title: K14-Actin.GFP; MMTV-PyMT (Interstitial fluid flow induced migration)

city: St. Louis

first: Greg

last: Longmore

state: MO

address: BJCIH, South Euclid Ave.

department: Medicine

institute: Washington University, St. Louis

description: 10x Genomics

data_processing:
Cell Ranger count was used to align samples to the reference genome (mm10), quantify reads and filter reads with a quality score below 30. All single cell RNA-sequencing (scRNAseq) data were analyzed using Partek Flow software. For quality control, nuclei with mitochondrial content >5% were removed. Nuclei that are doublets or multiplets were filtered out by two steps. First, nuclei with more than one marker gene expressed were removed. Then cells with high UMI and gene number per cell were filtered out. UMI counts were normalized following Partek Flow recommendations: for each UMI in each sample the number of raw reads was divided by the number of total mapped reads in that sample and multiplied by 1,000,000, obtaining a count per million value (CPM), the normalized expression value was log-transformed (pseudocount = 1).
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: organoids, Flow migration, scRNAseq

extract_protocol:
Primary breast tumor organoids were isolated from the microfluidic devices after 48 h of hypoxia (no signal) or after collective migration within the microfluidic devices in response to a SDF1 chemokine chemical gradient or interstitial (IF) flow gradient; 18 hours; average 150 m length of directional migration(Hwang et al., 2019)). Organoids were extracted from the device and isolated down to the single cell level by delivering a low concentration collagenase/trypsin digestion. After successful extraction, cells were stained for live/dead (FxCycle Violet; ThermoFisher), and live cells sorted via FACs (BD FACSAria II). After sorting, cells were centrifuged and resuspended in scRNA sequencing buffer and final concentration was adjusted to 1000 cells/ul and sent for scRNA processing
Library was performed according to the manufacter’s instructions. Samples were processed with each library sequenced on 0.125 NovaSeq S4 flow cell (300 cycles; 1.000 flow cell total). Read alignment, gene expression estimation, normalization and quality control were performed using the Cell Ranger Single-Cell Software Suite

value: heterogeneous tumor organoids

value: primary tumors

value: MMTV-PyMT

value: 10-12 weeks old


title: K14-Actin.GFP; MMTV-PyMT; DDR2-/- (SDF1 induced migration)

status: Public on Nov 25 2022

type: SRA

country: USA

description: 10x Genomics

library_source: transcriptomic single cell

molecule: total RNA

organism: Mus musculus

source_name: DDR2-/- organoids, SDF1 migration, scRNAseq

tag: cell type

tag: tissue

tag: strain

tag: age


title: BacKan20191030_4

city: Yokohama

first: motoaki

last: seki

state: Kanagawa

address: Suehiro-cho 1-7-22, Tsurumi-ku

department: CSRS

country: Japan

institute: RIKEN

library_source: transcriptomic

data_processing:
base-calling:RTA2 and bclfastq-v2.20.0
alignment: Tophat2
Genome_build: Manihot esculenta v6
Supplementary_files_format_and_content: FPKM

organism: Manihot esculenta

source_name: Leaf

growth_protocol: The cultivation were conducted at a field in Bac Kan province and Hanoi in Vietnam. KU50, one of popular cassava varieties in Southeast Asia, was used for this study. A 30-40 cm cutting of a properly lignified stem (about one-year-old) was vertically planted at 1.6 m x 1.6 m spacing. As for fertilizer, we supplied similar amount of  NPK (Nitrogen, Phosphorous, and Potassium) as descrieved in manuscript.

extract_protocol:
Leaf was collected in RNA later (Thermo). Total RNA was extracted by Plant RNA reagent (Thermo) and the RNA extraction was purified by RNeasy Plant Mini Kit (QIAGEN) .
2 µg of total RNA was used for cDNA synthesis by Superscript IV reverse transcriptase (Invitrogen) for the construction of sequencing libraries. After adaptor ligation, the cDNA libraries were enriched by 14 cycles of PCR.

tag: tag

tag: sampling date

tag: sampling site

value: BacKan


title: K14-Actin.GFP; MMTV-PyMT (SDF1 induced migration)

description: 10x Genomics

source_name: organoids, SDF1 migration, scRNAseq


title: JMO3

city: Boston

first: Jonathan

middle: M

last: Dreyfuss

state: MA

address: 1 Joslin Pl

department: Bioinformatics & Biostatistics Core

institute: Joslin Diabetes Center

data_processing:
The reads were trimmed for adapters and filtered by sequencing Phred quality (>= Q15) using fastp. The count table was generated by aligning reads to the mouse transcriptome (Ensembl version 98) using kallisto and converting transcript counts to gene counts using tximport.
Assembly: mouse transcriptome (Ensembl version 98)
Supplementary files format and content: A CSV file of counts

source_name: Brown preadipocytes

extract_protocol:
Total RNA was isolated from cells using TRIzol reagent (Thermo Fisher Scientific). The KAPA mRNA HyperPrep kit for Illumina sequencing was used.
mRNA was pulled down using oligo-dT beads, and the resulting mRNA was converted into cDNA. The resulting cDNA then became a library through adapter ligation and post-PCR Cleanup.

value: Brown preadipocytes

tag: genotype

value: JMO

tag: treatment

value: unstimulated


title: Single 2 cell embryo Exp3 NT 5

city: Munich

first: Pavel

middle: Andreevich

last: Kravchenko

state: Planegg

address: Am Klopferspitz 18

department: Totipotency

country: Germany

institute: Max-Planck-Institute of Biochemistry

description:
txi.kallisto_counts_normalized.csv
txi.kallisto_counts_batchcorrected_counts.csv
txi.kallisto_counts_raw.csv
C88_KD_RNA-Seq_DESeq2_all.csv
C88_KD_RNA-Seq_DESeq2_10th_percentile_th.csv

data_processing:
Base calling was performed using bcl2fastq Conversion Software by the Department of Totipotency, MPIB
Low quality reads were trimmed out using TrimGalore (version 0.6.2) using parameters: --nextera --trim-n --paired --quality 20 --nextera
Reads have been checked for contamination with BBMap (version 38.90) using parameters: ref=mm10,hg19 ambig2=all
Read pseudoalignment was done using Kallisto (version 0.46.1) using parameters: -b 100. All reads were aligned to mm10 genome index file.
Count tables have been created in R (version 3.5.1) with tximport (version 1.20.0). Batch correction have been done with BatchCorrectedCounts from CountClust (version 1.18.0). Differential expression was assesed with DESeq2 (version 1.32.0).
Genome_build: mm10
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

molecule: polyA RNA

source_name: single embryo

growth_protocol: Isolated mouse oocytes were cultured in microdrops under 5% O2, 5% CO2, 90% N2. Oocytes were isolated in M2 medium supplemented with dbcAMP (Sigma, 300 mM) and FBS (20%), microinjected and further cultured for 5 hours in M16 supplemented with dbcAMP. Oocytes were released from dbcAMP and cultured for 12 hours in M16, followed by in vitro fertilization (In Vitro Fert, Cooks; supplemented with GSH (Sigma)). Fertilized embryos were cultured in KSOM

extract_protocol:
Single embryo SmartSeq2 protocol with oligo dT priming
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Isolated GV oocytes were microinjected with sets of two siRNAs against targets (20µM each) or control. As a control of successful injection 150 ng/µl H2B-EGFP (for control) or 150 ng/µl H2B-rsEGFP (for target) was co-injected.

tag: developmental stage

value: 2 cell

value: negative control


title: Single 2 cell embryo Exp3 NT 3


title: BacKan20191030_3


title: K14-Actin.GFP; MMTV-PyMT (no migration)

description: 10x Genomics

source_name: organoids, no migration, scRNAseq


title: BacKan20191030_2


title: 3 _ CD43+CD27-

type: protein

city: Leuven

first: Xavier

last: Bossuyt

address: Herestraat 49

country: Belgium

institute: UZ Leuven

hyb_protocol: Provided cell culture supernatants (approx. 200 μL) were thawed on ice, diluted 1:2 with 200 μL 2X assay buffer (2X PBS pH 7.4 0.1% Triton X-100 1.5% non-fat dry milk powder) and carefully mixed by resuspending. 200 μL of Dulbecco’s Modified Eagle Medium (DMEM) were used as blank. Also, DMEM was spiked with 50 μg of human IgG pooled from 10 healthy individuals as positive control.  Microarrays were blocked for 30 min at RT in DIG Easy HybTM (Roche), followed by three washing steps in wash buffer (1X PBS 0.1% Triton X-100) for 5min each, rinsing with ultrapure water and spin drying (900 rpm, 4 min, RT). Blocking, detection and all washing steps were performed with slight agitation.  400 μL of sample mix were applied to each array, Hyb Chambers (Agilent) closed and incubated for 16h in a hybridization oven with gentle rotation (12 rpm) at 25°C. Slides were washed three times with wash buffer, rinsed with ultrapure water and spin dried. Detection was carried out in glass tanks using a 1:10,000 dilution of Alexa Fluor® 647 Goat Anti-Human IgG (H+L) in 1X PBS pH 7.4 0.1% Triton X-100 3% non-fat dry milk powder for 1h in the dark (RT). Slides were again washed three times with wash buffer, rinsed with ultrapure water and spin dried. Image acquisition was performed with the Tecan PowerScannerTM (laser intensity 50%, PMT gain 220%).

scan_protocol: Image acquisition was performed with the Tecan PowerScannerTM (laser intensity 50%, PMT gain 220%). Microarrays were then scanned and fluorescence intensities from array-images extracted using Gene-Pix7 software.

data_processing: Log2- transformed - background corrected and median intensity normalised fluorescent intensities are given. BRB-ArrayTools was used to normalise and analyse the data and the following settiings were applied:  •  Spot Filters:  Threshold the intensity at the minumum value if the intensity is below the minimum value: 50  •  Average the replicate spots within an array: ON  •  Normalization:  Normalize (center) each array using relative median over all genes.  Used 'slot24_human (User Selected)' array as reference array.  •  Gene Filters: OFF  •  Gene Subsets: OFF

label: Alexa Fluor® 647 Goat Anti-Human IgG

molecule: protein

organism: Homo sapiens

label_protocol: not applicable; a fluorescently lableled anti-human-IgG detection antibody is used for detection (see below)

growth_protocol: 50.103 sorted CD43+CD27-, CD43+CD27+, CD43-CD27- and CD43-CD27+ B cells were cultured in 125 µL RPMI supplemented with 10% FCS with or without 1 µg/mL CpG_2006 (Invivogen).

extract_protocol: The supernatants of CD43-CD27+ and CD43+CD27- cells were concentrated.

tag: donor

tag: cell population


title: 2 _ CD43+CD27-

treatment_protocol: 50.103 sorted CD43+CD27-, CD43+CD27+, CD43-CD27- and CD43-CD27+ B cells were cultured in 125 µL RPMI supplemented with 10% FCS with or without 1 µg/mL CpG_2006 (Invivogen).


title: JMO1


title: 1 _ CD43-CD27+


title: JMO2


title: Single 2 cell embryo Exp3 NT 25


title: Single 2 cell embryo Exp3 NT 24


title: Single 2 cell embryo Exp3 NT 23


title: Single 2 cell embryo Exp3 NT 22


title: 3 _ CD43-CD27+


title: Human IgG pool

source_name: 50 µg of human IgG pooled from 10 healthy individuals in 200 µL of Dulbecco’s Modified Eagle Medium (DMEM) - DMEM used similar to cell culture superantant samples of P6 and P8

value: control


title: Single 2 cell embryo Exp3 NT 20


title: Single 2 cell embryo Exp3 NT 21


title: BacKan201901005_4


title: 2 _ CD43-CD27+


title: BacKan20191030_1


title: Single 2 cell embryo Exp3 NT 2


title: CT_stim1

value: CT

value: stimulated with insulin


title: Single 2 cell embryo Exp3 NT 19


title: CT3


title: Single 2 cell embryo Exp3 NT 4


title: BacKan201901005_2


title: BacKan201901005_3


title: CT2


title: Single 2 cell embryo Exp3 NT 18


title: BacKan201901005_1

value: Hanoi


title: Single 2 cell embryo Exp3 NT 16


title: Single 2 cell embryo Exp3 NT 15


title: 1 _ CD43+CD27-


title: Single 2 cell embryo Exp3 NT 17


title: Single 2 cell embryo Exp3 NT 14


title: CT1


title: BacKan20190911_4


title: Single 2 cell embryo Exp3 NT 11


title: Single 2 cell embryo Exp3 NT 13


title: Single 2 cell embryo Exp3 NT 12


title: KD_stim3

value: KD


title: KD_stim2


title: KD_stim1


title: KD3


title: KD2


title: Single 2 cell embryo Exp3 C88 6

value: knockdown


title: Single 2 cell embryo Exp3 NT 1


title: Single 2 cell embryo Exp3 C88 7


title: Single 2 cell embryo Exp3 C88 9


title: Single 2 cell embryo Exp3 C88 8


title: Single 2 cell embryo Exp3 NT 10


title: Single 2 cell embryo Exp3 C88 5


title: Single 2 cell embryo Exp3 C88 4


title: BacKan20190911_1


title: BacKan20190815_4


title: KD1


title: BacKan20190911_2


title: BacKan20190815_3


title: BacKan20190911_3


title: BacKan20190815_2


title: BacKan20190726_4


title: BacKan20190815_1


title: IR_stim2

value: IR


title: Single 2 cell embryo Exp3 C88 20


title: Single 2 cell embryo Exp3 C88 3


title: Single 2 cell embryo Exp3 C88 23


title: Single 2 cell embryo Exp3 C88 21


title: Single 2 cell embryo Exp3 C88 22


title: Single 2 cell embryo Exp3 C88 2


title: IR_stim1


title: BacKan20190726_3


title: IR3


title: Single 2 cell embryo Exp3 C88 19


title: BacKan20190726_2


title: Single 2 cell embryo Exp3 C88 17


title: IR2


title: Single 2 cell embryo Exp3 C88 16


title: IR_stim3


title: Single 2 cell embryo Exp3 C88 13


title: Single 2 cell embryo Exp3 C88 15


title: Single 2 cell embryo Exp3 C88 14


title: IR1


title: DKO2

value: DKO


title: Single 2 cell embryo Exp3 C88 11


title: Single 2 cell embryo Exp3 C88 12


title: DKO1


title: Single 2 cell embryo Exp2 NT 8


title: Single 2 cell embryo Exp2 NT 7


title: Single 2 cell embryo Exp3 C88 1


title: BacKan20190629_4


title: Single 2 cell embryo Exp3 C88 18


title: Single 2 cell embryo Exp2 NT 6


title: BacKan20190629_3


title: BacKan20190629_1


title: BacKan20190629_2


title: BacKan20190726_1


title: Single 2 cell embryo Exp2 NT 5


title: Single 2 cell embryo Exp2 NT 4


title: DKO3


title: BacKan20190531_4


title: BacKan20190531_3


title: Single 2 cell embryo Exp2 NT 2


title: Cardiac Endothelial Cells_WT_male_rep 3

city: Philadelphia

first: Yemin

last: Lan

state: PA

address: 3400 Civic Center Blvd

institute: University of Pennsylvania

description:
WT.M.1011f1
polyA-selected mRNA

data_processing:
Quality of raw fastq reads was assessed using FastQC version 0.11.5 (Andrews et al., 2015).
Reads were aligned to the GRCm38/mm10 reference using STAR version 2.4.0i with default parameters and maximum fragment size of 2000 bp (Dobin et al., 2013). Only properly paired primary alignments were retained for downstream analysis using Samtools version 1.9.
Count matrices were generated using FeatureCounts version 1.6.2 against RefSeq gene annotation and read into DESeq2 (Love, Huber and Anders, 2014) to perform normalization and statistical analysis.
Assembly: mm10 (GRCm38)
Supplementary files format and content: raw_count.txt: Tab-delimited read count table for RefSeq genes.

source_name: Cardiac Endothelial Cells

extract_protocol:
E12.5 hearts were lysed with Collagenase (Sigma-Aldrich), Dispase II (Sigma-Aldrich), and DNase I (Sigma-Aldrich). Cardiac endothelial cells were collected using MACS CD31 microbeads (Miltenyi Biotec, Bergisch Gladbach, Germany) and RNA was isolated using RNeasy Micro kit (Qiagen).
After confirming RNA integrity using Bioanalyzer (Agilent Technologies, Santa Clara, CA), mRNA library was generated from 25ng RNA using NEBNext Poly(A) mRNA Magnetic Isolation Module and Ultra II RNA Library Prep Kit (New England Biolabs). Library quality was assessed by Bioanalyzer (Agilent Technologies) and TapeStation (Agilent Technologies).

value: CD31+ Cardiac Endothelial Cells

value: WT

tag: Sex

value: male


title: Cardiac Endothelial Cells_WT_male_rep 2

description:
WT.M.0929f3
polyA-selected mRNA


title: Cardiac Endothelial Cells_WT_male_rep 4

description:
WT.M.998f7
polyA-selected mRNA


title: Single 2 cell embryo Exp3 C88 10


title: Single 2 cell embryo Exp2 C88 9


title: BacKan20190531_2

value: BacKan


title: Cardiac Endothelial Cells_WT_male_rep 1

description:
WT.M.0928f6
polyA-selected mRNA


title: Single 2 cell embryo Exp2 C88 8


title: BacKan20190531_1


title: Single 2 cell embryo Exp2 C88 7


title: Single 2 cell embryo Exp2 C88 6


title: Single 2 cell embryo Exp2 C88 5


title: Cardiac Endothelial Cells_WT_female_rep 4

description:
WT.F.755f7
polyA-selected mRNA

value: female


title: Cardiac Endothelial Cells_WT_female_rep 3

description:
WT.F.1011f7
polyA-selected mRNA


title: Hanoi20191010_4


title: Hanoi20191010_2


title: Hanoi20191010_3


title: lactate treatment, anti-H3K18la IP (PTM-1406, PTM BIO), biol rep 2

city: Marburg

first: Ho Ryun

last: Chung

address: Hans-Meerwein-Straße 6

department: Institute for Medical Bioinformatics and Biostatistics

institute: Philipps University of Marburg

description:
50 bases reads
LL3_lactate_antiH3K18la_NA_peaks.broadPeak
gainedpeaks_nearestgenes.txt

library_source: genomic

data_processing:
bwa mem (v0.7.17) was used for mapping.
samtools (v1.9) was used to generate sorted BAM output.
Peaks were called using MACS2 (v2.2.7.1) with the broad option.
A custom R script (see supplemental data) was used to identify peaks gained in both replicates after lactate treatment and to retrieve the Ensembl ID of the closest gene for each peak.
Assembly: GRCm38(mm10)
Supplementary files format and content: MACS broadPeak: Genomic intervals
Supplementary files format and content: gainedpeaks_nearestgenes.txt: Gene IDs

molecule: genomic DNA

source_name: T cells, Th17 differentiated

growth_protocol: Cells from spleens and lymph nodes were pooled and CD4+ T and CD8+ T cells were purified by negative isolation kit (Miltenyi Biotec). Purity of T lymphocytes was consistently higher than 95%. Isolated T cells were stimulated with plate-bound anti-CD3 (5 μg/ml, Biolegend) and soluble anti-CD28 (1 μg/ml, Biolegend). Th17 cells were differentiated in the presence of anti-IFN-γ (5 μg/ml, Biolegend), anti-IL-4, IL-2 (25 U/ml), TGF-β1 (1 ng/ml, Peprotech) and IL-6 (40 ng/ml, Peprotech).

extract_protocol:
Cells were fixated with formaldehyde and then harvested and washed two times with ice cold PBS, then resuspended in 1 ml ChIP lysis buffer I (5 mM PIPES pH 8.0, 85 mM KCl, 0,5% (v/v) NP40) and incubated on ice for 20 min. The pellets were then incubated in 1 ml ChIP lysis buffer II (10 mM Tris-HCl pH 7.5, 150 mM NaCl, 1% (v/v) NP40, 1% (w/v) sodium deoxycholate, 0.1% (w/v) SDS, 1 mM EDTA) on ice for 10 min. Chromatin was sheared using an ultrasound desintegrator. Pre-clearing was performed with 100 μl of IgG-linked blocked protein A sepharose (45 min, 4°C, rotator). A 1 % aliquot of each sample was taken as input. Per 2 μg antibody, 220 μl of soluble chromatin was used and immune precipitation was performed. 50 μl of blocked protein A sepharose per sample was added and incubated for 1 h at 4°C. The beads were then washed with wash buffer I (20 mM Tris pH 8.1, 150 NaCl, 1% (v/v) Triton X-100, 0.1% SDS, 2mM EDTA), wash buffer II (20 mM Tris pH 8.1, 500 mM NaCl, 1% Triton X-100, 0.1 SDS, 2 mM EDTA) and wash buffer III (10 mM Tris pH 8.1, 250 mM LiCl, 1% NP40, 1% sodium deoxycholate, 1 mM EDTA) and kept on ice. Afterwards, the samples were washed with Tris buffer (Qiagen EB). Elution was performed by adding 200 μl elution buffer (0.1 M NaHCO3, 1% SDS) and then the samples were incubated for 20 min on a shaker. The samples were then de-crosslinked by adding 16 μl of de-crosslinking buffer and incubated at 65°C overnight. 2.2 ml of binding buffer was added and then the samples were run over a DNA binding column (Qiagen). Elution was performed with 2 x 30-50 μl elution buffer EB.
MicroPlex Library Preparation Kit v2

treatment_protocol: Treatment for 24 h with vehicle or 25 mM sodium lactate.

tag: antibody

value: T cells, Th17 differentiated

value: 25 mM sodium lactate


title: Single 2 cell embryo Exp2 C88 4

value: 2 cell


title: Single 2 cell embryo Exp2 C88 3


title: Single 2 cell embryo Exp2 NT 3

value: negative control


title: lactate treatment, IgG IP (neg. ctrl.), biol rep 2

value: IgG


title: Hanoi20191010_1


title: control treatment, IgG IP (neg. ctrl.), biol rep 2

description:
50 bases reads
CL3_control_antiH3K18la_NA_peaks.broadPeak
gainedpeaks_nearestgenes.txt

value: vehicle


title: Single 2 cell embryo Exp2 C88 2


title: Cardiac Endothelial Cells_phIC1_male_rep 3

description:
phIC1.M.0928f7
polyA-selected mRNA


title: Cardiac Endothelial Cells_phIC1_male_rep 4

description:
phIC1.M.998f4
polyA-selected mRNA


title: Single 2 cell embryo Exp2 C88 16


title: Hanoi20190807_4


title: Single 2 cell embryo Exp2 C88 15


title: Hanoi20190807_3


title: control treatment, anti-H3K18la IP (PTM-1406, PTM BIO), biol rep 1

description:
50 bases reads
CL2_control_antiH3K18la_NA_peaks.broadPeak
gainedpeaks_nearestgenes.txt


title: Cardiac Endothelial Cells_phIC1_male_rep 1

description:
phIC1.M.0804f1
polyA-selected mRNA


title: Cardiac Endothelial Cells_phIC1_male_rep 2

description:
phIC1.M.0928f2
polyA-selected mRNA


title: Single 2 cell embryo Exp2 C88 14


title: Cardiac Endothelial Cells_WT_female_rep 2

description:
WT.F.1010f7
polyA-selected mRNA


title: control treatment, anti-H3K18la IP (PTM-1406, PTM BIO), biol rep 2


title: Hanoi20190807_2


title: Cardiac Endothelial Cells_phIC1_female_rep 6

description:
phIC1.F.996f3
polyA-selected mRNA


title: Single 2 cell embryo Exp2 C88 13


title: lactate treatment, IgG IP (neg. ctrl.), biol rep 1

description:
50 bases reads
LL2_lactate_antiH3K18la_NA_peaks.broadPeak
gainedpeaks_nearestgenes.txt


title: Hanoi20190713_4


title: Hanoi20190807_1


title: Single 2 cell embryo Exp2 C88 12


title: Cardiac Endothelial Cells_phIC1_female_rep 5

description:
phIC1.F.1011f8
polyA-selected mRNA


title: control treatment, IgG IP (neg. ctrl.), biol rep 1


title: Control6 [PN3]

city: Guangzhou

first: Yongjun

last: Jiang

state: Guangdong

address: 250, Changgang East Road 250

country: China

institute: Guangzhou Medical University

data_processing:
Reads filtering under criteria removing reads with 20% of the base quality lower than 13
HISAT2.1.0 mapping to reference genome
count counting
Assembly: Rnor_6.0
Supplementary files format and content: TXT file contain counts for each sample

organism: Rattus norvegicus

source_name: Brain

extract_protocol:
Total RNA was extracted from cell or animal tissue by Trizol reagent (Invitrogen) separately, The RNA quality was checked by Bioanalyzer 2200 (Aligent) and kept at -80℃.The RNA with RIN >8.0 is right for cDNA library construction.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: 3 rats was performed with pontine infarction. 3 rats was performed with MCAO.

value: Sprague Dawley

value: Brain

value: post natal day 21

tag: group

value: sham


title: Cardiac Endothelial Cells_phIC1_female_rep 4

description:
phIC1.F.1011f3
polyA-selected mRNA


title: Single 2 cell embryo Exp2 C88 11

value: knockdown


title: Cardiac Endothelial Cells_phIC1_female_rep 3

description:
phIC1.F.0928f4
polyA-selected mRNA


title: Hanoi20190713_3


title: Single 2 cell embryo Exp2 C88 10


title: Control4 [PN1]


title: Control5 [PN2]


title: Hanoi20190713_2


title: lactate treatment, anti-H3K18la IP (PTM-1406, PTM BIO), biol rep 1


title: PI3 [PS3]

value: pontine infarction


title: Single 2 cell embryo Exp2 C88 1


title: Hanoi20190713_1


title: Hanoi20190524_4

value: Hanoi


title: Cardiac Endothelial Cells_phIC1_female_rep 1

description:
phIC1.F.0801f7
polyA-selected mRNA

value: CD31+ Cardiac Endothelial Cells


title: Cardiac Endothelial Cells_mdH19phIC1_male_rep 5

description:
mdH19phIC1.M.998f6
polyA-selected mRNA

value: male


title: Single 2 cell embryo Exp1 NT 8


title: PI1 [PS1]


title: PI2 [PS2]


title: Hanoi20190524_3


title: Single 2 cell embryo Exp1 NT 7


title: Single 2 cell embryo Exp1 NT 6


title: Control2 [LN2]


title: Cardiac Endothelial Cells_mdH19phIC1_male_rep 4

description:
mdH19phIC1.M.996f5
polyA-selected mRNA


title: Cardiac Endothelial Cells_mdH19phIC1_male_rep 3

description:
mdH19phIC1.M.755f8
polyA-selected mRNA


title: Cardiac Endothelial Cells_mdH19phIC1_male_rep 2

description:
mdH19phIC1.M.1011f6
polyA-selected mRNA


title: Hanoi20190524_2


title: Cardiac Endothelial Cells_phIC1_female_rep 2

description:
phIC1.F.0928f1
polyA-selected mRNA


title: Control1 [LN1]


title: Single 2 cell embryo Exp1 NT 9


title: Single 2 cell embryo Exp1 NT 5


title: Single 2 cell embryo Exp1 NT 4


title: MCAO3 [LS3]

value: middle cerebral artery occlusion


title: AbSeq tag oligo library

city: Hong Kong

first: Zhiwu

last: Tan

address: 21 Sassoon Road, Pokfulam

department: Microbiology

country: Hong Kong

institute: University of Hong Kong

data_processing:
Average high-quality (> Q30) base calls of 84%
Sequenced reads were trimmed to 75 bp
Raw reads were process with BD Rhapsody SBG cloud pipeline
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every T cell subset
Supplementary_files_format_and_content: sample tag metrics: HC1_Sample_Tag_Metrics.csv
Supplementary_files_format_and_content: Δ42PD-1-PD-1- T cell subsets: HC1_SampleTag01_hs_neg_DBEC_MolsPerCell.csv
Supplementary_files_format_and_content: Δ42PD-1+ T cell subsets: HC1_SampleTag02_hs_d42_DBEC_MolsPerCell.csv
Supplementary_files_format_and_content: PD-1+ T cell subsets: HC1_SampleTag03_hs_pd1_DBEC_MolsPerCell.csv

molecule: other

organism: synthetic construct

source_name: Ab tag oligo

extract_protocol:
isolated Δ42PD-1+, PD-1+ T and Δ42PD-1-PD-1- T cells were labeled with sample tag and Ab tag before loaded into BD Phapsody for RNA exraction, RNA was extracted according to BD Rhapsody protocol
library was prepared according to BD Rhapsody protocol

tag: disease

tag: molecule

value: AbSeq tag


title: Cardiac Endothelial Cells_mdH19phIC1_male_rep 1

description:
mdH19phIC1.M.1002f1
polyA-selected mRNA

tag: cell type


title: Single 2 cell embryo Exp1 NT 3


title: Cardiac Endothelial Cells_mdH19phIC1_female_rep 5

description:
mdH19phIC1.F.998f3
polyA-selected mRNA

value: female


title: MCAO2 [LS2]

tag: tissue


title: Cardiac Endothelial Cells_mdH19phIC1_female_rep 4

description:
mdH19phIC1.F.996f2
polyA-selected mRNA

tag: strain


title: PTX activation, PTX 5 hr, rep 5

city: Moscow

first: Alexander

last: Beletsky

address: Butlerova street, building 5a

country: Russia

institute: IHNA

data_processing:
Sequenced reads were mapped to сombined Rattus Norvegicus transcriptome (acquired by merging mRatBN7.2.105 versions of rat genome GTF and GTF from custom long-read assembly from all sequenced samples with gffcompare (ver. 0.11.7)) using minimap2 (ver. 2.17) with parameters: minimap2 -N 100 -p 1 -ax map-ont
Resulting BAM files were sorted using samtools (ver. 1.9) and used for read counting with Salmon (ver 1.7.0), with parameters suitable for long-reads: --libType A --noLengthCorrection --noErrorModel
Read counts were loaded into R using tximport package (ver. 1.17.6) and normalized by “median-of-ratios” method from DESeq2 (v 1.29) R-package.
Assembly: mRatBN7
Supplementary files format and content: tab-delimited text file, that includes normalized expression values for each sample (column).

source_name: Hippocampal primary neuronal culture

growth_protocol: Primary neuronal cultures were prepared from hippocampi of newborn Wistar rat pups. Briefly, the dissected hippocampi were trypsinised with 0.25% trypsin (MP Biomedicals, USA), washed with sterile DMEM (PanEco, Russia) contained 15 mM HEPES pH 7.0 and resuspended in the neurobasal medium (NBM; Gibco, USA) supplemented with B27 (Thermo Fisher Scientific, USA) and GlutaMAX (Thermo Fisher Scientific, USA). The cells were then counted and plated at a density of 250,000 cells per well on Poly-L-lysine hydrobromide 1 mg/ml (PanEco, Russia) coated 4-well plates (SPL Life Sciences, Republic of Korea). 1 h after the cell plating, the medium was changed to fresh NBM. Hippocampal neurons were cultured in 1 ml of NBM for two weeks at 37°C in a 5% CO2 incubator and supplemented with 1/3 of fresh medium each 3 days starting from DIV7.

extract_protocol:
RNA isolation was carried out according to the improved method of RNA phenol-chloroform extraction [Toni et al. MethodsX 2018, doi:10.1016/j.mex.2018.05.011].
To reverse transcribe RNA and amplify full-length cDNA, TeloPrime Full-Length cDNA Amplification kit V2 (Lexogen, Austria) was used. For preparation of barcoded cDNA libraries, Native Barcoding Expansion 1-12 (EXP-NBD104) and Ligation Sequencing Kit (SQK-LSK109) (Oxford Nanopore Technologies, UK) were used. All kits were used according to the manufacturer’s protocol.

treatment_protocol: On DIV15, the PTX activation (the final concentration of PTX was 30 μM; PTX was dis-solved in DMSO, Sigma-Aldrich, USA) was performed. Cells were incubated with PTX for either 30 min, 1 h or 5 h before the cultures were harvested in QIAzol (QIAGEN, Germany) lysis reagent. Control samples had no PTX treatment.

tag: cell line

value: Hippocampal primary neuronal culture

value: Wistar

tag: batch

value: PTX 5 hr.

tag: treatment result

value: No response


title: PTX activation, PTX 60 min, rep 5

value: PTX 60 min.


title: CT_stim2

value: Brown preadipocytes

value: CT

value: stimulated with insulin


title: MCAO1 [LS1]

value: Sprague Dawley

value: Brain

tag: age

value: post natal day 21


title: Control3 [LN3]

value: sham


title: PTX activation, PTX 30 min, rep 5

value: PTX 30 min.


title: Cardiac Endothelial Cells_mdH19phIC1_female_rep 2

description:
mdH19phIC1.F.755f4
polyA-selected mRNA

value: CD31+ Cardiac Endothelial Cells

tag: genotype


title: Single 2 cell embryo Exp1 NT 23

value: 2 cell

tag: treatment

value: negative control


title: Hanoi20190524_1

tag: tag

tag: sampling date

tag: sampling site

value: Hanoi


title: Single 2 cell embryo Exp1 NT 22

tag: developmental stage


title: Cardiac Endothelial Cells_mdH19phIC1_female_rep 1

description:
mdH19phIC1.F.1011f2
polyA-selected mRNA

tag: Sex

value: female


title: PTX activation, control, rep 5

value: Hippocampal primary neuronal culture

value: Wistar

value: Control


title: Cardiac Endothelial Cells_mdH19_male_rep 5

description:
mdH19.M.996f4
polyA-selected mRNA

value: male


title: PTX activation, PTX 5 hr, rep 4

value: PTX 5 hr.

value: No response


title: Wt 7 dpi_TDP-43 cleaved repl.1

city: Planegg-Martinsried

first: Jovica

last: Ninkovic

state: Bayern

address: Großhaderner Straße 9

department: Department for Cell Biology

institute: LMU München

description: 4 animals were pooled per each sample

data_processing:
Primary processing of raw sequencing data to fastq files was carried out with the program bcl2fastq v2.20.0.422 (from Illumina).
Alignment was performed using Cell Ranger 4.0.0 against the Danio rerio reference genome assembly GRCz11 (Ensembl Release 100).
Quality Control of mapped cells was performed adjusting the recommendations from previous publication ("Current best practices in single-cell RNA-seq analysis: a tutorial", Luecken et al., 2019) (gene counts ≥ 350; 40000 ≤ reads per cell ≥ 800; mitochondrial fraction ≤ 0.2).
Batch-correction and integration of different scRNA-seq datasets was performed using Scanorama ("Efficient integration of heterogeneous single-cell transcriptomes using Scanorama", Hie et al., 2019).
Assembly: GRCz11
Supplementary files format and content: barcodes.tsv.gz files include barcode sequences (Cell Ranger 4.0.0)
Supplementary files format and content: features.tsv.gz files include feature Gene ID and Gene name in the first and second column of the (unzipped) features.tsv.gz file, respectively. The third column identifies the type of the feature, in this case gene expression (Cell Ranger 4.0.0)
Supplementary files format and content: matrix.mtx.gz files include UMI counts for each barcode/gene pair (Cell Ranger 4.0.0)

organism: Danio rerio

source_name: Telencephalon

extract_protocol:
Telencephali were extracted and dissociated into single cell suspension using the papain kit (Worthington), according to manufacturer´s instructions
Single-Cell RNA Sequencing libraries were prepared according to Chromium Single Cell 3´Reagent Kit v3 and v3.1 (10X Genomics) and sequenced on NovaSeq6000 (Illumina) with recommended number of cycles (28-8-91) for sample 8 and (28-10-10-90) for samples 9-12.

treatment_protocol: For Sample 10, animals were injured and immersed in water containing lipoamide for the whole duration of the experiment until sacrifice. For samples 11 and 12, animals were injured and phase-separated TDP-43 was injected while performing the injury

value: Telencephalon

value: wildtype

tag: lesioned

value: yes

value: injected with TDP while performing injury


title: PTX activation, PTX 60 min, rep 4

value: PTX 60 min.


title: Single 2 cell embryo Exp1 NT 20


title: Single 2 cell embryo Exp1 NT 24


title: Wt 7 dpi_TDP-43 cleaved repl.2

description: 4 animals were pooled per each sample


title: Wt Intact repl.3

description: 4 animals were pooled per each sample

value: no


title: Mutant 7 dpi_Lipoamide repl.2

description: 4 animals were pooled per each sample

value: grna-/-;grnb-/-

value: treated with lipoamide for 7 days


title: Single 2 cell embryo Exp1 NT 2

value: 2 cell

value: negative control


title: PTX activation, PTX 30 min, rep 4

value: PTX 30 min.


title: PTX activation, control, rep 4

value: Hippocampal primary neuronal culture


title: Wt Intact repl.2

description: 4 animals were pooled per each sample


title: Cardiac Endothelial Cells_mdH19_male_rep 1

description:
mdH19.M.1010f1
polyA-selected mRNA

value: CD31+ Cardiac Endothelial Cells


title: Cardiac Endothelial Cells_mdH19_male_rep 3

description:
mdH19.M.926f1
polyA-selected mRNA


title: Cardiac Endothelial Cells_mdH19_male_rep 4

description:
mdH19.M.926f5
polyA-selected mRNA


title: Single 2 cell embryo Exp1 NT 19


title: Cardiac Endothelial Cells_mdH19_female_rep 3

description:
mdH19.F.926f6
polyA-selected mRNA

value: female


title: Single 2 cell embryo Exp1 NT 18


title: PTX activation, PTX 60 min, rep 3

value: Wistar

value: Activated


title: Single 2 cell embryo Exp1 NT 17


title: PTX activation, PTX 30 min, rep 3


title: PTX activation, PTX 5 hr, rep 3

value: PTX 5 hr.


title: Cardiac Endothelial Cells_mdH19_female_rep 1

description:
mdH19.F.1010f5
polyA-selected mRNA


title: Single 2 cell embryo Exp1 NT 15


title: Single 2 cell embryo Exp1 NT 16


title: Cardiac Endothelial Cells_mdH19_female_rep 2

description:
mdH19.F.1010f6
polyA-selected mRNA


title: Single 2 cell embryo Exp1 NT 21


title: Cardiac Endothelial Cells_md38phIC1_male_rep 5

description:
md38phIC1.M.249f3
polyA-selected mRNA

value: male


title: Cardiac Endothelial Cells_mdH19_male_rep 2

description:
mdH19.M.755f6
polyA-selected mRNA


title: Cardiac Endothelial Cells_md38phIC1_male_rep 4

description:
md38phIC1.M.0929f1
polyA-selected mRNA


title: Single 2 cell embryo Exp1 NT 14


title: PTX activation, PTX 5 hr, rep 2


title: Single 2 cell embryo Exp1 NT 13


title: Cardiac Endothelial Cells_md38phIC1_male_rep 3

description:
md38phIC1.M.0928f3
polyA-selected mRNA


title: Cardiac Endothelial Cells_md38phIC1_male_rep 2

description:
md38phIC1.M.0804f8
polyA-selected mRNA


title: PTX activation, control, rep 2

value: Control


title: PTX activation, PTX 30 min, rep 2


title: Single 2 cell embryo Exp1 NT 11


title: Single 2 cell embryo Exp1 NT 10


title: Cardiac Endothelial Cells_md38phIC1_female_rep 5

description:
md38phIC1.F.249f1
polyA-selected mRNA


title: PTX activation, PTX 5 hr, rep 1


title: Cardiac Endothelial Cells_md38phIC1_male_rep1

description:
md38phIC1.M.0801f5
polyA-selected mRNA


title: Single 2 cell embryo Exp1 NT 1


title: PTX activation, control, rep 3


title: PTX activation, PTX 60 min, rep 1


title: Cardiac Endothelial Cells_md38phIC1_female_rep 4

description:
md38phIC1.F.0929f2
polyA-selected mRNA


title: Single 2 cell embryo Exp1 C88 9

value: knockdown


title: PTX activation, PTX 60 min, rep 2


title: PTX activation, PTX 30 min, rep 1


title: Telencephalon, Mutant 7 dpi_Lipoamide

description:
Sample 7
4 animals were pooled per each sample

data_processing:
Primary processing of raw sequencing data to fastq files was carried out with the program bcl2fastq v2.20.0.422 (from Illumina).
Alignment was performed using Cell Ranger 4.0.0 against the Danio rerio reference genome assembly GRCz11 (Ensembl Release 100).
Quality Control of mapped cells was performed adjusting the recommendations from previous publication ("Current best practices in single-cell RNA-seq analysis: a tutorial", Luecken et al., 2019) (gene counts ≥ 350; 40000 ≤ reads per cell ≥ 800; mitochondrial fraction ≤ 0.2).
Batch-correction and integration of different scRNA-seq datasets was performed using Scanorama ("Efficient integration of heterogeneous single-cell transcriptomes using Scanorama", Hie et al., 2019).
Genome_build: GRCz11
Supplementary_files_format_and_content: barcodes.tsv.gz files include barcode sequences (Cell Ranger 4.0.0)
features.tsv.gz files include feature Gene ID and Gene name in the first and second column of the (unzipped) features.tsv.gz file, respectively. The third column identifies the type of the feature, in this case gene expression (Cell Ranger 4.0.0)
matrix.mtx.gz files include UMI counts for each barcode/gene pair (Cell Ranger 4.0.0)

extract_protocol:
Telencephali were extracted and dissociated into single cell suspension using the papain kit (Worthington), according to manufacturer´s instructions
Single-Cell RNA Sequencing libraries were prepared according to Chromium Single Cell 3´Reagen Kit v3 (10X Genomics) and sequenced on NovaSeq6000 (Illumina) with recommended number of cycles (28-8-91).
scRNA-seq

treatment_protocol: For Sample 7, animals were injured and immersed in water containing lipoamide for the whole duration of the experiment until sacrifice

value: Telencephalon

value: yes

tag: time

value: 7 dpi


title: PTX activation, control, rep 1


title: Cardiac Endothelial Cells_md38phIC1_female_rep 1

description:
md38phIC1.F.0804f7
polyA-selected mRNA


title: Telencephalon, Mutant 7 dpi

description:
Sample 6
4 animals were pooled per each sample

value: grna-/-;grnb-/-

value: no


title: Cardiac Endothelial Cells_md38phIC1_female_rep 2

description:
md38phIC1.F.0928f5
polyA-selected mRNA


title: Single 2 cell embryo Exp1 C88 7

value: 2 cell


title: Telencephalon, Wt 7 dpi

description:
Sample 5
4 animals were pooled per each sample

value: wildtype


title: Single 2 cell embryo Exp1 C88 6


title: Single 2 cell embryo Exp1 NT 12

value: negative control


title: Telencephalon, Mutant 3 dpi

description:
Sample 4
4 animals were pooled per each sample

value: 3 dpi


title: Cardiac Endothelial Cells_md38_male_rep 3

description:
md38.M.0804f6
polyA-selected mRNA

value: CD31+ Cardiac Endothelial Cells


title: ML infected liver, 30M, rep3

city: Rockville

first: Yanggu

last: Shi

address: 9430 Key West AVe #128

institute: Arraystar

description: Liver samples from M. leprae infected adult nine-banded armadillos for 30 months

data_processing:
raw data files in FASTQ format were generated from the Illumina sequencer
The trimmed reads (trimmed 5’, 3’-adaptor bases using cutadapt (v1.17)) were aligned to the reference genome (Dasypus novemcinctus, Dasnov3.0, GCA_000208655.2 Ensembl) using Hisat2 software (v2.1.0)
The transcript abundances in FPKM at gene and transcript levels were assembled and computed with StringTie (v1.3.3). The differential gene expression was analysed using R package Ballgown (v2.10.0). The novel genes and transcripts not present in the reference genome/transcriptome were predicted by StringTie and their protein coding potentials were scored by CPAT (v1.2.4)
Assembly: Dasnov3.0
Supplementary files format and content: Expression_Gene.tsv is Tab Separated Values file that includes Ensembl IDs and FPKM values of gene expression for each Sample
Supplementary files format and content: Expression_Transcript.tsv is Tab Separated Value file that includes Enembl IDs and FPKM values of transcript isoform expression for each Sample

organism: Dasypus novemcinctus

source_name: Liver

extract_protocol:
After storage in RNAlater, total RNA was extracted using TRIzol and chloroform/isopropanol. Total RNA was resuspended in distilled, Rnase-free water and quantified using a Nanodrop ND-1000 Spectrophotometer.
1-2 μg total RNA was used to prepare the sequencing libraries. Library preparation involved oligo (dT) magnetic bead mRNA enrichment, highly strand-specific dUTP method using KAPA Stranded RNA-Seq Library Prep Kit, library size distribution and yield QC with Agilent 2100 Bioanalyzer and by absolute quantification qPCR.

treatment_protocol: Adult armadillos were inoculated with freshly harvested M. leprae, monitored and liver tissue harvested at the experimental end-points. These were compared to ininfected armadillo livers.

value: Liver

value: ML infected


title: ML infected liver, 30M, rep2


title: Single 2 cell embryo Exp1 C88 5


title: Telencephalon, Wt 3 dpi

description:
Sample 3
4 animals were pooled per each sample


title: ML infected liver, 30M, rep1


title: Single 2 cell embryo Exp1 C88 4


title: Single 2 cell embryo Exp1 C88 8


title: Telencephalon, Mutant Intact

description:
Sample 2
4 animals were pooled per each sample


title: ML infected liver, 24M, rep3

description: Liver samples from M. leprae infected adult nine-banded armadillos for 24 months


title: Single 2 cell embryo Exp1 C88 3


title: Cardiac Endothelial Cells_md38_male_rep 2

description:
md38.M.0804f5
polyA-selected mRNA


title: Cardiac Endothelial Cells_md38_male_rep 1

description:
md38.M.0801f8
polyA-selected mRNA


title: Telencephalon, Wt Intact

description:
Sample 1
4 animals were pooled per each sample


title: Single 2 cell embryo Exp1 C88 2


title: Cardiac Endothelial Cells_md38_female_rep 3

description:
md38.F.0804f4
polyA-selected mRNA

value: female


title: Cardiac Endothelial Cells_md38_male_rep 4

description:
md38.M.249f4
polyA-selected mRNA


title: Genomic DNA from a pheochromocytoma sample carrying co-occurrent mutations in NF1 and DLST.

type: genomic

city: Madrid

first: Alberto

last: Cascón

address: Melchor Fernández Almagro 3

department: Human Cancer Genetics Program

country: Spain

institute: Spanish National Cancer Research Centre (CNIO)

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium MethylationEPIC BeadChip using standard Illumina protocol

scan_protocol: Arrays were imaged using iScan using standard recommended Illumina scanner setting

data_processing: GenomeStudio software v2011

label: Cy5 and Cy3

source_name: Pheochromocytoma sample carrying co-occurrent mutations in NF1 and DLST.

label_protocol: Standard Illumina Protocol

extract_protocol: genomic DNA was obtained with the Covaris S2 System (Covaris) for FFPE tissues according to manufacturers’ instructions

tag: gender

tag: sample type

value: Primary tumor


title: ML infected liver, 24M, rep2

tag: tissue


title: Single 2 cell embryo Exp1 C88 16

tag: strain


title: Control liver, 30M, rep3

description: Liver samples from normal adult nine-banded armadillos, controls


title: Cardiac Endothelial Cells_md38_female_rep 2

description:
md38.F.0804f3
polyA-selected mRNA

tag: cell type


title: ML infected liver, 24M, rep1


title: 4weeks, DR2, retina

first: Min

last: Fu

address: No. 253, Industrial Avenue Middle, Haizhu District

institute: The Second Clinical School, Southern Medical University

description: 10x Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v3.0.1 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: Rattus_norvegicus.Rnor_6.0.dna.toplevel.fa
Supplementary files format and content: Tab-separated values files and matrix files

source_name: retina

extract_protocol:
Animals that were considered diabetic were maintained on a high-sugar diet, and tail vein blood samples were collected and measured regularly for assessment of glucose levels. The rats in the experimental group (2 weeks, 4 weeks, 8 weeks) and the control group were anesthetized by intraperitoneal injection and fixed in the supine position. First, the eyeballs were removed, and then the corneoscleral limbus was cut. The eyeballs were radially incised, the anterior segment and vitreous were removed, and the iris structure was slowly separated from the intact retina and placed in protective solution.  The tissues were transported in sterile culture dishes with 10 ml of 1x Dulbecco's phosphate-buffered saline (DPBS; Thermo Fisher, Cat. No. 14190144) on ice. The residual tissue storage solution was removed, and the tissues were then minced on ice. We used 0.25% trypsin (dissociation enzyme; Thermo Fisher, Cat. No. 25200-072) and 10 µg/mL DNase I (Sigma, Cat. no. 11284932001) dissolved in PBS with 5% fetal bovine serum (FBS; Thermo Fisher, Cat. No. SV30087.02) to digest the tissues. The tissues were dissociated at 37°C with a shaking speed of 50 RPM for approximately 40 min. We repeatedly collected the dissociated cells at intervals of 20 min to increase cell yield and viability. The cell suspensions were filtered using a 40 µm nylon cell strainer, and red blood cells were removed by 1X Red Blood Cell Lysis Solution (Thermo Fisher, Cat. No. 00-4333-57). The dissociated cells were washed with 1x DPBS containing 2% FBS. The cells were stained with 0.4% Trypan Blue (Thermo Fisher, Cat. No. 14190144), and viability was assessed on a Countess® II Automated Cell Counter (Thermo Fisher).
Beads with unique molecular identifiers (UMIs) and cell barcodes were loaded close to saturation so that each cell was paired with a bead in gel beads-in-emulsion (GEMs). After exposure to cell lysis buffer, polyadenylated RNA molecules hybridized to the beads. The beads were retrieved into a single tube for reverse transcription. In cDNA synthesis, each cDNA molecule was tagged on the 5’ end (that is, the 3’ end of the messenger RNA transcript) with the UMI and a cell label indicating its cell of origin. Briefly, 10× beads were subjected to second-strand cDNA synthesis, adaptor ligation, and universal amplification. Sequencing libraries were prepared using randomly interrupted whole-transcriptome amplification products to enrich the 3’ ends of the transcripts linked with the cell barcodes and UMIs. All the remaining procedures, including library construction, were performed according to the standard manufacturer’s protocol (CG000206 Rev D). The sequencing libraries were quantified using a High Sensitivity DNA Chip (Agilent) on a Bioanalyzer 2100 and with a Qubit High Sensitivity DNA Assay (Thermo Fisher Scientific). The libraries were sequenced on a NovaSeq6000 instrument (Illumina) in 2 x 150 bp mode.

value: retina

value: SD

value: retinal cells

value: STZ molding for 4 weeks


title: Single 2 cell embryo Exp1 C88 15

value: knockdown


title: 2weeks, DR1, retina

description: 10x Genomics

value: STZ molding for 2 weeks


title: Control liver, 30M, rep1

value: Control


title: AntiCD47 4

city: New York

first: Fang

last: Li

state: NY

institute: Columbia University Irving Medical Center

data_processing:
FASTQ files were quantified with Salmon v1.3.0 to obtain transcript abundance counts using an annotation made from GRCm39 GENCODE V.M27.
The resulting counts were summarized to the gene level using tximport v1.20.0.
Differential expression was assessed using DESeq2 v1.32.0.
Genome_build: Genome Reference Consortium Mouse Build 39
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample
Supplementary_files_format_and_content: Comma separated file contains Log2FoldChange and false discover rate-adjusted P value for every gene by comparing CD47-treated group versus IgG-treated group

extract_protocol:
Total mRNA was extracted from the liver tissues of anti-CD47 or IgG treated mice using RNeasy Mini Kit (Qiagen, #74104).
The libraries were constructed using Illumina TruSeq chemistry.

value: Male

value: CD47 antibody


title: Single 2 cell embryo Exp1 C88 13

value: 2 cell


title: Control liver, 24M, rep3


title: AntiCD47 3


title: PI3 [scRNA-seq]

data_processing:
Basecalls performed using CASAVA version 1.8
cellranger (v3.1.0) was utilized to calculate the feature-barcode matrices. Cells contained over 200 expressed genes and mitochondria UMI rate below 20%  passed the cell quality filtering and mitochondria genes were removed in the expression table.   Seurat package (version: 2.3.4 , https://satijalab.org/seurat/) was used for cell normalization and regression based on the expression table according to the UMI counts of each sample and percent of mitochondria rate to obtain the scaled data.   PCA was constructed based on the scaled data with top 2000 high variable genes and top 10 principals  were used for tSNE construction and UMAP construction. Utilizing graph-based cluster method, we acquired the unsupervised cell cluster result based the PCA top 10  principal and we calculated the marker genes by FindAllMarkers function with wilcox rank sum test algorithm under following criteria:1. lnFC > 0.25; 2. pvalue<0.05; 3. min.pct>0.1.
Assembly: Rat_Ensembl93
Supplementary files format and content: MTX file and TSV file contain counts for each barcodes and genes

extract_protocol:
Single-cell gel beads in emulsion (GEMs) were generated on a GemCode Single Cell Instrument (10x Genomics). Single-cell RNA-seq cDNA libraries were prepared using Chromium™ Single Cell 3’ V3.1 Reagent Kits (10x Genomics) according to manufacturer's protocol.
RNA libraries were generated by 10xGenomics Single Cell 3’ V3.1 Library Gel Bead Kit and prepared for sequencing using standard Illumina protocols

treatment_protocol: 3 rats was performed with pontine infarction.

value: Sprague Dawley

value: Brain

value: post natal day 21

tag: group

value: pontine infarction


title: Control liver, 24M, rep2

value: Liver


title: PI2 [scRNA-seq]


title: Control liver, 24M, rep1


title: Single 2 cell embryo Exp1 C88 11


title: Cardiac Endothelial Cells_md38_female_rep 4

description:
md38.F.249f5
polyA-selected mRNA

value: CD31+ Cardiac Endothelial Cells

value: female


title: PI1 [scRNA-seq]


title: Single 2 cell embryo Exp1 C88 10


title: IgG4

value: IgG


title: AntiCD47 2


title: IgG3


title: Single 2 cell embryo Exp1 C88 1


title: NC3 [scRNA-seq]

value: sham


title: Cardiac Endothelial Cells_md38_female_rep 1

description:
md38.F.0804f2
polyA-selected mRNA


title: Single 2 cell embryo Exp1 C88 12


title: Control liver, 30M, rep2


title: HCC mRNA, sample tag and AbSeq library, Jun08

data_processing:
Average high-quality (> Q30) base calls of 84%
Sequenced reads were trimmed to 75 bp
Raw reads were process with BD Rhapsody SBG cloud pipeline
Matrix table with raw gene counts for every gene and every T cell subset
Supplementary_files_format_and_content:
Jun08_Sample_Tag_Metrics.csv (sample tag metrics)
Jun08_SampleTag08_hs_07neg_DBEC_MolsPerCell.csv (Δ42PD-1-PD-1- T cell subsets (#07patient))
Jun08_SampleTag07_hs_07d42_DBEC_MolsPerCell.csv (Δ42PD-1+ T cell subsets (#07patient))
Jun08_SampleTag10_hs_03neg_DBEC_MolsPerCell.csv (Δ42PD-1-PD-1- T cell subsets (#03patient))
Jun08_SampleTag09_hs_03d42_DBEC_MolsPerCell.csv (Δ42PD-1+ T cell subsets (#03patient))

source_name: PBMCs

extract_protocol:
isolated Δ42PD-1+, PD-1+ T and Δ42PD-1-PD-1- T cells were labeled with sample tag and Ab tag before loaded into BD Phapsody for RNA exraction, RNA was extracted according to BD Rhapsody protocol
library was prepared according to BD Rhapsody protocol
single-cell RNA-seq

value: PBMCs

tag: disease

value: HCC

value: treated patients

tag: molecule

value: mRNA, sample tag, AbSeq tag


title: HCC mRNA, sample tag and AbSeq library, J12

data_processing:
Average high-quality (> Q30) base calls of 84%
Sequenced reads were trimmed to 75 bp
Raw reads were process with BD Rhapsody SBG cloud pipeline
Matrix table with raw gene counts for every gene and every T cell subset
Supplementary_files_format_and_content:
J12_Sample_Tag_Metrics.csv (sample tag metrics)
J12_SampleTag06_hs_neg_DBEC_MolsPerCell.csv (Δ42PD-1-PD-1- T cell subsets)
J12_SampleTag04_hs_d42_DBEC_MolsPerCell.csv (Δ42PD-1+ T cell subsets)
J12_SampleTag05_hs_pd1_DBEC_MolsPerCell.csv (PD-1+ T cell subsets)

value: untreated patients


title: HCC mRNA, sample tag and AbSeq library, JUL14

data_processing:
Average high-quality (> Q30) base calls of 84%
Sequenced reads were trimmed to 75 bp
Raw reads were process with BD Rhapsody SBG cloud pipeline
Matrix table with raw gene counts for every gene and every T cell subset
Supplementary_files_format_and_content:
JUL14_Sample_Tag_Metrics.csv (sample tag metrics)
JUL14_SampleTag10_hs_1cneg_DBEC_MolsPerCell.csv (Δ42PD-1-PD-1- T cell subsets (before treatment))
JUL14_SampleTag09_hs_1cd42_DBEC_MolsPerCell.csv (Δ42PD-1+ T cell subsets (before treatment))
JUL14_SampleTag08_hs_1cpd1_DBEC_MolsPerCell.csv (PD-1+ T cell subsets (before treatment))
JUL14_SampleTag12_hs_B1neg_DBEC_MolsPerCell.csv (Δ42PD-1-PD-1- T cell subsets (after treatment))
JUL14_SampleTag11_hs_B1d42_DBEC_MolsPerCell.csv (Δ42PD-1+ T cell subsets (after treatment))

value: before and after treatment


title: NC2 [scRNA-seq]

tag: age


title: Single 2 cell embryo Exp1 C88 14

data_processing:
Base calling was performed using bcl2fastq Conversion Software by the Department of Totipotency, MPIB
Low quality reads were trimmed out using TrimGalore (version 0.6.2) using parameters: --nextera --trim-n --paired --quality 20 --nextera
Reads have been checked for contamination with BBMap (version 38.90) using parameters: ref=mm10,hg19 ambig2=all
Read pseudoalignment was done using Kallisto (version 0.46.1) using parameters: -b 100. All reads were aligned to mm10 genome index file.
Count tables have been created in R (version 3.5.1) with tximport (version 1.20.0). Batch correction have been done with BatchCorrectedCounts from CountClust (version 1.18.0). Differential expression was assesed with DESeq2 (version 1.32.0).
Genome_build: mm10
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

tag: treatment

value: knockdown


title: IgG2

value: Male


title: Embryo scRNA-seq data 1

city: Rehovot

first: Nimrod

last: Rappoport

state: Shfela

address: 234 Herzl St.

country: Israel

institute: Weizmann Institute of Science

description:
UMI_counts.txt
metacell_expression.txt

data_processing:
scRNA-seq:
.Read_1 files were mapped into mm9 using bowtie2, using default parameters.
.Demultiplexing and UMI counting (UMI and cell barcodes are in read 2) was performed using the pipeline described in Jaitin et al. 2014 (10.1126/science.1247651).
UMI counts were analyzed using the metacell package as described in Baran et al. 2019 (https://doi.org/10.1186/s13059-019-1812-2), and the results of the analysis are in metacell_expression.txt
scHiC: Standard Illumina base-calling pipeline.
Sequence processing pipeline Paired-end reads of sequencing batches were de-multiplexed to single cell datasets based on the two 8 bp unique identification tags attached to each cell during the Tn5-transposase tagmentation. Reads lacking a perfect match were discarded. Reads were broken down to segments on their matches to the MboI recognition site (GATC), concatenating segments shorter than 16 bp with their adjacent segment. Each segment was independently mapped to the Mus Musculus genome (assembly mm9) using Bowtie2 in end-to-end alignment mode. The uniquely mapped (MAPQ > 36) segments from each paired-end read were consolidated into a chain of segments by merging segments mapped to overlapping genomic regions. Next, the segments chain was translated to a chain of fragment-ends (fends) by associating each segment with its downstream fend. Finally, adjacent fend pairs from all chains were used to comprise the contact map of the cell. All the analysis following used the distinct contacts, ignoring the number of times each contact appeared in the map.
Fends were then mapped to 40kb genomic bins. The genomic_bin_coverage_per_cell counts the number of fends mapped to every genomic bin.
Parts of the genome were designated as strict-A and strict-B regions, and for every 40kb genomic bin the numbers of contacts between the bin and strict-A or strict-B regions were counted (in the genomic_bin_a_score_per_cell files).
Genome_build: mm9

source_name: Mouse embryo

extract_protocol:
Pregnant C57BL/6 mice were sacrificed at day 9.5 post-coitum and embryos were dissected under a microscope. The yolk sack was mechanically removed from each embryo, leaving the embryo proper only, and the embryo morphology was validated to match that of a wildtype embryo of the appropriate age. To create single-cells suspension, each embryo was moved to a 1.5ml tube containing 200µl of trypsin-EDTA (0.05% trypsin, 0.02% EDTA) and incubated at 37ºC for 5 minutes. 800µl of cold MEF medium was then added to each tube to inactivate the trypsin.
Single-cells were FACS-sorted directedly into a lysis solution (ddH2O, 0.1% triton-X100, RNAsin plus RNAse inhibitors) in 384-well plates. Plates were frozen and kept at -80C. lysis solution was then evaporated and reverse transcription was performed directly in the wells.  MARSseq library prepartion was performed as described in Jaitin et al. 2014 (10.1126/science.1247651). Briefly, cDNA from different cells (barcoded in the Reverse Transcripiton step) was pooled and amplified by in vitro-transcription. Amplified RNA was then fragmented, reverse transcribed, and Illumina adaptors were added by PCR (14 cycles).

value: mouse embryos

tag: embryonic day


title: HCC mRNA and sample tag library

source_name: PBMCs, sample tag oligo

value: mRNA, sample tag


title: NC1 [scRNA-seq]

value: Sprague Dawley

value: Brain

value: post natal day 21


title: AntiCD47 1

value: Liver

value: CD47 antibody


title: Evi5_MO_1

status: Public on Nov 24 2022

city: Shanghai

first: Gufa

last: Lin

address: 1239 Siping road Tongji university

department: Key Laboratory of Spine and Spinal Cord Injury Repair and Regeneration of Ministry of Education, Orthopaedic Department of Tongji Hospital, School of Life Sciences and Technology, Tongji University

institute: Tongji University

data_processing:
The raw paired end reads were trimmed and quality controlled by Trimmomatic with parameters (SLIDINGWINDOW:4:15 MINLEN:75). Then clean reads were separately aligned to reference genome with orientation mode using hisat2 (https://ccb.jhu.edu/software/hisat2/index.shtml) software.
Assembly: XENLA_XenBase_GeneNames
Supplementary files format and content: fPKM

organism: Xenopus laevis

source_name: limb bud

extract_protocol:
Tadpole were anesthetized with 0.02% MS-222 and collect 10 limb buds in a group. Total RNA was extracted from the cells using TRIzol® Reagent (Invitrogen) and genomic DNA was removed using DNase I (TaKara)
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: For limb amputation, animals were anesthetized with 0.02% MS-222, NF stage 52-53 tadpole hindlimbs were amputated with a surgical scissor at the level of presumptive knee, and froglet forelimbs and axolotl hindlimbs were amputated at midulna/radius. Microinjection and electroporation in the tadpoles were performed as described (Zhang et al., 2018b). Briefly, animals of selected stages were anesthetized with 0.02% MS-222 (Sigma-Aldrich) and injected with control or evi5 Mo.

value: limb bud

tag: genotype

value: Wild type

value: Evi5 morpholino injected


title: Evi5_MO_2


title: Evi5_MO_3


title: IgG1

value: IgG


title: Embryo scRNA-seq data 2

description:
UMI_counts.txt
metacell_expression.txt


title: Control_MO_3

value: Control morpholino injected


title: Control_MO_1


title: U2OS siMDC1 replicate 2, DRB, 30 min release

city: København

first: Lea

middle: Haarup

last: Gregersen

address: Blegdamsvej 3B,

department: ICMM

country: Denmark

institute: University of Copenhagen

data_processing:
Illumina bcl2fastq v1.8 software used for basecalling.
Paired-reads were aligned to the GRCh38 version of the human genome using BWA-MEM v0.7.12 with default settings
Assembly: GRCh38
Supplementary files format and content: bigWig files were generated by converting BAM files to bedGraph format using pybedtools' genomeCoverageBed function (-bg -split -scale 1).  bedGraph files were in turn converted to bigWig format using the bedGraphToBigWig function from the KentTools package.  Unscaled read depth coverage over chr1-22, X, Y (UCSC naming convention) is represented.
Library strategy: DRB/TTchem-seq

growth_protocol: U-2 OS cell lines were cultured in high-glucose Dulbecco's Modified Eagle Medium (DMEM) plus GlutaMax supplemented with 10% FBS, 100 μg/ml streptomycin and 100 U/ml penicillin at 37ºC and 5% CO2

extract_protocol:
RNA was extracted by TRIzol (Thermo Fisher Scientific, 15596026) accordingly to the manufacturer’s instructions. As a control for equal sample preparation, we spiked-in S. cerevisiae (strain BY4741, MATa, his3D1, leu2D0, met15D0, ura3D0) 4-thiouracil (4TU)-labelled RNA. S. cerevisiae were grown in YPD medium overnight, diluted to an OD600 of 0.1, and grown to mid-log phase (OD600 of 0.8) and labelled with 5 mM 4TU (Sigma-Aldrich, 440736) for 6 min. Total RNA was extracted using the PureLink RNA Mini kit (Thermo Fisher Scientific, 12183020) following the enzymatic protocol. For purification of 4SU labelled RNA, 100 μg mammalian 4SU labelled RNA was spiked-in 1/100 of 4TU-labelled S. cerevisiae RNA. The 101 μg RNA was fragmented by addition of 20 μL 1 M NaOH to fragment RNA and left on ice for 20 min. Fragmentation was stopped by addition of 80 μL 1 M Tris pH 6.8 and cleaned up twice with Micro Bio-Spin™ P-30 Gel Columns (BioRad, 7326223) according to the manufacturer’s instructions. Biotinylation of 4SU-residues were carried out in a total volume of 250 μl, containing 10 mM Tris-HCl [pH 7.4], 1 mM EDTA and 5mg MTSEA biotin-XX linker (Biotium, BT90066) for 30 min at room temperature in the dark. RNA was then purified by phenol:chloroform extraction, denatured by 10 min incubation at 65°C and added to 200 μL μMACS Streptavidin MicroBeads (Miltenyi, 130-074-101). RNA was incubated with beads for 15 min at room temperature and beads applied to a μColumn in the magnetic field of a μMACS magnetic separator. Beads were washed twice with pull-out wash buffer (100 mM Tris-HCl, pH 7.4, 10 mM EDTA, 1 M NaCl and 0.1% Tween20). 4SU-RNA was eluted twice by addition of 100 mM DTT and RNA cleaned up using the RNeasy MinElute kit (Qiagen, 74204).
NEBNext Ultra II directional RNA kit (NEB, E7760) using Unique Dual Index UMI Adaptors (NEB, E7416) following the protocol for degraded RNA (RIN 1-2) without additional RNA fragmentation.

treatment_protocol: 3.5 hrs pre-treatment with 100uM DRB (5,6-dichloro-1-β-D-ribofuranosylbenzimidazole), followed by release from DRB inhibition for 10, 20, 30 or 40 min (including 10 min 1mM 4-thiouridine pulse)

tag: cell line

value: osteosarcoma

value: female

value: siMDC1 transfected, 100uM DRB (5,6-dichloro-1-β-D-ribofuranosylbenzimidazole) for 3.5 hrs, release from DRB inhibition for 30 min (including 10 min 1mM 4-thiouridine pulse)


title: U2OS siMDC1 replicate 1, DRB, 40 min release

value: siMDC1 transfected, 100uM DRB (5,6-dichloro-1-β-D-ribofuranosylbenzimidazole) for 3.5 hrs, release from DRB inhibition for 40 min (including 10 min 1mM 4-thiouridine pulse)


title: U2OS siControl replicate 2, DRB, 30 min release

value: siControl transfected, 100uM DRB (5,6-dichloro-1-β-D-ribofuranosylbenzimidazole) for 3.5 hrs, release from DRB inhibition for 30 min (including 10 min 1mM 4-thiouridine pulse)


title: U2OS siMDC1 replicate 1, DRB, 30 min release


title: U2OS siControl replicate 2, DRB, 40 min release

value: siControl transfected, 100uM DRB (5,6-dichloro-1-β-D-ribofuranosylbenzimidazole) for 3.5 hrs, release from DRB inhibition for 40 min (including 10 min 1mM 4-thiouridine pulse)


title: U2OS siControl replicate 1, DRB, 30 min release


title: U2OS siMDC1 replicate 2, DRB, 40 min release


title: U2OS siMDC1 replicate 1, DRB, 20 min release

value: siMDC1 transfected, 100uM DRB (5,6-dichloro-1-β-D-ribofuranosylbenzimidazole) for 3.5 hrs, release from DRB inhibition for 20 min (including 10 min 1mM 4-thiouridine pulse)


title: U2OS siControl replicate 2, DRB, 20 min release

value: siControl transfected, 100uM DRB (5,6-dichloro-1-β-D-ribofuranosylbenzimidazole) for 3.5 hrs, release from DRB inhibition for 20 min (including 10 min 1mM 4-thiouridine pulse)


title: U2OS siControl replicate 1, DRB, 20 min release


title: U2OS siMDC1 replicate 2, DRB, 10 min release

value: siMDC1 transfected, 100uM DRB (5,6-dichloro-1-β-D-ribofuranosylbenzimidazole) for 3.5 hrs, release from DRB inhibition for 10 min (including 10 min 1mM 4-thiouridine pulse)


title: U2OS siControl replicate 1, DRB, 10 min release

value: siControl transfected, 100uM DRB (5,6-dichloro-1-β-D-ribofuranosylbenzimidazole) for 3.5 hrs, release from DRB inhibition for 10 min (including 10 min 1mM 4-thiouridine pulse)


title: U2OS siControl replicate 2, DRB, 10 min release


title: U2OS siMDC1 replicate 2, DRB, 20 min release


title: U2OS siMDC1 replicate 1, DRB, 10 min release


title: V12-3

city: tsukuba

first: Ichiro

last: Chihara

state: Ibaraki

address: 1-1-1 tennodai

department: Urology

institute: University of TSUKUBA

data_processing:
FASTQ files were analyzed using CLC Genomics Workbench (Version 7.5.1; Qiagen, Redwood City, CA).
Assembly: mm10
Supplementary files format and content: CSV files were generated usingCLC Genomics Workbench (Version 7.5.1; Qiagen, Redwood City, CA).

source_name: whole bladder

extract_protocol:
Total RNA from whole blood samples was isolated using a PAX gene Blood RNA kit (PreAnalytix) according to the manufacturer’s instructions. The globin RNA was removed from total RNA using a GLOBINclear-Human Kit (Thermo Fisher SCIENTIFIC).
For RNA sequencing, 500 ng total RNA were rRNA-depleted using the NEBNext rRNA Depletion Kit (New England Biolabs) according to the manufacturer's instructions. Library preparation was performed using an NEBNext Ultra Directional RNA Library Prep Kit (New England Biolabs).

treatment_protocol: After bilateral adrenalectomy of the mice, corticosterone was administered at inactive timing pending recovery.

tag: operation

value: bilateral adrenalectomy

value: vehicle only

value: whole bladder


title: V20-3


title: V16-3


title: V08-3


title: V24-3


title: Control_MO_2

value: limb bud

value: Wild type


title: C24-3

value: CORT


title: V04-3


title: C20-3


title: U2OS siControl replicate 1, DRB, 40 min release


title: C16-3


title: C12-3


title: C08-3


title: C04-3


title: Single cell RNA-Seq 65729 WT ZygG1

data_processing:
Base calling was performed using bcl2fastq Conversion Software by the NGS core facility of the Vienna BioCenter
Fastq files were pseudo-aligned by Kallisto (kallisto quant --threads=8) to Mus musculus cDNA (mm10)
Kallisto results were imported to R by txiimport on the gene level. Differential expression was analysed by DESeq2 in R and DeSeq2 tables were generated.
To generate bam files, read mapping was done with tophat using the parameters -N 2 --read-gap-length 2 --read-edit-dist 2 -I  500000. All reads were mapped to mm10 genome.
Fastq files can be re-generated from bam files with picard SamToFastq: java -XX:ParallelGCThreads=8 -jar picard.jar SamToFastq.
Genome_build: mm10

source_name: small batch of oocytes/embryos

growth_protocol: Isolated mouse oocytes were cultured in microdrops under 5% O2, 5% CO2, 90% N2. s Oocytes were released from dbcAMP and cultured for 12 hours in M16, followed by in vitro fertilization (In Vitro Fert, Cooks; supplemented with GSH (Sigma)). Fertilized embryos were cultured in KSOM

extract_protocol:
Small batch (10-15 oocytes/embryos) SmartSeq2 protocol with oligo dT priming
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: no treatment

tag: developmental stage

value: G1 zygote

value: untreated


title: Single cell RNA-Seq 65732 WT ZygG2

value: G2 zygote


title: Single cell RNA-Seq 65735 WT 2cellG2

value: G2 2C embryo


title: Single cell RNA-Seq 65730 WT ZygG1


title: Single cell RNA-Seq 65733 WT ZygG2


title: Single cell RNA-Seq 72600 WT 2cellG2


title: Single cell RNA-Seq 65736 WT 2cellG2


title: Single cell RNA-Seq 65734 WT ZygG2


title: Single cell RNA-Seq 72602 WT 2cellG2


title: Single cell RNA-Seq 72601 WT 2cellG2


title: Single cell RNA-Seq 72593 WT ZygG2


title: Single cell RNA-Seq 72592 WT ZygG2


title: Single cell RNA-Seq 72588 WT ZygG1


title: Single cell RNA-Seq 72586 WT MIIegg

value: MII egg


title: Single cell RNA-Seq 72587 WT MIIegg


title: Single cell RNA-Seq 72589 WT ZygG1


title: Single cell RNA-Seq 72585 WT MIIegg


title: Single cell RNA-Seq 72590 WT ZygG1


title: Single cell RNA-Seq 72591 WT ZygG2


title: mCherry IP_b input

city: beijing

first: lei

last: chen

address: NO.1 Beichen West  Road, Chaoyang District, Beijing 100101, China

institute: the institute of microbiology chinese academy of sciences

data_processing:
RNA-seq:
Basecalls performed using CASAVA version 1.4
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to JEC21α whole genome using Hisat2 v2.1.0 with parameters  hisat -p -x  -S --rna-strandness RF (for strand-specific RNA-seq)
Framents Per Kilobase of exon per Megabase of library size (TPM) were calculated using Stingtie v1.3.3 with parameters stringtie -p -e -G -o -A-C
The differential expression of genes (DEGs) was assessed using DEseq2 v1.16.1 of R package
ChIP-Seq:
The raw data were aligned using Bowtie2 (version 2.1.0) (Langmead et al., 2012) with default parameters. Indexed and sorted bam files of each datasets were created using SAMtools (version 1.5)
ChIP-Seq peaks were called using MACS2 (version 2.1.1.20160309) (Zhang et al., 2008). Annotation used ChIPseeker (R 1,12,1) to locate the each peaks to promoter regions of related genes. Chromosomal traces were plotted using Integrative Genomics Browser 9.0.0 (Broad Institute).
Overlap between biological replicates of FLAG and mCherry tag enriched genes was high. For subsequent analysis, we only included genes whose promoters had at least one ChIP-Seq peak in overlaped genes.
ChIP-Seq peaks of mCherry and FLAG tag were merged using homer (4.9.1), and 50 bps of upstrem and downstrem of merged peaks were selected to find the conserved binding motif (homer 4.9.1). Motifs were generated for widths of 6–14 bps for both strands represented by the sequences, the length of the motif reported was determined by the lowest p-value.
Genome_build: JEC21α
Supplementary_files_format_and_content: TPM values for each Sample; bigwig files generated using  MACS version 2.1.1.20160309

organism: Cryptococcus deneoformans XL280

source_name: mCherry IP_b input

growth_protocol:
RNA-Seq: 50 ODs of cells from overnight YPD cultures were washed twice in water and resuspended in water at a final concentration of 1 DO600, dropped onto V8 (pH7) plates, and incubated for 12 hours at 25℃ in dark.
ChIP-Seq: strains expressing Cqs2-Flag (Anti-FLAG M2 Magnetic Beads (M8823, SIGMA) and Cqs2-mCherry (RFP-Trap Magnetic Agarose (rtma-20, ChromoTek)  were cultured in 100 ml YPD (with 25μM copper), cells were collected and washed two times with sterile water. Cells were diluted to OD600=1 in water and then spotted onto V8 plate containing 200 μM BCS for 8 hours at 25 °C in the dark.

extract_protocol:
RNA-Seq: Frozen pellets were ground in liquid nitrogen and total RNA was purified using the Ultrapure RNA Kit (Kangweishiji, CW0581S) according to the manufacturer's instructions, and then reverse-transcribed with the Fastquant RT Kit (Tiangen KR106-02, with gDNase).
RNA-Seq: Illumina cDNA libraries were generated using VAHTSTM mRNA-seq v2 Library Prep Kit (Vazyme Biotech Co., Ltd, Nanjing, China) as described by the manufacture. Samples were clustered using VAHRS RNA adapters set1/set2 and then sequenced using Illunima Hiseq 4000 platform in a 2x150 pair-ended manner.
ChIP-Seq: Cell lysates were resuspended in MNase reaction Buffer (50 mM Tris-HCl (pH 7.9), 5mM CaCl2), and the protein concentration of each lysate was quantified using BCA assay (#) described as manufacturer’s instructions. For each sample, the protein concentrations was diluted to 1 mg ml-1 with total volume of 4 microliters. Chromatin was digested in 2 U μl-1 MNase (#) for 15 min at 37 °C, followed by quenching with 50 μl 0.5 M EDTA. Pellet nuclei and resuspend nuclei in 2 microliters lysis buffer
ChIP-Seq: For library construction, 5 ng of raw ChIP material was used for library construction. Illumina libraries were constructed using a modified custom paired-end protocol28. In brief, samples were end-repaired (1_ T4 DNA ligase buffer, 0.4mM dNTP mix, 2.25U T4 DNA polymerase, 0.75U Klenow DNA polymerase and 7.5U T4 polynucleotide kinase; 30 min at 21–25 _C), A-tailed (1_ NEB buffer 2, 0.4mM dNTPs and 3.75U of Klenow (exo-); 30 min at 37 _C) and ligated (1_ rapid DNA ligation buffer, 1mM Illumina PE adapters and 1,600U DNA ligase; 1–8 h at 21–25 _C). Ligated fragments were amplified using indexed primers (Illumina) for 8–10 PCR cycles. DNA was purified with 1.8_volume Ampure XP DNA purification beads between each step

treatment_protocol:
RNA-Seq: Total RNA was purified using the Ultrapure RNA Kit. Illumina cDNA libraries were generated using VAHTSTM mRNA-seq v2 Library Prep Kit.
ChIP-Seq: Cells were harvested and crosslinked with 1% formaldehyde at room temperature for 15 min. Glycine (2.5 M) was then added to a final concentration of 125 mM and the treated cultures were incubated for another 5 min at room temperature. Cells were harvested by centrifugation at 4000rpm for 5 min at 4°C and washed three times with ice-cold water. Cells were grounded to a fine powder in liquid nitrogen. Chromatin fragmentation was performed by using Microccocal Nuclease digestion described as previously

value: serotype D XL280 MATalpha

tag: genotype/variation

value: expressing Cqs2-mCherry

tag: culture condition

value: V8 agar (5% v/v V8 juice, 0.5g/l KH2PO4, 4% agar)  at 25°C, 8h


title: mCherry IP_a input

source_name: mCherry IP_a input


title: mCherry IP_b

source_name: mCherry IP_b

tag: chip antibody

value: RFP-Trap Magnetic Agarose (rtma-20, ChromoTek)


title: mCherry IP_a

source_name: mCherry IP_a


title: FLAG IP_b input

source_name: FLAG IP_b input

value: expressing Cqs2-Flag


title: FLAG IP input

source_name: FLAG IP input


title: FLAG IP_a

source_name: FLAG IP_a

value: Anti-FLAG M2 Magnetic Beads (M8823, SIGMA)


title: Single cell RNA-Seq 65731 WT ZygG1

first: Pavel

last: Kravchenko

institute: Max-Planck-Institute of Biochemistry


title: cqs2OE_V8_24h_3 [RNA-seq]

value: V8 agar (5% v/v V8 juice, 0.5g/l KH2PO4, 4% agar)  at 25°C, 24h


title: cqs2OE_V8_24h_2 [RNA-seq]


title: cqs2OE_V8_24h_1 [RNA-seq]


title: cqs2OE_V8_12h_3 [RNA-seq]

value: V8 agar (5% v/v V8 juice, 0.5g/l KH2PO4, 4% agar)  at 25°C, 12h


title: cqs2OE_V8_12h_2 [RNA-seq]


title: cqs2OE_V8_12h_1 [RNA-seq]


title: vea2Δ_V8_24h_1 [RNA-seq]


title: vea2Δ_V8_12h_3 [RNA-seq]


title: vea2Δ_V8_24h_2 [RNA-seq]


title: FLAG IP_b

source_name: FLAG IP_b


title: WT_V8_24h_2 [RNA-seq]

value: wild type


title: vea2Δ_V8_12h_2 [RNA-seq]


title: vea2Δ_V8_12h_1 [RNA-seq]


title: WT_V8_24h_3 [RNA-seq]


title: WT_V8_24h_1 [RNA-seq]


title: WT_V8_12h_3 [RNA-seq]


title: WT_V8_12h_2 [RNA-seq]


title: WT_V8_12h_1 [RNA-seq]


title: vea2Δ_V8_24h_3 [RNA-seq]


title: M15vM16

type: RNA

city: Magdalenka

first: Adrian

middle: Mateusz

last: Stankiewicz

state: Mazovia

address: Jastrzebiec, ul. Postepu 36A

department: Animal Behaviour

country: Poland

institute: Institute of Genetics and Animal Breeding of the Polish Academy of Sciences

hyb_protocol: 300 ng of cRNA from control (Cy3-labelled) and corticosterone-treated (Cy5-labelled) mice were hybridized together on two-color microarrays without pooling of samples from the same groups. Both control and corticosterone-treated animals from all analyzed time points were assigned to each slide in a pseudorandom way. Gene Expression Hybridization Kit was used for fragmentation and hybridization and Gene Expression Wash Buffer Kit was used for washing slides after hybridization.

scan_protocol: Acquisition and analysis of hybridization intensities were performed using Agilent DNA Microarray Scanner G2505C. Data were extracted and background subtracted using the standard procedures included in the Agilent Feature Extraction Software version 10.7.3.1. Data extraction included Lowess normalization.

data_processing: The ‘normexp’ + 50 offset background correction method [A comparison of background correction methods for two-colour microarrays] was used. The background correction was followed by within-array normalization carried out with the ‘loess’ procedure and between-array normalization conducted with the ‘Aquantile’ method [Normalization of cDNA microarray data].

label_protocol: RNA Spike In Kit (Agilent Technologies, USA) was used as an internal control, the Low Input Quick Amp Labeling Kit was applied to amplify and label (Cy3 or Cy5) target RNA to generate complementary RNA.

growth_protocol: 48 Swiss-Webster male mice (weighing 39.0 ± 3.8g (mean ± SD) and 12 weeks of age) were used in the experiment. Mice were obtained from the breeding colony located at the Institute of Genetics and Animal Biotechnology (Jastrzebiec). Animals were housed in cages with fine sawdust bedding (4-5 mice per cage) at standard conditions (12/12 h light cycle, 22±2°C, and 55±5 % humidity). The animals had an enriched environment and free access to dry food and tap water.

extract_protocol: Brains were removed for hippocampal dissection, which was performed according to protocol described in details in following paper: Jaszczyk, A., A. M. Stankiewicz and G. R. Juszczak (2022). Dissection of Mouse Hippocampus with Its Dorsal, Intermediate and Ventral Subdivisions Combined with Molecular Validation. Brain Sci 12(6). DOI: 10.3390/brainsci12060799. Total RNA was extracted from the individual hippocampal samples using GeneMATRIX universal RNA purification kit (Eurx) following protocol provided by the manufacturer. The quantity and quality of all RNA samples were assessed by spectrophotometry (ND-1000, Nanodrop) and microcapillary electrophoresis (Bioanalyzer 2000)

treatment_protocol: Experimental animals received corticosterone dissolved in drinking water (100 µg/ml) with addition of hydroxypropyl-β-cyclodextrin (0.45%). Control mice received only water with addition of hydroxypropyl-β-cyclodextrin (0.45%). Mice received the new bottles with either corticosterone solution or vehicle at the end of the light phase followed by 12 hours of dark phase constituting period of mouse activity. The next day, the animals were sacrificed at a three time points to collect samples for analysis. The first group of corticosterone-treated mice and assigned control subjects were sacrificed during the first hour of the light phase when animals are still awake although their activity is declining while remaining corticosterone-treated and control mice were sacrificed during the 5th and 9th hour when animals sleep. Cages with animals intended for sample collection were quietly transferred from experimental room to adjacent dissection room immediately before the sacrifice performed by cervical dislocation followed by decapitation. Animals from control and corticosterone groups were sacrificed in alternating order.

value: hippocampus

value: Swiss-Webster

tag: Sex

value: male

value: vehicle

tag: timepoint

value: corticosterone


title: M33vM24

tag: tissue

tag: strain


title: M43vM44


title: 8weeks, DR3, retina

description: 10x Genomics

value: retina

value: SD

tag: cell type

value: retinal cells

value: STZ molding for 8 weeks


title: M7vM18


title: M31vM32


title: M37vM38


title: M9vM10


title: M19vM20


title: M47vM48


title: M49vM50


title: M23vM22


title: T-ALL cell line CCRF-CEM

city: Tampa

first: Rafael

last: Renatino Canevarolo

state: FL

address: 12902 USF Magnolia Dr

department: Cancer Physiology

institute: H Lee Moffitt Cancer Center & Research Institute

description: Gene expression data from acute lymphoblastic leukemia cell lines

hyb_protocol: Samples were hybridized on HG-U133 Plus 2.0 Arrays (Affymetrix) according to the manufacturer recommendations

scan_protocol: Arrays were scanned using a GeneChip Scanner 3000-7G and Gene Chip Operating Software v 1.4 .

data_processing: Expression values were obtained with the iterPLIER+16 algorithm using the Affymetrix Expression Console with default settings.

label: biotin

source_name: T-ALL

label_protocol: Samples were processed with the One-Cycle Target Labeling and Control Reagents Kit (Affymetrix, Santa Clara, CA, USA)

growth_protocol: Cell lines (10 × 10e7) were cultured in RPMI-1640 medium, 10% fetal bovine serum (FBS), and penicillin/streptomycin at 37°C and 5% CO2 for 30 hours

extract_protocol: RNA was extracted by the phenol-chloroform method and purified with the RNAeasy Mini Kit (Qiagen, Inc., Valencia, CA, USA)

treatment_protocol: No treatment was performed

tag: phenotype

value: T-ALL

value: CCRF-CEM


title: M29vM30


title: T-ALL cell line Jurkat

value: Jurkat


title: T-ALL cell line P12-ICHIKAWA


title: M59vM60


title: M13vM14


title: M25vM26


title: T-ALL cell line HPB-ALL

value: HPB-ALL


title: M3vM4


title: T-ALL cell line ALL-SIL

value: ALL-SIL


title: M5vM6


title: M11vM12


title: T-ALL cell line TALL-1


title: T-ALL cell line Molt4


title: BCP-ALL cell line Nalm16

source_name: BCP-ALL

value: BCP-ALL


title: BCP-ALL cell line Nalm30


title: M17vM56


title: M57vM58


title: 12A

city: SHenyang

first: Shuang

last: Chen

address: 77 Puhe road, Shenbei new district, Shenyang city, Liaoning province

institute: China Medical University

data_processing:
The reads were first mapped to the latest UCSC transcript set using Bowtie2 version 2.1.0 and the gene expression level was estimated using RSEM v1.2.15
TMM (trimmed mean of M-values) was used to normalize the gene expression. Differentially expressed genes were identified using the edgeR program. Genes showing altered expression with p < 0.05 and more than 1.5 fold changes were considered differentially expressed
For circRNA expression analysis, the reads were to mapped genome using the STAR and DCC was used to identify the cirRNA and to estimate the circRNA expression
Genome_build: hg19
Supplementary_files_format_and_content: txt TMM normalized junction read counts

source_name: cutaneous squamous cell carcinoma tissues

extract_protocol:
total RNA  was extracted with TRIzol® Reagent (Life technologies)
RNA sequencing libraries were prepared from 2μg of total RNA using the KAPA RNA HyperPrep Kit with RiboErase (HMR) for Illumina®（Kapa Biosystems, Inc., Woburn, MA）. Instead of purifying poly-A RNA using poly-dT primer beads, we removed ribosomal RNA using the Ribo-Zero rRNA Removal Kit (Illumina, Inc.). Linear RNA was removed using RNase R (Epicentre, Inc). Next, the  RNA was fragmented, and then first-strand and directional second-strand syntheses were performed. Subsequently, a tailing/adapter ligation approach was performed with the purified cDNA. Finally, the purified, adapter ligated DNA was amplified. Each library was diluted to 10 nM and pooled equimolar prior to clustering.All of the steps were performed according to the manufacturer's protocols.

value: year 58

value: cutaneous squamous cell carcinoma


title: 12B

source_name: adjacent non-cancerous tissues

value: adjacent non-cancerous


title: 120 min-2

city: Toon

first: Tomohisa

last: Sakaue

address: Shitsukawa

department: Cardiovascular and Thoracic Surgery

institute: Ehime University

data_processing:
Sequence data were mapped on the mouse genome (mm10) using Tophat and analyzed by Cufflinks.
Normalizations were performed  using iDEGES/edgeR
Assembly: mm10

source_name: Lung

extract_protocol:
The total RNA was purified from the lung tissues using Isogen II (NipponGene, Tokyo, Japan), according to the manufacturer's instructions.
RNA (500 ng) was subjected to RNA sequencing using the NEBNext Ultra Directional RNA Library Prep Kit for Illumina and NEBNext rRNA Depletion Kit (Human/Mouse/Rat) (New England Bio Labs, Cambridge, UK).

treatment_protocol: After the induction of anesthesia, the mice were intubated orotracheally with a 20G angiocatheter and placed on a VentElite small animal ventilator (Harvard Apparatus, Holliston, MA, USA). The mice were ventilated at a tidal volume of 0.25 mL and respiratory rate of 120/min and maintained under general anesthesia with a mixture of sevoflurane and 100% oxygen. Left thoracotomy was performed through the third intercostal space. For RNA sequencing and qRT-PCR of S100A8 or S100A9, mice undergoing IR were subjected to 60-min left lung ischemia followed by 30-, 60-, and 120-min reperfusion via the left hilar occlusion with a microvascular clamp (n = 3).

value: Lung

value: WT

value: Ischemia 30 min, reperfusion 120 min


title: 120 min-3


title: 1B

value: year 61


title: 10B

value: year 57


title: BCP-ALL cell line 697


title: BCP-ALL cell line RS4,11


title: 10A


title: 1A

source_name: cutaneous squamous cell carcinoma tissue


title: M51vM40

value: hippocampus

value: Swiss-Webster

value: male

value: vehicle

value: corticosterone


title: BCP-ALL cell line Nalm6


title: M53vM54


title: MPASMCs_hypoxia 8h_rep3, SUP

city: 南京市栖霞区迈皋桥街道合班村122号职防所

first: xinwei

last: shi

address: 迈皋桥街道

institute: 江苏省疾病预防控制中心职防所

description:
H8-3.txt
Biological replicate 3 of 3.Mouse pulmonary artery smooth muscle cells treated with hypoxia for 8 hours

hyb_protocol: Cy3 and Cy5 labeled cRNAs were combined together and hybridized to Arraystar Mouse mRNA&lncRNA Epitranscriptomic Arrays(8*60K,Artraystar) at 65℃ for 17 hours in an Agilent Hybridization Oven.

scan_protocol: After washing,slides were scanned with Agilent Scanner G2505C.

data_processing: Data was extracted using Agilent Feature Extraction software. The probe signals passing P or M QC flags in at least 3 samples were retained for further analysis.IP (Cy5-labelled) intensities were normalized as relative intensities by the RNA spike-in calibration controls. The normalized IP intensities represent the m6A quantity of the transcript comparable across samples.Differentially m6A-methylated mRNAs, lncRNAs and other ncRNAs based on m6A quantity passing fold change and statistical significance cutoffs were identified and compiled.Hierarchical clustering heatmap analysis was performed for differentially m6A-methylated RNAs. Differentially m6A-methylated mRNAs were analyzed for GO and pathway enrichment.

label_protocol: IP and SUP RNAs are amplified as cRNAs and labeled with Cy5 and Cy3 respectively using Arraystar Super RNA Labeling Kit.

growth_protocol: The mouse pulmonary artery smooth muscle cell（MPASMCs） line was cultured in complete medium containing 89%DMEM, 10% fetal bovine serum, and 1% penicilin-streptomycin at 37 ° C and 5%CO2.For MPASMCs in the experimental group（H8-1、H8-2、H8-3）, the culture conditions were changed to 37℃, 1%O2, 5%CO2, and removed after 8 hours of hypoxic culture. For control group（N2、N3、N4）, the original culture conditions were maintained.

extract_protocol: Total RNAs were immunoprecipitated with anti-N6-methyladenosine(m6A) antibody.The immunoprecipitated IP fraction contained enriched m6A methylated RNAs,and the supernatant SUP fraction contained unmodified RNAs.

treatment_protocol: The purity and amount of total RNA samples were determined with NanoDrop ND-1000.RNA integrity was assessed by Bioanalyzer 2100 or Mops electrophoresis.

value: Hypoxia

tag: discription

value: Unmodified RNAs(SUP)


title: MPASMCs_normoxia_rep1, SUP

city: 南京市栖霞区迈皋桥街道合班村122号职防所

institute: 江苏省疾病预防控制中心职防所

description:
N2.txt
Biological replicate 1 of 3.Control mouse pulmonary artery smooth muscle cells.Normoxia

source_name: Mouse pulmonary artery smooth muscle cells

value: Normoxia


title: MPASMCs_hypoxia 8h_rep2, SUP

city: 南京市栖霞区迈皋桥街道合班村122号职防所

institute: 江苏省疾病预防控制中心职防所

description:
H8-2.txt
Biological replicate 2 of 3.Mouse pulmonary artery smooth muscle cells treated with hypoxia for 8 hours


title: M45vM46


title: MPASMCs_normoxia_rep2, IP

city: 南京市栖霞区迈皋桥街道合班村122号职防所

institute: 江苏省疾病预防控制中心职防所

description:
N3.txt
Biological replicate 2 of 3.Control mouse pulmonary artery smooth muscle cells.Normoxia

value: Modified RNAs(IP)


title: 60 min-2

value: Ischemia 30 min, reperfusion 60 min


title: 60 min-3


title: 60 min-1


title: 120 min-1


title: MPASMCs_hypoxia 8h_rep3, IP

city: 南京市栖霞区迈皋桥街道合班村122号职防所

institute: 江苏省疾病预防控制中心职防所


title: BCP-ALL cell line REH

value: BCP-ALL

value: REH


title: MPASMCs_hypoxia 8h_rep1, SUP

city: 南京市栖霞区迈皋桥街道合班村122号职防所

institute: 江苏省疾病预防控制中心职防所

description:
H8-1.txt
Biological replicate 1 of 3.Mouse pulmonary artery smooth muscle cells treated with hypoxia for 8 hours


title: MPASMCs_normoxia_rep3, SUP

city: 南京市栖霞区迈皋桥街道合班村122号职防所

institute: 江苏省疾病预防控制中心职防所

description:
N4.txt
Biological replicate 3 of 3.Control mouse pulmonary artery smooth muscle cells.Normoxia


title: MPASMCs_hypoxia 8h_rep2, IP

city: 南京市栖霞区迈皋桥街道合班村122号职防所

institute: 江苏省疾病预防控制中心职防所


title: M1vM28


title: MPASMCs_normoxia_rep2, SUP

city: 南京市栖霞区迈皋桥街道合班村122号职防所

institute: 江苏省疾病预防控制中心职防所


title: MPASMCs_hypoxia 8h_rep1, IP

city: 南京市栖霞区迈皋桥街道合班村122号职防所

institute: 江苏省疾病预防控制中心职防所


title: 30 min-3

value: Lung

value: Ischemia 30 min, reperfusion 30 min


title: 30 min-2

value: WT


title: MPASMCs_normoxia_rep1, IP

city: 南京市栖霞区迈皋桥街道合班村122号职防所

institute: 江苏省疾病预防控制中心职防所


title: 44_18

city: Marseille

first: Franck

last: Galland

address: 163 avenue de Luminy

country: France

institute: centre d'immunologie de Marseille Luminy

data_processing:
Image analysis and base calling were performed using RTA 2.7.3 and bcl2fastq 2.17.1.14.
Reads were mapped onto the hg38 assembly of the Homo sapiens genome using Tophat 2.0.14 and bowtie version 2-2.1.0.
Quantification of gene expression has been performed using HTSeq-0.6.1 with annotations coming from Ensembl 87. Only no-ambiguously assigned reads have been retained for further analyses.
Genome_build: hg38
Supplementary_files_format_and_content: a text file, containing ENSembl ID and associated raw counts.

source_name: intestinal biopsy

extract_protocol: RNA extraction from colonic biopsies was performed using the Qiagen AllPrep RNA/DNA Mini Kit. RNA integrity was measure by AGILENT bioanalyzer.

value: intestinal biopsy

tag: disease state

value: healthy control

tag: disease activity


title: 43_9

tag: treatment


title: 45_41


title: 0 min-3

tag: genotype

value: Ischemia 30 min


title: 42_2


title: 38_90_AS_Cort

value: Ulcerative colitis (UC)

value: severe activity (AS)

value: corticoids (Cort)


title: 36_55_AM_TNF

value: moderate activity (AM)

value: anti-TNFbiologics  (TNF)


title: 0 min-2


title: 0 min-1


title: 32_20_AM_5ASA


title: MPASMCs_normoxia_rep3, IP

city: 南京市栖霞区迈皋桥街道合班村122号职防所

institute: 江苏省疾病预防控制中心职防所


title: 31_20_AM_5ASA


title: XX3 neurons

city: Jerusalem

first: Ithai

last: Waldhorn

address: Kiryat Hadassah

department: Goldyne Savad Institute of Gene Therapy

institute: Hebrew University

data_processing:
Read trimming and base quality filtering with trim_galore version 0.3.7 and cutadapt 1.18, quality score cutoff of 20 and minimal trimmed sequence length of 20bp. Quality test with fastQC  V0.11.8.
Mapping to the transcriptome with Salmon version 0.13.1, gcBias and validateMapping enabled.
Differential gene expression analysis with DESeq2 package version 1.24.0. Intreface to Salmon output with  tximport version 1.12.3.
Genome_build: hg38
Supplementary_files_format_and_content: Tab-delimited text files including gene based TPM and Salmon calculated read count estimates for each of the six samples. Each row represents a gene and includes Symbol name, gene length and gene effective length.

source_name: Neural progenitor cells

growth_protocol: hiPSCs were plated in 96-well plates with NPC differentiation. NPC differentiation medium contained Nutristem(-) media with HSA (20 µM/ml), bFGF (20ng/ml), LDN (100nM) and SB431542 (5µM). Rock inhibitor (10 µM) was added only on day 0. Medium was changed at day 2 and then twice a week. After day 5, SB431542 was discontinued and differentiation continued until day 19. Nutristem(-) was replaced by phenol red-free DMEM/F12 medium to eliminate hormonal effects.

extract_protocol:
Total RNA was extracted from hiPSCs and NPCs using the miRNeasy Micro Kit (QIAGEN, Hilden, Germany). For quality control of RNA or DNA yield and library synthesis products RNA ScreenTape kit, D1000 ScreenTape kit (both from AGILENT TECHNOLOGIES), Qubit® RNA HS Assay kit, Qubit® DNA HS Assay kit (Invitrogen) were used for each specific step. mRNA libraries were prepared from 1 mg RNA using KAPA Stranded mRNA-Seq Kit, with mRNA Capture Beads (kapabiosystems, KK8421).
mRNA libraries were prepared from 1 mg RNA using KAPA Stranded mRNA-Seq Kit, with mRNA Capture Beads (kapabiosystems, KK8421). Each library was eluted in 20µl elution buffer, adjusted to 10 mM, then 10µl (50%) from each sample were collected and pooled into one tube. The multiplex samples pool (1.5 pM including PhiX 1%) was loaded on NextSeq 500/550 High Output v2 kit (75 cycles) cartridge, and loaded on NextSeq 500 System (Illumina)

value: ES-derived neural progenitor cells

tag: sex chromosome complement


title: XY3 neurons


title: XY1 neurons


title: 29_85_AM_5ASA


title: 30 min-1


title: XY2 neurons


title: 28_85_AM_5ASA


title: XX2 neurons


title: XX1 neurons


title: 22_1_Q_5ASA

value: quiescent (Q)


title: 24_22_Q_5ASA


title: ErbB4_mut_P15_S1_5

city: Paris

first: Pierre

last: de la Grange

address: 29, rue du Faubourg Saint-Jacques

department: Paris Biotech Santé

institute: GenoSplice technology

data_processing:
Sequencing, data quality, reads repartition (e.g., for potential ribosomal contamination), and insert size estimation were performed using FastQC, Picard-Tools, Samtools and rseqc
Reads were mapped using STAR_2.4.0
Assembly: Count on FAST DB gene annotations (GenoSplice) and normalization using Deseq2
Supplementary files format and content: mm10
Supplementary files format and content: Tab-delimited text file includes deseq normalized expression values for each gene and for each sample. Annotations from Human FAST DB v2021_1 were also provided

source_name: cerebral cortex synaptosomes

extract_protocol:
Cortices from P15 Lhx6-Cre;Erbb4+/+;Rpl22HA/HA and Lhx6-Cre;Erbb4F/F;Rpl22HA/HA mice were rapidly dissected in ice-cold RNase-free PBS and immediately homogenized in SynPER Synaptic Protein Extraction Reagent (ThermoScientific) supplemented with 1x cOmplete EDTA-free protease inhibitors (Sigma-Aldrich), 1 mg/ml Heparin (Sigma-Aldrich), 200 U/ml RNAsin (Promega), 100 μg/ml cycloheximide, and 1 mM DTT (Sigma-Aldrich). Synaptosomes were then prepared according to the manufacturer’s instructions. The final synaptosome pellets were resuspended in supplemented SynPER, and Igepal-CA630 (Sigma-Aldrich) was added to the samples to a final concentration of 1%. 100 μl of anti-HA magnetic beads (Pierce #88837) were washed in supplemented SynPER and added to the samples for 3-4 h at 4ºC with gentle rotation. After incubation, beads were washed 3 times in ice-cold washing buffer (300 mM KCl, 1% Igepal- CA630, 50 mM Tris-HCl pH 7.5, 12mM MgCl2, 1mM DTT and 100 μg/ml cycloheximide) and eluted in 350 μl of RLT Plus buffer from the RNAeasy Plus Micro kit (Qiagen) supplemented with 2-mercaptoethanol (Bio-Rad). RNA purification of immunoprecipitated RNA was performed using the RNeasy Plus Micro kit (Qiagen) following the manufacturer’s protocol.
Library preparation for all samples was performed with 1 ng of total RNA using the SMARTer Ultra Low RNAkit for ultra-low RNA. Samples were then sequenced paired-end using an Illumina HiSeq 2500 platform to approximately 60-80 million mapped reads per sample.

value: cerebral cortex synaptosomes

tag: development stage

value: MGE-derived interneurons


title: 23_21_Q_5ASA


title: ErbB4_mut_P15_S1_3


title: ErbB4_mut_P15_S1_4


title: 8_47_Q_TNF

value: Crohn's disease (CD)


title: 41_96_AS_Cort


title: 46_50

value: heathy control


title: 40_44_AS_Cort


title: Ctrl_P15_C1_5


title: Ctrl_P15_C1_3


title: Ctrl_P15_C1_1


title: 37_55_AM_TNF