title: L01_DA06_MethodBlank_0

description:
L01_DA06
Hepatocyte_normcounts.csv


title: CLL-C210_PB_CD19

status: Public on Jan 01 2022

type: SRA

city: Bethesda

first: Mehdi

last: Pirooznia

state: MD

address: 12 SOUTH DR

country: USA

institute: National Institutes of Health

library_source: transcriptomic

data_processing:
Reads were aligned to hg38 using STAR (Dobin et al., 2013), summarized by featureCounts (Liao et al., 2014),
and normalized across samples (Law et al., 2014). Counts per million (CPM) were used to measure gene expression.
Genes with CPM > 1 in ≥ 3 samples were analyzed in downstream analysis.
Paired gene-level differential analysis was conducted using the limma package (Law et al., 2014).
Genome_build: hg38
Supplementary_files_format_and_content: log2CPM Text format

molecule: total RNA

organism: Homo sapiens

extract_protocol:
RNA was extracted from CD19+ cells or snap frozen lymph node biopsies using RNeasy kits (Qiagen, Germantown, MD, USA).
Total RNA libraries were prepared according to the Illumina TruSeq protocol.

tag: tissue

value: peripheral blood

tag: cd19+ selection

value: yes

tag: age

tag: Sex

value: M

tag: diagnosis

value: SLL

tag: ighv

value: U


title: L01_DA03_043_kerosine_100

city: RTP

first: John

middle: S.

last: House

state: NC

address: 111 TW Alexander Drive

department: Biostatistics & Computational Biology Branch

institute: National Instititute of Environmental Health Sciences

description:
L01_DA03
Hepatocyte_normcounts.csv

data_processing:
pipeline run to convert reads to counts https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5672545/
samples with counts < 100 average reads per transcript removed
normalized counts generated by cell type in DESEQ2
Genome_build: NA – Targeted Reads by BioSpyder
Supplementary_files_format_and_content: 6 normalized count matrix files in CSV with genes as rows and columns as samples.  The sample information in the hashfile.csv

source_name: Hepatocyte

extract_protocol:
described in https://www.altex.org/index.php/altex/article/view/1994
described in https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0178302

tag: tissue/celltype

value: iCell Hepatocytes

tag: treatment

value: KER

tag: dose


title: L01_DA10_180_VHGO_100

description:
L01_DA10
Hepatocyte_normcounts.csv

value: VHGO


title: CLL-C45_PB_CD19

value: F

value: CLL


title: CLL-C43_PB_CD19


title: L01_DA05_151_OLBO_100

description:
L01_DA05
Hepatocyte_normcounts.csv

value: BO


title: CLL-C46_PB_CD19


title: heat_24h_40C_A

city: St. Louis

first: Ru

last: Zhang

state: Missouri

address: 95 N Warson Rd

institute: Donald Danforth Plant Science Center

data_processing:
Samples were quality control filtered using the JGI BBDuk and BBMap pipelines
Samples were quality assessed using FastQC
Reads were mapped to the Chlamydomonas reinhardtii v5.6 genome (Merchant et al., 2007) using STAR (Dobin and Gingeras, 2015; Dobin et al., 2013) with the maximum number of mapped loci set to 1 and the maximum mismatches per read set to 1, resulting in >92% of all reads being uniquely mapped to the Chlamydomonas reinhardtii v5.6 genome.
Reads per feature were counted via HT-seq count (Anders et al., 2014).
The dataset was filtered for genes that met minimum read count cutoffs of at least 10 mapped reads in at least 10% of the samples, resulting in 15,541 genes for downstream analyses
Differential expression modeling was performed on transcripts per million (TPM) normalized read counts using a generalized linear mixed-effect model and a negative binomial distribution. Treatment time points were compared to pre-heat controls. Significant differential expression was defined as |log2 fold-change > 1, FDR < 0.05, and |(control mean TPM) – (treatment mean TPM)| ≥ 1. FDR correction was performed using the Benjamini-Hochberg method (Benjamini and Hochberg, 1995).
Genome_build: Chlamydomonas reinhardtii v5.6 genome
Supplementary_files_format_and_content: tab-delimited text files include TPM values for each Sample
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

molecule: polyA RNA

organism: Chlamydomonas reinhardtii

growth_protocol: Chlamydomonas reinhardtii wildtype strain (cc1690, also called 21gr, mt+) was used in all experiments. CC1690 were grown in standard Tris-acetate-phosphate (TAP) medium in 400mL photobioreactors (PBRs) (Photon System Instruments, FMT 150/400-RB). Cultures were illuminated with constant 100 µmol photons m-2 s-1 light (50% red: 50% blue), mixed by bubbling with filtered air at a flow rate of 1 L/minute. Algal growth was turbidostatically maintained using OD680 during the experiments, so the algal cultures were not limited by nutrients or light. After PBR inoculation, cultures were allowed to grow to a target cell density of 2.00x106 cells/mL corresponding to around 4.0 ug/mL chlorophyll content in log-phase growth at 25oC. The steady condition was maintained turbidostatically using OD680 for 4 days to allow cultures to adapt to steady growth conditions at 25oC before heat treatments

extract_protocol:
At each time point, approximately 4x106 cells were pelleted with Tween-20 (0.005%, v/v) by centrifugation at 1,100 x g and 4oC for 2 min. The cell pellet was flash frozen in liquid nitrogen and stored at -80oC before processing. Total RNA was extracted with the TRIzol reagent (Thermo Fisher Scientific, Cat No. 15596026) as described before with some modifications (Zones et al., 2015). RNA was purified by RNeasy mini-column (Qiagen, Cat No. 74106) after on column digestion with RNase-free DNase (Qiagen, Cat No. 79256) according to the manufacturer’s instructions. RNA was quantified with Qubit™ RNA BR Assay Kit, (Life technology, Cat No. Q10210). Total 0.4 μg RNA was reverse transcribed with oligo dT primers using SuperScript® III First-Strand Synthesis System (Life technology, Cat No. 18080-051) according to the manufacturer’s instructions. Quantitative real-time PCR (RT-qPCR) analysis was carried out using a CFX384 Real-Time System (C 1000 Touch Thermal Cycler, Bio-Rad, Hercules, California) using SensiFAST SYBR No-ROS kit (Bioline, BIO-98020). PCR was set up as follows: 2 min at 95˚C, followed by 40 cycles of 5 s at 95oC, 10 s at 60oC and 15 s at 72oC. Melting curve was checked right after all PCR cycles to make sure there are no primer dimers or unspecific PCR products. Expression of G-protein β-subunit-like polypeptide CBLP (Cre06.g278222), (Schloss, 1990) remain stable among all time points, and were used as internal controls (Xie et al., 2013). The relative expressions were calculated relative to its expression in pre-heat by the ΔΔCT method (Livak and Schmittgen, 2001b). The qPCR primers for tested genes (CBLP, HSP22A, HSP90A, and others) are listed in Supplementary Table 1. PCR efficiencies were checked and were employed to the 2−ΔΔCT method to calculate the relative expression as described previously (Livak and Schmittgen, 2001; Hellemans et al., 2007; Remans et al., 2014). Three biological replicates for each time point and treatment were conducted.
Library construction was perfored at the Department of Energy (DOE) Joint Genome Institute (JGI)

treatment_protocol: PBR temperatures were shifted to moderate or acute heat stress conditions (35oC and 40oC respectively in different PBRs) for 24 hours, then shifted back to 25oC for 48 hours for recovery.

tag: strain

value: 40C high temperature

tag: time point


title: reach_control_temp_40C_B

value: recovery following 40C high temperature

value: reach control temperature (0h)


title: heat_24h_40C_C


title: reach_control_temp_40C_A


title: heat_16h_40C_B


title: heat_24h_40C_B


title: reach_control_temp_40C_C


title: heat_16h_40C_A


title: L01_DA01_016_kerosine_100

description:
L01_DA01
Hepatocyte_normcounts.csv


title: heat_8h_40C_C


title: heat_8h_40C_B


title: L01_CH11_185_RAE_1

description:
L01_CH11
Hepatocyte_normcounts.csv

value: RAE


title: L01_DA08_006_HFO_100

description:
L01_DA08
Hepatocyte_normcounts.csv

value: HFO


title: recovery_2h_40C_C


title: L01_CH10_172_SRGO_1

description:
L01_CH10
Hepatocyte_normcounts.csv

value: SRGO


title: heat_8h_40C_A


title: heat_4h_40C_A


title: CLL-C41_PB_CD19

value: peripheral blood


title: heat_2h_40C_C


title: heat_4h_40C_C


title: CLL-C02_LN_CD19

value: lymph node

value: yes


title: L01_CH09_175_VHGO_1

description:
L01_CH09
Hepatocyte_normcounts.csv


title: CLL-C35_PB_CD19


title: CLL-C34_PB_CD19

value: M


title: heat_2h_40C_B


title: L01_CH08_084_UATO_1

description:
L01_CH08
Hepatocyte_normcounts.csv

value: UATO


title: CLL-C32_PB_CD19

value: U


title: L01_CH06_MethodBlank_0

description:
L01_CH06
Hepatocyte_normcounts.csv

value: iCell Hepatocytes


title: CLL-C30_PB_CD19


title: L01_CH05_085C_OLBO_1

description:
L01_CH05
Hepatocyte_normcounts.csv


title: CLL-C14_PB_CD19


title: heat_1h_40C_C


title: CLL-C08_PB_CD19


title: heat_4h_40C_B


title: CLL-C05_PB_CD19


title: heat_1h_40C_B


title: heat_1h_40C_A


title: L01_CH04_149_OLBO_1

description:
L01_CH04
Hepatocyte_normcounts.csv


title: L01_CH02_069_TDAE_1

description:
L01_CH02
Hepatocyte_normcounts.csv

value: TDAE


title: CLL-C01_PB_CD19

value: F


title: reach_high_temp_40C_A

value: reach high temperature (0h)


title: reach_high_temp_40C_C


title: reach_high_temp_40C_B


title: preheat_40C_C

value: control

value: pre-heat


title: L01_CG11_078_HFO_1

description:
L01_CG11
Hepatocyte_normcounts.csv


title: L01_CH01_049_kerosine_1

description:
L01_CH01
Hepatocyte_normcounts.csv

value: KER


title: preheat_40C_A


title: CLL-C33_PB_CD19

value: CLL


title: L01_CG10_139_OLBO_1

description:
L01_CG10
Hepatocyte_normcounts.csv

value: BO


title: CLL-C24_PB_CD19


title: preheat_40C_B


title: heat_2h_40C_A

value: 40C high temperature


title: heat_0.5h_40C_C


title: heat_0.5h_40C_B


title: CLL-C44_PB_CD19


title: CLL-C11_PB_CD19


title: L01_CG09_056_gasoline_1

description:
L01_CG09
Hepatocyte_normcounts.csv

value: NAPTHA


title: L01_CG06_MethodBlank_0

description:
L01_CG06
Hepatocyte_normcounts.csv


title: CLL-C03_PB_CD19

value: peripheral blood


title: L01_CG05_183_VHGOa_1

description:
L01_CG05
Hepatocyte_normcounts.csv

value: VHGO


title: recovery_48h_35C_B

value: recovery following 35C high temperature


title: recovery_48h_35C_C


title: recovery_48h_35C_A


title: recovery_8h_35C_B


title: recovery_24h_35C_B


title: recovery_8h_35C_C


title: recovery_24h_35C_A


title: L01_CG04_073_OLBO_1

description:
L01_CG04
Hepatocyte_normcounts.csv


title: CLL-C49_PB_CD19

value: yes


title: recovery_4h_35C_C


title: recovery_4h_35C_B


title: recovery_4h_35C_A


title: recovery_8h_35C_A


title: L01_CG03_072_OLBO_1

description:
L01_CG03
Hepatocyte_normcounts.csv


title: recovery_2h_35C_C


title: recovery_2h_35C_B


title: CLL-C47_PB_CD19

value: SLL


title: CLL-C37_PB_CD19

value: M


title: L01_CG02_064_UATO_1

description:
L01_CG02
Hepatocyte_normcounts.csv

value: iCell Hepatocytes

value: UATO


title: reach_control_temp_35C_C

value: reach control temperature (0h)


title: recovery_2h_35C_A


title: CLL-C36_PB_CD19

value: F

value: U


title: reach_control_temp_35C_B


title: L01_CG08_134_HFO_1

description:
L01_CG08
Hepatocyte_normcounts.csv

value: HFO


title: reach_control_temp_35C_A


title: L01_CG01_109_FO_1

description:
L01_CG01
Hepatocyte_normcounts.csv

value: FO


title: CLL-C31_PB_CD19

value: CLL


title: L01_CF06_MethodBlank_0

description:
L01_CF06
Hepatocyte_normcounts.csv


title: CLL-C25_PB_CD19


title: heat_24h_35C_C

value: 35C high temperature


title: heat_24h_35C_B


title: CLL-C13_PB_CD19


title: L01_CE11_131_HFO_1

description:
L01_CE11
Hepatocyte_normcounts.csv


title: L01_CE10_177_VHGO_1

description:
L01_CE10
Hepatocyte_normcounts.csv


title: heat_16h_35C_B


title: heat_24h_35C_A


title: heat_16h_35C_C


title: heat_8h_35C_C


title: L01_CE09_012_CGO_1

description:
L01_CE09
Hepatocyte_normcounts.csv

value: CGO


title: heat_16h_35C_A


title: L01_CE08_066_OLBO_1

description:
L01_CE08
Hepatocyte_normcounts.csv

value: BO


title: CLL-C04_PB_CD19

value: peripheral blood


title: heat_8h_35C_A


title: CLL-C06_PB_CD19


title: heat_4h_35C_C


title: L01_CE07_007_HFO_1

description:
L01_CE07
Hepatocyte_normcounts.csv


title: heat_4h_35C_B


title: heat_4h_35C_A


title: heat_2h_35C_C


title: CLL-C02_PB_CD19


title: heat_2h_35C_B


title: L01_CE06_MethodBlank_0

description:
L01_CE06
Hepatocyte_normcounts.csv


title: heat_2h_35C_A


title: L01_CE05_173_OGO_1

description:
L01_CE05
Hepatocyte_normcounts.csv

value: OGO


title: T4

city: Changchun

first: Daoyu

address: Xinzhu street 1977

country: China

institute: Jilin University

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm8 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample ...

source_name: Breast cancer cells

growth_protocol: The breast cancer cells MDA-MB-231 were cultured in RPMI 1640 (Gibco, USA) supplemented with 10% fetal bovine serum (BI, Israel), 1% MEM Non-Essential Amino Acids (Gibco, USA), 1% GluMAX and 1% Penicillin-Streptomycin Solution (Gibco, USA).

extract_protocol:
Total RNA was extracted from MDA-MB-231 breast cancer cells using TRIzol reagent (invitrogen) according to the instruction. The RNA was reverse transcribed to cDNA with TransScript All-in-One First-Strand cDNA Synthesis SuperMix for qPCR (TRAN, Beijing, China).
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: 2.5μM 6-TG treated MDA-MB-231 cells for 48h

tag: cell type

value: MDA-MB-231 breast cancer cell line

tag: drug treatment

value: Thioguanine(Selleck, US)


title: CLL-C07_PB_CD19

value: yes


title: T3


title: L01_CE04_097_HFO_1

description:
L01_CE04
Hepatocyte_normcounts.csv


title: heat_1h_35C_C


title: heat_1h_35C_A


title: heat_1h_35C_B


title: T2


title: L01_CE03_113_OLBO_1

description:
L01_CE03
Hepatocyte_normcounts.csv


title: heat_0.5h_35C_C


title: heat_8h_35C_B


title: heat_0.5h_35C_B


title: T1


title: L01_CE02_192_BITUMENS_1

description:
L01_CE02
Hepatocyte_normcounts.csv

value: BIT


title: L01_CE01_111_petrolatum_1

description:
L01_CE01
Hepatocyte_normcounts.csv

value: iCell Hepatocytes


title: heat_0.5h_35C_A


title: reach_high_temp_35C_C

value: reach high temperature (0h)


title: L01_CD12_034_HFO_1

description:
L01_CD12
Hepatocyte_normcounts.csv


title: N4


title: reach_high_temp_35C_B


title: preheat_35C_B

value: control

value: pre-heat


title: N2


title: reach_high_temp_35C_A


title: N3


title: preheat_35C_C


title: L01_CD11_189_BITUMEN_1

description:
L01_CD11
Hepatocyte_normcounts.csv


title: In labor myometrium circRNA rep12

city: Guangzhou

first: Kaiyuan

last: Ji

address: No.9 Jinsui Road, Guangzhou, China

department: Guangzhou Women and Children’s Medical Center

institute: Guangzhou Medical University

data_processing:
fastq files were trimmed with SOAPnuke v1.5.2.
CIRI v2.0.5 and find_circ v1.2 were used to predict the circRNA. The reads were calulated from the average value of CIRI and find_circ sorfware.
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample.

source_name: Myometrium

extract_protocol:
Total RNA was treated with DNase I and Ribo-off rRNA Depletion Kit (Vazyme, Inc.) to degrade DNA and ribosomal RNA respectively.
Linear RNA was removed using RNase R (Epicentre, lnc). Purification was performed using Agencourt RNAClean XP magnetic beads. All other steps were performed according to the manufacturer's protocols. The library was quality and quantitated in two methods: check the distribution of the fragments size using the Agilent 2100 bioanalyzer, and quantify the library using BMG (OMEGA). Finally, the Qualified libraries were sequenced pair end on the BGISEQ-500.

tag: ga at delivery   (weeks+days)

tag: labor durations  (hours)

tag: cervical dilatation（cm）

tag: maternal age (years)

tag: fetal weight（g）


title: L01_CD10_031_HFO_1

description:
L01_CD10
Hepatocyte_normcounts.csv


title: L01_CD09_176_VHGO_1

description:
L01_CD09
Hepatocyte_normcounts.csv

value: VHGO


title: In labor myometrium circRNA rep11


title: In labor myometrium circRNA rep13


title: In labor myometrium circRNA rep14


title: In labor myometrium circRNA rep15


title: 5222

city: Maastricht

first: Julian

last: Krauskopf

address: Universiteitssingel 50

country: Netherlands

institute: Maastricht University

description:
serum circulating miRNAs
Sample_T48.fastq

data_processing:
data processing miRge pipeline v1
mapptin to miRBase release 21
Supplementary_files_format_and_content: contains mapped read counts, not normalized

source_name: serum

extract_protocol:
200 ul serum using Qiagen miRNeasy plasma/serum kit
Illumina Truseq small RNA prep kit

tag: gender

value: female

tag: subject id

tag: physical activity

value: resting

tag: exposure condition

value: low air pollution


title: 6213

description:
serum circulating miRNAs
Sample_T47.fastq

tag: age

value: cycling

value: high air pollution


title: In labor myometrium circRNA rep10


title: In labor myometrium circRNA rep9


title: In labor myometrium circRNA rep8


title: 5512

description:
serum circulating miRNAs
Sample_T46.fastq


title: L01_CD07_024_HFO_1

description:
L01_CD07
Hepatocyte_normcounts.csv

tag: tissue/celltype

value: HFO


title: L01_CD06_MethodBlank_0

description:
L01_CD06
Hepatocyte_normcounts.csv

tag: treatment


title: 6313

description:
serum circulating miRNAs
Sample_T45.fastq

value: male


title: L01_CD05_112_OLBO_1

description:
L01_CD05
Hepatocyte_normcounts.csv

value: BO

tag: dose


title: In labor myometrium circRNA rep6


title: preheat_35C_A

tag: strain


title: In labor myometrium circRNA rep4


title: L01_CD04_137_OLBO_1

description:
L01_CD04
Hepatocyte_normcounts.csv


title: In labor myometrium circRNA rep3


title: N1

value: MDA-MB-231 breast cancer cell line


title: In labor myometrium circRNA rep2


title: L01_CD03_174_OGO_1

description:
L01_CD03
Hepatocyte_normcounts.csv

value: OGO


title: In labor myometrium circRNA rep1


title: L01_CD02_020_HFO_1

description:
L01_CD02
Hepatocyte_normcounts.csv


title: 6414

description:
serum circulating miRNAs
Sample_T42.fastq


title: 5022

description:
serum circulating miRNAs
Sample_T41.fastq


title: Non-labor myometrium circRNA rep1


title: 4411

description:
serum circulating miRNAs
Sample_T40.fastq


title: miRNA In labor myometrium rep14

data_processing:
Expression level of RNAs was calculated using the Reads of exon model per Million mapped reads (RPM) method, RNAs with extremely low abundance (average RPM<1 in 17 samples) was excluded.
The correlation between RNAs expression level and labor duration or blood loss was calculated using the “cor.test” function of Pearson correlation, with corrected p-value < 0.01 as the threshold for statistical significance.
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text files include RPM values for each Sample.

extract_protocol:
Myometrium were removed, flash frozen on dry ice, and RNA was harvested using Trizol reagent.
Total RNA was separated by polyacrylamide gel electrophoresis (PAGE) and small RNA regions corresponding to the 18–30 nt bands in the marker lane (14-30 ssRNA Ladder Marker, TAKARA) were excised and recovered. Then the small RNAs were ligated to adenylated 3’ adapters annealed to unique molecular identifiers (UMI), followed by the ligation of 5’ adapters. The adapter-ligated small RNAs were transcribed into cDNA, and subsequently enriched by PCR. The target fragments 110~130 bp were selected by agarose gel electrophoresis, and purified by QIAquick Gel Extraction Kit (QIAGEN, V alencia, CA). The library was quality and quantitated in two methods: check the distribution of the fragments size using the Agilent 2100 bioanalyzer, and quantify the library using real-time quantitative PCR (qPCR) (TaqMan Probe). The final ligation PCR products were sequenced using the BGISEQ-500 platform (BGI-Shenzhen, China).


title: miRNA In labor myometrium rep15


title: miRNA In labor myometrium rep12


title: 5814

description:
serum circulating miRNAs
Sample_T44.fastq


title: In labor myometrium circRNA rep7


title: miRNA In labor myometrium rep11


title: miRNA In labor myometrium rep13


title: L01_CD01_003_CGO_1

description:
L01_CD01
Hepatocyte_normcounts.csv

value: CGO


title: 6814

description:
serum circulating miRNAs
Sample_T39.fastq


title: L01_CC10_188_SRGO_10

description:
L01_CC10
Hepatocyte_normcounts.csv

value: SRGO


title: miRNA In labor myometrium rep10


title: 4921

description:
serum circulating miRNAs
Sample_T43.fastq


title: 6821

description:
serum circulating miRNAs
Sample_T38.fastq


title: L01_CC08_175_VHGO_10

description:
L01_CC08
Hepatocyte_normcounts.csv

value: iCell Hepatocytes


title: In labor myometrium circRNA rep5


title: miRNA In labor myometrium rep9


title: miRNA In labor myometrium rep6


title: miRNA In labor myometrium rep8


title: miRNA In labor myometrium rep7


title: 6013

description:
serum circulating miRNAs
Sample_T37.fastq


title: L01_CC05_134_HFO_10

description:
L01_CC05
Hepatocyte_normcounts.csv


title: Non-labor myometrium circRNA rep2


title: 6612

description:
serum circulating miRNAs
Sample_T36.fastq


title: L01_CC06_MethodBlank_0

description:
L01_CC06
Hepatocyte_normcounts.csv


title: L01_CC03_120_gasoline_10

description:
L01_CC03
Hepatocyte_normcounts.csv

value: NAPTHA


title: miRNA In labor myometrium rep5


title: miRNA In labor myometrium rep4


title: 5523

description:
serum circulating miRNAs
Sample_T35.fastq


title: miRNA In labor myometrium rep3


title: miRNA In labor myometrium rep2


title: L01_CC01_092_OLBO_10

description:
L01_CC01
Hepatocyte_normcounts.csv


title: L01_CB11_186_RAE_1

description:
L01_CB11
Hepatocyte_normcounts.csv

value: RAE


title: 5821

description:
serum circulating miRNAs
Sample_T34.fastq


title: L01_CB10_171_SRGO_1

description:
L01_CB10
Hepatocyte_normcounts.csv


title: 5324

description:
serum circulating miRNAs
Sample_T32.fastq


title: miRNA Non-labor myometrium rep2


title: miRNA Non-labor myometrium rep1


title: 5213

description:
serum circulating miRNAs
Sample_T33.fastq


title: ICC-3

city: Shanghai

first: Qian

last: Cai

address: No.130 Dongan road

department: Immunology

institute: Fudan University

data_processing:
Illumina Casava1.7 software used for basecalling.
Raw reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence using SOAPnuke, then mapped to reference whole genome using bowtie v2.2.5 with parameters -q --phred64 --sensitive --dpad 0 --gbar 99999999 --mp 1,1 --np 1 --score-min L,0,-0.1 -p 16 -k 200.
Mapped reads were count using RSEM v1.2.12, and Fragments Per Kilobase of exon per Megabase of library size (FPKM) were calculated.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample ...

source_name: ICC Tumor cell

growth_protocol: To collect CM for stimulation, 5X105 CAFs or FAPkdCAFs within two passages or blood 2X105 CD33+MDSCs were cultured in serum-free DMEM-F12 and RPMI-1640 with 1%FBS, respectively, for 24 hrs. All CM were filtered and used for further study.

extract_protocol:
RNA was extracted from cells by TRIzol
RNA libraries were prepared for sequencing using standard BGI protocols

treatment_protocol: For human CD33+MDSCs isolation, single-cell suspensions of ICC tumor and blood of ICC patients were separated by gradient centrifugation using a 70%/35% Percoll gradient (GE Healthcare) and further purified by magnetic-activated cell sorting (MACS) using CD33 microbeads (#130-045-501, Miltenyi Biotech). For isolation of ICC CAFs and tumor cells, single-cell suspensions of ICC tumor were incubated with anti-human Fibroblast Microbeads (#130050601, Miltenyi Biotec) or anti-human EpCAM Microbeads (#130061101, Miltenyi Biotec), respectively, followed by magnetic beads separation. All CAFs used for in vitro experiments were cultured in advanced DMEM/F12 (#12634028, Gibco) with 1% FBS within two passages.FAP siRNA was transfected into CAFs using lipofectamine iMAX.

value: no treatment


title: ICC-2


title: L01_CB08_146_gasoline_1

description:
L01_CB08
Hepatocyte_normcounts.csv


title: L01_CB07_168_SRGO_1

description:
L01_CB07
Hepatocyte_normcounts.csv


title: 4222

description:
serum circulating miRNAs
Sample_T31.fastq


title: FAPkdCAF2

source_name: CAFs

value: FAP siRNA transfected


title: FAPkdCAF1


title: FAPkdCAF3


title: CAF-3


title: L01_CB06_MethodBlank_0

description:
L01_CB06
Hepatocyte_normcounts.csv


title: 6621

description:
serum circulating miRNAs
Sample_T29.fastq


title: CAF-2


title: L01_CB05_061_P_Hwax_1

description:
L01_CB05
Hepatocyte_normcounts.csv

value: WAX


title: CAF-1


title: miRNA In labor myometrium rep1


title: 5924

description:
serum circulating miRNAs
Sample_T28.fastq


title: T-MDSC-3

source_name: tumor-infiltrated MDSCs


title: L01_CB04_117_OLBO_1

description:
L01_CB04
Hepatocyte_normcounts.csv


title: T-MDSC-1


title: 6324

description:
serum circulating miRNAs
Sample_T27.fastq


title: MDSC-3

source_name: blood MDSCs


title: L01_CB03_147_OLBO_1

description:
L01_CB03
Hepatocyte_normcounts.csv


title: 6924

description:
serum circulating miRNAs
Sample_T26.fastq

value: resting


title: MDSC-1


title: L01_CB02_011_kerosine_1

description:
L01_CB02
Hepatocyte_normcounts.csv

value: KER


title: 5911

description:
serum circulating miRNAs
Sample_T25.fastq

value: female

value: cycling


title: FAP-MDSC1

value: FAP knockdown CAF conditional medium


title: L01_CA11_028_HFO_1

description:
L01_CA11
Hepatocyte_normcounts.csv

value: HFO


title: CAF-MDSC2

value: CAF conditional medium


title: 6022

description:
serum circulating miRNAs
Sample_T24.fastq

value: male

value: high air pollution


title: L01_CA10_085D_OLBO_1

description:
L01_CA10
Hepatocyte_normcounts.csv

value: BO


title: CAF-MDSC1


title: FAP-MDSC2


title: 5713

description:
serum circulating miRNAs
Sample_T23.fastq


title: L01_CA08_025_HFO_1

description:
L01_CA08
Hepatocyte_normcounts.csv


title: 5614

description:
serum circulating miRNAs
Sample_T22.fastq

value: low air pollution


title: 6422

description:
serum circulating miRNAs
Sample_T30.fastq


title: T-MDSC-2


title: F3_organoid_panel_neuropathology

type: RNA

city: Campinas

first: Simoni

last: Avansini

state: Sao Paulo

address: Tessalia Vieira Camargo Street,126

department: Translacional Medicine

country: Brazil

institute: University of Campinas

description: NanoString Human Neuropathology Panel

data_processing: The nSolver software (v4.0) by NanoString was used to normalize gene expression data

label: Nanostring

source_name: cortical organoids

growth_protocol: We cultived iPSCs in StemFlex media. Cortical organoids are generated according: https://doi.org/10.1016/j.stem.2019.08.002

extract_protocol: For RNA samples, we used RNeasy Micro Kit (Qiagen)

treatment_protocol: Not aplicable

tag: sample type

value: Patient


title: 4813

description:
serum circulating miRNAs
Sample_T21.fastq


title: MDSC-2


title: L01_CA06_MethodBlank_0

description:
L01_CA06
Hepatocyte_normcounts.csv

value: iCell Hepatocytes


title: F2_organoid_panel_neuropathology

description: NanoString Human Neuropathology Panel


title: L01_CA07_018_HFO_1

description:
L01_CA07
Hepatocyte_normcounts.csv


title: F4_organoid_panel_neuropathology

description: NanoString Human Neuropathology Panel


title: F1_organoid_panel_neuropathology

description: NanoString Human Neuropathology Panel


title: 5413

description:
serum circulating miRNAs
Sample_T20.fastq


title: 96hpi - infected - replicate 3

city: Muenster

first: Hans

middle: R

last: Schöller

state: NRW

address: Roentgenstrasse 20

department: Cell and Developmental Biology

country: Germany

institute: Max Planck Institute for Molecular Biomedicine

data_processing:
Samples were demultiplexed usign the Illumina software bcl2fastq v2.20.0
Alignment to a customized reference concatenation of human and SARS-CoV-2 genomes was done using STAR v2.7.7a
A table of read counts per gene was obtained  with STAR v2.7.7a and further processing was done in the statistical software environment R v4.0.3
Genome_build: GRCh38.p13 + NC_045512.2
Supplementary_files_format_and_content: Comma Separated Values (csv) matrix file of raw counts per gene for each sample

organism:
Homo sapiens
Severe acute respiratory syndrome coronavirus 2

source_name: retinal organoid

growth_protocol: Retinal organoid generation (based on Capowski et al. 2019)

extract_protocol:
TRIzol® reagent according manufacturer´s recommended protocol
NEBNext® Ultra TM II RNA Library Prep kit for Illumina®

treatment_protocol: Triplicates infected with SARS-CoV-2 and incubated for 24 and 96 hours

tag: tissue type

value: Retinal organoids derived from Gibco episomal iPSC line A18945

value: Infected with SARS-CoV-2

tag: incubation period

tag: day of organoid differentiation


title: L01_CA05_138_OLBO_1

description:
L01_CA05
Hepatocyte_normcounts.csv


title: 96hpi - infected - replicate 2


title: 121_organoid_panel_neuropathology

description: NanoString Human Neuropathology Panel

value: Control


title: 5013

description:
serum circulating miRNAs
Sample_T18.fastq


title: 4C_organoid_panel_neuropathology

description: NanoString Human Neuropathology Panel


title: 24hpi - infected - replicate 3


title: 96hpi - infected - replicate 1


title: L01_CA03_062_P_Hwax_1

description:
L01_CA03
Hepatocyte_normcounts.csv

value: WAX


title: 4313

description:
serum circulating miRNAs
Sample_T17.fastq


title: 24hpi - infected - replicate 2


title: L01_CA04_086_kerosine_1

description:
L01_CA04
Hepatocyte_normcounts.csv


title: WT83_organoid_panel_neuropathology

description: NanoString Human Neuropathology Panel


title: 24hpi - infected - replicate 1


title: L01_CA02_160_FO_1

description:
L01_CA02
Hepatocyte_normcounts.csv

value: FO


title: 4821

description:
serum circulating miRNAs
Sample_T16.fastq


title: L01_CA01_046_gasoline_1

description:
L01_CA01
Hepatocyte_normcounts.csv

value: NAPTHA


title: 4914

description:
serum circulating miRNAs
Sample_T15.fastq

value: female


title: 969_organoid_panel_neuropathology

description: NanoString Human Neuropathology Panel


title: 6114

description:
serum circulating miRNAs
Sample_T19.fastq

value: cycling


title: L01_BH06_MethodBlank_0

description:
L01_BH06
Hepatocyte_normcounts.csv


title: L01_BG11_058_HFO_1

description:
L01_BG11
Hepatocyte_normcounts.csv


title: KO_MeRIP_input

city: Hangzhou

first: Jia

last: Xiong

address: 866 Yuhangtang Road

institute: Zhejiang University

description: Macrophage colony-stimulating factor (M-CSF) treated the bone marrow cells for 7 days followed by co-culturing with MC38 cells

data_processing:
fastp software (https://github.com/OpenGene/fastp) were used to remove the reads that contained adaptor contamination, low quality bases and undetermined bases with default parameter. Then sequence quality of IP and Input samples were also verified using fastp. We used HISAT2 (http://daehwankimlab.github.io/hisat2) to map reads to the reference genomeMus musculus (Version: v101).
Mapped reads of IP and input libraries were provided for R package exomePeak (https://bioconductor.org/packages/exomePeak), which identifies m6A peaks with bed or bigwig format that can be adapted for visualization on the IGV software (http://www.igv.org).
MEME (http://meme-suite.org) and HOMER (http://homer.ucsd.edu/homer/motif) were used for de novo and known motif finding followed by localization of the motif with respect to peak summit. Called peaks were annotated by intersection with gene architecture using R package ChIPseeker (https://bioconductor.org/packages/ChIPseeker).
Then StringTie (https://ccb.jhu.edu/software/stringtie) was used to perform expression level for all mRNAs from input libraries by calculating FPKM (total exon fragments /mapped reads (millions) × exon length (kB)). The differentially expressed mRNAs were selected with log2 (fold change) >1 or log2 (fold change) <-1 and p value < 0.05 by R package edgeR (https://bioconductor.org/packages/edgeR).
Genome_build: mm10
Supplementary_files_format_and_content: Indentification and comparison of different m6A peak between indicated groups:  WT_MeRIP_IPVSWT_MeRIP_input_peak.txt; KO_MeRIP_IPVSKO_MeRIP_input_peak.txt; KO_MeRIPVSWT_MeRIP_diffPeak_result.txt; KO_MeRIPVSWT_MeRIP_diffPeak_Gene_differential_expression.txt

organism: Mus musculus

source_name: bone-marrow-derived macrophages

growth_protocol: M-CSF-inudced BMDM in vitro

extract_protocol:
Total RNA was isolated and purified using TRIzol reagent (Invitrogen, Carlsbad, CA, USA) following the manufacturer's procedure. The RNA amount and purity of each sample was quantified using NanoDrop ND-1000 (NanoDrop, Wilmington, DE, USA). The RNA integrity was assessed by Bioanalyzer 2100 (Agilent, CA, USA) with RIN number >7.0, and confirmed by electrophoresis with denaturing agarose gel. Poly (A) RNA is purified from 50μg total RNA using Dynabeads Oligo (dT)25-61005 (Thermo Fisher, CA, USA) using two rounds of purification. Then the poly(A) RNA was fragmented into small pieces using Magnesium RNA Fragmentation Module (NEB, cat.e6150, USA) under 86℃ 7min. Then the cleaved RNA fragments were incubated for 2h at 4℃ with m6A-specific antibody (No. 202003, Synaptic Systems, Germany) in IP buffer (50 mM Tris-HCl, 750 mM NaCl and 0.5% Igepal CA-630).
Then the IP RNA was reverse-transcribed to create the cDNA by SuperScript™ II Reverse Transcriptase (Invitrogen, cat. 1896649, USA), which were next used to synthesise U-labeled second-stranded DNAs with E. coli DNA polymerase I (NEB, cat.m0209, USA), RNase H (NEB, cat.m0297, USA) and dUTP Solution (Thermo Fisher, cat.R0133, USA）. An A-base is then added to the blunt ends of each strand, preparing them for ligation to the indexed adapters. Each adapter contains a T-base overhang for ligating the adapter to the A-tailed fragmented DNA. Single- or dual-index adapters are ligated to the fragments, and size selection was performed with AMPureXP beads. After the heat-labile UDG enzyme (NEB, cat.m0280, USA) treatment of the U-labeled second-stranded DNAs, the ligated products are amplified with PCR by the following conditions: initial denaturation at 95℃ for 3 min; 8 cycles of denaturation at 98℃ for 15 sec, annealing at 60℃ for 15 sec, and extension at 72℃ for 30 sec; and then final extension at 72℃ for 5 min. The average insert size for the final cDNA library was 300±50 bp.At last, we performed the 2×150bp paired-end sequencing (PE150) on an illumina Novaseq™ 6000 (LC-Bio Technology CO., Ltd., Hangzhou, China) following the vendor's recommended protocol.

treatment_protocol: MC38 cell co-culture for 24 h

tag: cell type

value: bone-marrow-derived macrophages

tag: genotype/variation

value: LysM-cre, Mettl3fl/fl

tag: antibody


title: 4424

description:
serum circulating miRNAs
Sample_T13.fastq


title: WT_MeRIP_IP


title: WT_MeRIP_input


title: KO_MeRIP_IP


title: L01_BG10_123_kerosine_1

description:
L01_BG10
Hepatocyte_normcounts.csv

value: KER


title: D5

city: boston

first: jing

last: liu

state: Massachusetts

address: 330 brookline ave

institute: BIDMC

description: Hi-Myc x KO_rep5

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 mm8 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: mm8
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample。

source_name: prostate tumor

extract_protocol:
Total RNA was extracted from prostate tissue or tumor of Otud6a+/y, or Otud6a-/y, or Hi-Myc; Otud6a+/y or Hi-Myc mice. NEBNext® Ultra™ Directional RNA Library Prep Kit was used with 1ug of total RNA for the construction of library
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: genotype

value: Hi-Myc; Otud6a-/y

tag: disease state

value: tumor

value: C57BL/6N x BALB/C


title: 6523

description:
serum circulating miRNAs
Sample_T12.fastq

tag: gender

tag: subject id

value: resting

value: high air pollution


title: L01_BG09_170_SRGO_1

description:
L01_BG09
Hepatocyte_normcounts.csv

value: iCell Hepatocytes

value: SRGO


title: D2

description: Hi-Myc x KO_rep5


title: D1

description: Hi-Myc x KO_rep5


title: D3

description: Hi-Myc x KO_rep5


title: C4

description: Hi-Myc x WT_rep4

value: Hi-Myc; Otud6a+/y


title: L01_BG08_102_CGO_1

description:
L01_BG08
Hepatocyte_normcounts.csv

value: CGO


title: 4721

description:
serum circulating miRNAs
Sample_T10.fastq

value: male

tag: physical activity

tag: exposure condition


title: C1

description: Hi-Myc x WT_rep1


title: L01_BG06_MethodBlank_0

description:
L01_BG06
Hepatocyte_normcounts.csv

tag: tissue/celltype


title: 4213

description:
serum circulating miRNAs
Sample_T9.fastq

tag: age

value: low air pollution


title: B4

source_name: prostate tissue

value: normal


title: D4

description: Hi-Myc x KO_rep5


title: 4322

description:
serum circulating miRNAs
Sample_T14.fastq

value: female


title: B3


title: B2


title: L01_BG04_106_CGO_1

description:
L01_BG04
Hepatocyte_normcounts.csv

tag: treatment

tag: dose


title: 4713

description:
serum circulating miRNAs
Sample_T8.fastq


title: B1

tag: strain


title: C5

description: Hi-Myc x WT_rep5


title: L01_BG03_153_OLBO_1

description:
L01_BG03
Hepatocyte_normcounts.csv

value: BO


title: A5


title: A4


title: 6511

description:
serum circulating miRNAs
Sample_T7.fastq


title: L01_BG02_202_Paraffinwax_1

description:
L01_BG02
Hepatocyte_normcounts.csv

value: WAX


title: A3


title: L01_BG01_121_CGO_1

description:
L01_BG01
Hepatocyte_normcounts.csv


title: A1


title: 5621

description:
serum circulating miRNAs
Sample_T5.fastq

value: cycling


title: 6121

description:
serum circulating miRNAs
Sample_T6.fastq


title: B5


title: 5724

description:
serum circulating miRNAs
Sample_T11.fastq


title: L01_BF10_070_CGO_1

description:
L01_BF10
Hepatocyte_normcounts.csv


title: B6_Lmajor_Gp63_KO-3

city: MONTREAL

first: David

last: Langlais

state: QC

address: 740 Ave Dr Penfield, rm 4203, McGill Genome Centre

department: Human Genetics

country: Canada

institute: McGill University

data_processing:
The quality of sequence reads was assessed with the FastQC tool (Babraham Bioinformatics)
The reads were trimmed using the paired end mode with the default settings in Trimmomatic (Bolger et al., 2014)
Reads were mapped to the mouse UCSC mm9 reference assembly using hisat2 v2.2.0 (Kim et al., 2015)
The number of reads mapping onto gene exons was quantified by counting the number of strand-specific reads using featureCounts (Liao et al., 2014).
TMM normalization and differential expression analysis was conducted using the edgeR Bioconductor package (Robinson and Oshlack, 2010). We retained genes that had an expression level of a minimum of five counts per million reads in at least 3 of the 12 samples, and pairwise differential gene expression analysis was performed by comparing L. major infected samples versus uninfected samples. Genes with changes in expression ≥|2| and adjusted p-values (<10-3) were considered significant.
For RNA-seq data visualization in IGV, bigwig files scaled per million reads mapped to exons were generated using genomeCoverageBed and wigToBigWig tools.
Genome_build: mm9
Supplementary_files_format_and_content: Tab-delimited text with raw gene counts for every gene in each sample as generated by featureCounts (gene annotation: UCSC mm9)

source_name: perioneal lavage

growth_protocol: The wild type Leishmania parasite used was NIH S (MHOM/SN/74/Seidman) clone A2. GP63 knockout (GP63KO) and GP63 rescue (GP63R) L. major were generously supplied by Dr. Robert McMaster (University of British Columbia, Canada). All parasites were cultured at 25 ºC, 5% CO2 in Schneider’s Drosophila Medium (SDM) supplemented with 10% heat-inactivated fetal bovine serum (FBS, Wisent, St.Bruno, QC, Canada), and 5mg/ml HEMIN and passaged every 3 to 4 days. Cultures of promastigotes growing at logarithmic phase (day 3-4 post passage) were passaged bi-weekly, and were grown to stationary phase (day 6-8 post passage) before used in infections for all experiments (12).

extract_protocol:
Total RNA was extracted from the aqueous phase from the Trizol lysates using EasyPure RNA columns as per the manufacturer’s protocol. RNA integrity was assessed using a Bioanalyzer RNA Pico kit (Agilent).
Ribosomal RNAs were depleted and libraries were prepared with the Kapa Hyperprep stranded total RNA kit (Roche). The indexed libraries were pooled and the pool was sequences on 2 lanes of Illumina NovaSeq 6000 in a paired-end 50bp configuration.

treatment_protocol: Groups of 3 C57BL/6 mice were infected with 10^8 wildtype Leishmania major parasites, L. major GP63 knockout and L. major GP63 rescue, injected into the intraperitoneal cavity, or PBS alone. Six hours post infection, the mice were sacrificed and 5ml of ice-cold endotoxin-free PBS was used to obtain lavages of the cavities. Total lavage was centrifuged at 1500 rpm for 10 mins to separate cells and supernatant. The cell pellet was resuspended in TRIzol reagent (Ambion life technologies) and frozen.

tag: Sex

value: L.major Gp63 KO

value: peritoneal lavage cells


title: B6_Lmajor_Gp63_rescue-1

value: L.major Gp63 rescued


title: 5422

description:
serum circulating miRNAs
Sample_T3.fastq


title: B6_Lmajor_Gp63_rescue-2


title: L01_BF08_148_OLBO_1

description:
L01_BF08
Hepatocyte_normcounts.csv


title: B6_Lmajor_Gp63_KO-1


title: 6912

description:
serum circulating miRNAs
Sample_T2.fastq


title: L01_BF07_114_OLBO_1

description:
L01_BF07
Hepatocyte_normcounts.csv


title: B6_Lmajor_WT-3

value: L.major WT


title: C2

description: Hi-Myc x WT_rep2

value: tumor

value: C57BL/6N x BALB/C


title: A2


title: 5313

description:
serum circulating miRNAs
Sample_T1.fastq


title: B6_Lmajor_WT-2


title: B6_Lmajor_WT-1


title: B6_Lmajor_Gp63_rescue-3


title: B6_Lmajor_Gp63_KO-2


title: B6_PBS-2

value: vehicle


title: L01_BF05_196_petrolatum_1

description:
L01_BF05
Hepatocyte_normcounts.csv

value: iCell Hepatocytes


title: L01_BF06_MethodBlank_0

description:
L01_BF06
Hepatocyte_normcounts.csv


title: B6_PBS-3


title: B6_PBS-1


title: L01_BF04_197_HFO_1

description:
L01_BF04
Hepatocyte_normcounts.csv

value: HFO


title: 6221

description:
serum circulating miRNAs
Sample_T4.fastq

value: high air pollution


title: L01_BF09_096B_UDAE_1

description:
L01_BF09
Hepatocyte_normcounts.csv

value: UDAE


title: 6832

description:
serum circulating miRNAs
Sample_46.fastq

value: male

value: resting

value: low air pollution


title: L01_BF03_178_VHGO_1

description:
L01_BF03
Hepatocyte_normcounts.csv

value: VHGO


title: 6643

description:
serum circulating miRNAs
Sample_47.fastq

value: female


title: 5434

description:
serum circulating miRNAs
Sample_45.fastq

value: cycling


title: L01_BF02_132_gasoline_1

description:
L01_BF02
Hepatocyte_normcounts.csv

value: NAPTHA


title: Lung endothelial cells - C70_R1R2_Adult_48h_ctrl_Lung

city: Helsinki

first: Sinem

last: Karaman

address: Haartmaninkatu 8

department: Individualized Drug Therapy Research Program / Faculty of Medicine

country: Finland

institute: University of Helsinki

description:
C70_R1R2_Adult_48h_ctrl+del_Lung_barcodes.tsv
C70_R1R2_Adult_48h_ctrl+del_Lung_genes.tsv
C70_R1R2_Adult_48h_ctrl+del_Lung_matrix.mtx

data_processing:
Data processing and analysis were performed using 10x Genomics Cell Ranger v2.1.1 pipelines
The “cellranger mkfastq” was used to produce FASTQ (raw data) files and “cellranger count” to perform alignment, filtering and UMI counting.
mkfastq was run using the Illumina bcl2fastq v2.2.0 and alignment was done against mouse genome mm10
Cellranger aggr pipeline was used to combine data from multiple samples into an experiment-wide gene-barcode matrix and analysis.
Analyses shown in manuscript were performed with Seurat V4.0 (Hao et al., 2021) and scVelo V (Bergen et al., 2020)
Genome_build: mm10
Supplementary_files_format_and_content: Aggregated matrix files (*matrix.mtx) containing cell counts and tab separated metadata files (*_genes.tsv and *_barcodes.tsv)

source_name: Lung

extract_protocol:
Single-cell suspensions were prepared from lung and heart tissues using a combination of Collagenases, Dispase II and DNAse. Endothelial cells were sorted with flow cytometry using BD Influx. 4% BSA in PBS was added to the cell suspension to a final concentration of 0.04% and the cell viability and concentration was measured.  Cells were kept on ice until continuation of the 10X Genomics Single Cell Protocol.
The Chromium Single Cell 3’RNAseq run and library preparation were done using the Chromium™ Single Cell 3' Reagent version 2 chemistry

treatment_protocol: Single or compound VEGFR deletion were induced in female mice (8-10 weeks of age) with 2 daily doses of Tamoxifen (2 mg per day, in 100 µL corn oil) via oral gavage using a feeding needle. Tissues were harvested at 48 hours from first tamoxifen administration.

tag: tissue

value: lung

value: endothelial cells

tag: developmental stage

value: adult

tag: timepoint


title: Lung endothelial cells - C59_R1R2R3_Adult_48h_ctrl_Lung

description:
C59_R1R2R3_Adult_48h_ctrl+del_Lung_barcodes.tsv
C59_R1R2R3_Adult_48h_ctrl+del_Lung_genes.tsv
C59_R1R2R3_Adult_48h_ctrl+del_Lung_matrix.mtx

tag: cell type


title: L01_BF01_075_OLBO_1

description:
L01_BF01
Hepatocyte_normcounts.csv

value: BO


title: Lung endothelial cells - C120_R2R3_Adult_48h_ctrl_Lung

description:
C120_R2R3_Adult_48h_ctrl+del_Lung_barcodes.tsv
C120_R2R3_Adult_48h_ctrl+del_Lung_genes.tsv
C120_R2R3_Adult_48h_ctrl+del_Lung_matrix.mtx


title: Lung endothelial cells - C59_R1R2R3_Adult_48h_del_Lung


title: Lung endothelial cells - C70_R1R2_Adult_48h_del_Lung


title: 5942

description:
serum circulating miRNAs
Sample_43.fastq


title: 5034

description:
serum circulating miRNAs
Sample_44.fastq


title: L01_BE11_188_SRGO_100

description:
L01_BE11
Hepatocyte_normcounts.csv

value: SRGO


title: Lung endothelial cells - C64_R3_Adult_48h_del_Lung

description:
C64_R3_Adult_48h_ctrl+del_Lung_barcodes.tsv
C64_R3_Adult_48h_ctrl+del_Lung_genes.tsv
C64_R3_Adult_48h_ctrl+del_Lung_matrix.mtx


title: L01_BE10_188_SRGO_1

description:
L01_BE10
Hepatocyte_normcounts.csv


title: Lung endothelial cells - C72_R2_Adult_48h_ctrl_Lung

description:
C72_R2_Adult_48h_ctrl+del_Lung_barcodes.tsv
C72_R2_Adult_48h_ctrl+del_Lung_genes.tsv
C72_R2_Adult_48h_ctrl+del_Lung_matrix.mtx


title: Lung endothelial cells - C64_R3_Adult_48h_ctrl_Lung


title: Lung endothelial cells - C69_R1_Adult_48h_ctrl_Lung

description:
C69_R1_Adult_48h_ctrl+del_Lung_barcodes.tsv
C69_R1_Adult_48h_ctrl+del_Lung_genes.tsv
C69_R1_Adult_48h_ctrl+del_Lung_matrix.mtx


title: 6031

description:
serum circulating miRNAs
Sample_40.fastq


title: Heart endothelial cells - C82_R1R2R3_Adult_48h_del_Heart

description:
C82_R1R2R3_Adult_48h_ctrl+del_Heart_barcodes.tsv
C82_R1R2R3_Adult_48h_ctrl+del_Heart_genes.tsv
C82_R1R2R3_Adult_48h_ctrl+del_Heart_matrix.mtx

source_name: Heart

value: heart


title: 4933

description:
serum circulating miRNAs
Sample_42.fastq


title: Lung endothelial cells - C120_R2R3_Adult_48h_del_Lung


title: 6532

description:
serum circulating miRNAs
Sample_39.fastq


title: Heart endothelial cells - C120_R2R3_Adult_48h_del_Heart

description:
C120_R2R3_Adult_48h_ctrl+del_Heart_barcodes.tsv
C120_R2R3_Adult_48h_ctrl+del_Heart_genes.tsv
C120_R2R3_Adult_48h_ctrl+del_Heart_matrix.mtx


title: L01_BE07_134_HFO_100

description:
L01_BE07
Hepatocyte_normcounts.csv

value: iCell Hepatocytes


title: Heart endothelial cells - C82_R1R2R3_Adult_48h_ctrl_Heart


title: L01_BE08_175_VHGO_1

description:
L01_BE08
Hepatocyte_normcounts.csv


title: Heart endothelial cells - C120_R2R3_Adult_48h_ctrl_Heart


title: Lung endothelial cells - C69_R1_Adult_48h_del_Lung


title: 4244

description:
serum circulating miRNAs
Sample_38.fastq


title: Heart endothelial cells - C83_R3_Adult_48h_ctrl_Heart

description:
C83_R3_Adult_48h_ctrl+del_Heart_barcodes.tsv
C83_R3_Adult_48h_ctrl+del_Heart_genes.tsv
C83_R3_Adult_48h_ctrl+del_Heart_matrix.mtx


title: 5731

description:
serum circulating miRNAs
Sample_37.fastq


title: L01_BE06_MethodBlank_0

description:
L01_BE06
Hepatocyte_normcounts.csv


title: Heart endothelial cells - C70_R1R2_Adult_48h_ctrl_Heart

description:
C70_R1R2_Adult_48h_ctrl+del_Heart_barcodes.tsv
C70_R1R2_Adult_48h_ctrl+del_Heart_genes.tsv
C70_R1R2_Adult_48h_ctrl+del_Heart_matrix.mtx


title: Heart endothelial cells - C70_R1R2_Adult_48h_del_Heart


title: 6132

description:
serum circulating miRNAs
Sample_41.fastq


title: Heart endothelial cells - C83_R3_Adult_48h_del_Heart


title: 4231

description:
serum circulating miRNAs
Sample_36.fastq


title: Heart endothelial cells - C72_R2_Adult_48h_del_Heart

description:
C72_R2_Adult_48h_ctrl+del_Heart_barcodes.tsv
C72_R2_Adult_48h_ctrl+del_Heart_genes.tsv
C72_R2_Adult_48h_ctrl+del_Heart_matrix.mtx


title: Lung endothelial cells - C72_R2_Adult_48h_del_Lung


title: L01_BE04_120_gasoline_100

description:
L01_BE04
Hepatocyte_normcounts.csv


title: 6044

description:
serum circulating miRNAs
Sample_35.fastq


title: L01_BE09_175_VHGO_100

description:
L01_BE09
Hepatocyte_normcounts.csv


title: Heart endothelial cells - C72_R2_Adult_48h_ctrl_Heart


title: Heart endothelial cells - C69_R1_Adult_48h_del_Heart

description:
C69_R1_Adult_48h_ctrl+del_Heart_barcodes.tsv
C69_R1_Adult_48h_ctrl+del_Heart_genes.tsv
C69_R1_Adult_48h_ctrl+del_Heart_matrix.mtx


title: L01_BE03_120_gasoline_1

description:
L01_BE03
Hepatocyte_normcounts.csv


title: 6941

description:
serum circulating miRNAs
Sample_34.fastq


title: L01_BE02_092_OLBO_100

description:
L01_BE02
Hepatocyte_normcounts.csv


title: L01_BD06_MethodBlank_0

description:
L01_BD06
Hepatocyte_normcounts.csv


title: Heart endothelial cells - C69_R1_Adult_48h_ctrl_Heart


title: L01_BE01_092_OLBO_1

description:
L01_BE01
Hepatocyte_normcounts.csv


title: Ad-Ctrl sh 3

city: New York

first: Liheng

last: Wang

state: NY

address: 1150 Saint Nicholas Avenue, Room 234

department: Department of Medicine

institute: Columbia University Medical Center

data_processing:
We use RTA (Illumina) for base calling and bcl2fastq2 (version 2.19) for converting BCL to fastq format, coupled with adaptor trimming.
We perform a pseudoalignment to a kallisto index created from transcriptomes (Human: GRCh38; Mouse: GRCm38) using kallisto (0.44.0).
We employed the R package limma (v3.44.3) to identify differentially expressed genes (DEG) between Ctrl sh and Tox4 sh with a |log2(Fold Change)| > 0.5 and Adjusted P-value < 0.1 (Ritchie et al., 2015).
We conducted the functional enrichment with a cutoff of FDR < 0.1 for upregulated and downregulated genes by gprofiler2 (v0.2.0), separately We conducted the functional enrichment with a cutoff of FDR < 0.1 for upregulated and downregulated genes by gprofiler2 (v0.2.0), separately (Raudvere et al., 2019).

source_name: Liver total RNA

extract_protocol:
9 days post viral injection, we fasted mice for 16-hr. Then we sac mice and liver tissues were frozen with liquid nitrogen. Liver total RNA were exacted with Trizol reagent and further purified by QIAGEN RNA mini kit.
We use poly-A pull-down to enrich mRNAs from total RNA samples,then proceed with library construction using Illumina TruSeq chemistry.
Libraries are then sequenced using Illumina NovaSeq 6000 at Columbia Genome Center. We multiplex samples in each lane, which yields targeted number of paired-end 100bp reads for each sample.

treatment_protocol: Adenovirus Ctrl- or Tox4-shRNA (2.5x10^8 particles/gram) were administered by tail vein injection to 8-10-wk-old C57BL/6J

value: Adenovirus Ctrl

value: 10-week old

tag: sac condition

value: Fast 16-hr


title: Ad-Tox4 sh 2


title: Ad-Tox4 sh 1


title: Ad-Tox4 sh 3


title: Ad-Ctrl sh 1


title: 6441

description:
serum circulating miRNAs
Sample_33.fastq

value: high air pollution


title: Ad-Ctrl sh 2


title: L01_BD04_177_VHGO_1

description:
L01_BD04
Hepatocyte_normcounts.csv

source_name: Hepatocyte


title: 6234

description:
serum circulating miRNAs
Sample_32.fastq

value: male


title: 6843

description:
serum circulating miRNAs
Sample_31.fastq

value: resting


title: 5843

description:
serum circulating miRNAs
Sample_29.fastq


title: 5642

description:
serum circulating miRNAs
Sample_30.fastq


title: L01_BD03_020_HFO_1

description:
L01_BD03
Hepatocyte_normcounts.csv

value: HFO


title: PERK_KO_M2_2

city: Columbus

first: Chan-Wang

middle: Jerry

last: Lio

state: Ohio

address: 460 W 12th Ave

institute: Ohio State University

data_processing:
Bowtie2 (v2.4.2)
Samtools (v1.10)
Deeptools (v3.5.1)
HOMER (v4.8)
DiffBind (v2.0.2)
Genome_build: mm10
Supplementary_files_format_and_content: Txt (peaks), Bigwig

source_name: Bone marrow

growth_protocol: Bone marrow cells were differentiated in the presence of recombinant mouse M-CSF (20 ng/ml) in complete medium (RPMI 1640 containing 10 mM glucose, 2 mM L-glutamine, 100 U/mL of penicillin/streptomycin and 10% FBS) for 7 days. Fresh complete medium with M-CSF was supplemented on day 6 prior to use.

extract_protocol:
Five millions of cells were fixed with 1% formaldehyde in media at 1x10^6 cells/mL for 10 min at room temperature with constant agitation. Fixation was stopped and quenched with 125 mM glycine for 5 min on ice. After one wash with PBS, cell pellets were snap-frozen with liquid nitrogen and store at -80°C until nuclei preparation. Nuclei were isolated using Lysis buffer (50 mM HEPES, 140 mM NaCl, 1 mM EDTA, 10% glycerol, 0.5% NP40, 0.25% Triton X-100) and were washed once with Wash buffer (10 mM Tris-HCl pH 8.0, 200 mM NaCl, 1 mM EDTA, 0.5 mM EGTA). The pellets were resuspended with Shearing buffer (10mM Tris-HCl pH 8.0, 1 mM EDTA, 0.1% SDS) and the chromatin were sheared using BioruptorPico (Diagenode) for 14 cycles (30s on; 30s off) at 4°C. 2.5 µg chromatin was diluted to a final of 300 µL RIPA buffer (50 mM Tris-HCl pH 8.0, 150 mM NaCl, 1 mM EDTA, 1% NP40, 0.1% SDS, 0.5% sodium deoxycholate) and incubated with 2.5 µg rabbit monoclonal anti-H3K27me3 antibody (CST, clone C36B11, lot 19) overnight at 4°C with constant rotation. For immunoprecipitation, the samples were incubated with 10µL pre-cleared Protein A Magnetic Beads (ThermoFisher) for 2h at 4°C. The beads were washed twice with RIPA buffer, once with High salt buffer (50 mM Tris-HCl pH 8.0, 500 mM NaCl, 1 mM EDTA, 1% NP40, 0.1% SDS), once with LiCl buffer (50 mM Tris-HCl pH 8.0, 250 mM LiCl, 1 mM EDTA, 1% NP40, 1% sodium deoxycholate), and finally once with TE buffer (10 mM Tris-HCl pH 8.0, 1mM EDTA). All washes were incubated for 5 mins at 4°C with constant rotation. After last wash, beads were resuspended with 200L elution buffer (100 mM NaHCO3, 1% SDS) with 0.5 mg/mL RNaseA (Qiagen), and incubated at 65°C on a thermoshaker for 20 min at 1200 rpm. For decrosslinking, proteinase K (0.5 mg/mL; Ambion) and NaCl (200 mM) were added into the eluted samples and incubated in thermocycler at 65°C overnight. The samples were purified by using Zymo PCR purification kit (Zymo).
Sequencing libraries were prepared using NEB Ultra II kits according to the standard protocol (NEB).

treatment_protocol: Day 7 bone marrow-derived macrophages were washed and either untreated or stimulated with IL-4 (20 ng/mL) or LPS (20ng/ml)+IFNg (50ng/ml) for 24 h at a density of 2 million cells per well in a 6-well plate.

value: bone marrow-derived macrophage

tag: genotype

value: Eif2ak3 fl/fl x LysMcre


title: PERK_KO_M1_2

value: LPS+IFNg


title: L01_BE05_134_HFO_1

description:
L01_BE05
Hepatocyte_normcounts.csv


title: PERK_KO_M1_1


title: L01_BD05_168_SRGO_1

description:
L01_BD05
Hepatocyte_normcounts.csv


title: PERK_WT_M2_1

value: Eif2ak3 fl/fl


title: 6332

description:
serum circulating miRNAs
Sample_28.fastq

value: cycling


title: PERK_WT_M2_2


title: PERK_WT_M1_2


title: L01_BD02_091_HFO_1

description:
L01_BD02
Hepatocyte_normcounts.csv


title: PERK_WT_M1_1


title: 5332

description:
serum circulating miRNAs
Sample_27.fastq

value: female

value: low air pollution


title: 5041

description:
serum circulating miRNAs
Sample_25.fastq


title: L01_BD01_184_VHGO_1

description:
L01_BD01
Hepatocyte_normcounts.csv

value: VHGO


title: PERK_KO_M2_1


title: PERK_WT_M0

value: unstimulated


title: 5441

description:
serum circulating miRNAs
Sample_26.fastq


title: PERK_KO_M0


title: L01_BC10_182_VHGO_1

description:
L01_BC10
Hepatocyte_normcounts.csv

value: iCell Hepatocytes


title: L01_BC11_193_OXASPH_1

description:
L01_BC11
Hepatocyte_normcounts.csv

value: BIT


title: L01_BC09_120_gasoline_1

description:
L01_BC09
Hepatocyte_normcounts.csv

value: NAPTHA


title: 4734

description:
serum circulating miRNAs
Sample_24.fastq


title: 6433

description:
serum circulating miRNAs
Sample_23.fastq


title: L01_BC08_130_CGO_1

description:
L01_BC08
Hepatocyte_normcounts.csv

value: CGO


title: KO3_Ma

data_processing:
Cutadapt software (https://cutadapt.readthedocs.io/en/stable/,version:cutadapt-1.9) was used to remove the reads that contained adaptor contamination,(command line: ~cutadapt -a ADAPT1 -A ADAPT2 -o out1.fastq -p out2.fastq in1.fastq in2.fastq -O 5 -m 100).
And After removed the low quality bases and undetermined bases ,we used HISAT2 software (https://daehwankimlab.github.io/hisat2/,version:hisat2-2.0.4) to map reads to the genome (for example:Homo sapiens Ensembl v96),(command line: ~hisat2 -1 R1.fastq.gz -2 R1.fastq.gz -S sample_mapped.sam).
The mapped reads of each sample were assembled using StringTie (http://ccb.jhu.edu/software/stringtie/,version:stringtie-1.3.4d.Linux_x86_64) with default parameters (command line: ~stringtie -p 4 -G genome.gtf -o output.gtf -l sample input.bam).
Then, all transcriptomes from all samples were merged to reconstruct a comprehensive transcriptome using gffcompare software(http://ccb.jhu.edu/software/stringtie/gffcompare.shtml,version:gffcompare-0.9.8.Linux_x86_64)
After the final transcriptome was generated, StringTie and ballgown(http://www.bioconductor.org/packages/release/bioc/html/ballgown.html) were used to estimate the expression levels of all transcripts and perform expression level for mRNAs by calculating FPKM (FPKM = [total_exon_fragments / mapped_reads(millions) × exon_length(kB)]),(command line: ~stringtie -e -B -p 4 -G merged.gtf -o samples.gtf samples.bam). The differentially expressed mRNAs were selected with fold change > 2 or fold change < 0.5 and p value < 0.05 by R package edgeR(https://bioconductor.org/packages/release/bioc/html/edgeR.html) or DESeq2(http://www.bioconductor.org/packages/release/bioc/html/DESeq2.html),and then analysis GO enrichment and KEGG enrichment to the differentially expressed mRNAs.
Genome_build: ensembl-101
Supplementary_files_format_and_content: 4_genes_fpkm_expression.txt: stringTie and ballgown(http://www.bioconductor.org/packages/release/bioc/html/ballgown.html) were used to estimate the expression levels of all transcripts and perform expression level for mRNAs by calculating FPKM (FPKM = [total_exon_fragments / mapped_reads(millions) × exon_length(kB)]),(command line: ~stringtie -e -B -p 4 -G merged.gtf -o samples.gtf samples.bam). The differentially expressed mRNAs were selected with fold change > 2 or fold change < 0.5 and p value < 0.05 by R package edgeR(https://bioconductor.org/packages/release/bioc/html/edgeR.html) or DESeq2(http://www.bioconductor.org/packages/release/bioc/html/DESeq2.html)

extract_protocol:
Total RNA was isolated and purified using TRIzol reagent (Invitrogen, Carlsbad, CA, USA) following the manufacturer's procedure. The RNA amount and purity of each sample was quantified using NanoDrop ND-1000 (NanoDrop, Wilmington, DE, USA). The RNA integrity was assessed by Bioanalyzer 2100 (Agilent, CA, USA) with RIN number >7.0, and confirmed by electrophoresis with denaturing agarose gel. Poly (A) RNA is purified from 1μg total RNA using Dynabeads Oligo (dT)25-61005 (Thermo Fisher, CA, USA) using two rounds of purification.
Then the poly(A) RNA was fragmented into small pieces using Magnesium RNA Fragmentation Module (NEB, cat.e6150, USA) under 94℃ 5-7min. Then the cleaved RNA fragments were reverse-transcribed to create the cDNA by SuperScript™ II Reverse Transcriptase (Invitrogen, cat. 1896649, USA), which were next used to synthesise U-labeled second-stranded DNAs with E. coli DNA polymerase I (NEB, cat.m0209, USA), RNase H (NEB, cat.m0297, USA) and dUTP Solution (Thermo Fisher, cat.R0133, USA）. An A-base is then added to the blunt ends of each strand, preparing them for ligation to the indexed adapters. Each adapter contains a T-base overhang for ligating the adapter to the A-tailed fragmented DNA. Single- or dual-index adapters are ligated to the fragments, and size selection was performed with AMPureXP beads. After the heat-labile UDG enzyme (NEB, cat.m0280, USA) treatment of the U-labeled second-stranded DNAs, the ligated products are amplified with PCR by the following conditions: initial denaturation at 95℃ for 3 min; 8 cycles of denaturation at 98℃ for 15 sec, annealing at 60℃ for 15 sec, and extension at 72℃ for 30 sec; and then final extension at 72℃ for 5 min.  The average insert size for the final cDNA library was 300±50 bp. At last, we performed the 2×150bp paired-end sequencing (PE150) on an Illumina Novaseq™ 6000 (LC-Bio Technology CO., Ltd., Hangzhou, China) following the vendor's recommended protocol.

treatment_protocol: BMDM were co-cultured with MC38 cell line for 24h

value: bone-marrow-derived macrophages

value: LysM-cre, Mettl3fl/fl

value: Co-cultured with MC38 for 24h


title: WT_MDSC

data_processing:
Cutadapt software (https://cutadapt.readthedocs.io/en/stable/,version:cutadapt-1.9) was used to remove the reads that contained adaptor contamination,(command line: ~cutadapt -a ADAPT1 -A ADAPT2 -o out1.fastq -p out2.fastq in1.fastq in2.fastq -O 5 -m 100).
And After removed the low quality bases and undetermined bases ,we used HISAT2 software (https://daehwankimlab.github.io/hisat2/,version:hisat2-2.0.4) to map reads to the genome (for example:Homo sapiens Ensembl v96),(command line: ~hisat2 -1 R1.fastq.gz -2 R1.fastq.gz -S sample_mapped.sam).
The mapped reads of each sample were assembled using StringTie (http://ccb.jhu.edu/software/stringtie/,version:stringtie-1.3.4d.Linux_x86_64) with default parameters (command line: ~stringtie -p 4 -G genome.gtf -o output.gtf -l sample input.bam).
Then, all transcriptomes from all samples were merged to reconstruct a comprehensive transcriptome using gffcompare software(http://ccb.jhu.edu/software/stringtie/gffcompare.shtml,version:gffcompare-0.9.8.Linux_x86_64)
After the final transcriptome was generated, StringTie and ballgown(http://www.bioconductor.org/packages/release/bioc/html/ballgown.html) were used to estimate the expression levels of all transcripts and perform expression level for mRNAs by calculating FPKM (FPKM = [total_exon_fragments / mapped_reads(millions) × exon_length(kB)]),(command line: ~stringtie -e -B -p 4 -G merged.gtf -o samples.gtf samples.bam). The differentially expressed mRNAs were selected with fold change > 2 or fold change < 0.5 and p value < 0.05 by R package edgeR(https://bioconductor.org/packages/release/bioc/html/edgeR.html) or DESeq2(http://www.bioconductor.org/packages/release/bioc/html/DESeq2.html),and then analysis GO enrichment and KEGG enrichment to the differentially expressed mRNAs.
Genome_build: MM10
Supplementary_files_format_and_content: MDSC_genes_fpkm_expression.txt: stringTie and ballgown(http://www.bioconductor.org/packages/release/bioc/html/ballgown.html) were used to estimate the expression levels of all transcripts and perform expression level for mRNAs by calculating FPKM (FPKM = [total_exon_fragments / mapped_reads(millions) × exon_length(kB)]),(command line: ~stringtie -e -B -p 4 -G merged.gtf -o samples.gtf samples.bam). The differentially expressed mRNAs were selected with fold change > 2 or fold change < 0.5 and p value < 0.05 by R package edgeR(https://bioconductor.org/packages/release/bioc/html/edgeR.html) or DESeq2(http://www.bioconductor.org/packages/release/bioc/html/DESeq2.html)

source_name: Myeloid-derived suppressor cel l(MDSC)

growth_protocol: MDSC were isolated from MC38-bearing micr by MACS

treatment_protocol: MDSC were co-cultured with MC38 cell line for 24h

value: Myeloid-derived suppressor cel l(MDSC)

value: From MC38-bearing mice


title: WT1_Ma


title: WT3_Ma


title: KO_MDSC

value: From MC39-bearing mice


title: KO1_Ma


title: L01_BC07_150_OLBO_1

description:
L01_BC07
Hepatocyte_normcounts.csv

data_processing:
pipeline run to convert reads to counts https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5672545/
samples with counts < 100 average reads per transcript removed
normalized counts generated by cell type in DESEQ2
Genome_build: NA – Targeted Reads by BioSpyder
Supplementary_files_format_and_content: 6 normalized count matrix files in CSV with genes as rows and columns as samples.  The sample information in the hashfile.csv

value: BO


title: 5633

description:
serum circulating miRNAs
Sample_22.fastq

source_name: serum

value: male

value: high air pollution


title: 5534

description:
serum circulating miRNAs
Sample_21.fastq

value: female

value: cycling


title: Spleen T  Rapamycin-loaded Polymerosome Treatment Rep5 [rPS7_S32]

city: Evanston

first: Reese

middle: Anthony Keith

last: Richardson

state: IL

address: 2145 Sheridan Road

department: Chemical and Biological Engineering

institute: Northwestern University

data_processing:
Sequenced reads were trimmed for adapter content with Trimmomatic v0.39. Parameters: PE ILLUMINACLIP:./TruSeq3-PE_custom.fa:2:30:10 LEADING:30 TRAILING:30 MINLEN:36 TruSeq3-custom.fa: >TruSeq3_IndexedAdapter AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC >TruSeq3_UniversalAdapter AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTA
Trimmed reads were aligned to Gencode M27 (GRCm39) mouse genome assembly (primary assembly) with STAR v2.7.5a. Parameters: --outFilterType BySJout --runThreadN 16 --outFilterMultimapNmax 100 --alignSJoverhangMin 8 --alignSJDBoverhangMin 1 --outFilterMismatchNoverLmax 0.05 --alignIntronMin 20 --alignIntronMax 1000000 --alignMatesGapMax 1000000 --outSAMattributes NH HI NM MD --outSAMstrandField intronMotif --outSAMmapqUnique 60 --outSAMtype BAM SortedByCoordinate --limitBAMsortRAM 30000000000
Alignments were quantified and differential expression analysis was performed with cuffdiff, cufflinks v2.1.1. Samples NT10_S6, PS1_S9, R10_S26, and RO1_S14 were excluded due to poor alignment quality. Parameters: -b ../genome_fasta/GRCm39.primary_assembly.genome.fa -u ../GTF/gencode.vM27.primary_assembly.annotation.gtf
Genome_build: Gencode M27 (primary annotation)
Supplementary_files_format_and_content: raw counts

source_name: Splenic T cells_ Rapamycin-loaded Polymerosome Treatment

extract_protocol: After 11 days, the mice were sacrificed, and spleens were harvested. The spleens were processed through 70 nm filters and treated with 1X red blood cell lysis buffer (Fisher) for 5 minutes on ice, washed with PBS and spun down. T cells were isolated using magnetic sorting (MojoSort; BioLegend) per the manufacturer’s instructions. RNA was isolated from the T cells using RNeasy Mini Kit with DNAse digestion (Qiagen).

treatment_protocol: Healthy 8 to 12-week-old, male C57BL/6J mice were purchased from Jackson Labs. Mice were housed in the Center for Comparative Medicine at Northwestern University. All animal protocols were approved by Northwestern University’s Institutional Animal Care and Use Committee (IACUC). Mice were subjected to a dosage regime consisting of 1 dose per day, for 11 days, totaling 11 doses. Rapamycin formulations were prepared at a concentration of 0.125 mg/ml and dosed at 1 mg rapamycin per kilogram body weight. Rapamune® (RO) was given orally via gavage. Rapamycin (R; Selleckchem; in 0.2% CMC) and rapamycin-loaded poly(ethylene glycol)-block-poly(propylene sulfide) polymersomes (rPS) were given subcutaneously in the neck scruff.  The rPS formulation contained approximately 7.5 mg/ml polymer. Polymer and volume equivalent dose of PS were injected as controls.

tag: strain background

value: Spleen

value: T Cells (CD3+)

value: Rapamycin-Loaded PEG-b-PPS Polymersomes (Subcutaneous; 11 doses, 1 dose per day, 7.5 mg polymer/ml, 60 mg polymer/kg body weight/dose, 0.125 mg rapamycin/ml, 1 mg rapamycin/kg body weight/dose)


title: Spleen T  Rapamycin-loaded Polymerosome Treatment Rep6 [rPS8_S33]


title: Spleen T  Rapamycin-loaded Polymerosome Treatment Rep4 [rPS6_S31]


title: L01_BC05_140_OLBO_1

description:
L01_BC05
Hepatocyte_normcounts.csv

extract_protocol:
described in https://www.altex.org/index.php/altex/article/view/1994
described in https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0178302

value: iCell Hepatocytes


title: Spleen T  Rapamycin-loaded Polymerosome Treatment Rep3 [rPS5_S30]


title: Spleen T  Rapamycin-loaded Polymerosome Treatment Rep2 [rPS4_S29]


title: 4344

description:
serum circulating miRNAs
Sample_20.fastq

tag: gender

value: resting

value: low air pollution


title: L01_BC04_036_OLBO_1

description:
L01_BC04
Hepatocyte_normcounts.csv


title: 5341

description:
serum circulating miRNAs
Sample_19.fastq

tag: subject id


title: Spleen T  Oral Rapamune Treatment Rep1 [RO11_S20]

source_name: Splenic T cells_ Oral Rapamune Treatment

value: Rapamune® (Oral; 11 doses, 1 dose per day, 0.125 mg rapamycin/ml, 1 mg rapamycin/kg body weight/dose)


title: Spleen T  Rapamycin-loaded Polymerosome Treatment Rep1 [rPS3_S28]


title: Spleen T  Rapamycin-loaded Polymerosome Treatment Rep7 [rPS9_S34]


title: 4742

description:
serum circulating miRNAs
Sample_18.fastq

tag: physical activity


title: 4442

description:
serum circulating miRNAs
Sample_17.fastq

tag: exposure condition


title: L01_BC01_179_VHGO_1

description:
L01_BC01
Hepatocyte_normcounts.csv

tag: tissue/celltype

value: VHGO


title: L01_BB11_115_OLBO_1

description:
L01_BB11
Hepatocyte_normcounts.csv


title: L01_BB10_085B_OLBO_1

description:
L01_BB10
Hepatocyte_normcounts.csv


title: 5234

description:
serum circulating miRNAs
Sample_16.fastq

tag: age


title: 5541

description:
serum circulating miRNAs
Sample_15.fastq


title: Spleen T  Oral Rapamune Treatment Rep7 [RO9_S19]

tag: treatment


title: Spleen T  Oral Rapamune Treatment Rep6 [RO7_S18]


title: Spleen T  Oral Rapamune Treatment Rep4 [RO5_S16]


title: Spleen T  Oral Rapamune Treatment Rep5 [RO6_S17]


title: Spleen T Rapamycin Treatment Rep6 [R6_S24]

source_name: Splenic T cells_Rapamycin Treatment

value: Rapamycin in 0.2% CMC (Subcutaneous; 11 doses, 1 dose per day, 0.125 mg rapamycin/ml, 1 mg rapamycin/kg body weight/dose)


title: Spleen T Rapamycin Treatment Rep2 [R11_S27]


title: Spleen T Rapamycin Treatment Rep7 [R8_S25]


title: Spleen T  Oral Rapamune Treatment Rep3 [RO4_S15]


title: Spleen T Rapamycin Treatment Rep5 [R5_S23]


title: L01_BB08_071_HFO_1

description:
L01_BB08
Hepatocyte_normcounts.csv

value: HFO

tag: dose


title: L01_BB09_190_BITUMENS_1

description:
L01_BB09
Hepatocyte_normcounts.csv

value: BIT


title: Spleen T Rapamycin Treatment Rep4 [R4_S22]


title: Spleen T Rapamycin Treatment Rep3 [R2_S21]


title: 4942

description:
serum circulating miRNAs
Sample_14.fastq


title: Spleen T Polymerosome Treatment Rep1 [PS10_S13]

source_name: Splenic T cells_Polymerosome Treatment

value: PEG-b-PPS Polymersomes (Subcutaneous; 11 doses, 1 dose per day, 7.5 mg polymer/ml, 60 mg polymer/kg body weight/dose)


title: L01_BC02_145_HRBO_1

description:
L01_BC02
Hepatocyte_normcounts.csv

value: BO


title: 6933

description:
serum circulating miRNAs
Sample_13.fastq

value: male


title: L01_BB07_166_HFO_1

description:
L01_BB07
Hepatocyte_normcounts.csv


title: 4433

description:
serum circulating miRNAs
Sample_12.fastq


title: Spleen T Polymerosome Treatment Rep4 [PS7_S11]


title: Spleen T Polymerosome Treatment Rep3 [PS6_S10]


title: Spleen T No Treatment Rep3 [NT12_S8]

source_name: Splenic T cells_No Treatment

value: Untreateed


title: 4331

description:
serum circulating miRNAs
Sample_11.fastq

value: female


title: Spleen T No Treatment Rep2 [NT11_S7]


title: Spleen T No Treatment Rep8 [NT8_S5]


title: Spleen T No Treatment Rep7 [NT5_S4]


title: 5933

description:
serum circulating miRNAs
Sample_10.fastq


title: Spleen T No Treatment Rep6 [NT3_S3]


title: 6143

description:
serum circulating miRNAs
Sample_9.fastq

value: high air pollution


title: 6242

description:
serum circulating miRNAs
Sample_8.fastq


title: Spleen T No Treatment Rep5 [NT2_S2]

value: Spleen


title: 5742

description:
serum circulating miRNAs
Sample_48.fastq


title: 6634

description:
serum circulating miRNAs
Sample_7.fastq


title: A-line HOM rep3

city: Madison

first: Hasan

last: Khatib

state: Wisconsin

address: 1675 Observatory Dr.

department: Animal and Dairy Sciences

institute: University of Wisconsin-Madison

data_processing:
Basecalls performed using bcl2fastq v2.20.0.422
Sequenced reads were trimmed for low-quality and adaptor sequences using Trimmomatic v.0.39 , then mapped to mm39 whole genome using STAR v.2.7.4a  with parameters –outSAMmapqUnique 60 --outFilterType BySJout --outSAMstrandField intronMotif --quantMode GeneCounts --twopassMode Basic
For gene-level expression, gene counts were estimated using “--quantMode GeneCounts” option in STAR (Dobin et al., 2013).
Genome_build: GRCm39
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: left ventricular

extract_protocol:
Total RNA was extracted from mouse left ventricles at the age of 2 month using TRIzol Reagent (Life technologies, Thermo Fisher Scientific, Waltham, MA) according to the manufacturer’s protocol. DNase I (#D9905K, Lucigen, Middleton, WI) treatment was applied to clean up genomic DNA before RNA-seq. The quantity and quality were determined by Nanodrop One (Thermo Fisher Scientific, Waltham, MA) and electrophoresis.
RNA libraries (Illumina TruSeq standard Total RNA Gold) were prepared for sequencing using standard Illumina protocols.

tag: strain

value: heart, left ventricular

value: 2 months


title: L01_BA06_MethodBlank_0

description:
L01_BA06
Hepatocyte_normcounts.csv

value: iCell Hepatocytes


title: L01_BB01_154_OLBO_1

description:
L01_BB01
Hepatocyte_normcounts.csv


title: A-line HOM rep1


title: A-line HOM rep2


title: A-line HET rep3


title: Spleen T Polymerosome Treatment Rep5 [PS9_S12]

value: T Cells (CD3+)


title: L01_AH11_090_FO_1

description:
L01_AH11
Hepatocyte_normcounts.csv

value: FO


title: 4834

description:
serum circulating miRNAs
Sample_6.fastq

value: resting

value: low air pollution


title: A-line HET rep2


title: L01_BB06_MethodBlank_0

description:
L01_BB06
Hepatocyte_normcounts.csv


title: L01_AH10_067_P_Hwax_1

description:
L01_AH10
Hepatocyte_normcounts.csv

value: WAX


title: A-line HET rep1


title: G-line HOM rep3


title: L01_BB05_091_HFO_1

description:
L01_BB05
Hepatocyte_normcounts.csv

value: HFO


title: 5241

description:
serum circulating miRNAs
Sample_5.fastq


title: L01_BB03_188_SRGO_1

description:
L01_BB03
Hepatocyte_normcounts.csv

value: SRGO


title: G-line HOM rep2


title: 5832

description:
serum circulating miRNAs
Sample_4.fastq

value: cycling


title: Spleen T No Treatment Rep4 [NT1_S1]


title: G-line HOM rep1


title: L01_AH09_079_HFO_1

description:
L01_AH09
Hepatocyte_normcounts.csv


title: G-line HET rep3


title: L01_AH07_021_HFO_1

description:
L01_AH07
Hepatocyte_normcounts.csv


title: 6544

description:
serum circulating miRNAs
Sample_2.fastq


title: WT rep3

value: WT


title: 4842

description:
serum circulating miRNAs
Sample_1.fastq


title: L01_AH05_096A_UDAE_1

description:
L01_AH05
Hepatocyte_normcounts.csv

value: UDAE


title: WT rep1


title: G-line HET rep1


title: 6341

description:
serum circulating miRNAs
Sample_3.fastq

value: male


title: G-line HET rep2


title: L01_AH03_060_OLBO_1

description:
L01_AH03
Hepatocyte_normcounts.csv

value: BO


title: L01_AH02_119_OLBO_1

description:
L01_AH02
Hepatocyte_normcounts.csv


title: NC_rep1

city: West Haven

first: Francesc

last: Lopez

state: CT

department: Department of Genetics

institute: Yale University

data_processing:
Illumina Casava1.8.2 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence.
The first 6 and last 7 nucleotides  were trimmed using FASTX-Toolkit trimmer.
Trimmed reads were mapped to the human reference genome (hg19) with a known transcriptome index (UCSC Known Gene annotation) with Tophat v2.0.10 using the very-sensitive preset, first strand library type, and providing the corresponding gene model annotation. Only the reads that mapped to a single unique location within the genome, with a maximum of two mismatches in the anchor region of the spliced alignment, were reported in these results.
Tophat alignments were then processed by Cuffdiff (v2.1.1) to obtain differential gene expression using first strand library type, providing gene model annotation and the genome sequence file for detection and correction of sequence-specific bias that random hexamer can cause during library preparation.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include RPKMs, fold changes, and p-values for each condition. Cuffdiff output format.

source_name: WA01 ES cells

growth_protocol: Human ESC/iPSC colonies digested with Accutase cell detachment solution (Innovative Cell Technologies) were re-suspended in differentiation medium plus CHIR 99021 (3 µM; #4423 Tocris Bioscience) plated at 20,000 cells per cm2 on Matrigel-coated surfaces. Differentiation medium contained DMEM/F12 medium supplemented with 2% B27 supplement (Life Technologies), 1× Glutamax (Life Technologies) and 0.5% bovine serum albumin (wt/vol) (A9647, Sigma-Aldrich). The ROCK inhibitor Y-27632 (10 µM; Tocris Bioscience) was added for the first two days.

extract_protocol:
Total RNAs were extracted using TRIzol reagent (Life Technologies) according to Manufacturer's instructions. Extracted RNAs were dissolved in H2O and kept at -80oC until ready for library construction.
Libraries were prepared from poly-adenylated (poly-A) mRNAs using a custom kit based on the Illumina’s mRNA-seq kit (Illumina, part # RS-122-2101)

value: Neural crest cells

tag: cell line

value: WA01 ES cells

tag: differentiation day

value: day 5

value: Wildtype


title: NC_rep2


title: WT rep2

tag: tissue

value: heart, left ventricular

value: 2 months


title: L01_AH04_128_kerosine_1

city: RTP

first: John

institute: National Instititute of Environmental Health Sciences

description:
L01_AH04
Hepatocyte_normcounts.csv

value: iCell Hepatocytes

value: KER


title: CI_d0

city: Toyonaka

first: Takamasa

last: Ito

state: Osaka

address: 1-1 Machikaneyama

department: Biological Science

country: Japan

institute: Osaka University

data_processing:
Raw sequence reads were trimmed to remove low-quality reads and adapter sequences using Trim Galore! and then mapped to the mm10 genome using HISAT2 with default parameter.
The Sam file was converted to a bam file using the Samtools.
Gene expression and transposon expression were counted and normalized using analyzeRepeats.pl in HOMER software.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited .txt files containing FPKM value for each samples

source_name: Embryonic stem cells

growth_protocol: All ESCs were cultured on mitomycin C-treated mouse embryonic fibroblasts (MEFs) in ESC medium [D-MEM/Ham’s F12 (Wako, Osaka, Japan), 10% fetal bovine serum (Corning, NY, USA), 1× penicillin-streptomycin and 2 mM L-glutamate (Gibco®, Thermo Fisher Scientific), 0.1 mM β-mercaptoethanol (Signa-Aldrich), and 10^3 U/ml ESGRO® LIF (Merck, Kenilworth, NJ, USA)] and grown under 5% CO2 at 37˚C. The medium was changed daily.

extract_protocol:
Total RNA was extracted using the RNeasy Mini Kit (Qiagen).
After the QC process, mRNA is enriched using oligo(dT) beads. First, mRNA is randomly fragmented by adding fragmentation buffer, cDNA is synthesized using mRNA template and random hexamers primer, and then second-stranded synthesis is performed by adding custom second-stranded synthesis buffer (illumina), dNTPs, RNase H and DNA polymerase. Next, terminal repair, A-ligation, and sequencing adapter ligation are followed by size selection and PCR enrichment to complete the double-stranded cDNA library.

treatment_protocol: First, feeder cells were removed from the trypsinized ESCs by incubating for 30 min in a 100-mm gelatin-coated dish. The non-adherent ESCs were collected and 2 × 10^7 ESCs were placed in a 100-mm Petri dish. To form embryoid bodies (EBs), the cells were then cultured in MEF medium [D-MEM supplemented with 10% FBS] for 1 day. One-day-old EBs were placed in a 6-well plate and adherent cells were cultured in the MEF medium for 3 days. The medium was changed daily.

tag: geno type

value: Dnmt1-/-,  DNMT1C1229S

tag: time point

value: day 0


title: 1KO_d2

value: day 2


title: CI_d2


title: 1KO_d4

value: day 4


title: 1KO_d0


title: preNC_rep2

tag: cell type

value: Pre-neural crest cells

value: day 3


title: L01_AH01_195_UDAE_1

last: House

address: 111 TW Alexander Drive

description:
L01_AH01
Hepatocyte_normcounts.csv

value: UDAE


title: preNC_rep1

tag: genotype


title: L01_AH06_MethodBlank_0

description:
L01_AH06
Hepatocyte_normcounts.csv


title: WT_d0

value: wild type


title: L01_AG11_191_BITUMEN_1

description:
L01_AG11
Hepatocyte_normcounts.csv

value: BIT


title: WT_d2


title: ES_rep2

value: Embryonic stem cells


title: SC35 ChIP-Seq wt_input

city: Pittsburgh

first: Bokai

last: Zhu

state: PA

address: 100 Technology Dr, Bridgeside point

institute: University of Pittsburgh

library_source: genomic

data_processing:
Replicates were pooled at each time for subsequent ChIP-Seq analysis. The sequences identified were mapped to the mouse genome (UCSC mm10) using BOWTIE function in Galaxy. Only the sequences uniquely mapped with no more than 2 mismatches were kept and used as valid reads. PCR duplicates were also removed.
Peak calling was carried out by MACS2 (version 2.1.1.20160309) in Galaxy (options --mfold 5, 50 --pvalue 1e-4), on each ChIP-seq file against the input in XBP1Flox or XBP1LKO mice using the broad region function.
To account for the different sequencing depths between samples, the signal files generated from MACS2 were RPKM normalized to sequencing depth
5,365 genes with at least one peak identified in the gene body region (from TSS to TTS) in at least one CT in XBP1Flox mice were identified
Genome_build: UCSC mm10
Supplementary_files_format_and_content: bigwig

molecule: genomic DNA

source_name: liver

growth_protocol: WT and XBP1 LKO mice were kept under constant darkness

extract_protocol:
ChIP for SC35 was performed using anti-SC35 antibody (ab11826, Abcam). Mouse liver samples were submerged in PBS + 1% formaldehyde, cut into small (~1 mm3) pieces with a razor blade and incubated at room temperature for 15 minutes. Fixation was stopped by the addition of 0.125 M glycine (final concentration). The tissue pieces were then treated with a TissueTearer and finally spun down and washed twice in PBS. Chromatin was isolated by the addition of lysis buffer, followed by disruption with a Dounce homogenizer. The chromatin was enzymatically digested with MNase. Genomic DNA (Input) was prepared by treating aliquots of chromatin with RNase, Proteinase K and heated for reverse-crosslinking, followed by ethanol precipitation. Pellets were resuspended and the resulting DNA was quantified on a NanoDrop spectrophotometer. An aliquot of chromatin (30 μg) was precleared with protein A agarose beads (Invitrogen). Genomic DNA regions of interest were isolated using 4 μg of antibody. Complexes were washed, eluted from the beads with SDS buffer, and subjected to RNase and proteinase K treatment. Crosslinking were reversed by incubation overnight at 65 °C, and ChIP DNA was purified by phenol-chloroform extraction and ethanol precipitation.
The DNA libraries were prepared at University of Pittsburgh and sequenced at Gene by Gene, Ltd per standard protocols. DNA libraries were prepared with Ovation® Ultralow V2 DNA-Seq library preparation kit (NuGen) using 1ng input DNA. The size selection for libraries were performed using SPRIselect beads (Beckman Coulter) and purity of the libraries were analyzed using the High Sensitivity DNA chip on Bioanalyzer 2100 (Agilent). The prepared libraries pooled and sequenced using Nova-Seq 6000 (Illumina), generating ~40 million 101 bp single-end reads per samples.

treatment_protocol: Liver samples were collected every 4 hours for a total of 48 hours from WT and XBP1 LKO mice

tag: Sex

value: male

value: WT

value: 3-4 months

value: liver

tag: time

tag: chip antibody

value: anti-SC35 (ab11826, Abcam)


title: L01_AG10_164_HFO_1

description:
L01_AG10
Hepatocyte_normcounts.csv

value: iCell Hepatocytes

value: HFO


title: ES_rep1

value: WA01 ES cells

value: Wildtype


title: SC35 ChIP-Seq WT_CT4B


title: SC35 ChIP-Seq WT_CT8A


title: SC35 ChIP-Seq WT_CT4A


title: CI_d4

value: Dnmt1-/-,  DNMT1C1229S


title: SC35 ChIP-Seq WT_CT44C


title: L01_AG08_108_OLBO_1

description:
L01_AG08
Hepatocyte_normcounts.csv

value: BO


title: L01_AG07_136_slackwax_1

description:
L01_AG07
Hepatocyte_normcounts.csv

value: WAX


title: SC35 ChIP-Seq WT_CT36B


title: WT_d4

value: day 4


title: SC35 ChIP-Seq WT_CT28AC


title: L01_AG06_MethodBlank_0

description:
L01_AG06
Hepatocyte_normcounts.csv


title: SC35 ChIP-Seq WT_CT40AB


title: SC35 ChIP-Seq WT_CT36A


title: SC35 ChIP-Seq WT_CT32A


title: L01_AG04_181_VHGO_1

description:
L01_AG04
Hepatocyte_normcounts.csv

value: VHGO


title: L01_AG05_135_TDAE_1

description:
L01_AG05
Hepatocyte_normcounts.csv

value: TDAE


title: SC35 ChIP-Seq WT_CT24B


title: SC35 ChIP-Seq WT_CT24A


title: SC35 ChIP-Seq WT_CT20A


title: L01_AG09_104_kerosine_1

description:
L01_AG09
Hepatocyte_normcounts.csv

value: KER


title: SC35 ChIP-Seq WT_CT12A


title: SC35 ChIP-Seq WT_CT16A


title: L01_AG03_017_HFO_1

description:
L01_AG03
Hepatocyte_normcounts.csv


title: SC35 ChIP-Seq WT_CT12C


title: L01_AG02_187_2__OGO_1

description:
L01_AG02
Hepatocyte_normcounts.csv

value: OGO


title: SC35 ChIP-Seq WT_CT0C

value: male


title: SC35 ChIP-Seq WT_CT44AB

value: WT


title: SC35 ChIP-Seq WT_CT0A

value: 3-4 months


title: L01_AF06_MethodBlank_0

description:
L01_AF06
Hepatocyte_normcounts.csv


title: L01_AF05_183_VHGOa_1

description:
L01_AF05
Hepatocyte_normcounts.csv


title: SC35 ChIP-Seq LKO_CT4

value: XBP1 LKO

value: liver


title: RVX208, rep1

city: Daejeon

first: Byungho

last: Lim

address: 141 Gajeong-ro, Yuseong-gu, Daejeon 34114, Korea

country: South Korea

institute: KRICT

description: Gene expression data from drug treated AML cells

hyb_protocol: Approximately 5.5 μg of labeled DNA target was hybridized to the Affymetrix GeneChip Array at 45°C for 16hour.

scan_protocol: Hybridized arrays were washed and stained on a GeneChip Fluidics Station 450 and scanned on a GCS3000 Scanner (Affymetrix).

data_processing: Array data export processing and analysis was performed using Affymetrix® GeneChip Command Console® Software (AGCC).

label: biotin

source_name: RVX208 treatment

label_protocol: The sense cDNA was then fragmented and biotin-labeled with TdT (terminal deoxynucleotidyl transferase) using the GeneChip WT Terminal labeling kit.

growth_protocol: MV4-11 leukimia cells were cultured in RPMI1640 medium supplemented with 10% fetal bovine serum (FBS) in a CO2 incubator.

extract_protocol: Total RNA was extracted by using RNeasy mini kit (Qiagen).

treatment_protocol: During 24h, DMSO, DW-71374 (300 nM), DW-71177 (300 nM), OTX-015 (300 nM), and RVX-208 (5 uM) were treated to 5x105 MV4-11 cells plated on 6-well plates in triplicates.

tag: cancer type

value: AML


title: OTX015, rep3

source_name: OTX015 treatment


title: SC35 ChIP-Seq LKO_CT8

value: anti-SC35 (ab11826, Abcam)


title: RVX208, rep3


title: DW71374, rep3

source_name: DW71374 treatment


title: OTX015, rep2


title: OTX015, rep1


title: DW71374, rep1


title: SC35 ChIP-Seq LKO_CT36


title: L01_AF04_192_BITUMENS_1

description:
L01_AF04
Hepatocyte_normcounts.csv

value: iCell Hepatocytes

value: BIT


title: SC35 ChIP-Seq LKO_CT40


title: L01_AF03_076_gasoline_1

description:
L01_AF03
Hepatocyte_normcounts.csv

value: NAPTHA


title: SC35 ChIP-Seq LKO_CT44


title: RVX208, rep2


title: SC35 ChIP-Seq LKO_CT32


title: SC35 ChIP-Seq LKO_CT20


title: SC35 ChIP-Seq LKO_CT28


title: L01_AF02_083_UATO_1

description:
L01_AF02
Hepatocyte_normcounts.csv

value: UATO


title: DW71374, rep2


title: DW71177, rep3

source_name: DW71177 treatment


title: L01_AF01_043_kerosine_1

description:
L01_AF01
Hepatocyte_normcounts.csv

source_name: Hepatocyte


title: SC35 ChIP-Seq LKO_input


title: SC35 ChIP-Seq LKO_CT16


title: DW71177, rep2


title: SC35 ChIP-Seq LKO_CT12


title: L01_AE11_124_gasoline_1

description:
L01_AE11
Hepatocyte_normcounts.csv


title: SC35 ChIP-Seq LKO_CT0


title: L01_AE10_085A_OLBO_1

description:
L01_AE10
Hepatocyte_normcounts.csv

value: BO


title: ADPKD_Inh_2

city: Tianjin

first: Zhiheng

last: Liu

state: Tianjin

address: No.22 Qixiangtai Road

department: Tianjin Research Center for Basic Medical Science

institute: Tianjin Medical University

data_processing:
HISAT2 (version 2.1.0) was used to align paired-end reads to mouse (mm10) genome. Only unique mapped reads were used in further analysis.
FeatureCounts (version 1.6.0) was used to count reads number for each sample.
R package DESeq2 was used to identify differentially expressed genes, cut-offs were set at foldchange = 1.5 and FDR at 0.05.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text file includes reads number for each gene/sample.

source_name: freshly isolated DBA positive cell

extract_protocol:
DBA positive cells were isolated from mouse kidney. Total RNA was extracted using TRIzol (Invitrogen). Total RNAs from whole kidney were subjected to Oligo dT selection and adaptor ligation.
Construction of RNA-seq library was finished by Novogene company (Beijing, China).

treatment_protocol: 5 mg/kg 666-15 or appropriate amount of vehicle was given once daily for five consecutive days, followed by 2 days rest. 666-15 treatment was started from P11 and continued for 3 weeks.

value: kidney

value: Dolichos biflorus lectin (DBA) positive cells

value: ADPKD

value: Inh


title: ADPKD_DMSO_2

value: DMSO


title: ADPKD_Inh_1


title: SC35 ChIP-Seq LKO_CT24

value: male


title: DMSO, rep3

source_name: DMSO treatment


title: DW71177, rep1


title: L01_AE09_092_OLBO_1

description:
L01_AE09
Hepatocyte_normcounts.csv


title: WT_Inh_2

value: WT


title: WT_Inh_1


title: L01_AE08_107_P_Hwax_1

description:
L01_AE08
Hepatocyte_normcounts.csv

value: WAX


title: WT_DMSO_2


title: ADPKD_K4M3

data_processing:
Library strategy: CUT&RUN
Bowtie2 (version 2.3.4.1) was used to align paired-end 150 bp sequence reads to human (hg38) genome
HOMER (version 4.10) findPeaks command was used to call peak
BamCoverage within deeptools (version 3.3.0) were used to generate bigwig files from bam files.
Genome_build: hg38 or mm10
Supplementary_files_format_and_content: Bigwig

extract_protocol:
For ChIP-seq. Cells were cross-linked with 1% formaldehyde in 1 mL PBS for 10 min at RT. The crosslink was quenched by adding 67 μL of 2.5 M glycine(150 mM final). Cells were washed with PBS and harvested using ChIP lysis buffer. Cells were then sonicated to obtain fragments (200-500 bp) with Sonicator. Immunoprecipitation was performed with indicated antibodies. After elution and reversal cross-linking, DNA was purified for library preparation. For CUT&RUN. Cells were permeabilized with digitonin. DNA were cleaved in situ using a protein A-micrococcal nuclease fusion recruited by an antibody to chromatin associated protein. Then DNA was purified for library preparation.
Library construction were performed using VAHTS Universal DNA Library Prep Kit (Vazyme, ND607-02) and VATHS DNA Adapters set2 for Illumina (Vazyme Biotech, Cat.N802-01)

value: Millipore, 05-745R


title: L01_AE06_MethodBlank_0

description:
L01_AE06
Hepatocyte_normcounts.csv


title: ADPKD_K27ac

value: Abcam, ab4729


title: WT_DMSO_1


title: L01_AE07_087_kerosine_1

description:
L01_AE07
Hepatocyte_normcounts.csv

value: KER


title: ADPKD_pCREB

value: Cell Signaling Technology, #9198


title: L01_AE05_065_P_Hwax_1

description:
L01_AE05
Hepatocyte_normcounts.csv

value: iCell Hepatocytes


title: human atria, tachycardia, 21A+21B

city: Graz

first: Karin

last: Wagner

state: Styria

address: Stiftingtalstrasse 24

department: Molecular Biology

country: Austria

institute: Medical University Graz

description: HA TC6 21A+B

hyb_protocol: Affymetrix Human Gene 2.0 ST Array (Cat No. 902112);  Affymetrix GeneChip® HT hybridization, Wash and Stain Kit (Cat No. 900720);   Affymetrix Genechip®  fluidics station 450: protocol FS450_0002 for Cartridge Arrays

scan_protocol: Affymetrix Scanner: GCS3000; AGCC (Command Console Software  AGCC 4.0.0)

data_processing: Affymetrix Genexpression Console (1.3.1) using Affymetrix default analysis settings for generation of CEL-files.

label: Biotin

source_name: isolated atrial multicellular trabeculae

label_protocol: NuGen Ovation Pico WTA System V2, M01224v2 (Cat No. 3302); Encore Biotin Module, M01111v6 (Cat No. 4200);

growth_protocol: Atrial appendages were obtained from patients undergoing CABG surgery. Trabeculae were isolated in maximal diameter of 1mm and immediatelly put in an organ bath setup were they were kept for the whole duration of the experiment.

extract_protocol: miRNeasyMICRO (Qiagen CatNo: 74004) incl DNase Treatment on column (RNase-Free DNase Set; Qiagen CatNo: 79254)

treatment_protocol: Trabeculae were either stretched to maximal phisiological length or subjected to 2,5 Hz pacing frequency for a duration of 6h.

value: tachycardia

value: atrial appendage


title: GA Muscle 122 EV5

city: SANDIEGO

first: XIANHUI

last: RUAN

address: 9500 Gilman Dr (#0612), La Jolla

department: PATHOLOGY

institute: UCSD

data_processing:
RNA-seq and data processing were performed by Novogene Co., Ltd. Downstream analysis was performed using a combination of programs including STAR, HTseq, Cufflink and Novogene's wrapped scripts. Alignments were parsed using Tophat program and differential expressions were determined through DESeq2/edgeR.
Reference genome and gene model annotation files were downloaded from genome website browser (NCBI/UCSC/Ensembl) directly. Indexes of the reference genome was built using STAR and paired-end clean reads were aligned to the reference genome using STAR (v2.5). STAR used the method of Maximal Mappable Prefix(MMP) which can generate a precise mapping result for junction reads.
HTSeq v0.6.1 was used to count the read numbers mapped of each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene. FPKM, Reads Per Kilobase of exon model per Million mapped reads, considers the effect of sequencing depth and gene length for the reads count at the same time, and is currently the most commonly used method for estimating gene expression levels (Mortazavi et al., 2008).
Genome_build: mm10
Supplementary_files_format_and_content: tab delimited text file including FPKM values for each sample.

source_name: Muscle

growth_protocol: Female NOD scid gamma (NSG) mice were maintained in a standard mouse facility in sterile conditions.

extract_protocol:
Homogenized GA tissue (~20 mg) was used to extract RNA by using 1 ml of Trizol reagent (Invitrogen). The RNA pellet was dissolved in RNase-free water, and subjected to library construction and deep sequencing.
RNA libraries were prepared for sequencing using standard Illumina protocols by Novogene Co., Ltd.
mRNA is purified from total RNA using poly-T oligo-attached magnetic beads. The mRNA is first fragmented randomly by addition of fragmentation buffer.

treatment_protocol: Mice received tail-vein injections of EVs twice a week for 5 weeks (~10 ug EV per injection). Two days after the last injection, GA muscle was collected for immediate RNA extraction.

value: NSG

value: GA Muscle

value: week 12

value: Wild Type

value: MCF-10A/miR122 EV


title: ADPKD_DMSO_1

value: kidney

value: Dolichos biflorus lectin (DBA) positive cells

value: ADPKD


title: human atria, tachycardia, 13B

description: HA TC6 13B


title: DMSO, rep2

value: AML


title: DMSO, rep1


title: GA Muscle 122 EV4


title: L01_AE03_076_gasoline_1

description:
L01_AE03
Hepatocyte_normcounts.csv

value: NAPTHA


title: L01_AE01_169_SRGO_1

description:
L01_AE01
Hepatocyte_normcounts.csv

value: SRGO


title: GA Muscle 122 EV1


title: human atria, tachycardia, 20A

description: HA TC6 20A


title: human atria, tachycardia, 8A+8B

description: HA TC6  8A+B


title: L01_AD10_089_UDAE_1

description:
L01_AD10
Hepatocyte_normcounts.csv

value: UDAE