title: Hamster HFD-T070 5% 8

status: Public on Jun 30 2023

type: SRA

city: Riom

first: Cédric

last: Langhi

address: 20-22 rue Henri et Gilberte Goudier

country: France

institute: Valbiotis

library_source: transcriptomic

data_processing:
FASTQ files were generated using bcl2fastq (Illumina).
Reads were trimmed with Trimmomatic (version 0.36) to filter poor quality reads and to cut adapters. Filtered reads were mapped to the reference genome (Mesocricetus auratus, assembly MesAur1) using STAR (version 2.7.10). The STAR software was also used to produce the count matrix to assign reads to features using transcriptome annotations from the GTF file.
The differential analysis was performed with the edgeR R package. TMM normalization was applied. The glmQLFit and glmQLFTest functions were used to identify differentially expressed genes in the three groups (ND, HFD and HFD-T070 5%).
Assembly: Mesocricetus auratus, assembly MesAur1
Supplementary files format and content: A single tab-delimited text file including raw counts for each sample as a column

molecule: total RNA

organism: Mesocricetus auratus

source_name: Liver

extract_protocol:
RNA was extracted from snap-frozen tissues using TRIzol.
Fragmented double-strand cDNA was synthesized using the NEBNext Ultra II Directional RNA Library Prep Kit (New England Biolabs) according to the manufacturer’s instructions.

treatment_protocol: Hamster were fed with either a Normal Diet, a High Fat Diet or a High Fat Diet mixed with Totum-070 mixed in the diet at 5% for 6 complet weeks.

tag: tissue

value: Liver

tag: genotype

value: WT

tag: treatment

value: High Fat Diet + Totum-070 5%


title: Hamster HFD-T070 5% 7


title: Hamster HFD-T070 5% 6


title: Hamster HFD-T070 5% 4


title: Hamster HFD 6

value: High Fat Diet


title: Hamster HFD 7


title: Hamster HFD 5


title: Hamster HFD-T070 5% 1


title: Hamster HFD 3


title: Hamster HFD 1


title: Hamster HFD 2


title: Hamster ND 8

value: Normal Diet


title: Hamster ND 5


title: Hamster ND 2


title: Hamster HFD-T070 5% 5


title: Hamster HFD-T070 5% 3


title: Hamster ND 1


title: population T, 5 hours after treatment 3

city: Fort Collins

first: Todd

last: Gaines

state: CO

address: 1177 Campus Delivery

department: Agricultural Biology

country: USA

institute: Colorado State University

data_processing:
Raw reads were trimmed by trimmomatic
Trimmed reads were pseudoaligned to the transcriptome of Conyza canadensis (Laforest et al., 2020, Pest Management Science) using Salmon
Assembly: GenBank assembly accession: GCA_010389155.1
Supplementary files format and content: tab-delimited files showing transcript lengths, number of reads from each transcript and the transcripts per million sourced from each transcript

molecule: polyA RNA

organism: Conyza sumatrensis

source_name: leaf

extract_protocol: Zymo Direct-zol RNA Miniprep Plus

value: leaf

value: T


title: Hamster HFD-T070 5% 2


title: population T, 5 hours after treatment 2


title: Hamster HFD 8


title: population T, prior to treatment 3

value: untreated


title: population T, prior to treatment 4


title: Hamster HFD 4


title: Hamster ND 6


title: population S, prior to treatment 3

value: S


title: Hamster ND 7


title: population S, 5 hours after treatment 2


title: Hamster ND 3


title: Hamster ND 4


title: population R, 5 hours after treatment 2

value: R


title: population S, prior to treatment 1


title: population R, prior to treatment 4


title: population T, 5 hours after treatment 4


title: population R, prior to treatment 3


title: population R, prior to treatment 2


title: population T, 5 hours after treatment 1


title: population S, 5 hours after treatment 4


title: population T, prior to treatment 2


title: population T, prior to treatment 1


title: population S, 5 hours after treatment 3


title: population S, 5 hours after treatment 1


title: population S, prior to treatment 2


title: IVT_24hr_6_S54

city: Seattle

first: Sonali

last: Arora

state: WA

address: 1100 Fairview Ave N,

institute: FHCRC

description: 24  hr rep 6

data_processing:
Sequencing was performed using an NextSeq 2000in Rapid Run mode and  employed a Paired end, 150 base read length  sequencing strategy.
Files were aligned to guides using bowtie2 for each sample. Next, the barcodes for WT and mutant were  segregated for each sample.
log2 CPM values for each barcode using edgeR.
Assembly: hg38
Supplementary files format and content: tab-delimited text files include log2 cpm  values for each Sample.

organism: Homo sapiens

source_name: cell line

growth_protocol: RNA was isolated from samples collected in TRIzol using a chloroform-isopropanol protocol. 200µL chloroform was added to 1mL TRIzol samples, transferred to a heavy phase-lock gel tube (QuantaBio), and spun in a microcentrifuge at 12,000xg for 15 minutes at 4°C.

extract_protocol:
After 10 minutes of incubation at room temperature, sample was spun at 20,000xg for 20 minutes at 4°C, then RNA pellet washed with fresh 75% ethanol before drying and resuspending in 40µL water.
isolated mRNA was DNase treated using Turbo DNase in reactions consisting of 11µL (~15µg) RNA and 1.5µL Turbo DNase according to manufacturer’s protocol. DNase-treated RNA was purified using lithium chloride precipitation as described in mMESSAGE mMACHINE T7 ULTRA Transcription Kit (Invitrogen). 2µg RNA per sample was reverse transcribed into cDNA using SuperScript III First-Strand Synthesis System (Invitrogen) and MPRA RNA-specific primer (Table **, primer #22).

treatment_protocol: the aqueous layer was transferred to a new tube containing 1µL of glycogen and equal volume isopropanol added

tag: time point


title: IVT_24hr_5_S53

description: 24  hr rep5


title: population R, 5 hours after treatment 3


title: IVT_24hr_4_S52

description: 24  hr rep4


title: IVT_24hr_3_S51

description: 24  hr rep 3


title: IVT_24hr_2_S50

description: 24   hr rep 2


title: population R, 5 hours after treatment 1


title: garid(-) gametocyte, rep3

city: tsu

first: masao

last: yuda

state: mie

address: edobashi 2-174

country: Japan

institute: mie university

data_processing:
Sequence data were mapped onto the P. berghei genome sequence (PlasmoDB, version 3) by HISAT2. Parameters of HISAT2 were set to default except for the option “--max-intron” which was set to 1000. The SAM files were then sorted using samtools to produce BAM files.
Using the BAM files, number of reads mapped on each gene was counted by featureCounts.
Assembly: PlasmoDB, version 3
Supplementary files format and content: txt, raw read count

organism: Plasmodium berghei ANKA

source_name: Gametocyte

growth_protocol: Parasites were inoculated in Balb/c mice.

extract_protocol:
Total RNA was extracted using the ISOGEN II (NIPPON GENE, Japan) according to the manufacturer’s instructions.
Libraries were constructed from total RNA using KAPA mRNA Hyperprep kit (KAPA Biosystems), and sequencing was performed with DNBSEQ (Paired-end read - MGI DNBSEQ-G400),

treatment_protocol: Infected mice were treated with sulfadiazine in their drinking water for 2 days in order to deplete asexual blood-stage parasites.

tag: Stage

value: gametocyte

tag: strain

value: ANKA

value: garid(-)


title: garid(-) gametocyte, rep1


title: WT gametocyte, rep3


title: WT gametocyte, rep2


title: WT gametocyte, rep1


title: IVT_12hr_5_S47

description: 12 hr rep5


title: IVT_12hr_6_S48

description: 12 hr rep 6


title: IVT_24hr_1_S49

description: 24  hr rep1


title: IVT_12hr_4_S46

description: 12 hr rep4


title: IVT_12hr_2_S44

description: 12  hr rep 2


title: IVT_12hr_1_S43

description: 12 hr rep1


title: population R, prior to treatment 1


title: IVT_6hr_5_S41

description: 6 hr rep5


title: IVT_6hr_4_S40

description: 6 hr rep4


title: IVT_6hr_6_S42

description: 6 hr rep 6


title: garid(-) gametocyte, rep2


title: IVT_6hr_2_S38

description: 6  hr rep 2


title: IVT_6hr_3_S39

description: 6 hr rep 3


title: IVT_6hr_1_S37

description: 6 hr rep1


title: IVT_3hr_6_S36

description: 3 hr rep 6


title: IVT_3hr_5_S35

description: 3 hr rep5


title: IVT_3hr_4_S34

description: 3 hr rep4


title: IVT_3hr_3_S33

description: 3 hr rep 3


title: IVT_12hr_3_S45

description: 12 hr rep 3


title: IVT_1hr_6_S30

description: 1 hr rep 6


title: IVT_3hr_2_S32

description: 3  hr rep 2


title: IVT_3hr_1_S31

description: 3 hr rep1


title: IVT_1hr_5_S29

description: 1 hr rep5


title: IVT_1hr_3_S27

description: 1 hr rep 3


title: IVT_1hr_2_S26

description: 1  hr rep 2


title: IVT_1hr_1_S25

description: 1 hr rep1


title: Control_NM_4

city: Spokane

first: Michelle

last: Pearson

address: 3410 W Whistalks Way MS3280

department: Life Sciences

institute: Spokane Falls Community College

description: Non-drought without mycorrhizal fungus

data_processing:
Read quality was good and adapter sequences were not overrepresented, so no trimming occurred; quality assessed by FastQC v0.11.5 (Andrews, 2016)
Reads were pseudo-aligned with Kallisto v0.42.3 (Bray et al., 2016).
Data were analyzed using the sleuth package (Pimentel et al., 2017) in R 3.5.2 (R Core Team, 2019).
Genome_build: The transcriptomes for Daucus carota v2 and Rhizophagus irregularis 197198 v2 were merged; transcripts were aligned agained this merged transcriptome.
Supplementary_files_format_and_content: tsv files contain the read abundance quantified with Kallisto v0.42.3

organism: Daucus carota

source_name: Fine roots of carrot

growth_protocol: Carrots (mycorrhizal and non-mycorrhizal) grew for 50 days prior to subjection to drought treatment. All plants received regular watering and nutrient addition using Enshi solution (a nutrient solution well-suited for carrots)

extract_protocol:
RNA extraction: PureLink RNA Mini Kit; removal of DNA contaminants: Turbo DNA-free kit (Life Technologies, Carlsbad, CA, USA)
Library preparation by Novogene LTD Co., Sacramento, CA, USA; secquenced on Illumina NovaSeq 6000

treatment_protocol: During the last 10 days of growth, carrots in the drought treatment group received water less frequently than controls, diminishing until sample collection. Nutrient inputs were the same for both control and drought groups.

tag: cultivar

value: Napoli

tag: infected with

value: not infected

tag: drought treatment status

value: non-drought

value: fine roots


title: Drought_NM_3

description: Drought without mycorrhizal fungus

value: drought


title: Control_NM_2

description: Non-drought without mycorrhizal fungus


title: Drought_NM_1

description: Drought without mycorrhizal fungus


title: IVT_1hr_4_S28

description: 1hr rep4


title: Drought_NM_2

description: Drought without mycorrhizal fungus


title: Control_NM_3

description: Non-drought without mycorrhizal fungus


title: Control_NM_1

description: Non-drought without mycorrhizal fungus


title: Drought_NM_4

description: Drought without mycorrhizal fungus


title: Ctr_rep3

city: chengdu

first: Yong

last: Dong

state: sichuan

address: Xindu road 783, Xindu district

department: Immunology

country: China

institute: Chengdu medical college

data_processing:
All the clean data were aligned to the zebrafish genome by hisat2 software.
Supplementary files format and content: Raw_count.txt

organism: Danio rerio

source_name: whole fish

extract_protocol:
Total RNA of wild type or mcm5 mutated zebrafish at 3.5dpf was extracted, and mRNA was enriched by olig(T) beads.
Add Fragmentation Buffer to randomly break mRNA into short fragments. Reverse transcription synthesis of cDNA using short fragments as templates, and then perfom end repair and A-tail addition for all cDNA.  Following add UMI tags and sequencing adapters onto the cDNAs. Finally, PCR amplification was performed to obtain the library.. All the DNA libraries were sequenced by HiSeq X Ten. And the clean data were generated from the raw data by removing the adapters.

value: whole fish

value: control


title: Ctr_rep2


title: Ctr_rep1


title: Mcm5_mut_rep1

value: mcm5 mutants


title: Mcm5_mut_rep2


title: Mcm5_mut_rep3


title: R93 5 9 Grays of WBIR

type: RNA

city: Gainesville

first: Robert

last: Maile

state: FL

address: 1600 SW Archer Road

department: Surgery

institute: University of Florida

hyb_protocol: Standard nanostring miRNA hybridisation protocols.

data_processing: nsolver v3

organism: Mus musculus

source_name: Plasma Extracellular Vesicles

extract_protocol: Collected peripheral blood was centrifuged at 2,000g for 35 minutes for plasma separation. Plasma was removed and at 2,000g for 30 minutes to remove cellular debris. The supernatant was removed and centrifuged at 10,000gs for 30 minutes to remove larger EVs. The supernatant was removed and centrifuged at 21,000gs for 60 minutes. The supernatant was discarded and the pellet was resuspended in 50ul of sterile-filtered PBS.

tag: wbir

value: yes


title: Sham 4

label_protocol: Standard nanostring miRNA hybridisation protocols.

value: no


title: Sham 3


title: Sham 1


title: Sham 2


title: R23 4 2 Grays of WBIR


title: R93 4 9 Grays of WBIR


title: R93 2 9 Grays of WBIR


title: R93 3 9 Grays of WBIR


title: R93 1 9 Grays of WBIR


title: R23 5 2 Grays of WBIR


title: R23 1 2 Grays of WBIR


title: R23 2 2 Grays of WBIR


title: R23 3 2 Grays of WBIR


title: AT12_Subject 12 after bromocriptine treatment [miRNA_seq]

city: Solna

first: Nageswara Rao

last: Boggavarapu

state: stockholm

address: Visionsgatan 4

department: Women and Children health

country: Sweden

institute: Karolinska Institutet

data_processing:
Bioinformatic analyses were performed using Partek Flow Genomic Analysis Software (Partek, St. Louis, Missouri, USA).
Sequenced raw FASTQ files were trimmed for adapters and contaminants such as ribosomal DNA, mitochondrial DNA respectively.
Trimmed reads were mapped to the reference genome hg38 using STAR aligner.
Mapped reads were further filtered and quantified to transcripts and genes using hg38 assembly and Ensemble transcripts release 99 for mRNA nad miRbase v22 for miRNA.
Genome_build: hg38
Supplementary_files_format_and_content: Filtered Gene Counts in a txt format

source_name: Endometrial Biopsy

growth_protocol: Not applicable

extract_protocol:
Total RNA was extracted from tissue stored in RNA later using RNeasy total RNA Kit (Qiagen, Hilden, Germany) as per the manufacturer protocol.
cDNA library was constructed using well established Smart-seq2 protocol (Picelli et al. 2013, Picelli et al. 2014), tagmentation step was accomplished using Nextera XT kit (Illumina) , miRNA sequencing was performed as per the Hagemann et al 2018 protocol and sequencing was done in Illumina NextSeq 550® at the bioinformatics expression analysis facility at Karolinska University hospital, Sweden.

treatment_protocol: Twelve women diagnosed with diffuse adenomyosis were administered for six months with a daily dose of 5mg vaginal bromocriptine. Endometrial biopsies were collected at baseline and at the end of treatment.

tag: subject id

value: Subject 12

tag: subject status

value: diagnosed with diffuse adenomyosis

tag: treatment/time point

value: after bromocriptine treatment

value: Endometrial Biopsy


title: 9M cKO, NP 4

city: Philadelphia

first: Shira

middle: N

last: Johnston

state: PA

address: 1025 Walnut St., Suite 511 College Bldg.

institute: Thomas Jefferson University

hyb_protocol: Gene chips, Mouse Clariom S were hybridized with 2.5 μg fragmented and biotin-labeled cDNA in 100 μl of hybridization cocktail. Arrays were washed and stained with GeneChip hybridization wash & stain kit using Gene chip Fluidic Station 450.

scan_protocol: Chips were scanned on an Affymetrix Gene Chip Scanner 3000 7G, using Command Console Software. Quality Control of the experiment was performed by Expression Console Software v 1.4.1.

data_processing:
Chp files were generated by sst-rma normalization from Affymetrix .cel file using Expression Console Software. Experimental group was compared with control group by using Transcriptome array console 4.0 and DEGs with a Fold Change ±2, p-value or FDR<0.05. PANTHER tool was used to compute enriched pathways in DEGs that are altered with a Fold Change ±2, p-value <0.05.
Tukey's Bi-weight average of exon intensity of all the samples in a condition; log2(Expression).

label: biotin

source_name: Nucleus pulposus from 9-month-old GLUT1cKO mice

label_protocol: Fragmented biotin labeled cDNA (from 100 ng of RNA) was synthesized using the GeneChip WT Plus kit according to ABI protocol (Thermo Fisher Scientific).

growth_protocol: GLUT1f/f and K19Cre; GLUT1f/f Mice were aged to 9-months-old

extract_protocol: NP tissues were scooped into RNAlater and processed using Qiagen RNeasy Mini Kit

treatment_protocol: GLUT1f/f and K19Cre; GLUT1f/f Mice were injected 3 days in a row with 100ug/gbw Tamoxifen at 3-months-old

value: nucleus pulposus

value: K19Cre; Glut1f/f (cKO)

tag: age


title: 9M WT, NP 6

source_name: Nucleus pulposus from 9-month-old wildtype mice

value: Glut1f/f (WT)


title: 9M cKO, NP 1


title: WT IMQ 1

city: Taipei City

first: Yeh Fong

last: Tan

state: Taipei

address: No. 128, Section 2, Academia Rd, Nangang District

department: Institute of BioMedical Sciences

country: Taiwan

institute: Academia Sinica

data_processing:
Combination of Ubuntu 22.04.1 LTS, Trimmomatic, Hisat2, SAMtools, StringTie and prepDE python package.
Separate fastq files are merged using Terminal of Ubuntu.
Sequence reads were trimmed for adaptor sequence/low-quality sequence using Trimmomatic (MinLen: 36, Phred33).
Trimmed sequence reads were mapped to GrCM38.dna.toplevel.fa.gz using Hisat2.
Aligned sequence were converted from SAM to BAM using SAMtools.
Read count extraction was performed using StringTie. Files are then converted into CSV format using prepDE.py3 package.
Assembly: GrCM38.dna.toplevel.fa.gz
Supplementary files format and content: Comma separated value file including gene count for each sample

source_name: Ear

extract_protocol:
RNA from isolated Langerhans cells was extracted using R2060 DirectZol RNA MicroPrep kit (Zymo Research). 10 to 70 ng of total RNA was used for construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using SMARTer Stranded Total RNA-Seq Kit v2- Pico Input Mammalian according to manufacturer's protocols.

value: Ear

tag: cell type

value: Langerhans cell

value: Wild type

value: Imiquimod treated


title: 9M cKO, NP 5


title: AT6_Subject 6 after bromocriptine treatment [miRNA_seq]

value: Subject 6


title: AT10_Subject 10 after bromocriptine treatment [miRNA_seq]

value: Subject 10


title: AT3_Subject 3 after bromocriptine treatment [miRNA_seq]

value: Subject 3


title: 9M cKO, NP 2


title: AT9_Subject 9 after bromocriptine treatment [miRNA_seq]

value: Subject 9


title: 9M cKO, NP 3


title: AT7_Subject 7 after bromocriptine treatment [miRNA_seq]

value: Subject 7


title: AT4_Subject 4 after bromocriptine treatment [miRNA_seq]

value: Subject 4


title: 9M WT, NP 5


title: AT5_Subject 5 after bromocriptine treatment [miRNA_seq]

value: Subject 5


title: 9M WT, NP 4


title: AT8_Subject 8 after bromocriptine treatment [miRNA_seq]

value: Subject 8

value: diagnosed with diffuse adenomyosis


title: 9M cKO, NP 6


title: 9M WT, NP 3


title: Bach1KO

city: Bethesda

first: Sivaranjani

last: Namasivayam

address: 33 North Drive

department: NIAID

institute: NIH

library_source: transcriptomic single cell

data_processing:
Alignment, tagging, gene and transcript counting, and clustering analysis was performed using Cellranger 6.1.2
Supplementary files format and content: Tab sepearated value files and matrix files

source_name: Lung

extract_protocol:
Lung lobes isolated from mice were washed with sterile 1X PBS, dissected into small pieces and then digested in RPMI containing Liberase  TL (0.33mg/ml; Sigma-Aldrich, USA) and DNase I (0.1mg/ml; Sigma-Aldrich, USA) at 37oC for 45 min under agitation (200 rpm), followed by adding FBS to block the enzymatic digestion. Lung tissue was dispersed by passage through a 70-mm pore-size cell strainer. Red blood cells were lysed with ACK buffer (Gibco, USA) at room temperature for 3 min. Lung cells were washed with 1X PBS supplemented with 10% FBS, centrifuged at 1500 rpm for 5 min and the cell pellet resuspended in RPMI supplemented with 10% FBS. Equal number of live cells from each sample of a Bach1-/- and BL/6 WT groups were pooled, stained with propidium-iodide at a dilution of 1:100 and live cells were sorted for each group. 10,000 cells from this sorted population of each group were loaded per lane on a 10X Genomics Next GEM chip, and single-cell GEMs were generated using a 10X Chromium Controller.
Library construction was performed as manufacterer's instructions (10X Genomics v3.1)

value: Lung

value: Bach1 KO


title: 9M WT, NP 1

value: nucleus pulposus


title: WT


title: 9M WT, NP 2

value: Glut1f/f (WT)


title: AB10_Subject 10 adenomyosis baseline [miRNA_seq]

value: adenomyosis baseline

value: Endometrial Biopsy


title: AT2_Subject 2 after bromocriptine treatment [miRNA_seq]

value: Subject 2

value: after bromocriptine treatment


title: AT11_Subject 11 after bromocriptine treatment [miRNA_seq]

value: Subject 11


title: AB11_Subject 11 adenomyosis baseline [miRNA_seq]


title: AB9_Subject 9 adenomyosis baseline [miRNA_seq]


title: AT1_Subject 1 after bromocriptine treatment [miRNA_seq]

value: Subject 1


title: AB6_Subject 6 adenomyosis baseline [miRNA_seq]

value: Subject 6


title: AB5_Subject 5 adenomyosis baseline [miRNA_seq]


title: AB4_Subject 4 adenomyosis baseline [miRNA_seq]


title: AB2_Subject 2 adenomyosis baseline [miRNA_seq]


title: AT12_Subject 12 after bromocriptine treatment [RNA_seq]

value: Subject 12


title: AT8_Subject 8 after bromocriptine treatment [RNA_seq]


title: AT11_Subject 11 after bromocriptine treatment [RNA_seq]


title: AT3_Subject 3 after bromocriptine treatment [RNA_seq]

value: Subject 3


title: AT10_Subject 10 after bromocriptine treatment [RNA_seq]

value: Subject 10


title: AB1_Subject 1 adenomyosis baseline [miRNA_seq]


title: AT4_Subject 4 after bromocriptine treatment [RNA_seq]

value: Subject 4


title: AT1_Subject 1 after bromocriptine treatment [RNA_seq]


title: AB11_Subject 11 adenomyosis baseline [RNA_seq]


title: AT6_Subject 6 after bromocriptine treatment [RNA_seq]


title: AB7_Subject 7 adenomyosis baseline [RNA_seq]

value: Subject 7


title: AT2_Subject 2 after bromocriptine treatment [RNA_seq]

value: diagnosed with diffuse adenomyosis


title: AB10_Subject 10 adenomyosis baseline [RNA_seq]


title: AT7_Subject 7 after bromocriptine treatment [RNA_seq]


title: AB6_Subject 6 adenomyosis baseline [RNA_seq]


title: AB3_Subject 3 adenomyosis baseline [miRNA_seq]


title: AT5_Subject 5 after bromocriptine treatment [RNA_seq]

value: Subject 5


title: AB8_Subject 8 adenomyosis baseline [RNA_seq]

value: Subject 8


title: AB9_Subject 9 adenomyosis baseline [RNA_seq]

value: Subject 9


title: AB5_Subject 5 adenomyosis baseline [RNA_seq]


title: AT9_Subject 9 after bromocriptine treatment [RNA_seq]


title: AB12_Subject 12 adenomyosis baseline [RNA_seq]


title: AB7_Subject 7 adenomyosis baseline [miRNA_seq]


title: AB8_Subject 8 adenomyosis baseline [miRNA_seq]


title: AB4_Subject 4 adenomyosis baseline [RNA_seq]


title: AB3_Subject 3 adenomyosis baseline [RNA_seq]


title: AB1_Subject 1 adenomyosis baseline [RNA_seq]


title: AB2_Subject 2 adenomyosis baseline [RNA_seq]


title: scRNA-Seq Day 30 Zbtb20 KO OT-I

city: Lebanon

first: Edward

last: Usherwood

state: NH

address: Rubin Building, Level 7, 710-53

department: Microbiology and Immunology

institute: Geisel School of Medicine at Dartmouth College

data_processing:
Barcode processing, demultiplexing, read mapping, and quantification were performed using the Cell Ranger (v.3.1.0) count pipeline with default parameters
Assembly: hg38 for human samples and mm10 for mouse samples
Supplementary files format and content: Barcode matrices in HDF5 format

source_name: Splenocytes

growth_protocol: OT-I transgenic CD8 T cells expressing the congenic CD45.1 surface marker were expandedinvivowith listeria-actA-Ova. These cells were isolated from splenocytes at the indicated time points using FACS to collect CD45.1 expressing cells.

extract_protocol:
For isolation of CD8 T cells 10 and 35 days after infection, single-cell suspensions were generated from four mice per recipient group by grinding spleens through nylon filters. CD8 T cells were enriched from these suspensions using Stemcell’s EasySep™ Mouse CD8 T Cell Isolation Kit (#19853). These samples were FcR blocked then stained with antibodies and live/dead stain (LIVE/DEAD™ Fixable Violet Dead Cell Stain Kit, # L34955) for 30 minutes on ice shielded from light. The antibodies used for cell surface staining from BioLegend were as follows; PE anti-mouse CD8b Antibody (YTS156.7.7) and APC anti-mouse CD45.1 Antibody (A20). Samples were subsequently washed twice and ~1X10^6 congenically marked OT-I cells were purified using fluorescence activated cell sorting for each group of recipients. The samples purified in this way from each group of recipients were then suspended in 100μL buffer and labeled with 1μg of Total-seq A antibodies (Biologend) per sample. Cell suspensions were loaded onto a 10x Genomics ChIP G and processed using the NextGEM 3' v3.1 protocol according to manufacturer's instructions.
Libraries from single cell cDNA were constructed using the 10x Genomics NextGEM 3' v3.1 chemistry according to manufacturer's instructions.

treatment_protocol: Please reference treatment protocol

value: Splenocytes

value: CD8 T cells

value: Gransyme B Cre, Zbtb20 f/f, CD45.1, OT-I

value: LM-actA-OVA

value: Day 35 post-infection

value: TotalSeq-A0198 anti-mouse CD127 (A7R34), TotalSeq-A0250 anti-mouse/human KLRG1 (2F1/KLRG1), TotalSeq-A0073 anti-mouse/human CD44 (IM7) and TotalSeq-A0112 anti-mouse CD62L (MEL-14)


title: scRNA-Seq Day 30 WT OT-I

value: WT, OT-I


title: scRNA-Seq Day 10 WT OT-I

value: Day 10 post-infection


title: scRNA-Seq Day 10 Zbtb20 KO OT-I


title: CD8_T_Cells_Zbtb20-3XFLAG_IgG

library_source: genomic

data_processing:
Raw reads were trimmed with Cutadapt (v2.4) and aligned to hg38 using Bowtie (v2.2.6) in “--local” mode with parameters “-no-mixed-discordant”
Unmapped & multi-mappoing reads were removed and duplicate reads were identified and removed using MarkDuplicates (Picard Tools) to create filtered BAMs
Alignments were sorted into nucleosome-free regions (fragment length <=125bp) or nucleosomal-regions (fragment length >150bp) amd processed separately in downstream analysis
Peaks were called using MACS2 (v2.2.7.1) callpeak command with parameters “-f BAMPE --keep-dup all -p 1.0E-4” and filtered against the ENCODE hg38 blacklist (H3K4me3 analysis was run in -broadPeak mode). Parameter -g was set to 2913022398 and 2652783500 for human and mouse data, respectively.
Irreproducible Discovery Rate (IDR) method was applied, using parameters --rank signal.value "--peak-merge-method avg". Peaks with an IDR threshold of 0.05 and fold change above background >4 were retained for further analysis
Normalized signal tracks (BigWig files) were generated using deepTools (v 3.3.0) command BamCoverage with parameters “–binSize 20 –smoothLength 60 –scaleFactor sfi” where sfi corresponds to the sample specific scale factor calculated using E.coli spike-in DNA
Assembly: hg38 for human samples and mm10 for mouse samples
Supplementary files format and content: peak files in BED format
Supplementary files format and content: Normalized signal tracks in BigWig format

molecule: genomic DNA

extract_protocol:
CUT&RUN experiments were carried out using EpiCypher’s CUT&RUN kit version 1.0 (#14-1048) as directed by the CUTANA user manual version 1.0. Briefly, 500,000 cells (either HEK 293 or CD8 T cells) expressing Zbtb20-3XFLAG were crosslinked with 1% formaldehyde for 5 minutes and subsequently quenched with 125mM glycine. Considerations for performing CUT&RUN on crosslinked cells as described in the CUTANA user manual version 1.0 were then applied for the remainder of the procedure. The anti-FLAG (M2) antibody from Sigma-Aldrich was used for detection of Zbtb20-3XFLAG by CUT&RUN.
CUT&RUN library preparation and sequencing was performed according to the method described in the CUTANA Library Kit Manual v1.0 (EpiCypher). Briefly, 5ng of CUT&RUN DNA fragments were prepared for Illumina sequencing using the NEB Ultra II DNA kit with the following modifications: Step 3B.2 – 1.1x AmPure bead cleanup; Step 4.1.3 – PCR amplification with 45s @98C for initial denaturation followed by 14 cycles of 15s @98C, 10s @ 60C and 1m @ 72C final extension. Libraries were quantified by qubit and run on a Fragment Analyzer (Agilent) for sizing. Libraires were pooled and sequenced to a depth of 10M, 75bp paired-end reads/sample on a NextSeq500 instrument.

value: CD8 T cell

tag: cut&run antibody

value: Rabbit IgG (Cat# 13-0042k) from EpiCypher


title: CD8_T_Cells_Zbtb20-3XFLAG_Anti-FLAG_2

value: anti-FLAG (M2) antibody from Sigma-Aldrich


title: CD8_T_Cells_Zbtb20-3XFLAG_Anti-FLAG_1


title: C13, LPS, biol rep 3

city: Seville

first: Cintia

last: Roodveldt

address: CABIMER-Av. Americo Vespucio 24, Cartuja 93

country: Spain

institute: University of Seville

data_processing:
Illumina  Basespace Sequence Hub applications were used for data processing.
RNA-Seq data were filtered using the FASTQ Toolkit v2.2.0 program.
The TopHat Alignment Version 2.1.0 was used using the mus musculus genome build mm10.
Cufflinks Assembly and DE Version 2.1.0 was used for differential expression analysis.
Assembly: mm10
Supplementary files format and content: Excel file with FPKM values for each Sample

source_name: Brain, newborn (<3d)

growth_protocol: Cells were maintained in DMEM-F12 culture medium that was supplemented with 10% FBS, 2mM L-glutamine, nonessential amino acids (NEAAs), 100 U/ml penicillin, and 100 ug/ml streptomycin

extract_protocol:
mRNA was isolated using poly-dT-coated beads
Libraries were prepared by using the TruSeq Stranded mRNA kit (Illumina).
After library amplification by PCR and all recommended qualiity control assays, individual libraries were pooled together at equimolar ratios and diluted to ca. 1.4 pM.

treatment_protocol: RNA was harvested using RNeasy mini plus kit (Qiagen). 1.3 ug of total RNA was used for the construction of sequencing libraries.

value: Brain, newborn (<3d)

value: Primary microglia


title: CD8_T_Cells_Zbtb20-3XFLAG_Anti-H3K4me3

value: anti-H3K4me3 (Cat# 13-0041k) from EpiCypher


title: scATAC-Seq Day 10 WT OT-I

data_processing:
Barcode processing, demultiplexing, read mapping, peak calling and counting were performed using Cell Ranger ATAC (v.1.1.0) pipelines "mkfastq" and "count" using default parameters
Assembly: hg38 for human samples and mm10 for mouse samples
Supplementary files format and content: Barcode matrices in HDF5 format, fragments in tsv format, single cell  metadata in csv format

extract_protocol:
For isolation of CD8 T cells 10 and 35 days after infection, single-cell suspensions were generated from four mice per recipient group by grinding spleens through nylon filters. CD8 T cells were enriched from these suspensions using Stemcell’s EasySep™ Mouse CD8 T Cell Isolation Kit (#19853). These samples were FcR blocked then stained with antibodies and live/dead stain (LIVE/DEAD™ Fixable Violet Dead Cell Stain Kit, # L34955) for 30 minutes on ice shielded from light. The antibodies used for cell surface staining from BioLegend were as follows; PE anti-mouse CD8b Antibody (YTS156.7.7) and APC anti-mouse CD45.1 Antibody (A20). Samples were subsequently washed twice and ~1X10^6 congenically marked OT-I cells were purified using fluorescence activated cell sorting for each group of recipients. The samples purified in this way from each group of recipients were then suspended in 100μL buffer and labeled with 1μg of Total-seq A antibodies (Biologend) per sample. DNA tagmentation and single cell capture and barcoding were performed using the 10x Genomics Single Cell ATAC v1 chemistry according to manufacturer's instructions.
Libraries from single cell-barcoded ATAC fragements were constructed using the 10x Genomics Single Cell ATAC v1 chemistry according to manufacturer's instructions.


title: C13, LPS, biol rep 2


title: Vehicle,LPS, biol rep 3

value: DMSO (1h), LPS (5h)


title: scATAC-Seq Day 10 Zbtb20 KO OT-I


title: C13, LPS, biol rep 1


title: scATAC-Seq Day 30 Zbtb20 KO OT-I


title: scATAC-Seq Day 30 WT OT-I


title: Vehicle LPS, biol rep 2


title: Vehicle,LPS, biol rep 1


title: Terminally exhausted T cells from ctrl Ig-treated mice - VDJ

city: Toulouse

first: Liliana

middle: Elisa

last: Lucca

address: 2 Avenue Hubert Curien

institute: CRCT

description: 10x Genomics

data_processing:
Fastq files were generated from Illumina BCL files with the 'mkfastq' pipeline of cellranger v3.0.2
Fastq files from the two sequencing runs were aligned and demultiplexed with cellranger count or cellranger vdj.
Cellranger count was rerun with the option --force-cells to correct for inconsistencies between the number of cells identified in the first round of alignment/demultiplexing and the number of cells calculated upon inspection of the barcode rank plot. The following inputs were given to the --force-cells arguments: 13553 for the 137_PT_Ex sample, 10015 for the 137_TermTex sample, and 13188 for the Ig_PT_Ex sample.
Assembly: mm10
Supplementary files format and content: For generation of the processed file "aCD137_sorted_subsets_TcR_clonotypes.txt", the files "filtered_contig_annotations.csv" generated for each sample by the cellranger vdj pipeline were imported into an R session, concatenated and exported as a single file.
Supplementary files format and content: The processed file "aCD137_sorted_subsets_norm_counts.rds" was generated as follows: the contents of the "filtered_feature_bc_matrix" folder generated by the cellranger count pipeline were imported into Seurat v4.0.0. Counts were Log-normalized and cells were filtered out if they had more than 10% mitochondrial reads or less than 500 or more than 4000 unique genes detected. Cells were scored for cell cycle genes (https://github.com/hbc/tinyatlas/blob/master/cell_cycle/Mus_musculus.csv) with the Seurat function "CellCycleScoring". Data were scaled and cell cycle scores were regressed. Batch effects present between samples were corrected by running Harmony v0.1.0. Cells were clustered based on the first 10 harmonized PCs at a resolution of 0.4 with the Seurat function "FindClusters". Based on inspection of the cluster-specific expression of lineage genes, two clusters of contaminating B cells were excluded. Detection of hypervariable genes, scaling, PCA, dimensionality reduction with UMAP and clustering (resolution 0.3) were repeated on the subsetted object. The normalized count matrix was exported as an .rds file ("aCD137_sorted_subsets_norm_counts.rds"), while the metadata as well as the UMAP cell embeddings were exported as a .txt file ("aCD137_sorted_subsets_metadata.txt").

source_name: spleen

extract_protocol:
Five C57BL/6 mice were treated with anti-CD137 (10ug, clone 3H3) twice a week for 14 days. Ten C57BL/6 mice were treated with an Ig control (100ug, clone HRPN) also twice a week for 14 days. Mice were sacrificed and spleens were harvested for T cell sort. Teff cells were sorted as CD44hiPD1-, precursor exhausted T cells were sorted as CD44hiPD1+Slamf6+Tim3-, and exhausted T cells as CD44hiPD1+Slamf6-Tim3+.
Single-cell libraries (5′ gene expression) were generated using the Chromium Controller Instrument and Chromium Next GEM Single Cell 5’ Library & Gel Bead Kit v1.1 according to the manufacturer’s protocol (10× Genomics)
The libraries were sequenced twice on a NextSeq 550 (Illumina) in pair-end sequencing 28 bp (read1) × 91 bp (read2) and a single index 8 bp in length.

value: spleen

value: T cell

value: wild-type

value: Ig control


title: Terminally exhausted T cells from ctrl Ig-treated mice - GEX

description: 10x Genomics


title: p50, Sema4F-GOF, Male, scRNAseq_2

city: HOUSTON

first: emmet

last: huang-hobbs

state: TX

address: 1 baylor plaza, N1120

department: CAGT

institute: Baylor College of Medicine

description:
10x Genomics
S4F_50.rds

data_processing:
Sample alignment was done by 10X Cell Ranger (v3.0.2)
Quality control was performed using Seurat (v4.1.0) by following criteria: nUMI/cell threshold > 200, gene/cell threshold > 250, log10gene/UMI threshold > 0.8, mitochondria ratio < 0.3, and ribosome ration > 0.01
DoubletFinder
FindMarkers by Seurat
Assembly: mm10 + EGFP
Supplementary files format and content: Seurat Object .rds

source_name: Brain

extract_protocol:
Tissue was dissociated by using MACS neural dissociation kit
Illumina sequencing libraries were prepared by Chromium Single Cell Gene Expression 3v3.1 kit (10x Genomics)

tag: agent

tag: Sex

value: Male

value: GBM + TME

value: Brain

value: 50 days old


title: p50, Saline treated, Male scRNAseq

description:
10x Genomics
S4F_50.rds

value: Saline treated

tag: tissue


title: p50, CNO treated, Male, scRNAseq

description:
10x Genomics
S4F_50.rds

value: CNO treated


title: p50, Saline treated, Female, scRNAseq

description:
10x Genomics
S4F_50.rds

value: Female


title: p50, Sema4F-GOF, Male, scRNAseq_1

description:
10x Genomics
S4F_50.rds


title: p50, CNO treated, Female, scRNAseq

description:
10x Genomics
S4F_50.rds


title: Precursor exhausted T cells from ctrl Ig-treated mice - VDJ

description: 10x Genomics

tag: genotype

tag: treatment


title: Precursor exhausted T cells from ctrl Ig-treated mice - GEX

description: 10x Genomics


title: Effector T cells from ctrl Ig-treated mice - VDJ

description: 10x Genomics


title: Effector T cells from ctrl Ig-treated mice - GEX

description: 10x Genomics


title: Terminally exhausted T cells from aCD137-treated mice - VDJ

description: 10x Genomics


title: Terminally exhausted T cells from aCD137-treated mice - GEX

description: 10x Genomics


title: Precursor exhausted T cells from aCD137-treated mice - VDJ

description: 10x Genomics


title: Precursor exhausted T cells from aCD137-treated mice - GEX

description: 10x Genomics


title: Effector T cells from aCD137-treated mice - GEX

description: 10x Genomics


title: Effector T cells from aCD137-treated mice - VDJ

description: 10x Genomics


title: MEFs, NELFB f/-, Ad-Cre; Pol II ChIP-seq, biol rep 1

city: Washington

first: Haihui

last: Pan

state: DC

address: 2121 I St NW

department: Biochemistry and Molecular Medicine

institute: George Washington University

data_processing:
Raw ChIP-seq data in FASTQ format was aligned to mm10 reference genome using bowtie2
The Sequence Alignment Map (SAM) file was converted to a Binary Alignment Map (BAM) file, and then sorted by Samtools. Alignments with MAPQ score smaller than 30 were skipped.
The coverage (the number of reads per bin) track was generated by deepTools. The size of each bin was set at 1bp and the coverage was normalized by Reads Per Kilobase per Million mapped reads (RPKM).
Scores for each gene were calculated by computeMatrix command. The gene bodies were scaled to 3kb and the region between 1kb upstream to TSS and 1.5kb downstream of TES were included in the analysis.
Assembly: mm10
Supplementary files format and content: bigwig

source_name: Embryos

growth_protocol: 10% FBS in DMEM

extract_protocol:
Cells were treated with IAA at 0.5mM for 6 hours, if indicated, and then fixed with 1% formaldehyde for 10 minutes. After quenching and cell lysis, chromatin was fragmented with micrococcal nuclease and immunoprecipitated with Pol II or flag antibodies.
ChIP-seq libraries were prepared using the KAPA Hyperprep Library Preparation Kit complemented with Roche SeqCap Adapter Kit A.  Post amplification libraries were size selected at 0.7-0.9X using Kapa cleanup beads. Libraries were validated using the Agilent High Sensitivity DNA Kit.

value: Embryos

tag: cell line

value: Mouse Embryonic Fibroblasts (MEFs)

value: Fibroblasts

tag: chip antibody

value: Pol II (8wg16, Santa Cruz #56767)

value: Nelfb f/-

value: Nelfb f/-; Ad-Cre; Day 7; Pol II ChIP


title: MEFs, NELFB-AID, Myr-AKT1, +IAA, spike-in, Pol II ChIP-seq, biol rep 1

value: Nelfb -/-; NELFB-AID

value: pLenti-NELFB-AID; pCDH-osTIR1-mCherry; Ad-Cre; single clone isolation; pWZL-Myr-AKT1; +IAA; Spike-in; Pol II ChIP


title: MEFs, NELFB f/-, Ad-GFP; Pol II ChIP-seq, biol rep 1

value: Nelfb f/-; Ad-GFP; Day 7; Pol II ChIP


title: MEFs, NELFB-AID, Myr-AKT1, +IAA, spike-in, Pol II ChIP-seq, biol rep 2


title: MEFs, NELFB f/-, Ad-Cre; Pol II ChIP-seq, biol rep 2


title: MEFs, NELFB-AID, NELFB, +IAA, spike-in, Pol II ChIP-seq, biol rep 1

value: pLenti-NELFB-AID; pCDH-osTIR1-mCherry; Ad-Cre; single clone isolation; pLenti-NELFB; +IAA; Spike-in; Pol II ChIP


title: MEFs, NELFB-AID, EV, +IAA, spike-in, Pol II ChIP-seq, biol rep 2

value: pLenti-NELFB-AID; pCDH-osTIR1-mCherry; Ad-Cre; single clone isolation; pLenti-EV; +IAA; Spike-in; Pol II ChIP


title: MEFs, NELFB-AID, NELFB, +IAA, spike-in, Pol II ChIP-seq, biol rep 2


title: MEFs, NELFB f/-, Ad-GFP; Pol II ChIP-seq, biol rep 2


title: MEFs, NELFB-AID, Myr-AKT1, +IAA, spike-in, Pol II ChIP-seq, biol rep 3


title: MEFs, NELFB-AID, EV, +IAA, spike-in, Pol II ChIP-seq, biol rep 3


title: Dep24 (learned helpless in the acute paradigm)

city: Miami

first: Eleonore

last: Beurel

address: 1011 NW 15th Street Gautier room 415

department: Psychiatry

institute: University of Miami, Miller School of Medicine

data_processing:
Single-cell transcriptome sequencing raw reads were processed using 10X Genomics CellRanger (v2.2.0 for Dep24 and ND24, and v3.0.1 for others) pipeline
Count matrix was processed using Seurat (v2.3.4) R package for normalization, batch effect correction, dimensionality reduction and clustering
All the 6 individual samples were merged (using Seurat’s merge function) and further to correct unwanted technical variations, number of UMIs/cell and the 10x run of the sample (3 in total) were regressed out.
Cell-type annotation was carried out using Garnett (v0.2.11) R package using marker genes listed in the manuscript
Genome_build: mm10
Supplementary_files_format_and_content: CountMatrix-raw.tsv.gz: Raw count matrix (genes in rows and cells in columns)
Supplementary_files_format_and_content: CountMatrix-normalized.tsv.gz: Raw count matrix (genes in rows and cells in columns)
Supplementary_files_format_and_content: CellMetadata.tsv: Each cells additional processed information, TSNE coordinates and cell type annotation [only for post-filtered cells]

source_name: hippocampus

extract_protocol:
Immediately after learned helplessness, mice were anesthetized, spleens were recovered, and mice were transcardially perfused with PBS. Briefly, the hippocampi were dissected excluding meninges and choroid plexus, passed through a 70 μm cell strainer (BD Bioscience) and the cell suspension was mixed (vol/vol) to obtain a 30% Percoll/R1 medium [RPMI 1640 medium (Corning) supplemented with 1% FBS (Gibco), 100 IU/mL penicillin (Gibco), 100 μg/mL streptomycin (Gibco), 1 x non-essential amino acids (Gibco), 1 μM sodium pyruvate (Gibco), 2.5 μM β-mercaptoethanol (Sigma) and 2 mM L-glutamine (Gibco)]. The cellular suspension was overlaid on 70% Percoll/R1 medium in a centrifuge tube, and centrifuged at 2000 rpm for 20 min without using the brake. The cells at the interface of the 30/70% Percoll gradient were recovered, washed once, resuspended in R10 medium. For cell sorting, cells were stained for 30 min with FITC-conjugated anti-CD45 antibodies (clone 30-F11, ebioscience) and live dead fixable aqua dead cell dye (L34957, Molecular Probes), and sorted on a FACS Aria II, to recover CD45+Live dead- cells.
The libraries were prepared using the Chromium Single cell 5’ Library & Gel Bead Kit v1.0 and the Chromium Single Cell A Chip kit (10X Genomics) according to the manufacturer’s instructions, and run on an Illumina NextSeq 500.

treatment_protocol: Acute paradigm: mice received 180 inescapable footshocks of 0.3 mA, of 6-10 s duration, with 5-45 s rest interval on the first day, and were tested in 30 trials of 24 s. Chronic paradigm: mice received the acute paradigm and were restested weekly for 3 weeks with the second day of escapable foot shocks escapable shocks with 30 s rest interval on the second day.

tag: strain

value: learned helpless in the acute paradigm

value: brain

tag: region

value: Hippocampus

value: sorted Live CD45+ cells


title: MEFs, NELFB-AID, EV, +IAA, spike-in, Pol II ChIP-seq, biol rep 1


title: NS (non shocked)

value: non shocked


title: ND24 (non-learned helpless in the acute paradigm)


title: PBS_3

city: Basel

first: DBM Bioinformatics

last: Core Facility

state: BS

address: Hebelstrasse 20

department: Departement of Biomedicine

country: Switzerland

institute: University of Basel

data_processing:
Single-cell sequencing files (basecalls) were processed using the Cell Ranger Single Cell Software Suite (v2.2.0) to perform quality control, sample de-multiplexing, barcode processing, alignment to mm10 genome with STAR (version 2.6.1a), and read counting on Ensembl 84 gene model (https://support.10xgenomics.com/single-cell-gene-expression/software/overview/welcome).
Default parameters were used for Cell Ranger, except for the STAR parameters outSAMmultNmax set to 1 and alignIntronMax set to 10000.
UMI were counted by extracting read counts from the .h5 files generated by Cell Ranger, using R (v3.5.1). The UMI matrix was filtered to keep only cells with a count of at least 100 genes detected, and not likely to be empty droplets based on the emptyDrops function of the dropletUtils Bioconductor package (version 1.2.2). We retained a total of 6,954 cells (28,692 genes). The UMI counts matrix is provided as file UMIsMatrix.txt.gz.
Further quality controls and analyses were performed using the scran (11.10.2) and scatter (1.10.1) Bioconductor packages, and following the simpleSingleCell  Bioconductor workflow. The filtered dataset used for further analyses included expression values for 12,182 genes for 4,612 cells.
Genome_build: mm10
Supplementary_files_format_and_content: TSV file (tab separated values) with raw UMI counts for ensembl release 84 gene models; columns correspond to: 1. ENSEMBL ID, 2. and remaining columns contain UMI counts for each cell; column headers include the cell barcode sequence and the sample ID separated by a dash (e.g., "AAAAAAAAAAAAAAAT-DEP_11")

source_name: colon monocytes and macrophages from control (PBS-treated) mouse

growth_protocol: Mice were ordered from Charles River Laboratories (Germany) and kept in the animal facility of the Department of Biomedecine, University of Basel, Switzerland, under SPF conditions.

extract_protocol:
Single cells were extracted from suspensions of lamina propria of each individual mouse replicate.
Cells were sorted by flow cytometry (using a FACSAria III, BD Biosciences) and gated for Cd11b+, and Ly6c2+ or Cd64+ expression.
Sorted cell suspensions from each mouse were loaded into a single well of a 10× Genomics Chromium Single Cell Controller.
Single-cell capture and cDNA and library preparation were performed with a Single Cell 3’ v2 Reagent Kit (10× Genomics) according to manufacturer’s instructions.

treatment_protocol: Mice were orally gavaged 5 days a week for approximately 6 months with either 12ug diesel exhaust particles (DEP) disolved in 200uL PBS, or only PBS as control.

value: monocytes and macrophages

value: male


title: ND4w (nonlearned helpless in the chronic paradigm)


title: R4w (recovered, mice were learned helpless and stop being learned helpless overtime)


title: NR4w (non recovered)

value: non recovered


title: PBS_2


title: DEP_13

source_name: colon monocytes and macrophages from DEP-treated mouse


title: DEP_11


title: MEFs, NELFB-AID, NELFB, +IAA, spike-in, Pol II ChIP-seq, biol rep 3

value: Embryos

value: Mouse Embryonic Fibroblasts (MEFs)

value: Fibroblasts


title: DSS 3

first: Zhang

last: RuiBin

address: No. 37, Shi Er Qiao Road, JinNiu District

institute: chengdu university of traditional chinese medicine

description: DSS 3_Count

data_processing:
Oxford Nanopore Technologies Long Read Processing
As a first step, the original reads were filtered to select those with a minimum mean quality score of 7 and a minimum length of 500 bases.
Then, we mapped ribosomal RNA to the rRNA database and discarded it. After looking for primers on both ends of each read, FLNC (full-length, non-chimeric) transcripts were identified and mapped to the reference genome by MIMimap2.
Consensus subtypes were obtained by polishing within each cluster by Pinfish. By using GFFCompare, transcripts were validated against reference transcript annotations.
Assembly: mm10
Supplementary files format and content: tab-delimited text files include gene COUNTS values for each Sample

source_name: colon

extract_protocol:
Total RNA was extracted from the tissue using TRIzol reagent (Takara, Kyoto, Japan) according to the manufacturer’s instructions. RNA purity was tested using the Nano Photometer spectrophotometer (IMPLEN, Westlake Village, USA).
cDNA libraries were constructed from 1 μg of total RNA by using a cDNA-PCR Sequencing Kit (SQKPCS109) according to the protocol. Briefly, the reverse transcriptase was used to enrich full-length cDNAs and added defined PCR adapters to both ends of the first-strand of cDNA and following cDNA PCR for 14 circles with LongAmp Tag DNA polymerase (New England Biolabs, Ipswich, MA, USA) (8 min for elongation time). The PCR products were then subjected to ONT adaptor ligation using T4 DNA ligase (New England Biolabs, Ipswich, MA, USA). Agencourt XP beads (Beckman Coulter, Brea,USA) were used for DNA purification. The final cDNA libraries were subjected to FLOMIN109 flow cells and analyzed on a PromethION platform at Biomarker Technology Company (Beijing, China).

treatment_protocol:
We divided the mice into a control, dextran sodium sulfate (DSS), and DSS combined with the EA (DSS + EA) groups.
In the DSS and DDS + EA groups, mice were given 2.5% DSS (MP Biomedicals, California, USA) in drinking water for 7 days whereas the control group received distilled water.
After 5 days of UC modeling, mice in the DSS + EA group were treated with EA once a day for 5 days. A custom-made mouse frame was used to hold the animals and both of the Zusanli acupoint points (ST36, located ~3 mm below the capitulum fibulae) were targeted by EA for 30 minutes (2 Hz, 0.2 mA).

value: colon

value: DSS


title: EA ST36 1

description: EA ST36 1_Count

value: DSS + EA


title: EA ST36 2

description: EA ST36 2_Count


title: EA ST36 3

description: EA ST36 3_Count


title: CON 3

description: CON 3_Count

value: Control (water)


title: DSS 2

description: DSS 2_Count


title: DSS 1

description: DSS 1_Count


title: CON 2

description: CON 2_Count


title: CON 1

description: CON 1_Count


title: Ssdp[2082-G4]/+ head RNA, experiment, rep3

city: Doha

first: Safa

last: Salim

state: Qatar

address: 21, Kuwari Building, Khaleel Bin Ahmed Street, Umm-Ghuwailina

country: Qatar

institute: Hamad Bin Khalifa University

data_processing:
The dm6 was used as a reference Drosophila genome. Bowtie2 aligner was used to paired-end reads to the reference transcriptome. Known genes and transcripts were assembled with StringTie based. After assembly, the abundance of gene/transcript was calculated in the read count and normalized values as FPKM (Fragments Per Kilobase of transcript per Million mapped reads) and TPM (Transcripts Per Kilobase Million) for a sample. DEG (Differentially Expressed Genes) analysis was performed on a comparison pair (SSDP_vs_CTL) using DESeq2, genes were selected if they satisfied |fc|>=1.5 & nbinomWaldTest raw p-value<0.05 conditions in a comparison pair (3 SSDP_vs_ 3 CTL).
Assembly: dm6
Supplementary files format and content: Microsoft Excel file, contains significant genes with satisfies |fc|≥1.45 & raw.p<0.05 conditions in at least one of total comparison pairs.

organism: Drosophila melanogaster

source_name: head

extract_protocol:
RNA was extracted from 20 fly heads per sample using TRI reagent. Isolated RNA was stored in 80% ethanol. |RNA was quantified using Qubit 3.0. Further RNA integrity was checked on high sensitivity tape (Agilent TapeStation 2200). Samples with RIN number >8.5 were selected for library construction.
Three w1118 and three Ssdp[2082-G4] /+ samples were used to prepare 100bp paired sequencing library using the TruSeq Stranded mRNA Library prep kit and >40M read per sample were sequenced on an Illumina NovaSeq6000.

value: head

value: 3-4 days


title: w1118 head RNA, control, rep3


title: w1118 head RNA, control, rep2


title: Ssdp[2082-G4]/+ head RNA, experiment, rep2


title: Ssdp[2082-G4]/+ head RNA, experiment, rep1


title: w1118 head RNA, control, rep1


title: maize_leaf, SG200, 6dpi, rep3

city: Cologne

first: Gunther

last: Doehlemann

address: Zuelpicher Str. 47a

country: Germany

institute: University of Cologne

description: 6dpi, SG200, rep3

data_processing:
The Trinity software (v2.9.1) option trimmomatic was used for quality filtering of the paired-end reads.
bowtie2 (2.3.5.1) was used for the mapping of the quality-filtered reads to the reference genome of maize.
The R package Rsubread (v1.34.7) was used to count the mapped reads.
edgeR (3.26.8) was used for the differential gene expression analysis.
Assembly: Combined assembly of Ustilago maydis and Zea mays B73 version 5
Supplementary files format and content: Gzipped text files containing transcript counts for each sample.

organism: Zea mays

source_name: Ustilago maydis-infected leaf

extract_protocol:
RNA was harvested from frozen and homogenized samples using TRIzol reagent (Invitrogen, Darmstadt, Germany). The Turbo DNA-Free Kit from Ambion (Ambion Life TechnologiesTM, Carlsbad, USA) was used to exclude DNA contamination.
Messenger RNA was purified from total RNA using poly-T oligo-attached magnetic beads. After fragmentation, the first strand cDNA was synthesized using random hexamer primers followed by the second strand cDNA synthesis. The library was ready after end repair, A-tailing, adapter ligation, size selection, amplification, and purification.

value: Ustilago maydis-infected leaf

tag: cultivar

value: Golden Bantam

tag: fungal strain

tag: time point


title: maize_leaf, SG200, 6dpi, rep2

description: 6dpi, SG200, rep2


title: maize_leaf, Sts2-ko, 6dpi, rep1

description: 6dpi, Sts2-ko, rep1

value: SG200 Sts2-ko


title: maize_leaf, Sts2-ko, 6dpi, rep3

description: 6dpi, Sts2-ko, rep3


title: maize_leaf, Sts2-ko, 6dpi, rep2

description: 6dpi, Sts2-ko, rep2


title: maize_leaf, SG200, 3dpi, rep3

description: 3dpi, SG200, rep3


title: maize_leaf, SG200, 3dpi, rep2

description: 3dpi, SG200, rep2


title: maize_leaf, Sts2-ko, 3dpi, rep2

description: 3dpi, Sts2-ko, rep2


title: maize_leaf, SG200, 3dpi, rep1

description: 3dpi, SG200, rep1


title: maize_leaf, Sts2-ko, 3dpi, rep3

description: 3dpi, Sts2-ko, rep3


title: maize_leaf, SG200, 6dpi, rep1

description: 6dpi, SG200, rep1


title: maize_leaf, Sts2-ko, 3dpi, rep1

description: 3dpi, Sts2-ko, rep1


title: maize_leaf, mock, 6dpi, rep3

description: 6dpi, mock, rep3

source_name: leaf

value: leaf

value: mock (water)


title: maize_leaf, mock, 6dpi, rep2

description: 6dpi, mock, rep2


title: maize_leaf, mock, 3dpi, rep3

description: 3dpi, mock, rep3


title: maize_leaf, mock, 3dpi, rep1

description: 3dpi, mock, rep1


title: maize_leaf, mock, 3dpi, rep2

description: 3dpi, mock, rep2


title: maize_leaf, mock, 6dpi, rep1

description: 6dpi, mock, rep1


title: HCC816pre

city: Kanagawa

first: Satoko

last: Takizawa

state: Kamakura

institute: Toray Industries, Inc.

hyb_protocol: Hybridized for 16 h at 32 C with rotary shake (250 rpm). Hybridization buffer and washing protocol was followed by the protocol supplied by TORAY Industries, Inc..

scan_protocol: 3D-Gene Scanner ((Toray Industries Inc., Tokyo, Japan) was used for scanning. Images were quantified using Extraction(Toray Industries Inc., Tokyo, Japan).

data_processing: The raw data of each spot was normalized by substitution with a mean intensity of the background signal determined by all blank spots’ signal intensities of 95%

source_name: serum

label_protocol: Extracted total RNA was labeled with Cy5 using the 3D-Gene miRNA labeling kit (Toray Industries Inc., Tokyo, Japan).

growth_protocol: Serum was collected from the blood.

extract_protocol: Total RNA from serum was extracted commercially available kit (miReasy mini kit (Qiagen)).

treatment_protocol: Blood was collected before surgical treatment.

tag: disease/diagnosis

value: hepatocellular carcinoma

tag: sample collection time

value: before operation

tag: molecule subtype

value: miRNA


title: HCC818pre


title: ICC824pre

value: Cholangiocellular carcinoma


title: HCC815pre


title: HCC817pre


title: AB12_Subject 12 adenomyosis baseline [miRNA_seq]

data_processing:
Bioinformatic analyses were performed using Partek Flow Genomic Analysis Software (Partek, St. Louis, Missouri, USA).
Sequenced raw FASTQ files were trimmed for adapters and contaminants such as ribosomal DNA, mitochondrial DNA respectively.
Trimmed reads were mapped to the reference genome hg38 using STAR aligner.
Mapped reads were further filtered and quantified to transcripts and genes using hg38 assembly and Ensemble transcripts release 99 for mRNA nad miRbase v22 for miRNA.
Genome_build: hg38
Supplementary_files_format_and_content: Filtered Gene Counts in a txt format

source_name: Endometrial Biopsy

extract_protocol:
Total RNA was extracted from tissue stored in RNA later using RNeasy total RNA Kit (Qiagen, Hilden, Germany) as per the manufacturer protocol.
cDNA library was constructed using well established Smart-seq2 protocol (Picelli et al. 2013, Picelli et al. 2014), tagmentation step was accomplished using Nextera XT kit (Illumina) , miRNA sequencing was performed as per the Hagemann et al 2018 protocol and sequencing was done in Illumina NextSeq 550® at the bioinformatics expression analysis facility at Karolinska University hospital, Sweden.

tag: subject id

value: Subject 12

tag: subject status

value: diagnosed with diffuse adenomyosis

tag: treatment/time point

value: adenomyosis baseline

value: Endometrial Biopsy


title: HCC813pre


title: HCC812pre


title: HCC814pre


title: HCC811pre


title: HCC810pre


title: HCC800pre


title: HCC809pre


title: ICC808pre


title: HCC802pre


title: HCC804pre


title: HCC807pre


title: HCC806pre


title: HCC803pre


title: HCC798pre


title: HCC799pre


title: HCC801pre


title: ICC805pre


title: HCC795pre


title: ICC797pre


title: HCC792pre


title: ICC796pre


title: HCC794pre


title: HCC791pre


title: HCC790pre


title: HCC785pre


title: HCC786pre


title: ICC783pre


title: HCC787pre


title: ICC777pre


title: ICC779pre


title: HCC780pre


title: HCC775pre


title: HCC778pre


title: HCC761pre


title: HCC753pre


title: HCC764pre


title: HCC774pre


title: HCC752pre


title: HCC763pre


title: HCC766pre


title: HCC769pre


title: HCC788pre


title: HCC789pre


title: ICC768pre


title: HCC748pre


title: HCC740pre


title: HCC742pre


title: HCC733pre


title: ICC762pre


title: HCC732pre


title: HCC738pre


title: HCC737pre


title: HCC722pre


title: HCC726pre


title: HCC739pre


title: HCC720pre


title: HCC751pre


title: HCC721pre


title: HCC736pre


title: HCC717pre


title: HCC730pre


title: HCC718pre


title: HCC716pre


title: HCC735pre


title: HCC707pre


title: ICC712pre


title: ICC708pre


title: HCC711pre


title: HCC706pre


title: HCC705pre


title: HCC703pre


title: HCC713pre


title: HCC715pre


title: ICC694pre


title: HCC714pre


title: HCC709pre


title: HCC699pre


title: HCC690pre


title: HCC688pre


title: HCC700pre


title: HCC704pre


title: HCC687pre


title: HCC684pre


title: HCC674pre


title: HCC678pre


title: HCC702pre


title: HCC679pre


title: HCC697pre


title: HCC750pre


title: HCC689pre


title: HCC691pre


title: HCC692pre


title: HCC673pre


title: HCC685pre


title: HCC682pre


title: HCC680pre


title: HCC661pre


title: HCC683pre


title: HCC660pre


title: HCC657pre


title: HCC654pre


title: HCC665pre


title: HCC659pre


title: HCC650pre


title: HCC653pre


title: HCC655pre


title: HCC652pre


title: HCC676pre


title: HCC664pre


title: HCC649pre


title: ICC666pre


title: HCC648pre


title: HCC662pre


title: HCC670pre


title: HCC671pre


title: HCC647pre


title: HCC642pre


title: HCC639pre


title: HCC638pre


title: HCC644pre


title: HCC643pre


title: HCC645pre


title: HCC641pre


title: HCC631pre


title: HCC632pre


title: HCC637pre


title: HCC633pre


title: HCC646pre


title: HCC622pre


title: HCC628pre


title: HCC625pre


title: ICC614pre


title: HCC617pre


title: HCC618pre


title: ICC619pre


title: HCC611pre


title: ICC616pre


title: HCC612pre


title: HCC613pre


title: HCC604pre


title: HCC609pre


title: HCC607pre


title: HCC606pre


title: HCC608pre


title: HCC601pre


title: HCC600pre


title: HCC602pre


title: HCC590pre


title: HCC592pre


title: ICC597pre


title: ICC594pre


title: HCC588pre


title: HCC580pre


title: HCC568pre


title: HCC571pre


title: HCC575pre


title: HCC593pre


title: HCC591pre


title: HCC583pre


title: HCC553pre


title: ICC551pre


title: ICC536pre


title: HCC509pre


title: ICC534pre


title: HCC545pre


title: HCC508pre


title: HCC510pre


title: HCC515pre


title: HCC497pre


title: HCC505pre


title: HCC496pre


title: HCC494pre


title: HCC472pre


title: HCC476pre


title: HCC538pre


title: HCC434pre


title: ICC443pre


title: HCC488pre


title: HCC449pre


title: HCC460pre


title: ICC407pre


title: HCC415pre


title: HCC399pre


title: HCC420pre


title: ICC404pre


title: HCC394pre


title: ICC424pre

value: Gall bladder cancer


title: HCC423pre


title: HCC467pre


title: ICC409pre


title: HCC380pre


title: HCC349pre


title: HCC334pre


title: ICC336pre


title: HCC296pre


title: ICC298pre


title: ICC283pre


title: ICC279pre


title: ICC285pre


title: ICC278pre


title: ICC267pre


title: HCC355pre


title: HAP1_IFNG4h_SnxB_Rep3

city: COLUMBIA

first: HAO

last: JI

state: SC

address: 715 SUMTER ST CLS RM 109

department: College of Pharmacy

institute: University of South Carolina

description:
Pre-treated with 1uM Senexin B for 1 hour and then treated with 10ng/mL IFN-gamma (with Presence of Senexin B) for 4 hours.
S12

data_processing:
Indexed sequences were checked quality by Fastqc.
Indexed sequences were trimmed adaptor sequence by TrimGalore-0.4.5.
Reads were mapped to the hg38 reference genome using STAR | version 2.7.2 with default parameters (generation of sam files).
Convert .sam files to .bam files using samtools | version: 1.5 with parameters -bh -F 3840 -q 255.
Read counts over annotated genes were obtained using featureCount (subreads | version: 1.5.3) with parameters -p -B -M -O --fraction -T 10.
Assembly: GRCh38.98
Supplementary files format and content: HAP1_IFNG_SnxB_geneCounts.txt: Tab-delimited text file includes gene counts for each sample.

source_name: HAP-1 cells treated with 10ng/mL IFNG (with presence of 1µM Senexin B) for 4 hours, biological replicate-#3

growth_protocol: HAP-1 cells were grown in DMEM (High-glucose) media with 10% FBS, 1% penicillin-streptomycin and 2 mM L-glutamine. The cells were plated in 12-well plate at the density of 3x10^5 cells per well. 24 hours post seeding, cells were treated as indicated.

extract_protocol:
Total RNA was extracted using RNeasy Mini Kit (Qiagen) and RNA quality was validated on RNA-1000 chip using Bioanalyzer (Agilent).
Sequencing libraries were generated using NEBNext Ultra II Directional RNA Library prep Kit.

treatment_protocol: Cells were pre-treated with vehicle control (0.1% DMSO) or 1 μM Senexin B for 1 hour, and then treated with or without 10ng/mL IFN-gamma for 4 hours.

value: 1uM Senexin B for 1 hour, then 10ng/mL IFN-gamma (with presence of Senexin B) for 4 hours


title: CSC

city: Beijing

first: Yang

last: gu

address: 15 Datun Road

institute: institute of biophysics

data_processing:
A propriety Sub-pixel Registration algorithm developed by MGI was used for base call.
This project uses the filtering software SOAPnuke developed by BGI independently for filtering. The specific steps are as follows:
1) Remove the reads containing the adaptor(adaptor pollution);
2) Remove reads whose N content is greater than 5%;
3) Remove low-quality reads (we define reads with bases with a quality score less than 10 as the proportion of total bases in the reads that are greater than 20% as low-quality reads).
The filtered "Clean Reads" are saved in FASTQ format.
Bowtie2 was used to map the clean reads to the reference gene sequence (transcriptome), and then RSEM was used to calculate the gene expression level of each sample.
The DEseq2 was used to perform differential expression analysis.DESeq2: Qvalue (Adjusted Pvalue) <= 0.05
Assembly: GCF_000001405.39_GRCh38.p13
Supplementary files format and content: Matrix table with raw gene counts and FPKM values for each gene and each sample.

source_name: liver tumor

extract_protocol:
RNA was harvested using RNAprep Pure Micro Kit (Tiangen). 1.5 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries were constructed using MGIEasy RNA Library Prep Kit V3.0 (MGI-tech) following manufacturer's protocols.

value: liver tumor

value: HCC sample

tag: cell type

value: non liver cancer stem cells

value: WT


title: NC

tag: tissue

value: liver cancer stem cells


title: ICC244pre


title: HAP1_IFNG4h_SnxB_Rep2

description:
Pre-treated with 1uM Senexin B for 1 hour and then treated with 10ng/mL IFN-gamma (with Presence of Senexin B) for 4 hours.
S11

source_name: HAP-1 cells treated with 10ng/mL IFNG (with presence of 1µM Senexin B) for 4 hours, biological replicate-#2


title: ICC314pre


title: ICC229pre


title: HCC258pre


title: HAP1_IFNG4h_SnxB_Rep1

description:
Pre-treated with 1uM Senexin B for 1 hour and then treated with 10ng/mL IFN-gamma (with Presence of Senexin B) for 4 hours.
S10

source_name: HAP-1 cells treated with 10ng/mL IFNG (with presence of 1µM Senexin B) for 4 hours, biological replicate-#1


title: ICC179pre


title: HAP1_IFNG_4h_Rep3

description:
Pre-treated with 0.1% DMSO for 1 hour and then treated with 10ng/mL IFN-gamma for 4 hours.
S9

source_name: HAP-1 cells treated with 10ng/mL IFNG for 4 hours, biological replicate-#3

value: 0.1% DMSO for 1 hour, then 10ng/mL IFN-gamma for 4 hours


title: ICC169pre


title: HAP1_SnxB_5h_Rep3

description:
Treated with 1uM Senexin B for 5 hours.
S6

source_name: HAP-1 cells treated with 1μM Senexin B for 5 hours, biological replicate-#3

value: 1uM Senexin B for 5 hours


title: ICC077pre


title: HAP1_SnxB_5h_Rep2

description:
Treated with 1uM Senexin B for 5 hours.
S5

source_name: HAP-1 cells treated with 1μM Senexin B for 5 hours, biological replicate-#2


title: ICC172pre


title: HAP1_IFNG_4h_Rep1

description:
Pre-treated with 0.1% DMSO for 1 hour and then treated with 10ng/mL IFN-gamma for 4 hours.
S7

source_name: HAP-1 cells treated with 10ng/mL IFNG for 4 hours, biological replicate-#1


title: HCC026pre-2

value: hepatocellular carcinoma

value: before operation at 2nd recurrence


title: HAP1_SnxB_5h_Rep1

description:
Treated with 1uM Senexin B for 5 hours.
S4

source_name: HAP-1 cells treated with 1μM Senexin B for 5 hours, biological replicate-#1


title: HAP1_IFNG_4h_Rep2

description:
Pre-treated with 0.1% DMSO for 1 hour and then treated with 10ng/mL IFN-gamma for 4 hours.
S8

source_name: HAP-1 cells treated with 10ng/mL IFNG for 4 hours, biological replicate-#2


title: ICC004pre

value: before operation

value: miRNA


title: HCC013pre


title: ICC213pre

value: Cholangiocellular carcinoma


title: HCC051pre-2


title: HAP1_Ctrl_5h_Rep3

description:
Treated with 0.1% DMSO (vehicle conTrol) for 5 hours.
S3

source_name: HAP-1 cells treated with vehicle control (0.1% DMSO) for 5 hours, biological replicate-#3

value: 0.1% DMSO (vehicle control) for 5 hours


title: HAP1_Ctrl_5h_Rep2

description:
Treated with 0.1% DMSO (vehicle conTrol) for 5 hours.
S2

source_name: HAP-1 cells treated with vehicle control (0.1% DMSO) for 5 hours, biological replicate-#2


title: HM cell line

city: Chang Sha

first: Qi

last: Wang

state: Other (Non U.S.)

address: Tongzipo Road

institute: The Third Xiangya Hospital of Central South University

hyb_protocol: 1 μg of each labeled cRNA was fragmented by adding 5 μl 10 × Blocking Agent and 1 μl of 25 × Fragmentation Buffer, then heated the mixture at 60 °C for 30 min, finally 25 μl 2 × Hybridization buffer was added to dilute the labeled cRNA. 50 μl of hybridization solution was dispensed into the gasket slide and assembled to the circRNA expression microarray slide. The slides were incubated for 17 hours at 65°C in an Agilent Hybridization Oven.

scan_protocol: The hybridized arrays were washed, fixed and scanned using the Agilent Scanner G2505C.

data_processing: Agilent Feature Extraction software (version 11.0.1.1) was used to analyze acquired array images. Quantile normalization and subsequent data processing were performed using the R software package.Differentially expressed circRNAs between groups was screened by fold change and P-value.

source_name: The human melanocytes HM

label_protocol: Sample labeling and array hybridization were performed according to the manufacturer’s protocol (Arraystar Inc.). Briefly,circRNA weretreated with Rnase R (Epicentre, Inc.) to remove linear RNAs. Then, each sample was amplified and transcribed into fluorescent cRNA utilizing a random priming method (Arraystar Super RNA Labeling Kit; Arraystar). The labeled cRNAs were purified by RNeasy Mini Kit (Qiagen). The concentration and specific activity of the labeled cRNAs (pmol Cy3/μg cRNA) were measured by NanoDrop ND-1000.

extract_protocol: Total RNA was extracted from the cells using the RNA extraction kit according to the manufacturer's instructions and examined by 1% agarose gel electrophoresis.The purity and concentration of total RNA samples were determined with NanoDrop ND-1000.

treatment_protocol: The cells were incubated with Dulbecco's modified Eagle's medium containing 10% fetal bovine serum in a 5% CO2 incubator at 37˚C.

value: melanocytes

value: HM


title: HAP1_Ctrl_5h_Rep1

description:
Treated with 0.1% DMSO (vehicle conTrol) for 5 hours.
S1

source_name: HAP-1 cells treated with vehicle control (0.1% DMSO) for 5 hours, biological replicate-#1


title: WM451 melanoma cell line

source_name: the high-metastatic melanoma cell line WM451

value: high-metastatic melanoma


title: WM35 melanoma cell line

source_name: the low-metastatic melanoma cell line WM35

value: low-metastatic melanoma


title: HEK293_PMA2h_SnxB_Rep3

description:
Pre-treated with 1μM Senexin B for 1 hour and then treated with 30nM PMA (with Presence of Senexin B) for 2 hours.
S12

data_processing:
Indexed sequences were checked quality by Fastqc.
Indexed sequences were trimmed adaptor sequence by TrimGalore-0.4.5.
Reads were mapped to the hg38 reference genome using STAR | version 2.7.2 with default parameters (generation of sam files).
Convert .sam files to .bam files using samtools | version: 1.5 with parameters -bh -F 3840 -q 255.
Read counts over annotated genes were obtained using featureCount (subreads | version: 1.5.3) with parameters -p -B -M -O --fraction -T 10.
Assembly: GRCh38.98
Supplementary files format and content: HEK293_PMA2h_SnxB_geneCounts.txt: Tab-delimited text file includes gene counts for each sample.

source_name: HEK293 cells treated with 30nM PMA (with presence of 1µM Senexin B) for 2 hours, biological replicate-#3

growth_protocol: HEK293 cells were grown in DMEM (High-glucose) media with 10% FBS, 1% penicillin-streptomycin and 2 mM L-glutamine. The cells were plated in 12-well plate at the density of 3x10^5 cells per well. 24 hours post seeding, cells were treated as indicated.

treatment_protocol: Cells were pre-treated with vehicle control (0.1% DMSO) or 1 μM Senexin B for 1 hour, and then treated with 30nM PMA for 2 hours.

value: HEK293 (ATCC)

value: 1uM Senexin B for 1 hour, then 30nM PMA (presence of Senexin B) for 2 hours


title: HEK293_PMA2h_SnxB_Rep2

description:
Pre-treated with 1μM Senexin B for 1 hour and then treated with 30nM PMA (with Presence of Senexin B) for 2 hours.
S11

source_name: HEK293 cells treated with 30nM PMA (with presence of 1µM Senexin B) for 2 hours, biological replicate-#2


title: HEK293_PMA2h_SnxB_Rep1

description:
Pre-treated with 1μM Senexin B for 1 hour and then treated with 30nM PMA (with Presence of Senexin B) for 2 hours.
S10

source_name: HEK293 cells treated with 30nM PMA (with presence of 1µM Senexin B) for 2 hours, biological replicate-#1


title: HEK293_PMA2h_Rep2

description:
Pre-treated with 0.1% DMSO for 1 hour and then treated with 30nM PMA for 2 hours.
S8

source_name: HEK293 cells treated with 30nM PMA for 2 hours, biological replicate-#2

value: 0.1% DMSO for 1 hour, then 30nM PMA for 2 hours


title: HEK293_PMA2h_Rep3

description:
Pre-treated with 0.1% DMSO for 1 hour and then treated with 30nM PMA for 2 hours.
S9

source_name: HEK293 cells treated with 30nM PMA for 2 hours, biological replicate-#3


title: HEK293_SnxB_3h_Rep3

description:
Treated with 1μM Senexin B for 3 hours.
S6

source_name: HEK293 cells treated with 1μM Senexin B for 3 hours, biological replicate-#3

value: 1uM Senexin B for 3 hours


title: HEK293_SnxB_3h_Rep1

description:
Treated with 1μM Senexin B for 3 hours.
S4

source_name: HEK293 cells treated with 1μM Senexin B for 3 hours, biological replicate-#1


title: HEK293_Ctrl_3h_Rep3

description:
Treated with 0.1% DMSO (vehicle control) for 3 hours.
S3

source_name: HEK293 cells treated with vehicle control (0.1% DMSO) for 3 hours, biological replicate-#3

value: 0.1% DMSO (vehicle control) for 3 hours


title: SHP77 (RNA-Seq)

city: Hefei

first: fengmei

last: chao

state: Anhui

address: East Huanhu road

institute: Anhui Provincial Cancer Hospital

data_processing:
Illumina Bcl2FastQ  software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg19 whole genome using Hisat2 v2.1.0 with default parameters.
HTSeq v0.11.2 was subsequently employed to convert aligned short reads into read counts for each gene model.
Genome_build: Hg19
Supplementary_files_format_and_content: tab-delimited text file includes RPKM/COUNT values for each Sample

source_name: Small cell lung cancer cells

growth_protocol: The cells were cultured on 10cm cell culture dish in 1640 medium supplemented with 10% FBS.

extract_protocol:
Total RNA was isolated from cells using the Magzol Reagent (Magen, China)according to the manufacturer's protocol
The mRNA was enriched by oligo dT according to instructions of NEB Next® Poly(A) mRNA Magnetic Isolation Module (NEB,USA). And then fragmented to approximately 200bp. Subsequently, the RNA fragments were subjected to first strand and second strand cDNA synthesis following by adaptor ligation and enrichment with a low-cycle according to instructions of  NEBNext® Ultra™ RNA Library Prep Kit for Illumina. Libraries were sequenced on the Illumina HiSeq xten with paired-end 150bp following the manufacturer's protocols.

value: Small cell lung cancer cells

tag: cell source

value: Derived from a non-encapsulated primary lung tumor

value: untreated

tag: phenotype

value: Chemoresistance


title: H446 (RNA-Seq)

tag: cell line

value: Derived from metastatic site:pleural effusion

tag: treatment

value: Chemosensitivity


title: HEK293_Ctrl_3h_Rep2

description:
Treated with 0.1% DMSO (vehicle control) for 3 hours.
S2

source_name: HEK293 cells treated with vehicle control (0.1% DMSO) for 3 hours, biological replicate-#2


title: SHP77 (circRNA-Seq)

data_processing:
Illumina Bcl2FastQ  software used for basecalling.
Raw reads were treated with Trimmomatic tools(V0.36) to remove adapters. Following reads quality control:Scan the read with a 4-base wide sliding window, cutting when the average quality per base drops below 15, drop reads which are less than 35% of initiation read length. Then reads quality was inspected using the FastQC software then output statistical result.
Two algorithms, CIRI2 and CIRCexplorer2 were used to detect circRNAs. Reads were mapped to human reference genome GRCh37/ hg19 (http://genome.ucsc.edu/) by BWA-MEM or Tophat, respectively.
Back-spliced junction reads identified in CIRI2 were combined and scaled to RPM (Reads Per Million mapped reads, bwa mem mapping) to quantify every circRNAs.
The total number of reads spanning back-spliced junctions was used as an absolute measure of circRNA abundance.
Genome_build: Hg19
Supplementary_files_format_and_content: tab-delimited text files include RPM values and counts for each Sample

extract_protocol:
Total RNA was isolated from cells using the Magzol Reagent (Magen, China)according to the manufacturer's protocol
Briefly, rRNAs were removed from Total RNA using RiboCop rRNA Depletion Trial kit(LEXOGEN，Australia) , then RNA was treated with RNase R (Epicentre, USA) and fragmented to approximately 200bp. Subsequently, the purified RNA fragments were subjected to first strand and second strand cDNA synthesis following by adaptor ligation and enrichment with a low-cycle according to instructions of NEBNext® Ultra™ RNA Library Prep Kit for Illumina (NEB, USA). Libraries were sequenced on the Illumina HiSeq xten with paired-end 150bp following the manufacturer's protocols.


title: H1-D1-Input

city: Guangzhou

first: Weisheng

last: Cheng

address: 2nd Zhongshan Road

institute: Sun yat-sen University

data_processing:
Illumina Casava software used for basecalling.
Raw ChIP-seq sequenced reads were trimmed for adapters and low sequencing quality bases using fastp
BWA was used to map the 150 bp paired-end reads to the GRCh38/hg38 Homo sapiens reference genome
Mark duplicates by Picard and remove duplicates.
The SPP program was used to call peaks, and an IDR-based strategy was used to identify stable peaks across pseudo-replicates.
Genome_build: hg38
Supplementary_files_format_and_content: peak text file

source_name: human embryonic stem cells

extract_protocol:
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.
Libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit. ChIP-seq libraries were generated and sequenced an Illumina HiSeq X Ten with 150 bp paired-end reads by Novogene.

value: human embryonic stem cells (hESCs)

tag: differentiation time

tag: chip antibody


title: H446 (circRNA-Seq)


title: HEK293_SnxB_3h_Rep2

description:
Treated with 1μM Senexin B for 3 hours.
S5

source_name: HEK293 cells treated with 1μM Senexin B for 3 hours, biological replicate-#2


title: HC3

city: Tianjin

first: Chenchen

state: Tianjin

address: Nanjing Road 288

institute: State key laboratory of Experimental Hematology

data_processing:
Raw sequencing data was demultiplexed based on the cell-specific barcode sequences in read2 of paired-end reads. UMI sequences were extracted from read2 and assigned to paired read1 sequences by Perl script
Sequenced reads were trimmed for adaptor sequence using Trim Galore (version 0.4.4_dev; http://www.bioinformatics.babraham.ac.uk/projects/trim_galore/).
Then the clean reads were aligned to the human reference genome (GRCh38) using STAR 4 (version 2.5.3a) with the known gene annotation (Gencode v27). Gene expression levels were quantified based on the UMIs after removing duplicated reads using HTSeq 5 (version 0.9.1)
Genome_build: GRCh38
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and all sample. Cell IDs include patient diagnosis (HD = healthy, DBA = DBA) and cell type: 'B' are BFU-E cells and 'C' are CFU-E cells. e.g., L27-HD7-C289 = library 27- healthy control- CFU -cell.
Supplementary_files_format_and_content: Barcode list used for single cell RNA-seq library construction

source_name: BFU-E and CFU-E cells

extract_protocol:
BM mononuclear cells (BMMNC) were isolated by HISTOPAQUE® (Sigma, Cat# 10771) density gradient centrifugation
The single cells were obtained by a mouth pipette from sorted, bulk BFU-E and CFU-E cells.Sequencing libraries were constructed following a modified Smart-seq2 protocol as previously reported(Li et al., 2017); After RT and 18 cycles of PCR amplification, 3ml aliquots from each single cell cDNA-amplicon was pooled and purified using DNA Clean & Concentrator™ kit (ZYMO research, Cat# D4014) and AMPure XP Beads (Beckman, Cat# A63882). Library preparation was performed using 2X KAPA HiFi HotStart ReadyMix kit after biotin-indexing PCR.

value: Bone marrow

tag: diagnosis

value: mixed sample (healthy and DBA)


title: H1-D1-ATF4


title: HEK293_PMA2h_Rep1

description:
Pre-treated with 0.1% DMSO for 1 hour and then treated with 30nM PMA for 2 hours.
S7

source_name: HEK293 cells treated with 30nM PMA for 2 hours, biological replicate-#1


title: A_T_VIRENS_96H-3

city: SAN LUIS POTOSI

first: Cesaré

last: Ovando-Vázquez

state: SAN LUIS POTOSI

address: Camino a la Presa de San José 2055. Lomas 4 sección

department: CNS

country: Mexico

institute: CONACyT IPICyT

data_processing:
Mapping of the fragments was carried out using the HISAT2 software with default parameters
Mapped fragments were quantified with the featureCounts tool from the SubRead package
The differential gene expression analysis was performed with the edgeR package 57 using the count matrix. Normalization factors and variability were calculated with the calcNormFactors(x) and estimateDisp(x) functions respectively. Subsequently, the data were fitted with the function glmFit(x)
Assembly: TAIR10 + Trichoderma_atroviride_imi_206040_gca_000171015.TRIAT_v2.0 + Trichoderma_virens.ASM17099v1
Supplementary files format and content: counts.tab = Raw counts
Supplementary files format and content: cpm.tab = Counts per million

organism: Arabidopsis thaliana

source_name: leaf

growth_protocol: Columbia ecotype (Col-0) of Arabidopsis thaliana plants,      T. atroviride (IMI206040) and T. virens fungus as colonizing were used in this study. Trichoderma spp was grown in potato dextrose agar (PDA) (Becton, Dickinson and company) and incubated at 28°C under 12/12 light/dark cycles.

extract_protocol:
Briefly, frozen samples were macerated in extraction buffer. The cell lysate was carried out using the cationic detergent hexadecyltrimethylammonium bromide (CTAB). The recovery of the organic phase was carried out with 150 μL of phenol pH 8, and chloroform-isoamyl alcohol (24:1). Finally, the DNA was precipitated with isopropanol at -20 °C overnight. RNA integrity was visualized by agarose gel electrophoresis [0.8%] under denaturing conditions
To remove contaminating DNA, the samples were treated with DNAse using the commercial kit TURBO DNA-free™ KIT. RNA was quantified in an Epoch Microplate Spectrophotometer  at an OD of 260 and 280 nm (nanometers). RNA integrity was visualized by denaturing agarose gel electrophoresis [0.8%] and the samples were inspected using Agilent 2100 Bioanalyzer technology. Finally, 27 libraries were generated and sequenced in a paired manner with the illumina Hiseq 2500 technology

treatment_protocol: The 12-day-old Arabidopsis plants were inoculated with T. atroviride or T. virens. Uninoculated plants were used as controls. Subsequently, biological samples were collected at 48, 72, and 96 hours after inoculation (hpi) both for the control groups and for the different interactions.

value: leaf

tag: ecotype

value: T. virens

tag: time


title: A_T_VIRENS_96H-1


title: A_T_VIRENS_72H-2


title: A_T_VIRENS_48H-3


title: A_T_VIRENS_72H-1


title: A_T_VIRENS_48H-2


title: HEK293_Ctrl_3h_Rep1

description:
Treated with 0.1% DMSO (vehicle control) for 3 hours.
S1

source_name: HEK293 cells treated with vehicle control (0.1% DMSO) for 3 hours, biological replicate-#1


title: A_T_VIRENS_72H-3


title: A_T_ATROVI_96H-3

value: T. atroviride


title: A_T_ATROVI_96H-1


title: A_T_ATROVI_96H-2


title: A_T_VIRENS_96H-2


title: A_T_VIRENS_48H-1


title: A_T_ATROVI_72H-3


title: A_T_ATROVI_72H-1


title: A_T_ATROVI_72H-2


title: A_T_ATROVI_48H-3


title: A_T_ATROVI_48H-2


title: A_T_ATROVI_48H-1


title: A_THALIANA_96H-1

value: control


title: A_THALIANA_96H-2


title: A_THALIANA_72H-2


title: A_THALIANA_96H-3


title: A_THALIANA_72H-3


title: A_THALIANA_48H-1


title: A_THALIANA_72H-1


title: A_THALIANA_48H-2


title: A_THALIANA_48H-3


title: C13_NoAgg, biol rep 2

city: Cambridge

first: Lajos

last: Kalmar

address: Tennis Court Road

country: United Kingdom

institute: MRC Toxicology Unit, University of cambridge

data_processing:
SLAM-Seq analysis was done similar to previously reported (T. Neumann, et al., Quantification of experimentally induced nucleotide conversions in high-throughput sequencing datasets. BMC Bioinforma. 20, 258 (2019).
PMID: 31109287
Assembly: GRCm38
Supplementary files format and content: Raw gene counts table for nascent RNA in simple tab separated text format
Supplementary files format and content: Raw gene counts table for total RNA in simple tab separated text format

source_name: cell line

growth_protocol: SIM-A9 cells were maintained in DMEM-F12 that was supplemented with 10% FBS and 5% HS, 2 mM L-glutamine, 100 U/ml penicillin  and 100 ug/ml streptomycin.

extract_protocol:
RNA was harvested using easy-BLUE (iNtRON Biotechnology), under protection from direct light. After conjugating 4SU to iodoacetamide  in a 50 mM pH 8.0 phosphate buffer in DMSO/Water (1:1), the reaction was quenched with DTT and RNA was reprecipitated using ethanol and NaOAc.
Libraries were prepared using Quantseq 3’ mRNA-Seq Library Prep Kit (Lexogen).

treatment_protocol: SIM-A9 cells in culture were treated (by adding reagents in serum-free medium in all cases) with: 10 uM polymixin B (1h) and then either with 10 uM C13 or DMSO (1h). Subsequently, TDP-43- or sham-aggregates were added to 5 ug/mL (2.5 h), followed by addition of 4-thiouridine (S4U) to 100 uM  and further incubation for a further 90 min. (1.5 h).

value: cell line

value: Microglia, Mus musculus

tag: strain

value: C13 1h, Sham 4h (total)


title: DMSO_TDP43, biol rep 2

value: DMSO 1h, TDP43 4h (total)


title: C13_TDP43, biol rep 2

value: C13 1h, TDP43 4h (total)


title: DMSO_TDP43, biol rep 1


title: C13_TDP43, biol rep 1


title: C13_NoAgg, biol rep 1


title: C13_NoAgg, biol rep 3


title: DMSO_NoAgg, biol rep 3

value: DMSO 1h, Sham 4h (total)


title: C13_TDP43, biol rep 3


title: DMSO_NoAgg, biol rep 2


title: PTEN-null (PTEN-Mutant) [1]

city: Pamplona

first: Francisco

last: Exposito

state: Navarra

address: Irunlarrea SN, Research Building

department: Department of Pathology, Anatomy and Physiology, School of Medicine

institute: University of Navarra

data_processing:
Two hundred ng of total RNA were used to generate barcoded RNA-seq libraries using the NEBNext Ultra RNA Library preparation kit (New England Biolabs)
Poly A+ RNA was purified using poly-T oligonucleotides attached to magnetic beads, followed by fragmentation and first and second cDNA strand synthesis.
Libraries were sequenced using a HiSeq2500 equipment (Illumina)
FastQ files for each sample were obtained through the CASAVA v1.8 software (Illumina).
Assembly: mm10
Supplementary files format and content: tab delimited text contains raw counts for each sample

source_name: Lung Squamous cell carcinoma

growth_protocol: Cells were cultured in RPMI 1640 GlutaMAX supplemented with 10% HyClone Fetalclone III (FBS) and 1% penicillin-streptomycin in a humidified atmosphere 5%CO2 and 37ºC.

extract_protocol:
RNA extraction from cell lysates was performed with the NucleoSpin® RNA kit (Macherey-Nagel) and 200ng were use for generating the libraries.
Barcoded RNA-seq libraries using the NEBNext Ultra RNA Library preparation kit (New England Biolabs).

value: Lung Squamous cell carcinoma

tag: genotype

value: Pten Null

value: PTEN CRISPR mutant


title: DMSO_TDP43, biol rep 3


title: PTEN-null (PTEN-Mutant) [2]


title: 9m-input-100-2

first: Mingxue

last: Tan

address: North Campus, Sun Yat-Sen University, No. 74, 2nd Yat-Sen Street, Yuexiu District, Guangzhou City

department: Department of Toxicology

institute: School of Public Health, Sun Yat-sen University

description: Mouse, Liver, Input, CdCl2-100 mg/L, Exposed by drinking water, 9 months

data_processing:
Illumina Bcl2FastQ software used for basecalling.
Adaptor and low-quality bases were trimmed with Trimmomatictools(version:0.36), and the clean reads undergone rRNA deleting through RNAcentral to get effective reads.
Genomic alignment (hg19) was using Tophat(version:2.0.13)to get uniquely mapping reads.
MACS2(version 2.1.0.20151222) was employed to perform m6A peak calling.Then using Hommer (version:4.8) to annotate the m6A Peaks.
The nucleotides in m6A Peaks region were used for detection of the consensus m6A motif by DREME (version:4.11.1) and MEME(version:4.11.1). Motif central enrichment was performed by CentriMo (version:4.11.1). Differential methylation was determined by MetDiff.
Assembly: hg19/mm10/rn6
Supplementary files format and content: tab-delimited text files include TPM/counts for each Sample

source_name: Liver

extract_protocol:
Total RNA was isolated from tissues using the Magzol Reagent (Magen, China) according to the manufacturer’s protocol.
The quantity and integrity of RNA yield was assessed by using the K5500(Beijing Kaiao, China) and the Agilent 2200 TapeStation (Agilent Technologies, USA) separately. m6A antibody immunoprecipitation RNA was quality control with Qubit(Thermo Fisher Scientifc,USA) and Agilent 2200 TapeStation (Agilent Technologies, USA). Briefly, RNA were fragmented to approximately 200bp. Then, the RNA fragments were subjected to first strand and second strand cDNA synthesis following by adaptor ligation and enrichment with a low-cycle according to instructions of NEBNext® Ultra RNA LibraryPrep Kit for Illumina (NEB, USA).

value: Liver

value: WT

value: The exposure dose

value: 9 months


title: Empty-vector GFP (EVGFP-Control)

value: Control non targeting vector


title: 3m-input-100-2

description: Mouse, Liver, Input, CdCl2-100 mg/L, Exposed by drinking water, 3 months

value: 3 months


title: 9m-input-100-3


title: 3m-input-100-1


title: 9m-input-100-1


title: 3m-input-100-3


title: 3m-input-C-2

description: Mouse, Liver, Input, Control, 3 months


title: 9m-input-C-1

description: Mouse, Liver, Input, Control, 9 months


title: 3m-input-C-3

description: Mouse, Liver, Input, Control, 3 months


title: 9m-100-3

description: Mouse, Liver, CdCl2-100 mg/L, Exposed by drinking water, 9 months


title: DMSO_NoAgg, biol rep 1


title: 3m-100-3

description: Mouse, Liver, CdCl2-100 mg/L, Exposed by drinking water, 3 months


title: 3m-100-2


title: 9m-100-2


title: 9m-input-C-2

description: Mouse, Liver, Input, Control, 9 months


title: 3m-C-2

description: Mouse, Liver, Control, 3 months


title: 3m-100-1


title: 9m-C-2

description: Mouse, Liver, Control, 9 months


title: 9m-C-1

description: Mouse, Liver, Control, 9 months


title: 3m-C-3

description: Mouse, Liver, Control, 3 months


title: scRNAseq, patchseq, cortical IN,  33

city: Geneva

first: Denis

last: Jabaudon

state: Geneva

address: Centre Medical Universitaire, Rue Michel Servet 1

department: Department of Basic Neurosciences

institute: Geneva University

description:
PSeq08_IL03_R1.fastq.gz
PSeq_counts.csv
PSeq_33

data_processing:
gene expression counts matrix in csv format containing analyzed cortical upper layers Htr3a-GFP+/Hmx3-Cre;R26tdTOM+ patch-seqINs - samples in columns annotated by their position in C1 chip, genes in rows with gene symbol notation
Sequenced reads were aligned to the mouse genome using the read-mapping algorithm STAR and duplicated reads were corrected using UMI-tools. Non-ambiguously mapped exonic reads were quantified using GenomicAlignments in IntersectionStrict mode.
Cells containing at least 100.000 mapped reads, at least 25% exonically mapped and with less than 15% reads from mitochondrial genome were kept for  analysis.
mm10 v3.0.0.

source_name: somatosensory cortex

extract_protocol:
After whole-cell recording, nuclear and cytoplasmatic RNA from somatosensory cortex Htr3a-GFP+/Hmx3-Cre;R26tdTOM+ cells from mice between P14 and P25 was collected into the recording pipette by applying light suction. Pipette contents were transferred to RNAse-free PCR tubes containing nuclease-free water, lysis buffer from the SMART-Seq V4 3' DE Kit and RNase inhibitor.
Collected single cells were flash-frozen in dry ice and stored at -80°C until further processing.

value: somatosensory cortex

tag: developmental stage

value: Lamp5 Plch2 Dock5


title: scRNAseq, patchseq, cortical IN,  38

description:
PSeq10_IL02_R1.fastq.gz
PSeq_counts.csv
PSeq_38

value: Lamp5 Lsp1


title: scRNAseq, patchseq, cortical IN,  42

description:
PSeq11_IL02_R1.fastq.gz
PSeq_counts.csv
PSeq_42


title: scRNAseq, patchseq, cortical IN,  45

description:
PSeq11_IL05_R1.fastq.gz
PSeq_counts.csv
PSeq_45


title: scRNAseq, patchseq, cortical IN,  35

description:
PSeq08_IL05_R1.fastq.gz
PSeq_counts.csv
PSeq_35


title: scRNAseq, patchseq, cortical IN,  34

description:
PSeq08_IL04_R1.fastq.gz
PSeq_counts.csv
PSeq_34


title: scRNAseq, patchseq, cortical IN,  47

description:
PSeq11_IL07_R1.fastq.gz
PSeq_counts.csv
PSeq_47


title: scRNAseq, patchseq, cortical IN,  32

description:
PSeq08_IL02_R1.fastq.gz
PSeq_counts.csv
PSeq_32


title: scRNAseq, patchseq, cortical IN,  44

description:
PSeq11_IL04_R1.fastq.gz
PSeq_counts.csv
PSeq_44


title: scRNAseq, patchseq, cortical IN,  39

description:
PSeq10_IL05_R1.fastq.gz
PSeq_counts.csv
PSeq_39


title: scRNAseq, patchseq, cortical IN,  40

description:
PSeq10_IL06_R1.fastq.gz
PSeq_counts.csv
PSeq_40


title: scRNAseq, patchseq, cortical IN,  43

description:
PSeq11_IL03_R1.fastq.gz
PSeq_counts.csv
PSeq_43


title: scRNAseq, patchseq, cortical IN,  31

description:
PSeq08_IL01_R1.fastq.gz
PSeq_counts.csv
PSeq_31


title: scRNAseq, patchseq, cortical IN,  36

description:
PSeq08_IL07_R1.fastq.gz
PSeq_counts.csv
PSeq_36


title: scRNAseq, patchseq, cortical IN,  27

description:
PSeq07_IL07_R1.fastq.gz
PSeq_counts.csv
PSeq_27


title: scRNAseq, patchseq, cortical IN,  29

description:
PSeq07_IL11_R1.fastq.gz
PSeq_counts.csv
PSeq_29


title: scRNAseq, patchseq, cortical IN,  41

description:
PSeq10_IL07_R1.fastq.gz
PSeq_counts.csv
PSeq_41


title: scRNAseq, patchseq, cortical IN,  28

description:
PSeq07_IL09_R1.fastq.gz
PSeq_counts.csv
PSeq_28


title: scRNAseq, patchseq, cortical IN,  24

description:
PSeq07_IL03_R1.fastq.gz
PSeq_counts.csv
PSeq_24


title: scRNAseq, patchseq, cortical IN,  46

description:
PSeq11_IL06_R1.fastq.gz
PSeq_counts.csv
PSeq_46


title: scRNAseq, patchseq, cortical IN,  26

description:
PSeq07_IL06_R1.fastq.gz
PSeq_counts.csv
PSeq_26


title: scRNAseq, patchseq, cortical IN,  22

description:
PSeq06_IL06_R1.fastq.gz
PSeq_counts.csv
PSeq_22


title: scRNAseq, patchseq, cortical IN,  20

description:
PSeq06_IL02_R1.fastq.gz
PSeq_counts.csv
PSeq_20


title: scRNAseq, patchseq, cortical IN,  21

description:
PSeq06_IL05_R1.fastq.gz
PSeq_counts.csv
PSeq_21


title: scRNAseq, patchseq, cortical IN,  23

description:
PSeq06_IL07_R1.fastq.gz
PSeq_counts.csv
PSeq_23


title: scRNAseq, patchseq, cortical IN,  30

description:
PSeq07_IL12_R1.fastq.gz
PSeq_counts.csv
PSeq_30


title: scRNAseq, patchseq, cortical IN,  25

description:
PSeq07_IL05_R1.fastq.gz
PSeq_counts.csv
PSeq_25


title: scRNAseq, patchseq, cortical IN,  11

description:
PSeq05_IL01_R1.fastq.gz
PSeq_counts.csv
PSeq_11


title: scRNAseq, patchseq, cortical IN,  13

description:
PSeq05_IL03_R1.fastq.gz
PSeq_counts.csv
PSeq_13


title: scRNAseq, patchseq, cortical IN,  16

description:
PSeq05_IL06_R1.fastq.gz
PSeq_counts.csv
PSeq_16


title: scRNAseq, patchseq, cortical IN,  18

description:
PSeq05_IL08_R1.fastq.gz
PSeq_counts.csv
PSeq_18


title: scRNAseq, patchseq, cortical IN,  17

description:
PSeq05_IL07_R1.fastq.gz
PSeq_counts.csv
PSeq_17


title: scRNAseq, patchseq, cortical IN,  15

description:
PSeq05_IL05_R1.fastq.gz
PSeq_counts.csv
PSeq_15


title: scRNAseq, patchseq, cortical IN,  12

description:
PSeq05_IL02_R1.fastq.gz
PSeq_counts.csv
PSeq_12


title: scRNAseq, patchseq, cortical IN,  10

description:
PSeq04_IL10_R1.fastq.gz
PSeq_counts.csv
PSeq_10


title: scRNAseq, patchseq, cortical IN,  9

description:
PSeq04_IL09_R1.fastq.gz
PSeq_counts.csv
PSeq_9


title: scRNAseq, patchseq, cortical IN,  7

description:
PSeq04_IL06_R1.fastq.gz
PSeq_counts.csv
PSeq_7


title: scRNAseq, patchseq, cortical IN,  4

description:
PSeq03_IL12_R1.fastq.gz
PSeq_counts.csv
PSeq_4


title: scRNAseq, patchseq, cortical IN,  2

description:
PSeq03_IL03_R1.fastq.gz
PSeq_counts.csv
PSeq_2


title: scRNAseq, patchseq, cortical IN,  3

description:
PSeq03_IL10_R1.fastq.gz
PSeq_counts.csv
PSeq_3


title: scRNAseq, cortical IN P30,  581

description:
ROW40_9
CCHT7_counts.csv
CCHT7_581

data_processing:
gene expression counts matrix in csv format containing analyed cortical upper layers P30 Htr3a-GFP+/Hmx3-Cre;R26tdTOM+ and Htr3a-GFP+/Hmx3-Cre;R26tdTOM- INs - samples in columns annotated by their position in C1 chip, genes in rows with gene symbol notation
Fastq files were demultiplexed using the  barcode containing read  so can be treated as single-end. Sequenced reads were aligned to the mouse genome using the read-mapping algorithm STAR and duplicated reads were corrected using UMI-tools. Non-ambiguously mapped exonic reads were quantified using GenomicAlignments in IntersectionStrict mode.
Doublet cells or empty wells identified on the Fluidigm C1 plate imaging were excluded. Cells expressing < 1000 genes or <100.000 UMIs or <50.000 mapped reads or > 15% reads from mitochondrial genome were excluded from the analysis.
mm10 v3.0.0.

extract_protocol:
Htr3a-GFP/Hmx3-Cre;R26tdTOM P30 brains were extracted in ice-cold HBSS. After sectioning with a Mcllwain tissue chopper, upper layers of the somatosensory cortex were micro-dissected under a stereomicroscope. For digestion, the Worthinton Papain Dissociation Kit and protocol were used with adaptations, see article methods for details. After digestion, cells were mechanically dissociated via pipetting in EBSS and centrifuged 5 minutes at 300g. Cell pellet was then suspended in a solution containing EBSS, AP5 Kynurenic acyd, ovomucoid, DNase and trehalose. Following a last centrifugation at 70g for 6 minutes, the pellet was resuspended in 1ml DMEM/F12 with FBS, HS, AP5, Kynurenic acid and trehalose and incubated with Hoechst 33342.
Htr3a-GFP+/Hmx3-Cre;R26tdTOM+ and Htr3a-GFP+/Hmx3-Cre;R26tdTOM+ cells were FAC-sorted on a MoFloAstrios device gated for selecting independently GFP+/TOM+ or GFP+/TOM+ cells. Sorted cells were captured using integrated fluidic circuits and imaged prior to sequencing.

value: inconclusive