title: Type I SMA patient fibroblasts, treated flunarizine 4 hrs 3

status: Public on Apr 30 2020

type: SRA

city: 91400 Orsay

first: Florent

last: Dumont

state: Ile de France

address: 17 avenue des sciences

country: France

institute: Université Paris-Saclay

library_source: transcriptomic

data_processing:
Alignement:  STAR and bowtie2 aligner
counting reads : featureCounts v1.4.6
Differential analysis : DESeq2
Genome_build: hg19
Supplementary_files_format_and_content: GEO_RNAseq_featureCount_processeddata_4_55765.txt

molecule: total RNA

organism: Homo sapiens

source_name: flunarizine-treated immortalized Type I SMA patient fibroblast cell line

growth_protocol: cells are grown in DMEM-glutamax supplemented with 10% FBS, penicillin (100 U/ ml), streptomycin (100 mg/ml) at 37°C with 5% CO2

extract_protocol:
total RNAs were harvested with trizol (Ambion)
The rRNA-depleted RNAs were used to generate cDNA libraries according to the manufacturer's protocol (Ion total RNA-Seq kit V2, Thermo Fisher Scientific).

treatment_protocol: treated immortalized type I SMA patient fibroblasts with flunarizine or DMSO for 4hrs followed by the analysis of total RNA by RNA-seq on Ion Chef

tag: disease state

value: SMA type 1

tag: cell type

value: skin fibroblasts

tag: passages

value: passage 3 after thawing

tag: treatment

value: flunarizine


title: Type I SMA patient fibroblasts, treated flunarizine 4 hrs 2

value: passage 2 after thawing


title: Type I SMA patient fibroblasts, treated flunarizine 4 hrs 1


title: Type I SMA patient fibroblasts, DMSO 4hrs 1

description: DMSO

source_name: DMSO-treated immortalized Type I SMA patient fibroblast cell line

value: DMSO


title: Ova-11 A20_10_S12

city: Beer-Sheva

first: Nir

last: Bujanover

address: Ben Gurion 1

department: Immunology

country: Israel

institute: Ben-Gurion University

data_processing:
Base calling- Illumina's bcl2fastq v2.17
Filter contaminants (Bowtie 2) - v2.2.5 Partek. Filter out rDNA,mtrDNA
Alignment: STAR v2.5.3a , default parameters, reference index: mm10 - Ensembl Transcripts release 92
Quantification to annotation model (Partek E/M)) reference index: mm10 - Ensembl Transcripts release 92
Differential-expression analysis DEseq2 v3.5
Genome_build: mm10 - Ensembl Transcripts release 92
Supplementary_files_format_and_content: Normalized counts (after DEseq run)
Supplementary_files_format_and_content: raw gene counts

molecule: polyA RNA

organism: Mus musculus

source_name: Hematopoietic Stem Cells

extract_protocol:
Treated mice where euthanized, femur and tibia extracted, crashed in sample medium (PBSx1, EDTA 2mM, serum 2%) and loaded on Histopaq1083. this mononuclear enriched population was stained and sorted for Lineage-Sca1+cKit+CD150+Fgd5-mCherry+ cell, 100 cells from each sample, to 384 plate with lysis buffer also containing RNasin that blocks RNA degradation and stabilizes the RNA. library construction and sequencing was performed by the INCPM facility (Rehovot). in short - library preparation was done according to the Smart-seq2 protocol (Simone Picelli et al. Nature Protocols 2014) samples were pooled together and sequenced on one lane of the illumina HiSeq 2500 V4 instrument.
SMARTSeq-2 Ultra Low Input RNA V4 kit from Clontech (polyA based capture), with 14 cycles of cDNA amplification. The amplified cDNA was fragmented using the Covaris machine to around 450bp. Illumina libraries were constructed using the End repair, A base addition and adapter ligation (TruSeq like adapters:GATCGGAAGAGCACACGTCTGAACTCCAGTCACGTCGCCTTATCTCGTATGCCGTCTTCTG) and amplified using 13 PCR cycles. Performed by INCPM in the Weizmann institute of science.

treatment_protocol: Ova hypersensitivity treatment protocol adapted from (Zuany-Amorim et al. 1993), on day 0, 7 mice were injected subcutaneously (s.c.) with 100µg Ovalbumin (Ova, SIGMA- A5503-1G; lot:SLBK1399V), dissolved in PBSx1 and kept in aliquots at -20C) absorbed in 1.6mg aluminum hydroxide hydrate (stock dissolved in PBSx1 at 20mg/ml, kept in RT), shaken 1hr at RT prior to injection. On day 14 mice were injected with 10µg Ova, without adjuvant, and sacrificed on day 16, at 48 hrs after Ova-activation. Control-PBS  injected with PBS only. Positive-control were stimulated with polyinosinic–polycytidylic acid ( pIpC, Sigma P1530; 200 µg per mouse) intraperitoneally (IP) and sacrificed 24 hrs, as reported (Bujanover et al. 2018).

tag: strain

value: C57BL/6 Fgd5-mCherry


title: pIC-2 A23_12_S15


title: Ova-12 A21_10_S13


title: Ova-9 A18_9_S9


title: pIC-5 B5_13_S27


title: Ova-10 A19_10_S10


title: pIC-4 B1_14_S25


title: pIC-3 A24_13_S16


title: Ova-6 A15_8_S6


title: Ova-7 A16_9_S7


title: Ova-8 A17_9_S8


title: pIC-1 A22_12_S14


title: Ova-5 A14_8_S5


title: Ova-4 A13_7_S4


title: Ova-3 A12_7_S3


title: Ova-1 A10_6_S1


title: PBS-9 A9_5_S24


title: PBS-8 A8_5_S23


title: PBS-7 A7_5_S22


title: PBS-6 A6_4_S21


title: PBS-5 A5_4_S20


title: PBS-4 A4_4_S19


title: PBS-3 A3_3_S18


title: PBS-1 A1_3_S11


title: e-cig 48h Week2 S78

city: Southampton

first: Emmanuel

last: Minet

address: Regents Park Road

country: United Kingdom

institute: British American Tobacco

description:
qc: pass
S78

data_processing:
Illumina Casava1.7 software used for basecalling.
Samples were QC analyzed using the arrayQualityMetrics package in Bioconductor50. Outliers were identified based on 4 parameters, maplot, boxplot, heatmap and manual inspection. The RNAseq data was preprocessed and aligned to the human genome (GRCh38) using STAR aligner and the number of mapped read-pairs per gene were quantified based on the GENCODE v25 annotation. The resulting count data for the samples was normalized using TMM (Trimmed Mean of M-value) and transformed with VOOM to log2-counts per million with associated precision weights.
Genome_build: GRCh38
Supplementary_files_format_and_content: tab-delimited text file

source_name: MucilAir Bronchial donor MD046001

growth_protocol: Upon delivery MucilAir were given at least one week recovery before exposure experiments. The culture media was changed every two to three days.

extract_protocol:
The cells were lysed with QIAzol and the RNA was extracted using the QIAGEN miRNeasy Mini Kit (Hilden, Germany) and a QIACube workstation. All RNA samples had a RIN greater or equal to 8.0.
RNA libraries were prepared for sequencing using standard Illumina protocols
Sequencing was performed on an Illumina NextSeq 500 platform (Illumina, Sand Diego, CA, USA) at a depth of 40 million pair reads with 150 bp paired-end.

treatment_protocol: MucilAir™ cells were placed in exposure chambers (Adamson et al., 2011) with basal media and exposed to either vapour from the IS1(TT) prototype or to smoke from 1R6F cigarettes. Aerosols from both products were generated using a RM20S smoking machine (Borgwaldt KC, Germany). An air control was run alongside which received sterile air at an identical puffing regime to the product exposure.

tag: individual

value: Bronchial non smoker

tag: Stage

value: primary

tag: age

value: 64 yo

tag: gender

value: male

value: e-cig 48h post-exposure

value: in vitro primary airway cells


title: PBS-2 A2_3_S17


title: Ova-2 A11_6_S2


title: Air 48h Week1 S76

description:
qc: pass
S76

source_name: MucilAir Bronchial donor MD046002

value: 65 yo

value: Air 48h post-exposure


title: Air 24h Week1 S77

description:
qc: fail
S77

value: Air 24h post-exposure


title: 1R6Fcig 48h Week1 S73

description:
qc: pass
S73

value: 1R6Fcig 48h post-exposure


title: 1R6Fcig 24h Week1 S74

description:
qc: pass
S74

value: 1R6Fcig 24h post-exposure


title: e-cig 24h Week2 S72

description:
qc: pass
S72

value: e-cig 24h post-exposure


title: Air 48h Week1 S75

description:
qc: fail
S75


title: Ill_GM12878_TUC-seq_Rep2

city: irvine

first: Sorena

last: Rahmanian

state: ca

address: 2134 verano pl

department: Center for Complex Biological Systems

country: USA

institute: University of California Irvine

description: 8 hrs 1mM 4SU treated GM12878 + 3hrs osmium- replicate 2

data_processing:
we used Minimap2 v2.17 with iso-seq settings for mapping the PacBio data
TranscriptClean v2.0.2 was used on mapped PacBio data without mismatch correction. The splice junction file was obtained using GENCODE v29 using one of the accesory scripts
TALON v4.4.2 was used for annotation and quantification of PacBio data. The database was initialized with GENCODE v29
We used STAR 2.6 to map Illumina TUC-seq reads to Hg38 build
We created sub-categories of the illumina TUC-seq data based on the number of T to C substitutions in the reads to 4 groups: all reads, reads with > 2 , > 4 and > 6 T to C
For each categories in illumina data we counted the abundance for each transcript in gencode v29 annotation file using express v1.5.1
Genome_build: hg38
Supplementary_files_format_and_content: TXT table format, Pacbio abundance files generated by TALON and Illumina abundances generated by eXpress for each category of reads

growth_protocol: ENCODE protocol for GM12878 cell line specific

extract_protocol:
The RNeasy Plus Mini Kit was used for RNA extraction following the manufacturer instructions
The extracted RNA was treated with exonuclease for 1 hour and the SIV control set 3 was added at 0.03%, then we made cDNA following smart-seq II protocol
For PacBio samples we used "Preparing SMRTbell®  Libraries Using Express Template Prep Kit 2.0 With  Low DNA Input" and for illumina samples, we used "Nextra DNA library prep"

tag: 4su treatment

value: 8 hrs of  1mM 4SU

tag: osmium treatment

value: 3 hrs of osmium tetroxide

tag: library protocol

value: Illumina Nextra protocol

tag: cell line


title: Ill_GM12878_Osmium_ctrl_Rep1

description: Osmium-treated GM12878 cells without any 4SU incorporation-replicate 1

value: no 4SU


title: Ill_GM12878_Osmium_ctrl_Rep2


title: 1R6Fcig 24h Week1 S63

description:
qc: pass
S63


title: Air 24h Week2 S64

description:
qc: pass
S64


title: e-cig 48h Week2 S62

description:
qc: pass
S62


title: e-cig 48h Week2 S68

description:
qc: fail
S68


title: 1R6Fcig 48h Week1 S67

description:
qc: fail
S67


title: 1R6Fcig 48h Week1 S61

description:
qc: pass
S61


title: 1R6Fcig 24h Week1 S65

description:
qc: pass
S65


title: Air 48h Week2 S58

description:
qc: pass
S58


title: Air 48h Week2 S59

description:
qc: pass
S59


title: e-cig 24h Week2 S69

description:
qc: pass
S69


title: e-cig 24h Week2 S57

description:
qc: pass
S57


title: Air 24h Week1 S53

description:
qc: pass
S53


title: Ill_GM12878_TUC-seq_Rep1

description: 8 hrs 1mM 4SU treated GM12878 + 3hrs osmium- replicate 1


title: e-cig 48h Week2 S54

description:
qc: pass
S54


title: 1R6Fcig 24h Week1 S52

description:
qc: pass
S52


title: 1R6Fcig 48h Week1 S56

description:
qc: fail
S56


title: Air 24h Week1 S51

description:
qc: pass
S51


title: e-cig 24h Week2 S50

description:
qc: pass
S50


title: Air 24h Week1 S47

description:
qc: fail
S47


title: Air 24h Week1 S49

description:
qc: pass
S49


title: Air 48h Week2 S43

description:
qc: pass
S43


title: Air 48h Week2 S45

description:
qc: pass
S45


title: e-cig 48h Week2 S46

description:
qc: pass
S46


title: Air 24h Week2 S66

description:
qc: pass
S66


title: Air 48h Week1 S41

description:
qc: pass
S41


title: Air 48h Week1 S42

description:
qc: fail
S42


title: Air 24h Week1 S40

description:
qc: pass
S40


title: Air 24h Week2 S37

description:
qc: pass
S37


title: Air 48h Week1 S39

description:
qc: pass
S39


title: e-cig 48h Week2 S36

description:
qc: pass
S36


title: Air 48h Week1 S38

description:
qc: pass
S38


title: Air 24h Week2 S35

description:
qc: pass
S35


title: 1R6Fcig 24h Week1 S28

description:
qc: pass
S28


title: Air 24h Week2 S32

description:
qc: fail
S32


title: 1R6Fcig 48h Week1 S33

description:
qc: pass
S33


title: e-cig 24h Week2 S34

description:
qc: fail
S34


title: 1R6Fcig 48h Week1 S30

description:
qc: pass
S30


title: Air 48h Week1 S31

description:
qc: pass
S31


title: e-cig 24h Week2 S29

description:
qc: pass
S29


title: 1R6Fcig 24h Week1 S26

description:
qc: pass
S26


title: e-cig 24h Week2 S25

description:
qc: pass
S25


title: Air 24h Week1 S24

description:
qc: fail
S24


title: Air 48h Week2 S22

description:
qc: pass
S22


title: 1R6Fcig 24h Week1 S23

description:
qc: pass
S23


title: Air 48h Week2 S21

description:
qc: pass
S21


title: 1R6Fcig 48h Week1 S27

description:
qc: pass
S27


title: Air 24h Week2 S20

description:
qc: pass
S20


title: 1R6Fcig 24h Week1 S18

description:
qc: pass
S18


title: e-cig 24h Week2 S19

description:
qc: pass
S19


title: Air 24h Week2 S17

description:
qc: pass
S17


title: 1R6Fcig 24h Week1 S16

description:
qc: pass
S16


title: Air 48h Week2 S15

description:
qc: pass
S15


title: Air 24h Week1 S14

description:
qc: pass
S14


title: Air 48h Week2 S13

description:
qc: pass
S13


title: Air 48h Week2 S11

description:
qc: pass
S11


title: e-cig 48h Week2 S12

description:
qc: pass
S12


title: e-cig 24h Week2 S8

description:
qc: pass
S8


title: Air 48h Week1 S9

description:
qc: pass
S9


title: 1R6Fcig 48h Week1 S10

description:
qc: pass
S10


title: e-cig 48h Week2 S6

description:
qc: pass
S6


title: Air 24h Week1 S7

description:
qc: pass
S7


title: 1R6Fcig 48h Week1 S3

description:
qc: pass
S3


title: Air 24h Week2 S4

description:
qc: pass
S4


title: e-cig 48h Week2 S2

description:
qc: pass
S2


title: Air 48h Week1 S1

description:
qc: pass
S1


title: PDLSC-oD+Lev_Rep5

city: Würzburg

first: Richa

last: Bharti

state: Bavaria

address: Josef-Schneider-Straße 2 / Bau D15

department: IMIB,Core Unit Systemmedizin

country: Germany

institute: University of Wuerzburg

data_processing:
The generated raw reads were processed using FastQC 0.11.5 for assessing read quality, amount of duplicates and presence of adapter sequences.
After this, the Illumina TruSeq adaptors were cleaved using cutadapt (version 1.14) and resulting reads were further trimmed keeping a quality drop value below a mean of Q20.
Further, the processed sequences were mapped to the human genome using the short read aligner STAR (version-2.5.2b) with genome and annotation files retrieved from GENCODE (GRCh38, V25). For all the studied samples, the proportion of reads mapped to the human reference genome ranged between 83% and 86% in total.
The sequences aligning to specific genes were quantified using bedtools subcommand intersect (version 2.15.0).
Next, the differentially expressed genes were identified using DESeq2 (version 1.16.1). Only the genes having a Benjamini-Hochberg corrected p-value below 0.05 were classified as significantly differentially expressed (DEGs).
Genome_build: The data were visualized as MA plot using DESeq2’s function plotMA.
Supplementary_files_format_and_content: To compare the group, genes having p-adjusted values below 0.05 and an absolute log2 fold-change equal or above 2.

source_name: dental (periodontal ligament)

growth_protocol: Cells were cultivated in a humidified atmosphere at 37 °C and 5 % CO2 and the medium was changed twice a week. Cells were cultivated in DMEM Ham’s F12 (Life Technologies GmbH, Darmstadt Germany), 10 % FCS (Biochrom GmbH, now Merck KGaA, Darmstadt, Germany), 1% Penicillin/Streptomycin (Thermo Fisher Scientific, Bonn, Germany) and 50 µg/ml L-Ascorbat-2-Phosphate (Sigma Aldrich, now Merck KGaA, Darmstadt, Germany).

extract_protocol:
For isolation of stem cells from the periodontal ligament, which was left over after tooth (third molar) extraction, above all within the center and partially apical third of the root surface, was taken with sterile forceps and scalpels. The tissue was mechanically disrupted and enzymatically digested using 0.4 mg/ml collagenase and 4 mg/ml dispase in sterile PBS (1 h, 37 °C). Supernatant was discarded, and cells were transferred into a 25 cm2 culture flask with standard culture medium including 2.5 µg/ml Amphotericin B (Sigma Aldrich, now Merck KGaA, Darmstadt, Germany).
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: For osteogenic differentiation 5000 cells/cm2 were seeded and grew until confluence was reached prior to treatment with differentiation medium. Osteogenic differentiation medium contained DMEM High Glucose (4.5 g/l) (Life Technologies GmbH, Darmstadt Germany), 10 % FCS (Biochrom GmbH, now Merck KGaA, Darmstadt, Germany), 1 % Pen/Strep (Life Technologies GmbH, Darmstadt Germany), 50 µg/ml L-Ascorbat-2-phosphate, 10 mM ß-Glycerophosphate as well as 100 nM Dexamethasone (all Sigma-Aldrich, now Merck KGaA, Darmstadt, Germany). TNAP Inhibitor levamisole was purchased from Sigma-Aldrich, now Merck KGaA Darmstadt, Germany and used in a concentration of 1 mM.

value: osteogenic differentiation 2 weeks

value: treament with 1 mM levamisole

tag: tissue

value: periodontal ligament

value: dental stem cells


title: PDLSC-oD+Lev_Rep1


title: PDLSC-oD+Lev_Rep2


title: PDLSC-oD+Lev_Rep4


title: PDLSC-oD_Rep5

value: no treatment


title: PDLSC-oD_Rep3


title: PDLSC-oD_Rep2


title: PDLSC-oD+Lev_Rep3


title: PDLSC-oD_Rep4


title: cordBlood_TNrev_rep2 [2D-KV]

city: Birmingham

first: Paul

last: Moss

state: West Midlands

address: Vincent Drive

department: Immunology and Immunotherapy

institute: University of Birmingham

description:
2D-KV_S5
Chromatin accessibility of naive CD8 T cells from human cord blood, activated then maintained for 8 days in 25ng/ml IL-7

library_source: genomic

data_processing:
Basecalls performed using CASAVA version 1.8
ATAC-seq reads were aligned to the hg19 human genome assembly using Bowtie version 2 with default parameters and "--very-sensitive-local" flag
Data were filtered upon alignment using default filtering in bowtie2
Peaks were called using MACS version 2.2 with the settings: --keep-dup=auto --nomodel --shift -100 --extsize 200
Average tag counts at each peak were calculated using annotatePeaks program from HOMER version 4.8 and the flag -size 400
Genome_build: hg19
Supplementary_files_format_and_content: The txt file ATAC_raw_tag_counts.txt was produced from running annotatePeaks for all identified peak locations on each sample sequence alignment file. It contains annotations for the peak regions and raw read counts taken from a 400bp region centred on the peak summits for each sample

molecule: genomic DNA

source_name: Cord blood, naïve CD8, Anti-CD3 activated, 25ng/ml IL-7

growth_protocol: TN cells were enriched by immunomagnetic separation. Activation and de-differentiation was carried out in RPMI 1640 supplemented with 10% foetal bovine serum. Cultures were incubated  at 37 C in a humidified incubator with 5% CO2.

extract_protocol:
T cells sorted on Aria Fusion (Becton Dickinson, New Jersey, USA)  were  pelleted and resuspended in a 50-μl reaction cocktail containing 1 μl of 0.5% Digitonin (Promega, Madison, WI, USA), 2.5 μl of Tn5 transposase and 25 μl of TD buffer (Nextera DNA library preparation kit, Illumina, San Diego, CA, USA) and incubated for 30 min at 37°C with gentle shaking. The tagmented DNA was then purified using Minielute PCR Purification kit (Qiagen) and eluted into 11 μl of elution buffer.
Transposed DNA was then amplified using  2.5 μl of indexing primers and 25 μl of Nextera PCR master mix according to the PCR protocol previously described (Buenrostro, 2013, Nat. Methods). PCR clean-up was then performed using AMPure XP beads (Beckman Coulter, Brea, CA, USA), and resuspended in 30 μl of resuspension buffer. The libraries were quantified using Qubit fluorometer (Life Technologies), and the size was detemined using TapeStation (Agilent).

treatment_protocol: Chromatin accessibility analysis was performed on cells from 4 human cord blood samples, i.e. 4 freshly enriched CD8+ TN samples and 4 samples of CD8+ TN cells which had been activated with anti CD3 plus 300 U/ml IL-2, and after 6 days maintained for further 13 days in  25 ng/mL IL-7

value: cord blood

value: Revertant Naive-like CD8 T cell


title: cordBlood_TNrev_rep3 [4-517-Rev]

description:
4-517-Rev_S8
Chromatin accessibility of naive CD8 T cells from human cord blood, activated then maintained for 8 days in 25ng/ml IL-7


title: cordBlood_TEM_rep3 [3-517-EM]

description:
3--517-EM_S10_L002
Chromatin accessibility of naive CD8 T cells from human cord blood, activated then isolated EM phenotype

source_name: Cord blood, naïve CD8, Anti-CD3 activated, EM

value: Effector Memory CD8 T cell (TEM)


title: cordBlood_TEM_rep1 [1C-KV]

description:
1C-KV_S3
Chromatin accessibility of naive CD8 T cells from human cord blood, activated then isolated EM phenotype


title: cordBlood_TEM_rep2 [2C-KV]

description:
2C-KV_S6
Chromatin accessibility of naive CD8 T cells from human cord blood, activated then isolated EM phenotype


title: cordBlood_TNrev_rep4 [8-409-Rev]

description:
8-409-Rev_S2
Chromatin accessibility of naive CD8 T cells from human cord blood, activated then maintained for 8 days in 25ng/ml IL-7


title: cordBlood_TCM_rep3 [2-517-CM]

description:
2-517-CM_S11
Chromatin accessibility of naive CD8 T cells from human cord blood, activated then isolated CM phenotype

source_name: Cord blood, naïve CD8, Anti-CD3 activated, CM

value: Central Memory CD8 T cell (TCM)


title: cordBlood_TCM_rep1 [1B-KV]

description:
1B-KV_S4
Chromatin accessibility of naive CD8 T cells from human cord blood, activated then isolated CM phenotype


title: cordBlood_TCM_rep2 [2B-KV]

description:
2B-KV_S8
Chromatin accessibility of naive CD8 T cells from human cord blood, activated then isolated CM phenotype


title: cordBlood_TN_rep3 [1-517-N]

description:
1-517-N_S12
Chromatin accessibility of naïve CD8 T cells from human cord blood

source_name: Cord blood, naïve CD8

value: naive CD8 T cell


title: cordBlood_TN_rep4 [5-409-N]

description:
5-409-N_S7
Chromatin accessibility of naïve CD8 T cells from human cord blood


title: cordBlood_TN_rep2 [2A-KV]

description:
2A-KV_S7
Chromatin accessibility of naïve CD8 T cells from human cord blood


title: cordBlood_TNrev_rep1 [1D-KV]

description:
1D-KV_S1
Chromatin accessibility of naive CD8 T cells from human cord blood, activated then maintained for 8 days in 25ng/ml IL-7


title: cordBlood_TN_rep1 [1A-KV]

description:
1A-KV_S2
Chromatin accessibility of naïve CD8 T cells from human cord blood


title: hf2UVB

city: Geneva

first: Roman

last: Ulm

address: 30 Quai E. Ansermet

department: Department of Botany and Plant Biology

country: Switzerland

institute: University of Geneva

data_processing:
Illumina HiSeq 2500
Quality control was performed with FastQC v.0.10.2
Reads were mapped to Arabidopsis TAIR-10 genome using TopHat v2.0.13 software
Biological quality control was done with the PicardTools v1.80
The gene features were counted with HTSeq v.0.6.1 (htseq-count).
Normalization and differential expression analysis was performed with the statistical analysis R/Bioconductor package edgeR v.3.4.2 for the genes annotated in TAIR10
Genome_build: TAIR10
Supplementary_files_format_and_content: tab-delimited text files include rawcount values for each Sample
Supplementary_files_format_and_content: tab-delimited text files include normalized expression values (cpm = count per millions) for each Sample

organism: Arabidopsis thaliana

source_name: seedlings

growth_protocol: Arabidopsis seeds were surface sterilized with sodium hypochlorite and sown on half-strength Murashige and Skoog basal salt medium (MS; Duchefa) containing 1% (wt/vol) agar (Applichem) and 1% (wt/vol) sucrose. Seeds were germinated aseptically at 22°C in a standard growth chamber (Percival Scientific) that contains LED lampbanks (CLF floralLED series, CLF Plant Climatics) under constant white light (R:FR = 4.7) of 60 umol m-2 s-1 overall intensity measured using a LI-COR 250A light meter (LI-COR Biosciences. UV-B was supplemented for the indicated times with Philips TL20W/01RS narrowband UV-B tubes (0.06 mW cm−2 s-1; measured with a VLX-3W Ultraviolet Light Meter equipped with a CX-312 sensor, Vilber Lourmat). For low R:FR treatments, PAR remained constant with enrichment in FR provided by supplementary FR LEDs resulting in a R:FR ratio of 0.05 The UV-B range was modulated by the use of 3-mm transmission cut-off filters of the WG series (Schott Glaswerke) with half-maximal transmission at the indicated wavelength (WG304 for UV-B-treated and WG368 for non-UV-B-treated controls).

extract_protocol:
Whole seedlings material of 30 seedlings per sample were collected in 1.5ml eppendorf tubes.Plant materials were ground using silamat and RNA was isolated with Plant RNeasy kit (Qiagen) and treated with DNaseI according to the manufacturer’s instructions.DNase was heat inactivated in the presence of 2 mM EDTA.The libraries were prepared with 400 ng of total RNA as starting material and processed with the TruSeqUD Stranded mRNA (Illumina), and sequencing on an Illumina HiSeq 4000 System using 100 bp single-end reads protocol.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: On day 7, 1/4 of plates remained in white light (60 μmol m−2 s−1), 1/4 was transferred to white light supplemented with narrowband UV-B (0.06 mW cm−2 s-1) under WG304 filters, 1/4 was transferred to low R:FR (0.08) and 1/4 was transferred to a combination of narrowband UV-B and low R:FR (same light conditions described above)

tag: ecotype

tag: organ

value: whole seedlings

value: 7 days

tag: genotype

tag: light treatment

value: 3h with acclimation level UV-B


title: hf3UVB


title: hf1UVB


title: PDLSC-oD_Rep1

tag: cell type


title: 82UV


title: 81UVB


title: 83UVB


title: col1UVB

value: wild type


title: col3UVB


title: col2UVB


title: hf2FRUV

value: 3h low R:FR with acclimation level UV-B


title: hfr1FRUV1


title: hfr13FRUV


title: UV83FRUV


title: 81FRUV


title: 82FRUV


title: col2FRUV


title: col3FRUV


title: hfr13FR

value: 3h low R:FR


title: col1FRUV


title: hf1FR


title: 83FR


title: 82FR


title: hf2FR


title: 81FR


title: col3FR


title: col1FR


title: hf2WL

value: white light


title: hfr13WL


title: col2FR


title: hfr1WL1


title: 83WL


title: 8WL1


title: ColWL1


title: col2WL


title: col3WL


title: X18GMCerebellumCkoNdiF3

city: Chicago

first: Navdeep

last: Chandel

state: IL

address: 303 E Superior St, SQ5

department: Pulmonary and Critical Care

institute: Northwestern University

data_processing:
Raw BCL read files were demultiplexed and FASTQ files were generated using bcl2fastq and trimmed using Trimmomatic (Bolger et al., 2014).
Next, the reads were aligned to the mouse mm10 reference genome using STAR to generate BAM files (Dobin et al., 2013).
HTSeq was used to count reads in the exons of genes (Anders et al., 2015).
Genome_build: mm10
Supplementary_files_format_and_content: htseq.all.counts.txt is a tab delimited text file that contains counts data for all samples

source_name: cerebellum

extract_protocol:
6 mice per group (3 male and 3 female) were euthanized at approximately 7 weeks of age and the cerebellum was rapidly dissected and flash frozen in liquid nitrogen. Whole cerebellum RNA was extracted using a QIAGEN RNeasy Plus Mini Kit. Tissues were homogenized in RLT Plus Buffer + BME with a QIAGEN TissueRuptor II handheld rotor-stator homogenizer. After tissue homogenization, QIAshredder spin columns were used followed by gDNA elimination columns and an on column DNase digestion with Ambion RNase-free Dnase during the RNeasy RNA preparation manufacturer protocol.
RNA was quantified and QC was checked using an Agilent 4200 TapeStation RNA ScreenTape. mRNA libraries were prepared using NEBNext Ultra Kit with polyA selection (New England BioLabs).

value: cerebellum

tag: Sex

value: Female

value: 7 weeks


title: X19GMCerebellumCkoM1

value: cKO

value: Male


title: X20GMCerebellumCkoM2


title: X24GMCerebellumCkoF3


title: X21GMCerebellumCkoM3


title: X22GMCerebellumCkoF1


title: X17GMCerebellumCkoNdiF2


title: X23GMCerebellumCkoF2


title: X16GMCerebellumCkoNdiF1


title: X15GMCerebellumCkoNdiM3


title: X03GMCerebellumCreM3

value: Cre control


title: X01GMCerebellumCreM1


title: X09GMCerebellumNdiM3

value: NDI1 control


title: X08GMCerebellumNdiM2


title: X04GMCerebellumCreF1


title: X06GMCerebellumCreF3


title: snRNA-seq avMLPA_5

city: Boston

first: Sinisa

last: Hrvatin

state: MA

address: 220 Longwood ave, GB405

department: Neurobiology

institute: Harvard Medical School

description:
nuclear RNA, polyA captured
10X genomics single cell RNA-seq

data_processing:
The 10X Genomics package cellranger 3.1.0 was used to map transcripts to the mm10 reference mouse genome. Since single-nucleus RNA-seq captures unspliced pre-mRNA as well as mature mRNA, we create a custom “pre-mRNA” gene annotation file, in which all features are re-coded as exons, allowing us to map unspliced reads to these artificial exons and to assign them to the corresponding genes. Feature barcoding with custom features was used to assign viral mRNA reads to cells and distinguish between the transcript sequence from the initial AAV-DIO-Gq-DREADD-mCherry vector and the transcript sequence produced by the Cre-recombined vector in TRAPed neurons.
To bioinformatically detect and remove predicted doublets, each of the five libraries were independently processed using the scrublet package: scrub = scr.Scrublet(counts_matrix, expected_doublet_rate=0.10); doublet_scores, predicted_doublets = scrub.scrub_doublets(min_counts=2, min_cells=3, min_gene_variability_pctl=85, n_prin_comps=30)
The R software package Seurat 3.1.0, was used to assign cells to clusters. Any genes whose expression was present in fewer than three cells were removed from analysis. Data was normalized with the number of transcripts per cell and the percent transcripts derived from the mitochondrial genes regressed using the SCTransform function with default parameters. Initially 3,000 most variable genes were identified. To minimize the influence of these tissue processing-induced genes on the identification and molecular characterization of avMLPA cells, we removed from the initial list of 3,000 most variable genes any genes that were identified as mitochondrial, ribosomal protein-encoding or were the immediate-early genes Fos, Fosb, Fosl1, Fosl2, Egr1, and Npas4. To further diminish any potential effects of tissue-dissociation-induced expression changes on clustering, we identified and removed from the list of variable genes, any genes whose expression across all cells correlated with any mitochondrial, ribosomal protein-encoding or immediate-early genes listed above, Pearson correlation coefficient greater than 0.2 or smaller than -0.2). The final list contained 2,827 variable genes. Next, principal component analysis (PCA) was carried out using the RunPCA() function. The FindNeighbors() function, using the top 30 principal components (PCs) and the FindClusters(), was used to identify the initial 34 clusters. Clusters classified as neurons (28,103 of the 44,669 cells) were additionally processed to identify neuronal subtypes in the avMLPA. The same Seurat 3.1.0 pipeline was used as described above.
Feature barcoding with custom features identified for each nucleus the number of viral mRNA reads that were derived from the non-recombined AAV-DIO-Gq-DREADD-mCherry vector and the number of viral mRNA reads from the Cre-recombined AAV-DIO-Gq-DREADD-mCherry vector.
Genome_build: mm10

source_name: anteroventral medial and lateral preoptic area of the brain

extract_protocol:
The brains were extracted and sectioned into 300 μm coronal sections. Sections containing the MPA were microdissected to isolate the avMLPA.  The dissected avMLPA was dissected and placed into a Dounce with homogenization buffer (0.25 M sucrose, 25 mM KCl, 5 mM MgCl2, 20 mM Tricine-KOH, pH 7.8, 1 mM DTT, 0.15 mM spermine, 0.5 mM spermidine, protease inhibitors). The sample was homogenized using a tight pestle with 10 strokes. IGEPAL solution (5%, Sigma) was added to a final concentration of 0.32%, and 5 additional strokes were performed. The homogenate was filtered through a 40-μm filter, and OptiPrep (Sigma) was added to a final concentration of 25% iodixanol. The sample was layered onto an iodixanol gradient and centrifuged at 10,000g for 18 minutes as previously described. Nuclei were collected between the 30% and 40% iodixanol layers and diluted to 80,000-100,000 nuclei/mL for encapsulation. All buffers contained 0.15% RNasin Plus RNase Inhibitor (Promega) and 0.04% BSA. Single nuclei were captured and barcoded for whole-transcriptome libraries using the 10X Genomics Chromium v2 platform according to the manufacturer’s recommendations, collecting one library of approximately 10,000 nuclei from each of the 5 animals.
Libraries were processed according to manufacturer's (10X Genomics) protocols. The cDNA was amplified, fragmented and adapters were added for sequencing on a Nextseq 500 benchtop DNA sequencer (Illumina).     For enrichment of virally-derived transcripts, a fraction (1 μL) of the non-fragmented cDNA was PCR amplified. The forward primer (5’-GCATGGACGAGCTGTACA) was designed to anneal to the sequence uniquely present at the 3’ terminus of mCherry. The reverse primer (5’-CTACACGACGCTCTTCCG) was designed to anneal to the R1 sequence, uniquely present at the 5’ terminus, to the 10X barcode and UMI sequence which were introduced during the reverse transcription. The result of the PCR is preferential amplification of the viral-derived transcripts, while simultaneously retaining the cell-barcode sequence necessary to assign each viral transcript to a particular cell/nucleus. Following PCR amplification (18 cycles, Hot Start High-Fidelity Q5 polymerase, NEB # M0494S), the product was purified using 0.6X SPRI select reagent (Thermo Fisher Scientific # NC0406406) and 1ul of the 50ul eluent used in a second PCR reaction. The forward primer for the second PCR   (5’-GTGACTGGAGTTCAGACGTGTGCTCTTCCGATCTgtaaggcgcgccataac) was designed to anneal to the sequence uniquely present between the mCherry and loxP sites of the the AAV-DIO-Gq-DREADD-mCherry vector. In addition, this primer introduced the R2 sequence necessary for later library amplification. The reverse primer (5’-CTACACGACGCTCTTCCG) was the same as in the first PCR reaction. The result of the PCR is again preferential amplification of the viral-derived transcripts, while simultaneously retaining the cell-barcode sequence necessary to assign each viral transcript to a particular cell/nucleus. Following PCR amplification (18 cycles, Hot Start High-Fidelity Q5 polymerase, NEB # M0494S), all the libraries were indexed according to the 10X protocol, pooled, and sequenced on a Nextseq 500 benchtop DNA sequencer (Illumina).
10X snRNA-seq

value: FosTRAP2 (Jax 030323)


title: snRNA-seq avMLPA_2

value: anteroventral medial and lateral preoptic area of the brain


title: X10GMCerebellumNdiF1


title: X05GMCerebellumCreF2


title: X07GMCerebellumNdiM1


title: X11GMCerebellumNdiF2


title: X14GMCerebellumCkoNdiM2


title: X12GMCerebellumNdiF3


title: snRNA-seq avMLPA_4


title: snRNA-seq avMLPA_3


title: X02GMCerebellumCreM2


title: X13GMCerebellumCkoNdiM1


title: snRNA-seq avMLPA_1


title: WT_M1_8h_S3

first: Chih-Hao

last: Lee

state: Massachusetts

address: 665 Huntington Avenue, Bld. 1, room 406

department: Molecular Metabolism

institute: Harvard T.H. Chan School of Public Health

data_processing:
Sequencing was performed using an Illumina NextSeq 500 High Output Kit (75 cycles, 400 million total reads) on an Illumina NextSeq 500 instrument.
Raw data was processed using Qiagen CLC Genomics Workbench (v.10.1.1).
Raw sequencing reads were trimmed by removing adapter sequences, low-quality sequences (Phred quality score of < 20), and sequences with lengths >25 bp.
Quality control for individual samples were examined. Sequencing reads were mapped to the mouse genome assembly (mm10) from the University of California, Santa Cruz with the following parameters:  mismatches = 2, minimum fraction length = 0.9, minimum fraction similarity = 0.9, and maximum hits per read = 5.
Normalization and calculation of expression values were performed using the Differential Gene Expression for RNA-seq Tool in the Qiagen CLC Genomics Workbench v10.
Genome_build: Mouse genome assembly (mm10) from the University of California, Santa Cruz
Supplementary_files_format_and_content: Processed data represent fold-change based on transcripts per kilobase million (TPM) relative to sample 1.

source_name: Bone marrow-derived macrophages

growth_protocol: Differentiated 7 days in 30% L929-conditioned medium

extract_protocol:
Silica-based RNA spin column
RNA libraries were prepared with the TruSeq Stranded mRNA Library Preparation Kit (Illumina) according to the manufacturer’s instructions using 2 μg of RNA per sample.
Samples were quantified with Ribogreen (Life Technologies, CA) and RNA integrity was checked with a Bioanalyzer 2100 (Agilent, CA) prior to library construction.

treatment_protocol: Primed with Interferon gamma overnight without or with subsequent 8h lipopolysaccharide treatment

value: Bone marrow-derived macrophages

tag: primimg

value: Interferon gamma primed

tag: treatment

value: Stimulated with lipolysaccharide

value: Wild-type


title: WT_M1_8h_S2

tag: strain


title: M-BKO_Ifng_only_S3

value: No subsequent stimulation

value: Myeloid Bmal1 KO


title: M-BKO_M1_8h_S1


title: M-BKO_Ifng_only_S1


title: M-BKO_M1_8h_S3


title: M-BKO_Ifng_only_S2


title: M-BKO_M1_8h_S2


title: WT_M1_8h_S1


title: WT_Ifng_only_S3


title: WT_Ifng_only_S2


title: 82WL

value: whole seedlings

value: 7 days


title: E15.5 tdTom+ epicardium/epicardium-derived cells [plate6_H3_S366]

city: Oxford

first: Irina-Elena

last: Lupu

address: Sherrigton Building

department: DPAG

institute: University of Oxford

data_processing:
Illumina v2.19.1.403 bcl2fastq
reads trimmed and aligned to Mm10/GRCm38 using STAR (v2.3.3a) with Gencode (v.M16) annotations
cells with less than 200 reads and more than 5% mitochondrial content were discarded
genes not expressed in at least 3 cells were discarded
alternative cell cycle regression in Seurat was used to remove cell cycle differences and 12 PCAs and res 1 was used in FindClusters
Genome_build: Mm10
Supplementary_files_format_and_content: scaled data exported from Seurat object in R and associated metadata

extract_protocol:
FACS sorted tdTom+ heart cells dissociated using the Milteny neonatal heart dissociation kit
Illumina protocols (Nextera library prep kit); SMART-Seq2

tag: developmental stage

tag: genotype/variation

value: wild type

value: heart


title: E15.5 tdTom+ epicardium/epicardium-derived cells [plate6_F6_S276]


title: E15.5 tdTom+ epicardium/epicardium-derived cells [plate6_H5_S370]


title: E15.5 tdTom+ epicardium/epicardium-derived cells [plate6_G1_S314]


title: E15.5 tdTom+ epicardium/epicardium-derived cells [plate6_H4_S368]


title: E15.5 tdTom+ epicardium/epicardium-derived cells [plate6_G2_S316]


title: E15.5 tdTom+ epicardium/epicardium-derived cells [plate6_G6_S324]


title: E15.5 tdTom+ epicardium/epicardium-derived cells [plate6_G4_S320]


title: E15.5 tdTom+ epicardium/epicardium-derived cells [plate6_G3_S318]


title: E15.5 tdTom+ epicardium/epicardium-derived cells [plate6_F3_S270]


title: E15.5 tdTom+ epicardium/epicardium-derived cells [plate6_H2_S364]


title: E15.5 tdTom+ epicardium/epicardium-derived cells [plate6_F4_S272]


title: E15.5 tdTom+ epicardium/epicardium-derived cells [plate6_E5_S226]


title: E15.5 tdTom+ epicardium/epicardium-derived cells [plate6_G5_S322]


title: E15.5 tdTom+ epicardium/epicardium-derived cells [plate6_F1_S266]


title: E15.5 tdTom+ epicardium/epicardium-derived cells [plate6_F5_S274]


title: E15.5 tdTom+ epicardium/epicardium-derived cells [plate6_D6_S180]


title: E15.5 tdTom+ epicardium/epicardium-derived cells [plate6_E4_S224]


title: E15.5 tdTom+ epicardium/epicardium-derived cells [plate6_E2_S220]


title: E15.5 tdTom+ epicardium/epicardium-derived cells [plate6_E3_S222]


title: E15.5 tdTom+ epicardium/epicardium-derived cells [plate6_D4_S176]


title: E15.5 tdTom+ epicardium/epicardium-derived cells [plate6_E6_S228]


title: E15.5 tdTom+ epicardium/epicardium-derived cells [plate6_D5_S178]


title: E15.5 tdTom+ epicardium/epicardium-derived cells [plate6_E1_S218]


title: E15.5 tdTom+ epicardium/epicardium-derived cells [plate6_F2_S268]


title: E15.5 tdTom+ epicardium/epicardium-derived cells [plate6_C4_S128]


title: E15.5 tdTom+ epicardium/epicardium-derived cells [plate6_C3_S126]


title: E15.5 tdTom+ epicardium/epicardium-derived cells [plate6_C5_S130]


title: E15.5 tdTom+ epicardium/epicardium-derived cells [plate6_C2_S124]


title: WT_Ifng_only_S1


title: E15.5 tdTom+ epicardium/epicardium-derived cells [plate6_D1_S170]


title: E15.5 tdTom+ epicardium/epicardium-derived cells [plate6_B5_S82]


title: E15.5 tdTom+ epicardium/epicardium-derived cells [plate6_A1_S26]


title: E15.5 tdTom+ epicardium/epicardium-derived cells [plate6_A6_S36]


title: E15.5 tdTom+ epicardium/epicardium-derived cells [plate6_B2_S76]


title: E15.5 tdTom+ epicardium/epicardium-derived cells [plate6_B6_S84]


title: E15.5 tdTom+ epicardium/epicardium-derived cells [plate5_H4_S367]


title: E15.5 tdTom+ epicardium/epicardium-derived cells [plate6_A5_S34]


title: E15.5 tdTom+ epicardium/epicardium-derived cells [plate6_B3_S78]


title: E15.5 tdTom+ epicardium/epicardium-derived cells [plate6_B4_S80]


title: E15.5 tdTom+ epicardium/epicardium-derived cells [plate5_H3_S365]


title: E15.5 tdTom+ epicardium/epicardium-derived cells [plate6_C6_S132]


title: E15.5 tdTom+ epicardium/epicardium-derived cells [plate5_H5_S369]


title: E15.5 tdTom+ epicardium/epicardium-derived cells [plate6_C1_S122]


title: E15.5 tdTom+ epicardium/epicardium-derived cells [plate6_D2_S172]


title: E15.5 tdTom+ epicardium/epicardium-derived cells [plate5_G4_S319]


title: E15.5 tdTom+ epicardium/epicardium-derived cells [plate6_B1_S74]


title: E15.5 tdTom+ epicardium/epicardium-derived cells [plate6_D3_S174]


title: E15.5 tdTom+ epicardium/epicardium-derived cells [plate6_A3_S30]


title: E15.5 tdTom+ epicardium/epicardium-derived cells [plate6_A4_S32]


title: E15.5 tdTom+ epicardium/epicardium-derived cells [plate5_G5_S321]


title: E15.5 tdTom+ epicardium/epicardium-derived cells [plate6_A2_S28]


title: E15.5 tdTom+ epicardium/epicardium-derived cells [plate5_H2_S363]


title: E15.5 tdTom+ epicardium/epicardium-derived cells [plate5_H1_S361]


title: E15.5 tdTom+ epicardium/epicardium-derived cells [plate5_G3_S317]


title: E15.5 tdTom+ epicardium/epicardium-derived cells [plate5_G1_S313]


title: E15.5 tdTom+ epicardium/epicardium-derived cells [plate5_F4_S271]


title: E15.5 tdTom+ epicardium/epicardium-derived cells [plate5_F5_S273]


title: E15.5 tdTom+ epicardium/epicardium-derived cells [plate5_F2_S267]


title: E15.5 tdTom+ epicardium/epicardium-derived cells [plate5_F3_S269]


title: E15.5 tdTom+ epicardium/epicardium-derived cells [plate5_E1_S217]


title: E15.5 tdTom+ epicardium/epicardium-derived cells [plate5_D6_S179]


title: E15.5 tdTom+ epicardium/epicardium-derived cells [plate5_F1_S265]


title: E15.5 tdTom+ epicardium/epicardium-derived cells [plate5_D3_S173]


title: E15.5 tdTom+ epicardium/epicardium-derived cells [plate5_C6_S131]


title: E15.5 tdTom+ epicardium/epicardium-derived cells [plate5_C4_S127]


title: E15.5 tdTom+ epicardium/epicardium-derived cells [plate5_D1_S169]


title: E15.5 tdTom+ epicardium/epicardium-derived cells [plate5_C3_S125]


title: E15.5 tdTom+ epicardium/epicardium-derived cells [plate5_C2_S123]


title: E15.5 tdTom+ epicardium/epicardium-derived cells [plate5_E5_S225]


title: E15.5 tdTom+ epicardium/epicardium-derived cells [plate5_E3_S221]


title: E15.5 tdTom+ epicardium/epicardium-derived cells [plate5_B4_S79]


title: E15.5 tdTom+ epicardium/epicardium-derived cells [plate5_C1_S121]


title: E15.5 tdTom+ epicardium/epicardium-derived cells [plate5_G2_S315]


title: E15.5 tdTom+ epicardium/epicardium-derived cells [plate5_B5_S81]


title: E15.5 tdTom+ epicardium/epicardium-derived cells [plate5_B3_S77]


title: E15.5 tdTom+ epicardium/epicardium-derived cells [plate5_B2_S75]


title: E15.5 tdTom+ epicardium/epicardium-derived cells [plate5_F6_S275]


title: E15.5 tdTom+ epicardium/epicardium-derived cells [plate5_B1_S73]


title: E15.5 tdTom+ epicardium/epicardium-derived cells [plate5_A6_S35]


title: E15.5 tdTom+ epicardium/epicardium-derived cells [plate5_A4_S31]


title: E15.5 tdTom+ epicardium/epicardium-derived cells [plate5_A5_S33]


title: E15.5 tdTom+ epicardium/epicardium-derived cells [plate5_E6_S227]


title: E15.5 tdTom+ epicardium/epicardium-derived cells [plate5_C5_S129]


title: E15.5 tdTom+ epicardium/epicardium-derived cells [plate5_A2_S27]


title: E15.5 tdTom+ epicardium/epicardium-derived cells [plate5_E2_S219]


title: E15.5 tdTom+ epicardium/epicardium-derived cells [plate5_D5_S177]


title: E15.5 tdTom+ epicardium/epicardium-derived cells [plate5_D4_S175]


title: E15.5 tdTom+ epicardium/epicardium-derived cells [plate5_D2_S171]


title: E15.5 tdTom+ epicardium/epicardium-derived cells [plate5_A1_S25]


title: E15.5 tdTom+ epicardium/epicardium-derived cells [plate3_H5_S346]


title: E15.5 tdTom+ epicardium/epicardium-derived cells [plate3_H4_S344]


title: E15.5 tdTom+ epicardium/epicardium-derived cells [plate3_H3_S366]


title: E15.5 tdTom+ epicardium/epicardium-derived cells [plate3_H3_S342]


title: E15.5 tdTom+ epicardium/epicardium-derived cells [plate3_G3_S294]


title: E15.5 tdTom+ epicardium/epicardium-derived cells [plate3_G2_S316]


title: E15.5 tdTom+ epicardium/epicardium-derived cells [plate3_F5_S250]


title: E15.5 tdTom+ epicardium/epicardium-derived cells [plate3_F4_S272]


title: E15.5 tdTom+ epicardium/epicardium-derived cells [plate3_H4_S368]


title: E15.5 tdTom+ epicardium/epicardium-derived cells [plate3_H2_S364]


title: E15.5 tdTom+ epicardium/epicardium-derived cells [plate3_G6_S300]


title: E15.5 tdTom+ epicardium/epicardium-derived cells [plate3_F6_S276]


title: E15.5 tdTom+ epicardium/epicardium-derived cells [plate3_G5_S322]


title: E15.5 tdTom+ epicardium/epicardium-derived cells [plate3_G1_S314]


title: E15.5 tdTom+ epicardium/epicardium-derived cells [plate3_F5_S274]


title: E15.5 tdTom+ epicardium/epicardium-derived cells [plate3_G3_S318]


title: E15.5 tdTom+ epicardium/epicardium-derived cells [plate3_F4_S248]


title: E15.5 tdTom+ epicardium/epicardium-derived cells [plate5_A3_S29]


title: E15.5 tdTom+ epicardium/epicardium-derived cells [plate3_F3_S246]


title: E15.5 tdTom+ epicardium/epicardium-derived cells [plate3_F6_S252]


title: E15.5 tdTom+ epicardium/epicardium-derived cells [plate3_H5_S370]


title: E15.5 tdTom+ epicardium/epicardium-derived cells [plate3_G4_S320]


title: E15.5 tdTom+ epicardium/epicardium-derived cells [plate3_H2_S340]


title: E15.5 tdTom+ epicardium/epicardium-derived cells [plate3_G4_S296]


title: E15.5 tdTom+ epicardium/epicardium-derived cells [plate3_G5_S298]


title: E15.5 tdTom+ epicardium/epicardium-derived cells [plate3_G1_S290]


title: E15.5 tdTom+ epicardium/epicardium-derived cells [plate3_H1_S362]


title: E15.5 tdTom+ epicardium/epicardium-derived cells [plate3_G6_S324]


title: E15.5 tdTom+ epicardium/epicardium-derived cells [plate3_F3_S270]


title: E15.5 tdTom+ epicardium/epicardium-derived cells [plate3_F1_S242]


title: E15.5 tdTom+ epicardium/epicardium-derived cells [plate3_F2_S268]


title: E15.5 tdTom+ epicardium/epicardium-derived cells [plate3_G2_S292]


title: E15.5 tdTom+ epicardium/epicardium-derived cells [plate3_E6_S228]


title: E15.5 tdTom+ epicardium/epicardium-derived cells [plate3_E6_S204]


title: E15.5 tdTom+ epicardium/epicardium-derived cells [plate3_E5_S226]


title: E15.5 tdTom+ epicardium/epicardium-derived cells [plate3_E3_S198]


title: E15.5 tdTom+ epicardium/epicardium-derived cells [plate3_E4_S224]


title: E15.5 tdTom+ epicardium/epicardium-derived cells [plate3_E1_S194]


title: E15.5 tdTom+ epicardium/epicardium-derived cells [plate3_E2_S196]


title: E15.5 tdTom+ epicardium/epicardium-derived cells [plate3_E2_S220]


title: E15.5 tdTom+ epicardium/epicardium-derived cells [plate3_E4_S200]


title: E15.5 tdTom+ epicardium/epicardium-derived cells [plate3_E1_S218]


title: E15.5 tdTom+ epicardium/epicardium-derived cells [plate3_D6_S180]


title: E15.5 tdTom+ epicardium/epicardium-derived cells [plate3_D6_S156]


title: E15.5 tdTom+ epicardium/epicardium-derived cells [plate3_E5_S202]


title: E15.5 tdTom+ epicardium/epicardium-derived cells [plate3_D4_S176]


title: E15.5 tdTom+ epicardium/epicardium-derived cells [plate3_D2_S172]


title: E15.5 tdTom+ epicardium/epicardium-derived cells [plate3_E3_S222]


title: E15.5 tdTom+ epicardium/epicardium-derived cells [plate3_D5_S154]


title: E15.5 tdTom+ epicardium/epicardium-derived cells [plate3_D2_S148]


title: E15.5 tdTom+ epicardium/epicardium-derived cells [plate3_D3_S150]


title: E15.5 tdTom+ epicardium/epicardium-derived cells [plate3_C6_S132]


title: E15.5 tdTom+ epicardium/epicardium-derived cells [plate3_D1_S146]


title: E15.5 tdTom+ epicardium/epicardium-derived cells [plate3_F2_S244]


title: E15.5 tdTom+ epicardium/epicardium-derived cells [plate3_D1_S170]


title: E15.5 tdTom+ epicardium/epicardium-derived cells [plate3_D3_S174]


title: E15.5 tdTom+ epicardium/epicardium-derived cells [plate3_F1_S266]


title: E15.5 tdTom+ epicardium/epicardium-derived cells [plate3_C5_S106]


title: E15.5 tdTom+ epicardium/epicardium-derived cells [plate3_D4_S152]


title: E15.5 tdTom+ epicardium/epicardium-derived cells [plate3_C4_S128]


title: E15.5 tdTom+ epicardium/epicardium-derived cells [plate3_C3_S126]


title: E15.5 tdTom+ epicardium/epicardium-derived cells [plate3_D5_S178]


title: E15.5 tdTom+ epicardium/epicardium-derived cells [plate3_C4_S104]


title: E15.5 tdTom+ epicardium/epicardium-derived cells [plate3_C2_S100]


title: E15.5 tdTom+ epicardium/epicardium-derived cells [plate3_B6_S84]


title: E15.5 tdTom+ epicardium/epicardium-derived cells [plate3_C1_S122]


title: E15.5 tdTom+ epicardium/epicardium-derived cells [plate3_C3_S102]


title: E15.5 tdTom+ epicardium/epicardium-derived cells [plate3_C1_S98]


title: E15.5 tdTom+ epicardium/epicardium-derived cells [plate3_B6_S60]


title: E15.5 tdTom+ epicardium/epicardium-derived cells [plate3_B5_S82]


title: E15.5 tdTom+ epicardium/epicardium-derived cells [plate3_B4_S56]


title: E15.5 tdTom+ epicardium/epicardium-derived cells [plate3_B5_S58]


title: E15.5 tdTom+ epicardium/epicardium-derived cells [plate3_B4_S80]


title: E15.5 tdTom+ epicardium/epicardium-derived cells [plate3_A6_S36]


title: E15.5 tdTom+ epicardium/epicardium-derived cells [plate3_B2_S76]


title: E15.5 tdTom+ epicardium/epicardium-derived cells [plate3_B2_S52]


title: E15.5 tdTom+ epicardium/epicardium-derived cells [plate3_C5_S130]


title: E15.5 tdTom+ epicardium/epicardium-derived cells [plate3_B3_S78]


title: E15.5 tdTom+ epicardium/epicardium-derived cells [plate3_B3_S54]


title: E15.5 tdTom+ epicardium/epicardium-derived cells [plate3_C6_S108]


title: Preimplantation Morula embryo from L13a-/+ cross-6

city: Cleveland

first: Mark

last: Cameron

state: OH

address: 10900 Euclid Ave

department: Population and Quantitative Health Sciences

institute: Case Western Reserve University

description:
normalizedCounts.csv
rawCounts.csv

data_processing:
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence using skewer v0.2.2, then mapped to GRCm38 whole genome using Hisat2 v2.0.5
Read summarization was performed by the program featureCounts v1.5.0-p2 as part of the SubRead package using the NCBI Mus musculus Annotation release 105.
Quantile Normalized Counts were generated through the limma Library v3.36.5 in R
Genome_build: GRCm38
Supplementary_files_format_and_content: rawCounts.csv: counts as generated by featureCounts, rows are gene features, columns are samples
Supplementary_files_format_and_content: normalizedCounts.csv: Quantile normalize raw counts using the limma voom method

source_name: Embryo from L13a-/+ cross

growth_protocol: in vivo

extract_protocol:
Preimplanted embryos at the morula stage were collected by flashing the oviduct/uterus of pregnant L13a(+/-) mice at 3 d.p.c Each embryos were washed in PBS and transferred to 10ml of Cells-to-CDNA II Cell lysis buffer (Cat#AM8723 invitrogen) and boiled at 75 degree Centrigrade for 10 minutes, lysates were centrifuged briefly and transferred immediately on ice. RNA purification was performed using PicoPure RNA isolation it (Cat# KIT0214) following users manual. These samples were submitted for library construction and next generation sequencing.
Total RNA was normalized prior to oligo-dT capture and cDNA synthesis with Takara’s SMART-Seq v4. Libraries were generated using Illumina’s Nextera XT DNA Library Prep  kit.

treatment_protocol: no treatment

tag: background mouse strain

value: Preimplantation stage embryo from oviduct/uterus at 3 d.p.c


title: E15.5 tdTom+ epicardium/epicardium-derived cells [plate3_B1_S50]


title: E15.5 tdTom+ epicardium/epicardium-derived cells [plate3_B1_S74]


title: E15.5 tdTom+ epicardium/epicardium-derived cells [plate3_A6_S12]


title: Preimplantation Morula embryo from L13a-/+ cross-7

description:
normalizedCounts.csv
rawCounts.csv


title: E15.5 tdTom+ epicardium/epicardium-derived cells [plate3_A5_S34]


title: E15.5 tdTom+ epicardium/epicardium-derived cells [plate3_C2_S124]


title: Preimplantation Morula embryo from L13a-/+ cross-5

description:
normalizedCounts.csv
rawCounts.csv


title: E15.5 tdTom+ epicardium/epicardium-derived cells [plate3_A4_S32]


title: E15.5 tdTom+ epicardium/epicardium-derived cells [plate3_A5_S10]


title: E15.5 tdTom+ epicardium/epicardium-derived cells [plate3_A4_S8]


title: E15.5 tdTom+ epicardium/epicardium-derived cells [plate3_A3_S6]


title: Preimplantation Morula embryo from L13a-/+ cross-2

description:
normalizedCounts.csv
rawCounts.csv


title: Preimplantation Morula embryo from L13a-/+ cross-3

description:
normalizedCounts.csv
rawCounts.csv


title: Preimplantation Morula embryo from L13a-/+ cross-4

description:
normalizedCounts.csv
rawCounts.csv


title: Preimplantation Morula embryo from L13a-/+ cross-1

description:
normalizedCounts.csv
rawCounts.csv


title: E15.5 tdTom+ epicardium/epicardium-derived cells [plate3_A3_S30]


title: E15.5 tdTom+ epicardium/epicardium-derived cells [plate3_A2_S28]


title: E15.5 tdTom+ epicardium/epicardium-derived cells [plate3_A2_S4]


title: E15.5 tdTom+ epicardium/epicardium-derived cells [plate3_A1_S26]


title: E15.5 tdTom+ epicardium/epicardium-derived cells [plate2_H5_S369]


title: E15.5 tdTom+ epicardium/epicardium-derived cells [plate3_A1_S2]


title: M7_T1

city: Guangzhou

first: Dongqiang

last: Zeng

state: Guangdong

address: NO.1838 North Guangzhou Avenue

department: Medical oncology

country: China

institute: Southern Medical University

description:
primary colorectal cancer
M1 to M12 are applied to identity mice that the samples are originated from

data_processing:
FASTQ files were mapped by Hisat2
Hisat BAMs were quantified using HTSeq v0.6.0
Genome_build: mm10
Supplementary_files_format_and_content: raw counts

source_name: primary colon tumor

extract_protocol:
Total RNA was extracted from tissue specimens using Trizol and digested with DNase I. Then mRNA was purified from total RNA using oligo(dT)-attached magnetic beads and then fragmented.
Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s protocols.

tag: group

value: case (primary colon tumor)

tag: mouse id


title: M12_T1


title: M8_T1


title: M10_T1


title: E15.5 tdTom+ epicardium/epicardium-derived cells [plate2_H4_S367]


title: M6_T1


title: E15.5 tdTom+ epicardium/epicardium-derived cells [plate2_H3_S365]


title: M5_T1


title: E15.5 tdTom+ epicardium/epicardium-derived cells [plate2_H2_S363]


title: M4_T1


title: E15.5 tdTom+ epicardium/epicardium-derived cells [plate2_H1_S361]


title: M2_T1


title: E15.5 tdTom+ epicardium/epicardium-derived cells [plate2_G4_S319]


title: M12_H1

description:
pre-metastasis liver of colorectal cancer
M1 to M12 are applied to identity mice that the samples are originated from

source_name: pre-metastasis liver

value: case (pre-metastasis)


title: M1_T1


title: E15.5 tdTom+ epicardium/epicardium-derived cells [plate2_G3_S317]


title: M10_H1


title: E15.5 tdTom+ epicardium/epicardium-derived cells [plate2_G6_S323]


title: E15.5 tdTom+ epicardium/epicardium-derived cells [plate2_G5_S321]


title: M8_H1


title: E15.5 tdTom+ epicardium/epicardium-derived cells [plate2_G1_S313]


title: E15.5 tdTom+ epicardium/epicardium-derived cells [plate2_F6_S275]


title: M7_H1


title: E15.5 tdTom+ epicardium/epicardium-derived cells [plate2_G2_S315]


title: M4_H1


title: E15.5 tdTom+ epicardium/epicardium-derived cells [plate2_F5_S273]


title: E15.5 tdTom+ epicardium/epicardium-derived cells [plate2_F4_S271]


title: M2_H1


title: C7_H1

description: normal liver from sham operated mice with no tumors

source_name: normal liver

value: control (sham operated mice with no tumors)


title: E15.5 tdTom+ epicardium/epicardium-derived cells [plate2_F2_S267]


title: C6_H1


title: E15.5 tdTom+ epicardium/epicardium-derived cells [plate2_F1_S265]


title: E15.5 tdTom+ epicardium/epicardium-derived cells [plate2_E6_S227]


title: E15.5 tdTom+ epicardium/epicardium-derived cells [plate2_F3_S269]


title: M1_H1


title: C5_H1


title: E15.5 tdTom+ epicardium/epicardium-derived cells [plate2_E5_S225]


title: C1_H1


title: E15.5 tdTom+ epicardium/epicardium-derived cells [plate2_E4_S223]


title: C4_H1


title: E15.5 tdTom+ epicardium/epicardium-derived cells [plate2_E3_S221]


title: E15.5 tdTom+ epicardium/epicardium-derived cells [plate2_E2_S219]


title: NSDAD_LPS_3 [invivo]

city: Philadelphia

first: Hoang

last: Nguyen

state: PA

address: 3400 Civic Center Boulevard

institute: University of Pennsylvania Perelman School of Medicine

description:
invivo_counts.txt
WT C57Bl6, MHD3KO, NS-DAD mice and their control littermates of 8-week-old were intraperitoneally injected with either phosphate-buffered saline (PBS, Sigma) or 10 mg/kg of purified LPS (Sigma E. Coli O111:B4) at 4PM. Without thioglycolate stimulation, peritoneal cells were harvested 6h after LPS or PBS injection at 10PM and passed through pre-separation filters (Miltenyi Biotec, 130-041-407) to obtain a single-cell suspension. Peritoneal macrophages were then isolated by MACS (Magnetic-Activated Cell Sorting) as previously described40, following the manufacturer instructions (Miltenyi Biotec, 130-110-434) and using MiniMACS columns (Miltenyi Biotec, 130-042-201). RNA were isolated from purified cells using TRIzol (Invitrogen) with the RNeasy micro kit (Qiagen)

data_processing:
#genome alignment single read: STAR --genomeDir ~/STAR_mm10_GENOME_DIR  --runThreadN 20 --readFilesIn $i --outFileNamePrefix ${i/.fastq.gz/}_ --outFilterMultimapNmax 1 --outSAMtype BAM SortedByCoordinate --readFilesCommand zcat --outSAMstrandField intronMotif
#genome alignment paired-end read: STAR --outSAMtype BAM SortedByCoordinate --readFilesCommand zcat --runThreadN 20 --sjdbGTFfile ~/mm10/mm10_genes.gtf  --genomeDir ~/STAR_mm10_GENOME_DIR_150 --readFilesIn $f1 $f2 --outFileNamePrefix $out --outSAMstrandField intronMotif
#counting reads: featureCounts -t exon -g gene_id -a ~/mm10/mm10_genes.gtf -T 20
#DGE with edgeR
Genome_build: mm10
Supplementary_files_format_and_content: featureCounts read counts for all samples

source_name: peritoneal macrophages

growth_protocol: Control and MHD3KO mice were euthanized, and bone marrow were extracted for hindlimb femurs. Bone marrow cells were cultured for 7 days in DMEM supplemented with 10% FBS and 30% L929 media for 7 days on petri dishes to allow macrophage differentiation.

extract_protocol:
After treatment, cells were immediately lysed in trizol and RNA purified with RNeasy RNA isolation kit according to the manufacturers instructions.  Illumina Truseq Stranded RNA Total RNA library prep kit was used with 1ug RNA of total RNA for construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: After 7 days of differeniation, BMDM were replated, rested overnight before treated with BSA control, LPS(5ng/ml for 4 hours), IL4 (100ng/ml for 24hours). For rescue macrophages, retrovirus expressing Y298F or WT HDAC3 were added to BMDM 4 days post harvest from femurs. For siRNA experiments, siRNA were addded 24 hours after replating of the macrophages on the 7th day post harvest.

tag: age

value: 8 weeks

value: NSDAD

tag: agent

value: LPS


title: M6_H1


title: E15.5 tdTom+ epicardium/epicardium-derived cells [plate2_D6_S179]

tag: tissue


title: NSDAD_LPS_1 [invivo]


title: NSDAD_PBS_4 [invivo]

value: PBS


title: E15.5 tdTom+ epicardium/epicardium-derived cells [plate2_E1_S217]


title: NSDAD_LPS_2 [invivo]


title: NSDAD_PBS_2 [invivo]


title: NSDAD_PBS_1 [invivo]


title: E15.5 tdTom+ epicardium/epicardium-derived cells [plate2_D4_S175]


title: E15.5 tdTom+ epicardium/epicardium-derived cells [plate2_D5_S177]


title: E15.5 tdTom+ epicardium/epicardium-derived cells [plate2_D3_S173]


title: M5_H1


title: NSDAD_PBS_3 [invivo]


title: E15.5 tdTom+ epicardium/epicardium-derived cells [plate2_D2_S171]


title: E15.5 tdTom+ epicardium/epicardium-derived cells [plate2_C6_S131]


title: E15.5 tdTom+ epicardium/epicardium-derived cells [plate2_D1_S169]


title: E15.5 tdTom+ epicardium/epicardium-derived cells [plate2_C5_S129]


title: E15.5 tdTom+ epicardium/epicardium-derived cells [plate2_C3_S125]


title: E15.5 tdTom+ epicardium/epicardium-derived cells [plate2_C4_S127]


title: E15.5 tdTom+ epicardium/epicardium-derived cells [plate2_C2_S123]


title: E15.5 tdTom+ epicardium/epicardium-derived cells [plate2_B6_S83]


title: E15.5 tdTom+ epicardium/epicardium-derived cells [plate2_B5_S81]


title: E15.5 tdTom+ epicardium/epicardium-derived cells [plate2_C1_S121]


title: E15.5 tdTom+ epicardium/epicardium-derived cells [plate2_B4_S79]


title: E15.5 tdTom+ epicardium/epicardium-derived cells [plate2_B3_S77]


title: E15.5 tdTom+ epicardium/epicardium-derived cells [plate2_B2_S75]


title: E15.5 tdTom+ epicardium/epicardium-derived cells [plate2_B1_S73]


title: E15.5 tdTom+ epicardium/epicardium-derived cells [plate2_A6_S35]


title: E15.5 tdTom+ epicardium/epicardium-derived cells [plate2_A4_S31]


title: E15.5 tdTom+ epicardium/epicardium-derived cells [plate2_A1_S25]


title: E15.5 tdTom+ epicardium/epicardium-derived cells [plate2_A5_S33]


title: E15.5 tdTom+ epicardium/epicardium-derived cells [plate2_A3_S29]


title: E15.5 tdTom+ epicardium/epicardium-derived cells [plate2_A2_S27]


title: E15.5 tdTom+ epicardium/epicardium-derived cells [plate1_H5_S345]


title: E15.5 tdTom+ epicardium/epicardium-derived cells [plate1_H4_S343]


title: E15.5 tdTom+ epicardium/epicardium-derived cells [plate1_H2_S339]


title: E15.5 tdTom+ epicardium/epicardium-derived cells [plate1_H3_S341]


title: E15.5 tdTom+ epicardium/epicardium-derived cells [plate1_H1_S337]


title: E15.5 tdTom+ epicardium/epicardium-derived cells [plate1_G4_S295]


title: E15.5 tdTom+ epicardium/epicardium-derived cells [plate1_G5_S297]


title: E15.5 tdTom+ epicardium/epicardium-derived cells [plate1_G3_S293]


title: E15.5 tdTom+ epicardium/epicardium-derived cells [plate1_G6_S299]


title: E15.5 tdTom+ epicardium/epicardium-derived cells [plate1_G2_S291]


title: E15.5 tdTom+ epicardium/epicardium-derived cells [plate1_F6_S251]


title: E15.5 tdTom+ epicardium/epicardium-derived cells [plate1_G1_S289]


title: E15.5 tdTom+ epicardium/epicardium-derived cells [plate1_F4_S247]


title: E15.5 tdTom+ epicardium/epicardium-derived cells [plate1_F1_S241]


title: E15.5 tdTom+ epicardium/epicardium-derived cells [plate1_F5_S249]


title: E15.5 tdTom+ epicardium/epicardium-derived cells [plate1_F2_S243]


title: E15.5 tdTom+ epicardium/epicardium-derived cells [plate1_E5_S201]


title: E15.5 tdTom+ epicardium/epicardium-derived cells [plate1_F3_S245]


title: E15.5 tdTom+ epicardium/epicardium-derived cells [plate1_E4_S199]


title: E15.5 tdTom+ epicardium/epicardium-derived cells [plate1_E3_S197]


title: E15.5 tdTom+ epicardium/epicardium-derived cells [plate1_E6_S203]


title: E15.5 tdTom+ epicardium/epicardium-derived cells [plate1_E1_S193]


title: E15.5 tdTom+ epicardium/epicardium-derived cells [plate1_E2_S195]


title: E15.5 tdTom+ epicardium/epicardium-derived cells [plate1_D5_S153]


title: E15.5 tdTom+ epicardium/epicardium-derived cells [plate1_D6_S155]


title: E15.5 tdTom+ epicardium/epicardium-derived cells [plate1_D1_S145]


title: E15.5 tdTom+ epicardium/epicardium-derived cells [plate1_D2_S147]


title: E15.5 tdTom+ epicardium/epicardium-derived cells [plate1_D4_S151]


title: E15.5 tdTom+ epicardium/epicardium-derived cells [plate1_D3_S149]


title: E15.5 tdTom+ epicardium/epicardium-derived cells [plate1_C5_S105]


title: E15.5 tdTom+ epicardium/epicardium-derived cells [plate1_C6_S107]


title: E15.5 tdTom+ epicardium/epicardium-derived cells [plate1_C3_S101]


title: E15.5 tdTom+ epicardium/epicardium-derived cells [plate1_C2_S99]


title: E15.5 tdTom+ epicardium/epicardium-derived cells [plate1_C4_S103]


title: E15.5 tdTom+ epicardium/epicardium-derived cells [plate1_C1_S97]


title: E15.5 tdTom+ epicardium/epicardium-derived cells [plate1_B6_S59]


title: E15.5 tdTom+ epicardium/epicardium-derived cells [plate1_B4_S55]


title: E15.5 tdTom+ epicardium/epicardium-derived cells [plate1_B3_S53]


title: E15.5 tdTom+ epicardium/epicardium-derived cells [plate1_B2_S51]


title: E15.5 tdTom+ epicardium/epicardium-derived cells [plate1_A5_S9]


title: E15.5 tdTom+ epicardium/epicardium-derived cells [plate1_B1_S49]


title: E15.5 tdTom+ epicardium/epicardium-derived cells [plate1_A6_S11]


title: E15.5 tdTom+ epicardium/epicardium-derived cells [plate1_A3_S5]


title: E15.5 tdTom+ epicardium/epicardium-derived cells [plate1_A4_S7]


title: E15.5 tdTom+ epicardium/epicardium-derived cells [plate1_A2_S3]


title: E15.5 tdTom+ epicardium/epicardium-derived cells [plate1_A1_S1]


title: Mutant QKO scRNAseq

city: Houston

first: Kamryn

middle: Nicole

last: Gerner-Mauro

state: Texas

address: 6565 MD Anderson Blvd

department: Pulmonary Medicine

institute: MD Anderson Cancer Center

description: scRNA-Seq

data_processing:
Chromium single-cell RNA-seq output was processed with Cell Ranger using “cellranger count” and “cellranger aggr”.
Further analysis was carried out using Loupe Cell Browser (10x Genomics) or  R package Seurat/Monocle
Genome_build: mm10
Supplementary_files_format_and_content: tsv and mtx files can be opened with Seurat (R package) and analyzed with Seurat or Monocle. Cloupe file can be opened with Loupe cell browser to visualize the data.

source_name: Lung

extract_protocol:
FACS-purified lung ECs were processed through the Chromium Single Cell Gene Expression Solution Platform (10X Genomics) using the Chromium Single Cell 3' Library and Gel Bead Kit in accordance with the manufacturer’s user guide (v2, rev D).
The libraries were sequenced on an Illumina NextSeq500 using a 26X124 sequencing run format with 8 bp index (Read1).

value: Lung

value: epithelial cells

value: Embryonic day 15

value: LEF/TCF transcription factors knockouts


title: Control scRNAseq

description: scRNA-Seq

value: control


title: NIH3T3_T24

city: Pittsburgh

first: Jacob

last: Stewart-Ornstein

address: UPMC Hillman Cancer Center, 5117 Centre Avenue

department: computational and systems biology

institute: University of Pittsburgh, School of Medicine

description:
Gamma IR treated Mouse cell line
geo_mouse.txt

data_processing:
RNA-Seq: reads were mapped and analyzed by TopHat/Cufflinks RNA-seq analysis using Tophat version 2.1.0 and cufflinks version 2.1.1. Alignment was done against mm10 genome and mm10 RefSeq.gtf transcript annotations were used.
Genome_build: mm10
Supplementary_files_format_and_content: TSV files

extract_protocol:
Tissueed were thawed, ~50mg were minced, and dounced in 1ml trizol
RNA was extracted from tizol using the phenol chlorophorm method and quantified by nanodrop
1ug of RNA was polyA selected and RNA libraries constructed using the illumina Truseq kit
Tru-seq, non-directional cDNA prep and standard ligation based library construction

treatment_protocol: Tissues were removed from euthanized mice, placed in RNAlater, and frozen

tag: cell line


title: NIH3T3_T9


title: NIH3T3_T7


title: NIH3T3_T12


title: NIH3T3_T8


title: NIH3T3_T11


title: NIH3T3_T10


title: NIH3T3_T5


title: NIH3T3_T6


title: NIH3T3_T1


title: NIH3T3_T4


title: NIH3T3_T3


title: NIH3T3_T0


title: c57b6_TH_T24

description:
Gamma IR treated Mouse tissue
geo_mouse.txt

value: thymus


title: c57b6_TH_T7


title: c57b6_TH_T8


title: c57b6_TH_T6


title: c57b6_TH_T4


title: c57b6_TH_T5


title: c57b6_TH_T3


title: c57b6_TH_T2


title: c57b6_TH_T1


title: c57b6_TH_T0


title: c57b6_SP_T8

value: spleen


title: c57b6_SP_T7


title: c57b6_SP_T24


title: c57b6_SP_T6


title: c57b6_SP_T5


title: c57b6_SP_T4


title: c57b6_SP_T2


title: NIH3T3_T2


title: c57b6_LI_T24

value: large intestine


title: c57b6_SP_T1


title: c57b6_LI_T7


title: c57b6_LI_T5


title: c57b6_LI_T4


title: c57b6_LI_T8


title: c57b6_SP_T0


title: c57b6_LI_T3


title: c57b6_LI_T1


title: c57b6_LI_T6


title: c57b6_LI_T0


title: CD8TexStem_p45Tg_RNA_r1

city: Nutley

first: Haihui

last: Xue

state: NJ

address: 123 Metro Boulevard, Bldg. 123, Rm. 5527

department: Center for Discovery and Innovation

institute: Hackensack University Medial Center

data_processing:
Sequenced reads were trimmed for 30bp from both end to remove the low quality base. RNA-seq reads were then mapped to mm10 genome with hisat2 and only reads with MAPQ>30 were considered in following analysis. Expression index (RPKM) is generated by Stringtie. Differential expression analysis were performed by DESeq2 with adjusted p.value < 0.1, fold change >=1.5 and RPKM in higher expression condition >=1.
Genome_build: mm10
Supplementary_files_format_and_content: Tab-delimited text files (generated by HT-seq) include raw reads count of genes in each RNA-seq Sample.

source_name: exhausted CD8+ T cells

growth_protocol: CD45.2+ WT or p45Tg P14 TCR transgenic CD8 T cells were adoptively transferred into CD45.1+ B6.SJL recipients, followed by LCMV-clone 13 infection. On day 30 postinfection, the splenocytes were harvested, CD45.1+ cells were depleted, followed by cell sorting to collect CD45.2+Tex-stem or Tex-term cells for downstream analysis.

extract_protocol:
Tex-stem cells were sort-purified from the spleen and total RNA was extracted using standard Qiagen RNeasy columns
RNA libraries were prepared for sequencing using stardard Illumina protocol

value: splenocytes

value: p45 Tcf1 transgenic

tag: cell phenotype

value: CD8+, CXCR5+, Tim3–


title: CD8TexStem_WT_RNA_r2

tag: genotype

value: wild type


title: CD8TexStem_p45Tg_RNA_r2


title: c57b6_SI_T24

value: small intestine


title: c57b6_SI_T6


title: NW_ACB2E1_S10_L008

city: New York

first: Varshini

last: Vasudevaraja

state: NY

address: 550 1st Avenue

department: Pathology

institute: NYU Langone Health

description:
NW_no_ribosomedepletion
Animal cap explant dissected from embryo injected with Noggin + Wnt8 mRNAs

data_processing:
Base calling and demultiplexing was performed using Illumina bcl2fastq software.
The sequencing reads were aligned to the frog genome (build XL9.2, respectively) using the splice-aware STAR aligner.
The featureCounts program was utilized to generate counts for each gene.
The raw counts were normalized using the DESeq2 R package.
Heatmaps and other statistics was performed using R3.2
Genome_build: XL9_2
Supplementary_files_format_and_content: csv files include raw read counts table for genomic features and Transcript FPKM counts.

organism: Xenopus laevis

source_name: Noggin+Wnt8 no rRNA depletion, biological rep 2

extract_protocol:
Individual animal cap explants were homogenized and total RNA extracted using the RNeasy Micro Kit (Qiagen) according to the manufacturer’s instructions.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Xenopus laevis embryos were injected at the 2-cell stage with mRNA encoding noggin and wnt8 to induce neural crest progenitors. A subset of these embryos were co-injected with Sf3b4MO antisense oligonucleotides to interfere with neural crest foermation. At the blastula stage (stage 8/9), animal cap explants were dissected and cultured for 8 hours in a defined medium. Three replicate were performed for each condition.

value: Noggin+Wnt8 no rRNA depletion


title: c57b6_SI_T5


title: c57b6_SI_T8


title: c57b6_SI_T7


title: CD8TexStem_WT_RNA_r1


title: c57b6_SP_T3


title: NW_ACB1E1_S9_L008

source_name: Noggin+Wnt8 no rRNA depletion, biological rep 1


title: c57b6_SI_T4


title: NW_ACB1E1_S9_L007


title: c57b6_SI_T3


title: c57b6_SI_T2


title: c57b6_SI_T1


title: c57b6_LI_T2


title: NWS_ACB2E1_S13_L008

description:
NWS_no_ribosomedepletion
Animal cap explant dissected from embryo injected with Noggin + Wnt8 mRNAs and Sf3b4 antisense morpholino

source_name: Noggin+Wnt8+Sf3b4MO no rRNA depletion, biological rep 2

value: Noggin+Wnt8+Sf3b4MO no rRNA depletion


title: c57b6_SI_T0


title: NWS_ACB2E1_S13_L007

source_name: Noggin+Wnt8+Sf3b4MO no rRNA depletion, biological rep 1


title: NW_ACB3E1_S11_L008

source_name: Noggin+Wnt8 no rRNA depletion, biological rep 3


title: NWS_ACB1E1_S12_L007


title: WTres_LPS_3 [invitro_LPS]

source_name: bone marrow-derived macrophages

value: 8 weeks

value: MHD3KO +WT HDAC3

value: LPS


title: WTres_LPS_2 [invitro_LPS]


title: NW_ACB3E1_S11_L007


title: NW_ACB2E1_S10_L007


title: WTres_LPS_1 [invitro_LPS]


title: NW_ACB3E1_S12_L003

description:
NW_ribosomedepletion
Animal cap explant dissected from embryo injected with Noggin + Wnt8 mRNAs

source_name: Noggin+Wnt8 with rRNA depletion, biological rep 3

value: Noggin+Wnt8 with rRNA depletion


title: NW_ACB3E1_S12_L002


title: WTres_veh_2 [invitro_LPS]

value: PBS


title: NWS_ACB3E1_S14_L007


title: NWS_ACB3E1_S14_L008


title: WTres_veh_1 [invitro_LPS]


title: Y298F_LPS_4 [invitro_LPS]

value: MHD3KO +Y298F


title: NW_ACB2E1_S11_L002

source_name: Noggin+Wnt8 with rRNA depletion, biological rep 2


title: WTres_LPS_4 [invitro_LPS]


title: NW_ACB1E1_S10_L004

source_name: Noggin+Wnt8 with rRNA depletion, biological rep 1


title: Y298F_LPS_3 [invitro_LPS]


title: NW_ACB1E1_S10_L002


title: Y298F_LPS_1 [invitro_LPS]


title: NWS_ACB1E1_S12_L008


title: Y298F_veh_4 [invitro_LPS]


title: NWS_ACB3E1_S15_L003

description:
NWS_ribosomedepletion
Animal cap explant dissected from embryo injected with Noggin + Wnt8 mRNAs and Sf3b4 antisense morpholino

source_name: Noggin+Wnt8+Sf3b4MO with rRNA depletion, biological rep 3

value: Noggin+Wnt8+Sf3b4MO with rRNA depletion


title: Y298F_LPS_2 [invitro_LPS]


title: NW_ACB3E1_S12_L004


title: Y298F_veh_2 [invitro_LPS]


title: Y298F_veh_1 [invitro_LPS]


title: NWS_ACB2E1_S14_L003

source_name: Noggin+Wnt8+Sf3b4MO with rRNA depletion, biological rep 2


title: MHD3KO_LPS_4 [invitro_LPS]

value: MHD3KO+empty vector


title: NWS_ACB3E1_S15_L002


title: NWS_ACB2E1_S14_L004


title: NW_ACB2E1_S11_L004


title: WTres_veh_4 [invitro_LPS]


title: NW_ACB2E1_S11_L003


title: WTres_veh_3 [invitro_LPS]


title: NW_ACB1E1_S10_L003


title: NWS_ACB1E1_S13_L003

source_name: Noggin+Wnt8+Sf3b4MO with rRNA depletion, biological rep 1


title: MHD3KO_LPS_2 [invitro_LPS]


title: NWS_ACB1E1_S13_L004


title: NWS_ACB3E1_S15_L004


title: NWS_ACB1E1_S13_L002


title: MHD3KO_veh_3 [invitro_LPS]


title: MHD3KO_LPS_1 [invitro_LPS]


title: MHD3KO_veh_4 [invitro_LPS]


title: MHD3KO_veh_1 [invitro_LPS]


title: Control_LPS_3 [invitro_LPS]

value: control+empty vector


title: Control_LPS_4 [invitro_LPS]


title: Y298F_veh_3 [invitro_LPS]


title: MHD3KO_veh_2 [invitro_LPS]


title: Control_LPS_1 [invitro_LPS]


title: Control_veh_4 [invitro_LPS]


title: Control_veh_3 [invitro_LPS]


title: NWS_ACB2E1_S14_L002


title: Control_veh_1 [invitro_LPS]


title: UTER3886

city: Beltsville

first: George

middle: E.

last: Liu

state: Maryland (MD)

address: 10300 Baltimore Ave Bldg 306

institute: USDA-ARS

description:
mRNA sequencing 150bp paired-end
UMD3.1.1.fpkm.txt

data_processing:
we removed contaminating adapter molecules, reads containing poly-N, and low-quality reads using trimmomatic (version 0.39)
We then mapped the clean reads to the cattle reference genome UMD3.1.1 using  STAR (version 020201)
We used Ensembl genes as the gene annotation file, including 24,616 genes, and the gene expression levels were then determined by FPKM values for accounting for differences in sequence depth and gene length. The FPKM of genes were quantified using Cufflinks.
Genome_build: UMD 3.1.1
Supplementary_files_format_and_content: fpkm

organism: Bos taurus

source_name: Uterus

extract_protocol: Total RNA from 47 tissue samples was extracted using Trizol (Invitrogen, Carlsbad, CA, USA) followed by DNase digestion and Qiagen RNeasy column purification (Qiagen, Valencia, CA, USA). RNA integrity was verified using Agilent Bioanalyzer 2100 (Agilent, Palo Alto, CA, USA). High-quality RNA (RNA integrity number [RIN]: 9.0) was processed using an Illumina TruSeq RNA sample prep kit following the manufacturer’s instruction (Illumina, San Diego, CA, USA). After quality control (QC) procedures, individual RNA-seq libraries were pooled based on their respective sample-specific 6-bp (base pairs) adaptors and pair-end sequenced at 150 bp/sequence read (PE150) using an Illumina HiSeq 2500 sequencer (Illumina, Inc. San Diego, CA).

tag: breed

value: Holstein

value: Uterus

value: F


title: MHD3KO_LPS_3 [invitro_LPS]


title: UTER3842


title: Bone_1

city: Beijing

first: Shengli

last: Zhang

address: 2rd, Yuanmingyuan West Road

department: Colledge of Animal Science and Techonology

institute: China Agricultural University

description: WGBS; 150bp paired-end

data_processing:
Programs FastQC (0.11.5) and Trim Galore (0.4.5) were used to generate sequence quality reports and to trim/filter the sequences, respectively.
The cleaned data for each sample were merged and aligned to the reference genome (Bos taurus ARS-UCD1.2) using bowtie2 under the Bismark software (0.19.0)
The methylcytosine information was extracted using the bismark_methylation_extractor after deduplicating the duplication reads.
Genome_build: ARS-UCD1.2
Supplementary_files_format_and_content: The data files contain the methylatin information for the CG detected. The column names are: chrmosome, position,strand, coverage for methylated cytosine, coverage for unmethylated cytosine, CG type, three bases near the cytosine.

source_name: Bone

extract_protocol:
Genomic DNA was isolated according to the QIAamp DNA Mini Kit protocol (QIAGEN, Valencia, CA, USA).
The qualified genomic DNA from somatic tissues and sperm were used to construct libraries. Briefly, 3 μg of genomic DNA spiked with unmethylated lambda DNA were fragmented into 200-300 bp using a Covaris S220 (Covaris, Inc., Woburn, MA, USA), followed by teriminal repairing and A-ligation. Different cytosine methylated barcodes were ligated to sonicated DNA for different samples. The DNA bisufite conversion was performed using the EZ DNA Methylation Gold Kit (Zymo Research, Irvine, CA, USA). Then single-stranded DNA fragments were amplified using the KAPA HiFi HotStart Uracil + ReadyMix (2 X) (Kapa Biosystems, Wilmington, MA, USA). The library concentration was quantified using a Qubit 2.0 fluorometer (Life Technologies, Carlsbad, CA, USA) and qPCR (iCycler, BioRad Laboratories, Hercules, CA, USA), and the insert size was checked using the Agilent 2100.

value: Bone


title: Bone_2

description: WGBS; 150bp paired-end


title: SPLE3842

source_name: Spleen

value: Spleen


title: SPLE3886


title: 3842Mamdup RNA-seq

description: mRNA sequencing 150bp paired-end

data_processing:
we removed contaminating adapter molecules, reads containing ploy-N, and low-quality reads using trimmomatic (version 0.39)
We then mapped the clean reads to the cattle reference genome UMD3.1.1 using  STAR (version 020201)
We used Ensembl genes as the gene annotation file, including 24,616 genes, and the gene expression levels were then determined by FPKM values for accounting for differences in sequence depth and gene length. The FPKM of genes were quantified using Cufflinks.
Genome_build: UMD 3.1.1

source_name: Mammary

extract_protocol: Total RNA from 4 tissue samples was extracted using Trizol (Invitrogen, Carlsbad, CA, USA) followed by DNase digestion and Qiagen RNeasy column purification (Qiagen, Valencia, CA, USA). RNA integrity was verified using Agilent Bioanalyzer 2100 (Agilent, Palo Alto, CA, USA). High-quality RNA (RNA integrity number [RIN]: 9.0) was processed using an Illumina TruSeq RNA sample prep kit following the manufacturer’s instruction (Illumina, San Diego, CA, USA). After quality control (QC) procedures, individual RNA-seq libraries were pooled based on their respective sample-specific 6-bp (base pairs) adaptors and pair-end sequenced at 150 bp/sequence read (PE150) using an Illumina HiSeq 2500 sequencer (Illumina, Inc. San Diego, CA).

value: Hostein

value: Mammary


title: 3886Mamdup RNA-seq

description: mRNA sequencing 150bp paired-end


title: 4254Lym RNA-seq

description: mRNA sequencing 150bp paired-end

source_name: Lymphocyte

value: Lymphocyte

value: M


title: 4091Lym RNA-seq

description: mRNA sequencing 150bp paired-end


title: Control_LPS_2 [invitro_LPS]

value: 8 weeks


title: RUME3770

source_name: Rumen

value: Rumen


title: OVAR3842

source_name: Ovary

value: Ovary


title: SPLE3773


title: SPLE3770


title: RUME3886


title: RUME3842


title: OVAR3886


title: MAMP3886

source_name: Dry mammary gland

value: Dry mammary gland


title: Control_veh_2 [invitro_LPS]

value: PBS


title: LUNG3842

source_name: Lung

value: Lung


title: LYMP4254


title: MAMP3842

source_name: Lactating mammary gland

value: Lactating mammary gland


title: LUNG3886


title: LIVE3886

source_name: Liver

value: Liver


title: LUNG3773

value: Holstein


title: LIVE3842


title: LIVE3773


title: LIVE3770


title: LDOR3886

source_name: Muscle

value: Muscle


title: LDOR3842

value: F


title: LDOR3773


title: RUME3773


title: LDO3770


title: KIDN3886

source_name: Kidney

value: Kidney


title: ILEU3773

source_name: Ileum

value: Ileum


title: ILEU3886


title: Day28_LUNG_240_2500ppm_F

city: Research Triangle Park

first: Michael

middle: B.

last: Black

state: North Carolina

address: 100 Capitola Dr., Suite 106

institute: Scitovation, LLC.

description:
Day28-Lung 240
processed data: 4MEI_Day28_LUNG_Male_Female_Counts.txt

data_processing:
Illumina NextSeq 500 control software v2.1.0 with BCL files uploaded to Illumina BaseSpace for FASTQ file generation.
Sequences trimmed from both based on QC (TRIMMOMATIC, min base QC call of 21, min. retained read length 65bp), and mapped to Illumina iGenomes UCSC mm10 using BOWTIE2.
BAM files from each pair of paired-end files merged by sample with SAMTools, and gene counts extracted with HTSeq.
Genome_build: UCSC mm10 (Illumina iGenomes)
Supplementary_files_format_and_content: *_Male_Female_Counts.txt: Tab-delimited text files of gene counts.

extract_protocol: 1.0-2.0 μg total RNA using the manufacturer's standard procedure for the Illumina TruSeq® Stranded mRNA HT Kit.

treatment_protocol: Mice were exposed to 4-Methylimidazole for 2, 5 or 28 days.

tag: strain/background

value: Female

tag: dose

tag: exposure time

value: Day 28

tag: route

value: Feed


title: ILEU3842

tag: Sex


title: Day28_LUNG_236_2500ppm_F

description:
Day28-Lung 236
processed data: 4MEI_Day28_LUNG_Male_Female_Counts.txt

tag: treatment


title: Day28_LUNG_237_2500ppm_F

description:
Day28-Lung 237
processed data: 4MEI_Day28_LUNG_Male_Female_Counts.txt


title: HEAR3842

source_name: Heart

value: Heart


title: Day28_LUNG_234_2500ppm_F

description:
Day28-Lung 234
processed data: 4MEI_Day28_LUNG_Male_Female_Counts.txt


title: KIDN3770

value: M


title: HEAR3886


title: Day28_LUNG_230_2500ppm_M

description:
Day28-Lung 230
processed data: 4MEI_Day28_LUNG_Male_Female_Counts.txt


title: Day28_LUNG_235_2500ppm_F

description:
Day28-Lung 235
processed data: 4MEI_Day28_LUNG_Male_Female_Counts.txt


title: Day28_LUNG_231_2500ppm_M

description:
Day28-Lung 231
processed data: 4MEI_Day28_LUNG_Male_Female_Counts.txt


title: KIDN3842


title: LUNG3770


title: Day28_LUNG_229_2500ppm_M

description:
Day28-Lung 229
processed data: 4MEI_Day28_LUNG_Male_Female_Counts.txt


title: FRON3886

source_name: Frontal cortex

value: Frontal cortex


title: Day28_LUNG_228_2500ppm_M

description:
Day28-Lung 228
processed data: 4MEI_Day28_LUNG_Male_Female_Counts.txt


title: HEAR3770


title: Day28_LUNG_227_2500ppm_M

description:
Day28-Lung 227
processed data: 4MEI_Day28_LUNG_Male_Female_Counts.txt


title: FRON3770


title: FRON3773


title: Day28_LUNG_238_2500ppm_F

description:
Day28-Lung 238
processed data: 4MEI_Day28_LUNG_Male_Female_Counts.txt


title: ILEU3770


title: Day28_LUNG_225_2500ppm_M

description:
Day28-Lung 225
processed data: 4MEI_Day28_LUNG_Male_Female_Counts.txt


title: ADIP3886

source_name: Adipose

value: Adipose


title: KIDN3773


title: Day28_LUNG_223_1250ppm_F

description:
Day28-Lung 223
processed data: 4MEI_Day28_LUNG_Male_Female_Counts.txt


title: Day28_LUNG_222_1250ppm_F

description:
Day28-Lung 222
processed data: 4MEI_Day28_LUNG_Male_Female_Counts.txt


title: Day28_LUNG_221_1250ppm_F

description:
Day28-Lung 221
processed data: 4MEI_Day28_LUNG_Male_Female_Counts.txt


title: FRON3842


title: Day28_LUNG_220_1250ppm_F

description:
Day28-Lung 220
processed data: 4MEI_Day28_LUNG_Male_Female_Counts.txt


title: ADIP3773

description:
mRNA sequencing 150bp paired-end
UMD3.1.1.fpkm.txt


title: HEAR3773


title: Day28_LUNG_218_1250ppm_F

description:
Day28-Lung 218
processed data: 4MEI_Day28_LUNG_Male_Female_Counts.txt


title: ADIP3842


title: Kap114 KO rep3 [TAF1-d114-SALT-5_S10]

city: Taipei

first: Kuo-Chiang

last: Hsia

address: 128 Academia Road, Section 2, Nankang, Taipei 11529, Taiwan

department: Institute of Molecular Biology

country: Taiwan

institute: Academia Sinica

data_processing:
On-instrument base-calling with Illumina NextSeq 500 NCS v1.3 software/Real Time Analysis v2
Raw reads (76 bp) had their adapter sequences removed. General quality control of the raw reads was performed using FastQC.
Sequenced reads were trimmed for adaptor sequence,low quality sequences, then mapped to Saccharomyces_cerevisiae.R64-1-1.82 whole genome using CLC Genomics Workbench with parameters: mismatches=2, minimum fraction length =0.9, minimum fraction similarity=0.9, and maximum hits per read = 10.
RPKM and TPM were calculated using  CLC Genomics Workbench
Genome_build: Saccharomyces_cerevisiae.R64-1-1.82
Supplementary_files_format_and_content: multiple spreadsheets including RPKM, TPM, FC etc.

organism: Saccharomyces cerevisiae

source_name: Kap114 KO

growth_protocol: Wild type and Kap114 knockout yeast strains were grown in YPD medium in the presence of 1.5 M NaCl.

extract_protocol:
Total RNA was extracted using a RNeasy Mini Kit (QIAGEN).
2 ug of total RNA was used for RNA-seq library preparation using the TruSeq™ Stranded mRNA LT Sample .  RNA molecules were poly(A) selected, fragmented, and reverse transcribed . End repair, A-tailing, adaptor ligation, and library enrichment were performed as described in the TruSeq Stranded mRNA Sample Preparation Guide (Illumina). RNA libraries were assessed for quality and quantity with the Agilent 2100 BioAnalyzer and the Quant-iT HS dsDNA Assay Kit (Life Technologies). S

tag: strain background

tag: genotype/variation

value: Kap114 KO

tag: culture condition

value: high salt; 1.5M NaCl


title: Kap114 KO rep2 [TAF1-d114-SALT-4_S9]


title: Day28_LUNG_214_1250ppm_M

description:
Day28-Lung 214
processed data: 4MEI_Day28_LUNG_Male_Female_Counts.txt

value: Lung


title: Day28_LUNG_213_1250ppm_M

description:
Day28-Lung 213
processed data: 4MEI_Day28_LUNG_Male_Female_Counts.txt


title: WT ctrl rep2 [TAF1-SALT-2_S2]

source_name: WT ctrl

value: wild type


title: Kap114 KO rep1 [TAF1-d114-SALT-3_S8]


title: Day28_LUNG_217_1250ppm_F

description:
Day28-Lung 217
processed data: 4MEI_Day28_LUNG_Male_Female_Counts.txt


title: Day28_LUNG_215_1250ppm_M

description:
Day28-Lung 215
processed data: 4MEI_Day28_LUNG_Male_Female_Counts.txt


title: WT ctrl rep3 [TAF1-SALT-3_S3]


title: WT ctrl rep1 [TAF1-SALT-1_S1]


title: ADIP3770


title: Day28_LUNG_212_1250ppm_M

description:
Day28-Lung 212
processed data: 4MEI_Day28_LUNG_Male_Female_Counts.txt


title: Day28_LUNG_207_300ppm_F

description:
Day28-Lung 207
processed data: 4MEI_Day28_LUNG_Male_Female_Counts.txt

value: Vehicle

value: Vehicle (0ppm)


title: Day28_LUNG_208_300ppm_F

description:
Day28-Lung 208
processed data: 4MEI_Day28_LUNG_Male_Female_Counts.txt


title: siCtrl_2 siRNA control knockdown5 RNA-Seq

city: San Francisco

first: Wei

last: Wu

state: CA

address: 600 16th street

department: Department of Medicine

institute: University of California, San Franciso

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg19 genome using STAR_2.4.2a with default parameters.
The expression level of transcript per million (TPM) reads were quantified using RNA-Seq by Expectation-Maximization algorithm (RSEM v1.2.29).
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include TPM values for each Sample.

source_name: EC9706 esophageal cancer cells

extract_protocol:
Frozen tissues of surgically removed specimens or cells from cell culture were used for RNA extraction. RNA was harvested using Trizol reagent. NEBNext® Ultra™ RNA Library Prep Kit for Illumina® (#E7530L, NEB, USA)  was used with 2 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: esophageal squamouse carcinoma cell line


title: siYY1-2 siYY1 knockdown2 RNA-Seq

source_name: EC109 esophageal cancer cell


title: siMyc_2 siMyc knockdown2 RNA-Seq


title: siMyc_1 siMyc knockdown1 RNA-Seq


title: siYY1-1 siYY1 knockdown1 RNA-Seq


title: Day28_LUNG_209_1250ppm_M

description:
Day28-Lung 209
processed data: 4MEI_Day28_LUNG_Male_Female_Counts.txt


title: Day28_LUNG_202_300ppm_F

description:
Day28-Lung 202
processed data: 4MEI_Day28_LUNG_Male_Female_Counts.txt


title: siCTL-3 siRNA control knockdown3 RNA-Seq


title: Day28_LUNG_203_300ppm_F

description:
Day28-Lung 203
processed data: 4MEI_Day28_LUNG_Male_Female_Counts.txt


title: Day28_LUNG_196_300ppm_M

description:
Day28-Lung 196
processed data: 4MEI_Day28_LUNG_Male_Female_Counts.txt

value: Male


title: siCTL-1 siRNA control knockdown1 RNA-Seq


title: shESCCAL-1_3 shESCCAL-1 knockdown3 RNA-Seq


title: Day28_LUNG_204_300ppm_F

description:
Day28-Lung 204
processed data: 4MEI_Day28_LUNG_Male_Female_Counts.txt


title: shESCCAL-1_2 shESCCAL-1 knockdown2 RNA-Seq


title: Day28_LUNG_194_300ppm_M

description:
Day28-Lung 194
processed data: 4MEI_Day28_LUNG_Male_Female_Counts.txt


title: Day28_LUNG_197_300ppm_M

description:
Day28-Lung 197
processed data: 4MEI_Day28_LUNG_Male_Female_Counts.txt


title: shCtrl_3 shRNA control knockdown3 RNA-Seq


title: siCtrl_1 siRNA control knockdown4 RNA-Seq


title: Day28_LUNG_193_300ppm_M

description:
Day28-Lung 193
processed data: 4MEI_Day28_LUNG_Male_Female_Counts.txt


title: shCtrl_2 shRNA control knockdown2 RNA-Seq


title: siYY1-3 siYY1 knockdown3 RNA-Seq


title: Day28_LUNG_192_150ppm_F

description:
Day28-Lung 192
processed data: 4MEI_Day28_LUNG_Male_Female_Counts.txt


title: shESCCAL-1_1 shESCCAL-1 knockdown1 RNA-Seq


title: shCtrl_1 shRNA control knockdown1 RNA-Seq


title: Day28_LUNG_191_150ppm_F

description:
Day28-Lung 191
processed data: 4MEI_Day28_LUNG_Male_Female_Counts.txt


title: Tumor T15 RNA-Seq

description: Tumor

source_name: Esophageal Squamouse carcinoma

value: esophageal squamouse carcinoma

tag: tumor pathological stage

value: moderately differentiated

tag: tnm stage


title: Day28_LUNG_199_300ppm_M

description:
Day28-Lung 199
processed data: 4MEI_Day28_LUNG_Male_Female_Counts.txt


title: Day28_LUNG_190_150ppm_F

description:
Day28-Lung 190
processed data: 4MEI_Day28_LUNG_Male_Female_Counts.txt


title: Tumor T13 RNA-Seq

description: Tumor

value: highly differentiated


title: Tumor T12 RNA-Seq

description: Tumor

value: highly or moderately differentiated


title: Day28_LUNG_185_150ppm_F

description:
Day28-Lung 185
processed data: 4MEI_Day28_LUNG_Male_Female_Counts.txt

value: Day 28

value: Feed


title: Day28_LUNG_189_150ppm_F

description:
Day28-Lung 189
processed data: 4MEI_Day28_LUNG_Male_Female_Counts.txt


title: Day28_LUNG_195_300ppm_M

description:
Day28-Lung 195
processed data: 4MEI_Day28_LUNG_Male_Female_Counts.txt


title: Day28_LUNG_186_150ppm_F

description:
Day28-Lung 186
processed data: 4MEI_Day28_LUNG_Male_Female_Counts.txt


title: Tumor T11 RNA-Seq

description: Tumor


title: Day28_LUNG_183_150ppm_M

description:
Day28-Lung 183
processed data: 4MEI_Day28_LUNG_Male_Female_Counts.txt


title: Tumor T8 RNA-Seq

description: Tumor

value: moderately or poorly differentiated


title: Tumor T9 RNA-Seq

description: Tumor


title: Day28_LUNG_184_150ppm_M

description:
Day28-Lung 184
processed data: 4MEI_Day28_LUNG_Male_Female_Counts.txt


title: Day28_LUNG_181_150ppm_M

description:
Day28-Lung 181
processed data: 4MEI_Day28_LUNG_Male_Female_Counts.txt


title: Day28_LUNG_178_150ppm_M

description:
Day28-Lung 178
processed data: 4MEI_Day28_LUNG_Male_Female_Counts.txt


title: Tumor T2 RNA-Seq

description: Tumor


title: Tumor T6 RNA-Seq

description: Tumor


title: Tumor T7 RNA-Seq

description: Tumor


title: Day28_LUNG_180_150ppm_M

description:
Day28-Lung 180
processed data: 4MEI_Day28_LUNG_Male_Female_Counts.txt


title: Day28_LUNG_182_150ppm_M

description:
Day28-Lung 182
processed data: 4MEI_Day28_LUNG_Male_Female_Counts.txt


title: Tumor T1 RNA-Seq

description: Tumor


title: Day28_LUNG_211_1250ppm_M

description:
Day28-Lung 211
processed data: 4MEI_Day28_LUNG_Male_Female_Counts.txt

value: Female


title: normal N15 RNA-Seq

description: normal

source_name: Adjacent normal tissue

value: adjacent normal esophageal tissue


title: Day28_LUNG_173_VC_F

description:
Day28-Lung 173
processed data: 4MEI_Day28_LUNG_Male_Female_Counts.txt


title: Day28_LUNG_176_VC_F

description:
Day28-Lung 176
processed data: 4MEI_Day28_LUNG_Male_Female_Counts.txt


title: Day28_LUNG_172_VC_F

description:
Day28-Lung 172
processed data: 4MEI_Day28_LUNG_Male_Female_Counts.txt


title: normal N12 RNA-Seq

description: normal


title: normal N13 RNA-Seq

description: normal


title: normal N11 RNA-Seq

description: normal


title: Day28_LUNG_171_VC_F

description:
Day28-Lung 171
processed data: 4MEI_Day28_LUNG_Male_Female_Counts.txt


title: normal N8 RNA-Seq

description: normal


title: Day28_LUNG_170_VC_F

description:
Day28-Lung 170
processed data: 4MEI_Day28_LUNG_Male_Female_Counts.txt


title: Day28_LUNG_167_VC_M

description:
Day28-Lung 167
processed data: 4MEI_Day28_LUNG_Male_Female_Counts.txt


title: Day28_LUNG_206_300ppm_F

description:
Day28-Lung 206
processed data: 4MEI_Day28_LUNG_Male_Female_Counts.txt


title: Day28_LUNG_169_VC_F

description:
Day28-Lung 169
processed data: 4MEI_Day28_LUNG_Male_Female_Counts.txt


title: Day28_LUNG_168_VC_M

description:
Day28-Lung 168
processed data: 4MEI_Day28_LUNG_Male_Female_Counts.txt


title: normal N7 RNA-Seq

description: normal


title: normal N6 RNA-Seq

description: normal


title: normal N1 RNA-Seq

description: normal


title: Day28_LUNG_166_VC_M

description:
Day28-Lung 166
processed data: 4MEI_Day28_LUNG_Male_Female_Counts.txt


title: Tumor T15 WGBS

description: Tumor

data_processing:
Illumina Casava1.7 software used for basecalling.
Firstly, we trimmed using Trim Galore! (v0.4.1) to remove Illumina adaptors with the options of ' --paired --length 50 --clip_1 6 --clip_2 6 '. After trimming, around 90 Gbp of data remained per sample. Then trimmed reads were aligned to the HG19 reference genome using BSMAP (v2.89) with the option of '-p 8 -R'. Then SAMtools (v. 1.3.1) was used to sort by genomic coordination and make a bam file index. Picard Tools (v.1.92) is used to remove PCR duplicates. After deduplication, ~70Gbp remained per sample. Lastly, we ran MOABS (v. 1.3.4) to compute the methylation ratio per CpG with the option of '--cytosineMinScore 20  --skipRandomChrom 1 -p 4 --keepTemp 0 --processPEOverlapSeq 1 --requiredFlag 2 --excludedFlag 256 --minFragSize 110 --reportCpX G --qualityScoreBase 0 --trimRRBSEndRepairSeq 0  --trimWGBSEndRepairPE1Seq 5 --trimWGBSEndRepairPE2Seq 5'. Around 95% of CpGs are covered by at least five reads.
Given the methylation ratio and coordination computed, we built a data matrix, whose columns are samples and rows are CpGs.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include methylation ration (methylated reads/total reads at a given CpG)  for each Sample.

extract_protocol:
Frozen tissues of surgically removed specimens  were used for genomic DNA extraction.  Genomic DNA was extracted with QIAmp DNA Mini kits (Qiagen) from fresh frozen tissue samples. 1μg gDNA was fragmented by sonication with a base pair peak of 300 bp for the resulting fragment, and adaptors were then ligated to both ends of the fragments.  Bisulfite conversion was performed to whole genomes of ten pairs of ESCC and matched normal tissues, where converts cytosine residues of the dinucleotide CpG to uracil but leaves methylated cytosine unaffected. PCR amplification and purification were carried out. The uracil-binding pocket of KAPA HiFi DNA Polymerase has been inactivated, enabling amplification of uracil-containing DNA.
The high quality of the library was estimated by The Qubit® 3.0 Fluorometer. Bisulfite conversion success ratio is 99.18% and 99.49%, respectively in normal and ESCC samples
The WGBS library was sequenced on an Illumina HiSeq2500 sequencers and generated 400M of paired-end reads (2x125bp)


title: Day28_LUNG_164_VC_M

description:
Day28-Lung 164
processed data: 4MEI_Day28_LUNG_Male_Female_Counts.txt


title: Day28_LUNG_162_VC_M

description:
Day28-Lung 162
processed data: 4MEI_Day28_LUNG_Male_Female_Counts.txt


title: Day28-LIVER-240_2500ppm_F

description:
Day28-Liver 240
processed data: 4MEI_Day28_LIVER_Male_Female_Counts.txt

value: Liver


title: normal N9 RNA-Seq

description: normal


title: Tumor T12 WGBS

description: Tumor


title: Day28_LUNG_161_VC_M

description:
Day28-Lung 161
processed data: 4MEI_Day28_LUNG_Male_Female_Counts.txt


title: Tumor T13 WGBS

description: Tumor


title: Day28-LIVER-239_2500ppm_F

description:
Day28-Liver 239
processed data: 4MEI_Day28_LIVER_Male_Female_Counts.txt