU-MF59_MLN_0h_2

description:
m.MLN.TriFluMF59.00.2
Gene expression baseline at time 0 in lymph nodes before injection with Fluad.

source_name: draining medial iliac lymph nodes (MLN), 0hr, Fluad, replicate 2


title: 8-cell 011516_03 SPIA

source_name: 8-cell embryo

value: 8-cell embryo


title: D17.5_serum_C1


title: Norm179

value: Healthy Donor


title: D17.5_2i_C2


title: D17.5_2i_C1


title: D17_serum_C2


title: Norm285


title: genomic DNA from B1N1

description: breast tumor sample


title: D17.5_serum_C2


title: D17_serum_C1


title: genomic DNA from B1T1

description: breast tumor sample


title: PCa7


title: D17_2i_C1


title: SAL_MLN_0h_5

description:
m.MLN.saline.00.5
Gene expression baseline at time 0 in lymph nodes before injection with saline.

source_name: draining medial iliac lymph nodes (MLN), 0hr, Saline, replicate 5

value: saline


title: TriFLU_MLN_0h_4

description:
m.MLN.TriFlu.00.4
Gene expression baseline at time 0 in lymph nodes before injection with Agrippal.

source_name: draining medial iliac lymph nodes (MLN), 0hr, Agrippal, replicate 4


title: TriFLU_MLN_0h_3

description:
m.MLN.TriFlu.00.3
Gene expression baseline at time 0 in lymph nodes before injection with Agrippal.

source_name: draining medial iliac lymph nodes (MLN), 0hr, Agrippal, replicate 3


title: TriFLU_MLN_0h_2

description:
m.MLN.TriFlu.00.2
Gene expression baseline at time 0 in lymph nodes before injection with Agrippal.

source_name: draining medial iliac lymph nodes (MLN), 0hr, Agrippal, replicate 2


title: SAL_MLN_0h_4

description:
m.MLN.saline.00.4
Gene expression baseline at time 0 in lymph nodes before injection with saline.

source_name: draining medial iliac lymph nodes (MLN), 0hr, Saline, replicate 4


title: SAL_MLN_0h_3

description:
m.MLN.saline.00.3
Gene expression baseline at time 0 in lymph nodes before injection with saline.

source_name: draining medial iliac lymph nodes (MLN), 0hr, Saline, replicate 3


title: D16.5_2i_C2


title: D16.5_serum_C1


title: D16_serum_C2


title: D16.5_2i_C1


title: D17_2i_C2


title: genomic DNA from B1N2

description: breast tumor sample

value: breast tumor


title: SAL_MLN_0h_2

description:
m.MLN.saline.00.2
Gene expression baseline at time 0 in lymph nodes before injection with saline.

source_name: draining medial iliac lymph nodes (MLN), 0hr, Saline, replicate 2


title: D16_2i_C2


title: D16_serum_C1


title: D15.5_serum_C2


title: D16_2i_C1


title: PolyIC_MLN_0h_1

description:
m.MLN.PolyIC.00.1
Gene expression baseline at time 0 in lymph nodes before injection with Poly I:C.

source_name: draining medial iliac lymph nodes (MLN), 0hr, Poly I:C, replicate 1

value: PolyIC


title: PolyIC_MLN_0h_4

description:
m.MLN.PolyIC.00.4
Gene expression baseline at time 0 in lymph nodes before injection with Poly I:C.

source_name: draining medial iliac lymph nodes (MLN), 0hr, Poly I:C, replicate 4


title: PERT_MLN_0h_4

description:
m.MLN.Pertussis.00.4
Gene expression baseline at time 0 in lymph nodes before injection with Pentavac SD.

source_name: draining medial iliac lymph nodes (MLN), 0hr, Pentavac SD, replicate 4

value: Pentavac SD


title: PolyIC_MLN_0h_2

description:
m.MLN.PolyIC.00.2
Gene expression baseline at time 0 in lymph nodes before injection with Poly I:C.

source_name: draining medial iliac lymph nodes (MLN), 0hr, Poly I:C, replicate 2


title: D16.5_serum_C2

source_name: 2nd MEFs


title: SAL_MLN_0h_1

description:
m.MLN.saline.00.1
Gene expression baseline at time 0 in lymph nodes before injection with saline.

source_name: draining medial iliac lymph nodes (MLN), 0hr, Saline, replicate 1


title: D15.5_2i_C1


title: D15.5_2i_C2


title: PolyIC_MLN_0h_3

description:
m.MLN.PolyIC.00.3
Gene expression baseline at time 0 in lymph nodes before injection with Poly I:C.

source_name: draining medial iliac lymph nodes (MLN), 0hr, Poly I:C, replicate 3


title: PERT_MLN_0h_5

description:
m.MLN.Pertussis.00.5
Gene expression baseline at time 0 in lymph nodes before injection with Pentavac SD.

source_name: draining medial iliac lymph nodes (MLN), 0hr, Pentavac SD, replicate 5


title: PolyIC_MLN_0h_5

description:
m.MLN.PolyIC.00.5
Gene expression baseline at time 0 in lymph nodes before injection with Poly I:C.

source_name: draining medial iliac lymph nodes (MLN), 0hr, Poly I:C, replicate 5


title: D15_serum_C2


title: PERT_MLN_0h_3

description:
m.MLN.Pertussis.00.3
Gene expression baseline at time 0 in lymph nodes before injection with Pentavac SD.

source_name: draining medial iliac lymph nodes (MLN), 0hr, Pentavac SD, replicate 3


title: D15_serum_C1


title: D15.5_serum_C1


title: EMM1_shCNTL

city: Kumamoto

first: Yutaka

last: Okuno

state: Kumamoto

address: 1-1-1 Honko, Chuo Ku

department: Department of Hematology

country: Japan

institute: Kumamoto university of Medicine

data_processing:
Biomedical Genomics Workbench
Raw data filtering: Remove reads containing adapters, Remove reads containing N > 10% (N represents the base cannot be determined),  Remove reads containing low quality (Qscore<= 5) base which is over 50% of the total base.
Genome_build: hg19
Supplementary_files_format_and_content: text file with read counts and RPKM.

source_name: EMM1_control knockdown

growth_protocol: RPMI-1640 medium containing 10% FBS

extract_protocol:
Total RNA was isolated from cells using the ReliaPrep RNA Cell Miniprep System (Promega, Madison, WI, USA).
mRNA from eukaryotic organisms is enriched using oligo(dT) beads. For prokaryotic samples, rRNA is removed using the Ribo-Zero kit that leaves the mRNA. First, the mRNA is fragmented randomly by adding fragmentation buffer, then the cDNA is synthesized by using mRNA template and random hexamers primer, after which a custom second-strand synthesis buffer (Illumina) , dNTPs, RNase H and DNA polymerase I are added to initiate the second-strand synthesis. Second, after a series of terminal repair, A ligation and sequencing adaptor ligation, the double-stranded cDNA library is completed through size selection and PCR enrichment.

tag: cell line

tag: cell type

value: multiple myeloma


title: D15_2i_C2


title: D15_2i_C1


title: D14.5_serum_C2


title: EMM1_shMUC1

source_name: EMM1_MUC1 knockdown


title: D14.5_2i_C2


title: D14.5_serum_C1


title: D14.5_2i_C1


title: D13.5_serum_C2


title: D14_2i_C2


title: D14_serum_C1


title: D14_2i_C1


title: LPS_MLN_0h_3

description:
m.MLN.LPS.00.3
Gene expression baseline at time 0 in lymph nodes before injection with LPS.

source_name: draining medial iliac lymph nodes (MLN), 0hr, LPS, replicate 3

value: Female

value: LPS


title: LPS_MLN_0h_4

description:
m.MLN.LPS.00.4
Gene expression baseline at time 0 in lymph nodes before injection with LPS.

source_name: draining medial iliac lymph nodes (MLN), 0hr, LPS, replicate 4


title: PERT_MLN_0h_2

description:
m.MLN.Pertussis.00.2
Gene expression baseline at time 0 in lymph nodes before injection with Pentavac SD.

source_name: draining medial iliac lymph nodes (MLN), 0hr, Pentavac SD, replicate 2


title: LPS_MLN_0h_1

description:
m.MLN.LPS.00.1
Gene expression baseline at time 0 in lymph nodes before injection with LPS.

source_name: draining medial iliac lymph nodes (MLN), 0hr, LPS, replicate 1


title: WM1617RES

city: Debrecen

first: Viktoria

last: Koroknai

address: 26/B Kassai str.

department: Department of Public Health and Epidemiology

country: Hungary

institute: University of Debrecen

hyb_protocol: standard Affymetrix protocol

scan_protocol: standard Affymetrix protocol

data_processing: Affymetrix Genotyping Console was used for primary analysis. Copy number values were extracted and converted from CEL files into signal intensities using apt-copynumber-cyto 1.14.4 software, and CYCHP files were generated by Chromosome Analysis Suite (ChAS) 2.0 software according to the current protocol of UD-GenoMed Medical Genomic Technologies Ltd. ChAS 2.0 and Nexus 6.1 Copy Number Discovery softwares were used for further analysis.

label: biotin

source_name: melanoma cell line

label_protocol: Labeling, hybridization and image scan were performed according to the recent laboratory protocol of UD-GenoMed Medical Genomic Technologies Ltd.

growth_protocol: Human melanoma cell lines were maintained in RPMI 1640 medium supplemented with 10% foetal bovine serum, 300 mg/l L-glutamine and antibiotics.

extract_protocol: Genomic DNA was purified using Intron G-Spin Genomic DNA Extraction kit.

treatment_protocol: Human melanoma cell lines were switched to a medium containing 5 µM PLX4720 and cultured. The surviving cells were fed a medium containing PLX4720 every 3 days until they reached 80% confluence

tag: origin

value: generated from WM1617 metastatic melanoma cell line


title: LPS_MLN_0h_5

description:
m.MLN.LPS.00.5
Gene expression baseline at time 0 in lymph nodes before injection with LPS.

source_name: draining medial iliac lymph nodes (MLN), 0hr, LPS, replicate 5


title: LPS_MLN_0h_2

description:
m.MLN.LPS.00.2
Gene expression baseline at time 0 in lymph nodes before injection with LPS.

source_name: draining medial iliac lymph nodes (MLN), 0hr, LPS, replicate 2


title: PERT_MLN_0h_1

description:
m.MLN.Pertussis.00.1
Gene expression baseline at time 0 in lymph nodes before injection with Pentavac SD.

source_name: draining medial iliac lymph nodes (MLN), 0hr, Pentavac SD, replicate 1


title: D14_serum_C2


title: WM1617

value: metastatic melanoma tumor (primary pair:WM278)

tag: braf mutation status


title: D13.5_serum_C1


title: ENG_MLN_0h_5

description:
m.MLN.Engerix.00.5
Gene expression baseline at time 0 in lymph nodes before injection with Engerix B.

source_name: draining medial iliac lymph nodes (MLN), 0hr, Engerix B, replicate 5

value: Engerix B


title: WM278RES

value: generated from WM278 primary melanoma cell line


title: D13.5_2i_C2

source_name: 2nd MEFs

value: 2nd MEFs (OKSM)


title: IFA_MLN_0h_4

description:
m.MLN.IFA.00.4
Gene expression baseline at time 0 in lymph nodes before injection with IFA.

source_name: draining medial iliac lymph nodes (MLN), 0hr, IFA, replicate 4

value: draining medial iliac lymph nodes (MLN)

value: IFA


title: IFA_MLN_0h_2

description:
m.MLN.IFA.00.2
Gene expression baseline at time 0 in lymph nodes before injection with IFA.

source_name: draining medial iliac lymph nodes (MLN), 0hr, IFA, replicate 2


title: ENG_MLN_0h_4

description:
m.MLN.Engerix.00.4
Gene expression baseline at time 0 in lymph nodes before injection with Engerix B.

source_name: draining medial iliac lymph nodes (MLN), 0hr, Engerix B, replicate 4


title: IFA_MLN_0h_5

description:
m.MLN.IFA.00.5
Gene expression baseline at time 0 in lymph nodes before injection with IFA.

source_name: draining medial iliac lymph nodes (MLN), 0hr, IFA, replicate 5


title: ENG_MLN_0h_2

description:
m.MLN.Engerix.00.2
Gene expression baseline at time 0 in lymph nodes before injection with Engerix B.

source_name: draining medial iliac lymph nodes (MLN), 0hr, Engerix B, replicate 2


title: WM278

value: primary melanoma tumor (metastatic pair:WM1617)

tag: growth phase

value: VGP

tag: histologic type

value: NM


title: IFA_MLN_0h_1

description:
m.MLN.IFA.00.1
Gene expression baseline at time 0 in lymph nodes before injection with IFA.

source_name: draining medial iliac lymph nodes (MLN), 0hr, IFA, replicate 1


title: IFA_MLN_0h_3

description:
m.MLN.IFA.00.3
Gene expression baseline at time 0 in lymph nodes before injection with IFA.

source_name: draining medial iliac lymph nodes (MLN), 0hr, IFA, replicate 3


title: ENG_MLN_0h_1

description:
m.MLN.Engerix.00.1
Gene expression baseline at time 0 in lymph nodes before injection with Engerix B.

source_name: draining medial iliac lymph nodes (MLN), 0hr, Engerix B, replicate 1


title: D13.5_2i_C1


title: ENG_MLN_0h_3

description:
m.MLN.Engerix.00.3
Gene expression baseline at time 0 in lymph nodes before injection with Engerix B.

source_name: draining medial iliac lymph nodes (MLN), 0hr, Engerix B, replicate 3


title: TriFLU-MF59_BL_0h_5

description:
m.blood.TriFluMF59.00.5
Gene expression baseline at time 0 in blood before injection with Fluad.

source_name: Peripheral Blood, 0hr, Fluad, replicate 5

value: PBMC

value: Fluad


title: D13_serum_C2


title: WM983BRES

value: generated from WM983B metastatic melanoma cell line


title: WM983B

value: metastatic melanoma tumor (primary pair:WM983A)


title: D13_2i_C2


title: WM983ARES

value: generated from WM983A primary melanoma cell line


title: D13_serum_C1


title: TriFLU_MLN_0h_1

description:
m.MLN.TriFlu.00.1
Gene expression baseline at time 0 in lymph nodes before injection with Agrippal.

source_name: draining medial iliac lymph nodes (MLN), 0hr, Agrippal, replicate 1

value: Female

value: Agrippal


title: D13_2i_C1


title: WM983A

source_name: melanoma cell line

value: primary melanoma tumor (metastatic pair:WM983B)


title: TriFLU-MF59_BL_0h_2

description:
m.blood.TriFluMF59.00.2
Gene expression baseline at time 0 in blood before injection with Fluad.

source_name: Peripheral Blood, 0hr, Fluad, replicate 2


title: TriFLU-MF59_BL_0h_4

description:
m.blood.TriFluMF59.00.4
Gene expression baseline at time 0 in blood before injection with Fluad.

source_name: Peripheral Blood, 0hr, Fluad, replicate 4


title: TriFLU-MF59_BL_0h_1

description:
m.blood.TriFluMF59.00.1
Gene expression baseline at time 0 in blood before injection with Fluad.

source_name: Peripheral Blood, 0hr, Fluad, replicate 1


title: TriFLU-MF59_BL_0h_3

description:
m.blood.TriFluMF59.00.3
Gene expression baseline at time 0 in blood before injection with Fluad.

source_name: Peripheral Blood, 0hr, Fluad, replicate 3


title: D12.5_serum_C2

source_name: 2nd MEFs


title: TriFLU_BL_0h_4

description:
m.blood.TriFlu.00.4
Gene expression baseline at time 0 in blood before injection with Agrippal.

source_name: Peripheral Blood, 0hr, Agrippal, replicate 4


title: D12.5_serum_C1


title: TriFLU_BL_0h_5

description:
m.blood.TriFlu.00.5
Gene expression baseline at time 0 in blood before injection with Agrippal.

source_name: Peripheral Blood, 0hr, Agrippal, replicate 5


title: D12.5_2i_C2


title: YS B-1 RNA [036_RNA_031]

city: Kalamazoo

first: Momoko

last: Yoshimoto

address: 300 Portage St.

department: Investigative Medicine

institute: WMU Homer Stryker MD School of Medicine

data_processing:
Sequence reads were aligned to the mouse reference genome mm10 with STAR-2.4.2a.
featureCounts (subread-1.5.0) was used to quantify gene expression (parameters applied: "“-s 1 –Q 10")
Differential expression analysis was performed using edgeR.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files including raw read counts for each Sample

source_name: YS on OP9 for 10 days

growth_protocol: ES cells and E10 yolk sac cells were differentiated into B progenitors in co-culture with OP-9 stromal cells with IL-7 and Flt3-ligand. CD19+B220+ B progenitors were isolated rom fetal liver and adult BM and expanded on OP-9 stromal cells with IL-7 and Flt3-ligand.

extract_protocol: We used standard Ion Total RNA-Seq kit v2 protocol with RiboZero rRNA depletion

tag: strain/cell line

tag: tissue/cell type

value: yolk sac

tag: cell subtype

value: YS-derived B-1 progenitors


title: ES B-1 RNA [036_RNA_032]

source_name: Flk1 on OP9 for 14 days

value: ES cells

value: ES cell derived B-1 progenitors


title: BM B2 RNA-3 [036_RNA_029]

source_name: BM CD19+B220+ cells on OP9

value: bone marrow

value: BM-derived B-1 progenitors


title: D12_serum_C1

value: 2nd MEFs (OKSM)


title: BM B2 RNA-4 [036_RNA_030]


title: TriFLU_BL_0h_2

description:
m.blood.TriFlu.00.2
Gene expression baseline at time 0 in blood before injection with Agrippal.

source_name: Peripheral Blood, 0hr, Agrippal, replicate 2

tag: strain/background


title: D12_2i_C2


title: LIVER B1 d [029_RNA_028]

source_name: E14.5 fetal liver CD19+ cells on OP9 for 6 days

value: fetal liver

value: Fetal liver derived B-progenitors


title: BM B2 RNA-1 [036_RNA_022]


title: D12_2i_C1


title: TriFLU_BL_0h_1

description:
m.blood.TriFlu.00.1
Gene expression baseline at time 0 in blood before injection with Agrippal.

source_name: Peripheral Blood, 0hr, Agrippal, replicate 1

tag: gender

value: PBMC


title: LIVER B1 c [029_RNA_027]


title: SAL_BL_0h_5

description:
m.blood.saline.00.5
Gene expression baseline at time 0 in blood before injection with saline.

source_name: Peripheral Blood, 0hr, Saline, replicate 5

tag: tissue

value: saline


title: LIVER B1 b [029_RNA_026]


title: TriFLU_BL_0h_3

description:
m.blood.TriFlu.00.3
Gene expression baseline at time 0 in blood before injection with Agrippal.

source_name: Peripheral Blood, 0hr, Agrippal, replicate 3

tag: treatment


title: SAL_BL_0h_3

description:
m.blood.saline.00.3
Gene expression baseline at time 0 in blood before injection with saline.

source_name: Peripheral Blood, 0hr, Saline, replicate 3

tag: timepoint


title: D12.5_2i_C1


title: SAL_BL_0h_1

description:
m.blood.saline.00.1
Gene expression baseline at time 0 in blood before injection with saline.

source_name: Peripheral Blood, 0hr, Saline, replicate 1

tag: animal replicate


title: LIVER B1 a [029_RNA_025]


title: SAL_BL_0h_2

description:
m.blood.saline.00.2
Gene expression baseline at time 0 in blood before injection with saline.

source_name: Peripheral Blood, 0hr, Saline, replicate 2


title: BM B2 RNA-2 [036_RNA_023]


title: SAL_BL_0h_4

description:
m.blood.saline.00.4
Gene expression baseline at time 0 in blood before injection with saline.

source_name: Peripheral Blood, 0hr, Saline, replicate 4


title: D11.5_serum_C2

tag: cell types


title: PolyIC_BL_0h_5

description:
m.blood.PolyIC.00.5
Gene expression baseline at time 0 in blood before injection with Poly I:C.

source_name: Peripheral Blood, 0hr, Poly I:C, replicate 5

value: PolyIC


title: D11.5_serum_C1

tag: strain


title: D11.5_2i_C2


title: YS B1 d [029_RNA_024]


title: YS B1 c [029_RNA_023]


title: D11.5_2i_C1


title: D11_serum_C2


title: YS B1 a [029_RNA_021]


title: YS B1 b [029_RNA_022]


title: D11_serum_C1


title: D12_serum_C2


title: ESC B1 d [029_RNA_020]

source_name: Flk1 on OP9 for 13 days


title: D11_2i_C2

source_name: 2nd MEFs


title: PolyIC_BL_0h_4

description:
m.blood.PolyIC.00.4
Gene expression baseline at time 0 in blood before injection with Poly I:C.

source_name: Peripheral Blood, 0hr, Poly I:C, replicate 4


title: D11_2i_C1


title: D10.5_serum_C2


title: ESC B1 b [029_RNA_018]

source_name: VEcad on OP9 for 16 days


title: ESC B1 a [029_RNA_017]


title: ESC B1 c [029_RNA_019]


title: D10.5_serum_C1


title: PolyIC_BL_0h_3

description:
m.blood.PolyIC.00.3
Gene expression baseline at time 0 in blood before injection with Poly I:C.

source_name: Peripheral Blood, 0hr, Poly I:C, replicate 3


title: PolyIC_BL_0h_1

description:
m.blood.PolyIC.00.1
Gene expression baseline at time 0 in blood before injection with Poly I:C.

source_name: Peripheral Blood, 0hr, Poly I:C, replicate 1


title: F_NormalHead3

first: Debashis

last: Sahoo

state: California

address: 9500 Gillman Drive

department: Pediatrics

institute: UCSD

data_processing:
RNA-seq data was mapped with OLego (v.1.1.5) and normalized by using TPM (transcripts per millions) analysis
Total number of reads mapped to a known transcript annotation was estimated using featureCounts version v1.5.0-p2
Expression levels for each transcript were determined by normalizing the counts returned by featureCounts using a custom Perl script
Genome_build: dm6
Supplementary_files_format_and_content: tab-delimited text files include count number reads per gene for each Sample

organism: Drosophila melanogaster

source_name: Head

growth_protocol: The flies were maintained on reguler corn meal

extract_protocol:
The heads were collected from flies kept on liquid nitrogen with 10 seconds vortexing. The RNA for each biological replicate consist of ~100 heads. The RNA for the body was collected from 10 bodies.
Libraries were multiplexed and sequenced with 100 base pair (bp) paired end (PE100) Rapid Run to a depth of approximately 300 million reads per sample on an illumina HiSeq2500

treatment_protocol: For the high fat diet 5-7 day flies were kept on diet consisting of 20% coconut oil

tag: diet

value: Regular Diet

value: Head

tag: Stage

value: Adult


title: PolyIC_BL_0h_2

description:
m.blood.PolyIC.00.2
Gene expression baseline at time 0 in blood before injection with Poly I:C.

source_name: Peripheral Blood, 0hr, Poly I:C, replicate 2

value: Female


title: D10.5_2i_C1


title: D10_serum_C2


title: PERT_BL_0h_4

description:
m.blood.Pertussis.00.4
Gene expression baseline at time 0 in blood before injection with Pentavac SD.

source_name: Peripheral Blood, 0hr, Pentavac SD, replicate 4

value: Pentavac SD


title: D10_serum_C1


title: F_NormalHead2


title: D10_2i_C2


title: D10.5_2i_C2


title: PERT_BL_0h_3

description:
m.blood.Pertussis.00.3
Gene expression baseline at time 0 in blood before injection with Pentavac SD.

source_name: Peripheral Blood, 0hr, Pentavac SD, replicate 3


title: PERT_BL_0h_5

description:
m.blood.Pertussis.00.5
Gene expression baseline at time 0 in blood before injection with Pentavac SD.

source_name: Peripheral Blood, 0hr, Pentavac SD, replicate 5


title: F_NormalHead4


title: LPS_BL_0h_4

description:
m.blood.LPS.00.4
Gene expression baseline at time 0 in blood before injection with LPS.

source_name: Peripheral Blood, 0hr, LPS, replicate 4

value: LPS


title: PERT_BL_0h_2

description:
m.blood.Pertussis.00.2
Gene expression baseline at time 0 in blood before injection with Pentavac SD.

source_name: Peripheral Blood, 0hr, Pentavac SD, replicate 2


title: F_NormalBody3

source_name: Body without head

value: Body without head


title: D10_2i_C1


title: LPS_BL_0h_2

description:
m.blood.LPS.00.2
Gene expression baseline at time 0 in blood before injection with LPS.

source_name: Peripheral Blood, 0hr, LPS, replicate 2


title: WM1617

data_processing: Affymetrix Expression Console was used for primary analysis, RMA algorithm with default settings.

source_name: melanoma cell line

extract_protocol: Total RNA was isolated using Qiagen Rneasy Plus Mini kit.

tag: origin

value: metastatic melanoma tumor (primary pair:WM278)


title: D9.5_serum_C2


title: PERT_BL_0h_1

description:
m.blood.Pertussis.00.1
Gene expression baseline at time 0 in blood before injection with Pentavac SD.

source_name: Peripheral Blood, 0hr, Pentavac SD, replicate 1


title: WM278RES

value: generated from WM278 primary melanoma cell line


title: F_NormalBody2


title: F_HighHead4

value: High Fat Diet


title: LPS_BL_0h_5

description:
m.blood.LPS.00.5
Gene expression baseline at time 0 in blood before injection with LPS.

source_name: Peripheral Blood, 0hr, LPS, replicate 5


title: D9.5_serum_C1

source_name: 2nd MEFs


title: LPS_BL_0h_3

description:
m.blood.LPS.00.3
Gene expression baseline at time 0 in blood before injection with LPS.

source_name: Peripheral Blood, 0hr, LPS, replicate 3


title: F_HighHead3


title: WM983BRES

value: generated from WM983B metastatic melanoma cell line


title: WM1617RES

value: generated from WM1617 metastatic melanoma cell line


title: WM278

value: primary melanoma tumor (metastatic pair:WM1617)

value: VGP

value: NM

tag: braf mutation status


title: F_HighHead2


title: D9.5_2i_C2

value: 2nd MEFs (OKSM)


title: IFA_BL_0h_5

description:
m.blood.IFA.00.5
Gene expression baseline at time 0 in blood before injection with IFA.

source_name: Peripheral Blood, 0hr, IFA, replicate 5

value: PBMC

value: IFA


title: D9.5_2i_C1


title: LPS_BL_0h_1

description:
m.blood.LPS.00.1
Gene expression baseline at time 0 in blood before injection with LPS.

source_name: Peripheral Blood, 0hr, LPS, replicate 1


title: F_NormalBody4

value: Regular Diet


title: IFA_BL_0h_4

description:
m.blood.IFA.00.4
Gene expression baseline at time 0 in blood before injection with IFA.

source_name: Peripheral Blood, 0hr, IFA, replicate 4


title: D9_serum_C2


title: F_HighBody4

value: Adult


title: F_HighBody3

value: Female


title: WM983ARES

value: generated from WM983A primary melanoma cell line


title: IFA_BL_0h_3

description:
m.blood.IFA.00.3
Gene expression baseline at time 0 in blood before injection with IFA.

source_name: Peripheral Blood, 0hr, IFA, replicate 3


title: D9_2i_C2


title: F_HighBody2


title: M_NormalHead3

source_name: Head

value: Male

value: Head


title: D9_2i_C1


title: IFA_BL_0h_2

description:
m.blood.IFA.00.2
Gene expression baseline at time 0 in blood before injection with IFA.

source_name: Peripheral Blood, 0hr, IFA, replicate 2


title: D8.75_serum_C2


title: M_NormalHead1


title: ENG_BL_0h_5

description:
m.blood.Engerix.00.5
Gene expression baseline at time 0 in blood before injection with Engerix B.

source_name: Peripheral Blood, 0hr, Engerix B, replicate 5

value: Engerix B


title: D8.75_serum_C1


title: ENG_BL_0h_4

description:
m.blood.Engerix.00.4
Gene expression baseline at time 0 in blood before injection with Engerix B.

source_name: Peripheral Blood, 0hr, Engerix B, replicate 4


title: Cell Sample 1 condition 1b rep 3

city: San Francisco

first: Cassandra

middle: D

last: Belair

address: 35 Medical Center Way

department: Urology

institute: UCSF

description:
50ng input RNA; 3' adapter 0.85uM; 5' adapter 3.3uM unmodified; 14 cycles
processed data file: BCRB17_completeSummary.txt
BCRB17_4N_036_cell_PC3_50ng_original
processed data file: BCRB17_Mature_counts_raw.txt

data_processing:
demultiplex: CutAdapt v1.11 --no-trim -e 0 -O 20
trim adapters: CutAdapt v1.11 -u 4 -m 17 -e 0 -O 20
align to custom genomes using bowtie v1.1.2 or bowtie2 v2.2.5 sequentially removing adapter/marker "contaminant" sequences, mature miRNA, other small RNAs, then finally to genomic sequences
bowtie2 --local -L 17 (contaminant genome)
bowtie -n 0 -l 18 --best (all other genomes)
all files in BCRB17 set were aligned using STAR
(all small RNA genomes) params='--genomeLoad NoSharedMemory --outReadsUnmapped Fastx --outSAMtype BAM SortedByCoordinate --outSAMunmapped None  --outFilterMismatchNmax 0.05 --outFilterMatchNmin 16 --outFilterScoreMinOverLread 0 --outFilterMatchNminOverLread 0 --outFilterMultimapScoreRange 0 --outFilterMultimapNmax 1 --limitBAMsortRAM 4044427000'
(genomic) params2='--genomeLoad NoSharedMemory --outReadsUnmapped Fastx --outSAMtype BAM SortedByCoordinate --outSAMunmapped None  --outFilterMismatchNmax 0.5 --outFilterMatchNmin 16 --outFilterScoreMinOverLread 0 --outFilterMatchNminOverLread 0 --outFilterMultimapScoreRange 0 --outFilterMultimapNmax 1 --limitBAMsortRAM 2544427000'
custom bash script to generate counts
custom bash or r scripts to collapse PCR duplicates using UMI
Genome_build: hg19 for human genome, small RNAs downloaded from RNACentral Database release5
Supplementary_files_format_and_content: delimited files containing either counts or sequences

source_name: cell line

extract_protocol:
Qiagen micro miRNeasy kit modified to use 1:7 plasma:Trizol or 1:3 plasma:Trizol LS
see manuscript for details

tag: cell line

tag: Sex


title: WM983B

value: metastatic melanoma tumor (primary pair:WM983A)


title: WM983A

treatment_protocol: To select the invasive subpopulations, the invading cells in the lower layer chamber of Matrigel Invasion Assay were treated with a 0.5% trypsin/0.2% EDTA solution for recovery from the membrane and cultured using standard protocols until the RNA isolation.

value: primary melanoma tumor

tag: growth phase

tag: histologic type


title: D8.75_2i_C2


title: M_NormalBody3

value: Body without head


title: Total RNA from ground cells, Standard medium, biological replicate 3_array

city: Milan

first: Silvia

last: Bradamante

address: Via Golgi 19

institute: CNR-ISTM, Institute of Molecular Science and Technology

hyb_protocol: Hybridization was performed onto Affymetrix Gene Human 1.0 ST arrays (28.869 genes) (Affymetrix, Santa Clara, CA,USA).

scan_protocol: GeneChip arrays were scanned using an AffymetrixGeneChip® Scanner3000 7G using default parameters. AffymetrixGeneChip® Command Console software (AGCC) was used to acquire GeneChip® images and generate .DAT and .CEL files

data_processing:
Partek Genomics Suite v 6.4 was used for analysis of microarray data
The list of the differentially expressed genes was obtained using ANOVA. A 1.3-FC cutoff value coupled with p <0.05 and a false discovery rate (FDR) filter were used to distinguish statistically higher or lower gene expression from random variation

source_name: hBMSCs on ground cultured in osteogenic medium

label_protocol: 5-30 ng of high quality total RNA were used to synthesize Biotin-labeled cDNA targets. Double stranded cDNA synthesis and related cRNA was performed with Nugen® Pico WTA Systems V2 (NuGEN Technologies, Inc). With the Encore® Biotin Module (NuGEN Technologies, Inc) was synthesized the fragmented and labeled cDNA.

growth_protocol:
Standard Medium (SM): DMEM (Dulbecco’s Modified Eagle’s medium) supplemented with 12.5 mM HEPES, 10 U/mL heparin, 200 mM glutamine, 500 μg/mL streptomycin sulphate, 600 μg/mL penicillin.
Osteogenic Medium (OM): SM added with 0.1 M ascorbic acid, 10 mM b-glycerophosphate, and 10-8 M 1,25(OH)2D3 (Vit D3).

extract_protocol: Samples were preserved in RNAlater; resuspended by scraping in Trizol (Thermo Fisher Scientific) for total RNA extraction.

tag: cell type

value: bone marrow mesenchymal stem cells

tag: location

value: ground

tag: medium

value: standard


title: Total RNA from ground cells, Standard medium, biological replicate 1_array


title: M_NormalHead2

tag: gender

tag: tissue


title: IFA_BL_0h_1

description:
m.blood.IFA.00.1
Gene expression baseline at time 0 in blood before injection with IFA.

source_name: Peripheral Blood, 0hr, IFA, replicate 1

tag: strain/background

tag: treatment

tag: timepoint


title: ENG_BL_0h_3

description:
m.blood.Engerix.00.3
Gene expression baseline at time 0 in blood before injection with Engerix B.

source_name: Peripheral Blood, 0hr, Engerix B, replicate 3

tag: animal replicate


title: Total RNA from ground cells, Osteogenic medium, biological replicate 1_array

value: osteogenic


title: ENG_BL_0h_2

description:
m.blood.Engerix.00.2
Gene expression baseline at time 0 in blood before injection with Engerix B.

source_name: Peripheral Blood, 0hr, Engerix B, replicate 2


title: Total RNA from ground cells, Osteogenic medium, biological replicate 2_array


title: Total RNA from ground cells, Standard medium, biological replicate 2_array


title: Total RNA from ground cells, Osteogenic medium, biological replicate 3_array


title: D8.75_2i_C1

tag: cell types

value: 2nd MEFs (OKSM)

tag: strain


title: ENG_BL_0h_1

description:
m.blood.Engerix.00.1
Gene expression baseline at time 0 in blood before injection with Engerix B.

source_name: Peripheral Blood, 0hr, Engerix B, replicate 1

value: PBMC


title: Cell Sample 1 condition 1b rep 2

description:
50ng input RNA; 3' adapter 0.85uM; 5' adapter 3.3uM unmodified; 14 cycles
processed data file: BCRB17_completeSummary.txt
BCRB17_4N_035_cell_PC3_50ng_original
processed data file: BCRB17_Mature_counts_raw.txt


title: Total RNA from flight cells, Standard medium, biological replicate 3_array

source_name: hBMSCs on board the ISS cultured in standard medium

value: on board ISS


title: M_NormalBody2

source_name: Body without head

tag: diet

value: Regular Diet

tag: Stage


title: Total RNA from flight cells, Standard medium, biological replicate 4_array


title: D8.5_serum_C2

source_name: 2nd MEFs


title: M_NormalBody1

value: Adult


title: Total RNA from flight cells, Standard medium, biological replicate 2_array


title: Cell Sample 1 condition 1b rep 1

description:
50ng input RNA; 3' adapter 0.85uM; 5' adapter 3.3uM unmodified; 14 cycles
processed data file: BCRB17_completeSummary.txt
BCRB17_4N_034_cell_PC3_50ng_original
processed data file: BCRB17_Mature_counts_raw.txt

tag: cell line


title: D9_serum_C1


title: Cell Sample 1 condition 1 rep 3

description:
500ng input RNA; 3' adapter 0.85uM; 5' adapter 3.3uM unmodified; 14 cycles
processed data file: BCRB17_completeSummary.txt
BCRB17_4N_033_cell_PC3_500ng_original
processed data file: BCRB17_Mature_counts_raw.txt

tag: Sex


title: M_HighHead4

value: High Fat Diet


title: D8.5_serum_C1


title: D8.5_2i_C2


title: D8.5_2i_C1


title: D8.25_serum_C2


title: Cell Sample 1 condition 1 rep 1

description:
500ng input RNA; 3' adapter 0.85uM; 5' adapter 3.3uM unmodified; 14 cycles
processed data file: BCRB17_completeSummary.txt
BCRB17_4N_031_cell_PC3_500ng_original
processed data file: BCRB17_Mature_counts_raw.txt


title: Plasma Sample3 condition 1b rep 3

description:
50 ul Plasma input; 3' adapter 0.85uM; 5' adapter 3.3uM unmodified; 14 cycles
processed data file: BCRB17_completeSummary.txt
BCRB17_4N_030_plasmaRB4_50ul_original
processed data file: BCRB17_Mature_counts_raw.txt

source_name: plasma

value: plasma


title: Total RNA from flight cells, Standard medium, biological replicate 1_array


title: M_HighHead2

value: Male


title: M_HighBody3


title: M_HighBody4


title: D8.25_serum_C1


title: Plasma Sample3 condition 1b rep 2

description:
50 ul Plasma input; 3' adapter 0.85uM; 5' adapter 3.3uM unmodified; 14 cycles
processed data file: BCRB17_completeSummary.txt
BCRB17_4N_029_plasmaRB4_50ul_original
processed data file: BCRB17_Mature_counts_raw.txt


title: M_HighBody2


title: Total RNA from flight cells, Osteogenic medium, biological replicate 3_array

source_name: hBMSCs on board the ISS cultured in osteogenic medium


title: Total RNA from flight cells, Osteogenic medium, biological replicate 2_array


title: D8.25_2i_C2


title: Plasma Sample2 condition 1b rep 3

description:
50 ul Plasma input; 3' adapter 0.85uM; 5' adapter 3.3uM unmodified; 14 cycles
processed data file: BCRB17_completeSummary.txt
BCRB17_4N_027_plasmaCB3_50ul_original
processed data file: BCRB17_Mature_counts_raw.txt

value: Female


title: Plasma Sample3 condition 1b rep 1

description:
50 ul Plasma input; 3' adapter 0.85uM; 5' adapter 3.3uM unmodified; 14 cycles
processed data file: BCRB17_completeSummary.txt
BCRB17_4N_028_plasmaRB4_50ul_original
processed data file: BCRB17_Mature_counts_raw.txt


title: D8_Dox_C2


title: Cell Sample 1 condition 1 rep 2

description:
500ng input RNA; 3' adapter 0.85uM; 5' adapter 3.3uM unmodified; 14 cycles
processed data file: BCRB17_completeSummary.txt
BCRB17_4N_032_cell_PC3_500ng_original
processed data file: BCRB17_Mature_counts_raw.txt


title: M_HighHead3

value: Head


title: Plasma Sample2 condition 1b rep 1

description:
50 ul Plasma input; 3' adapter 0.85uM; 5' adapter 3.3uM unmodified; 14 cycles
processed data file: BCRB17_completeSummary.txt
BCRB17_4N_025_plasmaCB3_50ul_original
processed data file: BCRB17_Mature_counts_raw.txt


title: Total RNA from flight cells, Osteogenic medium, biological replicate 1_array


title: D7.5_Dox_C1


title: D7.5_Dox_C2


title: Plasma Sample3 condition 1 rep 2

description:
250 ul Plasma input; 3' adapter 0.85uM; 5' adapter 3.3uM unmodified; 14 cycles
processed data file: BCRB17_completeSummary.txt
BCRB17_4N_023_plasmaRB4_250ul_original
processed data file: BCRB17_Mature_counts_raw.txt


title: longterm non-infected donor 4

city: Berlin

first: Hans-Joachim

last: Mollenkopf

address: Charitéplatz 1

country: Germany

institute: Max-Planck-Institute for Infection Biology

hyb_protocol: After precipitation, purification and quantification, 0.75µg labeled samples were hybridized according to the supplier's protocol (Agilent Technologies).

scan_protocol: Scanning of microarrays was performed with 3µm resolution using a G2565CA high resolution laser microarray scanner (Agilent Technologies).

data_processing: Microarray image data were extracted and analyzed with the Image Analysis / Feature Extraction software G2567AA (Version A.10.10.1, Agilent Technologies) using default settings and the GE1_1105_Oct12 extraction protocol. The extracted single-color raw data txt files were further analyzed using R and the associated BioConductor package limma. Background was removed using method normexp with offset 15, followed by quantile normalization.

source_name: D5 - longterm non-infected

label_protocol: RNA was labeled with the single-color Low Input Quick Amp Labeling Kit  (Agilent Technologies) according to manufacturer’s instructions.

growth_protocol: Epithelial progenitor isolation from fallopian tube samples and organoid culture was done as previously described (Nat Commun. 2015 Dec 8;6:8989. doi: 10.1038/ncomms9989.)

extract_protocol: Total RNA was isolated by the TRIzol Reagent RNA preparation method (Invitrogen, Karlsruhe, Germany) using Glycogen as carrier.

treatment_protocol:
For infection with Chlamydia trachomatis D (CtrD) 2 wells of organoids were released from MatrigelTM with cold DPBS, pooled and mechanically disrupted by passing them through a 26xG needle. The fragmented organoids were divided equally into 2 tubes for infection and mock control. After centrifugation (300xg, 5min) and removal of the supernatant, 10µl CtrD (from a frozen stock with 108 IFU/mL as determined by titration on HeLa cells) were added to one tube of the pelleted organoids. The suspension was mixed by pipetting and incubated for 15min at 35°C followed by 5min on ice. The mock control was treated the same, but without addition of CtrD. Finally, 50µL MatrigelTM was added to each tube, the organoids seeded and placed in a humidified incubator at 5% CO2 and 35°C. Splitting of organoids was done every 3-4 weeks. RNA samples were taken at 72h p.i. and 1M p.i. At 4 months p.i. the infection was cured by applying a mixture of Penicillin (100 U/mL) and Streptomycin (100 µg/mL) to the organoid culture for one week.
After curing, a re-infection was carried out identical to the first infection with mechanical splitting, adding of CtrD to one half of the organoids and mock treatment of the other half. Also, the control organoids that have not been infected with CtrD before were infected and mock treated again. 72h post seeding RNA samples were taken of the now 2x infected (chronic cured acute), chronic infected (chronic cured), acute infected (longterm acute) and the never infected organoids

tag: donor

tag: condition

value: LT-NI

value: fallopian tube organoid culture


title: Plasma Sample3 condition 1 rep 1

description:
250 ul Plasma input; 3' adapter 0.85uM; 5' adapter 3.3uM unmodified; 14 cycles
processed data file: BCRB17_completeSummary.txt
BCRB17_4N_022_plasmaRB4_250ul_original
processed data file: BCRB17_Mature_counts_raw.txt


title: longterm infected donor 4

source_name: D4 - longterm infected

value: LT-CtrD


title: Baseline  (early passage organoids) donor 4

source_name: D4 - Baseline  (early passage organoids)

value: Baseline


title: D7_Dox_C1


title: Plasma Sample2 condition 1b rep 2

description:
50 ul Plasma input; 3' adapter 0.85uM; 5' adapter 3.3uM unmodified; 14 cycles
processed data file: BCRB17_completeSummary.txt
BCRB17_4N_026_plasmaCB3_50ul_original
processed data file: BCRB17_Mature_counts_raw.txt


title: Baseline  (early passage organoids) donor 3

source_name: D3 - Baseline  (early passage organoids)


title: longterm infected donor 3

source_name: D3 - longterm infected


title: D8.25_2i_C1


title: Plasma Sample2 condition 1 rep 2

description:
250 ul Plasma input; 3' adapter 0.85uM; 5' adapter 3.3uM unmodified; 14 cycles
processed data file: BCRB17_completeSummary.txt
BCRB17_4N_020_plasmaCB3_250ul_original
processed data file: BCRB17_Mature_counts_raw.txt


title: D6.5_Dox_C2


title: D8_Dox_C1


title: Plasma Sample2 condition 1 rep 1

description:
250 ul Plasma input; 3' adapter 0.85uM; 5' adapter 3.3uM unmodified; 14 cycles
processed data file: BCRB17_completeSummary.txt
BCRB17_4N_019_plasmaCB3_250ul_original
processed data file: BCRB17_Mature_counts_raw.txt


title: Plasma Sample3 condition 1 rep 3

description:
250 ul Plasma input; 3' adapter 0.85uM; 5' adapter 3.3uM unmodified; 14 cycles
processed data file: BCRB17_completeSummary.txt
BCRB17_4N_024_plasmaRB4_250ul_original
processed data file: BCRB17_Mature_counts_raw.txt


title: Plasma Sample2 condition 1 rep 3

description:
250 ul Plasma input; 3' adapter 0.85uM; 5' adapter 3.3uM unmodified; 14 cycles
processed data file: BCRB17_completeSummary.txt
BCRB17_4N_021_plasmaCB3_250ul_original
processed data file: BCRB17_Mature_counts_raw.txt


title: D6.5_Dox_C1


title: D7_Dox_C2


title: D6_Dox_C2


title: D6_Dox_C1


title: Cell Sample 1 condition 7b rep 1

description:
50ng RNA input; 3' adapter 0.05uM; 5' adapter 0.33uM modified; 14 cycles
processed data file: BCRB17_completeSummary.txt
BCRB17_4N_016_cell_PC3_50ng_optimized
processed data file: BCRB17_Mature_counts_raw.txt


title: Cell Sample 1 condition 7b rep 2

description:
50ng RNA input; 3' adapter 0.05uM; 5' adapter 0.33uM modified; 14 cycles
processed data file: BCRB17_completeSummary.txt
BCRB17_4N_017_cell_PC3_50ng_optimized
processed data file: BCRB17_Mature_counts_raw.txt


title: D5.5_Dox_C2


title: Cell Sample 1 condition 7 rep 3

description:
500ng RNA input; 3' adapter 0.05uM; 5' adapter 0.33uM modified; 14 cycles
processed data file: BCRB17_completeSummary.txt
BCRB17_4N_015_cell_PC3_500ng_optimized
processed data file: BCRB17_Mature_counts_raw.txt


title: longterm non-infected donor 3

source_name: D3 - longterm non-infected


title: D5.5_Dox_C1


title: Cell Sample 1 condition 7b rep 3

description:
50ng RNA input; 3' adapter 0.05uM; 5' adapter 0.33uM modified; 14 cycles
processed data file: BCRB17_completeSummary.txt
BCRB17_4N_018_cell_PC3_50ng_optimized
processed data file: BCRB17_Mature_counts_raw.txt

source_name: cell line


title: 252665211272_1_4: D4 chronic (cured) acute vs. D4 naive (cured) acute

description:
(-) polarity
252665211272_1_4

hyb_protocol: Whole human genome microarrays were done according to the supplier’s protocol (Agilent Technologies) using the SSPE wash protocol

scan_protocol: Scanning of microarrays was performed with either 5 µm resolution and XDR setting for 4x44K arrays or 3 µm resolution for 8x60K arrays using a G2505C DNA microarray laser scanner (Agilent Technologies)

data_processing: Raw microarray image data were analyzed with the Image Analysis / Feature Extraction software G2567AA (Version A.11.5.1.1, Agilent). The extracted files were analyzed with the Rosetta Resolver Biosoftware (Rosetta Biosoftware) and with Bioconductor Gene Spring 12.6.1 software (Agilent Technologies).

source_name: D4 Ctr infection - cured - Ctr reinfection

label_protocol: RNA labeling was performed with the Quick Amp RNA Fluorescent Linear Amplification Kit (Agilent Technologies) according supplier's instructions.

extract_protocol: Total RNA was isolated by the Trizol (Invitrogen) method following the manufacturer´s protocol.

treatment_protocol:
For infection with Chlamydia trachomatis D (CtrD) 2 wells of organoids were released from MatrigelTM with cold DPBS, pooled and mechanically disrupted by passing them through a 26xG needle. The fragmented organoids were divided equally into 2 tubes for infection and mock control. After centrifugation (300xg, 5min) and removal of the supernatant, 10µl CtrD (from a frozen stock with 108 IFU/mL as determined by titration on HeLa cells) were added to one tube of the pelleted organoids. The suspension was mixed by pipetting and incubated for 15min at 35°C followed by 5min on ice. The mock control was treated the same, but without addition of CtrD. Finally, 50µL MatrigelTM was added to each tube, the organoids seeded and placed in a humidified incubator at 5% CO2 and 35°C. Splitting of organoids was done every 3-4 weeks. RNA samples were taken at 72h p.i. and 1M p.i.  At 4 months p.i. the infection was cured by applying a mixture of Penicillin (100 U/mL) and Streptomycin (100 µg/mL) to the organoid culture for one week.
After curing, a re-infection was carried out identical to the first infection with mechanical splitting, adding of CtrD to one half of the organoids and mock treatment of the other half. Also, the control organoids that have not been infected with CtrD before were infected and mock treated again. 72h post seeding RNA samples were taken of the now 2x infected (chronic cured acute), chronic infected (chronic cured), acute infected (longterm acute) and the never infected organoids

value: fallopial tube

value: organoid donor 4

tag: progression

value: chronic (cured) acute

source_name: D4 naive - cured - Ctr infection

value: naive (cured) acute


title: 252665211272_1_2: D4 chronic (cured) vs. D4 naive (cured)

description:
(-) polarity
252665211272_1_2

source_name: D4 Ctr infection - cured - naive

value: chronic (cured)

source_name: D4 naive - cured - naive

value: naive (cured)


title: Cell Sample 1 condition 7 rep 2

description:
500ng RNA input; 3' adapter 0.05uM; 5' adapter 0.33uM modified; 14 cycles
processed data file: BCRB17_completeSummary.txt
BCRB17_4N_014_cell_PC3_500ng_optimized
processed data file: BCRB17_Mature_counts_raw.txt


title: D5_Dox_C2

value: 2nd MEFs (OKSM)


title: Rb/p53-mutated PB1

city: TORONTO

first: Eldad

last: Zacksenhaus

state: ON

address: 67 College St.

country: Canada

institute: University of Toronto

description: RMA expression value derived from Expression Console software

hyb_protocol: Samples were hybridized with GeneChip Mouse Gene 1.0 ST Arrays (Affymetrix) and scanned at the Sickkids TCAG Facility.

scan_protocol: Array scanning was performed according to the manufacturer's instruction (Affymetrix)

data_processing: Data were process using Expression Console

source_name: Rb/p53-mutated PB1

label_protocol: Performed according to the manufacturer's instruction (Affymetrix)

extract_protocol: mRNA was extracted from mouse pineoblastoma and normal cerebellum using Trizol

value: Brain tumour


title: Normal cerebellum3

source_name: Normal cerebellum3

value: Normal cerebellum


title: 252665211272_1_3: D4 naive (cured) acute vs. D4 chronic (cured) acute

description:
(+) polarity
252665211272_1_3


title: Rb/p53-mutated PB5

source_name: Rb/p53-mutated PB5


title: Rb/p53-mutated PB2

source_name: Rb/p53-mutated PB2


title: Rb/p53-mutated PB3

source_name: Rb/p53-mutated PB3


title: Cell Sample 1 condition 7 rep 1

description:
500ng RNA input; 3' adapter 0.05uM; 5' adapter 0.33uM modified; 14 cycles
processed data file: BCRB17_completeSummary.txt
BCRB17_4N_013_cell_PC3_500ng_optimized
processed data file: BCRB17_Mature_counts_raw.txt


title: Normal cerebellum2

source_name: Normal cerebellum2


title: Normal cerebellum1

source_name: Normal cerebellum1


title: Rb/p53-deleted PB11

source_name: Rb/p53-deleted PB11


title: D5_Dox_C1

source_name: 2nd MEFs


title: Rb/p53-mutated PB4

source_name: Rb/p53-mutated PB4


title: D4.5_Dox_C2


title: D4.5_Dox_C1


title: Rb/p53-deleted PB9

source_name: Rb/p53-deleted PB9


title: 252665211274_1_3: D3 naive (cured) acute vs. D3 chronic (cured) acute

description:
(+) polarity
252665211274_1_3

source_name: D3 naive - cured - Ctr infection

value: organoid donor 3

source_name: D3 Ctr infection - cured - Ctr reinfection


title: D4_Dox_C2


title: Plasma Sample3 condition 7b rep 2

description:
50 ul Plasma input; 3' adapter 0.05uM; 5' adapter 0.33uM modified; 14 cycles
processed data file: BCRB17_completeSummary.txt
BCRB17_4N_011_plasmaRB4_50ul_optimized
processed data file: BCRB17_Mature_counts_raw.txt

source_name: plasma

value: plasma

value: Male


title: Plasma Sample3 condition 7b rep 1

description:
50 ul Plasma input; 3' adapter 0.05uM; 5' adapter 0.33uM modified; 14 cycles
processed data file: BCRB17_completeSummary.txt
BCRB17_4N_010_plasmaRB4_50ul_optimized
processed data file: BCRB17_Mature_counts_raw.txt


title: Plasma Sample2 condition 7b rep 3

description:
50 ul Plasma input; 3' adapter 0.05uM; 5' adapter 0.33uM modified; 14 cycles
processed data file: BCRB17_completeSummary.txt
BCRB17_4N_009_plasmaCB3_50ul_optimized
processed data file: BCRB17_Mature_counts_raw.txt

value: Female


title: D4_Dox_C1


title: 252665211272_1_1: D4 naive (cured) vs. D4 chronic (cured)

description:
(+) polarity
252665211272_1_1


title: 252665211274_1_2: D3 chronic (cured) vs. D3 naive (cured)

description:
(-) polarity
252665211274_1_2

source_name: D3 Ctr infection - cured - naive

source_name: D3 naive - cured - naive


title: D3.5_Dox_C2


title: Plasma Sample2 condition 7b rep 2

description:
50 ul Plasma input; 3' adapter 0.05uM; 5' adapter 0.33uM modified; 14 cycles
processed data file: BCRB17_completeSummary.txt
BCRB17_4N_008_plasmaCB3_50ul_optimized
processed data file: BCRB17_Mature_counts_raw.txt


title: Rb/p53-deleted PB7

source_name: Rb/p53-deleted PB7


title: 252665211274_1_4: D3 chronic (cured) acute vs. D3 naive (cured) acute

description:
(-) polarity
252665211274_1_4


title: Plasma Sample3 condition 7b rep 3

description:
50 ul Plasma input; 3' adapter 0.05uM; 5' adapter 0.33uM modified; 14 cycles
processed data file: BCRB17_completeSummary.txt
BCRB17_4N_012_plasmaRB4_50ul_optimized
processed data file: BCRB17_Mature_counts_raw.txt


title: Rb/p53-deleted PB10

source_name: Rb/p53-deleted PB10


title: 252665211273_1_4: D2 chronic (cured) acute vs. D2 naive (cured) acute

description:
(-) polarity
252665211273_1_4

source_name: D2 Ctr infection - cured - Ctr reinfection

value: organoid donor 2

source_name: D2 naive - cured - Ctr infection


title: Rb/p53-deleted PB6

source_name: Rb/p53-deleted PB6


title: Rb/p53-deleted PB5

source_name: Rb/p53-deleted PB5


title: 252665211274_1_1: D3 naive (cured) vs. D3 chronic (cured)

description:
(+) polarity
252665211274_1_1


title: Plasma Sample2 condition 7b rep 1

description:
50 ul Plasma input; 3' adapter 0.05uM; 5' adapter 0.33uM modified; 14 cycles
processed data file: BCRB17_completeSummary.txt
BCRB17_4N_007_plasmaCB3_50ul_optimized
processed data file: BCRB17_Mature_counts_raw.txt


title: D3.5_Dox_C1


title: D3_Dox_C2


title: Plasma Sample3 condition 7 rep 3

description:
250 ul Plasma input; 3' adapter 0.05uM; 5' adapter 0.33uM modified; 14 cycles
processed data file: BCRB17_completeSummary.txt
BCRB17_4N_006_plasmaRB4_250ul_optimized
processed data file: BCRB17_Mature_counts_raw.txt


title: Plasma Sample3 condition 7 rep 2

description:
250 ul Plasma input; 3' adapter 0.05uM; 5' adapter 0.33uM modified; 14 cycles
processed data file: BCRB17_completeSummary.txt
BCRB17_4N_005_plasmaRB4_250ul_optimized
processed data file: BCRB17_Mature_counts_raw.txt


title: D3_Dox_C1


title: Plasma Sample3 condition 7 rep 1

description:
250 ul Plasma input; 3' adapter 0.05uM; 5' adapter 0.33uM modified; 14 cycles
processed data file: BCRB17_completeSummary.txt
BCRB17_4N_004_plasmaRB4_250ul_optimized
processed data file: BCRB17_Mature_counts_raw.txt


title: Rb/p53-deleted PB4

source_name: Rb/p53-deleted PB4


title: 252665211273_1_3: D2 naive (cured) acute vs. D2 chronic (cured) acute

description:
(+) polarity
252665211273_1_3


title: 252665211273_1_2: D2 chronic (cured) vs. D2 naive (cured)

description:
(-) polarity
252665211273_1_2

source_name: D2 Ctr infection - cured - naive

source_name: D2 naive - cured - naive


title: Plasma Sample2 condition 7 rep 3

description:
250 ul Plasma input; 3' adapter 0.05uM; 5' adapter 0.33uM modified; 14 cycles
processed data file: BCRB17_completeSummary.txt
BCRB17_4N_003_plasmaCB3_250ul_optimized
processed data file: BCRB17_Mature_counts_raw.txt


title: Rb/p53-deleted PB8

source_name: Rb/p53-deleted PB8


title: Rb/p53-deleted PB3

source_name: Rb/p53-deleted PB3


title: Plasma Sample2 condition 7 rep 2

description:
250 ul Plasma input; 3' adapter 0.05uM; 5' adapter 0.33uM modified; 14 cycles
processed data file: BCRB17_completeSummary.txt
BCRB17_4N_002_plasmaCB3_250ul_optimized
processed data file: BCRB17_Mature_counts_raw.txt


title: Rb/p53-deleted PB2

source_name: Rb/p53-deleted PB2


title: 252665211273_1_1: D2 naive (cured) vs. D2 chronic (cured)

description:
(+) polarity
252665211273_1_1


title: 222665219460_1_2: D4 chronic vs. D4 naive

description:
(-) polarity
222665219460_1_2

source_name: D4 Ctr infection

value: chronic

source_name: D4 naive

value: naive


title: D2.5_Dox_C2

source_name: 2nd MEFs


title: ResBr2

city: St. Louis

first: Jinsheng

last: Yu

state: MO

address: 660 S. Euclid Ave.

department: Genetics

institute: Washington University School of Medicine

description:
3112_12197_ResBr2
Gene expression data from FACS-sorted CD11c+eYFP+ cells of brain.

hyb_protocol: Followed Affymetrix standard hybridization protocol for MoGene1.0 arrays.

scan_protocol: Chips were scanned with Affymetrix 7G scanner at the standard setting.

data_processing: The raw chip data files (.CEL) were processed through Affymetrix standard analysis pipeline for RMA background correction, median-polish summarization and quantile normalization. The .CHP files were generated at gene-level.

source_name: local-derived cells in brain

label_protocol: RNAs were amplified with the Nugen Ovation Pico WTA kit to generate cDNA targets labeled with biotin.

growth_protocol: Mice were perfused with 25 mL of ice-cold PBS. Subsequently, brains and spinal cords were collected from perfused mice and homogenized to obtain single cell suspensions. CNS cells were purified by centrifugation for 30 min in a 95% Percoll solution with EBSS.

extract_protocol: RNAs were extracted using Qiagen RNeasy Mini kit.

treatment_protocol: We induced active EAE in standard fashion. Briefly, mice were immunized with residues 35-55 of myelin oligodendrocyte glycoprotein (MOG35-55) emulsified in complete Freund’s adjuvant. 200 ng of pertussis toxin was administered at the time of immunization and two days later.

value: local-derived cells in brain

tag: cell type

value: resident DCs


title: Plasma Sample2 condition 7 rep 1

description:
250 ul Plasma input; 3' adapter 0.05uM; 5' adapter 0.33uM modified; 14 cycles
processed data file: BCRB17_completeSummary.txt
BCRB17_4N_001_plasmaCB3_250ul_optimized
processed data file: BCRB17_Mature_counts_raw.txt

source_name: plasma


title: D2_Dox_C2


title: D2_Dox_C1


title: 222665226355_1_1: D2 naive vs. D2 chronic

description:
(+) polarity
222665226355_1_1

source_name: D2 naive

value: fallopial tube

source_name: D2 Ctr infection


title: ResSp3

description:
3112_12195_ResSp3
Gene expression data from FACS-sorted CD11c+eYFP+ cells of spleen.

source_name: local-derived cells in spleen

value: local-derived cells in spleen


title: D1.5_Dox_C2


title: 222665219460_1_1: D4 naive vs. D4 chronic

description:
(+) polarity
222665219460_1_1

value: organoid donor 4


title: ML 48H

city: Los Angeles

first: Priscila

middle: Ribeiro

last: Andrade

state: CALIFORNIA

address: 615 Charles E Young Drive South, room 246

department: Medicine

institute: UCLA

data_processing:
Sequenced reads were demultiplexed and aligned to the human reference genome hg19 (UCSC) using TopHat (version 2.0.6) and Bowtie2 (version 2.0.2).
The HTseq package was then used to assign uniquely mapped reads to exons and genes using the gene annotation file for build hg19 from Ensembl in order to generate raw count data.
Once raw count data was generated, data normalization and differential expression analysis using a negative binomial model was performed in the R statistical programming environment using the DESeq (version 1.5) Bioconductor package.
Genome_build: hg19
Supplementary_files_format_and_content: 1 csv file of RPKM counts and another csv file for raw counts from all time points

source_name: monocyte derived macrophages (MDMs)

growth_protocol: Human CD14+ cells were obtained by magnetic bead separation of PBMCs from 1 healthy donor and differentiated in vitro for 5 days with 50ng/ml of MCSF into macrophages (37°C, 5% CO2)

extract_protocol:
Total RNA was then isolated using RNeasy Micro kit (Qiagen) according to manufacturer’s protocol and quantified by RiboQuantitation and Qubit.  All samples had a RNA integrity above 8.0 as determined by Bioanalyzer (Agilent Technologies).
Depletion of ribosomal RNA and library preparation was performed using Ribozero Gold Epidemiology (Illumina) and TruSeq Sample Preparation Kit (Illumina) as per manufacturer’s protocols.
Final libraries were reassessed for quality (Qubit and Bioanalyzer), multiplexed at two samples per lane (10µM each library), and sequenced on a HiSeq 2000 sequencer (Illumina) at 50bp single-end reads protocol.

treatment_protocol: One and a half million MDMs from one healthy donor were infected or not with M. leprae at multiplicity of infection of 10 in RPMI 1640 with 10% FCS at 33°C. Cells were lysed at 0h (uninfected) and at different time points (1h, 2h, 24h, 48h) post-infection using RLT Buffer (Qiagen) supplemented with 1% B-mercaptoethanol. Samples were added to Lysing Matrix B tubes containing 0.1mm silica beads (MP Biomedicals) and sonicated in FastPrep®-24 instrument (MP Biomedicals) for 2 cycles of 45 seconds at 6.5m/s with 1 minute interval on ice.

tag: time point

value: blood (CD14+ cells stimulated with 50ng/ml MCSF)

value: Healthy donor PBMCs


title: 222665226355_1_2: D2 chronic vs. D2 naive

description:
(-) polarity
222665226355_1_2


title: D2.5_Dox_C1

value: 2nd MEFs (OKSM)


title: ML 24H


title: D1.5_Dox_C1


title: 222665219460_1_4: D1 chronic vs. D1 naive

description:
(-) polarity
222665219460_1_4

source_name: D1 Ctr infection

value: organoid donor 1

source_name: D1 naive


title: 222665219460_1_3: D1 naive vs. D1 chronic

description:
(+) polarity
222665219460_1_3


title: ML 2H


title: Rb/p53-deleted PB1

source_name: Rb/p53-deleted PB1

value: Brain tumour


title: ResSp1

description:
3112_12193_ResSp1
Gene expression data from FACS-sorted CD11c+eYFP+ cells of spleen.


title: ResSp2

description:
3112_12194_ResSp2
Gene expression data from FACS-sorted CD11c+eYFP+ cells of spleen.


title: 252665226357_1_2: D3 acute vs. D3 naive

description:
(-) polarity
252665226357_1_2

source_name: D3 Ctr infection

value: organoid donor 3

value: acute

source_name: D3 naive


title: SenBr5

description:
3112_12192_SenBr5
Gene expression data from FACS-sorted CD11c+eYFP+ cells of brain.

source_name: BM-derived cells in brain

value: BM-derived cells in brain

value: radiation sensitive DCs


title: 252665226356_1_4: D2 acute vs. D2 naive

description:
(-) polarity
252665226356_1_4

value: organoid donor 2


title: 252665226356_1_3: D2 naive vs. D2 acute

description:
(+) polarity
252665226356_1_3


title: SenSp4

description:
3112_12186_SenSp4
Gene expression data from FACS-sorted CD11c+eYFP+ cells of spleen.

source_name: BM-derived cells in spleen

value: BM-derived cells in spleen


title: D1_Dox_C2


title: ML 1H


title: 252665226357_1_1: D3 naive vs. D3 acute

description:
(+) polarity
252665226357_1_1

value: naive


title: D1_Dox_C1


title: 252665226356_1_2: D1 acute vs. D1 naive

description:
(-) polarity
252665226356_1_2


title: 252665226356_1_1: D1 naive vs. D1 acute

description:
(+) polarity
252665226356_1_1


title: Plasma Sample 1 condition 6 rep4

description:
CB02_4N48_48N100
3' adapter 0.85uM; 5' adapter 3.3uM unmodified.
processed data file: Map_stats_CB02_trimmed_all.txt
processed data file: CB02_Libcontam_counts_raw.txt
processed data file: CB02_Mature_counts_raw.txt

data_processing:
Demultiplex: CutAdapt v1.11 --no-trim -e 0 -O 20
Trim adapters: CutAdapt v1.11 -u 4 -m 17 -e 0 -O 20
Align to custom genomes using bowtie v1.1.2 or bowtie2 v2.2.5 sequentially removing adapter/marker "contaminant" sequences, mature miRNA, other small RNAs, then finally to genomic sequences.
bowtie2 --local -L 17 (contaminant genome)
bowtie -n 0 -l 18 --best (all other genomes)
Custom bash script to generate counts.
Custom bash or r scripts to collapse PCR duplicates using UMI.
Genome_build: hg19 (GRCh37) for human genome, small RNAs downloaded from RNACentral Database release5.
Supplementary_files_format_and_content: *txt: Tab-delimited text files containing either counts or sequences.

extract_protocol:
Qiagen micro miRNeasy kit modified to use 1:7 serum:Trizol or 1:3 serum:Trizol LS.
See manuscript for details.

value: Plasma

value: Male


title: D0_Dox_C2


title: D0.5_Dox_C2


title: Plasma Sample 1 condition 6 rep2

description:
CB02_4N47_47N100
3' adapter 0.85uM; 5' adapter 3.3uM unmodified.
processed data file: Map_stats_CB02_trimmed_all.txt
processed data file: CB02_Libcontam_counts_raw.txt
processed data file: CB02_Mature_counts_raw.txt


title: D0.5_Dox_C1


title: D0_Dox_C1


title: Plasma Sample 1 condition 5 rep3

description:
CB02_4N45_45N100
3' adapter 0.2uM; 5' adapter 3.3 uM unmodified.
processed data file: Map_stats_CB02_trimmed_all.txt
processed data file: CB02_Libcontam_counts_raw.txt
processed data file: CB02_Mature_counts_raw.txt


title: ML 0H