title: pal2_01_B06


title: leaf 4, control, rep3

status: Public on Jul 10 2023

type: SRA

city: Bern

first: Matthias

last: Erb

address: Altenbergrain 21

department: Institute of Plant Sciences

country: Switzerland

institute: University of Bern

library_source: transcriptomic

data_processing:
BGISEQ
Sequencing reads were filtered for adaptors, reads with more than 5% unknown bases (N) and low quality reads with the software SOAPnuke.
Filtered reads were mapped to GCF_000005005.2_B73_RefGen_v4 using Bowtie2.
Reads count and gene expression level were deteremined by RSEM.
Assembly: GCF_000005005.2_B73_RefGen_v4
Supplementary files format and content: tab-delimited text file includes raw counts for each sample
Supplementary files format and content: tab-delimited text file includes FRKM counts for each sample

molecule: total RNA

organism: Zea mays

source_name: leaf

growth_protocol: Maize (Zea mays, line B73) seeds were sown directly into pots (9 cm x 9 cm x 10 cm) with commercial soil (Selmaterra, BiglerSamen, Switzerland). All plants were grown in a glasshouse supplemented with artificial lights (~300 μmol m-2 s-1) at 22 ± 2 °C, 40–60% relative humidity (RH), with a 14 h : 10 h, light : dark cycle.

extract_protocol:
Total RNA extraction was done with the GeneJET PCR Purification Kit (K0702, Thermo Scientific). DNAse I (M0303, New England BioLabs) treatment was done to minimize genomic DNA contamination. Total RNA sample quality control was done with the Agilent 2100 Bioanalyzer (Agilent RNA 6000 Nano Kit).
Library construction was done by BGI following the DNBSEQ protocol.

treatment_protocol: V4 seedlings were cut at the position of 2nd leaf with a razor blade. L4, L5 and L6 leaves were carefully separated, all leaves were further cut by 0.5 cm under water. For L4 leaves (mature leaves), an additional removal of leaf sheath was required before further cutting of the leaf blade under water. All plant materials were transferred into glass beakers (250 mL) with 150 mL Milli-Q water and allowed for recovery for at least 2 hours before treatment. Detached leaves were transferred into 12-ml plastic centrifuge tubes containing 10 ml Milli-Q water. These samples were then transferred into the glass cylinders supplied with clean airflow for at least 2 hours acclimation. ZmPep3 treatment was done by adding 10 μl of a 1mM ZmPep3 solution in the centrifuge tubes to achieve a final concentration of around 1 µM. HAC treatment was done using the volatile dispensers. Whole leaf samples were harvested with 6 biological replicates for each leaf type/treatment/time combination by flash freezing in liquid nitrogen.

tag: tissue

value: leaf

tag: genotype

tag: treatment

value: control


title: Blood_Platelets_Vumc-NSCLC-560

city: Amsterdam

first: Myron

last: Best

address: De Boelelaan 1117

department: Neurosurgery

country: Netherlands

institute: VU University Medical Center

data_processing:
Single-end 100 bp reads were subjected to pre-aligment 5'-end quality trimming and sequence adapter clipping using Trimmomatic.
Cleaned-up reads were mapped to the hg19 reference genome using STAR (version 2.3.0), using splice aware alignments and allowing for 10 mismatches.
Intron-spanning read summarization was performed using a samtools-based filtering step and HTSeq (version 0.6.1) using union-mode, unstranded reads and minimal mapping quality of 35, all guided by the Ensembl gene annotation version 75.
Assembly: hg19
Supplementary files format and content: Samples in the Rdata-file were processed according to the described protocol (after filtering for low-abundent RNAs).

organism: Homo sapiens

source_name: Thrombocytes

extract_protocol:
Blood platelets were isolated from whole blood in purple-cap BD Vacutainers containing the EDTA anti-coagulant. The cells and aggregates were removed by centrifugation at room temperature for 20 minutes at 120g, resulting in platelet-rich plasma. The platelets were isolated from the platelet-rich plasma by centrifugation at room temperature for 20 minutes at 360g. The platelet pellet was collected in 30 μl RNAlater (Life Technologies), incubated overnight at 4°C and frozen at -80°C for further use. Frozen platelets were thawed on ice and total RNA was isolated using the mirVana RNA isolation kit (Life Technologies) according to the manufacturers’ protocol. Complementary purification of small RNAs was included in the isolation procedure by addition of miRNA homogenate (Life Technologies). Total RNA was dissolved in 30 μl Elution Buffer (Life Technologies) and RNA quality and quantity was measured using Bioanalyzer 2100 with RNA 6000 Picochip (Agilent).
100-500 pg of platelet total RNA diluted in nuclease free H2O was subjected to cDNA synthesis and amplification using the SMARTer Ultra Low RNA Kit for Illumina Sequencing v3 (Clontech, cat. nr. 634853) according to the manufacturers’ protocol. Conversion and efficient amplification of cDNA was quality-controlled using the Bioanalyzer 2100 with DNA High Sensitivity chip (Agilent). Samples with detectable fragments in the 300-7500 bp region were selected for further processing and Covaris shearing by sonication (Covaris Inc). Sample preparation for Illumina sequencing was performed using the Truseq DNA Sample Preparation Kit (Illumina, cat nr. FC-121-2001) or Truseq Nano DNA Sample Preparation Kit (Illumina, cat nr. FC-121-4001). Sample quality and quantity was measured using the DNA 7500 chip or DNA High Sensitivity chip (Agilent). High-quality samples with product sizes between 300-500 bp were pooled in equimolar concentrations and submitted for 100 bp Single Read sequencing on the Hiseq 2500 or 4000 platform (Illumina).

value: Thrombocytes

tag: diagnosis

value: NSCLC

value: nonResponder


title: Blood_Platelets_Vumc-NSCLC-603

value: Responder


title: pal2_01_B12

city: Dresden

first: Maximina

last: Yun

state: Saxony

address: Fetscherstrasse 105

department: CRTD

country: Germany

institute: TUD

data_processing:
basecalling: Basecalls were done with Illumina bcl2fastq version 2.19.1.
preparation of reference:  Sequence and gene annotation of the axolotl nuclear genome assembly AmexG_v6.0-DD were downloaded from https://www.axolotl-omics.org. The gene models for the HoxA and HoxD genes were replaced with manual curated gene models (personal communication with Sergej Nowoshilow, axolotl-omics.org). Sequence and gene annotation of the mitochondrial genome assembly (NCBI GenBank, AY659991.1) and RNA spike-in control sequences (ERCC, Ambion; for quality control) were included as well.
mapping:  Reads were aligned to the axolotl reference genome AmexG_v6.0-DD using the aligner STAR (v2.7.6a) with AmexG_v6.0-DD splice sites as support (parameters:--outSAMmultNmax 1).
counts per feature:  Uniquely mapped fragments were compared based on their overlap to AmexG_v6.0-DD gene annotations using featureCounts (v2.0.1) to create a table of counts per gene and cell (parameters:  -a AmexG_v6_DD.gtf -s 0 -p -o bfx1267.AmexG_v6_DD.tsv -Q 1).
Assembly: AmexG_v6.0-DD
Supplementary files format and content: bfx1267.AmexG_v6_DD.tsv.gz is a tab-separated file with the output from FeatureCounts. Each row represents a gene and the columns contain the gene information followed by the sample counts and additional gene information. Column titles

molecule: polyA RNA

organism: Ambystoma mexicanum

source_name: Blastema

extract_protocol:
Blastemas samples were collected from mid- (13 dpa), late (15 dpa)- or palette-stage (18 dpa) animals at 48 h following GalNP(Rho) injection. Samples were dissociated in 400 ml of 1x Liberase (Roche) diluted in 0.8x PBS, using mechanical disruption with forceps together with smooth pipetting at room temperature for 30 min. For live/dead staining, suspensions were incubated in 0.8X PBS supplemented with 200 nM CellTrace calcein green AM (Invitrogen) and 12.5 uM SYTOX blue (Invitrogen) at room temperature for 15 min. Subsequently, cell suspensions were filtered through a 70-mm-diameter strainer to generate single-cell suspensions and immediately subjected to FACS. Alive cells were sorted using a FACSAria III equipped with a 100 mm nozzle (BD Biosciences) according to the presence or absence of rhodamine signal using blastemas from vehicle-injected axolotls as negative controls. Single rhodamine+ cells were sorted into 2 μl of lysis buffer (nuclease-free water, 0.2% Triton X100, 4U/μl RNase Inhibitor).
Processing of the samples for RNA-sequencing was done following a modified Smartseq-2 protocol (https://star-protocols.cell.com/protocols/1595). In brief, samples were thawed on ice and we added 0.5ul of dT-buffer to each sample, containing poly-dT oligos (final concentration of 0.5uM) for capturing mRNAs. Subsequently, we performed reverse transcription and cDNA amplification. Libraries were prepared with the Illumina® DNA Prep Tagmentation kit and sequenced on an Illumina NovaSeq 6000 S1 flow cell to an average of 0.85 mio PE50bp fragments/cell.

treatment_protocol: Axolotls were amputated through the upper limb, and injected with GalNP-rho at 48 hr prior to blastema collection

tag: strain

value: d/d

value: Blastema

tag: regeneration stage

value: Palette


title: Blood_Platelets_Vumc-NSCLC-551


title: Blood_Platelets_Vumc-NSCLC-764


title: Blood_Platelets_Vumc-NSCLC-734


title: Blood_Platelets_Vumc-NSCLC-546


title: Blood_Platelets_Vumc-NSCLC-533


title: pal2_01_B09


title: Blood_Platelets_Vumc-NSCLC-679


title: Blood_Platelets_Vumc-NSCLC-441


title: Blood_Platelets_Vumc-NSCLC-483


title: pal2_01_B03


title: pal2_01_B02


title: Blood_Platelets_Vumc-NSCLC-394


title: Blood_Platelets_Vumc-NSCLC-404


title: Blood_Platelets_Vumc-NSCLC-374


title: pal2_01_B01


title: Blood_Platelets_Vumc-NSCLC-335


title: pal2_01_B05


title: pal1_01_A24


title: Blood_Platelets_Vumc-NSCLC-317


title: Blood_Platelets_Vumc-NSCLC-285


title: pal2_01_B04


title: pal1_01_A23


title: pal1_01_A22


title: Blood_Platelets_Vumc-NSCLC-263


title: Blood_Platelets_Vumc-NSCLC-1333


title: pal1_01_A21


title: Blood_Platelets_Vumc-NSCLC-1308


title: Blood_Platelets_Vumc-NSCLC-323


title: Blood_Platelets_Vumc-NSCLC-1228


title: Blood_Platelets_Vumc-NSCLC-1092


title: Blood_Platelets_Vumc-NSCLC-253


title: Blood_Platelets_Vumc-NSCLC-273


title: pal1_01_A20


title: Blood_Platelets_Vumc-NSCLC-1156


title: pal1_01_A19


title: Blood_Platelets_Vumc-NSCLC-251


title: Blood_Platelets_Vumc-NSCLC-1064


title: Blood_Platelets_Vumc-NSCLC-1213


title: Blood_Platelets_UMCG-NSCLC-996


title: pal1_01_A18


title: Blood_Platelets_UMCG-NSCLC-988


title: Blood_Platelets_UMCG-NSCLC-986


title: Blood_Platelets_UMCG-NSCLC-987


title: pal1_01_A16


title: pal1_01_A15


title: Blood_Platelets_UMCG-NSCLC-982


title: pal1_01_A17


title: Mouse epidermis, no treatment, 38 weeks of age, C

type: genomic

city: Copenhagen

first: Olivia

last: Luxford Meyer

address: Frederik V's Vej 11

department: Department of Forensic Medicine

country: Denmark

institute: University of Copenhagen

description:
24-No-C
mouse-epidermis-24W-Ctrl-C

hyb_protocol: Standard Illumina Protocol

scan_protocol: Standard Illumina Protocol

data_processing: Data processed with the R package SeSAMe (Sensible Step-wise Analysis of DNA Methylation BeadChips) v. 1.14.2 using default parameters

label: Cy3, Cy5

molecule: genomic DNA

organism: Mus musculus

label_protocol: Standard Illumina Protocol

extract_protocol: Geonomic DNA extracted with DNeasy Blood and Tissue kit from Qiagen

treatment_protocol: Mice were euthanized in CO2-atmosphere. The skin of the back of each mice was removed and placed in sodium chloride solution (58.44 g/L) at room temperature for 24 hours. Afterwards, the epidermis was gently removed from dermis using a tweezer.

tag: Sex

value: female

value: C3.Cg-HRhr/TifBomTac hairless (Taconic)

value: epidermis

tag: age

value: 38 weeks


title: Blood_Platelets_UMCG-NSCLC-981


title: Blood_Platelets_UMCG-NSCLC-993


title: Blood_Platelets_UMCG-NSCLC-979


title: pal1_01_A14


title: Mouse epidermis, no treatment, 34 weeks of age, C

description:
20-No-C
mouse-epidermis-20W-Ctrl-C

value: 34 weeks


title: Blood_Platelets_UMCG-NSCLC-969


title: pal1_01_A13


title: Blood_Platelets_UMCG-NSCLC-968


title: Mouse epidermis, no treatment, 34 weeks of age, B

description:
X1
mouse-epidermis-20W-Ctrl-B


title: Mouse epidermis, UVR treatment, 38 weeks of age, A

description:
Y1
mouse-epidermis-24W-UVR-A
Mouse treated with three standard erythema doses of UVR 3x pr. week for 24 weeks

value: UVR


title: Mouse epidermis, no treatment, 38 weeks of age, B

description:
OE1
mouse-epidermis-24W-Ctrl-B


title: Blood_Platelets_UMCG-NSCLC-967


title: Blood_Platelets_UMCG-NSCLC-966


title: pal1_01_A12


title: Blood_Platelets_UMCG-NSCLC-965


title: Mouse epidermis, no treatment, 38 weeks of age, A

description:
AE1
mouse-epidermis-24W-Ctrl-A


title: Mouse epidermis, no treatment, 34 weeks of age, A

description:
W1
mouse-epidermis-20W-Ctrl-A


title: Mouse epidermis, UVR treatment, 34 weeks of age, C

description:
20-UV-C
mouse-epidermis-20W-UVR-C
Mouse treated with three standard erythema doses of UVR 3x pr. week for 20 weeks


title: Mouse epidermis, UVR treatment, 38 weeks of age, B

description:
Z1
mouse-epidermis-24W-UVR-B
Mouse treated with three standard erythema doses of UVR 3x pr. week for 24 weeks


title: Blood_Platelets_UMCG-NSCLC-964


title: Blood_Platelets_UMCG-NSCLC-962


title: pal1_01_A10


title: Blood_Platelets_UMCG-NSCLC-958


title: pal1_01_A11


title: pal1_01_A09


title: Mouse epidermis, UVR treatment, 34 weeks of age, B

description:
V1
mouse-epidermis-20W-UVR-B
Mouse treated with three standard erythema doses of UVR 3x pr. week for 20 weeks


title: Blood_Platelets_UMCG-NSCLC-1145


title: Blood_Platelets_UMCG-NSCLC-990


title: Mouse epidermis, no treatment, 30 weeks of age, C

description:
16-No-C
mouse-epidermis-16W-Ctrl-C

value: 30 weeks


title: pal1_01_A08


title: Blood_Platelets_UMCG-NSCLC-1141


title: Blood_Platelets_UMCG-NSCLC-1140


title: Blood_Platelets_UMCG-NSCLC-951


title: Blood_Platelets_UMCG-NSCLC-1137


title: Blood_Platelets_UMCG-NSCLC-1136


title: pal1_01_A07


title: Mouse epidermis, UVR treatment, 38 weeks of age, C

description:
24-UV-C
mouse-epidermis-24W-UVR-C
Mouse treated with three standard erythema doses of UVR 3x pr. week for 24 weeks


title: Mouse epidermis, no treatment, 30 weeks of age, A

description:
S1
mouse-epidermis-16W-Ctrl-A


title: pal1_01_A06


title: Mouse epidermis, no treatment, 26 weeks of age, C

description:
12-No-C
mouse-epidermis-12W-Ctrl-C

value: 26 weeks


title: Blood_Platelets_UMCG-NSCLC-1133


title: Blood_Platelets_UMCG-NSCLC-1132


title: Mouse epidermis, UVR treatment, 30 weeks of age, C

description:
16-UV-C
mouse-epidermis-16W-UVR-C
Mouse treated with three standard erythema doses of UVR 3x pr. week for 16 weeks


title: pal1_01_A05


title: Blood_Platelets_UMCG-NSCLC-1130


title: Blood_Platelets_UMCG-NSCLC-1127


title: Blood_Platelets_UMCG-NSCLC-1124


title: Mouse epidermis, no treatment, 30 weeks of age, B

description:
T1
mouse-epidermis-16W-Ctrl-B


title: Blood_Platelets_UMCG-NSCLC-1120


title: pal1_01_A03


title: pal1_01_A04


title: Mouse epidermis, UVR treatment, 30 weeks of age, B

description:
R1
mouse-epidermis-16W-UVR-B
Mouse treated with three standard erythema doses of UVR 3x pr. week for 16 weeks


title: Blood_Platelets_UMCG-NSCLC-1119


title: Blood_Platelets_UMCG-NSCLC-1104


title: Blood_Platelets_UMCG-NSCLC-1117


title: pal1_01_A02


title: Blood_Platelets_UMCG-NSCLC-1103


title: Blood_Platelets_UMCG-NSCLC-1101


title: Blood_Platelets_UMCG-NSCLC-1099


title: Blood_Platelets_UMCG-NSCLC-1098


title: Mouse epidermis, no treatment, 26 weeks of age, A

description:
O1
mouse-epidermis-12W-Ctrl-A


title: Blood_Platelets_UMCG-NSCLC-1097


title: pal1_01_A01


title: Mouse epidermis, UVR treatment, 26 weeks of age, C

description:
12-UV-C
mouse-epidermis-12W-UVR-C
Mouse treated with three standard erythema doses of UVR 3x pr. week for 12 weeks


title: Mouse epidermis, UVR treatment, 30 weeks of age, A

description:
Q1
mouse-epidermis-16W-UVR-A
Mouse treated with three standard erythema doses of UVR 3x pr. week for 16 weeks


title: AL1 cells, Etoposide + nutlin-3a, L78083

data_processing:
basecalling:  Basecalls were done with Illumina bcl2fastq version 2.20.0.
preparation of reference:  Sequence and gene annotation of the axolotl nuclear genome assembly AmexG_v6.0-DD were downloaded from https://www.axolotl-omics.org. The gene models for the HoxA and HoxD genes were replaced with manual curated gene models (personal communication with Sergej Nowoshilow, axolotl-omics.org). Sequence and gene annotation of the mitochondrial genome assembly (NCBI GenBank, AY659991.1) and RNA spike-in control sequences (ERCC, Ambion; for quality control) were included as well.
mapping:  Reads were aligned to the axolotl reference genome  AmexG_v6.0-DD using the aligner STAR (v2.7.7a) with AmexG_v6.0-DD splice sites as support (parameters:--outSAMmultNmax 1).
counts per feature:  Uniquely mapped fragments were compared based on their overlap to AmexG_v6.0-DD gene annotations using featureCounts (v2.0.1) to create a table of counts per gene and cell (parameters:  -a AmexG_v6_DD.gtf -s 2 -p -o bfx1729.AmexG_v6_DD.tsv -Q 1).
Assembly: AmexG_v6.0-DD
Supplementary files format and content: bfx1729.AmexG_v6_DD.tsv.gz is a tab-separated file with the output from FeatureCounts. Each row represents a gene and the columns contain the gene information followed by the sample counts and additional gene information.

growth_protocol: In vitro senescence induction was performed according to (Yu et al., 2022), whereby cells were seeded at 50% confluence and subsequently exposed to 10 μM etoposide and 1 μM nutlin-3a for 24h. Cells were then incubated with 1 μM nutlin-3a in fresh media for the following 11 days. Senescence induction was confirmed by positive SA-β-gal staining, a significant reduction in EdU incorporation, expansion of mitochondrial and lysosomal networks and persistent DNA damage foci (MitoTracker and Lysomitotracker, lysotracker, γH2AX, Yu et al., 2022). Control proliferating cells were seeded in parallel, treated only with identical volumes of DMSO, and passaged during the 12 day senescence induction to avoid confluence.

extract_protocol:
For RNA-seq analysis of AL1 cells, senescent or proliferating control cells in 10 cm dishes were harvested at 14 days post induction. Briefly, cells were rinsed twice with 0.8X PBS, trypsinised, and pelleted. Subsequently, pellets were lysed in 350 ml b-mercaptoethanol-supplemented RLT+ buffer. Total RNA was then extracted using RNeasy micro plus RNA extraction kit (Qiagen) according to manufacturer’s instructions. 1000 ng of total RNA was used as input for library preparation.
Processing of the samples for RNA-sequencing was done following  a modified Smartseq-2 protocol (https://star-protocols.cell.com/protocols/1595). In brief, samples were thawed on ice and we added 0.5ul of dT-buffer to each sample, containing poly-dT oligos (final concentration of 0.5uM) for capturing mRNAs. Subsequently, we performed reverse transcription and cDNA amplification. Libraries were prepared with the Illumina DNA Prep Tagmentation kit and sequenced on an Illumina NovaSeq 6000 to an average of ~40mio PE100bp fragments/sample.

tag: cell line

tag: cell type

value: Fibroblast

value: WT

value: Etoposide + nutlin-3a


title: Blood_Platelets_UMCG-NSCLC-952

value: Thrombocytes

value: NSCLC


title: AL1 cells, Etoposide + nutlin-3a, L78082


title: Blood_Platelets_UMCG-NSCLC-1083

value: nonResponder


title: Mouse epidermis, UVR treatment, 26 weeks of age, B

description:
N1
mouse-epidermis-12W-UVR-B
Mouse treated with three standard erythema doses of UVR 3x pr. week for 12 weeks


title: Blood_Platelets_UMCG-NSCLC-1093

value: Responder


title: Blood_Platelets_UMCG-NSCLC-1082


title: AL1 cells, Etoposide + nutlin-3a, L78081


title: AL1 cells, DMSO, L78080

value: DMSO


title: Blood_Platelets_UMCG-NSCLC-1077


title: Blood_Platelets_UMCG-NSCLC-1075


title: AL1 cells, DMSO, L78079


title: Blood_Platelets_UMCG-NSCLC-1080


title: Mouse epidermis, no treatment, 22 weeks of age, B

description:
L1
mouse-epidermis-8W-Ctrl-B

value: 22 weeks


title: Blood_Platelets_UMCG-NSCLC-1073


title: Blood_Platelets_UMCG-NSCLC-1070


title: Mouse epidermis, UVR treatment, 34 weeks of age, A

description:
U1
mouse-epidermis-20W-UVR-A
Mouse treated with three standard erythema doses of UVR 3x pr. week for 20 weeks

value: female


title: AL1 cells, DMSO, L78078


title: Mouse epidermis, UVR treatment, 22 weeks of age, C

description:
8-UV-C
mouse-epidermis-8W-UVR-C
Mouse treated with three standard erythema doses of UVR 3x pr. week for eight weeks

value: C3.Cg-HRhr/TifBomTac hairless (Taconic)


title: Mouse epidermis, UVR treatment, 26 weeks of age, A

description:
M1
mouse-epidermis-12W-UVR-A
Mouse treated with three standard erythema doses of UVR 3x pr. week for 12 weeks

value: epidermis


title: mid11_07_I10

value: d/d

value: Blastema

value: Mid


title: Blood_Platelets_UMCG-NSCLC-1066


title: Mouse epidermis, no treatment, 22 weeks of age, A

description:
K1
mouse-epidermis-8W-Ctrl-A


title: Blood_Platelets_UMCG-NSCLC-1064


title: mid11_07_I08


title: Blood_Platelets_UMCG-NSCLC-1053


title: Blood_Platelets_UMCG-NSCLC-1068


title: Blood_Platelets_UMCG-NSCLC-1051


title: 16s rRNA-seq cKO Sample 5

city: Gainesville

first: Liang

last: Zhou

state: Fl

address: 2015 SW 16th Ave

country: USA

institute: University of Florida

description:
cKO_5
ancom-results-family.tsv
ancom-results-species.tsv

library_source: genomic

data_processing:
library strategy: 16s rRNA-seq
Sequencing was performed on the Illumina MiSeq (Illumina, Inc., San Diego, CA). Raw FASTQ sequences were filtered and analyzed using QIIME2 (v2022.2.0) and Dada2. Operational taxonomic units were defined based on sequence similarity threshold of 97%. Taxonomy was assigned based on the Silva 138 reference database
Assembly: Silva 138
Supplementary files format and content: ancom-results-family.tsv
Supplementary files format and content: ancom-results-species.tsv

organism: feces metagenome

source_name: feces

extract_protocol:
For microbiome analyses, fecal DNA was isolated the Quick-DNA Fecal/Soil Microbe Miniprep Kit (ZYMO, 11-322).
Amplification and library generation was performed with the Quick-16S NGS Library Prep Kit (ZYMO, D6410) according to the manufacturer’s instructions.

value: feces

value: TfrcF/F Rorc-cre

value: Untreated

tag: molecule type

value: mouse fecal DNA


title: Mouse epidermis, UVR treatment, 22 weeks of age, B

description:
T2_8A
mouse-epidermis-8W-UVR-B
Mouse treated with three standard erythema doses of UVR 3x pr. week for eight weeks

value: UVR


title: 16s rRNA-seq cKO Sample 3

description:
cKO_3
ancom-results-family.tsv
ancom-results-species.tsv


title: mid11_07_I09


title: Blood_Platelets_UMCG-NSCLC-1047

value: Thrombocytes


title: mid11_07_I07


title: Mouse epidermis, no treatment, 22 weeks of age, C

description:
8-No-C
mouse-epidermis-8W-Ctrl-C


title: Blood_Platelets_UMCG-NSCLC-1057

value: NSCLC


title: 16s rRNA-seq cKO Sample 2

description:
cKO_2
ancom-results-family.tsv
ancom-results-species.tsv


title: Mouse epidermis, no treatment, 18 weeks of age, A

description:
T1_4A
mouse-epidermis-4W-Ctrl-A

value: 18 weeks


title: Blood_Platelets_UMCG-NSCLC-1043

value: nonResponder


title: Mouse epidermis, no treatment, 26 weeks of age, B

description:
P1
mouse-epidermis-12W-Ctrl-B

value: 26 weeks


title: mid11_07_I06


title: Mouse epidermis, UVR treatment, 18 weeks of age, A

description:
T1_1
mouse-epidermis-4W-UVR-A
Mouse treated with three standard erythema doses of UVR 3x pr. week for four weeks


title: Blood_Platelets_UMCG-NSCLC-1038


title: Mouse epidermis, no treatment, 18 weeks of age, C

description:
4-No-C
mouse-epidermis-4W-Ctrl-C


title: Blood_Platelets_UMCG-NSCLC-1037

value: Responder


title: Mouse epidermis, UVR treatment, 18 weeks of age, B

description:
T2_1
mouse-epidermis-4W-UVR-B
Mouse treated with three standard erythema doses of UVR 3x pr. week for four weeks

value: female


title: Blood_Platelets_UMCG-NSCLC-1035


title: Blood_Platelets_UMCG-NSCLC-1032


title: 16s rRNA-seq cKO Sample 1

description:
cKO_1
ancom-results-family.tsv
ancom-results-species.tsv


title: mid11_07_I05


title: 16s rRNA-seq Ctrl Sample 7

description:
Ctrl_7
ancom-results-family.tsv
ancom-results-species.tsv

value: TfrcF/F


title: Mouse epidermis, UVR treatment, 22 weeks of age, A

description:
T1_8A
mouse-epidermis-8W-UVR-A
Mouse treated with three standard erythema doses of UVR 3x pr. week for eight weeks

value: C3.Cg-HRhr/TifBomTac hairless (Taconic)

value: epidermis

value: 22 weeks


title: mid11_07_I04

value: d/d

value: Blastema

value: Mid


title: 16s rRNA-seq Ctrl Sample 6

description:
Ctrl_6
ancom-results-family.tsv
ancom-results-species.tsv

value: feces

value: Untreated


title: Blood_Platelets_UMCG-NSCLC-1031


title: Blood_Platelets_UMCG-NSCLC-1030


title: Blood_Platelets_UMCG-NSCLC-1029


title: 16s rRNA-seq cKO Sample 4

description:
cKO_4
ancom-results-family.tsv
ancom-results-species.tsv

value: TfrcF/F Rorc-cre

value: mouse fecal DNA


title: Mouse epidermis, UVR treatment, 18 weeks of age, C

description:
4-UV-C
mouse-epidermis-4W-UVR-C
Mouse treated with three standard erythema doses of UVR 3x pr. week for four weeks

value: UVR


title: mid11_07_I03


title: Blood_Platelets_UMCG-NSCLC-1027

value: Thrombocytes

value: NSCLC


title: Mouse epidermis, no treatment, 18 weeks of age, B

description:
T2_4A
mouse-epidermis-4W-Ctrl-B

value: 18 weeks


title: Blood_Platelets_UMCG-NSCLC-1023

value: Responder


title: Blood_Platelets_UMCG-NSCLC-1022

value: nonResponder


title: mid11_07_I02


title: Mouse epidermis, no treatment, 14 weeks of age, C

description:
0-B
mouse-epidermis-0W-C

value: female

value: 14 weeks


title: 16s rRNA-seq Ctrl Sample 4

description:
Ctrl_4
ancom-results-family.tsv
ancom-results-species.tsv

value: TfrcF/F


title: Blood_Platelets_UMCG-NSCLC-1021


title: Blood_Platelets_UMCG-NSCLC-1016


title: mid11_07_I01


title: Blood_Platelets_UMCG-NSCLC-1009


title: mid11_07_H24


title: 16s rRNA-seq cKO Sample 6

description:
cKO_6
ancom-results-family.tsv
ancom-results-species.tsv


title: 16s rRNA-seq Ctrl Sample 3

description:
Ctrl_3
ancom-results-family.tsv
ancom-results-species.tsv


title: mid11_07_H19


title: Blood_Platelets_UMCG-NSCLC-1071


title: Blood_Platelets_UMCG-NSCLC-1008


title: Blood_Platelets_UMCG-NSCLC-1003


title: Blood_Platelets_UMCG-NSCLC-1005


title: 16s rRNA-seq Ctrl Sample 1

description:
Ctrl_1
ancom-results-family.tsv
ancom-results-species.tsv


title: Blood_Platelets_UMCG-NSCLC-1002


title: Blood_Platelets_UMCG-NSCLC-1004


title: mid11_07_H18


title: 16s rRNA-seq Ctrl Sample 2

description:
Ctrl_2
ancom-results-family.tsv
ancom-results-species.tsv


title: Mouse epidermis, no treatment, 14 weeks of age, B

description:
0-A
mouse-epidermis-0W-B

value: C3.Cg-HRhr/TifBomTac hairless (Taconic)

value: epidermis


title: 16s rRNA-seq Ctrl Sample 5

description:
Ctrl_5
ancom-results-family.tsv
ancom-results-species.tsv


title: 48h_shBRD9_B

city: Worcester

first: Tapan

last: Sharma

state: MA

address: 368 Plantation Street

department: Gene Therapy Centre

institute: University of Massachusetts Medical School

data_processing:
Libraries were sequenced using the BGIseq platform, averagely generating about 9.06 Gb bases per sample. Reads were filtered to remove adaptor-polluted, low quality and high content of unknown base reads.
About 97% of the raw reads were identified as clean reads. Of these, about 97% reads were mapped to genome with approximately 84% reads uniquely mapped to mouse reference genome mm10 using HISAT.
Transcripts were reconstructed using StringTie, and novel transcripts were identified using Cuffcompare. All transcripts were then combined together and mapped to the mm10 reference transcriptome using Bowtie.
Gene expression levels were calculated using RSEM. DEseq2 algorithm was used to detect differentially expressed genes (DEG).
Genome_build: mm10
Supplementary_files_format_and_content: Spreadsheet files in xls format containing normalized differential gene expression data for all transcripts. Normalization was made to expression data from shScr control sample.

source_name: Immortalized myoblast cell line

growth_protocol: C2C12 cells were grown at 37℃ in 5% CO2 and maintained at a confluency of 70% or less in Dulbecco's Modified Eagle's Medium with high glucose (Gibco) supplemented with 10% fetal bovine serum (Gibco) and 1% penicillin-streptomycin solution (Gibco). For induction of differentiation, cells were allowed to become 90% confluent and media was changed to Dulbecco's Modified Eagle's Medium with high glucose (Gibco) supplemented with 2% horse serum (Gibco) and 1% penicillin-streptomycin solution (Gibco). Insulin was added freshly to a final concentration of (2ug/ml).

extract_protocol:
Cells were harvested 48h after inducing differentiation. RNA was extracted by Trizol-chloroform phase separation followed by iso-propanol precipitaion. RNA pellet was resuspended in nuclease-free water.
RNA libraries were prepared by BGI Americas according to their standard protocol.

treatment_protocol: C2C12 cells stably transfected with shRNA constructs targeting BAF250A, BAF180 and BRD9 were plated on culture plates in DMEM medium. At 80-90% confluency, the cells were induced for differentiation and samples were harvested at indicated times for further analysis.

value: Myoblasts

value: Cells from 48h differentiated stage, stably transfected with shRNA construct targeting the BRD9 subunit


title: mid11_07_H17

value: d/d

value: Blastema

value: Mid


title: Blood_Platelets_UMCG-NSCLC-1000


title: 48h_shBRD9_A


title: Blood_Platelets_UMCG-NCSLC-991


title: Blood_Platelets_UMCG-NCSLC-985


title: Blood_Platelets_UMCG-NSCLC-1015


title: 48h_shBAF250a_B

value: Cells from 48h differentiated stage, stably transfected with shRNA construct targeting the BAF250a subunit


title: mid11_07_H16


title: Mouse epidermis, no treatment, 14 weeks of age, A

description:
T1_3
mouse-epidermis-0W-A


title: Blood_Platelets_UMCG-NCSLC-1166


title: Blood_Platelets_UMCG-NCSLC-1154


title: 48h_shScr_B

value: Cells from 48h differentiated stage, stably transfected with non-targeting scrambled shRNA construct


title: mid11_07_H14


title: Blood_Platelets_UMCG-NCSLC-1162

value: Thrombocytes


title: Blood_Platelets_UMCG-NCSLC-1153

value: NSCLC


title: 48h_shBAF250a_A


title: mid11_07_H13


title: Blood_Platelets_UMCG-NCSLC-1151


title: 48h_shScr_A


title: mid11_07_H12


title: Blood_Platelets_UMCG-NCSLC-1150


title: mid11_07_H11


title: Blood_Platelets_UMCG-NCSLC-1149


title: Blood_Platelets_UMCG-NCSLC-1116


title: Blood_Platelets_UMCG-NCSLC-1144


title: Blood_Platelets_UMCG-NCSLC-1115


title: mid11_07_H10


title: Blood_Platelets_UMCG-NCSLC-1112


title: Blood_Platelets_UMCG-NCSLC-1111


title: mid11_07_H15


title: mid11_07_H09


title: Blood_Platelets_UMCG-NCSLC-1105


title: Blood_Platelets_UMCG-NCSLC-1096


title: Blood_Platelets_UMCG-NCSLC-1159


title: mid11_07_H08


title: Blood_Platelets_UMCG-NCSLC-1094


title: mid11_07_H07


title: Blood_Platelets_UMCG-NCSLC-1090


title: Blood_Platelets_UMCG-NCSLC-1076


title: Blood_Platelets_UMCG-NCSLC-1054


title: Blood_Platelets_UMCG-NCSLC-1081


title: Blood_Platelets_UMCG-NCSLC-1033


title: mid11_07_H06


title: mid11_07_H05


title: mid11_07_H04


title: Blood_Platelets_NKI-NSCLC-975


title: Blood_Platelets_NKI-NSCLC-895

description: Please note that the mapped and counted intron-spanning reads from both files corresponding to this sample were merged in silico to yield sufficient mapped reads for further analyses.


title: Blood_Platelets_NKI-NSCLC-882


title: Blood_Platelets_NKI-NSCLC-868


title: E7386 treated HSC3 cells, , biological replicate 1

type: RNA

city: Medford

first: Eric

middle: R

last: Reed

address: 419 Boston Ave.

department: Data Intensive Studies Center

institute: Tufts University

description: Gene expression data from HSC3 cells treated with E7386

hyb_protocol: Hybridized to Affymetrix Human Gene 2.0 ST Array for 18 hours in a GeneChip Hybridization oven 640 at 45C with rotation (60 rpm). The hybridized samples were washed and stained using an Affymetrix fluidics station 450.

scan_protocol: Affymetrix GeneArray Scanner 3000 7G Plus

data_processing: Raw expression values were normalized together using the Robust Multiarray Average (RMA) with the affy (v1.36.1) R package. A BrainArray Chip Definition File (v17.0.0) was used to map the probes on the array to unique Entrez Gene identifiers (http://brainarray.mbni.med.umich.edu/Brainarray/Database/CustomCDF).

label: biotin

source_name: E7386 treated HSC3 cells

label_protocol: Biotin labeling using the Ambion WT Expression Kit, followed by the GeneChip WT Terminal Labeling and Controls Kit.

growth_protocol: Three separate wells (triplicate) in 6 well plates were seeded by HSC3 cells (at 5 × 104/well).

extract_protocol: After 48–64 h, the cells were trypsinized and harvested for RNA purification using the miRNeasy Micro Kit.

treatment_protocol: After 12–24 h (i.e., ~ 50% confluency), the cells were treated with either 0.1% dimethyl sulfoxide (DMSO) or 0.1 μM E7386 in DMSO.


title: Blood_Platelets_NKI-NSCLC-865


title: mid11_07_H03


title: mid11_07_H02


title: Blood_Platelets_NKI-NSCLC-856


title: Blood_Platelets_NKI-NSCLC-706


title: E7386 treated HSC3 cells, biological replicate 3


title: E7386 treated HSC3 cells, biological replicate 2


title: DMSO treated HSC3 cells, biological replicate 3

description: Gene expression data from HSC3 cells treated with DMSO

source_name: DMSO treated HSC3 cells

value: DMSO


title: mid11_07_H01


title: Blood_Platelets_NKI-NSCLC-582


title: Blood_Platelets_NKI-NSCLC-5207


title: DMSO treated HSC3 cells, biological replicate 2


title: DMSO treated HSC3 cells, biological replicate 1


title: mid11_07_G24


title: Blood_Platelets_NKI-NSCLC-5021


title: mid11_07_G23


title: Blood_Platelets_NKI-NSCLC-879


title: TE_CNTRL_24_3

city: London

first: Vladimir

last: Zhurov

state: ON

address: 1151 Richmond Street

department: Biology

country: Canada

institute: University of Western Ontario

description: Gene expression of tomato control plants

hyb_protocol: 5.5 ug of single stranded cDNA was hybridized for 16 h at 45 °C on GeneChip EUTOM3 arrays. Arrays were washed and stained in the Affymetrix Fluidics Station 450 (Affymetrix, Santa Clara, CA).

scan_protocol: Scanning was done following Affymetrix guidelines on a GeneChip Scanner 3000 7G (Affymetrix, Santa Clara, CA).

data_processing: CEL files were processed in Bioconductor using RMA workflow with standard settings and GPL16358 platform CDF. Analysis was performed together with samples from series GSE70375 (GSM1726205-GSM1726208, GSM1726215-GSM1726224) and GSE61074 (GSM1496241-GSM1496243, GSM1496259-GSM1496261).

organism: Solanum lycopersicum

source_name: Control plants, bio rep 3

label_protocol: Biotin end labeled single strand cDNA was prepared according to the Affymetrix GeneChip Whole Transcript (WT) Sense Target Labelling Assay manual (Affymetrix, Santa Clara, CA).

growth_protocol: Plants were grown under 200-250 µmol m-2 s-1 cool-white fluorescent light at 25 °C with a 16:8 h (light/dark) photoperiod in controlled growth chambers.

extract_protocol: RNA samples were processed in triplicate from pooled samples of two plants per treatment. 3 terminal leaflets of leaf 3 were used. Total RNA was prepared using the RNeasy Plant RNA extraction kit (Qiagen, Venlo, Netherlands).

treatment_protocol: 100 adult female spider mites were applied onto terminal leaflet of leaf 3 per plant and allowed to feed for 24 h.

value: 3 terminal leaflets of leaf 3

tag: cultivar

value: Heinz 1706

value: 1 month old


title: Blood_Platelets_NKI-NSCLC-4987

value: nonResponder


title: Blood_Platelets_NKI-NSCLC-5000


title: TE_24_2

description: Gene expression of tomato plants after 24 h of spider mite herbivory.

source_name: 24 h spider mite treatment, bio rep 2


title: HA1800_ND1_D6_rep2_miRNA-seq

city: Detroit

first: Yang

last: Shi

state: MI

address: 4100 John R St MM03BI

department: Karmanos Cancer Institute

institute: Wayne State University Schhol of Medicine

data_processing:
For mRNA sequencing, the Fastq files were quantified using kallisto (v0.46.1) with the transcriptome indices built on the cDNA FASTA files from human genome assembly GRCh38. Differential expression analysis was performed using Deseq2 (v1.32.0).
For miRNA sequencing, the Fastq were trimmed using Trim Galore! 9 (v0.6.5) for adapter sequences and any trimmed reads greater than 30 bp were filtered. The remaining reads were aligned to the genomic DNA sequence from human genome assembly GRCh38 using Bowtie2 (v2.4.3), and the aligned reads for each miRNA were quantified with featureCounts in the Subread package (v2.0.3) according to the sequences of all miRNA hairpins from miRbase.  Differential expression analysis was performed using Deseq2 (v1.32.0).
Assembly: GRCh38
Supplementary files format and content: For mRNA sequencing, processed data files are tab-delimited text files include read counts and TPM values for each sample generated from  kallisto (v0.46.1)
Supplementary files format and content: For miRNA sequencing, processed data files are tab-delimited text files include read counts for each sample generated from Subread (v2.0.3)

growth_protocol: HA1800 cells were maintained in culture medium (DMEM/F12, 10% fetal bovine serum (FBS), B27 supplement, 3.5 mM glucose, 10 ng/ml FGF2, 10 ng/ml EGF, and penicillin–streptomycin).

extract_protocol:
Total RNAs were extracted from cultured cells by using TRIzol® reagent (Invitrogen).
mRNA and miRNA libraries were prepared using the Illumina TruSeq® Stranded mRNA and small RNA library kit, respectively, following manufacturer's protocols.

treatment_protocol: At one day post infection, replace medium with neuron differentiation medium (DMEM/F12, 0.5% FBS, N2, B27, vitamin C, Y27632 and penicillin–streptomycin).

value: human astrocytes

value: ND1 overexpression

tag: time


title: mid11_07_G22


title: HA1800_ND1_D6_rep3_miRNA-seq


title: Blood_Platelets_NKI-NSCLC-4916

value: Responder


title: TE_24_1

source_name: 24 h spider mite treatment, bio rep 1


title: HA1800_ND1_D6_rep1_miRNA-seq


title: Blood_Platelets_NKI-NSCLC-4861


title: TE_24_3

source_name: 24 h spider mite treatment, bio rep 3


title: TE_CNTRL_24_2

source_name: Control plants, bio rep 2


title: mid11_07_G21


title: TE_CNTRL_24_1

source_name: Control plants, bio rep 1


title: Blood_Platelets_NKI-NSCLC-4678


title: HA1800_ND1_D2_rep3_miRNA-seq


title: Blood_Platelets_NKI-NSCLC-4653


title: Blood_Platelets_NKI-NSCLC-4638


title: HA1800_ND1_D2_rep2_miRNA-seq


title: Blood_Platelets_NKI-NSCLC-5135


title: Blood_Platelets_NKI-NSCLC-4620


title: mid11_07_G20


title: Blood_Platelets_NKI-NSCLC-4618


title: mid11_07_G19


title: mid11_07_G18


title: Blood_Platelets_NKI-NSCLC-4524


title: Blood_Platelets_NKI-NSCLC-4518


title: mid11_07_G17


title: HA1800_GFP_D6_rep3_miRNA-seq

value: WT


title: Blood_Platelets_NKI-NSCLC-4509


title: Blood_Platelets_NKI-NSCLC-4488


title: Blood_Platelets_NKI-NSCLC-4486


title: mid11_07_G16


title: Blood_Platelets_NKI-NSCLC-4375


title: mid11_07_G15


title: HA1800_GFP_D6_rep1_miRNA-seq


title: HA1800_GFP_D2_rep3_miRNA-seq


title: Blood_Platelets_NKI-NSCLC-4369


title: mid11_07_G14


title: Blood_Platelets_NKI-NSCLC-4373


title: Blood_Platelets_NKI-NSCLC-4330


title: HA1800_GFP_D2_rep2_miRNA-seq


title: HA1800_ND1_D2_rep1_miRNA-seq


title: Blood_Platelets_NKI-NSCLC-4185


title: HA1800_GFP_D2_rep1_miRNA-seq


title: Blood_Platelets_NKI-NSCLC-4595


title: Blood_Platelets_NKI-NSCLC-4147


title: mid11_07_G12


title: HA1800_ND1_D6_rep3_RNA-seq


title: Blood_Platelets_NKI-NSCLC-4112


title: mid11_07_G11


title: HA1800_GFP_D6_rep2_miRNA-seq


title: Blood_Platelets_NKI-NSCLC-4021


title: Blood_Platelets_NKI-NSCLC-4377


title: HA1800_ND1_D6_rep2_RNA-seq


title: Blood_Platelets_NKI-NSCLC-3988


title: HA1800_ND1_D6_rep1_RNA-seq


title: Blood_Platelets_NKI-NSCLC-3951


title: mid11_07_G09


title: Blood_Platelets_NKI-NSCLC-3949


title: mid11_07_G10


title: mid11_07_G13


title: HA1800_ND1_D2_rep3_RNA-seq


title: Blood_Platelets_NKI-NSCLC-3851


title: Blood_Platelets_NKI-NSCLC-3736


title: Blood_Platelets_NKI-NSCLC-3723


title: Blood_Platelets_NKI-NSCLC-3899


title: Blood_Platelets_NKI-NSCLC-404


title: Blood_Platelets_NKI-NSCLC-3715


title: HA1800_ND1_D2_rep1_RNA-seq


title: HA1800_GFP_D6_rep3_RNA-seq


title: Blood_Platelets_NKI-NSCLC-3679


title: Blood_Platelets_NKI-NSCLC-3673


title: Blood_Platelets_NKI-NSCLC-3688


title: mid11_07_G05


title: Blood_Platelets_NKI-NSCLC-3658


title: mid11_07_G06


title: Blood_Platelets_NKI-NSCLC-4020


title: Blood_Platelets_NKI-NSCLC-3642


title: HA1800_GFP_D6_rep1_RNA-seq


title: Blood_Platelets_NKI-NSCLC-3639


title: mid11_07_G03


title: mid11_07_G08


title: HA1800_ND1_D2_rep2_RNA-seq


title: mid11_07_G07


title: Blood_Platelets_NKI-NSCLC-3589


title: mid11_07_G02


title: HA1800_GFP_D2_rep3_RNA-seq


title: Blood_Platelets_NKI-NSCLC-3588


title: HA1800_GFP_D2_rep2_RNA-seq


title: mid11_07_G01


title: Blood_Platelets_NKI-NSCLC-3486


title: Blood_Platelets_NKI-NSCLC-3575


title: Blood_Platelets_NKI-NSCLC-3406


title: Blood_Platelets_NKI-NSCLC-3382


title: HA1800_GFP_D6_rep2_RNA-seq


title: Blood_Platelets_NKI-NSCLC-3338


title: mid11_07_G04


title: mid11_07_F24


title: Blood_Platelets_NKI-NSCLC-3257


title: Blood_Platelets_NKI-NSCLC-3252


title: Blood_Platelets_NKI-NSCLC-3619


title: CD8+ T cells, TOXdeltaN Positive, rep 2

city: West Hollywood

first: AGCT

last: Core

state: CA

address: 8687 Melrose Ave, PDC B230

department: BMS

institute: Cedars Sinai Medical Center

description:
Short-GFP-P-2
Short-GFP-P-2_S15_R1_trimmed.genes.results

data_processing:
Raw sequencing data was demultiplexed and converted to fastq format by using bcl2fastq v2.20 (Illumina, San Diego, California).
Sequence reads were trimmed using Cutadapt with default parameters.
Then reads were aligned to the transcriptome using STAR (version 2.6.1) (Dobin A et al., 2013) and quantified using RSEM (version 1.2.28) (Li B and Dewey CN, 2011) with default parameters
Assembly: GRCm38
Supplementary files format and content: comma-delimited text containing raw counts for each sample

source_name: Spleen

extract_protocol:
8ng of total RNA was used as input for the construction of sequencing library.
Libraries were constructed per the manufacturer's protocol using the SMART-Seq v4 Ultra Low Input RNA Kit for Sequencing (Takara Bio USA), followed by the Nextera XT DNA Library Preparation Kit (Illumina).

value: Spleen

value: CD8+ T cell

value: OTI (C57BL/6-Tg(TcraTcrb)1100Mjb/J)

tag: genetic modification

value: TOXdeltaN+


title: CD8+ T cells, TOXdeltaN Positive, rep 1

description:
Short-GFP-P-1
Short-GFP-P-1_S14_R1_trimmed.genes.results


title: mid11_07_F22

value: d/d

value: Blastema

value: Mid


title: mid11_07_F23


title: Blood_Platelets_NKI-NSCLC-3236

value: Thrombocytes

value: NSCLC


title: CD8+ T cells, TOXdeltaN Negative, rep 2

description:
Short-GFP-N-2
Short-GFP-N-2_S13_R1_trimmed.genes.results

value: TOXdeltaN Neg (GFP-)


title: CD8+ T cells TOXdeltaN Negative, rep 1

description:
Short-GFP-N-1
Short-GFP-N-1_S12_R1_trimmed.genes.results


title: Blood_Platelets_NKI-NSCLC-3178


title: Blood_Platelets_NKI-NSCLC-3249


title: Blood_Platelets_NKI-NSCLC-3131


title: Blood_Platelets_NKI-NSCLC-3101


title: CD8+ T cells, TOXFL Positive, rep 2

description:
Long-GFP-P-2
Long-GFP-P-2_S19_R1_trimmed.genes.results

value: TOXFL+


title: CD8+ T cells, TOXFL Positive, rep 1

description:
Long-GFP-P-1
Long-GFP-P-1_S18_R1_trimmed.genes.results


title: Blood_Platelets_NKI-NSCLC-3177


title: HA1800_GFP_D2_rep1_RNA-seq


title: Blood_Platelets_NKI-NSCLC-3242


title: Blood_Platelets_NKI-NSCLC-3096


title: Blood_Platelets_NKI-NSCLC-3100


title: mid11_07_F19


title: Blood_Platelets_NKI-NSCLC-3083


title: CD8+ T cells, TOXFL Negative, rep 2

description:
Long-GFP-N-2
Long-GFP-N-2_S17_R1_trimmed.genes.results

value: TOXFL Neg (GFP-)


title: mid11_07_F18


title: Blood_Platelets_NKI-NSCLC-3038

value: nonResponder


title: mid11_07_F20


title: Blood_Platelets_NKI-NSCLC-3022


title: mid11_07_F21


title: Blood_Platelets_NKI-NSCLC-2993


title: mid11_07_F16


title: mid11_07_F15


title: mid11_07_F14


title: Blood_Platelets_NKI-NSCLC-2775


title: Blood_Platelets_NKI-NSCLC-2417


title: Blood_Platelets_NKI-NSCLC-2777


title: Blood_Platelets_NKI-NSCLC-2314


title: Blood_Platelets_NKI-NSCLC-2205


title: Blood_Platelets_NKI-NSCLC-2237


title: mid11_07_F13


title: Blood_Platelets_NKI-NSCLC-2220


title: mid11_07_F12


title: mid11_07_F17


title: Blood_Platelets_NKI-NSCLC-2153


title: Blood_Platelets_NKI-NSCLC-2150


title: mid11_07_F11


title: CD8+ T cells, TOXFL Negative, rep 1

description:
Long-GFP-N-1
Long-GFP-N-1_S16_R1_trimmed.genes.results


title: Blood_Platelets_NKI-NSCLC-2126


title: PO5_ROI_4_well_D09

city: Ottawa

first: Baptiste

last: Lacoste

state: Ontario

address: 451 Smyth Rd, Roger Guindon Hall

department: Cellular and Molecular Medicine

institute: University of Ottawa

description: Samples were pooled during library preparation and split across lanes. Individual FASTQ files were generated for each lane, forward & reverse primers. The Fastq files contain the same identifier as the sample name for aggregation.

data_processing:
dcc-metadata = true
save-interim-files = false
quality-trim-score = 20
2color-trimming = True
adapter1 = AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC
adapter2 = AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT
adapter-trim-match-length = 10
adapter-trim-max-mismatch = 3
barcode-max-mismatch = 1
stitching-max-mismatch = 2
dedup-hd = 1
threads = 4
Assembly: N/A, sequencing of synthetic tags and alignment to whitelist of RTS_IDs (probe barcodes) found in the config.ini output from the GeoMx DSP platform, see attached PKC file (Hs_R_NGS_WTA_COVID19_v1.0.pkc)
Supplementary files format and content: Digital Count Conversion (DCC) file format outputted from GeoMx NGS Pipeline, contains software versions, scan attributes, GeoMx NGS pipeline parameters and output metrics, Q30 scores, and list of deduplicated counts per RTS_ID (probe barcode)
Supplementary files format and content: Values represented in the collapsed target counts tab are the geometric mean of the probes for a given target--in the case that multiple probes were used-- and excludes any targets flagged as outliers. Analyzed counts represent the upper quartile normalized collapsed counts across the study after removing QC flagged segments and features.

source_name: Brain

extract_protocol:
Samples were incubated with DNA-oligo barcoded RNA-ISH probes which were conjugated with a UV-photocleavable linker following standard ISH protocols, along with flourescently labeled antibodies for visualization of morphological structures. Regions of interest within the tissue were illuminated with UV light and oligo barcodes were physically aspirated from the tissue and collected into microtiter plates by the GeoMx® Digital Spatial Profiler (DSP) platform. For more information about DSP protocols please see Merritt et al. Nature Biotech 2020 (doi: 10.1038/s41598-020-63539-x)
Each collection of oligo tags from one well (representing an ROI from the tissue section) was indexed with i7xi5 unique dual indexes using GeoMx SeqCode primers with 18 cycles of PCR.  After PCR, indexed AOIs were pooled and purified in two rounds of AMPure XP PCR purification using 1.2x bead:sample ratio.
OTHER: GeoMx Seq

value: Brain

tag: slide id

tag: roi number

tag: segment type

tag: area

tag: roi x coordinate

tag: roi y coordinate

tag: rawreads

tag: alignedreads

tag: deduplicatedreads

tag: trimmedreads

tag: stitchedreads

tag: sequencingsaturation


title: Blood_Platelets_NKI-NSCLC-2079

tag: tissue

tag: diagnosis

tag: treatment


title: PO5_ROI_6_well_E01


title: PO5_ROI_5_well_D10


title: PO5_ROI_5_well_D11


title: PO5_ROI_3_well_D07


title: PO5_ROI_4_well_D08


title: PO5_ROI_6_well_D12


title: Blood_Platelets_NKI-NSCLC-2932


title: mid11_07_F09

tag: strain

tag: regeneration stage


title: mid11_07_F10


title: Blood_Platelets_NKI-NSCLC-2006


title: Blood_Platelets_NKI-NSCLC-1946


title: PO5_ROI_2_well_D05

tag: slide id


title: mid11_07_F08


title: Blood_Platelets_NKI-NSCLC-1931


title: mid11_07_F07


title: Blood_Platelets_NKI-NSCLC-1924


title: Blood_Platelets_NKI-NSCLC-1922


title: Blood_Platelets_NKI-NSCLC-2149


title: mid11_07_F06


title: Blood_Platelets_NKI-NSCLC-1777


title: Blood_Platelets_NKI-NSCLC-1671


title: mid11_07_F05


title: Blood_Platelets_NKI-NSCLC-1725


title: PO5_ROI_1_well_D03

tag: roi number


title: PO5_ROI_3_well_D06

tag: segment type


title: PO5_ROI_2_well_D04

tag: area


title: PO5_ROI_1_well_D02

tag: roi x coordinate


title: Blood_Platelets_NKI-NSCLC-1589


title: Blood_Platelets_NKI-NSCLC-1665


title: Blood_Platelets_NKI-NSCLC-1653


title: PO3_ROI_6_well_C12

tag: roi y coordinate


title: PO5_ROI_6_well_D01

tag: rawreads


title: Blood_Platelets_NKI-NSCLC-1553


title: Blood_Platelets_NKI-NSCLC-1663


title: mid11_07_F02


title: mid11_07_F03


title: mid11_07_F04


title: Blood_Platelets_NKI-NSCLC-1544


title: PO3_ROI_5_well_C11

tag: alignedreads


title: mid11_07_F01


title: YYW_PBMC

city: Daejeon

first: Jong-Eun

last: Park

address: 291, Daehak-ro, Yuseong-gu

country: South Korea

institute: Korea Advanced Institute of Science and Technology

description: Single-cell RNA transcriptome analysis

data_processing:
All raw files of fastq format were mapped to the reference genome GRCh38 using the Cell Ranger Single Cell v.4.0.0 software (10x Genomics).
The Scanpy (version 1.8.1) Python package was used to load the cell-gene count matrix and for analysis
Cells with fewer than 2000 UMI counts and 500 detected genes were considered to be empty droplets and removed from the dataset. Cells with more than 7,000 detected genes were considered as potential doublets and removed from the dataset
Scrublet was used for doublet detection, the batch correction was performed using the Harmony algorithm
All count values were transformed to a log scale.
Genome_build: GRCh38
Supplementary_files_format_and_content: tab-delimited text files representing: mtx, barcodes, features.tsv

extract_protocol:
CSF was quickly transported and centrifuged at 700g for 10 min. After centrifugation, the supernatant was removed, and then the pellet was resuspended with 30 uL of CSF. A total of 10 μL of the single-cell suspension was counted in a Cellometer counting chamber (PD100, Nexcelom, MA, USA) through staining with acridine orange and propidium iodide (AO/PI) reagent (CS2-0106, Nexcelom, MA, USA). Only samples having more than 2,000 cells were selected for scRNA-seq.
PBMCs were isolated using Lymphoprep (07861, STEMCELL Technologies, BC, Canada) and SepMate-50 tubes (ST86450, STEMCELL Technologies, BC, Canada) according to the manufacturer’s protocol. Briefly, the enriched PBMCs were obtained from density gradient–medium centrifugation. The red blood cells were removed with an ACK lysing buffer (A1049201, Gibco, MA, USA). Cells were resuspended in complete RPMI medium containing 10% fetal bovine serum, 1% GlutaMax, and 1% penicillin/streptomycin up to 10 mL. All CSF/PBMC samples were processed without freezing in the RNA workflow.
Single-cell cDNA synthesis, amplification, and sequencing libraries were generated using the Single Cell 3′ Reagent Kit (10X Genomics) following the manufacturer’s instructions. Sequencing was carried out on an Illumina HiSeqXten and sequenced using the following parameters: Read1: 28 cycles, i7: 8 cycles, i5: 0 cycles, Read2: 91 cycles to generate paired-end reads.

tag: patient id

value: YYW

value: PBMC

tag: disease

value: MS


title: PO3_ROI_5_well_C10

tag: deduplicatedreads

tag: trimmedreads

tag: stitchedreads


title: YYW_CSF

description: Single-cell RNA transcriptome analysis

tag: tissue

value: CSF


title: Blood_Platelets_NKI-NSCLC-1844

tag: diagnosis

tag: treatment

value: Responder


title: YYS_PBMC

description: Single-cell RNA transcriptome analysis

value: YYS

value: Ab-mediated IDD


title: mid11_07_E24

tag: strain

value: d/d

tag: regeneration stage


title: PO3_ROI_4_well_C09

tag: slide id

tag: roi number

tag: sequencingsaturation


title: Blood_Platelets_NKI-NSCLC-1523


title: mid11_07_E23

value: Blastema


title: PO3_ROI_4_well_C08

tag: segment type

tag: area

tag: roi x coordinate


title: Blood_Platelets_NKI-NSCLC-1485


title: YYS_CSF

description: Single-cell RNA transcriptome analysis


title: mid11_07_E22

value: Mid


title: PO3_ROI_3_well_C07

tag: roi y coordinate

tag: rawreads

tag: alignedreads


title: YYJ_PBMC

description: Single-cell RNA transcriptome analysis

tag: patient id

value: YYJ

tag: disease


title: Blood_Platelets_NKI-NSCLC-1379

value: Thrombocytes

value: NSCLC


title: mid11_07_E21


title: YYJ_CSF

description: Single-cell RNA transcriptome analysis


title: SYG_PBMC

description: Single-cell RNA transcriptome analysis

value: SYG


title: PO3_ROI_3_well_C06

tag: deduplicatedreads

tag: trimmedreads

tag: stitchedreads


title: mid11_07_E19

tag: tissue


title: PO3_ROI_2_well_C05


title: Blood_Platelets_NKI-NSCLC-1349

tag: diagnosis

tag: treatment


title: mid11_07_E18

tag: strain

tag: regeneration stage


title: Blood_Platelets_NKI-NSCLC-1535


title: KYO_PBMC

description: Single-cell RNA transcriptome analysis

value: KYO

value: Normal


title: mid11_07_E20


title: PO3_ROI_2_well_C04

value: Brain

tag: slide id

tag: roi number

tag: sequencingsaturation


title: Blood_Platelets_NKI-NSCLC-1348


title: Blood_Platelets_NKI-NSCLC-1292

value: nonResponder


title: PO3_ROI_1_well_C03

tag: segment type

tag: area

tag: roi x coordinate


title: SYG_CSF

description: Single-cell RNA transcriptome analysis


title: mid11_07_E17


title: KYO_CSF

description: Single-cell RNA transcriptome analysis


title: PO3_ROI_1_well_C02

tag: roi y coordinate

tag: rawreads

tag: alignedreads


title: Blood_Platelets_NKI-NSCLC-1255


title: mid9_07_E16


title: Blood_Platelets_NKI-NSCLC-1369


title: Blood_Platelets_NKI-NSCLC-1244


title: KSH_PBMC

description: Single-cell RNA transcriptome analysis

tag: patient id

value: KSH

value: PBMC

tag: disease


title: PO2_ROI_6_well_C01

tag: deduplicatedreads

tag: trimmedreads

tag: stitchedreads


title: KSH_CSF

description: Single-cell RNA transcriptome analysis

tag: tissue

value: CSF


title: mid9_07_E15

tag: strain


title: mid9_07_E14

tag: regeneration stage


title: PO2_ROI_5_well_B11

tag: slide id


title: Blood_Platelets_NKI-NSCLC-1211

tag: diagnosis

tag: treatment


title: Blood_Platelets_NKI-NSCLC-1205

value: Responder


title: KJS_PBMC

description: Single-cell RNA transcriptome analysis

value: KJS

value: MS


title: mid9_07_E13

value: d/d


title: PO2_ROI_5_well_B10

tag: roi number

tag: segment type

tag: sequencingsaturation


title: KJS_CSF

description: Single-cell RNA transcriptome analysis


title: KHW_PBMC

description: Single-cell RNA transcriptome analysis

value: KHW

value: Ab-mediated IDD


title: PO2_ROI_4_well_B09

tag: area

tag: roi x coordinate

tag: roi y coordinate


title: Blood_Platelets_NKI-NSCLC-1198


title: Blood_Platelets_NKI-NSCLC-1143


title: mid9_07_E11

value: Blastema

value: Mid


title: JYJ_PBMC

description: Single-cell RNA transcriptome analysis

tag: patient id

value: JYJ


title: KHW_CSF

description: Single-cell RNA transcriptome analysis

tag: disease


title: Blood_Platelets_NKI-NSCLC-1128

value: Thrombocytes

value: NSCLC


title: mid9_07_E10


title: mid9_07_E12


title: mid9_07_E09


title: PO2_ROI_4_well_B08

tag: rawreads

tag: alignedreads

tag: deduplicatedreads


title: PO2_ROI_3_well_B07

tag: tissue

tag: trimmedreads

tag: stitchedreads


title: PO2_ROI_6_well_B12

tag: slide id


title: JYJ_CSF

description: Single-cell RNA transcriptome analysis


title: PO2_ROI_3_well_B06


title: Blood_Platelets_NKI-NSCLC-1109

tag: diagnosis


title: Blood_Platelets_NKI-NSCLC-107-602

tag: treatment


title: JSB_PBMC

description: Single-cell RNA transcriptome analysis

value: JSB

value: Normal


title: mid11_07_E07

tag: strain

tag: regeneration stage


title: Blood_Platelets_NKI-NSCLC-107-270

value: nonResponder


title: mid9_07_E08


title: mid11_07_E06


title: Blood_Platelets_NKI-NSCLC-107-245


title: mid11_07_E05


title: CYG_PBMC

description: Single-cell RNA transcriptome analysis

value: CYG


title: PO2_ROI_1_well_B02

value: Brain

tag: roi number

tag: segment type

tag: sequencingsaturation


title: PO2_ROI_1_well_B03

tag: area

tag: roi x coordinate

tag: roi y coordinate


title: CYG_CSF

description: Single-cell RNA transcriptome analysis

tag: patient id

value: CSF

tag: disease


title: PO1_ROI_6_well_B01

tag: rawreads

tag: alignedreads

tag: deduplicatedreads


title: JSB_CSF

description: Single-cell RNA transcriptome analysis

tag: tissue


title: mid11_07_E04


title: PO2_ROI_2_well_B04

tag: slide id

tag: trimmedreads

tag: stitchedreads


title: mid11_07_E03

tag: strain


title: Blood_Platelets_NKI-NSCLC-1041

tag: diagnosis

tag: treatment


title: PO1_ROI_6_well_A12

tag: roi number

tag: segment type


title: Normoxia

city: Shanghai

first: Huajian

last: Zhong

address: 415 Feng Yang Road

country: China

institute: Changzheng Hospital,Second Military 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
Genome_build: GRCh38
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample

source_name: nucleus pulposus

growth_protocol: Human nucleus pulposus cells were isolated from surgically discarded IVD tissues from patients, and cultured in Dulbecco’s modified Eagle’s medium supplemented with 10% fetal bovine serum and 1% Antibiotic-Antimycotic in a humidified atmosphere with 5% CO2 and 95% air.

extract_protocol:
Total RNA was extracted from cell  by Trizol reagent (Invitrogen) separately. The RNA quality was checked by Bioanalyzer 4200 (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: For hypoxic exposure, NP cells were maintained in a Modular Incubator Chamber (MIC101, Billups-Rothenberg, USA) with a mixture of 1% O2, 5% CO2, and 94% N2 for 24 h

tag: cell type

value: primary  nucleus pulposus

tag: passages

tag: oxygen tension

value: normoxia


title: Blood_Platelets_NKI-NSCLC-1034


title: Blood_Platelets_NKI-NSCLC-1114


title: mid11_07_E02

tag: regeneration stage


title: PO1_ROI_5_well_A11

tag: area

tag: roi x coordinate

tag: roi y coordinate

tag: sequencingsaturation


title: PO2_ROI_2_well_B05

tag: tissue

tag: rawreads

tag: alignedreads

tag: deduplicatedreads


title: HiC_CJW_S9WT_rep2

city: Bloomington

first: Xindan

last: Wang

state: IN

address: 1001 E 3rd St

institute: Indiana University at Bloomington

data_processing:
Reads from each end of a DNA fragment were represented in each of the two FASTQ files generated by Illumina paired-end sequencing.
The sequencing reads were mapped to the combined B. burgdorferi genome (NCBI GCA_000008685.2_ASM868v2) by Distiller-nf using maqp_30 filter otherwise defult setting.
Assembly: Borrelia burgdorferi S9 NCBI GCA_000008685.2_ASM868v2
Supplementary files format and content: Files ending with .mcool: HDF5 format containing multiple matrices which can be viewed using HiGlass and munipulated using cooler and cooltools.

organism: Borreliella burgdorferi

source_name: Bacterial cell

extract_protocol:
Wild type and mutant cells of Borrelia burgdorferi S9 growing in BSK-II were crosslinked using 3% formaldehyde for 30min at room temperature and then lysed by treatment of lysosome and 1% SDS as previouly described (Wang et al 2015).
Standard library construction protocol was used for Illumina Nextseq500 sequencing platforms. Illumina Truseq indexes were used.

tag: strain

value: Bacterial cell

tag: genotype

value: WT


title: HiC_CJW_S9WT_rep1


title: Blood_Platelets_NKI-NSCLC-1019

tag: diagnosis

tag: treatment

value: Responder


title: mid11_07_E01

value: d/d


title: Blood_Platelets_NKI-NSCLC-1043


title: PO1_ROI_4_well_A09

tag: slide id

tag: roi number

tag: segment type

tag: trimmedreads

tag: stitchedreads


title: PO1_ROI_5_well_A10

tag: area


title: Blood_Platelets_NKI-NKI-004957-NSCLC


title: Blood_Platelets_GRON-Gron-1118-NSCLC


title: mid9_07_D24

value: Blastema

tag: regeneration stage


title: mid9_07_D23

value: Mid


title: HiC_CJW_Bb609_rep2

tag: cell type

value: Bb609 mutant


title: mid9_07_D22


title: PO1_ROI_4_well_A08

tag: roi x coordinate

tag: roi y coordinate

tag: sequencingsaturation


title: hypoxia

tag: passages

tag: oxygen tension

value: hypoxia


title: HiC_CJW_Bb609_rep1

tag: strain


title: PO1_ROI_3_well_A07

tag: tissue

tag: rawreads

tag: alignedreads

tag: deduplicatedreads


title: HiC_CJW_Bb366_rep2

tag: genotype

value: Bb366 mutant


title: HiC_CJW_Bb605_rep2

value: Bb605 mutant


title: HiC_CJW_Bb605_rep1


title: mid9_07_D20


title: siGAPDH [si-14-p_S66]

first: Christopher

last: Rhodes

state: Hammersmith and Fulham

address: Hammersmith Campus, Du Cane Rd

country: United Kingdom

institute: Imperial College London

data_processing:
salmon estimation of transcript reads
combination of transcripts to genes by tx2gene
Assembly: GENCODE 28
Supplementary files format and content: csv raw gene estimated tpm from salmon

source_name: HPAEC

extract_protocol:
Qiagen RNAeasy kits to extract total RNA from hPAEC cell lysates from confluent 6-well plates.
Each RNA sample will be quantified using Qubit and run on a Tapestation to assess sample integrity. mRNA will be isolated from total RNA using oligo dT beads. After fragmentation the sample will be converted to double stranded DNA and ligated to Illumina adapters. The second strand cDNA is then degraded by the UNG enzyme providing directional information to the library. Indexing of each sample will be performed by PCR. For each pool of libraries, Tapestation will be used to assess fragment distribution and presence of artefacts. Each submitted pool will also be quantified by Qubit and/or qPCR prior to sequecing. Sequencing will be performed using a HiSeq4000.
pooled and sequenced across multiple lanes

tag: agent

value: siGAPDH

value: HPAEC


title: siGAPDH [si-03-p_S68]


title: siGAPDH [si-12-p_S67]


title: PO1_ROI_3_well_A06

tag: slide id

tag: roi number

tag: segment type

tag: trimmedreads


title: mid9_07_D21

tag: regeneration stage


title: mid9_07_D19


title: HiC_CJW_Bb366_rep1

tag: cell type


title: PO1_ROI_2_well_A04

tag: area

tag: roi x coordinate

tag: roi y coordinate

tag: stitchedreads


title: PO1_ROI_2_well_A05

tag: sequencingsaturation


title: mid9_07_D18

tag: strain

tag: tissue


title: HiC_CJW_Bb354_rep2

value: Bb354 mutant


title: negativeSIRNA [si-12-n_S64]

value: negativeSIRNA


title: negativeSIRNA [si-03-n_S63]


title: mid9_07_D17


title: PO1_ROI_1_well_A03

value: Brain

tag: rawreads

tag: alignedreads


title: HiC_CJW_Bb354_rep1

tag: genotype


title: mid9_07_D16


title: HiC_CJW_Bb353_rep2

value: Bb353 mutant


title: mid9_07_D15


title: HiC_CJW_Bb353_rep1


title: PO1_ROI_1_well_A02

tag: deduplicatedreads


title: siGAPDH [si-16-p_S65]

tag: agent


title: HiC_CJW_Bb288_rep1

value: Bb288 mutant


title: HiC_CJW_Bb288_rep2

value: Bacterial cell


title: mid9_07_D14


title: mid9_07_D13


title: siSOX17 [si-03-17_S51]


title: siSOX17 [si-12-17_S52]


title: negativeSIRNA [si-16-n_S61]


title: negativeSIRNA [si-14-n_S62]


title: mid9_07_D12


title: siSOX17 [si-14-17_S50]


title: HiC_CJW_Bb287_rep2

value: Bb287 mutant


title: siSOX17 [si-16-17_S49]


title: mid9_07_D11


title: HiC_CJW_Bb287_rep1


title: Control

city: Jinan

first: Wei

last: Lin

state: Shandong

address: 6699 Qingdao Road, Huaiyin District, Jinan, Shandong , China

department: School of Clinical and Basic Medicine

institute: Shandong First Medical University & Shandong Academy of Medical Sciences

description: 10× Genomics

library_source: transcriptomic single cell

data_processing:
Raw FASTQ files were mapped to the mouse Reference genome using Cell Ranger 3.0 (10× Genomics). The references were rebuilt based on the instructions provided in 10× Genomics (https://support. 10× Genomics.com/single-cell-gene expression/software/pipelines/latest/advanced/references), which perform alignment, filtering, barcode counting, and UMI counting, to create Cell Ranger-compatible reference genomes. Digital gene expression (DGE) matrixes were generated for each sample and the combined samples following alignment. Merged 10× Genomics DGE files were generated using the aggregation function of the Cell Ranger pipeline. All cells in different batches were merged and controlized by equalizing the read depth among libraries. The matrix of all cells and their global genes was the final outcome. The gene expression matrixes were combined in R (version 4.1.3) and converted to a Seurat object using the Seurat R package. The single-cell expression matrix was calculated using Seurat (version 4.1.0) for filtering, data Controlization, dimensionality reduction, clustering, and differentially expressed gene analysis.
Supplementary files format and content: mm10
Supplementary files format and content: Tab-separated values and matrix files

source_name: ocular tissue

extract_protocol:
After separating the eyes from the mice, the dissected tissues were immediately placed in complete medium. After lens was removed. the dissected tissues were digested, and incubated with 5 mg/ml of collagenase IV (Sigma-Aldrich) and neutral protease (Sigma-Aldrich) on a shaking bed (180 rpm) and at a constant temperature (37℃ for 30 min. Finally, the dissociated cells were resuspended in Ca2+-free buffer (with 1% BSA) and filtered to ensure single-cell suspension using a 40 μm filter membrane. The single-cell suspension was washed twice with phosphate-buffered saline (PBS) and centrifuged (120 × g, 4°C, 3 min). The samples were resuspended with PBS and processed for cell viability test, cell counting, and single-cell arresting. The cells were stored on ice as much as possible during the entire single-cell acquisition procedure, which was completed within 90 min, to maintain cell activity
For the Control or EAU samples, single cells were independently arrested by the 10× Genomics system. Briefly, cell suspensions were loaded on a Chromium Single Cell Controller (10× Genomics) to generate single-cell gel beads in emulsion (GEMs) by using Single Cell 3' Library and Gel Bead Kit V3 (10x Genomics, 1000075) and Chromium Single Cell B Chip Kit (10x Genomic, 1000074) according to the manufacturer’s protocol. cDNA was generated and amplified, and quality was assessed using the Agilent 4200. Finally, sequencing was performed on an Illumina Novaseq6000 with a sequencing depth of at least 100,000 reads per cell and pair end 150bp (PE150).

value: ocular tissue

tag: Sex

value: female

tag: age

value: 6~8 weeks

tag: disease state

value: naïve


title: EAU

description: 10× Genomics

value: EAU


title: mid9_07_D10

source_name: Blastema

value: d/d

value: Blastema

tag: regeneration stage

value: Mid


title: HiC_CJW_Bb286_rep2

tag: cell type

value: Bb286 mutant


title: Signal 1-Repression [3-KR-43-4_S29]

value: Signal 1-Repression

value: HPAEC


title: mid9_07_D09


title: HiC_CJW_Bb286_rep1


title: HiC_CJW_Bb285_rep2

value: Bb285 mutant


title: HiC_CJW_Bb284_rep2

value: Bb284 mutant


title: HiC_CJW_Bb285_rep1


title: Control cells-Control [3-WT-4_S30]

value: Control cells-Control


title: BFP control-Repression [3-KR-BF-4_S25]

value: BFP control-Repression


title: Promoter-Repression [3-KR-14-4_S26]

value: Promoter-Repression


title: Control cells-Control [3-WT-3_S24]


title: HiC_CJW_Bb284_rep1

value: Bacterial cell


title: Promoter-Activation [3-SA-17-4_S28]

value: Promoter-Activation


title: Signal 1-Repression [3-KR-43-3_S23]


title: Vehicle, M[IL-4], rep1

first: Alexandre

last: Blais

address: 451 Smyth Road

data_processing:
Raw paired-end reads were trimmed of adapters using fastp before being aligned on the mouse genome (assembly GRCm38) using STAR in local mode and retaining only read pairs with mapq score of 40. Duplicate reads were marked but retained using Picard. Reads aligning to exons were counted and summarized to genes using Subread featureCounts. Differential expression testing was performed in R/Bioconductor using edgeR and the glmQLFTest function. For differential expression calls, a log2 fold-change value of 1 or -1 combined with a Benjamini-Hochberg-calculated FDR value less than 0.05 was judged significant.
Assembly: GRCm38
Supplementary files format and content: Tab-delimited file containing the featureCounts read summarization to gene counts for ENSEMBL genes (rows) and 18 RNA-seq samples (columns)

source_name: Bone marrow

growth_protocol: BMDMs were grown in 20 mL DMEM with 10% FBS and 1% FBS, supplemented with 20% L-929 culture supernatant in 15-cm dishes. On day 3, 5 mL of growth media was added. Cells were harvested on day 7 of culture.

extract_protocol:
Total RNA was isolated from BMDM using Tripure reagent and chloroform and subsequently purified using spin columns (PureLink RNA Mini, ThermoFisher).
Messenger RNA was purified from total RNA using poly-T oligo-attached magnetic beads. After fragmentation, the first strand cDNA was synthesized using random hexamer primers followed by the second strand cDNA synthesis. The library was ready after end repair, A-tailing, adapter ligation, size selection, amplification, and purification.

treatment_protocol: BMDMS were treated with vehicle (0.1% DMSO), 250 µM HC3, or 5 µM RSM-932a for 24h then polarized under naïve (M[0]) or 20 ng/mL IL-4 (M[IL-4]) for another 24h. Samples were prepared from 3 individual mice.

value: female

value: Bone marrow

value: macrophage

tag: treatment

value: Vehicle


title: HC3, M[IL-4], rep3

value: 250 uM HC3


title: RSM, M[IL-4], rep2

value: 5 uM RSM-932a


title: Vehicle, M[IL-4], rep2


title: HC3, M[IL-4], rep2


title: RSM, M[IL-4], rep1


title: RSM, M[IL-4], rep3


title: RSM, M[0], rep3


title: Vehicle, M[IL-4], rep3


title: HC3, M[0], rep3


title: scRNAseq from PH animal -2

city: Aurora

first: Sushil

last: Kumar

institute: University of Colorado Anschutz medical campus

description:
10x Genomics
DPA-HA-234

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v2.1.1 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Raw sequencing FASTQ read will be processed using the CellRanger (10X Genomic) software.
The CellRanger’s output count data will be analyzed using the Seurat v4.0 package. Briefly, samples will be filtered based on cell and gene levels integrity. Systematic bias and batch effect will be assessed using samples' metadata and cell cycle information.
Samples will be normalized using the SCTransform function, followed by Principal Component (PC) level selection.
The selected level of PC will be used to find cell clusters. The clusters' cell type identification will be conducted using the SingleR R package (Aran, et al.,). Differential gene expression analysis for each cluster will be performed using the FindMarker function.
Assembly: Bos_taurus.ARS-UCD1.2.104
Supplementary files format and content: Tab-separated values files and matrix files

organism: Bos taurus

source_name: distal pulmonary arteries (less than 2mm)

extract_protocol:
Freshly collected distal pulmonary vessels were washed with ice-cold PBS without (Mg2+/Ca2+). The 100mg tissue was then cut into small pieces. Single cells were generated by the digestion buffer containing collagenase I, DNase I, and Dispase, until all pieces become single cells (in 2 hours, but cells released from the vessels were collected in every 45 mins to avoid damage). Finally, all cells passing 30μm strainer were checked for cell viability (80% cell viability is required).
Library was performed according to the manufacter’s instructions (single cell 3’ v2 protocol, 10x Genomics). Briefly, GCs were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead-in-emulsion (GEM). The poly-A RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA, which contains an Ilumina R1 primer sequence, Unique Molecular Identifier (UMI) and the 10x Barcode. The pooled barcoded cDNA was then cleaned up with Silane DynaBeads, amplified by PCR and the apropiated sized fragments were selected with SPRIselect reagent for subsequent library construction. During the library construction Ilumina R2 primer sequence, paired-end constructs with P5 and P7 sequences and a sample index were added.

value: cells in vessels

value: male

tag: breed

value: holstein dairy calf

value: 2 weeks old


title: BFP control-Activation [3-SA-BF-4_S27]

value: BFP control-Activation

value: HPAEC


title: HC3, M[IL-4], rep1


title: Promoter-Activation [3-SA-17-3_S22]


title: scRNAseq from PH animal -3

description:
10x Genomics
DPA-HA-236

value: distal pulmonary arteries (less than 2mm)


title: scRNAseq from PH animal -1

description:
10x Genomics
DPA-HA-233


title: BFP control-Activation [3-SA-BF-3_S21]


title: RSM, M[0], rep2


title: scRNAseq from control animal-3

description:
10x Genomics
DPA-CO-235


title: HC3, M[0], rep2


title: Promoter-Repression [3-KR-14-3_S20]


title: Vehicle, M[0], rep2


title: BFP control-Repression [3-KR-BF-3_S19]

value: BFP control-Repression


title: scRNAseq from control animal-1

description:
10x Genomics
DPA-CO-14


title: RSM, M[0], rep1


title: HC3, M[0], rep1


title: Vehicle, M[0], rep3


title: F344 Male 14 weeks normal salt, rep8

city: Muenster

first: Anika

last: Witten

address: Domagkstr. 3

department: Institute of Human Genetics, Department Genetic Epidemiology

institute: University of Muenster

description:
37.2
direct hybridization assay

hyb_protocol: sample hybridization was performed following the WGGEX Direct Hybridization Assay Guide

scan_protocol: BAR standard

data_processing: The data were normalised using quantile normalisation and the different gene expression analysis were performed using the R packages systemsbio and limma

organism: Rattus norvegicus

source_name: Rat 14 weeks old, cardiac tissus, free wall left ventricle

label_protocol: biotin-cRNA was performed using the TargetAmp-Nano Labeling Kit for Illumina Expression BeadChip according to the manufacturer's instruction

growth_protocol: All animals were maintained under standard conditions of regular 12h diurnal cycles using an automated light switching device and climate-controlled conditions at a constant room temperature of 22°C. Animals had access to food and water ad libitum. All animal experiments were approved by the responsible local government committee in accordance with the guidelines of the Charité-Universitätsmedizin Berlin and national animal protection guidelines (Landesamt für Gesundheit und Soziales (LAGeSo) Berlin, Germany) for the use of laboratory animals. Male SHRSP and F344 rats were obtained from our colonies at the Forschungseinrichtung für Experimentelle Medizin (FEM), Charité - Universitätsmedizin, Berlin. To develop the consomic strain SHRSP-1F344 (Rat Genome Database (RGD)-ID: SHRSP-Chr 1F344/Rkb), we crossed the SHRSP strain with the F344 strain in accordance with our linkage results and introgressed the whole rat chromosome (RNO)1 from F344 into the SHRSP background.

extract_protocol: Hearts were dissected and arrested in diastole by rinsing in 1 M KCl solution and subsequently blotted dry. The atria were trimmed away and hearts and kidneys were weighed. LV tissue was separated from septum and right ventricle for determination of LV weight. RNA was isolated from the free wall LV by the TRIzol reagent according to the manufacturer's instructions and dissolved in DEPC-treated H2O. The quality and concentration of the purified total RNA were confirmed by spectroscopy.

treatment_protocol: normal salt for 14 weeks

value: Rat F344

value: cardiac, left ventricle

value: 14 weeks old


title: scRNAseq from control animal-2

description:
10x Genomics
DPA-CO-15


title: F344 Male 14 weeks normal salt, rep7

description:
38.2
direct hybridization assay


title: F344 Male 14 weeks normal salt, rep5

description:
30.2
direct hybridization assay


title: F344 Male 14 weeks normal salt, rep4

description:
40.2
direct hybridization assay


title: F344 Male 14 weeks normal salt, rep6

description:
39.2
direct hybridization assay


title: MAdCAM1_rep2

city: Maebashi

first: Naoya

last: Ozawa

state: None Selected

address: showamachi

country: Japan

institute: Gunma University, Graduate School of Medicine

data_processing:
Obtained reads (CAGE tags) were mapped to the  GRCm39 genome using BWA (version 0.7.17). Unmapped reads were then mapped by HISAT2 (version 2.0.5).
CAGE tag clustering, detection of differential expressed genes and motif discovery were performed by pipeline RECLU (Ohmiya et al., BMC Genetics 2014, 15:269). Tag count data were clustered using the modified Paraclu program. Clusters with count per million (CPM) < 0.1 were discarded.
Regions that have 90% overlap between replicates were extracted by BEDtools (version 2.12.0). The clusters with irreproducible discovery rate (IDR) >=0.1 and clusters longer than 200 bp were discarded.
Differentially expressed genes were detected using the edgeR package (version 3.22.5).  For motif analysis, the genomic DNA sequence of the region from 200bp upstream to 50bp downstream of differentially expressed CAGE peaks were subjected to de novo motif discovery tools: AMD, GLAM2, DREME and Weeder.
The occurrences of the motifs were examined by FIMO. The similarity of consensus motifs and the motifs in database JASPAR CORE 2016 vertebrates were evaluated by Tomtom. The list of differentially expressed genes detected by RECLU with false discovery rate (FDR) =< 0.05 were used for GO enrichment analysis by clusterProfiler package (Yu et al., OMICS 2012, 16:5).
Assembly: GRCm39
Supplementary files format and content: tab-delimited text files include CPM values for each sample.

source_name: colon

extract_protocol:
Total RNA was extracted from tissues of AOM/DSS mouse tumours using the RNeasy Kit (Qiagen, Hilden, Germany).
The total RNA of tumours in AOM/DSS mice was analyzed using CAGE. CAGE library preparation, sequencing, mapping, gene expression analysis, motif discovery analysis, and gene ontology (GO) enrichment analysis were performed using DNAFORM (Yokohama, Kanagawa, Japan). Total RNA quality was assessed using a Bioanalyzer (Agilent, Santa Clara, CA, USA) to ensure that the RNA integrity number (RIN) was >7.0. cDNAs were synthesized from total RNA using random primers. Ribose diols in the 5′ cap structures of RNA were oxidized and biotinylated. Biotinylated RNA/cDNA was selected using streptavidin beads (cap-trapping). After RNA digestion by RNaseONE/H and adaptor ligation to both ends of cDNA, double-stranded cDNA libraries (CAGE libraries) were constructed. The CAGE libraries were sequenced using single-end reads of 75 nt on a NextSeq 500 instrument (Illumina, San Diego, CA, USA). The reads obtained (CAGE tags) were mapped to the mouse GRCm39 genome using BWA (version 0.7.17). The unmapped reads were mapped using HISAT2 (version 2.0.5). CAGE tag clustering, detection of differentially expressed genes, and motif discovery were performed using the pipeline RECLU (Ohmiya et al., BMC Genetics 2014, 15:269). The tag count data were clustered using the modified Paraclu program. Clusters with count per million (CPM) <0.1 were discarded. Regions with 90% overlap between replicates were extracted using BED tools (version 2.12.0). Clusters with an irreproducible discovery rate (IDR) ≥0.1 and clusters longer than 200 bp were discarded. Differentially expressed genes were detected using the edgeR package (version 3.22.5). For motif analysis, the genomic DNA sequences of the region from 200 bp upstream to 50 bp downstream of differentially expressed CAGE peaks were subjected to the de novo motif discovery tools AMD, GLAM2, DREME, and Weeder. The occurrence of these motifs was examined using FIMO. The similarity of consensus motifs and motifs in the JASPAR CORE 2016 vertebrates was evaluated using TomTom. The list of differentially expressed genes detected by RECLU with a false discovery rate (FDR) ≤0.05 were used for GO enrichment analysis using the cluster Profiler package27.
CAGE library preparation, sequencing, mapping, gene expression, motif discovery analysis, and gene ontology (GO) enrichment analysis were performed by DNAFORM (Yokohama, Kanagawa, Japan). Qualities of total RNA were assessed by Bioanalyzer (Agilent) to ensure that RIN (RNA integrity number) is over 7.0. The cDNAs were synthesized from total RNA using random primers. The ribose diols in the 5’ cap structures of RNAs were oxidized, and then biotinylated. The biotinylated RNA/cDNAs were selected by streptavidin beads (cap-trapping). After RNA digestion by RNaseONE/H and adaptor ligation to both ends of cDNA, double-stranded cDNA libraries (CAGE libraries) were constructed. CAGE libraries were sequenced using single end reads of 75nt on a NextSeq 500 instrument (Illumina).

value: colon


title: Signal 1-Repression [3-KR-43-2_S17]

value: Signal 1-Repression


title: Promoter-Activation [3-SA-17-2_S16]

value: Promoter-Activation


title: Vehicle, M[0], rep1

value: female

value: Bone marrow

value: macrophage

value: Vehicle


title: Control cells-Control [3-WT-2_S18]

value: Control cells-Control


title: IgG_rep2


title: F344 Male 14 weeks normal salt, rep3

description:
36.2
direct hybridization assay

value: male


title: BALB/c WAS 2

city: Wuhan

first: Gen

last: Zheng

state: Wuhan

address: Zhongshan road

institute: Wuhan Union Hospital

description: WAS.hic

data_processing:
We used ChIA-PET2 software to process the BL-Hi-C sequencing data, including linker trimming, read alignment (BWA), PET formation, and duplicate removal. The PETs were further adapted to enable the software homer to generate contact matrixes and heatmaps, to allow the software ChIA-PET2 or MICC to perform peak calling or PET clustering, among other functions.(PMID:29158486)
Assembly: mm10
Supplementary files format and content: Hic

source_name: colon epithelium

extract_protocol:
Crosslinked colon epithelium crypts from each mouse were ground in 500 µl nucleus lysis buffer (10 mM Tris-HCl pH 8.0, 10 mM NaCl, 0.2% Igepal CA630, Roche protease inhibitors cocktail) on ice with 0.5 ml glass grinder, and the nuclei were filtered with 40 µm Falcon cell strainer.
The BL-Hi-C analysis was performed as described (PMID:29158486).

value: colon epithelium

value: epithelial

value: BALB/c WT

value: Water avoidance stress


title: F344 Male 14 weeks normal salt, rep2

description:
29.2
direct hybridization assay


title: BFP control-Activation [3-SA-BF-2_S15]

value: BFP control-Activation

value: HPAEC


title: Promoter-Repression [3-KR-14-2_S14]

value: Promoter-Repression


title: IgG_rep1


title: BALB/c control 2

description: CT.hic


title: MAdCAM1_rep1


title: PND4CKO4

city: University Park

first: Camilla

middle: H. K.

last: Hughes

state: PA

address: 439 Shortlidge Rd

department: Animal Science

institute: Penn State University

data_processing:
Data were analyzed using the GenPipes pipeline, version 4.3.0 (https://pubmed.ncbi.nlm.nih.gov/31185495/) using default settings, with Ensembl v.102 annotation.
Trimming was performed with trimmomatic.
Reads were aligned using STAR.
Raw count data was obtained using HTseq.
Raw count data were analyzed in DEseq2.
Assembly: GRCm38
Supplementary files format and content: Raw count data as txt, file name CountMatrixSFAMH_raw.txt.
Supplementary files format and content: DEseq2 results in Excel docs, one document for each relevant comparison, file names: Data_S1_ED17_5_con_vs_cko.xlsx; Data_S2_PND1_con_vs_cko.xlsx; Data_S3_PND4_con_vs_cko.xlsx; Data_S4_CON_ED17_5_vs_PND1.xlsx; Data_S5_CON_PND1_vs_PND4.xlsx; Data_S6_CKO_ED17_5_vs_PND1.xlsx; Data_S7_CKO_PND1_vs_PND4.

source_name: Whole ovary

extract_protocol:
RNA was isolated from whole ovaries using the Arcturus PicoPure RNA Isolation Kit (Thermo), according to the manufacturer’s protocol. Following isolation, ovaries from 3-5 PND1 or PND4 or 5 ED17.5 mice were pooled together within each age and genotype group and RNA was further purified and DNase-treated using the RNA Clean & Concentrator Kit (Zymo Research), also according to the manufacturer’s protocol. RNA purity was assessed by Nanodrop and all samples had absorbance ratio of A260/280 >1.8 and A260/230 > 1.1, with all samples but two having A260/230 > 1.7. RNA quality and quality were assessed on a Biorad experion according to the manufacturers’ protocol and all samples had an RQI > 8.0, indicating high RNA quality.
An RNA input of 100 ng was used for library construction. First, mRNA was separated using oligo-dT based purification, using the NEBNext® Poly(A) mRNA Magnetic Isolation Module (New England Biolabs). This purified mRNA was used directly as input for the Library construction with the NEBNext® Ultra™ II Directional RNA Library Prep Kit for Illumina (New England Biolabs), also conducted according to the manufacturer’s protocol.

value: Whole ovary

value: whole ovary (mixed)

value: CKO


title: BFP control-Repression [3-KR-BF-2_S13]

value: BFP control-Repression


title: PND4CKO3


title: PND4CKO2


title: BALB/c control 1

description: CT.hic


title: F344 Male 14 weeks normal salt, rep1

description:
35.2
direct hybridization assay

value: Rat F344

value: cardiac, left ventricle

value: 14 weeks old


title: BFP control-Activation [2-SA-BF-4_S11]


title: 6hpa_control_H3K9me3_rep2

first: Qianshu

last: Zhu

state: Shanghai

address: Siping Road

department: School of Life Science and Technology

institute: Tongji University

data_processing:
Low-quality and the adaptor sequences were trimmed from the reads using cutadapt (v1.16)with parameters: --trim-n -q 25,25 -m 75 -a AGATCGGAAGAGC -A AGATCGGAAGAGC.
Then, all CUT&RUN data reads were aligned to the mm10 reference genome used BWA with mem command.
Signal tracks were generated using the deepTools bamCoverage function with normalized to 1-million reads by sequencing depth of spike in.
Assembly: mm10
Supplementary files format and content: *.bw are bigWig files generated using deepTools.
Library strategy: CUT&RUN

growth_protocol: MII oocytes were retrieved from the dissected oviducts of super-ovulated B6D2F1 female mice at 13 h post hCG injection for subsequent SCNT procedure. To get fertilized embryos, the super-ovulated C57BL/6 female mice were mated with C57BL/6 male mice. Then, the zygotes were collected from the oviducts of the female mice at 20 h after hCG injection and were cultured in G-1 PLUS medium at 37℃ under 5% CO2 until blastocysts.

extract_protocol:
50 blastomeres were used per reaction. Each sample were bound with 5 μL concanavalin-coated magnetic beads and incubated with 1 μg antibody at 4℃ for 2 hours. Deluted pA-MNase was incubated with samples at 4℃ for 1 hour and chromatin cleavage was initiated with 100mM CaCl2,for 15 minutes at 0℃. RNA and proteins were then digested. Fragmented DNA was purified by phenol chloroform followed by ethanol purification.
Libraries were generated using the KAPA HyperPrep Kit for the Illumina platform (kk8504), following the manufacturer's instrunctions. Paired-end 150 bp sequencing was performed in NovaSeq (Illumina) platform in Berry Genomics and Novogen.

treatment_protocol: Three siRNAs against Suv39h2 were diluted and mixed in nuclease-free water to a working concentration of 20 μM per siRNA. Oocytes were injected with approximately 10 pL of siRNAs using a Piezo-driven micromanipulator. The injected oocytes underwent SCNT procedure after 20 min recovery. Embryos were collected at 6hpa for H3K9me3 CUT&RUN.

value: wild type

tag: chip antibody

value: H3K9me3 (Active Motif, 39161)

value: SCNT embryo 6 hpa


title: PND4CKO1


title: SHRSP-1F344 Male 14 weeks normal salt, rep6

description:
45.2
direct hybridization assay

value: Rat consomic SHRSP-1F344

value: male


title: SHRSP-1F344 Male 14 weeks normal salt, rep7

description:
52.2
direct hybridization assay


title: Promoter-Repression [2-KR-14-4_S10]


title: 6hpa_siSuv39h2_H3K9me3_rep2


title: SHRSP-1F344 Male 14 weeks normal salt, rep4

description:
53.2
direct hybridization assay


title: PND4CON4

value: CON


title: 6hpa_control_H3K9me3_rep1


title: SHRSP-1F344 Male 14 weeks normal salt, rep5

description:
46.2
direct hybridization assay


title: SHRSP-1F344 Male 14 weeks normal salt, rep2

description:
48
direct hybridization assay


title: Promoter-Activation [2-SA-17-4_S12]

value: Promoter-Activation


title: PND4CON3


title: Promoter-Activation [2-SA-17-2_S8]


title: PND4CON2


title: BALB/c WAS 1

description: WAS.hic

value: colon epithelium

value: epithelial

value: BALB/c WT

value: Water avoidance stress


title: 6hpa_siSuv39h2_H3K9me3_rep1


title: BFP control-Activation [2-SA-BF-2_S7]

value: BFP control-Activation

value: HPAEC


title: SHRSP-1F344 Male 14 weeks normal salt, rep3

description:
50.2
direct hybridization assay


title: 8781-MP-0002

city: Nashville

first: Mary

last: Philip

state: TN

address: 777 PRB, 2220 Pierce Ave

department: Medicine

institute: Vanderbilt University Medical Center

description: Sort-purified (live CD8+CD90.1+CD44-) transgenic TCRTAG CD8 T cells from spleen, rep 2

data_processing:
The quality of the sequenced reads was assessed with FastQC and QoRTs.
Sequenced reads were aligned with default parameters to the mouse reference genome (GRCm38.p6) using STAR v2.7.6a.
Gene expression estimates were obtained with featureCounts v2.0.1 using composite gene models from Gencode vM25
Assembly: GRCm38.p6
Supplementary files format and content: tab-delimited text files include raw abundance values for each sample as obtained from featureCounts

extract_protocol:
CD8 T cells were sorted directly into Trizol LS and frozen. Total RNA was extraced from sorted cells using the Rneasy Micro kit (Qiagen)and amplified using the SMART-Seq v4 UltraLow Input RNA Kit (Clontech).
Libraries were prepared using NEBNext polyA mRNA sample kits (NEB).

value: Spleen


title: 8781-MP-0003

description: Sort-purified (live CD8+CD90.1+CD44-) transgenic TCRTAG CD8 T cells from spleen, rep 3


title: SHRSP-1F344 Male 14 weeks normal salt, rep1

description:
47.2
direct hybridization assay


title: SHRSP Male 14 weeks normal salt, rep6

description:
41.2
direct hybridization assay

value: Rat SHRSP


title: PND4CON5

value: Whole ovary

value: whole ovary (mixed)


title: BFP control-Repression [2-KR-BF-4_S9]

value: BFP control-Repression


title: 8781-MP-0001

description: Sort-purified (live CD8+CD90.1+CD44-) transgenic TCRTAG CD8 T cells from spleen, rep 1


title: PND1CKO3

value: CKO


title: SHRSP Male 14 weeks normal salt, rep7

description:
51.2
direct hybridization assay

value: cardiac, left ventricle

value: 14 weeks old


title: SHRSP Male 14 weeks normal salt, rep5

description:
44.2
direct hybridization assay

value: male


title: SHRSP Male 14 weeks normal salt, rep2

description:
43.2
direct hybridization assay


title: SHRSP Male 14 weeks normal salt, rep3

description:
42.2
direct hybridization assay


title: Lrrc10 KO MI-3

city: La Jolla

first: Rebecca

middle: J.

last: Salamon

address: 9500 Gilman Drive

department: Pediatrics

institute: University of California, San Diego

description: Lrrc10 KO MI-3

data_processing:
Raw sequence data (.bcl files) generated from Illumina HiSeq was converted into fastq files of reads (ranging ~18-28Mil per sample) and de-multiplexed using Illumina's bcl2fastq 2.17 software. One mismatch was allowed for index sequence identification.
Cutadapt (Version 3.4) was used to trim adapter sequences, remove unpaired reads, and remove reads less than 36 nucleotides. The cut reads were checked for quality and adapter removal using FastQC.
Reads were aligned to the GRCm39 mouse genome using HiSAT2 (Version 2.2.1)
Gene-level counts were generated using RSEM (Version 1.1.17)
Differential gene expression analysis was performed DESeq2
Assembly: GRCm39
Supplementary files format and content: RSEM expected gene counts (txt)
Supplementary files format and content: TPM gene counts (xslx)

source_name: full heart ventricle

extract_protocol:
Sex-balanced groups were collected at 7 days post-surgery (Sham or MI), hearts were harvested, full ventricles (above and below MI ligation) were isolated, and immediately homogenized in Trizol (Invitrogen) according to the manufacturer's protocol. Mouse tissue samples suspended in TRIzol were submitted to the University of Wisconsin Biotechnology Center (UWBC) Gene Expression Center (Research Resource Identifier - RRID:SCR_017757) for RNA extraction. Total RNA was purified following the recommendations of the Qiagen RNeasy Mini (Qiagen, Hilden, Germany) procedure, which included on-column DNase treatment.
Total RNA was used as input material and libraries were prepared by following the SMARTer Stranded Total RNA Sample Prep Kit – HI Mammalian user manual (Takara Bio USA, Mountain View, CA, USA).

value: full heart ventricle

value: Lrrc10 KO

value: MI


title: BFP control-Repression [2-KR-BF-2_S5]


title: PND1CKO4


title: Promoter-Repression [2-KR-14-2_S6]

value: Promoter-Repression


title: Promoter-Activation [2-SA-17-1_S4]

value: Promoter-Activation


title: TIL_gdT

first: Linyan

last: Yu

address: 44 Wenhua West Road

institute: Shandong University

description:
γδ T lymphocytes
10x Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the cellranger-6.1.1 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger).
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files (barcodes.tsv, features.tsv, matrix.mtx).

source_name: colon tumor

extract_protocol:
Mouse tumor tissues were cut up into fragments that were smaller than 0.05 mm in length and digested. The cells were washed with incomplete medium by centrifugation at 400 g for 10 minutes, and then separated by Percoll density gradient centrifugation at 800 × g for 25 min at room temperature. A mixed cell suspension was obtained from the 40%/70% Percoll interface and washed.
Library was performed according to the manufacturer’s instructions (single cell 3’ v3 protocol, 10x Genomics). Briefly, GCs were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead-in-emulsion (GEM). The poly-A RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA, which contains an Illumina R1 primer sequence, Unique Molecular Identifier (UMI) and the 10x Barcode. The pooled barcoded cDNA was then cleaned up with Silane DynaBeads, amplified by PCR and the appropriately sized fragments were selected with SPRIselect reagent for subsequent library construction. During the library construction Illumina R2 primer sequence, paired-end constructs with P5 and P7 sequences and a sample index were added.

value: gamma-delta T lymphocytes

value: colon tumor

value: 18-20 weeks


title: SHRSP Male 14 weeks normal salt, rep4

description:
57.2
direct hybridization assay


title: Lrrc10 KO MI-2

description: Lrrc10 KO MI-2


title: BFP control-Activation [2-SA-BF-1_S3]

value: BFP control-Activation

value: HPAEC


title: PND1CKO2

value: Whole ovary


title: IEL_gdT

description:
γδ T lymphocytes
10x Genomics

source_name: normal colon tissue

value: normal colon tissue


title: PND1CKO1

value: whole ovary (mixed)


title: Promoter-Repression [2-KR-14-1_S2]


title: 5274-MP-3

description: Sort-purified (live CD8+CD90.1+CFSEhi) transgenic TCRTAG CD8 T cells isolated 6h post activation in liver tumors, rep 3

source_name: Liver

extract_protocol:
5,000 cells were sorted directly into Trizol LS and frozen. Total RNA was extraced from sorted cells using the Rneasy Micro kit (Qiagen)and amplified using the SMART-Seq v4 UltraLow Input RNA Kit (Clontech).
Libraries were prepared using NEBNext polyA mRNA sample kits (NEB).

value: Liver

tag: source


title: Lrrc10 KO MI-1

description: Lrrc10 KO MI-1


title: WT MI-4

description: WT MI-4

value: Lrrc10 WT


title: 5274-MP-2

description: Sort-purified (live CD8+CD90.1+CFSEhi) transgenic TCRTAG CD8 T cells isolated 6h post activation in liver tumors, rep 2


title: Lrrc10 KO MI-7

description: Lrrc10 KO MI-7


title: PND1CON4

value: CON


title: BFP control-Repression [2-KR-BF-1_S1]

value: BFP control-Repression


title: WT MI-3

description: WT MI-3

value: full heart ventricle


title: 5274-MP-1

description: Sort-purified (live CD8+CD90.1+CFSEhi) transgenic TCRTAG CD8 T cells isolated 6h post activation in liver tumors, rep 1


title: PND1CON2


title: PND1CON3


title: 5274-MP-9

description: Sort-purified (live CD8+CD90.1+CFSEhi) transgenic TCRTAG CD8 T cells isolated 24h post activation in liver tumors, rep 2


title: PND1CON1


title: Lrrc10 KO SH-4

description: Lrrc10 KO SH-4

value: Lrrc10 KO

value: Sham


title: DPC17CKO4

value: CKO


title: 5274-MP-7

description: Sort-purified (live CD8+CD90.1+CFSEhi) transgenic TCRTAG CD8 T cells isolated 24h post activation in liver tumors, rep 1


title: Lrrc10 KO SH-3

description: Lrrc10 KO SH-3


title: 5274-MP-6

description: Sort-purified (live CD8+CD90.1+CFSEhi) transgenic TCRTAG CD8 T cells isolated 12h post activation in liver tumors, rep 3


title: 5274-MP-5

description: Sort-purified (live CD8+CD90.1+CFSEhi) transgenic TCRTAG CD8 T cells isolated 12h post activation in liver tumors, rep 2


title: DPC17CKO3