title: 5_Tumour

description: GeoMx DSP Ncounter


title: Pax7 lineage - E12.5b2_90

status: Public on Apr 12 2022

type: SRA

city: Hong Kong

first: Angela

last: Wu

address: Clear Water Bay, Kowloon

department: Division of Life Science

country: Hong Kong

institute: Hong Kong University of Science and Technology

description:
ss2_filtered_count.csv
E12.5_b2_9

library_source: transcriptomic

data_processing:
Smart-seq2 samples basecalling were performed using bcl2fastq2; 10x samples were performed using bcl2fastq.
Smart-seq2 samples were quantified using kallisto 0.44.0, summarized using tximport in R; 10x samples were aligned using STAR and matrices were generated with cellranger count
Both datasets were loaded in R environment as Seurat object and filtered for poor quality reads.
Genome_build: mm10
Supplementary_files_format_and_content: csv containing raw counts

molecule: total RNA

organism: Mus musculus

source_name: Mouse embryonic cells

extract_protocol:
YFP+ signals reporting Pax7-lineage cells were FACS sorted. Additional sorting with antibody labeling were done for bulk samples regarding surface marker studies.
Sequencing libraries for single-cell samples were constructed using Smart-seq2 protocol or 10x protocol. Smart-seq2 was also applied to bulk samples.

treatment_protocol: The progeny Pax7-expressing cells during early developmental stage were traced by injecting a single dose of TMX (75 µg/g body weight) intraperitoneally into the pregnant mice at E9.5 to initiate Cre-Lox recombination in Pax7-expressing cells. Embryos were harvested later at E12.5, E14.5, and E16.5.

tag: tissue

value: embryonic cells

tag: method

tag: sequencng type

value: Single-cell

tag: time point

tag: plate batch

value: Plate 2

tag: sequence batch

value: Batch 2

tag: medium

tag: marker


title: 5_Stroma

type: protein

city: brisbane

first: Arutha

last: Kulasinghe

address: 37 kent st

country: Australia

institute: University of Queensland

description: GeoMx DSP Ncounter

data_processing: Ncounter data was exported and normalised by RUVseq. Differential expression was performed between primary and metastatic samples

label: DNA barcode

molecule: protein

organism: Homo sapiens

source_name: FFPE Resected Tumour

extract_protocol: Commercial HNSCC TMA was analysed by GeoMX DSP. Antibody incubations and Ncounter readout were performed as per standardised Nanostring GeoMX DSP protocol

value: FFPE Resected Tumour

tag: type

value: Primary Only

tag: followup(days)

tag: current status

value: DEATH


title: 4_Stroma

description: GeoMx DSP Ncounter

value: ALIVE


title: Pax7 lineage - E12.5b2_89

description:
ss2_filtered_count.csv
E12.5_b2_8


title: 7

city: Wien

first: Andreas

middle: B

last: Diendorfer

address: Leberstraße 20

country: Austria

institute: TAmiRNA GmbH

data_processing:
fastQ quality assessment
cutadapt adater trimming
bowtie1 genome alignment
miRDeep2 miRNA quantification
edgeR differential expression
Homo sapiens (hsa, TXID: 9606)
Supplementary files format and content: CSV with miRNA quantifications (raw and rpm)
Assembly: GRCh38.p12

source_name: Washed platelets

extract_protocol:
Total RNA was extracted using the miRNeasy Mini Kit (Qiagen, Cat. 217004).
Libraries were prepared using the CleanTag small RNA library preparation kit (Cat. L-3206-24, TriLink Biotechnologies).

tag: sample type

value: Supernatant

tag: platelet activation

value: stimulated

tag: donor


title: 4

source_name: PPP

value: Plasma


title: 7_Tumour

description: GeoMx DSP Ncounter


title: 6_Tumour

description: GeoMx DSP Ncounter


title: Pax7 lineage - E12.5b2_88

description:
ss2_filtered_count.csv
E12.5_b2_8


title: 3

source_name: PRP


title: RNA-seq data of Rabbit replicate 3

city: Chengdu

first: Mengnan

last: He

address: Huimin road 211#

country: China

institute: Sichuan Agriculture University

description:
rabbit_quant_TPM-1.txt
ployA
PE125
Specific

data_processing:
RNA sequencing reads were aligned to reference genomes applying the STAR (2.6.0c) (Dobin, A. et al.).
Transcript quantification was conducted with kallisto (0.44.0) (Bray, N. L. et al.)
Genome_build: Genome building GRCh38 of human, Mmul_8.0.1 of monkey, GRCm38 of mouse, Rnor_6.0 of rat, OryCun2.0 of rabbit, Felis_cattus_6.2 of cat, CanFam3.1 of dog, Sscrofa11.1 of pig, UMD3.1 of cow, Oar_v3.1 of sheep, GRCz10 of zebrafish, and Gallus_gallus-5.0 of chicken were used for read alignment.

organism: Oryctolagus cuniculus

source_name: Rex Rabbit Ear Skin Fibroblasts

growth_protocol: Most of the fibroblasts were grown in Dulbecco's Modified Eagle Medium (DMEM, 11995-065, Gibco) containing 10% Fetal Bovine Serum (FBS, 10099-141, Gibco) and 1× penicillin/streptomycin (P/S, 15140-122, Gibco), incubated at 37 °C in 5% CO2.

extract_protocol:
total RNA  of each cell sample was extracted by using the Trizol  (Invitrogen).
We used an rRNA depletion protocol (Epicentre Ribo-zero™ rRNA Removal Kit, Epicentre, USA) or  mRNA capture protocol (Oligo (dT) magnetic beads, Promega, USA) coupled with the strand specific or non-specific RNA-seq library protocol  for each sample.

tag: cell type

value: Fibroblasts

tag: tissue source

value: Ear Skin

tag: age

value: unknown


title: 7_Stroma

description: GeoMx DSP Ncounter

tag: tissue


title: Pax7 lineage - E12.5b2_87

description:
ss2_filtered_count.csv
E12.5_b2_8

tag: method


title: 10

source_name: Gel-filtrated platelets


title: RNA-seq data of Rabbit replicate 2


title: 8_Stroma

description: GeoMx DSP Ncounter


title: 8_Tumour

description: GeoMx DSP Ncounter


title: 2

source_name: Buffy coat

value: Cell pellet


title: Pax7 lineage - E12.5b2_86

description:
ss2_filtered_count.csv
E12.5_b2_8

tag: sequencng type


title: Pax7 lineage - E12.5b2_91

description:
ss2_filtered_count.csv
E12.5_b2_9

tag: time point


title: RNA-seq data of Rabbit replicate 1

source_name: Rabbit Embryo Fibroblasts

value: Embyo


title: 1

source_name: Erythrocytes


title: Pax7 lineage - E12.5b2_85

description:
ss2_filtered_count.csv
E12.5_b2_8

tag: plate batch


title: 6_Stroma

description: GeoMx DSP Ncounter


title: Hi-C data of Rabbit replicate 3

library_source: genomic

data_processing:
Read pair flies in fastq format were aligned to the reference genome, filtered and binned into raw and normalized 2D contact matrices using Hiclib.
TADs were identified using DomainCaller
Compartment A/B identification at 20-Kb was performed by using A-B index value which represented the comparative likelihood of a sequence interacting with A or B (100-Kb) as described previously (Rowley, M. J. et al. ). Bins at 20-Kb with positive values (more association with A at 100-Kb) were called as A compartments, while 20-Kb bins with negative values (more association with B at 100-Kb) were called as B compartments. These positive or negative values were termed as A-B index values.
Genome_build: Genome building GRCh38 of human, Mmul_8.0.1 of monkey, GRCm38 of mouse, Rnor_6.0 of rat, OryCun2.0 of rabbit, Felis_cattus_6.2 of cat, CanFam3.1 of dog, Sscrofa11.1 of pig, UMD3.1 of cow, Oar_v3.1 of sheep, GRCz10 of zebrafish, and Gallus_gallus-5.0 of chicken were used for read alignment.

molecule: genomic DNA

extract_protocol:
Briefly, about 20 to 25 million cells were crosslinked with 2% formaldehyde for 10 min at room temperature (20–25 °C), then used glycine to quench the formaldehyde in a final concentration of 0.25 M at room temperature for 5 min, and subsequently on ice for 15 min.
Dilution Hi-C was performed as a previous study (Lieberman-Aiden, E. et al. ). Nuclei were permeabilized by a Dounce homogenizer in the presence of cold lysis buffer (10 mM Tris-HCl, pH 8.0, 10 mM NaCl, 0.2% IGEPAL CA-630, and 1× protease inhibitor solution). DNA was digested with 400 units of HindⅢ, and the ends of restriction fragments were labeled using biotinylated nucleotides and ligated in a small volume (8 mL). After reversal of cross-links, ligated DNA was puriﬁed and prepped for Illumina sequencing.


title: Pax7 lineage - E12.5b2_84

description:
ss2_filtered_count.csv
E12.5_b2_8

tag: sequence batch


title: Hi-C data of Rabbit replicate 2


title: 9_Stroma

description: GeoMx DSP Ncounter


title: 10_Tumour

description: GeoMx DSP Ncounter


title: Pax7 lineage - E12.5b2_83

description:
ss2_filtered_count.csv
E12.5_b2_8

tag: medium


title: Hi-C data of Rabbit replicate 1


title: 10_Stroma

description: GeoMx DSP Ncounter


title: Pax7 lineage - E12.5b2_81

description:
ss2_filtered_count.csv
E12.5_b2_8

tag: marker


title: 9_Tumour

description: GeoMx DSP Ncounter

tag: type


title: Pax7 lineage - E12.5b2_80

description:
ss2_filtered_count.csv
E12.5_b2_8


title: Pax7 lineage - E12.5b2_79

description:
ss2_filtered_count.csv
E12.5_b2_7


title: Pax7 lineage - E12.5b2_78

description:
ss2_filtered_count.csv
E12.5_b2_7


title: 11_Tumour

description: GeoMx DSP Ncounter

tag: followup(days)


title: 11_Stroma

description: GeoMx DSP Ncounter

tag: current status


title: 12_Tumour

description: GeoMx DSP Ncounter


title: Pax7 lineage - E12.5b2_77

description:
ss2_filtered_count.csv
E12.5_b2_7


title: E171_5mg/kg/bw/day_day21_male_D

type: RNA

city: Maastricht

first: Danyel

last: Jennen

address: Universiteitssingel 40

department: Toxicogenomics

country: Netherlands

institute: Maastricht University

hyb_protocol: Hybridization was performed according to the manufacturer’s protocol on SurePrint G3 Mouse Gene Expression v2 8x60K Microarray slides.

scan_protocol: Microarray slides were scanned using an Agilent DNA Microarray Scanner with Surescan High-resolution Technology (Agilent Technologies, The Netherlands). The scanner was set to Dye Channel: G, Profil: AgilentG3_GX_1Color, Scan region: Agilent HD (61 x 21.3 mm), Scan resolution 3 µm, Tiff file dynamic range: 20-bit, Red PMT gain: 100 %, Green PMT gain: 100 %.

data_processing: Pre-processing of microarray raw data was performed as previously described [19]. Briefly, gene expression values were obtained from the microarray scans using Agilent’s Feature extraction software (FES) version 10.7.3.1). Next, the samples were checked for quality and normalized with ArrayQC, an in-house developed pipeline (https://github.com/arrayanalysis/arrayQC_Module) using the following steps: local background correction, flagging of bad spots, controls/spots point with too low intensity, log2 transformation, and quantile normalization. Bad spots were removed from the normalized data. Sixteen groups were defined, based on exposure and time points: 4 different exposure groups and 4 different time points. Spot identifiers were deleted when more than 40 % of samples in each group had a missing value, and when the average expression in each group was < 4. Missing values were imputed by the k-nearest neighbors using GenePattern ImputeMissingValues.KNN module v13 (k-value 15). Repeated Agilent probe identifiers were merged (setting: median) with Babelomics 5. Next, Agilent probe identifiers were re-annotated to EntrezGeneIDs and again merged (setting: median) with Babelomics 5. Differentially expressed genes (DEGs) were identified by performing a moderate t-test using LIMMA (version 1.0), which corrected the exposure samples with their time-matched controls. The cut-off values of fold-changes (FC) ≥ 1.5 or ≤ -1.5 (absolute FC ≥ 1.5) and p-value < 0.05 were used. Additionally, the false discovery rate (FDR) was applied according to the Benjamini-Hochberg method with a threshold q-value < 0.05.

label_protocol: Total RNA was synthesized into cRNA and labelled according to the One-Color Microarray-Based Gene Expression Analysis protocol version 6.6

growth_protocol: All animal experiments were reviewed and approved by the Animal Experimental Committee, which included an ethical testing framework from Maastricht University, The Netherlands. All mice were housed in polycarbonate cages and kept in a housing room (21°C, 50-60 % relative humidity, 12 h light/dark cycles, air filtered until 5 µm particles an exchanged 18 times/h). Mice received a standard chow diet and water ad libitum. Cardboard was removed from cages to avoid potential contamination with TiO2.

extract_protocol: RNA was isolated from the distal colon using the miRNeasy Mini Kit (Qiagen, The Netherlands) including a DNase treatment, according to the manufacturer’s protocols for “Animal Cells and Animal Tissues” .

treatment_protocol: For the gene expression study, the number of 112 CACTg/Tg;APC580S mice were randomly divided into 4 groups: three exposure groups with different concentrations of E171 (1, 2, and 5 mg/kgbw/day) and one control group exposed to sterile water. Mice were exposed 5 days a week. After 2, 7, 14, and 21 days of exposure, 28 mice were euthanized: 7 mice per group, 3 females, and 4 males in each group. Colon, liver, and spleen were sampled from every mouse and weighed.

value: Distal colon

tag: gender

value: male

tag: treatment

value: 21 days of exposure to 5 mg/kgbw/day of E171 in sterile water


title: 12_Stroma

description: GeoMx DSP Ncounter


title: 13_Tumour

description: GeoMx DSP Ncounter


title: Pax7 lineage - E12.5b2_76

description:
ss2_filtered_count.csv
E12.5_b2_7

value: embryonic cells

value: Single-cell

value: Plate 2


title: 13_Stroma

description: GeoMx DSP Ncounter

value: FFPE Resected Tumour

value: Primary Only


title: 14_Tumour

description: GeoMx DSP Ncounter

value: DEATH


title: Pax7 lineage - E12.5b2_74

description:
ss2_filtered_count.csv
E12.5_b2_7

value: Batch 2


title: E171_5mg/kg/bw/day_day21_female_B

value: female


title: 14_Stroma

description: GeoMx DSP Ncounter


title: KG1α shRELA-1

city: Zhengzhou

first: Ding

last: Li

state: Henan

address: Dongming Road 127

institute: The Affiliated Cancer Hospital of Zhengzhou University, Henan Cancer Hospital

description: Gene expression analysis after the construction of stable cell lines

hyb_protocol: Hybridization was performed according to the Agilent One-Color Microarray-Based Gene Expression Analysis protocol (Agilent Technology) with minor modifications. 1 μg of each labeled cRNA was fragmented by adding 5 μl 10 × Blocking Agent and 1 μl of 25 × Fragmentation Buffer, then heated the mixture at 60°C for 30 min, finally 25 μl 2 × GE Hybridization buffer was added to dilute the labeled cRNA. 50 μl of hybridization solution was dispensed into the gasket slide and assembled to the LncRNA expression microarray slide. The slides were incubated for 17 hours at 65°C in an Agilent Hybridization Oven. The hybridized arrays were washed, fixed and scanned with using the Agilent DNA Microarray Scanner (part number G2505C

scan_protocol: The arrays were then exposed for 2 hours to an Imaging Plate and scanned at 25-mm resolution with a BAS5000

data_processing: Agilent Feature Extraction software (version 11.0.1.1) was used to analyze acquired array images. Quantile normalization and subsequent data processing were performed with using the GeneSpring GX v12.1 software package (Agilent Technologies). After quantile normalization of the raw data, LncRNAs and mRNAs that at least 3 out of 6 samples have flags in Present or Marginal (“All Targets Value”) were chosen for further data analysis. Differentially expressed LncRNAs and mRNAs with statistical significance between the two groups were identified through P-value/FDR filtering. Differentially expressed LncRNAs and mRNAs between the two samples were identified through Fold Change filtering. Hierarchical Clustering and combined analysis were performed using homemade scripts

source_name: Acute myeloid leukemia

label_protocol: Sample labeling was performed according to the Agilent One-Color Microarray-Based Gene Expression Analysis protocol (Agilent Technology) with minor modifications. Briefly, mRNA was purified from total RNA after removal of rRNA (mRNA-ONLY™ Eukaryotic mRNA Isolation Kit, Epicentre). Then, each sample was amplified and transcribed into fluorescent cRNA along the entire length of the transcripts without 3' bias utilizing a random priming method (Arraystar Flash RNA Labeling Kit, Arraystar). The labeled cRNAs were purified by RNeasy Mini Kit (Qiagen). The concentration and specific activity of the labeled cRNAs (pmol Cy3/μg cRNA) were measured by NanoDrop ND-1000.

growth_protocol: KG1α shCtrl and KG1α shRELA cells  were cultured in RPMI 1640 medium,  supplemented with 10% fetal bovine serum and 1% penicillin-streptomycin. The cells were maintained in a humidified incubator at 37 °C with 5% CO2.

extract_protocol: 107  cells were  dissolved in 1mL trizol, and then total RNA was extracted following the manufacturer's recommendations. RNA quantification and quality assessment were performed with a NanoDrop ND-1000, and RNA integrity and gDNA contamination were tested by denaturing agarose gel electrophoresis.

treatment_protocol: KG1α shCtrl and KG1α shRELA cells were treated with 0.5 μM Daunorubicin (DNR) for 2 h, then DNR was washout and  cells were collected.

tag: cell line

tag: shRNA

value: RELA knockdown


title: E171_5mg/kg/bw/day_day21_female_C


title: KG1α shCtrl-3

value: shCtr vector


title: KG1α shRELA-3


title: RNA-seq data of Cat replicate 1

description:
cat_quant_TPM.txt
rRNA-remove
PE125
Specific

organism: Felis catus

source_name: British Shorthair Ear Skin Fibroblasts

tag: cell type

value: Fibroblasts

tag: tissue source

value: Ear Skin


title: Pax7 lineage - E12.5b2_72

description:
ss2_filtered_count.csv
E12.5_b2_7

tag: tissue


title: E171_5mg/kg/bw/day_day21_male_A


title: E171_5mg/kg/bw/day_day21_male_C


title: E171_2mg/kg/bw/day_day21_female_C

value: 21 days of exposure to 2 mg/kgbw/day of E171 in sterile water


title: E171_2mg/kg/bw/day_day21_male_A


title: Pax7 lineage - E12.5b2_75

description:
ss2_filtered_count.csv
E12.5_b2_7

tag: method


title: KG1α shRELA-2


title: KG1α shCtrl-1


title: RNAs from non inoculated seed et collected at 6 days after sowing - Col0_water 3

city: Angers

first: Jerome

last: Verdier

address: Rue Georges Morel

country: France

institute: INRAE / IRHS

data_processing:
The sequencing data was filtered with SOAPnuke (v1.5.2) [1] by (1) Removing reads containing sequencing adapter; (2) Removing reads whose low-quality base ratio (base quality less than or equal to 5) is more than 20%; (3) Removing reads whose unknown base ('N' base) ratio is more than 5%, afterwards clean reads were obtained and stored in FASTQ format.
SOAPnuke: version：v1.5.2, parameters: -l 15 -q 0.5 -n 0.1, website: https://github.com/BGI-flexlab/SOAPnuke
Transcript mapping against Arabidopsis reference transcriptome Araport v11 using Salmon algorithm
Transcript mapping against Arabidopsis reference transcriptome Araport v11 using Salmon algorithm. Transcript mapping against Alternaria brassicicola (Abra43) reference transcritome (Belmas et al. 2018) PHFN00000000 (GeneBank number) using Salmon algorithm.
Assembly: Araport11_genes.201606.cdna.fasta downlaoded from arabidopsis.org. abra_mygenomebrowser_011021_mrna.fasta downloaded from GenBank number PHFN00000000 (https://www.ncbi.nlm.nih.gov/nuccore/PHFN00000000)
Supplementary files format and content: tab-delimited text files include count values for each sample

organism: Arabidopsis thaliana

source_name: entire seed

growth_protocol: Seeds were sowed in petri dishes containing 0.8% agarose (SIGMA) and cultures were incubated in a controlled growth chamber for 3, 6 and 10 days under a 16 h photoperiod (170 µmol photons m2 s-1) at 22 °C (light period)/20 °C (dark period) and a constant 70% relative humidity

extract_protocol:
Seeds were collected at 3, 6 and 10 days after sowing. RNA extraction was performed using NucleoSpin® RNA Plus kit (Macherey-Nagel, Düren, Germany) according to the manufacturer's instructions. RNA quantification and quality was measured with a NanoDrop ND-100 (NanoDrop Technologies, DE, USA) and a 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA) respectively.
RNA samples were sent to Beijing Genomics Institute (BGI)  for cDNA library construction and paired-end sequencing (PE100, 40M) using the DNBseq™ technology

treatment_protocol: To select a fungal inoculum that allows optimal seed germination and generates infection, we evaluated germination and infection rate on seeds using concentrations 10², 10³, 10⁴, 10⁵ conidia/mL of Abra43 and a control corresponding to seeds inoculated with water only. The inoculum 10⁴ was chosen as optimal inoculum concentration. After, seeds were inoculated with 10⁴ conidia/mL of Abra43 and the non-inoculated seeds were imbibed in water.

tag: agent

tag: ecotype

value: Collected at 6 days after sowing

value: entire seed


title: RNAs from non inoculated seed et collected at 10 days after sowing - Col0_water 3

tag: time point

value: Collected at 10 days after sowing


title: RNAs from non inoculated seed et collected at 10 days after sowing - Col0_water 2


title: E171_2mg/kg/bw/day_day21_female_B

value: Distal colon


title: E171_5mg/kg/bw/day_day21_female_A

value: 21 days of exposure to 5 mg/kgbw/day of E171 in sterile water


title: Hi-C data of Cat replicate 2

tag: age

value: unknown


title: Pax7 lineage - E12.5b2_71

description:
ss2_filtered_count.csv
E12.5_b2_7

value: embryonic cells

tag: sequencng type

value: Single-cell

tag: plate batch

value: Plate 2

tag: sequence batch

tag: medium


title: RNAs from non inoculated seed et collected at 6 days after sowing - Col0_water 2


title: E171_2mg/kg/bw/day_day21_male_D

value: male


title: Hi-C data of Cat replicate 1


title: E171_1mg/kg/bw/day_day21_male_C

value: 21 days of exposure to 1 mg/kgbw/day of E171 in sterile water


title: E171_2mg/kg/bw/day_day21_female_A

value: female


title: RNA-seq data of Cat replicate 2


title: E171_1mg/kg/bw/day_day21_male_B


title: Pax7 lineage - E12.5b2_69

description:
ss2_filtered_count.csv
E12.5_b2_6

value: Batch 2

tag: marker


title: KG1α shCtrl-2

value: shCtr vector


title: RNAs from non inoculated seed et collected at 6 days after sowing - Col0_water 1


title: RNA-seq data of Cow replicate 2

description:
cow_quant_TPM.txt
ployA
PE125
non-Specific

organism: Bos taurus

source_name: Holstein Ear Skin Fibroblasts

value: Fibroblasts

value: Adult


title: Pax7 lineage - E12.5b2_67

description:
ss2_filtered_count.csv
E12.5_b2_6


title: RNAs from non inoculated seed et collected at 3 days after sowing - Col0_water 3

value: Collected at 3 days after sowing


title: E171_1mg/kg/bw/day_day21_female_C

tag: gender


title: Pax7 lineage - E12.5b2_68

description:
ss2_filtered_count.csv
E12.5_b2_6


title: RNAs from non inoculated seed et collected at 3 days after sowing - Col0_water 2


title: Pax7 lineage - E12.5b2_66

description:
ss2_filtered_count.csv
E12.5_b2_6


title: Hi-C data of Cow replicate 1

value: Ear Skin


title: RNAs from infected seed et collected at 10 days after sowing - Col0_inoc 3

value: inoculated with Abra43

value: entire seed


title: Hi-C data of Cow replicate 2


title: RNAs from non inoculated seed et collected at 3 days after sowing - Col0_water 1


title: Pax7 lineage - E12.5b2_63

description:
ss2_filtered_count.csv
E12.5_b2_6


title: RNAs from infected seed et collected at 10 days after sowing - Col0_inoc 1

value: Collected at 10 days after sowing


title: RNAs from infected seed et collected at 10 days after sowing - Col0_inoc 2


title: Pax7 lineage - E12.5b2_64

description:
ss2_filtered_count.csv
E12.5_b2_6


title: Pax7 lineage - E12.5b2_65

description:
ss2_filtered_count.csv
E12.5_b2_6


title: Pax7 lineage - E12.5b2_62

description:
ss2_filtered_count.csv
E12.5_b2_6


title: RNAs from non inoculated seed et collected at 10 days after sowing - Col0_water 1


title: RNA-seq data of Cow replicate 1


title: E171_1mg/kg/bw/day_day21_female_B

value: Distal colon

tag: treatment


title: No NNK : Saline 5

city: Fort Collins

first: Tara

middle: M

last: Nordgren

state: CO

address: Colorado State University, Physiology 133

department: Environmental and Radiological Health Sciences

country: USA

institute: Colorado State University

scan_protocol: Chip was imaged and quantified by a nCounter Sprint profiler.

data_processing: Gene expression data analysis was performed using the nCounter Analysis System, nSolver 4.0 software. Manual normalization of the expression data was performed using the geometric mean of the housekeeping genes EEF1G, OAZ1, RPL19, and SDHA. Proceeding sample nor-malization, 21 of the 24 samples passed the normalization parameters and were deemed viable for subsequent analyses. The samples breakdown are as follows: 6 saline-only, 4 HDE-only, 6 saline+NNK, and 5 HDE+NNK.

source_name: RNA from lung tissue, 24 wk saline treatment

label_protocol: We utilized the mouse PanCancer Immune Profiling Panel (NanoString Technologies, Seattle, WA, USA) codeset which is a pre-designed panel containing 770 target genes related to immune response and carcinogenesis. Sample preparation was performed by mixing 50 ng of total RNA with the codeset and reporter probes and hybridizing the mixture for 16 hrs to form the desired target-probe complex. The hybridized complex was then plated and run on a nCounter Sprint profiler to image and quantify the data.

growth_protocol: Male and female A/J mice 8-12 weeks of age were received from The Jackson Laboratory (Bar Harbor, ME, USA) and housed in micro-isolator cages (five per cage) at the University of California, Riverside animal barrier facilities. Mice were allowed unrestricted access to food and water, monitored for any behavioral or physiological changes, and weighed weekly. All experiments and procedures were approved by the University of California River-side Institutional Animal Care and Use Committee.

extract_protocol: Tumors were counted and excised from the left lungs following collection and half of the left lung was then stored in RNA later (Thermo Fisher, Waltham, MA, USA) for gene expression analyses. Left lung tissues were homogenized and RNA was extracted using the PureLink RNA Mini Kit (Invitrogen, Carlsbad, California, USA) and sample quality was quantified using the NanoDrop ND-100 (NanoDrop Technologies, Inc, Wilmington, DE, USA) and an Agilent 2100 Bioanalyzer (UC Riverside Core Facilities, Agilent Technologies, Santa Clara, CA, USA).

treatment_protocol: This study utilized a newly optimized mouse model of chronic lung disease using long-term exposure to HDE, which was adapted from prior acute and repetitive murine dust exposure models. We used a total of 20 A/J mice for the preliminary study with 10 of them being HDE-treated and the other 10 saline-treated. Each mouse was lightly anesthetized by isoflurane inhalation prior to receiving a single intranasal chal-lenge of either 50 uL of 12.5% HDE or 1x PBS, thrice weekly for 24 consecutive weeks. To study the tumorigenic potential of the dust in a chronic exposure setting, we used the tobacco-specific carcinogen NNK to induce lung tumorigenesis in the mice. At the start of week 4, we administered a one-time intraperitoneal injection (i.p.) of 100 mg/kg NNK, which has been well-established to generate lung adenomas in A/J mice 21 weeks post-injection. Of the 20 exposed mice, 5 HDE-exposed and 5 saline-exposed were administered an i.p injection of NNK while the other 5 from each respective group received 1x PBS via i.p injection as the control.

tag: nnk injection

value: no NNK Injected

tag: strain

value: A/J

value: 24 wk saline treatment


title: No NNK : Saline 4


title: Control_day21_male_D

value: 21 days of exposure to sterile water


title: No NNK : Saline 6


title: E171_1mg/kg/bw/day_day21_male_A

value: male


title: Pax7 lineage - E12.5b2_61

description:
ss2_filtered_count.csv
E12.5_b2_6

value: embryonic cells

value: Single-cell

value: Plate 2


title: Control_day21_male_C


title: No NNK : Saline 3

value: female


title: NNK : Saline 6

value: Single NNK Injection


title: Control_day21_male_A


title: Pax7 lineage - E12.5b2_60

description:
ss2_filtered_count.csv
E12.5_b2_6

value: Batch 2


title: E171_5mg/kg/bw/day_day14_male_C

value: 14 days of exposure to 5 mg/kgbw/day of E171 in sterile water


title: E171_5mg/kg/bw/day_day14_male_D


title: Control_day21_male_B


title: RNAs from infected seed et collected at 6 days after sowing - Col0_inoc 1

value: Collected at 6 days after sowing


title: NNK : Saline 5


title: Pax7 lineage - E12.5b2_73

description:
ss2_filtered_count.csv
E12.5_b2_7


title: Pax7 lineage - E12.5b2_59

description:
ss2_filtered_count.csv
E12.5_b2_5


title: RNAs from infected seed et collected at 6 days after sowing - Col0_inoc 3

value: inoculated with Abra43


title: Pax7 lineage - E12.5b2_57

description:
ss2_filtered_count.csv
E12.5_b2_5


title: No NNK : HDE 3

source_name: RNA from lung tissue, 24 wk HDE treatment

value: 24 wk HDE treatment


title: RNAs from infected seed et collected at 6 days after sowing - Col0_inoc 2

value: entire seed


title: Pax7 lineage - E12.5b2_56

description:
ss2_filtered_count.csv
E12.5_b2_5


title: No NNK : HDE 4


title: E171_5mg/kg/bw/day_day14_female_C

value: Distal colon


title: E171_5mg/kg/bw/day_day14_male_B


title: RNA-seq data of Sheep replicate 3

description:
sheep_quant_TPM.txt
ployA
PE125
non-Specific

organism: Ovis aries

source_name: Small Tailed Han Sheep Ear Skin Fibroblasts

tag: cell type

value: Fibroblasts

value: Ear Skin

value: Adult


title: E171_5mg/kg/bw/day_day14_male_A


title: NNK : HDE 5

value: A/J


title: RNA-seq data of Sheep replicate 2

tag: tissue source


title: No NNK : HDE 2

value: no NNK Injected

value: male


title: RNAs from infected seed et collected at 3 days after sowing - Col0_inoc 1

value: Collected at 3 days after sowing

tag: tissue


title: RNA-seq data of Sheep replicate 1


title: Pax7 lineage - E12.5b2_55

description:
ss2_filtered_count.csv
E12.5_b2_5

source_name: Mouse embryonic cells

value: embryonic cells

tag: method

value: Single-cell

value: Plate 2


title: E171_2mg/kg/bw/day_day14_male_D

value: 14 days of exposure to 2 mg/kgbw/day of E171 in sterile water


title: RNAs from infected seed et collected at 3 days after sowing - Col0_inoc 3

tag: agent


title: E171_5mg/kg/bw/day_day14_female_A

value: female

value: 14 days of exposure to 5 mg/kgbw/day of E171 in sterile water


title: No NNK : HDE 1


title: Pax7 lineage - E12.5b2_54

description:
ss2_filtered_count.csv
E12.5_b2_5

value: Batch 2


title: E171_5mg/kg/bw/day_day14_female_B


title: RNAs from infected seed et collected at 3 days after sowing - Col0_inoc 2

value: inoculated with Abra43

tag: ecotype


title: Hi-C data of Sheep replicate 1


title: NNK : HDE 4

value: Single NNK Injection

value: 24 wk HDE treatment


title: E171_2mg/kg/bw/day_day14_male_A

value: Distal colon


title: Hi-C data of Sheep replicate 3

value: Fibroblasts

value: Ear Skin


title: NNK : HDE 1

value: A/J


title: Pax7 lineage - E12.5b2_52

description:
ss2_filtered_count.csv
E12.5_b2_5

tag: time point


title: NNK : HDE 3


title: Hi-C data of Sheep replicate 2

tag: age

value: Adult


title: Pax7 lineage - E12.5b2_47

description:
ss2_filtered_count.csv
E12.5_b2_4

tag: sequencng type


title: NNK : Saline 4

value: male

value: 24 wk saline treatment


title: Pax7 lineage - E12.5b2_49

description:
ss2_filtered_count.csv
E12.5_b2_4

value: embryonic cells

tag: plate batch


title: E171_2mg/kg/bw/day_day14_female_B


title: E171_2mg/kg/bw/day_day14_male_B


title: E171_2mg/kg/bw/day_day14_female_A


title: NNK : Saline 3


title: E171_2mg/kg/bw/day_day14_male_C


title: Pax7 lineage - E12.5b2_51

description:
ss2_filtered_count.csv
E12.5_b2_5

value: Single-cell

tag: sequence batch


title: E171_2mg/kg/bw/day_day14_female_C


title: OA ACL2

city: guangzhou

first: dianbo

last: long

state: guangdong

address: Zhongshan second road

institute: First Affiliated Hospital of Sun Yat-sen University

description: Test

data_processing:
The normalization and all the data analysis were performed according to the manufacturers instructions using their web-based software package: https://www.thermofisher.cn/cn/zh/home/global/forms/ab-7900-software-reg.html
For the normalization it uses the average of three housekeeping genes: RNU6,SNORD43,SNORD95.
Target gene signals normalized to housekeeping genes; 2^-deltaCt, where deltaCt = (Ct_Target − Ct_HKG)]
The web-based software package automatically performs all deltadeltaCt based fold-change calculations from the uploaded raw threshold cycle data.

label: SYBR Green

source_name: Osteoarthritis anterior cruciate ligament cells

label_protocol: Arraystar SYBR® Green qPCR Master Mix(ROX+) (AS-MR-006-5, Arraystar)

growth_protocol: ACL cells were cultured in Dulbecco’s modified Eagle’s medium/Ham’s F-12 nutrient mixture (Gibco Life Technologies) containing 10% foetal bovine serum (Gibco Life Technologies) and 1% penicillin/streptomycin solution. For IL-1β treatment, ACL cells were cultured in the same medium containing IL-1β (5 ng/ml) for 48 h. Cells were incubated at 37 °C in a humidified atmosphere of 5% CO2, and the medium was changed every 2 days.

extract_protocol: Total RNA

treatment_protocol: no

value: Degeneration


title: OA ACL3

description: Test


title: Pax7 lineage - E12.5b2_50

description:
ss2_filtered_count.csv
E12.5_b2_5

value: Plate 2

tag: medium


title: No NNK : Saline 2

value: no NNK Injected


title: Pax7 lineage - E12.5b2_48

description:
ss2_filtered_count.csv
E12.5_b2_4

tag: marker


title: Pax7 lineage - E12.5b2_53

description:
ss2_filtered_count.csv
E12.5_b2_5


title: OA ACL1

description: Test


title: No NNK : Saline 1

tag: gender

value: female


title: NNK : HDE 2

tag: treatment


title: E171_1mg/kg/bw/day_day14_male_B

value: 14 days of exposure to 1 mg/kgbw/day of E171 in sterile water


title: E171_1mg/kg/bw/day_day14_male_D


title: Pax7 lineage - E12.5b2_45

description:
ss2_filtered_count.csv
E12.5_b2_4

value: Batch 2


title: NNK : Saline 1

tag: nnk injection

value: Single NNK Injection


title: E171_1mg/kg/bw/day_day14_male_C


title: Pax7 lineage - E12.5b2_40

description:
ss2_filtered_count.csv
E12.5_b2_4


title: Pax7 lineage - E12.5b2_44

description:
ss2_filtered_count.csv
E12.5_b2_4


title: HFE1R4: MDA-MB-436 Enhancer targeting sample 1 rep 4

city: Chapel Hill

first: Hector

middle: L

last: Franco

state: NC

address: 120 Mason Farm Rd

department: Genetics

institute: UNC Lineberger Cancer Center

description: RNA-seq

data_processing:
Merge multiple FASTQs together
Map the data with STAR 2.7.6a
Quantify the expression with Salmon 1.4.0
Perform QC by running Picard 2.22.4 CollectRnaSeqMetrics, and FastQC 0.11.9
Genome_build: hg38

source_name: dCas9-KRAB expressing MDA-MB-436 TNBC Cells

growth_protocol: MDA-MB-436 TNBC cells expressing dCas9-KRAB were routinely grown and replated in T75 flasks in Dulbecco's modified eagle media supplemented with 10% fetal bovine serum and 1% pen-strep

extract_protocol:
RNA was extracted and purified from cells 48 hrs post-transfection using the Zymo RNA miniprep kit (Cat# R1054).
RNA-seq libraries were constructed by Novogene. 250~300 bp insert cDNA library,PolyA selected, non-strand specific

treatment_protocol: Cells were seeded into 6-well plates and transiently transfected via Fugene 6 (Promega) with unique guide RNA plasmids to target dCas9-KRAB to the region of interest

tag: cell line

value: dCas9-KRAB expressing MDA-MB-436

value: triple-negative breast cancer

tag: condition

value: CSF1 enhancer targeting sample


title: NA ACL3

description: Control

source_name: Normal anterior cruciate ligament cells

tag: cell type

value: Normal


title: Pax7 lineage - E12.5b2_43

description:
ss2_filtered_count.csv
E12.5_b2_4

tag: tissue


title: Pax7 lineage - E12.5b2_38

description:
ss2_filtered_count.csv
E12.5_b2_3

tag: method


title: E171_1mg/kg/bw/day_day14_male_A

value: Distal colon


title: NA ACL1

description: Control


title: Pax7 lineage - E12.5b2_42

description:
ss2_filtered_count.csv
E12.5_b2_4


title: NA ACL2

description: Control


title: NNK : Saline 2

tag: strain

value: A/J


title: FT4: healthy fallopian tube donor 4

city: Ann Arbor

first: Qianyi

last: Ma

state: MI

address: 1141 E Catherine St

department: Human Genetics

institute: University of Michigan

data_processing:
Raw paired-end 10x scRNA-seq data were processed and aligned using CellRanger v4.
Raw gene expression matrix were filtered to keep cells with >500 detected genes and <10% mitochondrial transcripts.
Genome_build: GRCh38
Supplementary_files_format_and_content: raw gene expression matrix

source_name: Fallopian tube cells

extract_protocol:
Fresh human fallopian tube samples obtained from either surgical removal for benign indication and cadaver samples were used as tissue sources. The whole tissue sample was dissected into three anatomic segments (isthmus, ampulla, fimbria). These segments separately were used to create a single cell suspensions by mechanical dissociation and digestion with collagenase at 37C.  All live cells were selected by exclusion of DAPI positive cells by flow cytometry.
Single-cell suspensions were processed and single cell RNA-seq data were generated using the 10X Genomics Chromium platform.

value: Fallopian Tube

tag: donor ethnicity

value: Caucasian

tag: Sex

tag: bmi

tag: menopause

value: premenopausal

tag: source

value: Cadaver

tag: health

value: healthy


title: FT6: fallopian tube donor 6 with hydrosalphinx

tag: age

value: Surgical

value: diseased with hydropsalphinx


title: RNA-seq data of Chicken replicate 4

description:
chicken_quant_TPM.txt
rRNA-remove
PE125
non-Specific

organism: Gallus gallus

source_name: White Leghorn Embryo Fibroblasts

value: Fibroblasts

tag: tissue source

value: Embyo


title: Pax7 lineage - E12.5b2_41

description:
ss2_filtered_count.csv
E12.5_b2_4

value: embryonic cells

tag: sequencng type

value: Single-cell

tag: time point

tag: plate batch

value: Plate 2

tag: sequence batch

value: Batch 2

tag: medium

tag: marker


title: HFE1R1: MDA-MB-436 Enhancer targeting sample 1 rep 1

description: RNA-seq

tag: cell line

value: dCas9-KRAB expressing MDA-MB-436

tag: cell type

value: triple-negative breast cancer

tag: condition

value: CSF1 enhancer targeting sample


title: RNA-seq data of Chicken replicate 5

source_name: Chicken Embryo Fibroblasts


title: E171_1mg/kg/bw/day_day14_female_C

tag: tissue

value: Distal colon

tag: gender

value: female

tag: treatment

value: 14 days of exposure to 1 mg/kgbw/day of E171 in sterile water


title: RNA-seq data of Chicken replicate 3

description:
chicken_quant_TPM.txt
rRNA-remove
PE125
Specific


title: HFE2R3: MDA-MB-436 Enhancer targeting sample 2 rep 3

description: RNA-seq


title: Pax7 lineage - E12.5b2_39

description:
ss2_filtered_count.csv
E12.5_b2_3

tag: method


title: Control_day14_male_C

value: male

value: 14 days of exposure to sterile water


title: RNA-seq data of Chicken replicate 2


title: Hi-C data of Chicken replicate 5


title: E171_1mg/kg/bw/day_day14_female_B


title: E171_1mg/kg/bw/day_day14_female_A


title: Control_day14_male_D


title: Pax7 lineage - E12.5b2_36

description:
ss2_filtered_count.csv
E12.5_b2_3


title: RNA-seq data of Chicken replicate 1


title: Pax7 lineage - E12.5b2_35

description:
ss2_filtered_count.csv
E12.5_b2_3


title: Pax7 lineage - E12.5b2_37

description:
ss2_filtered_count.csv
E12.5_b2_3


title: Hi-C data of Chicken replicate 3


title: Pax7 lineage - E12.5b2_33

description:
ss2_filtered_count.csv
E12.5_b2_3


title: HFE1R3: MDA-MB-436 Enhancer targeting sample 1 rep 3

description: RNA-seq


title: HFG1R4: MDA-MB-436 Gene targeting sample 1 rep 4

description: RNA-seq

value: CSF1 TSS targeting sample


title: HFN2R4: MDA-MB-436 Negative control 2 rep 4

description: RNA-seq

value: Negative control


title: Pax7 lineage - E12.5b2_30

description:
ss2_filtered_count.csv
E12.5_b2_3


title: HFG2R3: MDA-MB-436 Gene targeting sample 2 rep 3

description: RNA-seq


title: HFN2R3: MDA-MB-436 Negative control 2 rep 3

description: RNA-seq


title: Control_day14_female_A


title: Hi-C data of Chicken replicate 2


title: Pax7 lineage - E12.5b2_32

description:
ss2_filtered_count.csv
E12.5_b2_3


title: Control_day14_female_B


title: Hi-C data of Chicken replicate 1


title: HFG1R1: MDA-MB-436 Gene targeting sample 1 rep 1

description: RNA-seq


title: Control_day14_male_A


title: Control_day14_male_B


title: Hi-C data of Chicken replicate 4


title: FOSL2_R2_Input

city: Turku

first: Sini

last: Junttila

address: Tykistökatu 6 A

department: Turku Bioscience Centre

country: Finland

institute: University of Turku

description:
181121_SNK268_B_L007_AIFW-10
Naive CD4+ T cells isolated from human umbilical cord blood were in vitro polarized to Th17-fate for 72h and further subjected to FOSL2 ChIP analysis

data_processing:
ChIP-seq reads were aligned to the hg38 genome assembly with Bowtie2 (v. 2.3.3.1)
Reads with mapping quality value < 30 were filtered out using samtools (v. 1.9) and duplicate reads were removed using Picard tool's (v. 2.20.2) MarkDuplicates function.
Peaks were called using MACS2 (v. 2.1.2_dev) with the following settings: -g hs -q 0.05
Genome_build: hg38
Supplementary_files_format_and_content: narrowPeak files were generated with MACS2 (v. 2.1.2_dev)

source_name: FOSL2 ChIP-seq

growth_protocol: Human CD4+ T cells were purified from umbilical cord blood of healthy neonates (Turku University Central Hospital, Finland). Mononuclear cells were isolated (Ficoll-Paque, GE Healthcare), after which CD4+ cells were collected (Dynal CD4 Positive Isolation Kit, Invitrogen). Cells were then stimulated for 72h with plate-bound α-CD3 (3.75 µg/ml; Immunotech) and soluble α-CD28 (1 μg/mL; Immunotech) in X-vivo 20 serum-free medium (Lonza) supplemented with L-glutamine (2 mM, Sigma-Aldrich) and antibiotics (50 U/mL penicillin and 50 μg/mL streptomycin; Sigma-Aldrich). Th17-polarization was induced using IL-6 (20 ng/mL; Roche), IL-1β (10 ng/mL), TGF-β (10 ng/mL)] and the neutralizing antibodies anti-IFN-γ (1 μg/mL) and anti-IL-4 (1 μg/mL). All cytokines and neutralizing antibodies used in the study were purchased from R&D Systems. All cultures were maintained at 37°C in a humidified atmosphere of 5% (v/v) CO2/air.

extract_protocol:
CD4+ T cells were cultured under Th17 cell polarizing conditions for 72h. Chromatin was prepared (Diagenode Chromatin shearing optimization kit) and further subjected to sonication (Bioruptor, Diagenode) to obtain chromatin fragments of 100–500 bps. Histone DNA complexes were isolated using antibodies against FOSL1, FOSL2 or BATF.
Libraries were prepared according to Illumina's instructions.

tag: cell source

value: Human umbilical cord blood

value: Human naive CD4+ T cells polarized to Th17-fate for 72h

tag: chip antibody

tag: biological replicate

value: Biological Replicate :2


title: Pax7 lineage - E12.5b2_31

description:
ss2_filtered_count.csv
E12.5_b2_3

value: embryonic cells


title: HFN1R4: MDA-MB-436 Negative control 1 rep 4

description: RNA-seq


title: E171_5mg/kg/bw/day_day7_male_D

value: 7 days of exposure to 5 mg/kgbw/day of E171 in sterile water


title: Pax7 lineage - E12.5b2_27

description:
ss2_filtered_count.csv
E12.5_b2_2

value: Single-cell

value: Plate 2


title: HFN2R1: MDA-MB-436 Negative control 2 rep 1

description: RNA-seq

value: dCas9-KRAB expressing MDA-MB-436


title: E171_5mg/kg/bw/day_day7_female_C


title: FOSL2_R2

description:
181121_SNK268_B_L007_AIFW-12
Naive CD4+ T cells isolated from human umbilical cord blood were in vitro polarized to Th17-fate for 72h and further subjected to FOSL2 ChIP analysis

value: anti-FOSL2; Cell Signaling Tech, Cat no.19967


title: E171_5mg/kg/bw/day_day7_male_C


title: Pax7 lineage - E12.5b2_26

description:
ss2_filtered_count.csv
E12.5_b2_2

value: Batch 2


title: Pax7 lineage - E12.5b2_29

description:
ss2_filtered_count.csv
E12.5_b2_2


title: HFN1R1: MDA-MB-436 Negative control 1 rep 1

description: RNA-seq

value: triple-negative breast cancer


title: Pax7 lineage - E12.5b2_28

description:
ss2_filtered_count.csv
E12.5_b2_2


title: HFG1R3: MDA-MB-436 Gene targeting sample 1 rep 3

description: RNA-seq


title: Pax7 lineage - E12.5b2_25

description:
ss2_filtered_count.csv
E12.5_b2_2


title: FOSL2_R1_Input

description:
181121_SNK268_B_L007_AIFW-7
Naive CD4+ T cells isolated from human umbilical cord blood were in vitro polarized to Th17-fate for 72h and further subjected to FOSL2 ChIP analysis

value: Biological Replicate :1


title: HFN1R3: MDA-MB-436 Negative control 1 rep 3

description: RNA-seq


title: FOSL1_C-12_R1_Input

description:
190517_SNK268_A_L002_AIFW-23
Naive CD4+ T cells isolated from human umbilical cord blood were in vitro polarized to Th17-fate for 72h and further subjected to FOSL1 ChIP analysis

source_name: FOSL1 ChIP-seq


title: E171_5mg/kg/bw/day_day7_male_A

value: Distal colon


title: E171_5mg/kg/bw/day_day7_female_A

value: female


title: Pax7 lineage - E12.5b2_23

description:
ss2_filtered_count.csv
E12.5_b2_2


title: Pax7 lineage - E12.5b2_21

description:
ss2_filtered_count.csv
E12.5_b2_2


title: BATF R3_Input

description:
190517_SNK268_A_L005_AIFW-33
Naive CD4+ T cells isolated from human umbilical cord blood were in vitro polarized to Th17-fate for 72h and further subjected to BATF ChIP analysis

source_name: BATF ChIP-seq


title: FOSL1_C-12_R2_Input

description:
190517_SNK268_A_L002_AIFW-26
Naive CD4+ T cells isolated from human umbilical cord blood were in vitro polarized to Th17-fate for 72h and further subjected to FOSL1 ChIP analysis


title: FOSL2_R1

description:
181121_SNK268_B_L007_AIFW-9
Naive CD4+ T cells isolated from human umbilical cord blood were in vitro polarized to Th17-fate for 72h and further subjected to FOSL2 ChIP analysis


title: FOSL1_C-12_R2

description:
190517_SNK268_A_L002_AIFW-27
Naive CD4+ T cells isolated from human umbilical cord blood were in vitro polarized to Th17-fate for 72h and further subjected to FOSL1 ChIP analysis

value: anti-FOSL1; Santacruz Biotechnology, Cat no.sc-28310


title: E171_5mg/kg/bw/day_day7_female_B


title: Pax7 lineage - E12.5b2_24

description:
ss2_filtered_count.csv
E12.5_b2_2


title: E171_2mg/kg/bw/day_day7_male_B

value: male

value: 7 days of exposure to 2 mg/kgbw/day of E171 in sterile water


title: Serum_free_5

city: Oslo

first: Thomas

last: Sæther

state: Oslo

address: Sognsvannsveien 9

department: Dept. of Molecular Medicine

country: Norway

institute: University of Oslo

description: serum free medium

data_processing:
50 bp paired end reads were sequenced on an Illumina Novaseq 600 intrument
BBDuk (BBMap v34.56) was used to remove/trim low-quality reads and adapter sequences
Reads were  mapped to a human reference genome/transcriptome (ENSEMBL release 101, GRCh38.101) using HiSat2 v.1.2.1
Read counting was done with FeatureCounts v1.4.6-p1
Genome_build: GRCh38.101
Supplementary_files_format_and_content: Normalized_gene_counts_TPM.csv is a csv file that containes normalised counts (Transcripts Per Million; TPM), for all samples, annotated to Ensembl IDs/EntrezGene IDs/HCGN. Unnormalised_feature_counts.csv is a csv file containing unnormalised counts for all samples, annotated to Ensembl IDs, generated in HiSat2 v.1.2.1

source_name: HepG2 cells

growth_protocol: HepG2 cells were grown in DMEM with 10% FBS (Sigma-Aldrich, Cat# D6546). For experiments, cells were kept in serum-free medium overnight, before they were incubated +/- human serum

extract_protocol:
RNA was isolated with a NucleoSpin RNA mini kit (Machery-Nagel), according to the manufacturer’s instructions.
Strand-Specific TruSeqTM mRNA-seq library preparation

treatment_protocol: Cells were incubated +/- 20% human serum for 6 hours. The serum samples were from a postprandial, randomised, controlled cross-over study where participants (n=5) consumed protein from salmon by-products (fishmeal) or whey. Serum was taken at 0 min (fasting) and 30 and 60 min after consumption. In addition, 6 wells were incubated with serum free medium.

tag: participant id

tag: timepoint

tag: supplement


title: Serum_free_4

description: serum free medium


title: FOSL1_C-12_R1

description:
190517_SNK268_A_L002_AIFW-24
Naive CD4+ T cells isolated from human umbilical cord blood were in vitro polarized to Th17-fate for 72h and further subjected to FOSL1 ChIP analysis

value: Human umbilical cord blood


title: Serum_free_3

description: serum free medium


title: Serum_free_6

description: serum free medium


title: E171_2mg/kg/bw/day_day7_male_D


title: BATF_R1_Input

description:
190517_SNK268_A_L005_AIFW-29
Naive CD4+ T cells isolated from human umbilical cord blood were in vitro polarized to Th17-fate for 72h and further subjected to BATF ChIP analysis

value: Human naive CD4+ T cells polarized to Th17-fate for 72h


title: Pax7 lineage - E12.5b2_19

description:
ss2_filtered_count.csv
E12.5_b2_1

tag: sequencng type

tag: time point

tag: plate batch


title: Pax7 lineage - E12.5b2_20

description:
ss2_filtered_count.csv
E12.5_b2_2

tag: sequence batch

tag: medium

tag: marker


title: E171_2mg/kg/bw/day_day7_male_C


title: BATF R1

description:
190517_SNK268_A_L005_AIFW-30
Naive CD4+ T cells isolated from human umbilical cord blood were in vitro polarized to Th17-fate for 72h and further subjected to BATF ChIP analysis

tag: cell type

value: anti-BATF; Cell Signaling, Cat no. 8638


title: Serum_free_2

description: serum free medium


title: E171_2mg/kg/bw/day_day7_male_A

tag: tissue


title: Pax7 lineage - E12.5b2_18

description:
ss2_filtered_count.csv
E12.5_b2_1

value: embryonic cells


title: Serum_free_1

description: serum free medium


title: Whey_60_ID15

description: 6 hours incubation with human serum

value: Whey


title: rep4 OE 72h GFP

description:
45-190038-C13_S45
Naive CD4+ T cells were nucleofected with control GFP RNA and polarized to Th17-phenotype for 72h

data_processing:
RNA-seq reads were aligned to the hg38 reference genome using align method of Rsubread (v. 1.34.6) package in R (v. 3.6.1)
Read counts for each gene were obtained using featureCount method of Rsubread (v. 1.34.6) package in R (v. 3.6.1)
Genome_build: hg38
Supplementary_files_format_and_content: txt file with raw gene counts for every gene and every sample

source_name: Human naive CD4+ T cells polarized to Th17-fate for 72h

growth_protocol: Human CD4+ T cells were purified from umbilical cord blood of healthy neonates (Turku University Central Hospital, Finland). Mononuclear cells were isolated (Ficoll-Paque, GE Healthcare), after which CD4+ cells were collected (Dynal CD4 Positive Isolation Kit, Invitrogen). Cells were then stimulated with plate-bound α-CD3 (3.75 µg/ml; Immunotech) and soluble α-CD28 (1 μg/mL; Immunotech) in X-vivo 20 serum-free medium (Lonza) supplemented with L-glutamine (2 mM, Sigma-Aldrich) and antibiotics (50 U/mL penicillin and 50 μg/mL streptomycin; Sigma-Aldrich). Th17-polarization was induced using IL-6 (20 ng/mL; Roche), IL-1β (10 ng/mL), TGF-β (10 ng/mL)] and the neutralizing antibodies anti-IFN-γ (1 μg/mL) and anti-IL-4 (1 μg/mL). All cytokines and neutralizing antibodies used in the study were purchased from R&D Systems. All cultures were maintained at 37°C in a humidified atmosphere of 5% (v/v) CO2/air.

extract_protocol:
RNA was isolated (RNeasy Mini Kit; QIAGEN, Cat no. 74104) and given on-column DNase treatment (RNase-Free DNase Set; QIAGEN) for 15 min. The removal of genomic DNA was ascertained by an additional treatment of the samples with DNase I (Invitrogen, Cat no. 18068-015). RNA was eluted in dH2O.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Naive CD4+ T cells were nucleofected with the following - (1) For BATF KD: Non-targeting (Scr) and si BATF (2) For FOSL KD: Non-targeting (Scr), si FOSL1, si FOSL2 and si FOSL1+FOSL2 (Double KD) (3) For FOSL OE: GFP control RNA, FOSL1 RNA, FOSL2 RNA and FOSL1+FOSL2 RNA (Double OE)

value: Human Umbilical Cord blood

tag: genotype/variation

value: nucleofected with control GFP RNA


title: BATF R3

description:
190517_SNK268_A_L005_AIFW-34
Naive CD4+ T cells isolated from human umbilical cord blood were in vitro polarized to Th17-fate for 72h and further subjected to BATF ChIP analysis

value: Biological Replicate :2


title: Pax7 lineage - E12.5b2_17

description:
ss2_filtered_count.csv
E12.5_b2_1

value: Single-cell

value: Plate 2


title: rep3 OE 72h GFP

description:
41-190038-C9_S41
Naive CD4+ T cells were nucleofected with control GFP RNA and polarized to Th17-phenotype for 72h


title: Whey_30_ID15

description: 6 hours incubation with human serum


title: Pax7 lineage - E12.5b2_16

description:
ss2_filtered_count.csv
E12.5_b2_1

value: Batch 2


title: Whey_F_ID15

description: 6 hours incubation with human serum

value: fasting


title: Pax7 lineage - E12.5b2_15

description:
ss2_filtered_count.csv
E12.5_b2_1


title: rep2 OE 72h GFP

description:
37-190038-C5_S37
Naive CD4+ T cells were nucleofected with control GFP RNA and polarized to Th17-phenotype for 72h


title: Pax7 lineage - E12.5b2_14

description:
ss2_filtered_count.csv
E12.5_b2_1


title: Fishmeal_60_ID15

description: 6 hours incubation with human serum

value: Fishmeal


title: rep4 OE 72h FOSL2GFP

description:
47-190038-C15_S47
Naive CD4+ T cells were nucleofected with FOSL2 OE RNA and polarized to Th17-phenotype for 72h

value: nucleofected with FOSL2 OE RNA


title: Fishmeal_F_ID15

description: 6 hours incubation with human serum


title: E171_1mg/kg/bw/day_day7_male_D

value: Distal colon

tag: gender

tag: treatment

value: 7 days of exposure to 1 mg/kgbw/day of E171 in sterile water


title: Fishmeal_30_ID15

description: 6 hours incubation with human serum


title: Pax7 lineage - E12.5b2_13

description:
ss2_filtered_count.csv
E12.5_b2_1

tag: method


title: Pax7 lineage - E12.5b2_12

description:
ss2_filtered_count.csv
E12.5_b2_1


title: rep2 OE 72h FOSL2GFP

description:
39-190038-C7_S39
Naive CD4+ T cells were nucleofected with FOSL2 OE RNA and polarized to Th17-phenotype for 72h

tag: cell source


title: rep3 OE 72h FOSL2GFP

description:
43-190038-C11_S43
Naive CD4+ T cells were nucleofected with FOSL2 OE RNA and polarized to Th17-phenotype for 72h

tag: biological replicate


title: E171_2mg/kg/bw/day_day7_female_B

value: female

value: 7 days of exposure to 2 mg/kgbw/day of E171 in sterile water


title: E171_2mg/kg/bw/day_day7_female_C


title: E171_1mg/kg/bw/day_day7_male_A

value: male


title: E171_1mg/kg/bw/day_day7_female_B


title: Pax7 lineage - E12.5b2_11

description:
ss2_filtered_count.csv
E12.5_b2_1


title: E171_1mg/kg/bw/day_day7_male_B


title: rep4 OE 72h FOSL1GFP

description:
46-190038-C14_S46
Naive CD4+ T cells were nucleofected with FOSL1 OE RNA and polarized to Th17-phenotype for 72h

value: nucleofected with FOSL1 OE RNA


title: E171_1mg/kg/bw/day_day7_female_C


title: Whey_60_ID14

description: 6 hours incubation with human serum

tag: participant id


title: Whey_30_ID14

description: 6 hours incubation with human serum

tag: timepoint


title: rep3 OE 72h FOSL1GFP

description:
42-190038-C10_S42
Naive CD4+ T cells were nucleofected with FOSL1 OE RNA and polarized to Th17-phenotype for 72h


title: E171_2mg/kg/bw/day_day7_female_A


title: Whey_F_ID14

description: 6 hours incubation with human serum

tag: supplement


title: Pax7 lineage - E12.5b2_9

description:
ss2_filtered_count.csv
E12.5_b2_9

value: embryonic cells

tag: sequencng type


title: rep2 OE 72h FOSL1GFP

description:
38-190038-C6_S38
Naive CD4+ T cells were nucleofected with FOSL1 OE RNA and polarized to Th17-phenotype for 72h


title: Fishmeal_60_ID14

description: 6 hours incubation with human serum


title: Pax7 lineage - E12.5b2_8

description:
ss2_filtered_count.csv
E12.5_b2_8

tag: time point


title: Fishmeal_30_ID14

description: 6 hours incubation with human serum


title: E171_1mg/kg/bw/day_day7_female_A


title: Pax7 lineage - E12.5b2_7

description:
ss2_filtered_count.csv
E12.5_b2_7

tag: plate batch


title: rep4 OE 72h DoubleOE

description:
48-190038-C16_S48
Naive CD4+ T cells were nucleofected with FOSL1 + FOSL2 OE RNA and polarized to Th17-phenotype for 72h

value: nucleofected with FOSL1 + FOSL2 OE RNA


title: Control_day7_male_B

value: 7 days of exposure to sterile water


title: Pax7 lineage - E12.5b2_6

description:
ss2_filtered_count.csv
E12.5_b2_6

tag: sequence batch


title: rep3 OE 72h DoubleOE

description:
44-190038-C12_S44
Naive CD4+ T cells were nucleofected with FOSL1 + FOSL2 OE RNA and polarized to Th17-phenotype for 72h

value: Human Umbilical Cord blood


title: rep2 OE 72h DoubleOE

description:
40-190038-C8_S40
Naive CD4+ T cells were nucleofected with FOSL1 + FOSL2 OE RNA and polarized to Th17-phenotype for 72h


title: Whey_60_ID13

description: 6 hours incubation with human serum

value: Whey


title: Whey_30_ID13

description: 6 hours incubation with human serum


title: Pax7 lineage - E12.5b2_4

description:
ss2_filtered_count.csv
E12.5_b2_4

value: Single-cell

tag: medium


title: Control_day7_male_D


title: Pax7 lineage - E12.5b2_5

description:
ss2_filtered_count.csv
E12.5_b2_5

value: Plate 2

tag: marker


title: rep4 KD 72h Scr

description:
29-190038-B13_S29
Naive CD4+ T cells were nucleofected with scr siRNA and polarized to Th17-phenotype for 72h

tag: cell type

value: nucleofected with scr siRNA


title: Control_day7_male_A

tag: tissue


title: Pax7 lineage - E12.5b2_3

description:
ss2_filtered_count.csv
E12.5_b2_3

value: Batch 2


title: rep3 KD 72h Scr

description:
21-190038-B5_S21
Naive CD4+ T cells were nucleofected with scr siRNA and polarized to Th17-phenotype for 72h

tag: genotype/variation


title: rep1 KD 72h Scr

description:
5-190038-A5_S5
Naive CD4+ T cells were nucleofected with scr siRNA and polarized to Th17-phenotype for 72h


title: Whey_F_ID13

description: 6 hours incubation with human serum

value: fasting


title: Pax7 lineage - E12.5b2_2

description:
ss2_filtered_count.csv
E12.5_b2_2


title: Control_day7_female_C

tag: gender


title: Fishmeal_F_ID14

description: 6 hours incubation with human serum

value: Fishmeal


title: rep4 KD 72h FOSL2

description:
31-190038-B15_S31
Naive CD4+ T cells were nucleofected with si FOSL2 and polarized to Th17-phenotype for 72h

value: nucleofected with si FOSL2


title: Fishmeal_30_ID13

description: 6 hours incubation with human serum


title: Control_day7_female_A

value: Distal colon

tag: treatment


title: rep3 KD 72h FOSL2

description:
23-190038-B7_S23
Naive CD4+ T cells were nucleofected with si FOSL2 and polarized to Th17-phenotype for 72h


title: E171_5mg/kg/bw/day_day2_male_D

value: 2 days of exposure to 5 mg/kgbw/day of E171 in sterile water


title: Control_day7_female_B

value: female


title: Pax7 lineage - E12.5b1_69

description:
ss2_filtered_count.csv
E12.5_b1_6

tag: method

value: Plate 1

value: Batch 1


title: E171_5mg/kg/bw/day_day2_male_C

value: male


title: Fishmeal_F_ID13

description: 6 hours incubation with human serum


title: E171_5mg/kg/bw/day_day2_male_A


title: Pax7 lineage - E12.5b1_67

description:
ss2_filtered_count.csv
E12.5_b1_6

value: embryonic cells


title: rep1 KD 72h FOSL2

description:
7-190038-A7_S7
Naive CD4+ T cells were nucleofected with si FOSL2 and polarized to Th17-phenotype for 72h

tag: cell source


title: E171_5mg/kg/bw/day_day2_male_B


title: Fishmeal_60_ID13

description: 6 hours incubation with human serum


title: Pax7 lineage - E12.5b1_68

description:
ss2_filtered_count.csv
E12.5_b1_6


title: Control_day7_male_C

value: 7 days of exposure to sterile water


title: Whey_F_ID12

description: 6 hours incubation with human serum


title: rep3 KD 72h FOSL1

description:
22-190038-B6_S22
Naive CD4+ T cells were nucleofected with si FOSL1 and polarized to Th17-phenotype for 72h

value: Human Umbilical Cord blood

value: nucleofected with si FOSL1

tag: biological replicate


title: rep4 KD 72h FOSL1

description:
30-190038-B14_S30
Naive CD4+ T cells were nucleofected with si FOSL1 and polarized to Th17-phenotype for 72h


title: Whey_30_ID12

description: 6 hours incubation with human serum

tag: participant id

value: Whey


title: E171_5mg/kg/bw/day_day7_male_B

value: 7 days of exposure to 5 mg/kgbw/day of E171 in sterile water


title: rep1 KD 72h FOSL1

description:
6-190038-A6_S6
Naive CD4+ T cells were nucleofected with si FOSL1 and polarized to Th17-phenotype for 72h


title: Pax7 lineage - E12.5b2_1

description:
ss2_filtered_count.csv
E12.5_b2_1

value: Single-cell

value: Plate 2


title: Pax7 lineage - E12.5b1_65

description:
ss2_filtered_count.csv
E12.5_b1_6


title: rep4 KD 72h DoubleKD

description:
32-190038-B16_S32
Naive CD4+ T cells were nucleofected with si FOSL1+ si FOSL2 and polarized to Th17-phenotype for 72h

value: nucleofected with si FOSL1+ si FOSL2


title: Pax7 lineage - E12.5b1_64

description:
ss2_filtered_count.csv
E12.5_b1_6


title: Whey_60_ID12

description: 6 hours incubation with human serum

tag: timepoint


title: rep3 KD 72h DoubleKD

description:
24-190038-B8_S24
Naive CD4+ T cells were nucleofected with si FOSL1+ si FOSL2 and polarized to Th17-phenotype for 72h


title: Fishmeal_30_ID12

description: 6 hours incubation with human serum

tag: supplement

value: Fishmeal


title: E171_5mg/kg/bw/day_day2_female_C


title: E171_5mg/kg/bw/day_day2_female_A


title: rep1 KD 72h DoubleKD

description:
8-190038-A8_S8
Naive CD4+ T cells were nucleofected with si FOSL1+ si FOSL2 and polarized to Th17-phenotype for 72h


title: Whey_60_ID11

description: 6 hours incubation with human serum


title: E171_2mg/kg/bw/day_day2_male_D

value: 2 days of exposure to 2 mg/kgbw/day of E171 in sterile water


title: Pax7 lineage - E12.5b1_62

description:
ss2_filtered_count.csv
E12.5_b1_6

tag: sequencng type


title: Pax7 lineage - E12.5b1_61

description:
ss2_filtered_count.csv
E12.5_b1_6

tag: time point


title: Fishmeal_F_ID12

description: 6 hours incubation with human serum

value: fasting


title: rep3 KD 24h Scr

description:
17-190038-B1_S17
Naive CD4+ T cells were nucleofected with scr siRNA and polarized to Th17-phenotype for 24h

source_name: Human naive CD4+ T cells polarized to Th17-fate for 24h

value: nucleofected with scr siRNA


title: Pax7 lineage - E12.5b1_66

description:
ss2_filtered_count.csv
E12.5_b1_6

tag: plate batch


title: Whey_30_ID11

description: 6 hours incubation with human serum


title: rep2 KD 24h Scr

description:
9-190038-A9_S9
Naive CD4+ T cells were nucleofected with scr siRNA and polarized to Th17-phenotype for 24h


title: E171_2mg/kg/bw/day_day2_male_A

value: Distal colon


title: Pax7 lineage - E12.5b1_60

description:
ss2_filtered_count.csv
E12.5_b1_6

value: Plate 1

tag: sequence batch


title: E171_2mg/kg/bw/day_day2_male_C


title: E171_2mg/kg/bw/day_day2_female_C

value: female


title: rep1 KD 24h Scr

description:
1-190038-A1_S1
Naive CD4+ T cells were nucleofected with scr siRNA and polarized to Th17-phenotype for 24h


title: E171_2mg/kg/bw/day_day2_male_B

value: male


title: rep3 KD 24h FOSL2

description:
19-190038-B3_S19
Naive CD4+ T cells were nucleofected with si FOSL2 and polarized to Th17-phenotype for 24h

value: nucleofected with si FOSL2


title: Pax7 lineage - E12.5b1_58

description:
ss2_filtered_count.csv
E12.5_b1_5

value: embryonic cells

value: Batch 1

tag: medium


title: Fishmeal_60_ID11

description: 6 hours incubation with human serum


title: Pax7 lineage - E12.5b1_63

description:
ss2_filtered_count.csv
E12.5_b1_6

tag: marker


title: Pax7 lineage - E12.5b1_59

description:
ss2_filtered_count.csv
E12.5_b1_5


title: Whey_F_ID11

description: 6 hours incubation with human serum


title: Fishmeal_F_ID11

description: 6 hours incubation with human serum


title: E171_1mg/kg/bw/day_day2_male_C

value: 2 days of exposure to 1 mg/kgbw/day of E171 in sterile water


title: Fishmeal_30_ID11

description: 6 hours incubation with human serum


title: Pax7 lineage - E12.5b1_57

description:
ss2_filtered_count.csv
E12.5_b1_5


title: rep2 KD 24h FOSL2

description:
11-190038-A11_S11
Naive CD4+ T cells were nucleofected with si FOSL2 and polarized to Th17-phenotype for 24h

value: Human Umbilical Cord blood

tag: cell type


title: rep1 KD 24h FOSL2

description:
3-190038-A3_S3
Naive CD4+ T cells were nucleofected with si FOSL2 and polarized to Th17-phenotype for 24h


title: E171_1mg/kg/bw/day_day2_male_D

tag: tissue


title: Isthmus3: Isthmus of healthy fallopian tube donor 3

description:
Isthmus3
1714-YS-3_GAGACGCACG-ATGTTCATAG

data_processing:
Raw paired-end sequence data were processed and aligned using CellRanger v4.
Raw gene expression matrix were filtere to keep cells with >500 detected genes and <10% mitochondrial transcripts.
Genome_build: GRCh38
Supplementary_files_format_and_content: raw gene expression matrix

source_name: Fallopian tube Isthmus cells

extract_protocol:
Fresh human fallopian tube samples obtained from either surgical removal for benign indication and cadaver samples were used as tissue sources. The whole tissue sample was dissected into three anatomic segments (isthmus, ampulla, fimbria). These segments separately were used to create a single cell suspensions by mechanical dissociation and digestion with collagenase at 37C.  All live cells were selected by exclusion of DAPI positive cells by flow cytometry.
10x Chromium scRNA-seq; Single-cell suspensions were processed and single cell RNA-seq data were generated using the 10X Genomics Chromium platform.

value: Fallopian Tube

tag: donor ethnicity

value: Caucasian

tag: age

tag: Sex

tag: bmi

tag: menopause

value: premenopausal

tag: source

value: Surgical

tag: health

value: healthy


title: Pax7 lineage - E12.5b1_56

description:
ss2_filtered_count.csv
E12.5_b1_5

tag: method

value: Single-cell


title: rep3 KD 24h FOSL1

description:
18-190038-B2_S18
Naive CD4+ T cells were nucleofected with si FOSL1 and polarized to Th17-phenotype for 24h

tag: cell source

tag: genotype/variation

value: nucleofected with si FOSL1

tag: biological replicate


title: Pax7 lineage - E12.5b1_55

description:
ss2_filtered_count.csv
E12.5_b1_5

tag: sequencng type

tag: time point

tag: plate batch


title: Ampulla3: Ampulla of healthy fallopian tube donor 3

description:
Ampulla3
1714-YS-2_CGTCCACCTG-GTCATGAATG

source_name: Fallopian tube Ampulla cells


title: Fimbria3: Fimbria of healthy fallopian tube donor 3

description:
Fimbria3
1714-YS-1_GAATTGGTTA-CTACTAGAGT

source_name: Fallopian tube Fimbria cells


title: Pax7 lineage - E12.5b1_54

description:
ss2_filtered_count.csv
E12.5_b1_5

tag: sequence batch

tag: medium

tag: marker


title: rep2 KD 24h FOSL1

description:
10-190038-A10_S10
Naive CD4+ T cells were nucleofected with si FOSL1 and polarized to Th17-phenotype for 24h

tag: cell type


title: rep1 KD 24h FOSL1

description:
2-190038-A2_S2
Naive CD4+ T cells were nucleofected with si FOSL1 and polarized to Th17-phenotype for 24h


title: E171_1mg/kg/bw/day_day2_male_A

tag: tissue

tag: gender

tag: treatment


title: Isthmus5: Isthmus and Ampulla of fallopian tube donor 5 with hydrosalphinx

description:
Isthmus5
1407-NU-2

tag: donor ethnicity

tag: age

tag: Sex

tag: bmi

tag: menopause

value: diseased with hydropsalphinx


title: Pax7 lineage - E12.5b1_53

description:
ss2_filtered_count.csv
E12.5_b1_5

tag: method


title: rep3 KD 24h DoubleKD

description:
20-190038-B4_S20
Naive CD4+ T cells were nucleofected with si FOSL1+ si FOSL2 and polarized to Th17-phenotype for 24h

tag: cell source

tag: genotype/variation

value: nucleofected with si FOSL1+ si FOSL2

tag: biological replicate


title: E171_1mg/kg/bw/day_day2_female_B

value: Distal colon


title: E171_1mg/kg/bw/day_day2_female_A

value: female


title: FimAmp5: Fimbria and Ampulla of fallopian tube donor 5 with hydrosalphinx

description:
FimAmp5
1407-NU-1

tag: source

tag: health


title: Pax7 lineage - E12.5b1_52

description:
ss2_filtered_count.csv
E12.5_b1_5

tag: sequencng type

tag: time point

tag: plate batch

value: Plate 1

tag: sequence batch

tag: medium


title: E171_1mg/kg/bw/day_day2_female_C

tag: tissue

tag: gender

tag: treatment


title: rep2 KD 24h DoubleKD

description:
12-190038-A12_S12
Naive CD4+ T cells were nucleofected with si FOSL1+ si FOSL2 and polarized to Th17-phenotype for 24h

tag: cell type


title: Isthmus2: Isthmus of healthy fallopian tube donor 2

description:
Isthmus2
1427-NU-3

tag: donor ethnicity

tag: age

tag: Sex

tag: bmi

value: Cadaver


title: E171_1mg/kg/bw/day_day2_male_B

value: male


title: Control_day2_male_C

value: 2 days of exposure to sterile water


title: Pax7 lineage - E12.5b1_51

description:
ss2_filtered_count.csv
E12.5_b1_5

value: embryonic cells

tag: method

value: Batch 1

tag: marker


title: Control_day2_male_B


title: Pax7 lineage - E12.5b1_50

description:
ss2_filtered_count.csv
E12.5_b1_5


title: Ampulla2: Ampulla of healthy fallopian tube donor 2

description:
Ampulla2
1427-NU-2

value: Fallopian Tube

tag: menopause

tag: source


title: Pax7 lineage - E12.5b1_49

description:
ss2_filtered_count.csv
E12.5_b1_4

tag: sequencng type


title: rep3 BATF 72h Scr

description:
59-190038-AST11_S59
Naive CD4+ T cells were nucleofected with siBATF and polarized to Th17-phenotype for 72h

tag: cell source

value: Human Umbilical Cord blood

tag: genotype/variation

value: nucleofected with siBATF

tag: biological replicate


title: rep2 BATF 72h Scr

description:
55-190038-AST7_S55
Naive CD4+ T cells were nucleofected with siBATF and polarized to Th17-phenotype for 72h


title: Fimbria2: Fimbria of healthy fallopian tube donor 2

description:
Fimbria2
1427-NU-1

value: Caucasian

value: premenopausal

tag: health


title: Pax7 lineage - E12.5b1_48

description:
ss2_filtered_count.csv
E12.5_b1_4

tag: tissue

value: Single-cell

tag: time point

tag: plate batch

tag: sequence batch

tag: medium


title: Control_day2_female_C

tag: gender

tag: treatment


title: Isthmus1: Isthmus of healthy fallopian tube donor 1

description:
Isthmus1
747-YS-3

tag: donor ethnicity

tag: age

tag: Sex

tag: bmi

value: perimenopausal

value: Surgical

value: healthy


title: Pax7 lineage - E12.5b1_47

description:
ss2_filtered_count.csv
E12.5_b1_4

tag: method

tag: marker


title: Ampulla1: Ampulla of healthy fallopian tube donor 1

description:
Ampulla1
747-YS-2

tag: menopause

tag: source


title: Pax7 lineage - E12.5b1_46

description:
ss2_filtered_count.csv
E12.5_b1_4

tag: sequencng type


title: sef1 azf1 double-deleted mutant, YPGly, repeat 3 [SAzG4]

city: Taipei

first: Po-Chen

last: Hsu

address: 128 Academia Road, Section 2, Nankang

department: Institute of Molecular Biology

country: Taiwan

institute: Academia Sinica

description:
LK_Deseq2_sef1azf1 vs azf1_YPG.xlsx
LK_Deseq2_sef1azf1 vs sef1_YPG.xlsx
LK_Deseq2_sef1azf1_YPG.xlsx
LK_Deseq2_YPG vs YPD_sef1azf1.xlsx

data_processing:
Raw reads were quality-trimmed using Trimmomatic v0.38 with options: “ILLUMINACLIP:2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:36”.
The relative abundance of each gene in units of TPM for each sample was quantified using Salmon v1.4.0 with options: “--numBootstraps 200 --validateMappings --gcBias”.
Tximport by default was used to convert the estimated transcript abundance files from Salmon to DESeq2 compatible dataset.
DESeq2 was used for the differential analysis of gene expression in R v4.0.4 with default settings.
Assembly: Lachancea kluyveri CBS_3082 (15-JUL-2013 Release from GRYC, http://gryc.inra.fr)
Supplementary files format and content: SF files from Salmon include TPM and NumReads (Estimated number of reads mapping to each transcript)
Supplementary files format and content: xlsx files (Excel files) from DESeq2 include log2FoldChange of each transcript between tested and reference samples.

organism: Lachancea kluyveri

source_name: JYL1897 derived strain

growth_protocol: Yeast strains were grown in YPD overnigh at 30°C and harvested.

extract_protocol:
About 10 OD600 of early-log-phase (0.5–1.0 OD600/ml) cells from subcultures were harvested. Total RNA was extracted by the phenol-chloroform method and treated with the TURBO DNA-freeTM kit (Ambion).
RNA-seq libraries were prepared with a TruSeq Stranded mRNA HT Sample Prep Kit (Illumina) by using 2 mg total RNA and sequenced by single-end 75 bp read length followed the protocol of NextSeq 500 High Output kit v2.5 (75 cycles) sequencing kit on the Illumina NextSeq 500 System.

treatment_protocol: YPD overnigh cells were diluted into YPD and YPGly at a cell density of 0.2 OD600/ml and subculcuted at 30°C for 5.5 hours.

tag: cell line

value: JYL1897 derived strain

tag: cell type

value: Yeast cell

tag: genotype

value: sef1 azf1 double knockout

value: YPGly, 30°C, 5.5 h


title: Fimbria1: Fimbria of healthy fallopian tube donor 1

description:
Fimbria1
747-YS-1

tag: tissue

value: female

tag: health


title: rep3 BATF 72h KD

description:
60-190038-AST12_S60
Naive CD4+ T cells were nucleofected with siBATF and polarized to Th17-phenotype for 72h

tag: cell source

tag: genotype/variation

tag: biological replicate


title: rep1 KD 24h DoubleKD

description:
4-190038-A4_S4
Naive CD4+ T cells were nucleofected with si FOSL1+ si FOSL2 and polarized to Th17-phenotype for 24h

value: nucleofected with si FOSL1+ si FOSL2


title: sef1 azf1 double-deleted mutant, YPGly, repeat 2 [SAzG3]

tag: treatment


title: Pax7 lineage - E12.5b1_45

description:
ss2_filtered_count.csv
E12.5_b1_4

data_processing:
Smart-seq2 samples basecalling were performed using bcl2fastq2; 10x samples were performed using bcl2fastq.
Smart-seq2 samples were quantified using kallisto 0.44.0, summarized using tximport in R; 10x samples were aligned using STAR and matrices were generated with cellranger count
Both datasets were loaded in R environment as Seurat object and filtered for poor quality reads.
Genome_build: mm10
Supplementary_files_format_and_content: csv containing raw counts

source_name: Mouse embryonic cells

extract_protocol:
YFP+ signals reporting Pax7-lineage cells were FACS sorted. Additional sorting with antibody labeling were done for bulk samples regarding surface marker studies.
Sequencing libraries for single-cell samples were constructed using Smart-seq2 protocol or 10x protocol. Smart-seq2 was also applied to bulk samples.

value: embryonic cells

tag: time point

tag: plate batch

value: Plate 1

tag: sequence batch

tag: medium


title: Control_day2_male_A

value: Distal colon

tag: gender

value: male

value: 2 days of exposure to sterile water


title: Pax7 lineage - E12.5b1_44

description:
ss2_filtered_count.csv
E12.5_b1_4

tag: method

value: Batch 1

tag: marker


title: S20-1

city: Beijing

first: Yan

last: Zhang

state: Not Applicable

address: Dongdajie street

institute: Beijing institute of Biotechnology

data_processing:
STAR 2.26 --genomeDir hg38.p13  --readFilesCommand zcat --outReadsUnmapped Fastx  --chimSegmentMin 15 --chimScoreMin 10 --clip3pAdapterMMp 0.1 --scoreGapNoncan -4 --scoreGapATAC -4  --chimJunctionOverhangMin 15
hisat2 -p 24 --dta -x hg38.p13 -1 Unmapped.out.mate1 -2 Unmapped.out.mate2  -S hg38_compent.sam
samtools sort -@ 16 -o hg38_STAR.bam Aligned.out.sam
samtools sort -@ 16 -o hg38_hisat2.bam hg38_compent.sam
samtools merge -@ 16  -h hg38_STAR.bam merged.bam hg38_STAR.bam hg38_hisat2.bam
stringtie -e -B -p 8 -G /STAR_genomeDIR/gencode.v33.chr_patch_hapl_scaff.annotation.gtf -o /BallgownDIR}/sample.GTF  {BAMDIR}/merged.bam
Genome_build: hg38.p13
Supplementary_files_format_and_content: stringtie used to evaluate gene and transcript expression for each sample.

source_name: whole blood total RNA

extract_protocol:
Blood samples were treated in Trizol reagent (ThermoFisher, USA), and RNA extraction was prepared following manufacturer’s manual; rRNA depleted total RNA. After RNA quantification using Nanodrop (ThermoFisher, USA) and Qubit 2.0 (ThermoFisher, USA).
RNA-seq libraries were prepared with 50ng input RNA material using SMARTer Stranded Total RNA-seq Kit v2—Pico Input Mammalian (Takara Bio USA Inc., USA), according to the manufacturer’s instructions.

tag: individual

tag: Stage

tag: time

value: whole blood


title: rep2 BATF 72h KD

description:
56-190038-AST8_S56
Naive CD4+ T cells were nucleofected with siBATF and polarized to Th17-phenotype for 72h

value: Human Umbilical Cord blood

tag: cell type

value: nucleofected with siBATF


title: rep1 BATF 72h KD

description:
52-190038-AST4_S52
Naive CD4+ T cells were nucleofected with siBATF and polarized to Th17-phenotype for 72h


title: Control_day2_female_A

tag: tissue


title: azf1-deleted mutant, YPGly, repeat 3 [AzG4]

description:
LK_Deseq2_azf1_YPG.xlsx
LK_Deseq2_sef1azf1 vs azf1_YPG.xlsx
LK_Deseq2_YPG vs YPD_azf1.xlsx

tag: cell line

tag: genotype

value: azf1 knockout


title: azf1-deleted mutant, YPGly, repeat 2 [AzG3]


title: Control_day2_female_B


title: azf1-deleted mutant, YPGly, repeat 1 [AzG2]


title: rep3 BATF 24h Scr

description:
57-190038-AST9_S57
Naive CD4+ T cells were nucleofected with siBATF and polarized to Th17-phenotype for 24h

tag: cell source

tag: genotype/variation


title: S17-1

value: healthy


title: Pax7 lineage - E12.5b1_43

description:
ss2_filtered_count.csv
E12.5_b1_4

tag: sequencng type

value: Single-cell


title: rep1 BATF 72h Scr

description:
51-190038-AST3_S51
Naive CD4+ T cells were nucleofected with siBATF and polarized to Th17-phenotype for 72h

tag: biological replicate


title: Pax7 lineage - E12.5b1_42

description:
ss2_filtered_count.csv
E12.5_b1_4

tag: time point

tag: plate batch


title: Pax7 lineage - E12.5b1_41

description:
ss2_filtered_count.csv
E12.5_b1_4

tag: sequence batch

tag: medium


title: rep1 BATF 24h Scr

description:
49-190038-AST1_S49
Naive CD4+ T cells were nucleofected with siBATF and polarized to Th17-phenotype for 24h


title: sef1-deleted mutant, YPGly, repeat 3 [SG4]

description:
LK_Deseq2_sef1_YPG.xlsx
LK_Deseq2_sef1azf1 vs sef1_YPG.xlsx
LK_Deseq2_YPG vs YPD_sef1.xlsx

value: JYL1897 derived strain

value: Yeast cell

value: sef1 knockout

tag: treatment


title: rep3 BATF 24h KD

description:
58-190038-AST10_S58
Naive CD4+ T cells were nucleofected with siBATF and polarized to Th17-phenotype for 24h


title: B6-2


title: sef1 azf1 double-deleted mutant, YPGly, repeat 1 [SAzG2]

value: sef1 azf1 double knockout

value: YPGly, 30°C, 5.5 h


title: B6-1


title: sef1-deleted mutant, YPGly, repeat 2 [SG2]


title: B4-2


title: S17-2


title: Pax7 lineage - E12.5b1_39

description:
ss2_filtered_count.csv
E12.5_b1_3

value: embryonic cells

tag: method

tag: marker


title: rep1 BATF 24h KD

description:
50-190038-AST2_S50
Naive CD4+ T cells were nucleofected with siBATF and polarized to Th17-phenotype for 24h


title: sef1-deleted mutant, YPGly, repeat 1 [SG1]


title: Pax7 lineage - E12.5b1_40

description:
ss2_filtered_count.csv
E12.5_b1_4

value: Plate 1


title: Pax7 lineage - E12.5b1_38

description:
ss2_filtered_count.csv
E12.5_b1_3


title: B3-2

tag: individual

tag: Stage


title: Wild type, YPGly, repeat 3 [WG3]

description:
LK_Deseq2_azf1_YPG.xlsx
LK_Deseq2_sef1_YPG.xlsx
LK_Deseq2_sef1azf1_YPG.xlsx
LK_Deseq2_YPG vs YPD_WT.xlsx

tag: cell type

value: wild-type


title: B4-1

tag: time

tag: tissue


title: rep2 BATF 24h Scr

description:
53-190038-AST5_S53
Naive CD4+ T cells were nucleofected with siBATF and polarized to Th17-phenotype for 24h


title: Pax7 lineage - E12.5b1_36

description:
ss2_filtered_count.csv
E12.5_b1_3


title: B3-1


title: B21-2


title: 20210629_Hide 062921_CD20 H3_06

city: cleveland

first: Hidetoshi

last: Tsuda

state: ohio

address: 9500 euclid ave

institute: cleveland clinic

description: Pancancer panel includes 784 probes including 6 positive control and 8 negative control.

hyb_protocol: Hybridization was followed NanoString nCounter XT gene expression assay protocol. Briefly,  for pereparation of master mix,  hybridization buffer was mixed with the Reporter CodeSet, the master mix, samples and Rnase-fee water were added to each tube and then Panel Capture codeset was added.All samples were incubated for 16 hours at 65 degree.

scan_protocol: Targeted mRNA hybridized with the capture probe was counted using the NanoString nCounter instrument (Nanostring)

data_processing: Raw Data  was normalized and analyzed in the nCounter Advanced Analysis 2.0 software (Nanostring)

source_name: mouse heart

label_protocol: Total RNA was reverse-transcribed using the High-Capacity cDNA Reverse Transcription Kit (Applied Biosystem) according to the instructions.

extract_protocol: Total RNA was extracted using an RNeasy Fibrous Tissue Mini kit (QIAGEN) for recovered grafts or an RNeasy Micro kit (QIAGEN) for microdissected vessels according to the instructions.

value: Apex of  the graft

tag: status

value: Alive

tag: Sex

value: Male

value: CD4 mAb+CD20mAb

tag: cartridgeid


title: 20210629_Hide 062921_CD20 H2_05


title: sef1 azf1 double-deleted mutant, YPD, repeat 3 [SAzD4]

description:
LK_Deseq2_sef1azf1 vs azf1_YPD.xlsx
LK_Deseq2_sef1azf1 vs sef1_YPD.xlsx
LK_Deseq2_sef1azf1_YPD.xlsx
LK_Deseq2_YPG vs YPD_sef1azf1.xlsx

tag: cell line

tag: genotype


title: Pax7 lineage - E12.5b1_35

description:
ss2_filtered_count.csv
E12.5_b1_3

tag: sequencng type

tag: time point

value: Batch 1


title: sef1 azf1 double-deleted mutant, YPD, repeat 2 [SAzD3]


title: B21-1

value: whole blood


title: Pax7 lineage - E12.5b1_34

description:
ss2_filtered_count.csv
E12.5_b1_3

tag: plate batch

tag: sequence batch


title: 20210629_Hide 062921_CD20 H1_04

tag: treatment


title: rep2 BATF 24h KD

description:
54-190038-AST6_S54
Naive CD4+ T cells were nucleofected with siBATF and polarized to Th17-phenotype for 24h

tag: cell source

value: Human Umbilical Cord blood

tag: genotype/variation

value: nucleofected with siBATF

tag: biological replicate


title: B9-2

tag: individual

tag: Stage

value: LRS

value: 52 days after diagnosis


title: 20210629_Hide 062921_AJB6H3_03

value: CD4 mAb


title: Wild type, YPGly, repeat 2 [WG2]

value: JYL1897 derived strain

tag: cell type

value: Yeast cell


title: azf1-deleted mutant, YPD, repeat 3 [AzD4]

description:
LK_Deseq2_azf1_YPD.xlsx
LK_Deseq2_sef1azf1 vs azf1_YPD.xlsx
LK_Deseq2_YPG vs YPD_azf1.xlsx

value: azf1 knockout


title: Pax7 lineage - E12.5b1_33

description:
ss2_filtered_count.csv
E12.5_b1_3

tag: tissue

value: embryonic cells

tag: method

value: Single-cell

tag: medium

tag: marker


title: 20210629_Hide 062921_AJB6H2_02

tag: status

tag: Sex

tag: cartridgeid


title: Pax7 lineage - E12.5b1_37

description:
ss2_filtered_count.csv
E12.5_b1_3

tag: sequencng type

tag: time point

value: Plate 1


title: Pax7 lineage - E12.5b1_32

description:
ss2_filtered_count.csv
E12.5_b1_3

tag: plate batch

tag: sequence batch


title: Wild type, YPGly, repeat 1 [WG1]

tag: cell line

tag: genotype

value: wild-type

tag: treatment

value: YPGly, 30°C, 5.5 h


title: B2-2

tag: individual

tag: time

value: 33 days after diagnosis


title: azf1-deleted mutant, YPD, repeat 2 [AzD3]

tag: cell type


title: Pax7 lineage - E12.5b1_31

description:
ss2_filtered_count.csv
E12.5_b1_3

tag: tissue


title: 20210430_Fairchild 043021_CD20 H2_08

value: CAV region of  the graft

value: Alive

value: Male

value: CD4 mAb+CD20mAb

value: Fairchild 043021


title: 20210629_Hide 062921_AJB6H1_01


title: azf1-deleted mutant, YPD, repeat 1 [AzD2]


title: B2-1

tag: Stage

value: LRS

value: whole blood


title: Fishmeal_60_ID12

description: 6 hours incubation with human serum

tag: participant id

tag: timepoint

tag: supplement

value: Fishmeal


title: sef1 azf1 double-deleted mutant, YPD, repeat 1 [SAzD2]

value: JYL1897 derived strain

value: sef1 azf1 double knockout


title: 20210430_Fairchild 043021_CD20 H1_07

tag: status

tag: Sex


title: S9-2

value: ERS

value: 30 days after diagnosis


title: sef1-deleted mutant, YPD, repeat 3 [SD3]

description:
LK_Deseq2_sef1_YPD.xlsx
LK_Deseq2_sef1azf1 vs sef1_YPD.xlsx
LK_Deseq2_YPG vs YPD_sef1.xlsx

value: Yeast cell

value: sef1 knockout


title: B9-1

value: 52 days after diagnosis


title: sef1-deleted mutant, YPD, repeat 2 [SD2]


title: Pax7 lineage - E12.5b1_30

description:
ss2_filtered_count.csv
E12.5_b1_3

value: embryonic cells

tag: method

tag: sequencng type

value: Single-cell

value: Plate 1

value: Batch 1

tag: medium

tag: marker


title: Pax7 lineage - E12.5b1_28

description:
ss2_filtered_count.csv
E12.5_b1_2

tag: time point

tag: plate batch

tag: sequence batch


title: Pax7 lineage - E12.5b1_29

description:
ss2_filtered_count.csv
E12.5_b1_2


title: 20210430_Fairchild 043021_AJB6H2_02

value: CAV region of  the graft

value: Alive

value: Male

tag: treatment

value: CD4 mAb

tag: cartridgeid


title: B7-2

tag: individual

value: LRS

tag: time

value: 42 days after diagnosis

value: whole blood


title: 20210430_Fairchild 043021_AJB6H1_01

tag: tissue

value: Fairchild 043021


title: sef1-deleted mutant, YPD, repeat 1 [SD1]

tag: cell line

value: JYL1897 derived strain

tag: cell type

tag: genotype


title: B7-1

tag: Stage


title: Wild type, YPD, repeat 3 [WD4]

description:
LK_Deseq2_azf1_YPD.xlsx
LK_Deseq2_sef1_YPD.xlsx
LK_Deseq2_sef1azf1_YPD.xlsx
LK_Deseq2_YPG vs YPD_WT.xlsx

value: wild-type


title: S9-1

value: ERS

value: 30 days after diagnosis


title: RNA-seq data of Mouse replicate 3

description:
mouse_quant_TPM-1.txt
ployA
PE125
Specific

data_processing:
RNA sequencing reads were aligned to reference genomes applying the STAR (2.6.0c) (Dobin, A. et al.).
Transcript quantification was conducted with kallisto (0.44.0) (Bray, N. L. et al.)
Genome_build: Genome building GRCh38 of human, Mmul_8.0.1 of monkey, GRCm38 of mouse, Rnor_6.0 of rat, OryCun2.0 of rabbit, Felis_cattus_6.2 of cat, CanFam3.1 of dog, Sscrofa11.1 of pig, UMD3.1 of cow, Oar_v3.1 of sheep, GRCz10 of zebrafish, and Gallus_gallus-5.0 of chicken were used for read alignment.

source_name: Mouse Embryo Fibroblasts

extract_protocol:
total RNA  of each cell sample was extracted by using the Trizol  (Invitrogen).
We used an rRNA depletion protocol (Epicentre Ribo-zero™ rRNA Removal Kit, Epicentre, USA) or  mRNA capture protocol (Oligo (dT) magnetic beads, Promega, USA) coupled with the strand specific or non-specific RNA-seq library protocol  for each sample.

value: Fibroblasts

tag: tissue source

value: Embyo

tag: age


title: Hi-C data of Mouse replicate 3

data_processing:
Read pair flies in fastq format were aligned to the reference genome, filtered and binned into raw and normalized 2D contact matrices using Hiclib.
TADs were identified using DomainCaller
Compartment A/B identification at 20-Kb was performed by using A-B index value which represented the comparative likelihood of a sequence interacting with A or B (100-Kb) as described previously (Rowley, M. J. et al. ). Bins at 20-Kb with positive values (more association with A at 100-Kb) were called as A compartments, while 20-Kb bins with negative values (more association with B at 100-Kb) were called as B compartments. These positive or negative values were termed as A-B index values.
Genome_build: Genome building GRCh38 of human, Mmul_8.0.1 of monkey, GRCm38 of mouse, Rnor_6.0 of rat, OryCun2.0 of rabbit, Felis_cattus_6.2 of cat, CanFam3.1 of dog, Sscrofa11.1 of pig, UMD3.1 of cow, Oar_v3.1 of sheep, GRCz10 of zebrafish, and Gallus_gallus-5.0 of chicken were used for read alignment.

extract_protocol:
Briefly, about 20 to 25 million cells were crosslinked with 2% formaldehyde for 10 min at room temperature (20–25 °C), then used glycine to quench the formaldehyde in a final concentration of 0.25 M at room temperature for 5 min, and subsequently on ice for 15 min.
Dilution Hi-C was performed as a previous study (Lieberman-Aiden, E. et al. ). Nuclei were permeabilized by a Dounce homogenizer in the presence of cold lysis buffer (10 mM Tris-HCl, pH 8.0, 10 mM NaCl, 0.2% IGEPAL CA-630, and 1× protease inhibitor solution). DNA was digested with 400 units of HindⅢ, and the ends of restriction fragments were labeled using biotinylated nucleotides and ligated in a small volume (8 mL). After reversal of cross-links, ligated DNA was puriﬁed and prepped for Illumina sequencing.


title: Pax7 lineage - E12.5b1_25

description:
ss2_filtered_count.csv
E12.5_b1_2

value: embryonic cells

tag: method

tag: sequencng type

value: Single-cell


title: S2-1

value: 40 days after diagnosis


title: Wild type, YPD, repeat 2 [WD3]

value: Yeast cell


title: S2-2


title: Wild type, YPD, repeat 1 [WD2]


title: Pax7 lineage - E12.5b1_24

description:
ss2_filtered_count.csv
E12.5_b1_2

value: Plate 1

value: Batch 1

tag: medium

tag: marker


title: CD19creSRBCd7GC_3

city: New York

first: Matt

last: Teater

state: NY

address: 445 E 69th St

institute: Weill Cornell Medical College

data_processing:
FASTQ data was aligned and processed using the proseq2.0 pipeline developed by Danko lab (https://github.com/Danko-Lab/proseq2.0).
All data was competitively aligned to a merged genome assembly of mm10 and dm3. Merging the two genome builds was performed using fastq merge.
Assembly: mm10 and dm3
Supplementary files format and content: PRO-seq libraries were competitively aligned to a genome resulted by merging mm10 assembly with D.melanogaster dm3 genome assembly. Alignment was performed using the proseq2.0 pipeline developed by the Danko lab (https://github.com/Danko-Lab/proseq2.0) using the parameters -PE --RNA5=R2_5prime --UMI1=6. Downstream analysis was performed in R, using Genomic Ranges (Lawrence M, Huber W, Pagès H, Aboyoun P, Carlson M, Gentleman R, Morgan M, Carey V (2013). “Software for Computing and Annotating Genomic Ranges.” PLoS Computational Biology, 9. doi: 10.1371/journal.) and BRgenomics1.1.3 (https://mdeber.github.io/index.html).
Library strategy: PRO-seq

source_name: Germinal center cells

extract_protocol:
RNA extraction, run-on, and library preparation were executed according to “Mahat, D. B. et al. Base-pair-resolution genome-wide mapping of active RNA polymerases using precision nuclear run-on (PRO-seq). Nat. Protoc. 11, 1455–1476 (2016).” (PMID: 27442863).
Library prep was performed using Illumina custom adapters: Reverse 3' RNA adapter (/5Phos/NNNNNNGAUCGUCGGACUGUAGAACUCUGAAC/3InvdT) and Reverse 5' RNA Adapter (5'-CCUUGGCACCCGAGAAUUCCA-3').

tag: dtag-13 treatment

value: Wild type

tag: replicate


title: CD19creSRBCd7GC_4


title: S5-2

value: 13 days after diagnosis


title: E171_2mg/kg/bw/day_day2_female_A

data_processing: Pre-processing of microarray raw data was performed as previously described [19]. Briefly, gene expression values were obtained from the microarray scans using Agilent’s Feature extraction software (FES) version 10.7.3.1). Next, the samples were checked for quality and normalized with ArrayQC, an in-house developed pipeline (https://github.com/arrayanalysis/arrayQC_Module) using the following steps: local background correction, flagging of bad spots, controls/spots point with too low intensity, log2 transformation, and quantile normalization. Bad spots were removed from the normalized data. Sixteen groups were defined, based on exposure and time points: 4 different exposure groups and 4 different time points. Spot identifiers were deleted when more than 40 % of samples in each group had a missing value, and when the average expression in each group was < 4. Missing values were imputed by the k-nearest neighbors using GenePattern ImputeMissingValues.KNN module v13 (k-value 15). Repeated Agilent probe identifiers were merged (setting: median) with Babelomics 5. Next, Agilent probe identifiers were re-annotated to EntrezGeneIDs and again merged (setting: median) with Babelomics 5. Differentially expressed genes (DEGs) were identified by performing a moderate t-test using LIMMA (version 1.0), which corrected the exposure samples with their time-matched controls. The cut-off values of fold-changes (FC) ≥ 1.5 or ≤ -1.5 (absolute FC ≥ 1.5) and p-value < 0.05 were used. Additionally, the false discovery rate (FDR) was applied according to the Benjamini-Hochberg method with a threshold q-value < 0.05.

extract_protocol: RNA was isolated from the distal colon using the miRNeasy Mini Kit (Qiagen, The Netherlands) including a DNase treatment, according to the manufacturer’s protocols for “Animal Cells and Animal Tissues” .

value: Distal colon

tag: gender

value: female

tag: treatment

value: 2 days of exposure to 2 mg/kgbw/day of E171 in sterile water


title: Pax7 lineage - E12.5b1_23

city: Hong Kong

first: Angela

last: Wu

address: Clear Water Bay, Kowloon

institute: Hong Kong University of Science and Technology

description:
ss2_filtered_count.csv
E12.5_b1_2

tag: time point

tag: plate batch

tag: sequence batch


title: S5-1

tag: individual

tag: time

tag: tissue

value: whole blood


title: CD19creSRBCd7GC_1


title: Pax7 lineage - E12.5b1_27

description:
ss2_filtered_count.csv
E12.5_b1_2


title: B17-2

tag: Stage

value: LRS

value: 57 days after diagnosis


title: Pax7 lineage - E12.5b1_22

description:
ss2_filtered_count.csv
E12.5_b1_2


title: CD19creSETD2HetSRBCd7GC_4

value: SETD2 heterozygote


title: Pax7 lineage - E12.5b1_26

description:
ss2_filtered_count.csv
E12.5_b1_2


title: B17-1


title: Pax7 lineage - E12.5b1_21

description:
ss2_filtered_count.csv
E12.5_b1_2


title: Pax7 lineage - E12.5b1_20

description:
ss2_filtered_count.csv
E12.5_b1_2


title: CD19creSETD2HetSRBCd7GC_3


title: CD19creSETD2HetSRBCd7GC_2


title: CD19creSETD2HetSRBCd7GC_1


title: B15-2

value: 39 days after diagnosis


title: B15-1


title: S3-1

value: ERS

value: 30 days after diagnosis


title: CD19creSRBCd7GC_2


title: Pax7 lineage - E12.5b1_18

description:
ss2_filtered_count.csv
E12.5_b1_1

value: embryonic cells

value: Single-cell


title: od4ex2wk8o

city: Tucson

first: Katherine

last: Rhodes

state: AZ

address: 1657 East Helen street

department: Immunobiology

institute: University of Arizona

description:
inoculum dose 2
od4ex2wk8o.ENA_CP060415_CP060415.1.insert_site_plot.gz
od4ex2wk8o.ENA_CP060414_CP060414.1.insert_site_plot.gz
joined_output.pass2wk8o_CP060414.csv
joined_output.pass2wk8o_CP060415.csv
oralvinocplasmid.csv
oralvinocula.csv

data_processing:
Basecalling with Illumina RTA 1.18.54
Read files were merged by sample
Samples were trimmed and filtered on Tn5 sequences using cutadapt V 1.18, pairs lacking Tn5 end  were discarded: -g CTAGAGTCGACCTGC -G cactctttccctacacgacgctcttccgatct --trim-n -m 20 --discard-untrimmed -pair-filter=first
remaining  adaptors were removed with cutadapt  v.1.18 -g AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT -m 20 -pair-filter=first
Reads were mapped to the Nmus chromosome and plasmid using BWA v 0.7.17: bwa mem -k 16 -a -T 25, output files were converted to sorted bam format using samtools v.1.11
Tn5 insertions were plotted using tradis_plot script implemented in BioTradis pipeline V 1.4.5, using reads with mapping quality > 30
Gene insertions were determined using tradis_gene_insert_sites, joined samples by library, sample site and time point using nw831 refseq anotation in embl format. Ignored insertions in 3' 10% of the gene
tradis_essentiality.R used to determine single condition essentiality.
tradis_comparison.R used to quantify abundance of host passage samples in relation to inoculum. -f -t 1
Genome_build: Neisseria musculi NW831 strain AP2031 assembly ASM1429759v1
Supplementary_files_format_and_content: tradis_plot output; insertion counts per nucleotide, tradis_gene_insert_sites output; insertions counts per annotated gene in .csv format of samples merged by library,dose, sample site and timepoint, tradis_essentiality.R output files; .csv format of gene essentiality assignments based on gamma fit distribution of in vitro passage samples, tradis_comparison.R output files; .csv  files of normalized gene abundance  control v. condition calculated via edgeR implemented in biotradis using gene insertion files as input.

organism: Neisseria musculi

source_name: oral CFU

growth_protocol: Bacteria for inoculum were recovered from freezer on  GCB Rif Km media for  24 hours, then lawned on a fresh GCB Rif Km plate for an additional 36 hours. DNA was isolated from recovery passage, and initial inoculum after adjustment in PBS to dose OD600

extract_protocol:
Lysis in TES buffer (50 mM Tris pH 8, 20 mM EDTA, 50 mM NaCl) with 1% SDS, Rnase A treatment followed by 25:24:1 Phenol chloroform isoamyl alcohol extraction with ethanol precipitation.
DNA was sheared to 500 bp. Tn5 junction enrichment was performed on samples post end repair, A tailing and ligation to custom adaptors via NEBnext DNA kit. Amplicons from 100-600 bp were size selected and indexed by Nextera V2 dual index Kit. Samples were sequenced on an Illumina MiSeq as 75 bp paired end samples

treatment_protocol: Bacteria were inoculated into oral cavity of mice, and recovered from oral and fecal samples at various timepoints post inoculation on GCB Rif Km prior to DNA extraction.

tag: library replicate

value: library replicate 2

tag: condition

value: mouse passage

tag: timepoint

value: week 8 post inoculation

tag: sample site

value: oral cavity


title: Pax7 lineage - E12.5b1_19

description:
ss2_filtered_count.csv
E12.5_b1_1

tag: method

tag: sequencng type

value: Plate 1

value: Batch 1

tag: medium


title: S1-2

value: 19 days after diagnosis


title: od4ex1wk8o

description:
inoculum dose 2
od4ex1wk8o.ENA_CP060415_CP060415.1.insert_site_plot.gz
od4ex1wk8o.ENA_CP060414_CP060414.1.insert_site_plot.gz
joined_output.lib1wk8o_CP060414.csv
joined_output.lib1wk8o_CP060415.csv
oralvinocplasmid.csv
oralvinocula.csv

value: library replicate 1


title: Pax7 lineage - E12.5b1_16

description:
ss2_filtered_count.csv
E12.5_b1_1

tag: marker


title: S1-1

value: whole blood


title: RNA from PC3 METTL1 KO cells (clon 117 C1) 3

city: Salamanca

first: Sandra

last: Blanco

address: Campus Miguel de Unamuno

country: Spain

institute: Cancer Research Institute (CIC) - Instituto de Biología Molecular y Celular  del Cáncer (IBMCC-CSIC)

hyb_protocol: Labelling and hybridizations were performed according to protocols from Affymetrix. Briefly, 100 ng of total RNA were amplified and labelled using the WT Plus reagent kit (Affymetrix) and then hybridized to Clariom S human Array (Affymetrix).

scan_protocol: Washing and scanning were performed using GeneChip System of Affymetrix (GeneChip Hybridization Oven 645, GeneChip Fluidics Station 450 and GeneChip Scanner 7G).

data_processing: R/Bioconductor. The data normalization was done using the RMA algorith implemented in the oligo package. For the downstream statistical anlysis the limma package was used. The pvalues were corrected using the Benjamini–Hochberg method.

label: Biotin

source_name: Prostate cancer cell line PC3

growth_protocol: PC3 were cultured in DMEM with L-Glutamine and pyruvate (Gibco) supplemented with 10% FBS (Gibco) and 1% Penicillin/streptomycin, a humidified atmosphere at 37°C and 5% CO2. Cell cultures were tested for mycoplasma monthly and maintained mycoplasma-free.

extract_protocol: Total RNA was extracted from purified cell populations using NZY Total RNA Isolation kit (RNA Purification – NZYTech) according to the manufacturer’s instructions. The RNA integrity was assessed using Agilent 2100 Bioanalyzer (Agilent, Palo Alto, CA).

tag: genotype

value: METTL1 KO

tag: cell line