title: BF_24h_samp 3_Co-10

source_name: Peri-implant mucosa + biofilm, 24 h, sample 3, experiment Co-10


title: mammary gland tissue, age 24M, 12 months CYP19A1 transgene induction, biol rep 3 [4379AROM12M24M_S7]

status: Public on Aug 22 2022

type: SRA

city: Cheonan

first: Keunsoo

last: Kang

address: 119 Dandae-ro

country: South Korea

institute: Dankook University

library_source: transcriptomic

data_processing:
Sequencing quality was checked using FastQC (version 0.11.9; https://www.bioinformatics.babraham.ac.uk/projects/fastqc/).
Contaminated adaptor and/or row quality portions of sequenced reads were trimmed using Trim Galore (version 0.6.5; https://github.com/FelixKrueger/TrimGalore).
Trimmed reads were aligned to the reference mouse genome (mm10), using STAR (version 2.7.9a) (Dobin et al. Bioinformatics 2013).
Batch effect was normalized using RUVSeq (version 1.26.0) with the RUVg method (Risso et al. Nat Biotech. 2014).
Normalized expression levels were estimated by means of transcripts per million (TPM) using RSEM (version 1.3.1) (Li and Dewey, BMC Bioinformatics 2011)
Assembly: mm10
Supplementary files format and content: tab-delimited text files include TPM values for each sample

molecule: total RNA

organism: Mus musculus

source_name: mammary gland

extract_protocol:
Thoracic (second) mammary glands were flash frozen in liquid nitrogen and stored at -80℃ until processing. Glands were thawed in Invitrogen Trizol reagent (ThermoFisher Scientific) and homogenized using a Qiagen Tissuruptor and Qiashredder (Qiagen). RNA was then isolated using Direct Zol RNA miniprep kit (Zymo Research), quantified on a Qubit 2.0 or 4.0 Fluorometer (Qiagen) and analyzed for RNA integrity using the Agilent 2100 Bioanalyzer.
Indexed, single-index sequencing libraries prepared from total RNA (1 microgram/sample) using the Illumina TruSeq Stranded Total RNA Library Preparation Human/Mouse/Rat Kit (rRNA depletion and random-primed cDNA synthesis)
Sequencing using the Illumina NextSeq 550, SE 75 bp read length; minimum reads ≥50M per sample

tag: tissue

value: mammary gland

tag: age

tag: genotype

tag: treatment

value: 12 months CYP19A1 transgene induction


title: Xenopus laevis Embryos, Total RNA, 5 hpf, Rep 2 [All_5hpf_rep2]

city: Philadelphia

first: Matthew

middle: C

last: Good

state: PA

address: Room 1140, 421 Curie Blvd

department: Cell and Developmental Biology

country: USA

institute: University of Pennsylvania

data_processing:
Fastq files were aligned to transcripts annotated in Xenopus laevis genome build 9.2 (xenbase.org) using salmon v0.12.0 yeilding raw counts per transcript.
Raw counts quantified from salmon were normalized to library size using DESeq2.
Assembly: Xenopus laevis genome build 9.2  (xenbase.org)
Supplementary files format and content: DESeq2 normalized reads per transcript, comma separated values text file

organism: Xenopus laevis

source_name: Embryo

growth_protocol: Xenopus laevis embryos were cultured in 0.1× Marc’s Modified Ringer’s (MMR) medium. All embryo experiments were performed at room temperature (22℃ ± 0.5 ℃)

extract_protocol:
Total RNAs were isolated using the RNeasy Mini Kit (Qiagen), following the instructions provided by the manufacturer. Nascent EU-RNAs were biotinylated using bisulfide biotin azide via click reaction and purified using streptavidin beads following the instructions provided by the Click-iTTM Nascent RNA Capture Kit (Thermo Fisher Scientific, Cat# C10365).
The cDNA libraries for 'All' (Total RNA), 'Bead' (Nascent transcripts), 'FL' (Flowthrough RNA) and 'Egg' (Maternal RNA) were prepared using the Universal RNA-seq with NuQuant® kit (NuGEN, Cat# 0364), following the manual provided by the manufacturer. Ribosomal RNAs were depleted using the custom designed AnyDeplete Probe Mix for Xenopus laevis provided by the kit.

treatment_protocol: Embryos at 1-cell stage were microinjected with 10 nl of 50 mM EU. The final concentration of EU is at ~ 0.5 mM. Embryos developed to blasula stages at 5-9 hpf were collected for RNA extraction.

value: Embryo

tag: developmental stage

value: Blastula

tag: time

value: 5 hpf

value: Wildtype

value: EU microinjected

tag: batch

value: Experiment 1


title: mammary gland tissue, age 24M, 12 months CYP19A1 transgene induction, biol rep 2 [4370AROM24M12M_S7]


title: Xenopus laevis Embryos, CHX, 7.5 hpf, Rep 2 [CHX_7.5hpf_rep2]

extract_protocol:
Total RNAs were isolated using the RNeasy Mini Kit (Qiagen), following the instructions provided by the manufacturer. Nascent EU-RNAs were biotinylated using bisulfide biotin azide via click reaction and purified using streptavidin beads following the instructions provided by the Click-iTTM Nascent RNA Capture Kit (Thermo Fisher Scientific, Cat# C10365).
The cDNA libraries for purified ascent transcripts were prepared using the Universal RNA-seq with NuQuant® kit (NuGEN, Cat# 0364), following the manual provided by the manufacturer. Ribosomal RNAs were depleted using the custom designed AnyDeplete Probe Mix for Xenopus laevis provided by the kit.

treatment_protocol: Embryos at 1-cell stage were microinjected with 10 nl of 50 mM EU. The final concentration of EU is at ~ 0.5 mM. Embryos developed to 5 hpf blastula stage were treated with 0.2 mg/ml of cycloheximide (CHX) up to 7.5 hpf. Control and CHX-arrested embryos were collected for RNA extraction.

value: 7.5 hpf

value: Wild type

value: EU microinjected, CHX treated


title: mammary gland tissue, age 24M, 6 months CYP19A1 transgene induction, biol rep 3 [4230AROM6M24M_S6]

value: 6 months CYP19A1 transgene induction


title: COV010

city: New York City

first: Coen

last: van Solingen

state: New York

address: 435 E30th street, Science Building 723T, Science Building 723T

department: Cardiology/Medicine

institute: NYU School of Medicine

data_processing:
Fastq qualtiy assessed via FastQC 0.11.7
Sample contamination assessed via fastqscreen v0.13.0
Fastq files trimmed via Trimmomatic v0.36
Fastq files aligned to the HG38 human genome via STAR v2.7.3a
Reads counted via featurecounts v1.6.3
Genome_build: hg38
Supplementary_files_format_and_content: Raw count table as a .txt file

molecule: polyA RNA

organism: Homo sapiens

source_name: whole blood

extract_protocol:
QIAsymphony PAXgene RNA isolation
Sequencing libraries were barcoded and prepared using the Clontech SMART-Seq HT with Nxt HT kit (Takara Bio USA) as per the manufacturer's instruction

value: whole blood

tag: cohort

value: COVID

tag: Sex

value: Female

value: Dead


title: mammary gland tissue, age 24M, 12 months CYP19A1 transgene induction, biol rep 1 [4321AROM24M12M_S7]


title: Xenopus laevis Embryos, Total RNA, 6 hpf, Rep 2 [All_6hpf_rep2]

value: 6 hpf


title: THR-238

value: Control

value: Male


title: C_24h_samp 3_Co-10

type: RNA

city: Hannover

first: Carina

last: Mikolai

address: Carl-Neuberg-Str. 1

department: Department of Prosthetic Dentistry and Biomedical Materials Science

country: Germany

institute: Hannover Medical School

description: Gene expression of mucosa without biofilm after 24h

hyb_protocol: cRNA fragmentation, hybridization and washing steps were carried-out as recommended in the ‘One-Color Microarray-Based Gene Expression Analysis Protocol V5.7’ by use of 1650ng of labelled cRNA for hybridization.

scan_protocol: Slides were scanned on the Agilent Micro Array Scanner G2565CA (pixel resolution 3 µm, bit depth 20).

data_processing: Data extraction was performed with the ‘Feature Extraction Software V10.7.3.1’ using the extraction protocol file ‘GE1_107_Sep09.xml’. Measurements of on-chip replicates (quintuplicates) were averaged using the geometric mean of processed intensity values of the green channel, ‘gProcessedSignal’ (gPS) to retrieve one resulting value per unique non-control probe. Single Features were excluded from averaging, if they i) were manually flagged, ii) were identified as Outliers by the Feature Extraction Software, iii) lay outside the interval of ‘1.42 x interquartile range‘ regarding the normalized gPS distribution of the respective on-chip replicate population, or, iv) showed a coefficient of variation of pixel intensities per Feature that exceeded 0.5.   Averaged gPS values were normalized by global linear scaling: All gPS values of one sample were multiplied by an array-specific scaling factor. This factor was calculated by dividing a ‘reference 75th Percentile value’ (set as 1500 for the whole series) by the 75th Percentile value of the particular Microarray to be normalized (‘Array I’ in the formula shown below). Accordingly, normalized gPS values for all samples (microarray data sets) were calculated by the following formula:   normalized gPSArray i = gPSArray i  x (1500 / 75th PercentileArray i)    Subsequently, a lower intensity threshold (surrogate value) was defined based on intensity distribution of negative control features. This value was fixed at 15 normalized gPS units. All of those measurements that fell below this intensity cutoff were substituted by the respective surrogate value of 15.

source_name: Peri-implant mucosa control, 24 h, sample 3, experiment Co-10

label_protocol: Synthesis of Cy3-labeled cRNA was performed with the ‘Quick Amp Labeling kit, one color’ (#5190-0442, Agilent Technologies) using 500ng of total RNA as input and according to the manufacturer’s recommendations, except that reaction volumes were halved.

growth_protocol: Organotypic peri-implant mucosa construction: Human gingiva fibroblasts were embeeded in a collagen typer-I hydrogel and a HGF-colonized titanium disk was integrated. Immortalized human oral keratinocytes were seede on the top of the HGF-collagen and stimulated in order to epithelial differentitaion. The peri-implant mucosa models were cultivated at 37 °C in a humidified 5% CO2 atmosphere.

extract_protocol: RNA was isolated by using the RNeasy Mini Kit (Qiagen) with On-column DNase digestion according to the manufacturer’s protocol.

treatment_protocol: Peri-implant mucosa was exposed to multispecies biofilm for 24 or 48 h at 37 °C in a humidified 5% CO2 atmospehere. Untreated peri-implant mucosa models served as control.

value: organotypic oral mucosa

tag: time point

value: without biofilm


title: BF_24h_samp 2_Co-10

description: Gene expression of mucosa after biofilm exposure for 24h

source_name: Peri-implant mucosa + biofilm, 24 h, sample 2, experiment Co-10

value: with biofilm


title: THR-303


title: C_24h_samp 1_Co-09

source_name: Peri-implant mucosa control, 24 h, sample 1, experiment Co-09


title: Xenopus laevis Embryos, CHX, 7.5 hpf, Rep 1 [CHX_7.5hpf_rep1]

value: Embryo

value: Blastula


title: COV008


title: Xenopus laevis Embryos, Total RNA, 5 hpf, Rep 1 [All_5hpf_rep1]

value: 5 hpf

value: Wildtype

value: EU microinjected

value: Experiment 1


title: COV009

value: Alive


title: Xenopus laevis Embryos, Control, 7.5 hpf, Rep 2 [Control_7.5hpf_rep2]

value: 7.5 hpf

value: Wild type


title: COV007

value: whole blood

value: COVID


title: BF_24h_samp 1_Co-09

source_name: Peri-implant mucosa + biofilm, 24 h, sample 1, experiment Co-09


title: mammary gland tissue, age 24M, no CYP19A1 transgene induction, biol rep 3 [4388AROM24M0D_S5]

value: mammary gland

value: no CYP19A1 transgene induction


title: C_24h_samp 2_Co-10

source_name: Peri-implant mucosa control, 24 h, sample 2, experiment Co-10


title: mammary gland tissue, age 24M, 6 months CYP19A1 transgene induction, biol rep 2 [4212AROM6M24M_S6]

value: 6 months CYP19A1 transgene induction


title: Xenopus laevis Embryos, Control, 5 hpf, Rep 1 [Control_5hpf_rep1]


title: mammary gland tissue, age 24M, 6 months CYP19A1 transgene induction, biol rep 1 [4200AROM6M24M_S6]


title: Xenopus laevis Embryos, Control, 5 hpf, Rep 2 [Control_5hpf_rep2]


title: COV005

value: Male


title: mammary gland tissue, age 24M, no CYP19A1 transgene induction, biol rep 1 [4409AROM24M0D_S5]


title: ΔRsfS_18h_Ribo-seq_rep1_dataset2

city: guangzhou

first: zhang

last: hong

state: guangdong province

address: Huangpu Boulavard West Jinan uinversity

country: China

institute: zhanghong

description:
Ribo RNA
BW25113_ΔRsfS
ΔRsfS_18h_Ribo-seq_rep1, dataset2
processed data file: r3_1f.txt

data_processing:
Library strategy: Ribo-seq
Basecalls performed using bcl2fastq2 Version 2.17.
Sequenced reads were trimmed for adaptor sequence (Illumina), and masked for low-complexity or low-quality sequence.
Mapped to GCF_000005845.2_ASM584v2_cds_from_genomic using FANse3g.
Genome_build: ASM584v2 (GCF_000005845.2)
Supplementary_files_format_and_content: *.txt: Tab-delimited text files include RPKM values.

organism: Escherichia coli BW25113

source_name: Culture grown in M9 minimal medium

growth_protocol: Cultures were grown aerobically at 37 °C in 50 mL volumes of M9 minimal medium, supplemented with MgSO4 (1 mM), CaCl2 (0.1 mM), and glucose (4 g/L) in vigorously shaken (200 rpm) Fernbach flasks.

extract_protocol:
Trizol method.
Ribo-seq libraries were prepared for sequencing using standard VAHTS Small RNA Library Prep Kit for Illumina.

treatment_protocol: Exponentially growing cells were poured over crushed ice containing 100 μg/ml chloramphenicol and harvested by centrifugation at 5000g for 10min at 4℃, followed by 3 washed with pre-chilled phosphate buffered saline (PBS). The cell pellet was resuspended in 6ml pre-chilled sucrose-buffer solution [16mM Tris pH 8.1 supplemented with 0.5M RNase-free sucrose, 50mM KCL, 8.75mM EDTA,100 μg/ml chloramphenicol,12.5mg/ml lysozyme] and gently stirred for 5min on ice. 0.3ml of 1M MgCl2 was added to inhibit lysozome and the suspension was spun at 6000g for 10min at 4℃. The pellet was resuspended in 0.6ml freshly prepared lysis buffer (10mM Tris pH 7.8 containing 50mM NH4Cl, 0.01M MgCl2, 0.2% TritonX-100, 100μg/ml chloramphenicol and 10U DNaseⅠ(RNase-free, Thermo)). The lysate was clarified by centrifugation at 12000g for 10min at 4℃. Up to 0.6ml of clarified lysate was layered onto 35% (w/v) sucrose buffer (10mM Tris pH7.8 containing 50mM NH4Cl, 10mM MgCl2, 0.2% Triton X-100,100μg/ml chloramphenicol) and centrifuged for 5h at 42500 r.p.m in type 70Ti rotor (Beckman) at 4℃. The pellet was slowly resuspended in 0.2ml Micorcocol buffer (50mM Tris pH7.9 containing 5mM CaCl2 and 12mM MgCl2). An aliquot of 1 A260 units of ribosome-bound mRNA fraction was subjected to nucleolytic digestion with 800 units micrococcal nuclease (NEB) for 20min at 25℃. The total RNA extraction was performed by Trizol method.

tag: strain

tag: growth time


title: mammary gland tissue, age 18M, 1 week CYP19A1 transgene induction, biol rep 3 [AROM1WDoxy18M_3722-AROM_S4]

value: 1 week CYP19A1 transgene induction


title: COV004

value: Female

value: Dead


title: ΔRsfS_3h_Ribo-seq_rep2_dataset2

description:
Ribo RNA
BW25113_ΔRsfS
ΔRsfS_3h_Ribo-seq_rep2, dataset2
processed data file: r1_2f.txt


title: ΔRsfS_3h_Ribo-seq_rep1_dataset2

description:
Ribo RNA
BW25113_ΔRsfS
ΔRsfS_3h_Ribo-seq_rep1, dataset2
processed data file: r1_1f.txt


title: Xenopus laevis Embryos, Vegetal Pole (VP), 9 hpf, Rep 4 [VP_9hpf_rep4]

treatment_protocol: Embryos at 1-cell stage were microinjected with 10 nl of 50 mM EU. The final concentration of EU is at ~ 0.5 mM. Embryos developed to blasula stages at 5-9 hpf were dissected, and the AP and VP regions were collected for RNA extraction.

value: Embryo

value: Blastula

value: 9 hpf

value: Experiment 2


title: mammary gland tissue, age 18M, 1 week CYP19A1 transgene induction, biol rep 2 [AROM1WDoxy18M_3678-AROM_S3]


title: mammary gland tissue, age 24M, no CYP19A1 transgene induction, biol rep 2 [4403AROM24M0D_S5]


title: Xenopus laevis Embryos, Control, 7.5 hpf, Rep 1 [Control_7.5hpf_rep1]

value: EU microinjected

value: Experiment 1


title: mammary gland tissue, age 18M, 1 week CYP19A1 transgene induction, biol rep 1 [AROM1WDoxy18M_3674-AROM_S2]


title: ΔRsfS_28h_Ribo-seq_rep1

description:
Ribo RNA
BW25113_ΔRsfS
processed data file: r4_1f.txt


title: PolII_ChIP_DRBCA_R2

city: Leicester

first: Michael

last: Tellier

state: Select State

address: Lancaster Road

department: Department of Molecular and Cell Biology

country: United Kingdom

institute: University of Leicester

library_source: genomic

data_processing:
Adapters were trimmed with Cutadapt v1.18.
Mapping to the hg38 and mm10 genomes was performed with STAR v2.7.3a.
Extraction of properly paired and properly mapped reads and Bam files sorting and indexing were done with SAMtools v1.9.
SAMtools was used to PCR deduplicate and subsampling.
Bigwig files were generated with the Deeptools2 v3.4.2 bamCoverage tool.
Genome_build: hg38 (GRCh38)
Supplementary_files_format_and_content: bigwig files: Genome-coverage files for all samples.

molecule: genomic DNA

growth_protocol: HeLa and BV2a cells were maintained in DMEM with 10% fetal bovine serum.

extract_protocol:
DNA was purified following standard ChIP-seq protocol.
Libraries were prepared according to the protocol of NEBNext(R) Ultra(TM) II DNA Library Prep Kit for Illumina(R) (NEB).

treatment_protocol: Cells were treated with DMSO, DRB, CA, or DRB & CA for the amount of time indicated in the sample's name.

tag: cell line

value: HeLa

tag: spiked-in mouse cell line

value: DRBCA

tag: antibody

value: RNA pol II antibody (mAb), 39097, Active Motif


title: Xenopus laevis Embryos, Vegetal Pole (VP), 8 hpf, Rep 4 [VP_8hpf_rep4]

value: 8 hpf

value: Wildtype


title: Xenopus laevis Embryos, Vegetal Pole (VP), 7 hpf, Rep 5 [VP_7hpf_rep5]

value: 7 hpf


title: PolII_ChIP_DRBCA_R1


title: ΔRsfS_12h_Ribo-seq_rep2_dataset2

description:
Ribo RNA
BW25113_ΔRsfS
ΔRsfS_12h_Ribo-seq_rep2, dataset2
processed data file: r2_2f.txt


title: ΔRsfS_18h_Ribo-seq_rep1_dataset1

description:
Ribo RNA
BW25113_ΔRsfS
ΔRsfS_18h_Ribo-seq_rep1, dataset1
processed data file: r3_1f.txt


title: COV001

value: whole blood

value: COVID

value: Alive


title: ΔRsfS_12h_Ribo-seq_rep2_dataset1

description:
Ribo RNA
BW25113_ΔRsfS
ΔRsfS_12h_Ribo-seq_rep2, dataset1
processed data file: r2_2f.txt


title: PolII_ChIP_DRB_R2

value: DRB


title: Xenopus laevis Embryos, Vegetal Pole (VP), 8 hpf, Rep 5 [VP_8hpf_rep5]


title: Xenopus laevis Embryos, Vegetal Pole (VP), 6 hpf, Rep 4 [VP_6hpf_rep4]

value: 6 hpf


title: ΔRsfS_28h_Ribo-seq_rep2

description:
Ribo RNA
BW25113_ΔRsfS
processed data file: r4_2f.txt


title: Xenopus laevis Embryos, Vegetal Pole (VP), 9 hpf, Rep 5 [VP_9hpf_rep5]

value: Embryo


title: mammary gland tissue, age 12M, 1 week CYP19A1 transgene induction, biol rep 1 [AROM1WDoxy12M_3820-AR0M_S3]

value: mammary gland

value: 1 week CYP19A1 transgene induction


title: ΔRsfS_3h_Ribo-seq_rep1_dataset1

description:
Ribo RNA
BW25113_ΔRsfS
ΔRsfS_3h_Ribo-seq_rep1, dataset1
processed data file: r1_1f.txt


title: Xenopus laevis Embryos, Animal Pole (AP), 9 hpf, Rep 4 [AP_9hpf_rep4]

value: Blastula

value: 9 hpf

value: Experiment 2


title: BW25113_3h_Ribo-seq_rep1_dataset2

description:
Ribo RNA
BW25113_3h_Ribo-seq_rep1, dataset2
processed data file: b1_1f.txt


title: mammary gland tissue, age 12M, no CYP19A1 transgene induction, biol rep 3 [AROM012M_3866-AROM_S2]

value: no CYP19A1 transgene induction


title: PolII_ChIP_CA_R2

value: HeLa

value: CA


title: COV002

value: Male


title: mammary gland tissue, age 18M, no CYP19A1 transgene induction, biol rep 3 [AROM018M_3885-AROM_S5]


title: Xenopus laevis Embryos, Animal Pole (AP), 8 hpf, Rep 5 [AP_8hpf_rep5]

value: 8 hpf

value: Wildtype

value: EU microinjected


title: ΔRsfS_18h_Ribo-seq_rep2

description:
Ribo RNA
BW25113_ΔRsfS
processed data file: r3_2f.txt


title: mammary gland tissue, age 18M, no CYP19A1 transgene induction, biol rep 1 [AROM018M_3735-AROM_S5]


title: mammary gland tissue, age 18M, no CYP19A1 transgene induction, biol rep 2 [AROM018M_3872-AROM_S1]


title: Input_DRBCA_R2

value: DRBCA


title: mammary gland tissue, age 12M, no CYP19A1 transgene induction, biol rep 2 [AROM012M_3865-AROM_S7]


title: Xenopus laevis Embryos, Animal Pole (AP), 8 hpf, Rep 4 [AP_8hpf_rep4]


title: Xenopus laevis Embryos, Vegetal Pole (VP), 6 hpf, Rep 5 [VP_6hpf_rep5]


title: mammary gland tissue, age 12M, 1 week CYP19A1 transgene induction, biol rep 3 [AROM1WDoxy12M_3829-AROM_S4]


title: BW25113_3h_Ribo-seq_rep2_dataset2

description:
Ribo RNA
BW25113_3h_Ribo-seq_rep2, dataset2
processed data file: b1_2f.txt


title: ΔRsfS_12h_Ribo-seq_rep1

description:
Ribo RNA
BW25113_ΔRsfS
processed data file: r2_1f.txt


title: Input_DRBCA_R1


title: mammary gland tissue, age 12M, no CYP19A1 transgene induction, biol rep 1 [AROM012M_3848b-AROM_S6]


title: Xenopus laevis Embryos, Vegetal Pole (VP), 7 hpf, Rep 4 [VP_7hpf_rep4]

value: 7 hpf


title: BW25113_12h_Ribo-seq_rep2

description:
Ribo RNA
processed data file: b2_2f.txt


title: ΔRsfS_3h_Ribo-seq_rep2_dataset1

description:
Ribo RNA
BW25113_ΔRsfS
ΔRsfS_3h_Ribo-seq_rep2, dataset1
processed data file: r1_2f.txt


title: Xenopus laevis Embryos, Animal Pole (AP), 9 hpf, Rep 5 [AP_9hpf_rep5]


title: mammary gland tissue, age 30M, 18 months Esr1 transgene induction, biol rep 3 [4550CERM18M30M_S4 ]

value: 18 months Esr1 transgene induction


title: PolII_ChIP_DMSO_R1

value: DMSO

value: RNA pol II antibody (mAb), 39097, Active Motif


title: mammary gland tissue, age 12M, 1 week CYP19A1 transgene induction, biol rep 2 [AROM1WDoxy12M_3826-AROM_S8]

value: mammary gland


title: Input_CA_R1


title: BW25113_18h_Ribo-seq_rep1

description:
Ribo RNA
processed data file: b3_1f.txt


title: Xenopus laevis Embryos, Animal Pole (AP), 7 hpf, Rep 4 [AP_7hpf_rep4]

value: Embryo


title: Input_DRB_R2

value: DRB


title: Xenopus laevis Embryos, Animal Pole (AP), 6 hpf, Rep 5 [AP_6hpf_rep5]

value: Blastula

value: 6 hpf


title: Xenopus laevis Embryos, Animal Pole (AP), 7 hpf, Rep 5 [AP_7hpf_rep5]

value: Experiment 2


title: PolII_ChIP_DMSO_R2

value: HeLa


title: PolII_ChIP_DRB_R1


title: Xenopus laevis Embryos, Animal Pole (AP), 6 hpf, Rep 4 [AP_6hpf_rep4]


title: PolII_ChIP_CA_R1

value: CA


title: mammary gland tissue, age 30M, 18 months Esr1 transgene induction, biol rep 2 [4629CERM18M30M_S4]


title: Input_CA_R2


title: Input_DRB_R1


title: mammary gland tissue, age 24M, 12 months Esr1 transgene induction, biol rep 3 [4728CERM12M24M_S3]

value: 12 months Esr1 transgene induction


title: BW25113_3h_Ribo-seq_rep2_dataset1

description:
Ribo RNA
BW25113_3h_Ribo-seq_rep2, dataset1
processed data file: b1_2f.txt


title: Xenopus laevis Embryos, Vegetal Pole (VP), 9 hpf, Rep 3 [VP_9hpf_rep3]

value: 9 hpf

value: Experiment 1


title: BW25113_18h_Ribo-seq_rep2

description:
Ribo RNA
processed data file: b3_2f.txt


title: Input_DMSO_R2


title: BW25113_3h_Ribo-seq_rep1_dataset1

description:
Ribo RNA
BW25113_3h_Ribo-seq_rep1, dataset1
processed data file: b1_1f.txt


title: mammary gland tissue, age 24M, 12 months Esr1 transgene induction, biol rep 2 [4754CERM12M24M_S3]


title: Xenopus laevis Embryos, Vegetal Pole (VP), 9 hpf, Rep 2 [VP_9hpf_rep2]

value: Wildtype

value: EU microinjected


title: BW25113_12h_Ribo-seq_rep1

description:
Ribo RNA
processed data file: b2_1f.txt


title: Day 6.0 rabbit embryos

city: BRON

first: Wilhelm

last: Bouchereau

state: Rhone-Alpes

address: 18 Avenue du Doyen Lépine

country: France

institute: INSERM

data_processing:
Illumina RTA software used for basecalling.
Sequenced reads were demultiplexed using Cell Ranger v3.0.2, then their quality was assessed using FastQC software and they were screened for contaminant using bowtie2 alignement tool of FastQC software.
The reads were mapped to OryCun2 v95 whole genome using Cell Ranger v3.0.2.
The 6 different datasets were combined using the cellranger aggr function of Cell Ranger v3.0.2.
Genome_build: OryCun2_ensembl v95
Supplementary_files_format_and_content: tab-delimited text files include single-cell barcodes as sample names
Supplementary_files_format_and_content: tab-delimited text files include features ENSG identity and Gene Symbol
Supplementary_files_format_and_content: Matrix table with raw gene counts for every feature and every sample

organism: Oryctolagus cuniculus

extract_protocol:
The embryos were depellucidated using protease from Streptomyces griseus treatment and gentle mechanical dissociation. Cell singularization was achieved using trypsine 2 %, TryPLE 1 %, and gentle mechanical dissociation. Cell suspensions were loaded on a Chromium controller (10x Genomics, Pleasanton, CA, USA) to generate single-cell Gel Beads-in-Emulsion (GEMs).
Single-cell RNA-Seq libraries were prepared using Chromium Single cell 3’RNA Gel Bead and Library Kit

tag: Stage

value: Day 6.0

tag: tissues

value: dissected embryonic disk


title: mammary gland tissue, age 24M, 12 months Esr1 transgene induction, biol rep 1 [4816CERM12M24M_S3]

tag: tissue


title: Day 6.6 rabbit embryos

value: Day 6.6


title: Xenopus laevis Embryos, Vegetal Pole (VP), 9 hpf, Rep 1 [VP_9hpf_rep1]


title: Day 5.0 rabbit embryos

value: Day 5.0

value: whole embryo


title: mammary gland tissue, age 24M, 6 months Esr1 transgene induction, biol rep 3 [1702CERM6M24M_S2]

value: mammary gland

tag: age

value: 6 months Esr1 transgene induction


title: Input_DMSO_R1

value: DMSO


title: Xenopus laevis Embryos, Vegetal Pole (VP), 8 hpf, Rep 3 [VP_8hpf_rep3]

value: Embryo

value: Blastula

value: 8 hpf

tag: genotype


title: mammary gland tissue, age 30M, 18 months Esr1 transgene induction, biol rep 1 [4607CERM30m18M_S1]

tag: treatment

value: 18 months Esr1 transgene induction


title: Xenopus laevis Embryos, Vegetal Pole (VP), 8 hpf, Rep 2 [VP_8hpf_rep2]

tag: developmental stage


title: mammary gland tissue, age 24M, 6 months Esr1 transgene induction, biol rep 1 [4709CERM6m24M_S2]


title: Recovery 3 [R3]

city: Houston

first: Yulin

last: Li

state: Texas

address: 6670 Bertner Avenue

institute: Houston Methodist Research Institute

data_processing:
kallisto (version 0.46.2) was used to pseudoalign paired-end reads to a reference transcriptome under default settings.
Genome_build: The reference transcriptome used to build the kallisto index consisted of the "Protein-coding transcript sequences" and "Long non-coding RNA transcript sequences" FASTA files from Human Release 38 (GRCh38.p13) of GENCODE.
Supplementary_files_format_and_content: Tab-delimited text files containing trascript IDs and transcript-level estimated counts and TPMs.

source_name: pancreatic ductal adenocarcinoma cells

growth_protocol: MIA PaCa-2 cells were cultured in DMEM media supplemented with 10% fetal bovine serum and 1% penicillin/streptomycin in a 5% CO2 humidified incubator.

extract_protocol:
RNA samples were extracted using Qiagen RNeasy Plus kit (QIAGEN)
Library construction and RNA sequencing were performed by Novogene as a service. Briefly, ribosomal RNA was removed from total RNA by rRNA removal kit, and rRNA free residue was cleaned up by ethanol precipitation. After fragmentation, the first strand cDNA was synthesized using random hexamer primers. Then the second strand cDNA was synthesized and dUTPs were replaced with dTTPs in the reaction buffer. The directional library was ready after end repair, A-tailing, adapter ligation, size selection, USER enzyme digestion, amplification, and purification.

treatment_protocol: Control cells were the MIA PaCa-2 cultured under normal conditions. Torin1-treated cells were MIA PaCa-2 treated with Torin 1 (100nM) for 9 days. Persister cells were collected following combined treatment with gemcitabine (100nM) plus Torin 1 (100nM) for 9 days. The recovery cells were the persister cells further cultured in drug-free normal media for 12 days.

value: MIA PaCa-2

tag: cell type

value: pancreatic ductal adenocarcinoma cells

value: Gemcitabine (100 nM) plus Torin 1 (100 nM)

tag: treatment time

value: 9 days followed by culture in drug-free normal media for 12 days


title: mammary gland tissue, age 24M, 6 months Esr1 transgene induction, biol rep 2 [4641CERM6M24M_S2]


title: Xenopus laevis Embryos, Vegetal Pole (VP), 8 hpf, Rep 1 [VP_8hpf_rep1]

tag: time

value: Wildtype

value: EU microinjected

tag: batch

value: Experiment 1


title: Day 3.5 rabbit embryos

value: Day 3.5


title: Recovery 2 [R2]


title: Day 3.0 rabbit embryos

value: Day 3.0


title: Recovery 1 [R1]


title: mammary gland tissue, age 24M, no Esr1 transgene induction, biol rep 3 [4925CERM24M0D_S4]

value: no Esr1 transgene induction


title: Day 4.0 rabbit embryos

value: Day 4.0

value: whole embryo


title: Xenopus laevis Embryos, Vegetal Pole (VP), 7 hpf, Rep 3 [VP_7hpf_rep3]

value: 7 hpf


title: mammary gland tissue, age 24M, no Esr1 transgene induction, biol rep 2 [4892CERM24M0D_S1]

value: mammary gland


title: Persisters 3 [gT3]

value: 9 days


title: mammary gland tissue, age 24M, no Esr1 transgene induction, biol rep 1 [4942CERM0-24M_S1]


title: Persisters 2 [gT2]


title: Torin1-treated 3 [T3]

value: Torin 1 (100 nM)


title: Xenopus laevis Embryos, Vegetal Pole (VP), 7 hpf, Rep 2 [VP_7hpf_rep2]

value: Embryo

value: Blastula


title: mammary gland tissue, age 18M, 1 week Esr1 transgene induction, biol rep 2 [CERM1WDoxy18M_4222-CERM_S8]

value: 1 week Esr1 transgene induction


title: Persisters 1 [gT1]

value: MIA PaCa-2

value: pancreatic ductal adenocarcinoma cells

value: Gemcitabine (100 nM) plus Torin 1 (100 nM)


title: mammary gland tissue, age 18M, 1 week Esr1 transgene induction, biol rep 3 [CERM1WDoxy18M_4223-CERM_S1]


title: Torin1-treated 1 [T1]


title: mammary gland tissue, age 18M, 1 week Esr1 transgene induction, biol rep 1 [CERM1WDoxy18M_4219-CERM_S6]


title: Xenopus laevis Embryos, Vegetal Pole (VP), 7 hpf, Rep 1 [VP_7hpf_rep1]

value: Wildtype

value: EU microinjected


title: pt_173_nk

city: St. Louis

first: Eric

last: Tycksen

state: Missouri

address: 4444 Forest Park Avenue

department: McDonnell Genome Institute

institute: Washington University in St. Louis School of Medicine

description: NK cell JDM

data_processing:
Basecalling with Illumina RTA 1.9
Demultiplexing with Illumina bcl2fastq2
Fastq files were combined and aligned with STAR 2.4.0b
Gene counts quantitated with Subread:featureCount 1.45 with CPM and RPKM transformations added with custom Rscripting.
Assembly: Ensembl GRCm38.76
Supplementary files format and content: Gene counts with CPM and RPKM in tab-delimitted text format

source_name: enriched live PBMC

extract_protocol: Clontech SMARTer v1

treatment_protocol: highly riched live N cell, T cell, and B cells were sorted from previously alquoted PBMCs from Jnew onset DM patients or controls

value: human peripheral blood


title: Torin1-treated 2 [T2]


title: pt_173_b

description: B cell JDM


title: pt_172_nk

description: NK cell JDM


title: Xenopus laevis Embryos, Vegetal Pole (VP), 6 hpf, Rep 3 [VP_6hpf_rep3]

value: 6 hpf

value: Experiment 1


title: Xenopus laevis Embryos, Vegetal Pole (VP), 6 hpf, Rep 2 [VP_6hpf_rep2]


title: pt_172_t

description: T cell JDM


title: pt_168_nk

description: NK cell JDM


title: Control 2 [C2]

value: Untreated


title: pt_168_t

description: T cell JDM


title: Control 3 [C3]


title: pt_172_b

description: B cell JDM


title: pt_168_b

description: B cell JDM


title: Xenopus laevis Embryos, Vegetal Pole (VP), 5 hpf, Rep 3 [VP_5hpf_rep3]

value: 5 hpf


title: Control 1 [C1]


title: mammary gland tissue, age 18M, no Esr1 transgene induction, biol rep 2 [CERM018M_4235-CERM_S1]

value: no Esr1 transgene induction


title: pt_173_t

description: T cell JDM


title: pt_144_t

description: T cell JDM


title: mammary gland tissue, age 12M, 1 week Esr1 transgene induction, biol rep 3 [CERM1WDoxy12M_4107-CERM_S4]

value: mammary gland


title: Xenopus laevis Embryos, Animal Pole (AP), 9 hpf, Rep 3 [AP_9hpf_rep3]

value: 9 hpf


title: Xenopus laevis Embryos, Vegetal Pole (VP), 5 hpf, Rep 1 [VP_5hpf_rep1]


title: ChIP-seq MYC ONS76 rep3

city: Nashville

first: Jing

last: Wang

state: TN

address: 2220 Pierce Avenue

institute: Vanderbilt University Medical Center

description: MYC ChIP-seq of ONS76 cells

data_processing:
ChIP-seq reads were aligned to the hg19 genome assembly using Bowtie2.
Peaks were called by MACS2 with a q-value of 0.05.
Genome_build: hg19
Supplementary_files_format_and_content: ChIP-seq: one peak file per Sample

source_name: Medulloblastoma cell line

growth_protocol: ONS76 cells  were maintained in DMEM + 10% FBS + penicillin/streptomycin

extract_protocol:
Cells were crosslinked in 1% formaldehyde and subject to sonication. The resulting sheared chromatin was combined overnight with antibody.
Libraries were prepared using NEBnext Ultra II DNA Library Prep Kit and NEBNext Multiplex Oligos for Illumina, following the manufacturer's instructions.

tag: engineered genotype

value: Inducible SOX2

value: MYC (Y69)


title: Xenopus laevis Embryos, Vegetal Pole (VP), 6 hpf, Rep 1 [VP_6hpf_rep1]

value: Embryo

value: Blastula


title: mammary gland tissue, age 18M, no Esr1 transgene induction, biol rep 3 [CERM018M_4312-CERM_S7]


title: Xenopus laevis Embryos, Animal Pole (AP), 9 hpf, Rep 2 [AP_9hpf_rep2]


title: ChIP-seq MYC ONS76 rep1

description: MYC ChIP-seq of ONS76 cells


title: pt_144_nk

description: NK cell JDM


title: mammary gland tissue, age 12M, 1 week Esr1 transgene induction, biol rep 1 [CERM1WDoxy12M_4098IIb-CERM_S3]

value: 1 week Esr1 transgene induction


title: mammary gland tissue, age 12M, 1 week Esr1 transgene induction, biol rep 2 [CERM1WDoxy12M_4099-CERM_S5]


title: mammary gland tissue, age 18M, no Esr1 transgene induction, biol rep 1 [CERM018M_4226-CERM_S2]


title: ChIP-seq MYC ONS76 rep2

description: MYC ChIP-seq of ONS76 cells


title: pt_144_b

description: B cell JDM


title: ChIP-seq IgG ONS76 rep3

description: Normal IgG ChIP-seq of ONS76 cells

value: Normal IgG


title: Xenopus laevis Embryos, Animal Pole (AP), 8 hpf, Rep 3 [AP_8hpf_rep3]

value: 8 hpf


title: Xenopus laevis Embryos, Animal Pole (AP), 9 hpf, Rep 1 [AP_9hpf_rep1]

value: Wildtype


title: ctrl_170_nk

description: NK cell control


title: ctrl_170_t

description: T cell control


title: Xenopus laevis Embryos, Animal Pole (AP), 8 hpf, Rep 2 [AP_8hpf_rep2]

value: EU microinjected


title: ChIP-seq IgG ONS76 rep2

description: Normal IgG ChIP-seq of ONS76 cells


title: mammary gland tissue, age 12M, no Esr1 transgene induction, biol rep 3 [CERM012M_4171a-CERM_S7]


title: mammary gland tissue, age 12M, no Esr1 transgene induction, biol rep 1 [CERM012M_4162-CERM_S6]


title: ChIP-seq IgG ONS76 rep1

description: Normal IgG ChIP-seq of ONS76 cells


title: Xenopus laevis Embryos, Vegetal Pole (VP), 5 hpf, Rep 2 [VP_5hpf_rep2]


title: Xenopus laevis Embryos, Animal Pole (AP), 8 hpf, Rep 1 [AP_8hpf_rep1]


title: ctrl_170_b

description: B cell control

value: human peripheral blood


title: Sample 2 - Single-cell RNA-seq - Technical Replicate B

city: Ann Arbor

first: Kelly

last: Bakulski

state: MI

address: 1415 Washington Heights

department: Epidemiology

institute: University of Michigan

description:
Raw files are demultiplexed asymmetric paired-end fastq reads from cDNA libraries barcoded and constructed on the Chromium platform from 10x Genomics, Single Cell 3' v2 chemistry. Processed data file is the Seurat object as an .Rdata file used for the analysis and includes all demultiplexed samples listed here.
processed_single_cell_Seurat_object.rda

data_processing:
Single-cell RNA-sequencing read preprocessing and alignment: raw reads were processed, deconvoluted, droplet filtered, and aligned at the gene level with the CellRanger pipeline using default settings (v4.0.0), 10X Genomics)
Single-cell RNA-sequencing fetal/maternal identity and mosaic doublet removal: the freemuxlet function in the latest version (accessed 2021/12/05) of the ‘popscle’ package was used to assign fetal or maternal origin and identify 120 mosaic doublets for removal based on single nucleotide polymorphisms with minor allele frequency greater than 10% from the 1000 Genomes Phase 3 reference panel (released 2013/05/02).
Single-cell RNA-sequencing cell quality control: per cell quality control criteria were total RNA molecules, unique genes, and percentage of mitochondrial gene mapping reads. We excluded 1,398 low-quality outlier cells defined as cells that exceeded four median absolute deviations in samples 1 and 2 or three median absolute deviations in samples 3, 4, and 5 using the quickQCPerCell function in ‘scater’ (R package, version 1.18.6) with default settings.
Single-cell RNA-sequencing clustering and cluster annotation: maternal and fetal cells were split into separate datasets for clustering. Mutual nearest neighbor batch correction by biological replicate with default settings was used to identify cell type clusters and visualize clustering results via uniform manifold projection using FastMNN from ‘SeuratWrapper’ (R package, version 0.3.0). Iterative clustering and sub-clustering with ‘Seurat’ (R package, version 4.0.1) function FindClusters at different resolution parameters were evaluated using cluster stability via clustering trees in ‘clustree’. A priori canonical cell type marker gene expression patterns and cluster marker genes were used to assign cell types to cell clusters. Cells that fell outside cell type clusters and outlying in doublet density calculated with computeDoubletDensity were removed as putative doublets and doublet clusters.were identified with findDoubletClusters for removal in ‘scDblFinder’ (R package, version 1.4.0)
Bulk RNA-sequencing of placental tissue and cell types alignment and feature counts: Reads were aligned to the GRCh38.p12/ GENCODEv28 reference transcriptome using ‘STAR’ v2.6.0c with default settings [57]. featureCounts from ‘subread’ v1.6.1 was used to quantify and summarize gene expression with default settings [83]
Genome_build: For single-cell RNA-sequencing, reads were aligned to the GRCh38 GENCODEv32/Ensembl 98 reference transcriptome. For bulk RNA-sequencing, reads were aligned to the GRCh38.p12/ GENCODEv28 reference transcriptome
Supplementary_files_format_and_content: Processed files are .Rdata objects ready for analysis formatted as a Seurat object for the single-cell RNA-seq data or as DESeq object for the bulk RNA-sequencing data. Code used to generate these files is available (https://github.com/bakulskilab).

source_name: Placental Villous Tissue

extract_protocol:
Placentas were collected shortly after delivery from healthy, full term, singleton uncomplicated Cesarean sections at the University of Michigan Von Voigtlander Women’s Hospital. Villous placental tissue biopsies were collected and minced for dissociation after cutting away the basal and chorionic plates and scraping villous tissue from blood vessels. We subjected approximately 1g minced dissected villous tissue to the Miltenyi Tumor Dissociation Kit on the GentleMACS Octo Dissociator with Heaters (Miltenyi Biotec) to yield single-cell suspensions of viable placental cells in 5μM StemMACS™ Y27632 (Miltenyi Biotec) in RPMI 1640 (Gibco) according to manufacturer’s instructions for “soft” tumor type. Red blood cells were depleted using RBC lysis buffer (Biolegend) according to manufacturer’s protocol A. Single-cell suspensions were size-filtered at 100μm and subsequently 40μm. To collect a syncytiotrophoblast-enriched fraction, the fraction between 40μm and 100μm was washed from the 40μm strainers. Single-cell suspensions <40μm were cryogenically stored in 5μM StemMACS™ Y27632 90% heat-inactivated fetal bovine serum (Gibco)/10% dimethyl sulfoxide (Invitrogen). For each placenta, additional whole villous tissue samples were stored in RNALater (Qiagen).
For single-cell RNA-sequencing, single cells were barcoded, and cDNA libraries constructed on the Chromium platform (10X Genomics, Single Cell 3' v2 chemistry).
For bulk RNA-sequencing, ribosomal RNAs were depleted with RiboGone (Takara) and libraries were prepared with the SMARTer Stranded RNA-Seq v2 kit (Takara).

value: Placental Villous Tissue


title: Sample 2 - Single-cell RNA-seq - Technical Replicate A


title: amc_016_t

description: T cell control


title: amc_016_nk

description: NK cell control


title: Sample 1 - Single-cell RNA-seq - Technical Replicate B


title: Xenopus laevis Embryos, Animal Pole (AP), 7 hpf, Rep 2 [AP_7hpf_rep2]

value: 7 hpf

value: Experiment 1


title: mammary gland tissue, age 12M, no Esr1 transgene induction, biol rep 2 [CERM012M_4170II-CERM_S8]


title: amc_016_b

description: B cell control


title: Xenopus laevis Embryos, Animal Pole (AP), 7 hpf, Rep 1 [AP_7hpf_rep1]


title: Sample 1 - Single-cell RNA-seq - Technical Replicate A


title: amc_013_t

description: T cell control


title: HT-29_NHT_rep3

city: Freiburg

first: Geoffroy

last: Andrieux

address: Breisacherstr 153

institute: University clinics Freiburg

hyb_protocol: 5.5 µg of fragmented and labeled ss-cDNA were hybridized for 17 h at 45°C on Applied BiosystemsT human ClariomT S Array, according to the Affymetrix WT PLUS Reagent Kit user manual.

scan_protocol: Gene Expression Microarrays were scanned using the Affymetrix GeneChip® Scanner 3000 according to GeneChip® Expression Wash, Stain and Scan Manual for Cartridge Arrays.

data_processing: CEL files were analysed using the oligo R package. RMA method, log2 transformed were used to normalized the probe intensities.

label: Biotin

source_name: human intestinal epithelial cell line HT-29, CRISPR/Cas9 control non-human target (nht)

label_protocol: The Applied BiosystemsT WT PLUS Reagent Kit was used to generate labeled ss-cDNA from input amounts of 100 ng total RNA.

growth_protocol: HT-29 control (non-human target: nht) and USP22 knockout single clones X16 and X62 cells were seeded at equal densities. After two days of cultivation and 80% confluency, RNA was isolated.

extract_protocol: RNA was isolated using the peqGOLD total RNA isolation kit (Peqlab, Erlangen, Germany), according to the manufacturer’s protocol.

treatment_protocol: No treatment was performed. Culture medium was removed before starting RNA extraction protocol.

value: crispr/cas9 guide rna non-human target (nht)

value: control


title: siDDX5_rep2

city: Rome

first: Valerio

last: Licursi

address: via degli Apuli, 4

department: c/o Dept. Biology and Biotechnologies "C. Darwin", Sapienza University of Rome

country: Italy

institute: Institute of Molecular Biology and Pathology (IBPM), National Research Council (CNR)

data_processing:
Processing raw data for both format conversion and de-multiplexing by Bcl2Fastq 2.20 version of the Illumina pipeline
Reads quality was evaluated using FastQC (version 0.11.8, Babraham Institute  Cambridge, UK) tool, then adapter sequences were masked with Cutadapt version 1.11 from raw fastq data using the following parameters: --anywhere (on both adapter sequences) --overlap 5 --times 2 --minimum-length 35 --mask-adapter
Reads were mapped to the human Ensembl GRCh38 transcriptome index (release 96) using kallisto (version 0.46.0)
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text files of kallisto output table with TPM values for each Sample

source_name: rhabdomyosarcoma alveolar cell line

extract_protocol:
Cells were harvested and centrifuged at 3000 rpm for 5 min at 4°C. Supernatant was then removed and cell pellet was resuspended in 1 ml of ice-cold PBS and centrifuged at 2000 rpm for 5 min at 4°C. After removing the supernatant, cell pellet was resuspended in 1 mL of TRIzol reagent (Invitrogen) and RNA extraction was carried out following Invitrogen protocol. RNA was then quantified using Nanodrop.
TruSeq Stranded mRNA kit (Illumina, San Diego, CA) has been used for library preparation following the manufacturer’s instructions (library type: fr-firstrand). RNA samples were quantified and quality tested by Agilent 2100 Bioanalyzer RNA assay (Agilent technologies, Santa Clara, CA) or Caliper (PerkinElmer, Waltham, MA). Final libraries were checked with both Qubit 2.0 Fluorometer (Invitrogen, Carlsbad, CA) and Agilent Bioanalyzer DNA assay or Caliper (PerkinElmer, Waltham, MA).

tag: gene fusion

value: pax3-foxo1 fusion positive cell line

tag: knockdown


title: Xenopus laevis Embryos, Animal Pole (AP), 7 hpf, Rep 3 [AP_7hpf_rep3]


title: Xenopus laevis Embryos, Animal Pole (AP), 6 hpf, Rep 1 [AP_6hpf_rep1]

value: 6 hpf


title: siDDX5_rep1

tag: cell line


title: siDDX5_rep3


title: Xenopus laevis Embryos, Animal Pole (AP), 6 hpf, Rep 2 [AP_6hpf_rep2]


title: amc_012_t

description: T cell control


title: amc_012_nk

description: NK cell control


title: amc_013_b

description: B cell control


title: Xenopus laevis Embryos, Animal Pole (AP), 5 hpf, Rep 3 [AP_5hpf_rep3]

value: 5 hpf


title: CTR_rep3


title: CTR_rep2


title: amc_013_nk

description: NK cell control


title: Xenopus laevis Embryos, Animal Pole (AP), 6 hpf, Rep 3 [AP_6hpf_rep3]


title: Xenopus laevis Embryos, Animal Pole (AP), 5 hpf, Rep 1 [AP_5hpf_rep1]


title: P22354_121

status: Public on Aug 21 2022

city: Stockholm

first: Mikael

last: Sandell

state: Solna

address: Akademiska stråket 1

department: Clinical Neuroscience

country: Sweden

institute: Karolinska Institutet

data_processing:
Salmon for alignment and quantification
DESeq2 for count normalization and transformation
Genome_build: Genome_build: Sscrofa11.1
Supplementary_files_format_and_content: count matrix of reads mapped to genes

organism: Sus scrofa

source_name: Kidney vessel

extract_protocol:
RNAdvance Tissue kit with modifications: Reduce reagent volumes by dividing with 13. Use vortexing + centrifugation to homogenize samples. SMARTer Pico
SMARTer Pico

value: Peripheral kidney artery

tag: device used

value: 3D-printed microbrush

tag: pigid


title: P22354_119

source_name: Liver vessel

value: Peripheral liver artery


title: amc_012_b

description: B cell control


title: Xenopus laevis Embryos, Animal Pole (AP), 5 hpf, Rep 2 [AP_5hpf_rep2]

value: Embryo

value: Blastula


title: HT-29_USP22 KO #62_rep1

source_name: human intestinal epithelial cell line HT-29, subjected to CRISPR/Cas9 mediated knockout of USP22, single clone #62

value: crispr/cas9 guide rna USP22

value: USP22 knockout

tag: clone


title: P22354_117

source_name: Whole blood

value: Blood


title: HT-29_USP22 KO #62_rep3


title: HT-29_NHT_rep2


title: HT-29_USP22 KO #16_rep3

source_name: human intestinal epithelial cell line HT-29, subjected to CRISPR/Cas9 mediated knockout of USP22, single clone #16


title: HT-29_NHT_rep1


title: HT-29_USP22 KO #62_rep2


title: P22354_114


title: P22354_115


title: HT-29_USP22 KO #16_rep1


title: P22354_116

value: Nitinol wire


title: P22354_113

source_name: Vessel

value: Aorta


title: HT-29_USP22 KO #16_rep2


title: P22354_118


title: P22354_111


title: P22354_112


title: P22354_105


title: P22354_120


title: P22354_108


title: P22354_106


title: CTR_rep1


title: P22354_103


title: P22354_102


title: P22354_101


title: P22354_109


title: P22354_104


title: BuP_1.0

city: Nowon-gu

first: Kitae

last: Kim

address: Gongneung-ro

institute: Seoul national university of science and technology

data_processing:
The adapter sequences and the ends of the reads less than Phred quality score 20 were trimmed and simultaneously the reads shorter than 50 bp were removed by using cutadapt v.2.8
Filtered reads were mapped to the reference genome related to the species using the aligner STAR v.2.7.1a following ENCODE standard options
Gene expression estimation was performed by RSEM v.1.3.1 considering the direction of the reads which are corresponding to the library protocol using option --strandedness.
To normalize sequencing depth among samples, FPKM and TPM values were calculated.
Assembly: GRCz11
Supplementary files format and content: tab-delimited text files include RPKM and TPM values for each Sample

organism: Danio rerio

source_name: Brain

extract_protocol: The libraries were prepared for 151bp paired-end sequencing using TruSeq stranded mRNA Sample Preparation Kit (Illumina, CA, USA).

value: Brain

value: WT

value: BuP 1.0 mg/L


title: BuP_0.1

value: BuP 0.1 mg/L


title: P22354_107


title: P22354_110


title: BuP_0.01

value: BuP 0.01 mg/L


title: Control

value: DMSO 0.1%


title: RAD21 WT siGLO, Rep1

city: Chapel Hill

first: Jill

last: Dowen

state: NC

address: 250 Bell Tower Drive

institute: University of North Carolina at Chapel Hill

data_processing:
Any samples that were split scross sequencing lanes were treated as technical replicates and "L1" and "L2" were concatenated for each sample. If the sample was paired-end, only the first read of the pair was used for analysis (samples with "R1").
Alignment: reads were aligned to a hybrid mm10+hg38 genome with  bowtie v 1.2.3 with parameters -v 2 -p 24 -S -m 1 --best --strata
PCR Duplicate Removal: duplicates removed with samtools v 1.11 fixmate -m followed by markdup -r -s
Peak Calling: peaks were called using MACS (v2.2.7.1) with parameters -f BED -g mm -q 0.01
Spike-In Normalization Factor: reads mapping to each genome (mouse and human) were counted. Normalization factor = 1/(number human reads / 1,000,000)
Coverage File Generation: bigwig files were generated using bedtools (v 2.29.0) genomecov with parameters -bga -g mm10.chrom.sizes -scale (Normalization Factor) followed by ucsctools (v 320) bedGraphToBigWig
Assembly: Custom built bowtie index of Mus musculus build mm10 plus Homo sapiens build hg38
Supplementary files format and content: For each ChIP sample, a BigWig coverage track of merged replicates is provided for viewing in a genome browser.

source_name: Mouse embryonic stem cells v6.5

growth_protocol: Murine embryonic stem cells (v6.5, male) were grown on gelatinized tissue culture dishes under standard ESC conditions as previously described (Kagey et al. 2010).

extract_protocol:
mESCs were crosslinked in 1% formaldehyde for 5 minutes before quenching with 2.5M glycine. After chromatin extraction, 5% of HEK293T chromatin was added to the mESC samples to be later used as a spike-in normalization for the indicated experiments. Crosslinked cells were lysed using Lysis Buffer 1 and Lysis Buffer 2 before washing and resuspension in Shearing Buffer. Sonication of nuclei was performed on a Covaris E220 with the following settings: Duty Factor 5, PIP/W 140, and 200 cycles per burst for 12 minutes. Chromatin fragments of 200-1000 base pairs were generated. The antibodies were incubated with 30uL and 50uL Protein G Dynabeads for RAD21 and PDS5 IPs respectivly, for 6 hours prior to addition of chromatin. The chromatin in shearing buffer was spiked with NaCl and Triton X-100 to be in a ChIP buffer. Chromatin from 1 x 10^7 cells was added to antibody conjugated beads and incubated rotating overnight at 4C. Beads were then washed with ChIP Buffer and Wash Buffers 1, 2, and 3. Chromatin was eluted and crosslinks were reversed overnight via incubation at 65C and addition of 5ul Proteinase K. The next day, DNA was purified using a Zymo ChIP DNA Clean and Concentrate kit. Sequencing libraries were prepared using Kapa Hyper Prep Kit.
Sequencing libraries were prepared using Kapa Hyper Prep Kit (Kapa Biosystems).

treatment_protocol: As indicated, cells were counted and 5 x 10^5 were plated per well in 6-well plates. Each well was treated with 50nM of siRNA or siGLO transfection control using DharmaFECT (Dharmacon) transfection reagent following manufacturer’s instructions: siGLO (D-001630-01-0) and siPds5b (M-058400-01-0005). Cell were harvested after 48 hours for crosslinking.

value: Wildtype

value: mouse embryonic stem cells (mESCs)

tag: chip antibody

value: Abcam ab992


title: RAD21 Pds5a-KO, Rep2

description:
RAD21_Pds5a-KO_Merge.bw
Samples were split across two lanes on the sequencer. These were treated as technical replicates and "L1" and "L2" were concatenated for each sample.

value: Pds5a knockout


title: RAD21 Pds5a-KO, Rep1


title: RAD21 WT siGLO, Rep2


title: RAD21 Pds5b-KO, Rep2

description:
RAD21_Pds5b-KO_Merge.bw
Samples were split across two lanes on the sequencer. These were treated as technical replicates and "L1" and "L2" were concatenated for each sample.

value: Pds5b knockout


title: RAD21 Pds5b-KO, Rep1


title: L56C5 YTB LTBI- turned LTBI+

city: Tyler

first: Tanmoy

last: Mukherjee

state: TX

department: Pulmonary Immunology

institute: University of Texas Health Science Center at Tyler

data_processing:
MATLAB
Differential gene expression analysis included the following steps. 1. Construction of the 'reference group' by identifying a group of genes expressed above background with inherently low variability as determined by an F test. The 'reference group' presents an internal standard of equal expression. As such, the 'reference group' is used to assess the inherent variability resulting from technical factors alone (technological variation). By creating an estimate of the technological variation, we were able to select a group of biologically stable genes.
Replications were selected using the commonly accepted significance threshold of p<0.05 with the Student’s t test. This selection maintains the commonly accepted sensitivity level; however, a significant proportion of genes identified as differentially expressed at this threshold will represent false-positive determinations. 3. An associative T test in which the replicated residuals for each gene from the experimental group are compared with the entire set of residuals from the reference group defined above. The Ho hypothesis was checked to determine whether the levels of gene expression in the experimental group presented as replicated residuals (deviations from the averaged control group profile) were associated with a highly representative (several hundred members) normally distributed set of residuals of gene expression values in the reference group. The significance threshold was then corrected to render the appearance of false-positive determinations improbable: in the current case, the threshold was set at p<0.0001. Only genes that passed both tests were presented in the final selections. Additional restrictions were applied to the minimal gene expression level (RPKM>2) and fold change (>1.5). The two-step normalization procedure and the associated analysis functions were implemented in MATLAB (Mathworks, MA). Functional analysis of identified genes was performed based on an Ingenuity Pathway Analysis (IPA; Ingenuity® Systems, Redwood City, CA, http://www.ingenuity.com).
Assembly: hg38
Supplementary files format and content: Microsoft excel worksheet files include RPKM values for each sample

source_name: PBMC

growth_protocol: Freshly isolated PBMCs were cultured in 24-well plates at 1 × 106 cells/well in RPMI 1640 containing 1% penicillin/streptomycin (Sigma), L-glutamine and 10% heat-inactivated human serum with or without CFP-10 + ESAT-6 (10 μg/ml) or γ-irradiated Mtb at 37 °C in a humidified atmosphere with 5% CO2.

extract_protocol:
Total RNA from unstimulated and ESAT-6+CFP-10-stimulated PBMCs of nonconverters and converters was extracted with TRIzol reagent according to the manufacturer's instructions.
RNA libraries for RNA-seq were prepared using TruSeq RNA Library Prep Kit following manufacturer's protocols.

tag: donor groups

value: Converters

tag: time point

value: Baseline

value: ESAT6+CFP10 stimulated

value: PBMC


title: M55C3F4 YTB LTBI- turned LTBI+

value: Follow-up


title: M16C3F5 YTB LTBI- remained LTBI-

value: Non-converters


title: M16C3 UN LTBI- remained LTBI-

value: Unstimulated


title: L56C5F5 UN LTBI- turned LTBI+


title: L14C3F6 UN LTBI- turned LTBI+


title: L56C5F5 YTB LTBI- turned LTBI+


title: M55C3F4 UN LTBI- turned LTBI+


title: M16C3 YTB LTBI- remained LTBI-


title: L14C3 YTB LTBI- turned LTBI+


title: M55C3 UN LTBI- turned LTBI+


title: M10C1 YTB LTBI- remained LTBI-


title: L14C3F6 YTB LTBI- turned LTBI+


title: M10C1F6 UN LTBI- remained LTBI-


title: L33C1F4 UN LTBI- remained LTBI-


title: M16C3F5 UN LTBI- remained LTBI-


title: M10C1 UN LTBI- remained LTBI-


title: L33C1 YTB LTBI- remained LTBI-


title: L33C1 UN LTBI- remained LTBI-


title: L33C1F4 YTB LTBI- remained LTBI-


title: L14C3 UN LTBI- turned LTBI+


title: M55C3 YTB LTBI- turned LTBI+


title: M10C1F6 YTB LTBI- remained LTBI-


title: 47513

city: Bethesda

first: Mallikarjuna

middle: Rao

last: Gedda

state: MD

address: 6 Center Dr

institute: NEI

hyb_protocol: Hybridisation at 65°C for 16 hours using PCR,

scan_protocol: Post hybridization steps and scanning were performed on the nCounter Prep Station and Digital Analyzer

data_processing: R (Version 4.1.1)

source_name: COVID convalenscent whole blood

extract_protocol: RNA extraction, Nanodrop, Bioanalyser .

treatment_protocol: ACK Lysis of Whole Blood

value: plate 14

tag: date

tag: generlf

tag: systemapf

tag: fovcount

tag: fovcounted

tag: scannerid

tag: stageposition

tag: bindingdensity

tag: cartridgeid

value: tcr diversity plate 14 wb 12212020


title: L56C5 UN LTBI- turned LTBI+

tag: treatment

tag: cell type


title: 47750_22

value: plate 15

value: tcr diversity plate 15 wb 12212020


title: 47614_22

value: plate 16

value: tcr diversity plate 16 wb 12212020


title: 31552_33

value: plate 24

value: tcr diversity plate 24 wb 12302020


title: 31602_22

value: plate 25

value: tcr diversity plate 25 wb 12302020


title: 47511


title: 31309_32

value: plate 19

value: tcr diversity plate 19 wb 12282020


title: 31449_44

value: plate 22

value: tcr diversity plate 22 wb 12292020


title: 15375 Healthy

source_name: healthy whole blood

value: plate 26

value: tcr diversity plate 26 wb 12302020

value: 15375 Healthy


title: 31172_22


title: 31193_22


title: 31514_22

value: plate 23

value: tcr diversity plate 23 wb 12292020


title: 31504_22


title: 31063_43

value: plate 12

value: tcr diversity plate 12 wb 12162020


title: 31097_22


title: 15298 Healthy

value: 15298 Healthy


title: 31306_54


title: 15337_22


title: 15349 Healthy

value: 15349 Healthy


title: 31540_33

value: plate 24


title: 31260_22

value: plate 18

value: tcr diversity plate 18 wb 12212020


title: 31643_22

value: plate 25

value: tcr diversity plate 25 wb 12302020


title: 31196_22

value: plate 16

value: tcr diversity plate 16 wb 12212020


title: 47511

source_name: COVID convalenscent Whole Blood

extract_protocol: RNA extraction, Nanodrop, Bioanalyser.

value: host response panel plate 14 wb 11232020

tag: cartridgebarcode


title: 47513


title: 47614_22

value: host response panel plate 15 wb 11242020


title: 15277 Healthy

value: 15277 Healthy


title: 47750_22


title: 31643_22

value: host response panel plate 25 wb 11292020


title: 31602_22

value: host response panel plate 24 wb 11292020


title: 15173 Healthy

value: plate 20

value: tcr diversity plate 20 wb 12282020

value: 15173 Healthy


title: 31309_32

value: host response panel plate 19 wb 11262020


title: 31306_54


title: 31260_22

value: host response panel plate 17 wb 11252020


title: 15021_33

value: plate 26

value: tcr diversity plate 26 wb 12302020


title: 15027 Healthy

value: plate 13

value: tcr diversity plate 13 wb 12212020

value: 15027 Healthy


title: 15213 Healthy

value: plate 21

value: tcr diversity plate 21 wb 12292020

value: 15213 Healthy


title: 15244 Healthy

value: plate 22

value: tcr diversity plate 22 wb 12292020

value: 15244 Healthy


title: 14990_55


title: 15375 Healthy

source_name: Healthy Whole Blood

value: host response panel plate 26 wb 11302020

value: 15375 Healthy


title: 15169 Healthy

value: plate 19

value: tcr diversity plate 19 wb 12282020

value: 15169 Healthy


title: 15110 Healthy

value: plate 16

value: tcr diversity plate 16 wb 12212020

value: 15110 Healthy


title: 31097_22

value: host response panel plate 12 wb 11222020


title: 31449_44

value: host response panel plate 21 wb 11272020


title: 31514_22

value: host response panel plate 22 wb 11272020


title: 15038 Healthy

value: plate 14

value: tcr diversity plate 14 wb 12212020

value: 15038 Healthy


title: 15337_22


title: 14906 Healthy

value: plate 12

value: tcr diversity plate 12 wb 12162020

value: 14906 Healthy


title: 31552_33

value: host response panel plate 23 11282020

value: host response panel plate 23 wb 11282020


title: 15071 Healthy

value: 15071 Healthy


title: 15298 Healthy

value: host response panel plate 26 wb 11302020

value: 15298 Healthy


title: 15124 Healthy

value: plate 17

value: tcr diversity plate 17 wb 12212020

value: 15124 Healthy


title: 15006_44

value: plate 26

value: tcr diversity plate 26 wb 12302020


title: 31193_22

value: host response panel plate 15 wb 11242020


title: 14991_33


title: 31504_22

value: host response panel plate 22 wb 11272020


title: 31540_33


title: 15244 Healthy

value: 15244 Healthy


title: 15080 Healthy

value: plate 15

value: tcr diversity plate 15 wb 12212020

value: 15080 Healthy


title: 31063_43

value: host response panel plate 11 wb 11222020


title: 15136 Healthy

value: plate 18

value: tcr diversity plate 18 wb 12212020

value: 15136 Healthy


title: 14972 Healthy

value: plate 13

value: tcr diversity plate 13 wb 12212020

value: 14972 Healthy


title: 14770 Healthy

value: plate 9

value: tcr diversity plate 9 wb 12162020

value: 14770 Healthy


title: 31196_22


title: 15173 Healthy

value: host response panel plate 25 wb 11292020

value: 15173 Healthy


title: 14959 Healthy

value: plate 12

value: tcr diversity plate 12 wb 12162020

value: 14959 Healthy


title: 31172_22

value: host response panel plate 14 wb 11232020


title: 15349 Healthy

value: host response panel plate 26 wb 11302020

value: 15349 Healthy


title: 15038 Healthy

value: host response panel plate 24 wb 11292020

value: 15038 Healthy


title: 15277 Healthy

value: 15277 Healthy


title: 15027 Healthy

value: 15027 Healthy


title: 15110 Healthy

value: 15110 Healthy


title: 14669_33

value: plate 25

value: tcr diversity plate 25 wb 12302020


title: 15136 Healthy

value: 15136 Healthy


title: 14721 Healthy

value: plate 8

value: tcr diversity plate 8 wb 12142020

value: 14721 Healthy


title: 14843 Healthy

value: plate 10

value: tcr diversity plate 10 wb 12162020

value: 14843 Healthy


title: 15213 Healthy

value: host response panel plate 25 wb 11292020

value: 15213 Healthy


title: 14653 Healthy

value: plate 6

value: tcr diversity plate 6 wb 12142020

value: 14653 Healthy


title: 14757_22


title: 15124 Healthy

value: 15124 Healthy


title: 15169 Healthy

value: 15169 Healthy


title: 14893 Healthy

value: plate 11

value: tcr diversity plate 11 wb 12162020

value: 14893 Healthy


title: 15071 Healthy

value: host response panel plate 24 wb 11292020

value: 15071 Healthy


title: 14788 Healthy

value: 14788 Healthy


title: 14755 Healthy

value: plate 9

value: tcr diversity plate 9 wb 12162020

value: 14755 Healthy


title: 14817_21

value: plate 26

value: tcr diversity plate 26 wb 12302020


title: 14685_22

value: plate 25

value: tcr diversity plate 25 wb 12302020


title: 14866 Healthy

value: 14866 Healthy


title: 15006_44

value: host response panel plate 26 wb 11302020


title: 14605 Healthy

value: plate 6

value: tcr diversity plate 6 wb 12142020

value: 14605 Healthy


title: 14893 Healthy

value: host response panel plate 14 wb 11232020


title: 15080 Healthy

value: 15080 Healthy


title: 14704 Healthy

value: plate 8

value: tcr diversity plate 8 wb 12142020

value: 14704 Healthy


title: 14594_55

value: plate 24

value: tcr diversity plate 24 wb 12302020


title: 14611_33


title: 14972 Healthy

value: host response panel plate 17 wb 11252020

value: 14972 Healthy


title: 14589 Healthy

value: plate 5

value: tcr diversity plate 5 wb 12142020

value: 14589 Healthy


title: 14991_33


title: 14672 Healthy

value: plate 7

value: tcr diversity plate 7 wb 12142020

value: 14672 Healthy


title: 15021_33

value: host response panel plate 26 wb 11302020


title: 14664 Healthy

value: 14664 Healthy


title: 14562_44


title: 14554_43


title: 14639_22

value: plate 25

value: tcr diversity plate 25 wb 12302020


title: 14556_22


title: 14637_55


title: 14990_55


title: 14621_22


title: 14906 Healthy

value: host response panel plate 15 wb 11242020

value: 14906 Healthy


title: 14649_22


title: 14721 Healthy

value: host response panel plate 8 wb 11202020

value: 14721 Healthy


title: 14770 Healthy

value: host response panel plate 10 wb 11212020

value: 14770 Healthy


title: 14548 Healthy

value: 14548 Healthy


title: 14540_33

value: plate 23

value: tcr diversity plate 23 wb 12292020


title: 14866 Healthy

value: host response panel plate 13 11232020

value: host response panel plate 13 wb 11232020

value: 14866 Healthy


title: 14817_21


title: 14482_22


title: 14959 Healthy

value: host response panel plate 16 wb 11242020

value: 14959 Healthy


title: 14443 Healthy

value: plate 4

value: tcr diversity plate 4 wb 12102020

value: 14443 Healthy


title: 14575_55

value: plate 24

value: tcr diversity plate 24 wb 12302020


title: 14433


title: 14424 Healthy

value: plate 3

value: tcr diversity plate 3 wb 12102020

value: 14424 Healthy


title: 14788 Healthy

value: host response panel plate 11 wb 11222020

value: 14788 Healthy


title: 14435 Healthy

value: 14435 Healthy


title: 14757_22

value: host response panel plate 25 wb 11292020


title: 14843 Healthy

value: host response panel plate 12 wb 11222020

value: 14843 Healthy


title: 14755 Healthy

value: host response panel plate 9 wb 11212020

value: 14755 Healthy


title: 14653 Healthy

value: host response panel 4 wb

value: 14653 Healthy


title: 14481_32

value: plate 23

value: tcr diversity plate 23 wb 12292020


title: 14622_33

value: host response panel plate 23 11282020

value: host response panel plate 23 wb 11282020


title: 14669_33

value: host response panel plate 24 wb 11292020


title: 14414_22

value: plate 22

value: tcr diversity plate 22 wb 12292020


title: 14470_33


title: 14685_22


title: 14704 Healthy

value: host response panel plate 7 wb 11 20 2020

value: 14704 Healthy


title: 14480_54


title: 14664 Healthy

value: host response panel plate 5 wb 11 19 2020

value: 14664 Healthy


title: 14649_22


title: 14639_22


title: 14621_22


title: 14672 Healthy

value: host response panel plate 6 wb 11192020

value: host response panel plate 6 wb 11 19 2020

value: 14672 Healthy


title: 14594_55


title: 14611_33


title: 14398_22


title: 14386 Healthy

value: plate 3

value: tcr diversity plate 3 wb 12102020

value: 14386 Healthy


title: 14589 Healthy

value: host response panel 4 wb

value: 14589 Healthy


title: 14575_55

value: host response panel plate 23 11282020


title: 14605 Healthy

value: 14605 Healthy


title: 14421_22


title: 14411_22


title: 14637_55

value: host response panel plate 24 wb 11292020


title: 14362_21

value: plate 22


title: 14389_33

value: tcr diversity plate 22 wb 12292020


title: 14402_44


title: 14381


title: 14359 Healthy

value: plate 2

value: tcr diversity plate 2 wb 12102020

value: 14359 Healthy


title: 14361


title: 14556_22

value: host response panel plate 23 wb 11282020


title: 14540_33

value: host response panel plate 22 wb 11272020


title: 14335_22

value: plate 21

value: tcr diversity plate 21 wb 12292020


title: 14554_43


title: 14482_22


title: 14562_44


title: 14511_33


title: 14338


title: 14300 Healthy

value: plate 1

value: tcr diversity plate 1 wb 12102020

value: 14300 Healthy


title: 14329 Healthy

value: 14329 Healthy


title: 14284_22


title: 14470_33


title: 14480_54


title: 14443 Healthy

value: host response panel 3 wb

value: 14443 Healthy


title: 14442_55


title: 14481_32


title: 14211


title: 14336 Healthy

value: 14336 Healthy


title: 14435 Healthy

value: 14435 Healthy


title: 14424 Healthy

value: host response panel 2 wb

value: 14424 Healthy


title: 14210


title: 14209


title: 14208


title: 14205_21


title: 14433


title: 14197_21


title: 14193_43


title: 14414_22

value: host response panel plate 21 wb 11272020


title: 14421_22


title: 14402_44


title: 14398_22


title: 14389_33


title: 14279


title: 14190

value: plate 20

value: tcr diversity plate 20 wb 12282020


title: 14386 Healthy

value: 14386 Healthy


title: 14169


title: 14192_44


title: 14249


title: 14548 Healthy

value: 14548 Healthy


title: 14186


title: 14411_22


title: 14381


title: 14167


title: 14362_21


title: 14166_22


title: 14361


title: 14336 Healthy

value: host response panel  1 wb

value: host response panel wb 1


title: 14359 Healthy

value: 14359 Healthy


title: 14160


title: 14338


title: 14335_22


title: 14095_54


title: 14083


title: 14165_22


title: 14300 Healthy


title: 14329 Healthy


title: 14284_22


title: 14107_42


title: 14044_21

value: plate 19

value: tcr diversity plate 19 wb 12282020


title: 14279

value: host response panel plate 20 wb 11262020


title: 14249


title: 14038


title: 13996_21


title: 14079_54


title: 14022


title: 13994


title: 14210


title: 14209


title: 13988_22


title: 14208


title: 14205_21


title: 13981_43

value: plate 18

value: tcr diversity plate 18 wb 12212020


title: 13985


title: 14192_44


title: 14197_21


title: 13977_43


title: 14193_43


title: 13975


title: 13974_21


title: 14190


title: 14211


title: Colon_HSD16wk-5

city: Vandoeuvre-lès-Nancy

first: Sebastien

last: Hergalant

address: Faculté de Médecine. 9 avenue de la forêt de Haye

department: Bioinformatics

description: colon extract from long high sucrose diet mice

hyb_protocol: Samples were hybridized to Affymetrix Mouse Clariom S catridges following the manufacturer’s instructions.

scan_protocol: The arrays were washed and scanned according to the protocol GeneChip® Expression Wash, Stain and Scan for Cartridge Arrays.

data_processing: Fluorescence values corresponding to raw expression data were extracted from CEL files using the R oligo package with the corresponding platform definitions (pd.clariom.s.mouse). Positive and negative control probes were removed.

label: biotin

source_name: High Sucrose Diet long replicate 5

label_protocol: RNA samples were aliquoted and stored at −80 °C, and later amplified and biotinylated using the Affymetrix GeneChip® WT PLUS reagent kit.

growth_protocol: Male C57BL/6J mice were purchased from Janvier Labs (Le Genest-Saint-Isle, France). All procedures were performed in accordance with guidelines established by the European Convention for the protection of Laboratory Animals and with a project approval (authorization N°APAFIS#16630) delivered by the French ministry of research. The animals were maintained on a strict 12-h light-dark cycle and were housed at 22–23°C, in cages containing a maximum of 5 animals, with ad libitum access to food and water. All animal experiments were repeated at least two times on two separate occasions. Before dietary interventions, mice were randomized to ensure that no incidental pre-diet differences in body weight existed between the different groups. Mice were fed with HSD for 8/16 weeks (U8960 v5, Safe Diets, Augy, France) or normal control diet (A04, Safe Diets, Augy, France).

extract_protocol: Total RNA was extracted from 20 mg of colon using Trizol (Invitrogen, Carlsbad, California, USA) according to the manufacturer’s recommendations. RNA was further digested with TurboTM DNase (Thermo Fisher, Waltham, Massachusetts, USA) and phenol-chloroform extracted. Quality of total RNAs was attested by O.D. 260 nm/O.D. 280 nm and O.D. 260 nm/O.D. 230 nm determination by spectrophotometry using a Nanodrop ND-1000 (NanoDrop Technologies; Wilmington, DE, USA) and using a 2100 Bioanalyzer (Agilent Technologies; Massy, France).

treatment_protocol: Mice were continued on the same diet during colitis, induced by administration of 3% dextran sulphate sodium (DSS, molecular weight 36 000-50 000, MP Biomedicals, Strasbourg, France) dissolved in drinking water for 5 days. DSS solution was replaced thereafter by normal drinking water for another 5 days. Mice were sacrificed at day 10 or upon reaching endpoint (i. e. > 20% weight loss).

tag: genotype

tag: tissue

value: Colon

tag: Sex

value: Male

tag: age

value: 26 weeks

tag: diet

value: High Sucrose Diet

tag: diet duration

value: 16 weeks

tag: weight (g)


title: 14186

tag: date

tag: generlf

tag: systemapf


title: 13968_21

tag: fovcount

tag: fovcounted

tag: scannerid


title: Colon_HSD+CD-2

description: colon extract from high sucrose diet switching to control diet mice

source_name: High Sucrose Diet switch Control Diet replicate 2

value: High Sucrose Diet + Control Diet


title: 13967_32

tag: stageposition

tag: bindingdensity

tag: cartridgeid


title: 14166_22

value: host response panel plate 19 wb 11262020

tag: cartridgebarcode


title: 14167


title: 13962_22


title: 14107_42


title: 14169


title: 14165_22


title: 13959_22


title: 14044_21


title: 14095_54


title: 14079_54


title: 14160


title: 13957_31


title: 14034_54

value: host response panel plate 18 wb 11252020


title: Colon_HSD8wk/DSS-3

description: colon extract from short high sucrose diet with colitis mice

source_name: High Sucrose Diet short + Colitis replicate 3

tag: genotype

value: 18 weeks

value: 8 weeks

tag: treatment

value: Dextran Sulfate Sodium (DSS)  3% 5 days


title: 13956_21

value: plate 17

value: tcr diversity plate 17 wb 12212020


title: 13955_53


title: Colon_HSD16wk-4

source_name: High Sucrose Diet long replicate 4

tag: tissue

tag: Sex


title: Colon_CD-2

description: colon extract from control mice

source_name: Control Diet replicate 2

tag: age

tag: diet

value: Control


title: Colon_CD-3

description: colon extract from control mice

source_name: Control Diet replicate 3

tag: diet duration

tag: weight (g)


title: 14022

tag: date

tag: generlf


title: Colon_CD-4

description: colon extract from control mice

source_name: Control Diet replicate 4


title: 14083

tag: systemapf

tag: fovcount


title: 13996_21

tag: fovcounted

tag: scannerid


title: 14038

tag: stageposition

tag: bindingdensity


title: Colon_HSD16wk/DSS-2

description: colon extract from long high sucrose diet with colitis mice

source_name: High Sucrose Diet long + Colitis replicate 2


title: 13935_32

tag: cartridgeid


title: 13914_22


title: 13981_43

tag: cartridgebarcode


title: 13985


title: 13988_22


title: 13975


title: 13911_22


title: 13974_21


title: 13977_43


title: 13929


title: 13994


title: 13950


title: 13902_21


title: 13908_21


title: 13890_22

value: plate 16

value: tcr diversity plate 16 wb 12212020


title: 13967_32

value: host response panel plate 17 wb 11252020


title: 13959_22


title: 13972_32


title: 13968_21


title: Colon_HSD+CD-1

source_name: High Sucrose Diet switch Control Diet replicate 1

tag: genotype

value: Colon

tag: treatment


title: 13957_31


title: 13962_22


title: 13955_53


title: 13956_21


title: 13934


title: Colon_HSD8wk/DSS-5

source_name: High Sucrose Diet short + Colitis replicate 5

tag: tissue

tag: Sex

value: Male


title: Colon_HSD16wk/DSS-1

source_name: High Sucrose Diet long + Colitis replicate 1

tag: age

value: 26 weeks

tag: diet


title: 13893_32


title: Colon_HSD16wk/DSS-3

source_name: High Sucrose Diet long + Colitis replicate 3

value: High Sucrose Diet

tag: diet duration

tag: weight (g)


title: 13950

tag: date

tag: generlf


title: 13911_22

value: host response panel plate 16 wb 11242020

tag: systemapf

tag: fovcount


title: 13901_32

tag: fovcounted

tag: scannerid


title: 13929

tag: stageposition

tag: bindingdensity


title: 13914_22

tag: cartridgeid

tag: cartridgebarcode


title: 13935_32


title: 13934


title: Colon_CD/DSS-3

description: colon extract from control colitis mice

source_name: Control Diet + Colitis replicate 3

tag: genotype

value: 16 weeks

tag: treatment


title: Colon_CD/DSS-2

description: colon extract from control colitis mice

source_name: Control Diet + Colitis replicate 2

tag: tissue

tag: Sex


title: Colon_HSD+CD-3

source_name: High Sucrose Diet switch Control Diet replicate 3

tag: age

tag: diet

value: High Sucrose Diet + Control Diet


title: Colon_HSD16wk/DSS-4

source_name: High Sucrose Diet long + Colitis replicate 4

tag: diet duration

tag: weight (g)


title: Colon_CD/DSS-4

description: colon extract from control colitis mice

source_name: Control Diet + Colitis replicate 4


title: Colon_HSD8wk-1

description: colon extract from short high sucrose diet mice

source_name: High Sucrose Diet short replicate 1


title: 13884_22

source_name: COVID convalenscent whole blood

tag: date

tag: generlf


title: 13885_22

tag: systemapf

tag: fovcount


title: 13908_21

source_name: COVID convalenscent Whole Blood

tag: fovcounted

tag: scannerid


title: 13902_21

tag: stageposition

tag: bindingdensity


title: Colon_HSD+CD/DSS-3

description: colon extract from high sucrose diet switching to control diet with colitis mice

source_name: High Sucrose Diet switch Control Diet + Colitis replicate 3


title: 13885_22

tag: cartridgeid

tag: cartridgebarcode


title: 13884_22


title: 13901_32


title: 13890_22


title: 13893_32


title: 13830_21


title: 13838_22


title: 13847_22


title: 13838_22

value: host response panel plate 15 wb 11242020


title: 13795_21


title: 13830_21


title: 13872_32


title: 13808


title: 13847_22


title: 13808

value: plate 15

value: tcr diversity plate 15 wb 12212020


title: 13816


title: Colon_HSD8wk-5

source_name: High Sucrose Diet short replicate 5

tag: genotype

value: 18 weeks

value: 8 weeks

tag: treatment


title: Colon_HSD+CD-4

source_name: High Sucrose Diet switch Control Diet replicate 4

tag: tissue

tag: Sex


title: Colon_HSD8wk/DSS-1

source_name: High Sucrose Diet short + Colitis replicate 1

tag: age

tag: diet

value: Dextran Sulfate Sodium (DSS)  3% 5 days


title: 13788


title: 13788


title: 13784_22

value: host response panel plate 14 wb 11232020


title: Colon_CD-1

description: colon extract from control mice

source_name: Control Diet replicate 1

value: Control

tag: diet duration

tag: weight (g)


title: Colon_HSD+CD/DSS-2

source_name: High Sucrose Diet switch Control Diet + Colitis replicate 2


title: Colon_HSD8wk-2

source_name: High Sucrose Diet short replicate 2


title: Colon_CD/DSS-1

description: colon extract from control colitis mice

source_name: Control Diet + Colitis replicate 1

value: Dextran Sulfate Sodium (DSS)  3% 5 days 3% 5 days


title: Colon_CD-5

description: colon extract from control mice

source_name: Control Diet replicate 5


title: 13775

tag: date

tag: generlf


title: Colon_HSD8wk/DSS-2

source_name: High Sucrose Diet short + Colitis replicate 2


title: 13785_22

tag: systemapf

tag: fovcount


title: 13785_22

tag: fovcounted

tag: scannerid


title: 13755

tag: stageposition

tag: bindingdensity


title: 13777

tag: cartridgeid

tag: cartridgebarcode


title: 13739_42


title: Colon_HSD16wk-2

source_name: High Sucrose Diet long replicate 2

tag: genotype

tag: treatment


title: 13777


title: 13738_43

value: host response panel plate 13 11232020

value: host response panel plate 13 wb 11232020


title: 13720


title: Colon_HSD16wk-3

source_name: High Sucrose Diet long replicate 3

tag: tissue

value: Colon

tag: Sex

value: Male


title: 13816


title: 13795_21


title: 13754


title: 13713_33


title: 13700


title: 13754

value: plate 14

value: tcr diversity plate 14 wb 12212020


title: 13784_22


title: 13748


title: 13698_42


title: 13721


title: 13724


title: 13716


title: Colon_HSD+CD-5

source_name: High Sucrose Diet switch Control Diet replicate 5

tag: age

value: 26 weeks

tag: diet


title: 13701


title: 13755


title: 13739_42


title: Colon_HSD16wk-1

source_name: High Sucrose Diet long replicate 1

value: High Sucrose Diet

tag: diet duration

value: 16 weeks

tag: weight (g)


title: 13738_43

tag: date

tag: generlf


title: 13697_53

tag: systemapf

tag: fovcount


title: 13693

tag: fovcounted

tag: scannerid


title: Colon_HSD+CD/DSS-4

source_name: High Sucrose Diet switch Control Diet + Colitis replicate 4

value: High Sucrose Diet + Control Diet


title: 13775

source_name: COVID convalenscent whole blood

value: plate 15

tag: stageposition

tag: bindingdensity

value: tcr diversity plate 15 wb 12212020


title: Colon_HSD8wk-3

source_name: High Sucrose Diet short replicate 3

value: 18 weeks

value: 8 weeks


title: 13673

source_name: COVID convalenscent Whole Blood

value: host response panel plate 12 wb 11222020

tag: cartridgeid

tag: cartridgebarcode


title: Colon_HSD8wk-4

source_name: High Sucrose Diet short replicate 4

tag: genotype

tag: treatment


title: 13692_21


title: 13685_22


title: Colon_HSD8wk/DSS-4

source_name: High Sucrose Diet short + Colitis replicate 4

tag: tissue

tag: Sex

value: Dextran Sulfate Sodium (DSS)  3% 5 days


title: Injecting CpOGA_DM_RNA-seq_rep1

city: Changsha

first: Yaowen

last: Zhang

address: Xiangya hospital, Xiangya Road

institute: Central South University

data_processing:
Illumina Casava1.8 software was used for basecalling.
For ChIP-seq and RNA-seq, The raw sequenced reads were cleaned using trim_galore (v0.6.0) with default parameters, and then mapped to the reference D. melanogaster genome (dm6, version BDGP6).
For ChIP-seq, Using Bowtie2 (v2.3.5.1) with the default parameters that look for multiple alignments but only report the one with the best mapping quality.  For RNA-seq, The key alignment parameters were as follows: “--outFilterMismatchNoverLmax 0.04  --outSAMtype BAM SortedByCoordinate --outFilterMultimapNmax 500 --outMultimapperOrder Random --outSAMmultNmax 1”
For ChIP-seq, Peak calling was performed using MACS2 v2.2.6 (parameters: -g dm --nomodel --broad --broad-cutoff 0.1).  For RNA-seq, Genes expression was quantified using featureCounts v1.6.5 based on dm6 RefSeq genes annotation file.
For ChIP-seq, Bigwig tracks were generate using bamCompare from deeptools (parameters: --skipNAs –scaleFactorsMethod readCount –operation subtract). The ChIP-Seq profiles were generated by computeMatrix and plotHeatmap in deepTools. IGV v.2.9.2 was used to visualize the bigwig tracks.  For RNA-seq, Differential expression analysis was performed based on the negative binomial distribution using the functions “DESeq” and “results” from DESeq2.
Genome_build: dm6
Supplementary_files_format_and_content: bw files were generated using bamCoverage.
Supplementary_files_format_and_content: peak excel files
Supplementary_files_format_and_content: CPM table for every gene and every sample

organism: Drosophila melanogaster

source_name: early embryo

extract_protocol:
Embryos lysates were clarified from sonicated nuclei and protein-DNA complexes were isolated with antibodies. And 100ng total RNA was harvested using Trizol reagent from a single embryo.
The sequencing libraries were prepared using the NEBNext Ultra II DNA Library Prep Kit for Illumina (NEB) following the manufacturer’s instructions. RNA libraries were prepared for sequencing using standard Illumina protocols.

tag: developmental stage

value: early embryo

value: Injecting CpOGA_DM


title: 13724


title: 13720


title: 13675_41


title: Injecting CpOGA_DM_RNA-seq_rep2


title: Colon_HSD+CD/DSS-1

source_name: High Sucrose Diet switch Control Diet + Colitis replicate 1

tag: age

tag: diet

tag: diet duration


title: 13721

tag: date

tag: generlf


title: Injecting CpOGA_WT_RNA-seq_rep1

value: Injecting CpOGA_WT


title: 13645

tag: systemapf

tag: fovcount


title: 13648_32

tag: fovcounted

tag: scannerid


title: 13643_22

tag: stageposition

tag: bindingdensity


title: 13713_33

value: plate 13

tag: cartridgeid

value: tcr diversity plate 13 wb 12212020


title: Injecting CpOGA_WT_RNA-seq_rep2


title: 13667_53

tag: cartridgebarcode


title: 13716

value: plate 14


title: 13608

value: host response panel plate 11 wb 11222020


title: 13601


title: CpOGA_WT_Input

value: collected 30 min and aged for 160 min

tag: chip antibody

tag: treatment

value: overexpressing CpOGA_WT


title: CpOGA_WT_IP_H3K27me3

tag: tissue


title: 13604_32


title: CpOGA_WT_IP_H2AK119ub

tag: developmental stage


title: CpOGA_DM_IP_polII

value: pol II (Abcam, ab817)

value: overexpressing CpOGA_DM


title: 13559


title: 13570


title: 13589


title: 13700

value: plate 26

value: tcr diversity plate 26 wb 12302020


title: 13701


title: 13534_42


title: 13544


title: 13594


title: CpOGA_DM_IP_H3K27me3


title: 13693


title: 13697_53


title: 13698_42


title: 13505_31


title: 13497

value: host response panel plate 10 wb 11212020


title: 13557


title: CpOGA_DM_IP_H2AK119ub


title: CpOGA_WT_IP_polII


title: CpOGA_DM_Input


title: 13588


title: 13685_22


title: 13463_22


title: 13675_41


title: 13449


title: 13424_22


title: 13426_21


title: MKN45_Capecitabine_5

city: Kajiwara

first: YUJI

last: SANO

state: Kamakura

country: Japan

institute: Chugai Pharmaceutical Co., Ltd

data_processing:
The RNAseq reads were mapped to human (GRCh38) and mouse (GRCm38) RefSeq transcripts  using  bowtie 1.1.2
Reads mapped to the transcripts of both organisms were excluded
The calculation of fragments per kilobase of transcript per million reads mapped (FPKM) using RSEM v1.2.31
Assembly: GRCh38 + CRCm38 with RefSeq annotations
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

organism:
Homo sapiens
Mus musculus

growth_protocol: MKN45 were expanded in vitro, and inoculated into the huNOG mice.

extract_protocol:
RNA was harvested from the tumors using RNeasy mini kit (Qiagen). Total RNA was used for RNAseq.
RNA libraries for RNA-seq were prepared using TruSeq Stranded mRNA Library Prep Kit following manufacturer's protocols.

treatment_protocol: When tumor was established, 359 mg/kg capecitabine orally was administered one day before the administration of 5 mg/kg ERY974 for 5 consective days in the combination group. In the monotherapy group, each agent was administered as described above. Then, tumours were collected on day 14 after ERY974 administration and used for RNA analysis.

tag: cell line

tag: cell type

value: Gastric tumor

value: Capecitabine

tag: time

value: Day 14


title: MKN45_Capecitabine_6


title: 13673

tag: date


title: 13444_21

tag: generlf


title: 13460_31

tag: systemapf


title: 13414_31

tag: fovcount


title: 13387

value: host response panel plate 9 wb 11212020

tag: fovcounted


title: 13472_21

tag: scannerid


title: MKN45_ERY974+capecitabine_6


title: MKN45_ERY974+capecitabine_4


title: MKN45_ERY974+capecitabine_5


title: 13667_53

value: plate 12

tag: stageposition

value: tcr diversity plate 12 wb 12162020


title: 13399

tag: bindingdensity


title: 13376_21

tag: cartridgeid


title: 13645


title: 13648_32


title: MKN45_Capecitabine_4


title: 13392

tag: cartridgebarcode


title: 13479_21


title: 13359_52


title: 13643_22


title: 13362_21


title: 13608


title: MKN45_ERY974_6


title: MKN45_ERY974_4


title: 13692_21

value: plate 13


title: MKN45_vehicle_6

value: Vehicle


title: 13343


title: 13341_21


title: 13372_32


title: 13589

value: plate 11

value: tcr diversity plate 11 wb 12162020


title: 13348_22


title: 13317_22

value: host response panel plate 8 wb 11202020


title: 13594


title: 13588


title: 13310_21

value: host response panel plate 26 wb 11302020


title: 13601


title: 13278_52


title: 13280_31


title: 13265 _21


title: 13604_32


title: 13308


title: 13333_21


title: 13570


title: 13312_53


title: 13245


title: 13231_21

value: host response panel plate 7 wb 11 20 2020


title: MKN45_vehicle_4


title: 13559


title: 13226


title: 13262_21


title: LHX6_KO_5

city: LONDON

first: Nicoletta

last: Kessaris

state: LONDON

address: Gower Street

department: WIBR

institute: University College London

data_processing:
Raw sequence data were adapter and quality trimmed (fastp v0.20.1), aligned to the genome with STAR (v2.7b) and reads per transcript determined with FeatureCounts (v1.6.4).
Differential expression was performed using DESeq2 in R
Sex-linked genes were filtered out (using GTF version M23 GRCm38.p6 from GENECODE) to eliminate the effect of uneven sex distribution within control and mutant samples which was skewing the data
Genome_build: UCSC mm10
Supplementary_files_format_and_content: Tables showing raw gene counts for every gene in every sample

source_name: Sorted fluorescent migrating embryonic cortical cells

extract_protocol:
Cortical tissue was dissected in ice-cold Hanks' Balanced Salt Solution, digested with Accutase, dissociated, resuspended and filtered using cell strainers. YFP+ve cells were sorted using MoFlo XDP Cell Sorter directly into tubes prefilled with 300 µl Neurobasal medium. Total RNA was isolated from freshly sorted cells without freezing using RNeasy Plus Micro Kit (Qiagen, #74034) according to manufacturer’s manual. RNA quality was assessed using TapeStation RNA ScreenTape (Agilent) according to manufacturer’s manual.
The NEBNext Single Cell/Low Input RNA Library Prep Kit was used to generate indexed amplified cDNAs libraries total RNA. The libraries were pooled sqeuenced on the NextSeq 500  (lllumina) using a single 75bp read configuration.

tag: strain

value: MGE-derived cortical cells

tag: age

value: embyonic day 14.5


title: MKN45_vehicle_5

tag: treatment


title: LHX6_KO_6

tag: tissue


title: 13557


title: LHX6_CTRL_3


title: 13173_21


title: 13172_21


title: LHX6_KO_3


title: 13168


title: LHX6_KO_2


title: 13261_52


title: 13155_42

value: host response panel plate 6 wb 11192020

value: host response panel plate 6 wb 11 19 2020


title: 13505_31


title: 13544


title: 13194


title: 13184_32


title: 13158


title: 13479_21

value: plate 23

value: tcr diversity plate 23 wb 12292020


title: 13186


title: 13497


title: LHX6_CTRL_2


title: 13534_42


title: LHX6_CTRL_4


title: 13178_52


title: 13147


title: LHX6_CTRL_1


title: 13146


title: 13130_31


title: 13154_31


title: 13472_21

value: plate 10

value: tcr diversity plate 10 wb 12162020


title: MTG8_KO_4


title: 13107_21


title: 13463_22


title: 13119_41


title: 13092


title: MTG8_KO_2


title: MTG8_KO_3


title: 13449


title: 13089


title: 13060


title: MTG8_CTRL_4


title: 13068

value: host response panel plate 5 wb 11 19 2020


title: MTG8_CTRL_2


title: 13041_31

value: host response panel plate 25 wb 11292020


title: 13424_22


title: 13032


title: 13049_21


title: 13118_42


title: 13414_31


title: hfdKO6

city: Baton Rouge

first: Carrie

middle: M

last: Elks

state: LA

address: 6400 Perkins Road

institute: Pennington Biomedical Research Center

data_processing:
Lexogen Quantseq pipeline V1.8.8 on the Bluebee platform, quality control, mapping, and read count tables
Annotation and preparation for analysis, R V4.0.3, Rstudio V1.3.1093 and biomaRt V2.46.0
DESeq2  V1.30 differential gene expression
JMP Genomics V9 quality control, principal components, ANOVA, hierarchical clustering
Genome_build: Mouse – GRCm38.84  mm10
Supplementary_files_format_and_content: tab-delimited text containing DESeq2 normalized counts

source_name: gWAT

growth_protocol: Animals fed diet (5015 or HFD) for 20 weeks prior to tissue collection.

extract_protocol:
gWAT tissue was collected and flash frozen in liquid nitrogen. RNA was extracted using Qiagen Lipid Tissue kit (catalog #74804).
Lexogen Quant-Seq
indexed and pooled samples, 50bp forward read

treatment_protocol: Epididymal fat pads were dissected from a) 6 male wild-type and 6 male adipocyte-specific LAMA4 knockout mice following 20 weeks of regular diet (5015) feeding,  and b)  6 male wild-type and 6 male adipocyte-specific LAMA4 knockout mice following 20 weeks of 45% fat diet (HFD) feeding,

value: LFKO

tag: genotype

value: LAMA4 knockout

tag: diet

value: HFD

value: gWAT


title: 13069


title: 13027_21


title: 13444_21


title: 13399

value: plate 9

value: tcr diversity plate 9 wb 12162020


title: 13022_21


title: LHX6_KO_1


title: MKN45_ERY974_5

tag: cell line

tag: cell type

value: Gastric tumor

tag: time

value: Day 14


title: hfdKO5


title: 12990_41

tag: date

tag: generlf

tag: systemapf


title: 13426_21

tag: fovcount

tag: fovcounted

tag: scannerid


title: 13392

tag: stageposition

tag: bindingdensity

tag: cartridgeid


title: hfdKO4

tag: strain


title: 12983_21

tag: cartridgebarcode


title: 12981_41


title: 12968


title: hfdKO3

tag: tissue


title: hfdKO2

tag: genotype


title: hfdKO1

tag: diet


title: 13387


title: 12954_21

value: host response panel 4 wb


title: 13376_21


title: 12929


title: hfdWT5

value: wild type (floxed)


title: 12955_21


title: 13372_32


title: 12966


title: 12915_21


title: 12917_51


title: hfdWT6


title: 12907


title: hfdWT4


title: 13362_21


title: 12896_52


title: 13359_52


title: 12889_31


title: 13343


title: hfdWT3


title: 12967


title: 12862_21


title: hfdWT2


title: 12830_51


title: MTG8_CTRL_1

value: MGE-derived cortical cells

tag: age

value: embyonic day 14.5


title: 12792_21

value: host response panel 3 wb


title: 12812_31


title: 13348_22


title: 12786_21


title: 12900


title: rdKO6


title: hfdWT1


title: 12774


title: 12781


title: 12772_31


title: rdKO5


title: 13341_21


title: 12766


title: rdKO4


title: 13312_53

value: plate 8

value: tcr diversity plate 8 wb 12142020


title: 13310_21


title: 12751_41


title: 12745

value: host response panel 2 wb


title: 12736


title: 13317_22


title: 13333_21


title: rdKO3


title: 12733


title: 13308


title: 13265 _21


title: 12727


title: 12726_21


title: 13225

value: host response panel plate 7 wb 11 20 2020


title: 13262_21


title: rdKO1

value: LFKO


title: rdWT6


title: 12709_21


title: 12700_21

value: host response panel  1 wb

value: host response panel wb 1


title: 12708 _51


title: 13231_21

value: plate 7

value: tcr diversity plate 7 wb 12142020


title: rdWT5

value: gWAT


title: 13245


title: rdWT4


title: 12672


title: rdWT3


title: 12694_21


title: rdKO2

value: LAMA4 knockout


title: 12693_21


title: 12688_41


title: 12707_31


title: rdWT2


title: 13226


title: 12650


title: 12721


title: 12591_51


title: 13194


title: 13225


title: 12590


title: Mouse alveolar organoids, BLM48h, rep3

city: Hamamatsu

first: Yasunori

last: Enomoto

state: Shizuoka

address: 1-20-1 Handayama

department: Department of Regenerative and Infectious Pathology

institute: Hamamatsu University School of Medicine

data_processing:
Sequence reads were trimmed for adaptor sequence/low-quality sequence using Trim galore ver. 0.6.5
Trimmed sequence reads were mapped to UCSC GRCm39/mm39 using HISAT2 ver. 2.2.1 with default parameters
Read count extraction was performed using StringTie ver. 2.1.4
Normalization was performed using edgeR ver. 3.32.1
Supplementary files format and content: GRCm39/mm39
Supplementary files format and content: tab-delimited text files include CPM values for each sample

source_name: Lung

extract_protocol:
RNA was harvested using ISOGEN (NIPPON GENE). 250 ng of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using Illumina Stranded mRNA Prep, Ligation following manufacturer's protocols.

value: Lung

tag: description

value: primary cells

tag: cell type

value: Alveolar epithelial cell type 2

tag: treatment

value: Bleomycin (100μM), 48h


title: 13186

value: plate 6

tag: date

tag: generlf

value: tcr diversity plate 6 wb 12142020


title: 12645_21

tag: systemapf

tag: fovcount


title: Mouse alveolar organoids, BLM48h, rep2


title: MInt3APC

city: Kansas City

first: Shiyuan

middle: (Cynthia)

last: Chen

state: MO

department: Computational Biology

institute: Stowers Institute for Medical Research

data_processing:
Raw reads were demultiplexed into Fastq format allowing up to one mismatch using Illumina bcl2fastq2 v2.18. Reads were aligned to UCSC genome mm10 with STAR aligner (version STAR_2.6.1c ), using Ensembl 91 gene models. TPM values were generated using RSEM (version v1.3.0 ).
Genome_build: mm10
Supplementary_files_format_and_content: TPM gene expression in csv file

source_name: Intestine

extract_protocol:
1. Sort into clear RNase free tube containing 200ul of Trizol, use 27G needle to homogenize cells. 2. Filled samples up to 1ml with Trizol, and added 200µl chloroform per 1ml of Trizol to each sample. 3. Incubation 10 min and Centrafuge. 4.Transferred 400µl of the upper aqueous layer to a new tube repeat step 2-3.  5.Transferred ~400 of upper aqueous layer to the tube had 1.5µl glycogen. 6. Added 450µl Isopropanol to each sample and mix well. 7. Incubation 10 min and Centrafuge.  8.  Removed supernatant and Added 1ml 75% EtOH/DEPC H2O. 9. After centrafuge, removed supernatant and circled pellet with marker, air dried for 20 min. 10. Add adequate amount f DEPC H2O to each sample for 10min, mix well and keep at-80 ℃ until use.
Libraries were prepared according to manufacturer’s instructions using the TruSeq Stranded mRNA Prep Kit (Illumina) and NEXTflex DNA barcodes (Perkin Elmer). The resulting libraries were purified using the Agencourt AMPure XP system (Beckman Coulter) then quantified using a Bioanalyzer (Agilent Technologies) and a Qubit fluorometer (Life Technologies).  Libraries were re-quantified, normalized, pooled and sequenced on an Illumina NextSeq 500 instrument as High Output 75bp single read runs. Following sequencing, Illumina NextSeq Real Time Analysis version 2.4.11 and bcl2fastq2 version 2.20 were run to demultiplex reads and generate FASTQ files.

tag: strain/genotype

value: APCmin/+ mutant

value: M-Myeloid-derived suppressor cells

value: Intestine


title: Mouse alveolar organoids, CTRL48h, rep2

value: None, 48h


title: Mouse alveolar organoids, CTRL48h, rep3


title: 13261_52

value: plate 8

tag: fovcounted

tag: scannerid

tag: stageposition

value: tcr diversity plate 8 wb 12142020


title: Mspl3APC

source_name: Spleen

value: Spleen


title: Mouse alveolar organoids, CTRL48h, rep4


title: GInt3APC

value: G-Myeloid-derived suppressor cells


title: rdWT1

tag: strain

value: LFKO

value: wild type (floxed)


title: Gspl3APC


title: Mouse alveolar organoids, CTRL48h, rep1


title: 13172_21

value: plate 7

tag: bindingdensity

tag: cartridgeid

value: tcr diversity plate 7 wb 12142020


title: 13173_21