title: H171.03

description: RNA expression from breast tumors


title: H1620.13

status: Public on Mar 20 2024

type: RNA

city: Chicago

first: Olufunmilayo

middle: I

last: Olopade

state: IL

address: 900 E. 57th Street

country: USA

institute: University of Chicago

description: RNA expression from breast tumors

hyb_protocol: Extracted RNA samples were hybridized to capture and reporter probes for the measured genes. These multiplexed hybridizations were carried out in a single-tube for 15-21 hours at 65˚C using 100 ng RNA.

scan_protocol: The signals were scanned on the nCounter Analysis system according to the manufacture’s protocols.

data_processing:
For the algorithm to produce precise results, data for the test samples had to meet a minimum threshold for expression of normalizing genes.
The normalized gene expression profile of each breast tumor sample was correlated to the prototypical gene expression profiles of the main breast cancer intrinsic subtypes.

label: Biotin

molecule: total RNA

organism: Homo sapiens

source_name: Breast Tumor

label_protocol: The target-probe complexes were processed on the nCounter Analysis system according to the manufacture’s protocols.

extract_protocol: Total RNA was extracted from FFPE breast tumors using an RNA extraction kit (Roche)

treatment_protocol: Formalin-fixed paraffin-embedded (FFPE) tumor blocks from the surgical specimen

tag: tissue

value: Breast Tumor

tag: gender

value: Female

tag: ethnicity

value: Nig

value: Basal


title: PFitness_41

type: SRA

city: Los Angeles

first: Matteo

last: Pellegrini

address: 610 Charles Young Drive East

institute: University of California, Los Angeles

library_source: genomic

data_processing:
Adapter sequences were trimmed off from the raw reads using Cutadapt (Martin, 2011) and only reads with minimum 10bp were kept for downstream analysis. Reads were aligned to GRCh38 reference genome using bsbolt align function and the duplicated reads were marked with samtools markdup function before calling methylation using bsbolt callmethylation function (Farrell et al, 2021). CGmaps from all samples were aggregated into one methylation count matrix using bsbolt aggregatematrix function with parameters -min-coverage 30 -min-sample 1.0.
Assembly: hg38
Supplementary files format and content: comma-separated text file containing methylation level per CpG site for each sample.

molecule: genomic DNA

source_name: Blood

extract_protocol:
500 ng of extracted DNA were used for TBS-seq library preparation. Fragmented DNA was subject to end repair, dA-tailing and adapter ligation using the NEBNext Ultra II Library prep kit using custom pre-methylated adapters (IDT). Pools of 16 purified libraries were hybridized to the biotinylated probes according to the manufacturer’s protocol. Captured DNA was treated with bisulfite prior to PCR amplification using KAPA HiFi Uracil+(Roche) with the following conditions: 2 min at 98◦C; 14 cycles of (98◦C for 20 sec; 60◦C for 30 sec; 72◦C for 30 sec); 72◦C for 5 minutes; hold at 4◦C.
Library QC was performed using the High-Sensitivity D1000 Assay on a 2200 Agilent TapeStation. Pools of 96 libraries were sequenced on a NovaSeq6000 (S1 lane) as paired-end 150 bases.

value: Blood

tag: cell type

value: PBMC

tag: age


title: H1587.14

description: RNA expression from breast tumors


title: H1587.14_206422710217_H1626.14_03

description: RNA expression from breast tumors


title: PFitness_3


title: PFitness_40


title: H1551.12_31020642253_01_11

description: RNA expression from breast tumors

value: Normal


title: PFitness_39


title: H151.07

description: RNA expression from breast tumors

value: LumA


title: PFitness_38


title: H1543.13

description: RNA expression from breast tumors


title: H142.14

description: RNA expression from breast tumors


title: H135.14

description: RNA expression from breast tumors


title: H1345.06

description: RNA expression from breast tumors


title: PFitness_34


title: H1340.07

description: RNA expression from breast tumors


title: H1318.10

description: RNA expression from breast tumors


title: PFitness_37


title: PFitness_33


title: PFitness_32


title: PFitness_36


title: PFitness_31


title: H1309.03

description: RNA expression from breast tumors


title: H1151.13

description: RNA expression from breast tumors


title: H1212.12_31020642253_01_09

description: RNA expression from breast tumors


title: H108.99

description: RNA expression from breast tumors


title: PFitness_30


title: PFitness_2


title: H1153.13

description: RNA expression from breast tumors


title: PFitness_29


title: PFitness_28


title: H1076.13

description: RNA expression from breast tumors


title: PFitness_27


title: PFitness_25


title: H100.11

description: RNA expression from breast tumors


title: H1048.12_206422610217_01_10

description: RNA expression from breast tumors

value: LumB


title: BC219.07

description: RNA expression from breast tumors


title: PFitness_35


title: BC221.06

description: RNA expression from breast tumors


title: PFitness_24


title: BC192.11_31020642253_01_07

description: RNA expression from breast tumors


title: PFitness_23


title: PFitness_22


title: PFitness_42


title: BC178.11_31020642253_01_05

description: RNA expression from breast tumors


title: PFitness_21


title: BC169.11_31020642253_01_02

description: RNA expression from breast tumors


title: PFitness_19


title: PFitness_18


title: H1015.10

description: RNA expression from breast tumors


title: BC164.13

description: RNA expression from breast tumors


title: BC154.13

description: RNA expression from breast tumors


title: PFitness_17


title: BC161.13

description: RNA expression from breast tumors


title: PFitness_26


title: PFitness_14


title: PFitness_15


title: BC160.08

description: RNA expression from breast tumors


title: BC150.13

description: RNA expression from breast tumors


title: BC147.13

description: RNA expression from breast tumors


title: PFitness_12


title: PFitness_110


title: BC153.05

description: RNA expression from breast tumors


title: PFitness_11


title: PFitness_10


title: BC135.13

description: RNA expression from breast tumors


title: BC190.08

description: RNA expression from breast tumors


title: PFitness_1


title: PFitness_100


title: BC133.13_206422550217_01_07

description: RNA expression from breast tumors


title: PFitness_101


title: BC133.12_31020642252_01_08

description: RNA expression from breast tumors


title: P41019081704275


title: P41019081704257


title: BC123.13

description: RNA expression from breast tumors


title: BC122.13

description: RNA expression from breast tumors


title: P41019081704251


title: P41019081704253


title: BC120.13

description: RNA expression from breast tumors


title: BC134.13

description: RNA expression from breast tumors


title: P41019081704254


title: P41019081704248


title: P41019081704246


title: P41019081704250


title: BC116.13

description: RNA expression from breast tumors


title: P41019081704242


title: BC103.13

description: RNA expression from breast tumors


title: P41019081704247


title: BC100.12_206422610217_01_04

description: RNA expression from breast tumors


title: P41019081704240


title: P41019081704239


title: P41019081704241


title: BC095.13

description: RNA expression from breast tumors


title: BC092.13

description: RNA expression from breast tumors


title: BC097.13

description: RNA expression from breast tumors


title: BC130.13

description: RNA expression from breast tumors


title: BC088.13

description: RNA expression from breast tumors


title: P41019081704238


title: BC085.12_31020642252_01_05

description: RNA expression from breast tumors


title: P41019081704236


title: BC085.08

description: RNA expression from breast tumors


title: P41019081704235


title: BC084.13

description: RNA expression from breast tumors


title: BC098.13

description: RNA expression from breast tumors


title: BC098.13_206422550217_01_12

description: RNA expression from breast tumors


title: P41019081704227


title: P41019081704226


title: BC081.13_206422550217_01_11

description: RNA expression from breast tumors


title: P41019081704224


title: P41019081704230


title: BC082.13

description: RNA expression from breast tumors


title: P41019081704225


title: BC080.13

description: RNA expression from breast tumors


title: BC075.13

description: RNA expression from breast tumors


title: BC066.14

description: RNA expression from breast tumors


title: BC066.08

description: RNA expression from breast tumors


title: P41019081704222


title: P41019081704223


title: BC063.13

description: RNA expression from breast tumors


title: BC062.14

description: RNA expression from breast tumors


title: P41019081704220


title: P41019081704216


title: BC084.06

description: RNA expression from breast tumors


title: P41019081704217


title: P41019081704234


title: BC059.14..repeat.

description: RNA expression from breast tumors


title: BC056.14_206422400217_01_11

description: RNA expression from breast tumors


title: BC055.14_206422550217_01_04

description: RNA expression from breast tumors


title: BC059.14

description: RNA expression from breast tumors


title: P41019081704213


title: BC054.13

description: RNA expression from breast tumors


title: P41019081704210


title: P41019081704209


title: P41019081704207


title: P41019081704212


title: BC051.14_206422550217_01_02

description: RNA expression from breast tumors


title: P41019081704206


title: BC051.14

description: RNA expression from breast tumors


title: P41019081704205


title: P41019081704204


title: P41019081704203


title: P41019081704215


title: P41019081704221


title: P41019081704202


title: BC048.14_206422420217_01_12

description: RNA expression from breast tumors


title: BC047.14

description: RNA expression from breast tumors


title: BC047.10

description: RNA expression from breast tumors


title: BC060.13

description: RNA expression from breast tumors


title: P41019081704201


title: BC055.14

description: RNA expression from breast tumors


title: P41019081704197


title: P41019081704199


title: BC046.14

description: RNA expression from breast tumors


title: BC047.06

description: RNA expression from breast tumors


title: BC046.12_31020642251_01_02

description: RNA expression from breast tumors


title: BC046.07

description: RNA expression from breast tumors


title: P41019081704195


title: BC051.08

description: RNA expression from breast tumors


title: BC044.13.1

description: RNA expression from breast tumors


title: P41019081704194


title: BC047.14_206422420217_01_01

description: RNA expression from breast tumors


title: BC044.14_206422550217_01_01

description: RNA expression from breast tumors


title: BC044.13.2

description: RNA expression from breast tumors


title: BC048.14

description: RNA expression from breast tumors


title: P41019081704200


title: P41019081704191


title: P41019081704190


title: P41019081704189


title: P41019081704188


title: BC044.12_31020642251_01_01

description: RNA expression from breast tumors


title: P41019081704187


title: BC037.14

description: RNA expression from breast tumors


title: BC041.13_206422420217_01_11

description: RNA expression from breast tumors


title: P41019081704185


title: BC041.12_206422590217_01_03

description: RNA expression from breast tumors


title: BC035.06

description: RNA expression from breast tumors


title: BC036.13_206422420217_01_09

description: RNA expression from breast tumors


title: P41019081704182


title: P41019081704181


title: P41019081704183


title: P41019081704196


title: P41019081704193


title: BC033.13_206422420217_01_08

description: RNA expression from breast tumors


title: BC034.14_206422400217_01_07

description: RNA expression from breast tumors


title: BC036.13

description: RNA expression from breast tumors


title: P41019081704180


title: P41019081704179


title: P41019081704178


title: BC033.13

description: RNA expression from breast tumors


title: P41019081704177


title: BC030.13

description: RNA expression from breast tumors


title: BC031.13

description: RNA expression from breast tumors


title: BC026.13

description: RNA expression from breast tumors


title: P41019081704149


title: BC023.13

description: RNA expression from breast tumors


title: BC017.13

description: RNA expression from breast tumors


title: P41019081704176


title: P41019081704147


title: BC020.12

description: RNA expression from breast tumors


title: P41019081704140


title: BC020.11_206301581116_01_08

description: RNA expression from breast tumors


title: BC018.13

description: RNA expression from breast tumors


title: BC006.12_206301581116_01_02

description: RNA expression from breast tumors


title: P41019081704138


title: BC004.14_206301581116_01_01

description: RNA expression from breast tumors


title: P41019081704136


title: BC004.14

description: RNA expression from breast tumors


title: P41019081704133


title: BC004.13

description: RNA expression from breast tumors


title: BC003.14

description: RNA expression from breast tumors


title: BC001.14

description: RNA expression from breast tumors


title: BC016.06

description: RNA expression from breast tumors


title: P41019081704139


title: P41019081704130


title: P41019081704175


title: P41019081704126


title: P41019081704143


title: P41019081704124


title: Msl3_MledF_adult_2

city: Moscow

first: Anastasia

last: Revel-Muroz

address: 34/5 Vavilov St.

country: Russia

institute: Institute of Gene Biology, Russian Academy of Sciences

data_processing:
Adapters, poly-N and poly-A read ends were removed using cutadapt software (Martin 2011). Cutadapt was also used for trimming low-quality ends (quality threshold was set to 20, reads with the length less than 20 bp after trimming were discarded).
The remaining reads were aligned to build version dm6 of the Drosophila melanogaster genome using Bowtie version 2 (Langmead and Salzberg 2012). Only reads that aligned concordantly exactly one time were passed to further analysis.
After alignment, read duplicates were removed using Picard MarkDuplicates function (http://broadinstitute.github.io/picard/). Also, peaks overlapping with blacklist regions were discarded (blacklist regions were previously converted from dm3 to dm6 genome built version) (https://sites.google.com/site/anshulkundaje/projects/blacklists)
Peak calling was performed using MACS version 2 against preimmune control (Zhang et al. 2008) in paired-end mode (option format=BAMPE).
Peaks with p value less than 1x10-2 were passed to the IDR pipeline to access reproducibility of chip-seq replicates (https://sites.google.com/site/anshulkundaje/projects/idr).
Optimal set of reproduced peaks was chosen for each sample and passed to further analysis.
Assembly: dm6
Supplementary files format and content: Processed data was obtained by MACS2 and deeptools bamCoverage (binSize 50) and includes: extended bed (narrowPeak) peak calls regions and coverage (bedGraph)

organism: Drosophila melanogaster

source_name: whole organism

extract_protocol:
Chromatin samples containing 10–20 µg of DNA equivalent in 200 µL of nuclear lysis buffer (2 µL aliquots of such pre-cleared chromatin being stored as input material) were incubated overnight, at 4°C, with antibodies-Dynabeads complexes. After 3 rounds of washing with lysis buffer supplemented with 500 mM NaCl, and TE buffer (10 mM Tris-HCl, pH 8; 1 mM EDTA), the DNA was eluted with elution buffer (50 mM Tris-HCl, pH 8.0; 1 mM EDTA, 1% SDS), the cross-links were reversed, and the precipitated DNA was extracted by the ChIP DNA Clean &Concentrator kit (Zymoresearch).
The ChIP-seq libraries were prepared with NEBNext®_Ultra™_II DNA Library Prep kit, as described in the manufacturer's instructions. Amplified libraries were quantified using fluorometry with DS-11 (DeNovix, United States) and Bioanalyzer 2100 (Agilent, United States). Diluted libraries were clustered on a pair-read flowcell and sequenced using a NovaSeq 6000 system (Illumina, United States).

treatment_protocol: Chromatin was prepared from two- to three-day-old adult males. A 1 g of adult flies was ground in a mortar in liquid nitrogen and resuspended in 20 mL of buffer A (15 mM HEPES-KOH, pH 7.6, 60 mM KCl, 15 mM NaCl, 13 mM EDTA, 0.1 mM EGTA, 0.15 mM spermine, 0.5 mM spermidine, 0.5% NP-40, 0.5 mM DTT) supplemented with 0.5 mM PMSF and Calbiochem Cocktail V. The suspension was then homogenized subsequently in a Potter and Dounce homogenizer with tight pestle, filtered through 100 µm Nylon Cell Strainer (Miltenyi Biotec, United States), and cross-linked with 1% formaldehyde for 15 min at room temperature. Cross-linking was stopped by adding glycine to a final concentration of 125 mM. The nuclei were washed with three 10-mL portions of wash buffer (15 mM HEPES-KOH, pH 7.6, 60 mM KCl, 15 mM NaCl, 1 mM EDTA, 0.1 mM EGTA, 0.1% NP-40, protease inhibitors), one 5-mL portion of nuclear lysis basic buffer (15 mM HEPES, pH 7.6, 140 mM NaCl, 1 mM EDTA, 0.1 mM EGTA, 1% Triton X-100, 0.5 mM DTT, 0.1% sodium deoxycholate, protease inhibitors) and resuspended in 1 mL of nuclear lysis buffer (15 mM HEPES, pH 7.6, 140 mM NaCl, 1 mM EDTA, 0.1 mM EGTA, 1% Triton X-100, 0.5 mM DTT, 0.1% sodium deoxycholate, 0.5% SLS, 0.1% SDS, protease inhibitors). The suspension was sonicated in a Covaris ME220 focused-ultrasonicator (40 alternating 15-s ON and 45-s OFF intervals, peak power 75, duty % factor 25), and 50-µL aliquots were used to test extent of sonication and to measure DNA concentration. Debris was removed by centrifugation at 14 000 g, 4°C, for 10 min, and chromatin was pre-cleared with Protein A Dynabeads (Invitrogen). Corresponding antibodies were incubated for 1 hour at room temperature with 20 µL aliquots of Protein A (anti-Msl1, 1:100; anti-Msl2, 1:100; anti-Msl3, 1:500) Dynabeads (Invitrogen) mixed with 200 µL of PBST. Then antibodies-Dynabeads complexes were washed and equilibrated in nuclear lysis buffer.

tag: antibody source

value: rabbit

tag: strain

value: whole organism

tag: genotype

value: MLEdel


title: Msl2_MlewtF_adult_2

value: MLEwt


title: P41019081704132


title: P41019081704123


title: Msl3_MlewtF_adult_2


title: BC011.13

description: RNA expression from breast tumors


title: P41019081704128


title: Msl3_MlewtF_adult_1


title: Msl2_MledF_adult_2


title: P41019081704121


title: P41019081704127


title: P41019081704144


title: P41019081704120


title: P41019081704125


title: Msl1_MlewtF_adult_2


title: Msl3_MledF_adult_1


title: P41019081704122


title: Msl2_MlewtF_adult_1


title: Msl2_MledF_adult_1


title: Preimmune wt Chip-seq


title: Msl1_MlewtF_adult_1


title: P41019081704118


title: P41019081704117


title: BC002.13

description: RNA expression from breast tumors


title: P41019081704116


title: Msl1_MledF_adult_2


title: P41019081704115


title: P41019081704114


title: Msl1_MledF_adult_1


title: P41019081704112


title: P41019081704111


title: P41019081704110


title: P41019081704108


title: P41019081704100


title: P41019081704106


title: P41019081704090


title: P41019081704087


title: P41019081704109


title: Sample_PP11_PL

city: Bialystok

first: Iwona

last: Sidorkiewicz

address: Sklodowska-Curie Street 24a

department: Clinical Research Centre

country: Poland

institute: Medical University of Bialystok

hyb_protocol: The RNA concentration was measured using Qubit (Invitrogen, Carlsbad, USA) and 100 ng total RNA was used as input material. Next, the samples were prepared for nCounter miRNA expression profiling as per the manufacturer’s recommendations (NanoString Technologies, Seattle, WA, USA). Briefly, sample preparation involved a multiplexed annealing of the specific tags to their target miRNA, a ligation reaction, an enzymatic purification to remove unligated tags, followed by an overnight hybridization (65 °C) with nCounter Reporter and Capture probes. Subsequently, the samples were placed into the nCounter Prep Station for automated sample purification and reporter capture. Each sample was scanned (550 fields of view) on the nCounter Digital Analyzer for data collection.

scan_protocol: Each sample was scanned on the nCounter Digital Analyzer for data collection.

data_processing: nSolver 4.0 Analysis software (NanoString) was used for data analysis including normalization using the ligation method. The p-values were adjusted using the False Discovery Rate (FDR) correction for multiple comparisons, which was limited to 0.05

label: oligonucleotide probe

source_name: plasma

label_protocol: Specific oligonucleotide probe pairs that are bound to barcoded tags (Nanostring Technologies inc.) were conducted according to the manufacturer's protocol.

growth_protocol: not applicable

extract_protocol: Both amniotic fluid (5.0 mL) and venous blood (5.5 mL) samples were obtained from participants on the same day. Venous blood was centrifuged, and, subsequently, both plasma and amniotic fluid samples were transferred into DNase- and RNase-free tubes (Eppendorf, Hamburg, Germany), and stored at -80°C until assayed. miRNA was isolated from 200 µl of plasma and amniotic fluid samples using the miRNeasy Serum/Plasma Advanced Kit (Qiagen, Germany), following the manufacturer’s instructions. miRNA was eluted in a final volume of 15 μl.   The RNA concentration was measured using Qubit (Invitrogen, Carlsbad, USA) and 100 ng total RNA was used as input material.

treatment_protocol: not applicable

tag: pregnancy status

value: pregnant woman

tag: fetus

value: congenital diaphragmatic hernia


title: Sample_PP4_PL


title: Sample_PP8_PL


title: Sample_RK3_PL

value: spina bifida


title: Sample_RK7_PL


title: Sample_PP9_PL


title: Sample_PP2_PL


title: Sample_RK5_PL


title: Sample_PP1_PL


title: Ngn2 iNeurons REST WBS isoWBS DMSO 2

city: Milano

first: Alessandro

last: Vitriolo

state: MI

address: Via Rita Levi Montalcini 1

department: Neurogenomics

country: Italy

institute: Fondazione Human Technopole

description: RNA.restExperiment.SE.rds

library_source: transcriptomic

data_processing:
Quantification was done using Salmon 0.9.1 (Patro et al., 2017) on the ensembl 92 transcriptome.
Only protein-coding transcripts were retained, and counts were aggregated at the level of gene symbols.
Only genes with at least 20 reads in at least a number of samples corresponding to 75% of the smallest experimental group were included in the analysis.
Differential expression analysis was done using DESeq2 (Love et al., 2014), and for pairwise comparisons between groups foldchanges were shrunken using the apeglm method (Zhu et al., 2019). In addition, a regression on 7q11.23 copy-numbers was performed.
Assembly: GRCh38
Supplementary files format and content: RNA.SE.rds.zip are RNA.restExperiment.SE.rds.zip are R SummarizedExperiment objects containing the quantification and annotation for the different samples.

molecule: polyA RNA

source_name: isoWBS

growth_protocol: In order to obtain cortical glutamatergic neurons (iNeurons), iPSCs were dissociated with Accutase (GIBCO, Thermo Fisher Scientific) and plated on Matrigel-coated plates (final 2% v/v, Corning) in mTeSR™ or TeSR-E8 (Stemcell Technologies) supplemented with 5 μM Y-27632 (Sigma). iPSCs were then cultured in MEM1 (DMEM/F12 1:1 (Euroclone/Gibco) supplemented with NEAA 1%, N2 1%, BDNF 10 ng/ml, NT-3 10 ng/ml, Laminin 0,2 μg/ml and 2 μg/ml doxycycline hydrochloride, penicillin 100 U/ml and streptomycin 100 μg/ml) for 2 days. On the second day of MEM1, cells were selected with 1 μg/ml puromycin, to reassure that only the cells with Ngn2-inducible cassette will survive. For patient-derived iNeurons, after two days of MEM1, media was change to Neurobasal medium (NB, Thermo Fisher Scientific) supplemented with BDNF 10 ng/ml, NT-3 10 ng/ml, B27 (1:50), GlutaMax (Gibco, 1:100), penicillin 100 U/ml, streptomycin (100 μg/ml), which was previously conditioned on mouse astrocytes for 24 h. Half of media was changed every other day. Instead, for isogenic iNeurons after two days of MEM1, media was change to Neurobasal Plus medium (NB-Plus) composed of B-27™ Plus Neuronal Culture System (Thermo Fisher Scientific) supplemented with Glutamax 0.25% (Thermo Fisher Scientific), 2 μg/ml, doxycycline hydrochloride and penicillin 100 U/ml, streptomycin (100 μg/ml). The media was changed twice a week. On day 7-8, cells that already acquired neuron-like shape were dissociated with Accutase, counted and seeded into plates coated with 15 μg/ml of poly-D-lysine at a density of 1 x 10^6 cells/well of multiwell 6, 2 x10^6 in 6 cm dishes or 4 x10^6 in 10 cm dishes (Nunc Edge plates, Thermo Fisher Scientific) in conditioned NB or NB-Plus. Half of media was changed twice a week until day 30-35.

extract_protocol:
RNA was isolated using the RNeasy mini Kit (QIAGEN) and genomic DNA was removed using the RNase-Free DNase Set (QIAGEN). Retrotranscribed cDNA was obtained from 1 μg of total RNA using the SuperScript VILO Retrotranscription kit from Life Technologies according to the manufacturer’s instructions.
Library preparation for RNA-seq was done with the Ribo-Zero Total RNA sample preparation kit (Illumina), starting from 250 ng to 1 g of total RNA. The quality of cDNA libraries was assessed by Agilent 2100 Bioanalyzer using the High Sensitivity DNA Kit.

tag: cell line

value: isoWBS

value: Ngn2 iNeurons

value: WBS

tag: model

value: Isogenic

tag: group

value: REST

tag: treatment

value: DMSO


title: Ngn2 iNeurons REST WBS isoWBS DMSO 3

description: RNA.restExperiment.SE.rds


title: Ngn2 iNeurons REST WBS isoWBS DMSO 1

description: RNA.restExperiment.SE.rds


title: Ngn2 iNeurons REST WBS isoWBS REST inhibitor X5050 3

description: RNA.restExperiment.SE.rds

value: REST inhibitor X5050


title: Sample_80_PL

value: healthy euploid


title: Sample_82_PL


title: Sample_PP10_PL


title: Ngn2 iNeurons REST WBS isoWBS REST inhibitor X5050 2

description: RNA.restExperiment.SE.rds


title: Sample_PP12_PL


title: Sample_79_PL


title: Sample_53_PL


title: Ngn2 iNeurons REST WBS isoWBS REST inhibitor X5050 1

description: RNA.restExperiment.SE.rds


title: Sample_51_PL


title: Sample_74_PL


title: post_pat37_ACTCb_1

city: Athens

first: William

last: Bastian

state: Georgia

address: 250 W Green Street

department: Institute of Bioinformatics

institute: Universty of Georgia

data_processing:
Sequence reads were pseudoaligned to hg38 using Kallisto (parameters- bootstrap: 100
Estimated raw counts and normalization (TPM) were performed using Kallisto
Assembly: hg38
Supplementary files format and content: Kallisto estimated counts were save in a comma-seperated value file (.csv)
Supplementary files format and content: Kallisto TPM normalized counts were saved in a comma-seperated value file (.csv)

source_name: Breast

extract_protocol:
Tumor RNA extraction was performed using the E.Z.N.A. FFPE RNA kit (Omega Biotek). The concentration and integrity of the extracted total RNA were estimated using the Quant-iT™ RiboGreen® RNA Assay Kit (Thermo Fisher Scientific) and the Fragment Analyzer Systems using the RNA High Sense chip, respectively.
Up to 30ng of RNA with DV200>20% was used to prepare libraries using SMRTer Stranded Total RNAseq v2 (Clonetech) with slight modifications.

value: Breast

tag: nac simple

value: ACTCb

tag: nac

value: taxol/carboplatin, AC

tag: residual tumor

value: yes

tag: tissue with_residul

value: B

tag: patient id

tag: deceased

value: N

tag: mastectomy or_lumpectomy

value: L

tag: grade pre-nac

tag: residual tumor_size

tag: bmi


title: post_pat38_ACT_1

tag: tissue

value: ACT

value: AC, taxol

value: B+LN

value: M


title: post_pat35_ACT_1

value: AC, Taxotere, taxol

value: y


title: post_pat39_ACT_1


title: post_pat34_ACT_1


title: post_pat31_ACT_1


title: post_pat32_ACTCb_1

value: AC, carboplatin, taxol


title: Sample_RK17_AF

source_name: amniotic fluid

tag: pregnancy status

value: pregnant woman

value: spina bifida


title: Sample_RK22_AF

tag: fetus


title: Sample_150_PL

value: healthy euploid


title: Sample_123_PL


title: Sample_116_PL


title: post_pat36_ACT_1

value: Breast

value: 4 cycles of AC and 12 weeks of taxol


title: post_pat30_ACT_1


title: post_pat24_ACTCb_1

value: ACTCb

value: AC, taxol, carboplatin


title: Sample_44_PL


title: post_pat33_ACT_1

value: 4 cycles AC, 12 x taxol

value: yes

value: B


title: Sample_RK13_AF


title: Sample_PP24_AF

value: congenital diaphragmatic hernia


title: Sample_136_PL


title: Sample_PP21_AF


title: Sample_PP20_AF


title: Sample_PP23_AF


title: post_pat29_ACT_1

value: ACT

value: AC, taxol

value: N


title: post_pat28_ACT_1

value: L


title: post_pat23_AbT_1

value: AbT

value: carboplatin, taxol

value: M


title: Sample_PP19_AF

value: pregnant woman


title: Sample_118_PL

value: healthy euploid


title: post_pat21_CbT_1

value: Breast

value: CbT

value: carboplatin taxol


title: post_pat22_ACTCb_1

value: ACTCb

value: taxol/carboplatin, AC

value: tumor bed 3.5 (foci 0.1-0.2)


title: post_pat19_FEC_1

value: FEC

value: yes

value: B


title: post_pat20__1

value: 5FU, cyclophosphamide, epirubicin, zometa, taxol

value: y


title: Sample_PP18_AF

value: congenital diaphragmatic hernia


title: Sample_PP16_AF


title: Sample_PP15_AF


title: post_pat17_ACT_1

value: ACT

value: taxol x 12, AC x 4 cycles

value: N


title: post_pat16_CbD_1

value: CbD

value: 5/6 cycles taxotere/carboplatin

value: M

value: 4.0 (largest span, largest continuous 0.2)


title: post_pat18_ACT_1

value: Breast

value: 4 cycles AC, 12 x taxol


title: Sample_PP14_AF

value: pregnant woman


title: post_pat14_ACT_1

value: weekly taxol, AC

value: L


title: post_pat15_AC_1

value: AC

value: yes


title: post_pat12_ACT_1

value: doxorubicin/cyclophosphamide, taxol

value: B


title: Sample_PP9_AF

value: congenital diaphragmatic hernia


title: Sample_RK5_AF

value: spina bifida


title: Sample_RK3_AF


title: Sample_PP8_AF


title: post_pat13_ACT_1

value: ACT

value: AC taxol


title: Sample_RK7_AF


title: Sample_PP6_AF


title: post_pat09_ACT_1

value: N


title: B and T-cell Acute Lymphoblastic Leukemia (ALL)

city: Novosibirsk

first: Roman

middle: Yurievich

last: Perik-Zavodskii

state: Novosibirsk region

address: Yadrincevskaya 14

institute: "Research Institute of Fundamental and Clinical Immunology" (RIFCI)

description: Pooled normal Bone Marrow mononuclear cells (n = 4), B-cell ALL (n = 2), T-cell ALL (n = 1), cell acquired pre-treatment in the moment of diagnostic bone marrow biopsy

library_source: other

data_processing:
The BD Rhapsody V1.10 pipeline creates UMI matrices of polyA RNA and ADT molecules from FASTQ files and separates them using HTO (ST) information, HTO sequences are embedded into the pipeline.
Assembly: Targeted - Immune Response Panel
Library strategy: CITE-seq

molecule: other

source_name: Bone Marrow (BM)

extract_protocol:
We extracted mononuclear cells from Bone Marrow via Ficoll-paque density gradient centrifugation.
Library was prepared for sequencing using "mRNA Targeted, Sample Tag, and BD AbSeq Library Preparation Protocol" protocol.

value: Bone Marrow (BM)

tag: cell type

value: Mononuclear cells

tag: adt

tag: hto -_sample_tag_(st)

value: ST5 -  normal BM, ST8 - Pro B-cell ALL, ST9 - DP T-cell ALL, ST10 - Pre B-cell ALL


title: post_pat07_CbT_1

value: Breast

value: CbT

value: carboplatin/paclitaxel

value: M


title: post_pat08_ACT_1

value: 4 cycles of AC and 12 weeks of taxol


title: post_pat04__1

value: OSU 10011, taxol, carboplatin

value: y


title: Sample_PP4_AF

value: pregnant woman


title: Sample_PP2_AF


title: post_pat01_ACT_1

value: AC, Taxotere, taxol

value: yes

value: B


title: Sample_PP12_AF

value: congenital diaphragmatic hernia


title: Sample_PP11_AF


title: pre_pat66_ACTCb_0

value: ACTCb

value: AC, carboplatin, taxol

value: no


title: pre_pat65_ACT_0

value: ACT

value: AC, taxol

value: N


title: Sample_PP10_AF


title: Sample_063_AF

value: healthy euploid


title: Sample_PP1_AF


title: post_pat10_ACT_1

value: Breast

value: AC taxol

value: L


title: pre_pat64_ACT_0


title: pre_pat61_ACT_0

value: taxol, AC

value: M


title: Sample_388_AF

value: pregnant woman


title: pre_pat59_ACT_0


title: Sample_031_AF


title: pre_pat51_ACT_0


title: pre_pat50_AC_0

value: AC


title: pre_pat52_ACT_0

value: weekly taxol, AC


title: pre_pat49_ACT_0

value: doxorubicin/cyclophosphamide, taxol


title: pre_pat47_ACT_0


title: Sample_130_AF


title: Sample_033_AF


title: Sample_118_AF


title: pre_pat46_ACT_0


title: Sample_129_AF


title: Sample_091_AF


title: Sample_083_AF [miRNA4]


title: pre_pat45_ACT_0

value: 4 cycles AC, 12 weeks of taxol


title: Sample_090_AF


title: pre_pat42_CbT_0

value: CbT

value: taxol/carbo


title: Sample_084_AF


title: pre_pat40_ACT_0

value: no

value: Y


title: Sample_080_AF


title: Sample_062_AF


title: Sample_025_AF


title: Sample_053_AF


title: pre_pat39_ACT_1

value: ACT

value: AC, taxol

value: yes

value: B


title: Sample_044_AF

value: healthy euploid


title: pre_pat37_ACTCb_1

value: Breast

value: ACTCb

value: taxol/carboplatin, AC

value: N

value: L


title: Sample_093_AF

value: pregnant woman


title: Sample_123_AF


title: pre_pat30_ACT_1

value: AC, Taxotere, taxol

value: M


title: pre_pat27__1


title: Sample_092_AF


title: Sample_086_AF


title: pre_pat26_ACT_1

value: AC with neulasta, taxolx 4


title: pre_pat25_ACTCb_1

value: AC, carboplatin, taxol


title: dbsc, input, rep2

city: Blacksburg

first: Honglin

last: Jiang

state: VA

address: Litton Reaves Hall

department: School of Animal Sciences

institute: Virginia Tech

data_processing:
Adapters were trimmed using Trimmomatic
Trimmed sequencs were aligned to the bovine genome assembly using Hisat2
The aligned reads were sorted and merged using SAMtools
Peak calling of the aligned reads was made using MACS3
Assembly: BosTau 9
Supplementary files format and content: peak files in BigWig, no peak files for Input samples

organism: Bos taurus

source_name: muscle

growth_protocol: Bovine satellite cells were cultured in growth medium containing 10% fetal bovine serum for up to 10 days.

extract_protocol:
Cells were lysed to release nuclei; nuclei were sonicated; and histone-DNA complexes were immunoprecipitated with specific antibodies.
ChIP-seq libraries were prepared using the NEBNext ChIP-Seq Library Prep Reagent Set for Illumina (New England BioLabs), according to the supplier’s instructions.

treatment_protocol: Bovine satelltie cells cultured in growth medium were induced to differentiate into myofibers by replacing the growth medium with differentiation medium containing 2% horse serum.

value: muscle

value: satellite cells

tag: treatment

value: differentiation medium


title: pre_pat44_ACT_0

tag: nac simple

value: ACT

value: AC and taxol

value: no


title: pre_pat22_ACTCb_1

tag: nac

value: yes

value: B

value: tumor bed 3.5 (foci 0.1-0.2)


title: Sample_083_AF

value: healthy euploid


title: Sample_051_AF


title: pre_pat21_CbT_1

value: Breast

value: CbT

value: carboplatin taxol

tag: residual tumor

value: N


title: dbsc, h3k4me1, rep2


title: Sample_079_AF

value: pregnant woman


title: pre_pat43_CbT_0

value: taxol, carboplatin

tag: tissue with_residul

value: L


title: dbsc, input, rep1

value: muscle


title: dbsc, 3k27ac, rep1

value: satellite cells


title: pre_pat18_ACT_1

value: 4 cycles AC, 12 x taxol

tag: patient id

value: y

value: M


title: pre_pat20__1

value: 5FU, cyclophosphamide, epirubicin, zometa, taxol

tag: deceased


title: dbsc, h3k27me3, rep1

value: differentiation medium


title: pre_pat17_ACT_1

value: ACT

value: taxol x 12, AC x 4 cycles

value: yes

value: B

tag: mastectomy or_lumpectomy


title: pre_pat16_CbD_1

value: Breast

value: CbD

value: 5/6 cycles taxotere/carboplatin

tag: grade pre-nac

value: 4.0 (largest span, largest continuous 0.2)


title: dbsc, 3k27ac, rep2


title: dbsc, h3k4me1, rep1


title: pre_pat15_AC_1

value: AC

value: N

tag: residual tumor_size


title: pre_pat14_ACT_1

value: weekly taxol, AC

value: L

tag: bmi


title: pbsc, input, rep2

tag: tissue

value: muscle

value: satellite cells

value: growth medium


title: pbsc, h3k27me3, rep2


title: pre_pat23_AbT_1

value: AbT

value: carboplatin, taxol

value: M


title: pre_pat12_ACT_1

value: ACT

value: doxorubicin/cyclophosphamide, taxol


title: pbsc, input, rep1


title: dbsc, h3k27me3, rep2

value: differentiation medium


title: pbsc, h3k4me1, rep2


title: pre_pat09_ACT_1

value: Breast

value: AC taxol

value: yes

value: B


title: pbsc, 3k27ac, rep1


title: pre_pat10_ACT_1


title: pre_pat07_CbT_1

value: CbT

value: carboplatin/paclitaxel


title: pbsc, h3k4me1, rep1


title: pre_pat04__1

value: OSU 10011, taxol, carboplatin

value: y


title: ∆codY 24 hr biol rep 4

city: College Station

first: Paul

last: Straight

state: TX

address: 2128 TAMU

institute: Texas A&M University

data_processing:
RNAlysis V3.7.0
Sequences reads were trimmed for adaptor sequences with CutAdapt.
Trimmed sequence reads were mapped to open reading frames (ORFs) in the B. subtilis 168 genome (Gene Bank: NC_000964.3) plus sfp, swrA and ORFs in the plasmid pSB32 and then quantified with Kallisto (V0.48.0)
Normalized abundance of the reads was measured using DESeq2.
Assembly: B. subtilis 168 genome (Gene Bank: NC_000964.3) plus sfp, swrA and ORFs in the plasmid pSB32
Supplementary files format and content: comma separated file includes normalized abundance measurements via DESeq

organism: Bacillus subtilis

source_name: early stationary phase

growth_protocol: Wild-type and ∆codY strains were grown to early stationary phase and inoculated on GYM7 plates with and without 1 µM chlormphenicol followed by incubation at 30℃ for 6 and 24 hours.

extract_protocol:
RNA was harvested using TRI reagent and Turbo DNA-free kits.
RNA libraries for RNA-seq were prepared using the TruSeq Stranded mRNA kit per manufacturer's prtocol.

value: early stationary phase

tag: source

value: B. subtilis 168 genome (Gene Bank:NC_000964.3)

tag: genotype

value: [delta]codY

tag: time point

value: 24 hr


title: ∆codY 24 hr biol rep 3


title: ∆codY 24 hr biol rep 1


title: pre_pat03_ACT_1

value: 12 x paclitaxel, 4 X AC

value: L


title: pbsc, 3k27ac, rep2

value: muscle

tag: cell type

value: satellite cells

value: growth medium


title: pre_pat02__1

value: Breast

value: Taxol, Carbo, Gamma secretase inhibitor

value: N


title: pre_pat01_ACT_1

value: ACT

value: AC, Taxotere, taxol

value: yes

value: B

value: M


title: ∆codY 6 hr biol rep 3

value: early stationary phase

value: 6 hr


title: ∆codY 6 hr biol rep 4

value: B. subtilis 168 genome (Gene Bank:NC_000964.3)

value: [delta]codY


title: EV, Control female, CTRL19

city: Montreal

first: Gustavo

last: Turecki

state: Quebec

address: 6875 Boulevard LaSalle

department: Psychiatry

country: Canada

institute: McGill University

data_processing:
Data trimmed with bbduk.sh from bbmap v38.86
Extracellular RNA Communication Consortium’s (ERCC) exceRpt small RNA-Seq pipeline (v.4.6.3)
no mismatch allowed during alignment
filter: excluded miRNAs with less than 10 counts in 70% of subjects per group
Assembly: hg38
Supplementary files format and content: csv file contains filtered raw read counts

source_name: Anterior cingulate cortex-derived Evs

extract_protocol:
QIAzol lysis reagent was added at 5X to each sample, which were then incubated at room temperature for 5 min. 1X of chloroform was added, and the samples were incubated at room temperature for 3 min. They were centrifuged at 12000g at 4 °C for 15 min, and the aqueous phase was collected. 1.5 volumes of 100 % ethanol were added and mixed gently. The mixture was then added to QIAGEN MinElute columns, and the MiRNeasy Micro Kit was used according to the manufacturer’s protocol (QIAGEN).
Libraries were constructed follwing the Galas Lab - 4N library prep - Version 1.0 protocol

treatment_protocol: For each subject, 200-400 mg of brain tissue were cut into very fine pieces while still partially frozen. The tissue was then incubated in Hibernate E medium (800 µL / 100 mg of tissue) in the presence of 75 U/mL of collagenase type III at 37 oC for 20 min with gentle shaking. The reaction was then halted using protease (PI) and phosphatase (PS) inhibitors (1X) , and the sample was centrifuged at 300g for 5 min. The pellet was homogenized in phosphate buffered saline (PBS) with 1X PI/PS, while the supernatant was collected and centrifuged at 2,000g for 10 min. The supernatant was collected again and centrifuged at 10,000g for 30 min. The supernatant was overlaid on a size exclusion column for extracellular vesicle (EV) separation according to the manufacturer’s protocol. Samples were then concentrated using Amicon centrifugal filters. EVs were treated with Proteinase K at 37 °C for 30 min, then with PureLink RNAseA at room temperature for 2 min.

value: Anterior cingulate cortex-derived Evs

tag: gender

value: female

value: control


title: ∆codY 6 hr biol rep 2


title: EV, Suicide female, MDD20

value: MDD


title: EV, Suicide female, MDD19


title: ∆codY 6 hr biol rep 1


title: WT + cm 24 hr biol rep 3

value: WT

value: 24 hr


title: WT + cm 24 hr biol rep 2


title: pbsc, h3k27me3, rep1

value: muscle

value: satellite cells

tag: treatment

value: growth medium


title: EV, Suicide female, MDD17


title: EV, Suicide female, MDD16


title: ∆codY 24 hr biol rep 2


title: pre_pat06__1

value: Breast

tag: nac simple

value: taxol/bev/carbo,

value: y


title: pre_pat13_ACT_1

value: ACT

tag: nac

value: AC taxol

value: yes

value: B

value: N

value: M


title: WT + cm 6 hr biol rep 3

value: early stationary phase

value: B. subtilis 168 genome (Gene Bank:NC_000964.3)

value: 6 hr


title: EV, Suicide female, MDD18

value: Anterior cingulate cortex-derived Evs

value: female

value: MDD


title: EV, Control female, CTRL20

value: control


title: EV, Suicide female, MDD15


title: WT + cm 6 hr biol rep 1

value: WT


title: WT 24 hr biol rep 3

value: 24 hr


title: EV, Suicide female, MDD14


title: EV, Control female, CTRL17


title: WT 24 hr biol rep 2


title: WT 24 hr biol rep 1


title: EV, Suicide female, MDD13


title: EV, Suicide female, MDD11


title: EV, Suicide female, MDD12


title: EV, Control female, CTRL15


title: WT 6 hr biol rep 1


title: WT 6 hr biol rep 2


title: EV, Control female, CTRL18


title: EV, Control female, CTRL16


title: P8 nucleus pulposus cells treated with H-151 #2 for RNA-seq

city: Wuhan

first: Cao

last: Yang

state: Hubei

address: Jiefang average

country: China

institute: Wuhan Union Hospital

description:
STINGI_2
STINGI_DMSO_RPKM.txt

data_processing:
Illumina Casava 1.7 software was used for basecalling.
Sequenced reads were qualified using FastQC and masked for low-complexity or low-quality sequence, then mapped to Homo_sapiens.GRCH38.94 whole genome.
Read Per Kilobase of exon per Megabase of library size (RPKM)  were calculated using a procotol from Feng, Jianxing et al. Bioinformatics (Oxford, England) vol. 28,21 (2012): 2782-8. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling of the meta-transcript and by the size of the library.
Assembly: Homo_sapiens.GRCh38.94
Supplementary files format and content: RPKM

source_name: Nucleus pulposus tissue

growth_protocol: Nucleus pulposus cells were isolated from human no-degenerated nucleus pulposus tissues and cultured in DMEM:F12 supplemented with 10% fetal bovine serum and antibiotics in humidified atmosphere with 5% CO2. P2 and P8 nucleus pulposus cells were collected via serial passage.

extract_protocol:
Total RNA was isolated from samples using TRIzol reagent. Illumina TruSeq RNA Sample Pre Kit (Cat#FC-122-1001) was used with 1 Î¼g of total RNA for the construction of sequencing libraries.
Libraries were prepared according to instructions of Illumina HiSeq X ten accompanying the Ovation RNA-Seq System V2 (M01206 v9). Briefly,RNA was elutated according to the manuscription user guide. Then RNA was fragmented using fragment buffer. cDNA was synthed using dNTPs, DNA polymeraseI and RNaseH. Then cDNA was purified using AMPure XP beads. PCR Was used to amplify with Illumina primers for 15 cycles and library fragments of ~200bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel. The purified RNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Illumina HiSeq X ten following the manufacturer's protocols.

treatment_protocol: Human nucleus pulposus tissues were digested with 0.2% type II collagenase for 8 hours. Passage 8 nucleus pulposus cells were treated with STING pharmacological inhibitor (H-151) or vehicle (DMSO) for 24 hours.

value: Nucleus pulposus tissue

value: Nucleus pulposus cells

value: Treated with H-151 for 24 hours


title: P8 nucleus pulposus cells treated with H-151 #3 for RNA-seq

description:
STINGI_3
STINGI_DMSO_RPKM.txt


title: P8 nucleus pulposus cells treated with H-151 #1 for RNA-seq

description:
STINGI_1
STINGI_DMSO_RPKM.txt


title: WT + cm 6 hr biol rep 2


title: EV, Control female, CTRL13


title: P8 nucleus pulposus cells treated with DMSO #2 for RNA-seq

description:
DMSO_2
STINGI_DMSO_RPKM.txt

value: Treated with DMSO for 24 hours


title: WT + cm 24 hr biol rep 1


title: P8 nucleus pulposus cells treated with DMSO #3 for RNA-seq

description:
DMSO_3
STINGI_DMSO_RPKM.txt


title: EV, Suicide female, MDD10


title: EV, Control female, CTRL12


title: EV, Suicide female, MDD9


title: P8 nucleus pulposus cells treated with DMSO #1 for RNA-seq

description:
DMSO_1
STINGI_DMSO_RPKM.txt


title: EV, Control female, CTRL14


title: WT 6 hr biol rep 3


title: P2 nucleus pulposus cells #3 for RNA-seq

description:
P2_3
P8_P2_RPKM.txt


title: EV, Control female, CTRL11


title: EV, Suicide female, MDD8


title: P2 nucleus pulposus cells #1 for RNA-seq

description:
P2_1
P8_P2_RPKM.txt


title: EV, Control female, CTRL10


title: EV, Control female, CTRL9


title: P8 nucleus pulposus cells #2 for RNA-seq

description:
P8_2
P8_P2_RPKM.txt


title: EV, Suicide female, MDD7


title: P8 nucleus pulposus cells #1 for RNA-seq

description:
P8_1
P8_P2_RPKM.txt


title: No-degenerated nucleus pulposus cells #1 for RNA-seq

description:
NO_Degenerated_1
Degenerated_NO_Degenerated_RPKM.txt

source_name: No-degenerated nucleus pulposus tissue

value: No-degenerated nucleus pulposus tissue


title: No-degenerated nucleus pulposus cells #2 for RNA-seq

description:
NO_Degenerated_2
Degenerated_NO_Degenerated_RPKM.txt


title: No-degenerated nucleus pulposus cells #3 for RNA-seq

description:
NO_Degenerated_3
Degenerated_NO_Degenerated_RPKM.txt


title: Degenerated nucleus pulposus cells #2 for RNA-seq

description:
Degenerated_2
Degenerated_NO_Degenerated_RPKM.txt

source_name: Degenerated nucleus pulposus tissue

value: Degenerated nucleus pulposus tissue


title: EV, Control female, CTRL8


title: EV, Suicide female, MDD6


title: EV, Control female, CTRL7


title: EV, Suicide female, MDD5


title: EV, Control female, CTRL6


title: P2 nucleus pulposus cells #2 for RNA-seq

description:
P2_2
P8_P2_RPKM.txt


title: EV, Control female, CTRL4


title: BMDMs, 2mg_IL-4_24hrs_23

city: New Haven

first: Scott

middle: Dean

last: Pope

state: Connecticut

address: 300 Cedar St

department: Immunobiology

institute: Yale School of Medicine

data_processing:
Paired-end sequencing was performed with Next-seq 500 with paired end reads of 38 base pairs. Illumina fastq files were downloaded from Illumina Basespace and were aligned with Kallisto v0.46.1 using the “-b 100 and -t 20” options to obtain transcript abundances in transcripts per million (TPM) and estimated counts. The kallisto index used during transcript quantification was built from the Mus musculus transcriptome GRCm38. Transcripts were annotated using the Bioconductor package biomaRt v2.40.5.
Assembly: GRCm38
Supplementary files format and content: tab separated
Supplementary files format and content: TPM

organism: Mus musculus

source_name: bone marrow-derived macrophage

growth_protocol: BMDMs were differentiated from mouse bone marrow cells in macrophage growth media (MGM) composed of 30% L929-cell conditioned media and 70% complete RPMI media (cRPMI), which consisted of RPMI-1640 (Corning) supplemented with 10% heat-inactivated fetal bovine serum (FBS) (Gibco), 2 mM L-glutamine, 200 U/mL penicillin/streptomycin, 1 mM sodium pyruvate, and 10 mM HEPES. Bone marrow was prepared by crushing C57BL/6J mouse femurs and tibias to release marrow, followed by ACK (ammonium-chloride-potassium) lysis of red blood cells and passage through a 70-μm cell strainer. Bone marrow was plated at 5 × 106 cells in 20 mL of MGM in a non-tissue culture (non-TC) dish (Day 0). Every three days, cells were supplemented with 10 mL of MGM. After day 6, adherent cells were lifted with cold phosphate-buffered saline (PBS) containing 5 mM EDTA and used for experiments.

extract_protocol:
After stimulation for 16-28 hours, gels were transferred with curved, blunt, serrated forceps to a 24-well non-TC plate, rinsing forceps in PBS between handling each gel. RNA-Bee (Tel-Test) 1 ml was then added to each gel and allowed to sit for 5 minutes or until gels began to fragment. RNA-Bee and gel were pipetted up and down until the gel disintegrated and the solution was homogenous. This solution was processed for RNA purification.
Illumina TruSeq Stranded mRNA

treatment_protocol: recombinant murine IL-4 (Peprotech, 214-14) was used at 20 ng/mL. Three-dimensional collagen gels with embedded BMDMs were synthesized using high-concentration rat tail collagen I (Corning, 354249), using a protocol adapted from Corning’s “alternate gelation procedure” provided with the product. Briefly, Collagen was mixed with 10× PBS and sterile H2O to achieve the desired collagen concentration. Subsequently, 1 N NaOH was added to neutralize the acetic acid in the collagen solution until a pH of 7-7.5 was achieved, measured by pH strip. BMDMs were added to the collagen solution at 0.5-1 × 106 cells per gel. Cells were added such that they made up 1/8 of the volume of the gel. Collagen-cell solutions were then plated at 200 ul in 48-well non-TC plates. Until this step, collagen solution was kept on ice as much as possible. After collagen-cell solutions were plated, they were incubated for 45 minutes to 1.5 hours at 37˚C and 5% CO2 to achieve gelation. A small pipette tip was used to score around the edge of the gels to detach them from the walls of the wells and ensure that they float, in order to avoid cells interacting with the stiff bottom of the plate. Media (400 or 500 ul) was then added, including any stimulation or inhibitors at the appropriate concentrations, and the gels were scored once again before placing them back in the incubator for the duration of the experiment.

tag: strain

tag: replicate

value: bone marrow-derived macrophage

value: wild-type

value: 2mg collagen, 24 hrs IL-4


title: EV, Suicide female, MDD4


title: EV, Control female, CTRL3


title: P8 nucleus pulposus cells #3 for RNA-seq

description:
P8_3
P8_P2_RPKM.txt


title: EV, Control female, CTRL2


title: BMDMs, 2mg_Untx_24hrs_22

value: 2mg collagen


title: BMDMs, 2mg_IL-4_24hrs_24


title: BMDMs, 2mg_Untx_24hrs_21


title: EV, Control female, CTRL1


title: BMDMs, 7mg_IL-4_24hrs_20

value: 7mg collagen, 24 hrs IL-4


title: Degenerated nucleus pulposus cells #3 for RNA-seq

description:
Degenerated_3
Degenerated_NO_Degenerated_RPKM.txt


title: EV, Suicide female, MDD1

value: Anterior cingulate cortex-derived Evs


title: BMDMs, 7mg_Untx_24hrs_18

value: 7mg collagen


title: Degenerated nucleus pulposus cells #1 for RNA-seq

description:
Degenerated_1
Degenerated_NO_Degenerated_RPKM.txt


title: XAUT2-POOL-SCG12:HS1-BL HS2-BL HS3-BL HS4-BL HS6-BL HS7-BL HS8-BL HS9-BL HS10-BL HS11-BL HS12-BL HS13-BL HS14-BL HS15-BL

city: San Francisco

first: Michael

middle: George

last: Kattah

state: CA

address: 513 Parnassus Ave

department: Medicine-Gastroenterology

institute: UCSF

description:
10X genomics
Blood_RNAADT_Final.h5ad

data_processing:
Briefly, sequencer obtained bcl files were demultiplexed into individual library fastq trios using the mkfastq program from the Cellranger 3.0.2 suite of tools (https://support.10xgenomics.com). Feature-barcode matrices were obtained for each sample by aligning the raw fastqs to GRCh38 reference genome (annotated with Ensembl v85) using the Cellranger count. Raw feature-barcode matrices were loaded into Seurat 3.1.5 and low-quality cells (with fewer than 100 features), and features in 3 or fewer cells were dropped from the dataset. The remaining events were assessed for inter-sample doublet detection (generated due to libraries containing samples pooled prior to loading) using Freemuxlet (https://github.com/statgen/popscle), the genotype-free version of Demuxlet.
Clusters of cells belonging to the same patient were identified via SNP concordance to a “truth set” generated by bulk RNASeq.
Clusters of cells belonging to a unique sample were mapped to patients using their individual Freemuxlet-generated genotype, and ground truth genotypes per patient identified via bulk RNA-seq. The pairwise discordance between inferred and ground-truth genotypes was assessed using the bcftools gtcheck command.
Assembly: GRCh38
Supplementary files format and content: Freemuxlet format: clust1.samples.gz
Supplementary files format and content: anndata (.h5ad)
Supplementary files format and content: feature, barcode, and matrix files from Cellranger
Library strategy: CITE-seq, V(D)J

source_name: peripheral blood

extract_protocol:
peripheral blood leukocyte (PBL) isolation, peripheral blood was collected into EDTA tubes (BD, 366643). 2 mL aliquots of peripheral blood were treated with 30mL of RBC lysis buffer (Roche) for 5-8 minutes at room temperature with gentle mixing. Cells were resuspended in CryoStor CS10 (at 4°C) freezing medium. PBLs were thawed for 2min with gentle agitation in a 37 degree Celsius in water bath and then washed twice with complete DMEM (Thermo Fisher) supplemented with nonessential amino acids (Thermo Fisher Scientific), sodium pyruvate (Thermo Fisher Scientific), HEPES (10 mM; Corning), Glutamax (2 mM; Thermo Fisher Scientific), Normocin (100 μg/mL; Invivogen, ant-nr-2), penicillin-streptomycin (Thermo Fisher Scientific) and 10% Fetal Bovine Serum (VWR). Cells were incubated with ACK lysis buffer (Quality Biological) for 5min at room-temperature, washed twice with complete DMEM, treated with HBSS (Corning) containing 0.1 mg/mL DNAse I (Sigma-Aldrich, D4513)for 5 min, and then strained through a 20um pre-separation filter (Miltenyi). Cells were counted using a TC20 Automated Cell Counter (Bio-Rad) with 0.4% Trypan Blue Solution (Thermo Fisher Scientific). PBLs from each donor were pooled with equivelent number of cells for each patient and used for scRNA-seq with a final pooled viability of >85%. 60,000 cells were loaded per well and processed for single-cell encapsulation.
cDNA library generation using the Chromium Single Cell 5′ v2 Reagent Kits, following the detailed protocol provided by 10x Genomics.

value: peripheral blood

value: peripheral leukocytes

tag: adt

value: custom TotalSeq-C panel, (BioLegend)


title: XAUT2-POOL-SCG11:HS1-BL HS2-BL HS3-BL HS4-BL HS6-BL HS7-BL HS8-BL HS9-BL HS10-BL HS11-BL HS12-BL HS13-BL HS14-BL HS15-BL

description:
10X genomics
Blood_RNAADT_Final.h5ad


title: BMDMs, TC_IL-4_24hrs_16

value: 24 hrs. IL-4


title: XAUT2-POOL-SCG10:HS1-BL HS2-BL HS3-BL HS4-BL HS6-BL HS7-BL HS8-BL HS9-BL HS10-BL HS11-BL HS12-BL HS13-BL HS14-BL HS15-BL

description:
10X genomics
Blood_RNAADT_Final.h5ad


title: BMDMs, 7mg_Untx_24hrs_17


title: EV, Suicide female, MDD3

value: female

value: MDD


title: BMDMs, TC_Untx_24hrs_14


title: EV, Control female, CTRL5

value: control


title: XAUT2-POOL-SCG5: HS1-CL HS2-CL HS3-CL HS4-CL HS5-CL HS7-CL HS8-CL HS9-CL HS10-CL HS11-CL HS12-CL HS13-CL HS14-CL HS15-CL

description:
10X genomics
Biopsy_RNA_Final.h5ad

library_source: transcriptomic single cell

data_processing:
Briefly, sequencer obtained bcl files were demultiplexed into individual library fastq trios using the mkfastq program from the Cellranger 3.0.2 suite of tools (https://support.10xgenomics.com). Feature-barcode matrices were obtained for each sample by aligning the raw fastqs to GRCh38 reference genome (annotated with Ensembl v85) using the Cellranger count. Raw feature-barcode matrices were loaded into Seurat 3.1.5 and low-quality cells (with fewer than 100 features), and features in 3 or fewer cells were dropped from the dataset. The remaining events were assessed for inter-sample doublet detection (generated due to libraries containing samples pooled prior to loading) using Freemuxlet (https://github.com/statgen/popscle), the genotype-free version of Demuxlet.
Clusters of cells belonging to the same patient were identified via SNP concordance to a “truth set” generated by bulk RNASeq.
Clusters of cells belonging to a unique sample were mapped to patients using their individual Freemuxlet-generated genotype, and ground truth genotypes per patient identified via bulk RNA-seq. The pairwise discordance between inferred and ground-truth genotypes was assessed using the bcftools gtcheck command.
Assembly: GRCh38
Supplementary files format and content: Freemuxlet format: clust1.samples.gz
Supplementary files format and content: anndata (.h5ad)
Supplementary files format and content: feature, barcode, and matrix files from Cellranger

source_name: colon biopsy

extract_protocol:
Colon biopsies were obtained with standard cold endoscopic biopsy forceps from the colon. Six biopsies were collected in a conical tube with Basal Media (Advanced DMEM/F12 with NEAA and Sodium Pyruvate, Thermo cat. No. 12634-010; 2mM Glutamax, Thermo cat. No. 35050061; 10 mM HEPES (Corning); Penicillin-Streptomycin-Neomycin (PSN) Antibiotic Mixture, Thermo cat. No. 15640055; Normocin 100 μg/mL, Invivogen cat. No. ant-nr-2; 1 mM N-acetylcysteine, Sigma-Aldrich, A9165) with 10 μM Y-27632 (MedChem Express) at 4°C. Biopsies were transferred into cryovials containing freezing media (90% (v/v) FCS, 10% (v/v) DMSO and 10 μM Y-27632). Colon biopsies were thawed for 2min with gentle agitation in a 37 C water bath, transferred to a gentleMACS Tube (Miltenyi Biotec), washed twice with basal media containing 10 μM Y-27632, and then incubated in 2 mL digestion buffer (basal media, 10 μM Y-27632, 600 U/mL Collagenase IV (Worthington cat. No.LS004189), 0.1 mg/mL DNAse I (Sigma-Aldrich, D4513) and digested for 20 min at 37°C in a shaking incubator set at 225 rpm. Subsequently, samples were placed in the gentleMACS Dissociator, processed with the gentleMACS program m_intestine_01, followed by 15 min incubation at 37°C in a shaking incubator set at 225 rpm. The suspension was then strained through a 100 μm strainer (Miltenyi) and centrifuged at 450g for 5 min at RT. Two additional washes were performed in Hanks’ Balanced Salt Solution (HBSS) (Corning) containing 0.1 mg/mL DNAse I (Sigma-Aldrich, D4513). Dead cells were removed with the Dead Cell Removal Kit (Miltenyi) according to the manufacturer’s instructions. Cell suspensions were counted using a TC20 Automated Cell Counter (Bio-Rad) with 0.4% Trypan Blue Solution (Thermo Fisher Scientific). Live cell enriched colon single-cell suspensions were used for tissue scRNA-seq and CITE-seq, with a final pooled viability >75%. Colon single-cell suspensions from each patient were pooled with equivalent number of live cells. Samples from unique individuals were pooled, each sample could later be uniquely identified using demuxlet.
cDNA library generation using the Chromium Single Cell 5′ v2 Reagent Kits, following the detailed protocol provided by 10x Genomics.

value: colon biopsy


title: BMDMs, TC_Untx_24hrs_13


title: H3KO_3

city: COLUMBUS

first: Deqiang

last: Li

state: Ohio

address: 575 Children’s Crossroad, WB4321

institute: Nationwide Children's Hospital

description: 10x Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v2.1.1 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Supplementary files format and content: mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Total heart cells

extract_protocol: Library was performed according to the manufacter’s instructions (single cell 3’ v2 protocol, 10x Genomics). Briefly, GCs were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead-in-emulsion (GEM). The poly-A RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA, which contains an Ilumina R1 primer sequence, Unique Molecular Identifier (UMI) and the 10x Barcode. The pooled barcoded cDNA was then cleaned up with Silane DynaBeads, amplified by PCR and the apropiated sized fragments were selected with SPRIselect reagent for subsequent library construction. During the library construction Ilumina R2 primer sequence, paired-end constructs with P5 and P7 sequences and a sample index were added.

value: Total heart cells

tag: age

value: Hdac3f/f; Tie2-Cre/+; R26eYFP/+


title: XAUT2-POOL-SCG3: HS1-CL HS2-CL HS3-CL HS4-CL HS5-CL HS7-CL HS8-CL HS9-CL HS10-CL HS11-CL HS12-CL HS13-CL HS14-CL HS15-CL

description:
10X genomics
Biopsy_RNA_Final.h5ad


title: H3KO_4

description: 10x Genomics


title: XAUT2-POOL-SCG2: HS1-CL HS2-CL HS3-CL HS4-CL HS5-CL HS7-CL HS8-CL HS9-CL HS10-CL HS11-CL HS12-CL HS13-CL HS14-CL HS15-CL

description:
10X genomics
Biopsy_RNA_Final.h5ad


title: EV, Suicide female, MDD2


title: XAUT2-POOL-SCG1: HS1-CL HS2-CL HS3-CL HS4-CL HS5-CL HS7-CL HS8-CL HS9-CL HS10-CL HS11-CL HS12-CL HS13-CL HS14-CL HS15-CL

description:
10X genomics
Biopsy_RNA_Final.h5ad


title: H3CTL_4

description: 10x Genomics

value: Hdac3f/+; Tie2-Cre/+; R26eYFP/+


title: H3KO_2

description: 10x Genomics


title: H3KO_1

description: 10x Genomics


title: XAUT2-POOL-SCG4: HS1-CL HS2-CL HS3-CL HS4-CL HS5-CL HS7-CL HS8-CL HS9-CL HS10-CL HS11-CL HS12-CL HS13-CL HS14-CL HS15-CL

description:
10X genomics
Biopsy_RNA_Final.h5ad


title: BMDMs, 7mg_IL-4_24hrs_19

value: bone marrow-derived macrophage

value: wild-type


title: XAUT2-POOL-SCG7: HS1-CL HS2-CL HS3-CL HS4-CL HS5-CL HS7-CL HS8-CL HS9-CL HS10-CL HS11-CL HS12-CL HS13-CL HS14-CL HS15-CL

description:
10X genomics
Biopsy_RNAADT_Final.h5ad

data_processing:
Briefly, sequencer obtained bcl files were demultiplexed into individual library fastq trios using the mkfastq program from the Cellranger 3.0.2 suite of tools (https://support.10xgenomics.com). Feature-barcode matrices were obtained for each sample by aligning the raw fastqs to GRCh38 reference genome (annotated with Ensembl v85) using the Cellranger count. Raw feature-barcode matrices were loaded into Seurat 3.1.5 and low-quality cells (with fewer than 100 features), and features in 3 or fewer cells were dropped from the dataset. The remaining events were assessed for inter-sample doublet detection (generated due to libraries containing samples pooled prior to loading) using Freemuxlet (https://github.com/statgen/popscle), the genotype-free version of Demuxlet.
Clusters of cells belonging to the same patient were identified via SNP concordance to a “truth set” generated by bulk RNASeq.
Clusters of cells belonging to a unique sample were mapped to patients using their individual Freemuxlet-generated genotype, and ground truth genotypes per patient identified via bulk RNA-seq. The pairwise discordance between inferred and ground-truth genotypes was assessed using the bcftools gtcheck command.
ADT counts were centered log-ratio (CLR) normalized. The resulting Harmony components were used to generate batch corrected UMAP visualizations and cell clustering
Assembly: GRCh38
Supplementary files format and content: Freemuxlet format: clust1.samples.gz
Supplementary files format and content: anndata (.h5ad)
Supplementary files format and content: feature, barcode, and matrix files from Cellranger
Library strategy: CITE-seq

extract_protocol:
Colon biopsies were obtained with standard cold endoscopic biopsy forceps from the colon. Six biopsies were collected in a conical tube with Basal Media (Advanced DMEM/F12 with NEAA and Sodium Pyruvate, Thermo cat. No. 12634-010; 2mM Glutamax, Thermo cat. No. 35050061; 10 mM HEPES (Corning); Penicillin-Streptomycin-Neomycin (PSN) Antibiotic Mixture, Thermo cat. No. 15640055; Normocin 100 μg/mL, Invivogen cat. No. ant-nr-2; 1 mM N-acetylcysteine, Sigma-Aldrich, A9165) with 10 μM Y-27632 (MedChem Express) at 4°C. Biopsies were transferred into cryovials containing freezing media (90% (v/v) FCS, 10% (v/v) DMSO and 10 μM Y-27632). Colon biopsies were thawed for 2min with gentle agitation in a 37 C water bath, transferred to a gentleMACS Tube (Miltenyi Biotec), washed twice with basal media containing 10 μM Y-27632, and then incubated in 2 mL digestion buffer (basal media, 10 μM Y-27632, 600 U/mL Collagenase IV (Worthington cat. No.LS004189), 0.1 mg/mL DNAse I (Sigma-Aldrich, D4513) and digested for 20 min at 37°C in a shaking incubator set at 225 rpm. Subsequently, samples were placed in the gentleMACS Dissociator, processed with the gentleMACS program m_intestine_01, followed by 15 min incubation at 37°C in a shaking incubator set at 225 rpm. The suspension was then strained through a 100 μm strainer (Miltenyi) and centrifuged at 450g for 5 min at RT. Two additional washes were performed in Hanks’ Balanced Salt Solution (HBSS) (Corning) containing 0.1 mg/mL DNAse I (Sigma-Aldrich, D4513). Dead cells were removed with the Dead Cell Removal Kit (Miltenyi) according to the manufacturer’s instructions. Cell suspensions were counted using a TC20 Automated Cell Counter (Bio-Rad) with 0.4% Trypan Blue Solution (Thermo Fisher Scientific). Live cell enriched colon single-cell suspensions were used for tissue scRNA-seq and CITE-seq, with a final pooled viability >75%. Colon single-cell suspensions from each patient were pooled with equivalent number of live cells. Samples from unique individuals were pooled, each sample could later be uniquely identified using demuxlet.
1x10^6 cells of single-cell colon suspension pool was stained with a custom TotalSeq-C panel, (BioLegend) according to the manufacturer’s instructions and loaded into two wells. cDNA library generation using the Chromium Single Cell 5′ v2 Reagent Kits, following the detailed protocol provided by 10x Genomics.


title: H3CTL_2

description: 10x Genomics


title: H3CTL_3

description: 10x Genomics

value: Hdac3f/+; Tie2-Cre/+


title: BMDMs, TC_IL-4_24hrs_15


title: JY3

city: Jinzhou

first: shuang

last: tian

state: Liaoning

address: No.40，Section 3,Songpo Road

institute: Jinzhou Medical University

description: AT-II

data_processing:
Transcriptome analysis flow 1. Quality control  Samples are sequenced on the platform to get image files, which are transformed by the  software of the sequencing platform, and the original data in FASTQ format (Raw Data) is  generated. Sequencing data contains a number of connectors, low-quality Reads, so we use  Cutadapt (v1.15) software to filter the sequencing data to get high quality sequence（Clean  Data）for further analysis . 2. Reads mapping The reference genome and gene annotation files were downloaded from genome website. The filtered reads were mapping to the reference genome using HISAT2 v2.0.5. 3. Differential expression analysis:  we used HTSeq(0.9.1) statistics to compare the Read Count values on each gene as the  original expression of the gene, and then used FPKM to standardize the expression. Then  difference expression of genes was analyzed by DESeq (1.30.0) with screened conditions as  follows: expression difference multiple |log2FoldChange| > 1, significant P-value < 0.05. At  the same time, We used R language Pheatmap(1.0.8) software package to perform  bi-directional clustering analysis of all different genes of samples. We geted heatmap according to the expression level of the same gene in different samples and the expression  patterns of different genes in the same sample with Euclidean method to calculate the distance  and Complete Linkage method to cluster
Assembly: GRCh38
Supplementary files format and content: tab-delimited text files include FPKM value for each sample

source_name: uterus

growth_protocol: RL95-2 cells were cultured in DMEM/F12 medium supplemented with 10% fetal bovine serum, 100 U/ml penicillin,100 µg/ml strep-tomycin and 5 µg/ml insulin.

extract_protocol:
Total RNA was isolated using the Trizol Reagent (Invitrogen Life Technologies), after which the concentration, quality and integrity were determined using a NanoDrop spectrophotometer (Thermo Scientific).
Three micrograms of RNA were used as input material for the RNA sample preparations. Sequencing libraries were generated according to the following steps. Firstly, mRNA was purified from total RNA using poly-T oligo-attached magnetic beads. Fragmentation was carried out using divalent cations under elevated temperature in an Illumina proprietary fragmentation buffer. First strand cDNA was synthesized using random oligonucleotides and  Super Script II. Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and RNase H. Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities and the enzymes were removed. After adenylation of the 3' ends of the DNA fragments, Illumina PE adapter oligonucleotides were ligated to prepare for hybridization. To select cDNA fragments of the preferred 400-500 bp in length, the library fragments were purified using the AMPure XP system (Beckman Coulter,Beverly, CA, USA).  DNA fragments with ligated adaptor molecules on both ends were selectively enriched using Illumina PCR Primer Cocktail in a 15 cycle PCR reaction. Products were purified (AMPure XP system) and quantified using the Agilent high sensitivity DNA assay on a Bioanalyzer 2100 system (Agilent). The sequencing library was then sequenced on NovaSeq 6000 platform (Illumina) by genechem.

treatment_protocol: The RL95-2 cells were treated with AT-II or DMSO for 48h.

value: uterus

tag: cell line

value: endometrial cancer

value: WT

value: AT-II


title: JY2

description: AT-II


title: TG microglia (Me-X04 pos) 5

city: Kuopio

first: Flavia

last: Scoyni

address: Neulaniementie 2

department: A.I. Virtanen Institute for Molecular Sciences

country: Finland

institute: University of Eastern Finland

data_processing:
Raw reads were trimmed, aligned and mapped using the Qiagen Data Analysis Center.
Transcripts with low counts of CPM < 1 not present in at least 2 libraries above this threshold were considered not expressed and removed from the analysis.
Library sizes were subsequently normalised using TMM, batch corrected, and quasi-likelihood F-testing was used to estimate differential expression using edgeR (3.24.3).
Transcripts with a log2 FC of ≥ 1 or ≤ -1 and FDR < 0.01 were considered differentially expressed.
UMI corrected reads were subsequently used for differential gene expression.
Assembly: GRCm38

source_name: Brain

growth_protocol: Ex vivo microglia obtained from 5xFAD mouse brain

extract_protocol:
RNA extraction was performed with Qiagen Micro RNA kit (Qiagen)
RNA libraries for RNA-seq were prepared using QIAseq miRNA Library Kit following manufacturer's protocols.

treatment_protocol: Mice were injected with Methoxy-X04 amyloid beta staining previous to microglia isolation

value: Brain

value: Microglia (Cd11b-Cd45 positive)

value: Methoxy-X04(amyloid beta), Cd11b, Cd45 stained single cell sorting

tag: time

value: 6 months old mice


title: XAUT2-POOL-SCG6: HS1-CL HS2-CL HS3-CL HS4-CL HS5-CL HS7-CL HS8-CL HS9-CL HS10-CL HS11-CL HS12-CL HS13-CL HS14-CL HS15-CL

description:
10X genomics
Biopsy_RNA_Final.h5ad


title: XAUT2-POOL-SCG9:HS1-BL HS2-BL HS3-BL HS4-BL HS6-BL HS7-BL HS8-BL HS9-BL HS10-BL HS11-BL HS12-BL HS13-BL HS14-BL HS15-BL

description:
10X genomics
Blood_RNAADT_Final.h5ad

value: peripheral blood

value: peripheral leukocytes

value: custom TotalSeq-C panel, (BioLegend)


title: H3CTL_1

description: 10x Genomics

value: Total heart cells


title: TG microglia (Me-X04 pos) 4


title: DZ3

description: DMSO

value: DMSO


title: DZ2

description: DMSO


title: TG microglia (Me-X04 pos) 3


title: TG microglia (Me-X04 pos) 2


title: DZ1

description: DMSO


title: XAUT2-POOL-SCG8: HS1-CL HS2-CL HS3-CL HS4-CL HS5-CL HS7-CL HS8-CL HS9-CL HS10-CL HS11-CL HS12-CL HS13-CL HS14-CL HS15-CL

description:
10X genomics
Biopsy_RNAADT_Final.h5ad

value: colon biopsy


title: TG microglia (Me-X04 pos) 1


title: TG microglia (Me-X04 neg) 4


title: TG microglia (Me-X04 neg) 5


title: AT2-10_CONTROL_R2

city: McAllen

first: Satish

last: Kumar

state: Texas

address: 5300 North L Street (MBMRF-2.219)

department: Division of Human Genetics & South Texas Diabetes and Obesity Institute, UTRGV School of Medicine

institute: University of Texas Rio Grande Valley

description: iPSC-derived AT2 mRNA raw counts.txt

data_processing:
Raw fastq sequence files were generated and demultiplexed using Illumina bcl2fastq software (Illumina, Inc., San Diego, CA, USA).
The aligned reads were filtered based on read quality metrics and only high-quality aligned sequencing reads were retained and quantified using NGS software v3.4 (Strand Life Sciences Pvt. Ltd., Bangalore, India).
The aligned reads were filtered based on read quality metrics and only high-quality aligned sequencing reads were retained and quantified using NGS software v4.1 (Strand Life Sciences Pvt. Ltd., Bangalore, India).
The gene expression values as raw counts of sequencing reads were obtained and log2 transformation and ‘DESeq’ normalization was applied.
Assembly: hg38
Supplementary files format and content: Tab-delimited text file of raw sequencing read counts formatted as genes-vs-samples matrix table.

source_name: iPSC-derived alveolar epithelial cell type-2

growth_protocol: Existing validated iPSCs were differentiated into AT2s using a four-stage differentiation protocol. In the first stage (days 0-4), high-quality iPSCs were differentiated into multipotent definitive endoderm (DE) cells using a commercially available STEMdiff™ Definitive Endoderm Kit (Stem Cell Technologies Inc., Cambridge, MA, USA). In stage 2 (days 5-8), highly enriched multipotent DE cells (> 97 % cells expressing SOX17 and CXCR4 endodermal markers) were differentiated into Anterior Foregut Endoderm cells (AFECs) in an alveolar epithelial cell (AEC) basal medium containing 3:1 IMDM and Ham’s F12 Nutrient Mix, 1X N2 supplement, 1X B27 supplement, 2 mM GlutaMAX, 0.1% (w/v) bovine serum albumin Fraction V, 0.05 mg/ml L-ascorbic acid, 50U/ml Penicillin/Streptomycin (all from Thermo Fisher Scientific, Waltham, MA, USA), and  0.4 mM monothioglycerol (MilliporeSigma, St. Louis, MO, USA), and supplemented with 100 ng/ml of human recombinant Noggin (Thermo Fisher Scientific, Waltham, MA, USA) and 10 μM TGFβ receptor inhibitor SB-431542 (Bio-Techne Corporation, Minneapolis, MN, USA). In the third stage (days 9-13), highly enriched AFECs (> 95% cells expressing SOX2 and FOXA2) were differentiated into Ventralized Anterior Foregut Endoderm cells (vAFECs)/Lung Progenitor cells in the AEC basal medium (as described above) supplemented with 50 ng/ml of human recombinant BMP4 (Thermo Fisher Scientific, Waltham, MA, USA), 100 nM all-trans retinoic acid, and 3 μM CHIR99021 (MilliporeSigma, St. Louis, MO, USA). On Day 14, one part of the generated vAFECs were characterized by immunocytochemistry (ICC) analysis of NKX2-1 and CPM markers to assess differentiation efficiency. Magnetic Activated Cell Sorting (MACS) of CPM-positive cells was performed as necessary to achieve a highly enriched NKX2-1 positive vAFEC population. In stage 4 (days 14-21), NKX2-1 enriched vAFECs were resuspended in growth factor reduced Matrigel Matrix (Corning, Glendale, AZ, USA) at a cell density of ~350 cells/μl and seeded as 3D slabs in 6 well cell culture plates and then cultured in AT2 medium containing AEC basal medium (described above), 1X HEPES buffer, 0.8 mM of CaCl2, 3 μM CHIR99021, 50 nM dexamethasone, 0.1 mM 8-Bromoadenosine 3′, 5′- cyclic monophosphate sodium salt and 0.1 mM 3-Isobutyl-1-methylxanthine (all from MilliporeSigma, St. Louis, MO, USA), and 25 ng/ml human recombinant KGF (Thermo Fisher Scientific, Waltham, MA, USA). The alveolosphere outgrowths containing AT2s develop in the 3D Matrigel Matrix within 3-7 days. On Day 21-25, the differentiated AT2s were harvested by sequential digestion with 1U/ml Dispase (Stem Cell Technologies Inc., Cambridge, MA, USA), and 0.05% Trypsin (Thermo Fisher Scientific, Waltham, MA, USA), and were re-seeded as a monolayer (~1.5 x 105 cells/cm2) on Matrigel Matrix coated tissue culture plates for ICC characterization and SARS-CoV-2 infection assays.

extract_protocol:
Total RNA was extracted from each of the pre- and post- SARS-CoV-2 infection challenged AT2s (2 replicates each of the SARS-CoV-2 infected, and vehicle-treated cells per sample) using a commercially available RNeasy Mini Kit (Qiagen, Germantown, MD, USA) and the manufacturer’s protocol. RNA quality and quantity were assessed using a NanoDrop 2000 Spectrophotometer (Thermo Fisher Scientific, Waltham, MA, USA) and an Agilent 2200 TapeStation system (Agilent, Santa Clara, CA, USA).
1 µg of high-quality total RNA per sample per replicate and the reagents supplied in Illumina Stranded mRNA sample preparation kit v2 (Illumina, Inc., San Diego, CA, USA) were used to prepare mRNA sequencing libraries.

treatment_protocol: All SARS-CoV-2 viral procedures were performed in compliance with containment procedures in the BSL3 as approved by UTRGV’s Institutional Biosafety Committee and the Department of Environmental Health, Safety, and Risk Management. For the SARS-CoV-2 infection assay, the SARS-CoV-2 USA-WA1/2020 viral strain was used. For each sample, infection challenge was performed in triplicate, that is, three replicates of the generated AT2 cultures were infected with the SARS-CoV-2 WA1 strain and the other three replicates were treated with vehicle control. After 2 hours of viral inoculation, viral and vehicle control media were replaced with fresh medium, and cells were returned to the cell culture incubator for 48 hours. After 48 hours, one replicate of each of the pre- (vehicle treated) and post- SARS-CoV-2 infection challenged AT2s was fixed using 4% Paraformaldehyde solution (MilliporeSigma, St. Louis, MO, USA), and the other two replicates of each of the pre- and post- SARS-CoV-2 infection challenged cells were harvested by digestion with RNA extraction buffer. The tubes containing cell digest for RNA extraction were sealed, surface decontaminated, and transferred to the BSL2 laboratory for RNA extraction.

value: not applicable

value: alveolar epithelial cell type-2 (AT2)

value: vehicle-treated control


title: AT2-10_SARS-CoV-2_R3

description: iPSC-derived AT2 mRNA raw counts.txt

value: iPSC-derived alveolar epithelial cell type-2

value: SARS-CoV-2 infection


title: AT2-10_CONTROL_R3

description: iPSC-derived AT2 mRNA raw counts.txt


title: TG microglia (Me-X04 neg) 2


title: TG microglia (Me-X04 neg) 3


title: AT2-10_SARS-CoV-2_R2

description: iPSC-derived AT2 mRNA raw counts.txt


title: AT2-9_SARS-CoV-2_R3

description: iPSC-derived AT2 mRNA raw counts.txt


title: WT microglia (Me-X04 neg) 5

value: 2 months old mice


title: TG microglia (Me-X04 neg) 1


title: AT2-9_CONTROL_R3

description: iPSC-derived AT2 mRNA raw counts.txt


title: AT2-9_SARS-CoV-2_R2

description: iPSC-derived AT2 mRNA raw counts.txt


title: JY1

description: AT-II

value: uterus

value: endometrial cancer

value: WT

value: AT-II


title: AT2-9_CONTROL_R2

description: iPSC-derived AT2 mRNA raw counts.txt


title: WT microglia (Me-X04 neg) 4

value: Brain

value: Microglia (Cd11b-Cd45 positive)

value: Methoxy-X04(amyloid beta), Cd11b, Cd45 stained single cell sorting


title: AT2-8_SARS-CoV-2_R3

description: iPSC-derived AT2 mRNA raw counts.txt


title: WT microglia (Me-X04 neg) 3


title: Polysome bound mRNA seq of Oryzae sativa cv IR64 in drought stress - Drought 3

city: Faridabad

first: Ramu

last: Vemanna

address: NCR Biotech Science Cluster, Faridabad

country: India

institute: Regional Centre for Biotechnology

data_processing:
Read alignment was carried out using Hisat2 v2.1.0
The quantification of the gene expression level in FPKM (Fragments per kilobase of the transcript sequence per million base pairs sequenced) were done by StringTie (1.3.4) by counting the number of reads mapped to each gene.
The differential expression analysis was performed using the DESeq2 R package (2.11.38).
Assembly: RGAP 7
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample individually

organism: Oryza sativa

source_name: Leaf

extract_protocol:
Polysome bound RNA was extracted using TRIzol reagent(Sigma, T9424). All the solutions were prepared in DEPC water.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: cultivar

value: leaf

value: drought

tag: molecule subtype

value: Polysomal RNA


title: AT2-8_SARS-CoV-2_R2

description: iPSC-derived AT2 mRNA raw counts.txt

tag: tissue


title: AT2-8_CONTROL_R2

description: iPSC-derived AT2 mRNA raw counts.txt


title: Polysome bound mRNA seq of Oryzae sativa cv IR64 in drought stress - Drought 1


title: AT2-7_SARS-CoV-2_R3

description: iPSC-derived AT2 mRNA raw counts.txt


title: WT microglia (Me-X04 neg) 2


title: WT microglia (Me-X04 neg) 1


title: AT2-8_CONTROL_R3

description: iPSC-derived AT2 mRNA raw counts.txt


title: Polysome bound mRNA seq of Oryzae sativa cv IR64 in drought stress - Drought 2


title: AT2-7_CONTROL_R3

description: iPSC-derived AT2 mRNA raw counts.txt


title: Polysome bound mRNA  seq of Oryzae sativa cv IR64 control plants - Control 2

value: control


title: BV2 LPS miR-146a 4

data_processing:
Bulk RNA sequences of mRNA (dataset: BV2) have been aligned and quantified to the mouse genome of reference GRCm38 using the nf-core workflow (3.0 version of “rnaseq”).
We filtered out lowly expressed molecules in any condition using the function “filterByExpr” to increase the reliability of the mean-variance relationship. We removed the differences between samples due to the sequencing depth normalizing the count using the trimmed mean of M-values (TMM) method and applied a log transformation minimizing sum of sample-specific squared difference to enhance the true positive and negative ratio in the downstream analysis.
We checked for outliers and sample’s features inducing batch effect by performing a principal component analysis and unsupervised consensus clustering with Cola.
We finally created the design matrix for each pair of conditions to compare (contrast) and performed the differential expression analysis using limma/edgeR model controlling for the false discovery rate with Benjamini-Hochberg Procedure.
Assembly: GRCm38

growth_protocol: Murine glioblastoma cell line (BV2) cells were cultured in RPMI 1640 Medium, GlutaMAX™ Supplemented base medium (Gibco, 31966021), 1% Penicillin-Streptomycin and 10% heat inactivated and filtered FBS (Gibco, 10270106) in temperature controlled humidified incubator (37 °C, 5% CO2).

extract_protocol:
RNA extraction was performed with TRIzol™ Reagent (Invitrogen) following manufacturer's protocol
RNA libraries for RNA-seq were prepared using CORALL total RNA-Seq Library Prep Kit (Lexogen GmbH) after ribosomal RNA depletion with RiboCop rRNA Depletion Kit V1.2 (Lexogen GmbH) following manufacturer's protocols.

treatment_protocol: Cells were treated with 10ng/ml LPS or vehicle for 24h and then transfected with miRNA scramble negative control or miR-7a-5p, miR-29a-3p or miR-146a-5p

value: Glioblastoma

value: LPS 10ng/ml for 24h and overexpressing miR-146a-5p mimic


title: AT2-6_CONTROL_R3

description: iPSC-derived AT2 mRNA raw counts.txt

value: not applicable

value: alveolar epithelial cell type-2 (AT2)

value: vehicle-treated control


title: AT2-7_SARS-CoV-2_R2

description: iPSC-derived AT2 mRNA raw counts.txt

value: iPSC-derived alveolar epithelial cell type-2

value: SARS-CoV-2 infection


title: AT2-7_CONTROL_R2

description: iPSC-derived AT2 mRNA raw counts.txt


title: AT2-6_SARS-CoV-2_R3

description: iPSC-derived AT2 mRNA raw counts.txt


title: Polysome bound mRNA  seq of Oryzae sativa cv IR64 control plants - Control 1


title: AT2-6_SARS-CoV-2_R2

description: iPSC-derived AT2 mRNA raw counts.txt


title: AT2-6_CONTROL_R2

description: iPSC-derived AT2 mRNA raw counts.txt


title: Polysome bound mRNA  seq of Oryzae sativa cv APO in drought stress – Drought 3

value: APO


title: BV2 LPS miR-146a 2

value: WT

value: 6 months old mice


title: AT2-5_SARS-CoV-2_R3

description: iPSC-derived AT2 mRNA raw counts.txt


title: BV2 LPS miR-146a 1


title: AT2-5_SARS-CoV-2_R2

description: iPSC-derived AT2 mRNA raw counts.txt


title: Polysome bound mRNA  seq of Oryzae sativa cv APO in drought stress – Drought 2


title: AT2-5_CONTROL_R3

description: iPSC-derived AT2 mRNA raw counts.txt


title: BV2 vehicle miR-146a 4

value: Vehicle overexpressing miR-146a-5p mimic


title: AT2-5_CONTROL_R2

description: iPSC-derived AT2 mRNA raw counts.txt


title: Polysome bound mRNA  seq of Oryzae sativa cv APO in drought stress – Drought 1


title: AT2-4_SARS-CoV-2_R3

description: iPSC-derived AT2 mRNA raw counts.txt


title: pre_pat05_ACT_1

source_name: Breast

value: Breast

value: ACT

value: AC and taxol

tag: residual tumor

value: yes

tag: tissue with_residul

value: B

tag: patient id

tag: deceased

value: y

tag: mastectomy or_lumpectomy

value: M

tag: grade pre-nac

tag: residual tumor_size

tag: bmi


title: AT2-4_SARS-CoV-2_R2

description: iPSC-derived AT2 mRNA raw counts.txt

tag: cell type

tag: genotype

tag: treatment


title: BV2 vehicle miR-146a 3

value: Glioblastoma


title: Polysome bound mRNA  seq of Oryzae sativa cv APO control plants - Control 3

value: leaf

value: control

value: Polysomal RNA


title: AT2-4_CONTROL_R3

description: iPSC-derived AT2 mRNA raw counts.txt

value: iPSC-derived alveolar epithelial cell type-2

value: not applicable

value: alveolar epithelial cell type-2 (AT2)

value: vehicle-treated control


title: BV2 vehicle miR-146a 2

value: WT


title: AT2-4_CONTROL_R2

description: iPSC-derived AT2 mRNA raw counts.txt


title: Polysome bound mRNA  seq of Oryzae sativa cv APO control plants - Control 2

value: APO


title: BV2 vehicle miR-146a 1

value: Vehicle overexpressing miR-146a-5p mimic


title: AT2-3_SARS-CoV-2_R3

description: iPSC-derived AT2 mRNA raw counts.txt

value: SARS-CoV-2 infection


title: AT2-3_SARS-CoV-2_R2

description: iPSC-derived AT2 mRNA raw counts.txt


title: AT2-3_CONTROL_R3

description: iPSC-derived AT2 mRNA raw counts.txt


title: Polysome bound mRNA  seq of Oryzae sativa cv APO control plants - Control 1


title: AT2-2_SARS-CoV-2_R3

description: iPSC-derived AT2 mRNA raw counts.txt


title: BV2 LPS miR-29a 4

value: LPS 10ng/ml for 24h and overexpressing miR-29a-3p mimic

value: 6 months old mice


title: Polysome bound mRNA  seq of Oryzae sativa cv IR64 control plants - Control 3


title: AT2-2_SARS-CoV-2_R2

description: iPSC-derived AT2 mRNA raw counts.txt


title: BV2 LPS miR-29a 3


title: ISE6 cells, subolesin knockdown, 4s

city: Ciudad Real

first: Sara

last: Artigas Jerónimo

state: Ciudad Real

address: Ronda de Toledo 12

department: Sanidad y Biotecnología (SaBio)

country: Spain

institute: Instituto de Investigación en Recursos Cinegéticos (IREC)

data_processing:
Pre-processing steps: 1. Right trimming where quality<Q20; 2. Left trimming of the first 10 bases ; 3. Quality analysis of the processed data
Reads mapping to the reference with Tophat
Transcripts assembly with Cufflinks
Transcripts merge and comparison with the reference with Cuffmerge
Analysis of differences in gene expression with Cuffdiff. Reads were mapped to the reference genome with the tool Bowtie, integrated in the Tophat suite.
Assembly: IscaW1 assembly
Supplementary files format and content: Matrix table with abundance messurements for each gene and treatment. The Wald test p-value, the Benjamini-Hochberg adjusted p-value,  log2 fold change and gene ID and name for each gene are included in the same table.

organism: Ixodes scapularis

source_name: Ixodes scapularis embryo-derived cell line ISE6

extract_protocol:
Total RNA was extracted using the All Prep DNA/RNA/PROTEIN Mini Kit (Qiagen, Hilden, Germany) following manufacturer’s recommendations.
The samples were subjected to polyA enrichment followed by fragmentation, first and second strand synthesis, adenylation of 3’ ends, adapter ligation, DNA fragment enrichment, and real-time PCR quantification. TruSeq Stranded mRNA LT (Illumina) was used. Agilent 2100 Bioanalyzer (Agilent Technologies) assessed the size distribution of the amplified DNA.

value: Subolesin knockdown

value: iRNA


title: BV2 LPS miR-29a 2


title: AT2-2_CONTROL_R3

description: iPSC-derived AT2 mRNA raw counts.txt


title: ISE6 cells, WT, 2


title: AT2-1_SARS-CoV-2_R3

description: iPSC-derived AT2 mRNA raw counts.txt


title: AT2-2_CONTROL_R2

description: iPSC-derived AT2 mRNA raw counts.txt


title: AT2-1_SARS-CoV-2_R2

description: iPSC-derived AT2 mRNA raw counts.txt


title: BV2 LPS miR-29a 1


title: ISE6 cells, WT, 1


title: BV2 vehicle miR-29a 4

value: Vehicle overexpressing miR-29a-3p mimic


title: AT2-1_CONTROL_R2

description: iPSC-derived AT2 mRNA raw counts.txt


title: AT2-1_CONTROL_R3

description: iPSC-derived AT2 mRNA raw counts.txt


title: C57BL/6J mice subjected to myocardial IRI at time point ZT20, replicate 3

city: Houston

first: Holger

middle: K.

last: Eltzschig

department: Department of Anesthesiology

institute: The University of Texas Health Science Center at Houston

data_processing:
Alignment of RNA sequencing tags was restricted to those mapping to the same DNA strand as annotated in the GRCm38 reference genome, utilizing the STAR software. Quantification of transcripts was conducted by calculating the fragments per kilobase of transcript per million mapped reads (FPKM) values, along with transcript counts. In the preprocessing step of mRNA analysis, any gene identified as non-expressed, defined as having an FPKM expression level less than 1 in more than 80% of samples, was excluded. The normalized expression profiles of these mRNAs were then subjected to PCA for quality control and to evaluate sample similarity. Differential expression analysis was executed using the DESeq2 pipeline, with DEGs being identified based on a threshold of 1.5-fold change and an adjusted p-value below 0.05, as determined by the Benjamini-Hochberg method
Assembly: GRCm38
Supplementary files format and content: Gene quantification and differential expression

source_name: left ventricle

extract_protocol:
The AAR of the heart was harvested following 2h of reperfusion from the C57BL/6J mice subjected to myocardial IRI at either ZT8 or ZT20.
Total RNA was extracted using the RNeasy Mini kit (Qiagen) and employed to construct RNA-Seq libraries

value: left ventricle

value: male

value: myocardial IRI at ZT20


title: CD34-Y

city: Los Angeles

first: Feiyang

last: Ma

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

department: Molecular Biology Institute

institute: UCLA

data_processing:
Sequencing analysis was carried out using 10X Genomics’ CellRanger software. Fastq files were generated using the CellRanger mkfastq pipeline.
Raw reads were mapped to the human reference genome (refdata-cellranger-GRCh38-3.0.0) using the CellRanger count pipeline. The expression matrices from different samples were concatenated.
Assembly: hg38
Supplementary files format and content: Raw count expression matrix for scRNA-seq.

source_name: Bone Marrow

extract_protocol:
FACS-purified live BM MNCs or Lin-CD34+ cells were sequenced at the Advanced Technology Genomics Core facility at MDACC. Sample concentration and cell suspension viability were evaluated using a Countess II FL Automated Cell Counter (ThermoFisher Scientific) and manual counting.
Samples were normalized for input onto the Chromium Single Cell A Chip Kit (10x Genomics, Pleasanton, CA), in which single cells were lysed and barcoded for reverse-transcription. The pooled single-stranded, barcoded cDNA was amplified and fragmented for library preparation. Pooled libraries were sequenced on a NovaSeq6000 SP 100-cycle flow cell (Illumina, San Diego, CA).

value: Bone Marrow

value: Bone Marrow CD34+ cells

value: Pre-canakinumab


title: BV2 vehicle miR-29a 3

value: Glioblastoma


title: C57BL/6J mice subjected to myocardial IRI at time point ZT20, replicate 2


title: CD34-8

value: Canakinumab Cycle 2


title: CD34-4


title: AT2-3_CONTROL_R2

description: iPSC-derived AT2 mRNA raw counts.txt

value: iPSC-derived alveolar epithelial cell type-2

value: not applicable

value: alveolar epithelial cell type-2 (AT2)

value: vehicle-treated control


title: CD34-13


title: BV2 vehicle miR-29a 2

value: WT


title: BM-Y

value: Bone Marrow Mononuclear cells


title: BM-8


title: BM-4


title: C57BL/6J mice subjected to myocardial IRI at time point ZT8, replicate 3

value: myocardial IRI at ZT8


title: BV2 vehicle miR-29a 1


title: ISE6 cells, subolesin knockdown, 3s

value: Subolesin knockdown

value: iRNA


title: C57BL/6J mice subjected to myocardial IRI at time point ZT8, replicate 2

value: left ventricle


title: BV2 LPS miR-7a 4

value: LPS 10ng/ml for 24h and overexpressing miR-7a-5p mimic


title: C57BL/6J mice subjected to myocardial IRI at time point ZT20, replicate 1

value: male

value: myocardial IRI at ZT20


title: BM-13

value: Bone Marrow


title: BV2 LPS miR-7a 3


title: hFBO, 4 psi, without BMP2 [8680-PD-5]

city: Ann Arbor

first: Allen

last: Liu

state: Michigan

address: 2350 Hayward Street

department: Mechanical Engineering

institute: University of Michigan

data_processing:
Libraries were sequenced on a NovaSeq instrument (Illumina) using 151bp paired-end reads. The reads were demultiplexed into FASTQ files using the BCL Convert Conversion Software (Illumina, v4) and the adapters were trimmed using Cutadapt v2.3.
The reads were then mapped to the human GRCh38 reference genome (ENSEMBL 109) following ENCODE standards using STAR v2.7.8a and counts were assigned to genes using RSEM v1.3.3.
The excepted counts from RSEM were filtered to genes with at least 10 counts in at least one sample and transformed to log-scaled counts per million using the edgeR package (v3.40.2)
Assembly: GRCh38 (ENSEMBL 109)
Supplementary files format and content: Expected raw count matrix from RSEM

source_name: fetal osteoblast spheroid

extract_protocol:
Osteoblast spheroids from the ground experiments were collected in RNAlater and  frozen at -80°C for RNA collection.
Total RNA was isolated with the miRNeasy Micro kit (Qiagen) following manufacturer instructions. Libraries were prepared using the SMART-seq mRNA kit (Takara Bio).

value: fetal osteoblast spheroid

tag: pressure

value: 4 psi

value: Control


title: hFOB, 4 psi, with BMP2 [8680-PD-6]


title: C57BL/6J mice subjected to myocardial IRI at time point ZT8, replicate 1


title: hFOB, 2 psi, with BMP2 [8680-PD-4]

value: 2 psi


title: hFBO, 2 psi, without BMP2 [8680-PD-3]


title: hFOB, 0 psi, with BMP2 [8680-PD-2]

value: 0 psi


title: BV2 LPS miR-7a 2

tag: cell line

value: Glioblastoma


title: BV2 LPS miR-7a 1


title: hFOB, 0 psi, without BMP2 [8680-PD-1]