title: UK1_25h_2

city: Boston

first: Carol

middle: A

last: Kumamoto

state: MA

address: 150 Harrison Ave.

department: Department of Molecular Biology and Microbiology

institute: Tufts University

description:
Library name: Sample 8
10x Genomics

data_processing:
Initial data analysis including demultiplexing, barcode processing and aligning reads to the human genome was performed using Cell Ranger.
Assembly: human GRCh38
Supplementary files format and content: Tab-separated values files and matrix files

organism:
Clostridioides difficile
Homo sapiens

source_name: Colonoid line CJ50

growth_protocol: Preparation of colonoid monolayers on transwells. Colonoid line CJ50 was derived from colonic biopsies obtained from a 67 year old Chinese female undergoing routine outpatient colonoscopy for colorectal cancer screening at Tufts Medical Center (IRB #11652, principal investigator: Jatin Roper). The cells were propagated in Matrigel (Corning 356231) as described previously [29]. Medium compo-sition was as described [22] except that L-WRN conditioned medium (L-WRN cells ATCC CRL- 3276 [30]) was used at 65% instead of L-WNT3A, R-Spondin and Noggin conditioned media, Primocin (InvivoGen ant-pm-1) was used instead of pen-strep and 5 uM Y27632 (Rho kinase inhibitor, Sigma Y0503) was added for the first 48 hrs of culturing. For preparation of monolayers on transwells, colonoid spheres were recovered from Matrigel, washed with PBS and digested with TrypLE Express (Gibco 12605-010) for 2.5 min at 37oC. After digestion, cells were diluted with 1 volume advanced DMEM (Invi-trogen 12634-028), 1% Glutamax (Gibco 35050-061), 20% FBS (Fisher 26140079) and filtered through a 40 um cell strainer. Cells were diluted with 0.4% Trypan blue, counted with a Corning CytoSmart counter and diluted to 2.5 x 106 cells/ml with warmed 65% LWRN medium containing Y27632. Matrigel was diluted with CMGF- to 33 or 66 ug protein/mL, 125 ul was applied to each 6.5mm diameter, 0.4 um pore, polycarbonate filter transwell (Costar 3413) and incubated at 37oC for 2 hours. Liquid was removed from the transwell, the basolateral compartment was filled with 0.5 ml 65% medium and 50 ul of medium was added to the apical compartment. Cells (2.5 x 105 cells per 6.5 mm diameter transwell) were added and the seeded transwells were incubated in a tissue culture incubator with 5% CO2 at 37oC. The next day, transwells were given fresh 65% L-WRN medium containing 5 uM Y27632 (Sigma Y0503), replacing the basolateral medium and adding 0.2 ml to the apical compartment. The next day, the medium was changed to 65% without Y27632 (0.4 ml apically and 0.5 ml basolaterally) and was changed again after 2 days when the mono-layer was typically confluent. Confluent monolayers were differentiated by washing with CMGF-, followed by feeding with Differentiation Medium (DM) [22, 31] containing Primocin. Medium was changed the next day with DM containing Primocin. Monolayers were fed 2 days later (day 3) (DM without Primocin) and in the late afternoon of day 4 or in the morning of day 5 (DM without Primocin). Monolayers were inoculated with pre-germinated spores on day 5. For measurement of trans-epithelial electrical resistance (TEER), a Millicell ERS-2 volt/ohm meter was used following manufacturer’s protocol.

extract_protocol:
Monolayers were cultured on 12 mm diameter 0.4 um polycarbonate filters (Millicell PIHP01250) and differentiated as described above. Spores were treated with glycine and sodium cholate, as above, collected by centrifugation (Eppendorf 5415, 13200 rpm, 5 min) resuspended in PBS and 1 x 105 spores in 10 ul or PBS was added to the apical medium. Transwells were incubated as described above. After 4, 15, 20 or 25 hours of incubation, monolayers were washed with 100 ul PBS, EDTA 0.5 mM, pH 8 and incubated with TrypLE Express, 600 ul in the basolateral and 400 ul in the apical compartments at 37oC for 12 min. One hundred ul 50% FBS was added to the apical compartment and the cells were suspended by pipeting up and down several times. Cells were passed through a 40 um cell strainer and recovered in tubes precoated with 0.1% BSA. The transwells were then washed with 400 ul CMGF-, which was passed through the strainer and combined with the previous filtrate. Cells were collected by centrifugation at 300g x 5 min. Most of the supernatant was gently removed. Cells were resuspended in 1 ml of 0.04% BSA, 5 uM Y27632 and collected as above. Using a wide bore tip, the pellet was resuspended in the remaining supernatant by pipetting up and down. Cells were counted with a Corning Cytosmart counter and adjusted to 1 x 106 cells/ml.
The remaining steps were performed following manufacturer’s protocol. Briefly, the cell suspension was loaded along with reagents, barcoded Single Cell 3’ v3.1 Gel Beads and Partitioning Oil onto the Chromium Next GEM Chip G. Cells were partitioned into GEMS using the Chromium Controller. Gel beads were then dissolved, releasing primers, and the cells were lysed. Reverse transcription was performed to generate cDNA tagged with cell specific barcodes and Illumina TruSeq Read 1 sequencing primer. GEMS were broken and first strand cDNA was purified and PCR amplified. After enzymatic fragmentation followed by size selection, the cDNA was PCR amplified, incorporating a sample index and primers P5, P7, and TruSeq Read 2 for Illumina sequencing. Library quality was assessed using an Agilent Bioanalyzer. Paired end sequencing was performed by the Tufts University Genomics Core Facility.

treatment_protocol: Co-culturing C. difficile with colonoid monolayers. Pre-germinated spores (approximately 5 x 107 per ml) were prepared as above and 10ul of the preparation was added gently to the apical medium of the transwell. Control samples were inoculated with 10ul of buffer. The plates were wrapped with Parafilm and incubated in a standard tissue culture incubator (37oC, 5% CO2, room air). At various times, transwells were taken into the anaerobic chamber (2 transwells at a time) to estimate the number of bacteria per transwell. The first 170 ul of apical medium was carefully removed. This medium was not turbid and was discarded. The second approximately 170 ul of medium was collected into the pipet tip and used to wash the monolayer twice, then collected into a pre-weighed tube. For inoculated transwells, this sample was typically turbid. 10 ul of this sample was immediately diluted with 1 ml of pre-reduced PBS to measure CFU. The remainder of the sample was removed from the chamber and weighed to determine the volume recovered from each transwell after correction for the 10 ul removed for CFU. Transwell monolayers were removed from the chamber and fixed with 4% para-formaldehyde for 15 min at room temp, followed by washing 3 times with PBS at room temperature. Transwells were stored at 4oC in PBS. For some experiments, transwells were inoculated with vegetative C. difficile cells. Strains were grown in pre-reduced TY broth and harvested during log phase. A sample of each culture was diluted 1/50 into pre-reduced PBS. DM medium was pre-reduced and 0.4 ml was transferred to a gasketed screw cap tube for each inoculation. 10 ul of bacteria diluted in PBS was added to each tube (or PBS only for mock inoculation). The caps were screwed on tightly and tubes removed from the chamber. The transwells were inoculated by removing their apical medium and replacing it with the bacteria-containing medium. Transwells were inoculated with approximately 5 x 104 CFU.

value: Colonoid line CJ50

value: infected

tag: time point


title: GFPrep1

status: Public on Jul 29 2026

type: SRA

city: Kunming

first: lei

last: shi

state: Yunnan

address: No.17 Longxin Road

country: China

institute: Kunming Institute of Zoology

library_source: transcriptomic

data_processing:
Illumina  software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to GRCm39primary(https://www.gencodegenes.org/)whole genome using Hisat2
Fragments per kilobase of transcript per million mapped fragments (FPKM) were calculated. First step, align RNA seq reads to the genome by using  Hista2 ; and then Cufflinks2 will assemble transcripts and computed the FPKM vlues(http://cufflinks.cbcb.umd.edu/),following protocol from Pertea, M.et al  Nat Protoc 11, 1650-1667, (2016).
Assembly: GRCm39primary
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

molecule: total RNA

organism: Homo sapiens

extract_protocol:
Total RNA was extracted from the centrifuged cells by using RNeasy Mini Kit (QIAGEN, #74104)
RNA sequencing library construction followed VAHTs mRNA-seq V3 Library Prep Kit for Illumina (Vazyme, #NR611). The total RNA input was 0.7-1ug, mRNA (with ploy-A) binds to mRNA capture beads (with Oligo dT), mRNA is eluted from beads and then fragmented, synthesis of the 1st strand of cDNA using random primers, synthesis of the 2nd strand of cDNA after RNase H digestion. Size selection and library amplication after end repair and adapter ligation, the final RNA sequencing library length is between 320-420bp. Library quality determination analyzed by an Agilent Technologies 2100 Bioanalyzer.

tag: cell line

tag: cell type

value: neuroblastoma

tag: genotype

tag: treatment

value: transfected with pCS2-eGFP-N


title: UK1_25h_1

country: USA

description:
Library name: Sample 7
10x Genomics

library_source: transcriptomic single cell


title: UK1_4h_2

description:
Library name: Sample 6
10x Genomics


title: AB20858

city: Rehovot

first: Ido

last: Amit

address: 234 Herzl st.

department: Immunology

country: Israel

institute: Weizmann Institute of Science

description: Library name: Sample 18

data_processing:
bases2fastq version 2.2.0.1940753917 arguments --legacy-fastq
Sequences with RMT of low quality (defined as RMT with minimum Phred score of less than 27) were filtered out.
Pool-barcode used i5+i7 barcodes each of them is unique in run, 1 error was allowed.  well-barcode N7 folowed by UMI N8 in read 2.
Assembly: hg38
Supplementary files format and content: tab-delimited text files include mRNA molecule count values for each Sample

molecule: polyA RNA

source_name: PBMCs

extract_protocol:
After two additional days of culture, a macrophage killing assay was initiated by adding hTREM2 CAR cells at a 5:1 effector-to-target ratio. Cells were collected after 24h and sorted.
3' end mRNA libraries were prepared for sequencing using MARS-seq (Jaitin et al, Science 2014)

treatment_protocol: Human CD14+ monocytes were isolated from freshly prepared PBMCs and cultured 5 days in C10 medium with 50 ng/mL recombinant human M-CSF. On day 5, the medium was replaced with C10 supplemented with 50 ng/mL M-CSF and 20 ng/mL IL-4, or 50 ng/mL M-CSF, or 50 ng/mL M-CSF and 20ng/ml IFNg to promote macrophage polarization.

tag: tissue

value: PBMCs

value: monocytes

tag: sorting gate

value: MCSF+IFNg

tag: batch


title: AB20857

description: Library name: Sample 17


title: UK1_4h_1

description:
Library name: Sample 5
10x Genomics


title: AB20856

description: Library name: Sample 16


title: AB20854

description: Library name: Sample 14

value: MCSF


title: AB20855

description: Library name: Sample 15


title: AB20853

description: Library name: Sample 13


title: AB20849

description: Library name: Sample 12


title: AB20847

description: Library name: Sample 10


title: AB20845

description: Library name: Sample 8


title: AB20848

description: Library name: Sample 11


title: AB20844

description: Library name: Sample 7


title: AB20846

description: Library name: Sample 9


title: AB20840

description: Library name: Sample 6


title: AB20839

description: Library name: Sample 5


title: AB20838

description: Library name: Sample 4


title: AB20837

description: Library name: Sample 3


title: AB20836

description: Library name: Sample 2


title: appendix_UC5, BCR-derived cDNA

city: Suita

first: Daisuke

last: Motooka

state: Osaka

address: 3-1, Yamadaoka

country: Japan

institute: NGS core facility, Research Institute for Microbial Diseases, Osaka University

description:
Library name: GA61851
BCR V(D)J segments

data_processing:
Sequencing was performed on DNBSEQ-G400 platform in 28+100 or 100+100 base paired-end mode.
During the sequencing run, a control software automatically operates basecalling analysis software and delivers raw sequencing data outputs.
Generated reads were input into the cellranger pipeline (Cell Ranger v.7.1.0, 10x Genomics) for UMI counting of each gene-cell (barcode) combination and B cell and T cell receptor repertoire profiling.
Assembly: refdata-gex-GRCh38-2020-A and refdata-cellranger-vdj-GRCh38-alts-ensembl-7.0.0
Supplementary files format and content: sample_filtered_feature_bc_matrix.h5 : HDF5 format files including UMI counts data for each gene and cell (barcode) combination
Supplementary files format and content: vdj_b.tar :  tar archive of output folder "vdj_b" of Cell Ranger pipeline including information of detected BCR clonotypes
Supplementary files format and content: vdj_t.tar : tar archive of output folder "vdj_t" of Cell Ranger pipeline including information of detected TCR clonotypes

source_name: appendix

extract_protocol:
Sinlge cell droplets were generated by 10x Genomics Chromium Controller, and cDNAs with UMIs were generated at single-cell level.
The single cell libraries were prepared following the protocol outlined in the Chromium Next GEM Single Cell V(D)J Reagent Kits v1.1 User Guide. Libraries were converted to libraries for DNBSEQ using MGIEasy Universal Library Conversion Kit (App-A).

value: appendix

value: lamina propria mononuclear cells

tag: disease state

value: ulcerative colitis

value: lamina propria mononuclear cells with dead cells removed


title: AB20835

description: Library name: Sample 1


title: appendix_UC5, TCR-derived cDNA

description:
Library name: GA61852
TCR V(D)J segments


title: appendix_UC5, mRNA-derived cDNA

description:
Library name: GA61850
poly A RNA


title: appendix_control5, BCR-derived cDNA

description:
Library name: GA61078
BCR V(D)J segments

value: non-ulcerative colitis


title: appendix_control4, TCR-derived cDNA

description:
Library name: GA60776
TCR V(D)J segments


title: appendix_control5, TCR-derived cDNA

description:
Library name: GA61079
TCR V(D)J segments


title: appendix_control4, BCR-derived cDNA

description:
Library name: GA60775
BCR V(D)J segments


title: appendix_control5, mRNA-derived cDNA

description:
Library name: GA61077
poly A RNA


title: appendix_control4, mRNA-derived cDNA

description:
Library name: GA60774
poly A RNA


title: appendix_UC4, TCR-derived cDNA

description:
Library name: GA59301
TCR V(D)J segments


title: appendix_UC4, BCR-derived cDNA

description:
Library name: GA59300
BCR V(D)J segments


title: appendix_UC4, mRNA-derived cDNA

description:
Library name: GA59299
poly A RNA


title: appendix_UC3, TCR-derived cDNA

description:
Library name: GA59079
TCR V(D)J segments


title: appendix_UC3, BCR-derived cDNA

description:
Library name: GA59078
BCR V(D)J segments


title: appendix_UC3, mRNA-derived cDNA

description:
Library name: GA59077
poly A RNA


title: appendix_control3, TCR-derived cDNA

description:
Library name: GA56854
TCR V(D)J segments


title: appendix_control3, BCR-derived cDNA

description:
Library name: GA56853
BCR V(D)J segments


title: appendix_control3, mRNA-derived cDNA

description:
Library name: GA56852
poly A RNA


title: appendix_UC, TCR-derived cDNA

description:
Library name: GA55757
TCR V(D)J segments


title: appendix_UC, BCR-derived cDNA

description:
Library name: GA55755
BCR V(D)J segments


title: appendix_UC, mRNA-derived cDNA

description:
Library name: GA55753
poly A RNA


title: appendix_control2, TCR-derived cDNA

description:
Library name: GA55756
TCR V(D)J segments


title: appendix_control, TCR-derived cDNA

description:
Library name: GA54134
TCR V(D)J segments


title: appendix_control2, mRNA-derived cDNA

description:
Library name: GA55752
poly A RNA


title: appendix_control2, BCR-derived cDNA

description:
Library name: GA55754
BCR V(D)J segments


title: appendix_control, BCR-derived cDNA

description:
Library name: GA54133
BCR V(D)J segments


title: appendix_control, mRNA-derived cDNA

description:
Library name: GA54132
poly A RNA


title: E12.5+18h ureter cultures, BIO treated vs control, repl. #2

type: RNA

city: Hannover

first: Mark-Oliver

last: Trowe

address: Carl-Neuberg-Str. 1

department: Molekularbiologie

country: Germany

institute: Medizinische Hochschule Hannover

hyb_protocol: cRNA fragmentation, hybridization and washing steps were carried-out as recommended for 4-plex Microarray-Slides in the ‘Two-Color Microarray-Based Gene Expression Analysis Protocol V5.7’ (Agilent Technologies), except that 2500ng of each fluorescently labelled cRNA were used for hybridization.

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

data_processing: Data extraction was performed with the ‘Feature Extraction Software V10.7.3.1’ by use of the extraction protocol file ‘GE2_107_Sep09.xml’.  Measurements of on-chip replicates were averaged using the geometric mean of ‘ProcessedSignal’ (PS) values (for each channel independently) to retrieve one resulting value per unique non-control probe. Single Features were excluded from averaging, if they i) were manually flagged, ii) were identified as Outliers by the Feature Extraction Software, iii) lay outside the interval of ‘1.42 x interquartile range‘ regarding the PS distribution of the respective on-chip replicate population, or, iv) showed a coefficient of variation of pixel intensities per Feature that exceeded 0.5.  For inter-array normalization, averaged processed intensity values, ‘gProcessedSignal’ (gPS) and ‘rProcessedSignal’ (rPS), were further transformed as follows: All PS values (gPS and rPS) of one particular microarray (‘Array i’ in the formula shown below) were multiplied with a microarray-specific scaling factor. This factor was calculated by dividing a ‘reference 75th Percentile value’ (set as 1500 for the whole series) by the 75th Percentile value of the gPS values calculated by the Feature Extraction software for that microarray. Accordingly, normalized PS values for all samples (microarray data sets) were calculated by the following formula:  normalized PSArray i = PSArray i x (1500 / 75th Percentile gPSArray i)  Finally, a lower intensity threshold (surrogate value) was defined based on intensity distribution of negative control features. This value was fixed at 15 normalized PS units. All of those measurements that fell below this intensity cutoff were substituted by the respective surrogate value of 15.

organism: Mus musculus

source_name: control 2

label_protocol: 50 ng of total RNA equivalents were used to synthesize AlexaFluor555- or AlexaFluor647- (Invitrogen) labeled cRNA with the ‘Amino Allyl MessageAmp™ II aRNA Amplification Kit’ (#AM1753, Thermo Fisher Scientific) according to the manufacturer’s recommendations, except that the proportion of aminoallyl-UTP/UTP was adjusted to 1+11 (instead of 1+1), reaction volumes were halved, and just one round of T7 amplification was conducted.

extract_protocol: Extraction of total RNA was performed using the PeqGold RNAPure according to the manufacturer’s recommendations.

treatment_protocol: Ureters were mechanically dissected from E12.5 embryos and cultured on transwell membranes for 18h in culture medium (DMEM/F12 with 1x GlutaMAX, 1x Penicillin/Streptomycin, 1x NEAA, 1x Pyruvate) containing 10 µM BIO or in medium containing DMSO (2:1000, control).

tag: strain

value: NMRI

value: wildtype

tag: Sex

value: not determined

tag: developmental stage

tag: culture period

value: ureter

source_name: BIO treated 2

value: 10 µM BIO


title: E11.5+18h ureter cultures, IWP-2 treated vs control, repl. #2

hyb_protocol: cRNA fragmentation, hybridization and washing steps were carried-out as recommended for 4-plex Microarray-Slides in the ‘Two-Color Microarray-Based Gene Expression Analysis Protocol V5.7’ (Agilent Technologies), except that 1900 ng of each fluorescently labelled cRNA were used for hybridization.

label_protocol: 100 ng of total RNA equivalents were used to synthesize AlexaFluor555- or AlexaFluor647- (Invitrogen) labeled cRNA with the ‘Amino Allyl MessageAmp™ II aRNA Amplification Kit’ (#AM1753, Thermo Fisher Scientific) according to the manufacturer’s recommendations, except that the proportion of aminoallyl-UTP/UTP was adjusted to 1+11 (instead of 1+1), reaction volumes were halved, and just one round of T7 amplification was conducted.

extract_protocol: Extraction of total RNA was performed using the Rneasy Micro kit (QIAGEN) according to the manufacturer’s recommendations.

treatment_protocol: Ureters were mechanically dissected from E11.5 embryos and cultured on transwell membranes for 18h in culture medium (DMEM/F12 with 1x GlutaMAX, 1x Penicillin/Streptomycin, 1x NEAA, 1x Pyruvate) containing 10 µM IWP-2 or in medium containing DMSO (2:1000, control).

source_name: IWP-2 treated 2

value: 10 µM IWP-2


title: E11.5+18h ureter cultures, IWP-2 treated vs control, repl. #1

source_name: control 1

source_name: IWP-2 treated 1


title: E12.5+18h ureter cultures, BIO treated vs control, repl. #1

source_name: BIO treated 1


title: E14.5 ureters, Ctnnb1-cKO vs control, rep2

label_protocol: 200 ng of total RNA were used to synthesize AlexaFluor555- or AlexaFluor647- (Invitrogen) labeled cRNA with the ‘Amino Allyl MessageAmp™ II aRNA Amplification Kit’ (#AM1753, Thermo Fisher Scientific) according to the manufacturer’s recommendations, except that the proportion of aminoallyl-UTP/UTP was adjusted to 1+11 (instead of 1+1) and reaction volumes were halved, and just one round of T7 amplification was conducted.

treatment_protocol: Ureters were mechanically dissected from E14.5 embryos.

value: female

source_name: Ctnnb1KO 2


title: CAR-T Enterocolitis 6

city: New York

first: Saurabh

last: Mehandru

state: New York

address: 1425 Madison Avenue

institute: Icahn School of Medicine

description:
Library name: EC6
10X Genomics

data_processing:
The demultiplexing, barcode processing, gene counting and aggregation were made using the CellRanger software v5.0.1
Assembly: GRCh38 (2020-A)
Supplementary files format and content: Tab separated values files and matrix files

source_name: left colon

extract_protocol:
Tissue first underwent epithelial layer removal via two incubation steps (20 min, 37°C, rotating incubator 180 rpm) in 10mL of Hanks’ balanced salt solution (HBSS), EDTA (0.5 M, pH 8; Invitrogen), Hepes (1 M; Lonza), and fetal bovine serum. Tissue was vortexed, washed with HBSS, and incubated (40 min, 37°C, rotating incubator 180 rpm) in digestion media, containing RPMI, collagenase (Sigma-Aldrich), deoxyribonuclease 1 (Sigma-Aldrich), and fetal bovine serum. Tissue was then manually disrupted an 18-gauge needle and filtered through 100-μm and 40-μm cell strainers, yielding single cell suspension.
All four samples (CAR-TEC = 4) were prepared using 5′ V3 chemistry. Approximately 16,000 cells were loaded per channel, targeting a recovery rate of 10,000 cells per sample. Barcoded cDNA was extracted from the GEMs after Post-GEM RT-cleanup and amplified for 12 cycles. Amplified cDNA was fragmented and subjected to end-repair, poly A-tailing, adapter ligation, and 10x-specific sample indexing following the manufacturer’s protocol.

value: left colon

value: lamina propria

tag: age

value: M


title: E12.5+18h ureter cultures, IWP-2 treated vs control, repl. #4

source_name: control 4

treatment_protocol: Ureters were mechanically dissected from E12.5 embryos and cultured on transwell membranes for 18h in culture medium (DMEM/F12 with 1x GlutaMAX, 1x Penicillin/Streptomycin, 1x NEAA, 1x Pyruvate) containing 10 µM IWP-2 or in medium containing DMSO (2:1000, control).

source_name: IWP-2 treated 4


title: CAR-T Enterocolitis 7

description:
Library name: EC7
10X Genomics


title: CAR-T Enterocolitis 5

description:
Library name: EC5
10X Genomics

value: F


title: Normal Volunteer 14

description:
Library name: NV14
10X Genomics

extract_protocol:
Tissue first underwent epithelial layer removal via two incubation steps (20 min, 37°C, rotating incubator 180 rpm) in 10mL of Hanks’ balanced salt solution (HBSS), EDTA (0.5 M, pH 8; Invitrogen), Hepes (1 M; Lonza), and fetal bovine serum. Tissue was vortexed, washed with HBSS, and incubated (40 min, 37°C, rotating incubator 180 rpm) in digestion media, containing RPMI, collagenase (Sigma-Aldrich), deoxyribonuclease 1 (Sigma-Aldrich), and fetal bovine serum. Tissue was then manually disrupted an 18-gauge needle and filtered through 100-μm and 40-μm cell strainers, yielding single cell suspension.
Sixteen samples (NV = 11, CAR-TCTRL = 2, CAR-TEC = 3) were prepared using 3′ V3 chemistry, and five samples (CAR-TCTRL = 3, CAR-TEC = 2) using 5′ V3 chemistry. Approximately 16,000 cells were loaded per channel for both 3’ and 5’, targeting a recovery rate of 10,000 cells per sample. Barcoded cDNA was extracted from the GEMs after Post-GEM RT-cleanup and amplified for 12 cycles. Amplified cDNA was fragmented and subjected to end-repair, poly A-tailing, adapter ligation, and 10x-specific sample indexing following the manufacturer’s protocol.


title: E14.5 ureters, Ctnnb1-cKO vs control, rep1

value: male

source_name: Ctnnb1KO 1


title: E12.5+18h ureter cultures, IWP-2 treated vs control, repl. #3

source_name: control 3

source_name: IWP-2 treated 3


title: E12.5+18h ureter cultures, IWP-2 treated vs control, repl. #1


title: E12.5+18h ureter cultures, IWP-2 treated vs control, repl. #2


title: Normal Volunteer 12

description:
Library name: NV12
10X Genomics


title: Normal Volunteer 11

description:
Library name: NV11
10X Genomics


title: Normal Volunteer 8

description:
Library name: NV8
10X Genomics


title: Normal Volunteer 7

description:
Library name: NV7
10X Genomics


title: Normal Volunteer 6

description:
Library name: NV6
10X Genomics


title: Normal Volunteer 5

description:
Library name: NV5
10X Genomics


title: Normal Volunteer 4

description:
Library name: NV4
10X Genomics


title: Normal Volunteer 3

description:
Library name: NV3
10X Genomics


title: Normal Volunteer 2

description:
Library name: NV2
10X Genomics


title: Normal Volunteer 1

description:
Library name: NV1
10X Genomics


title: CAR-T Control 7

description:
Library name: CTRL7
10X Genomics


title: CAR-T Control 5

description:
Library name: CTRL5
10X Genomics


title: CAR-T Control 3

description:
Library name: CTRL3
10X Genomics


title: CAR-T Control 4

description:
Library name: CTRL4
10X Genomics


title: CAR-T Control 2

description:
Library name: CTRL2
10X Genomics


title: CAR-T Enterocolitis 4

description:
Library name: EC4
10X Genomics


title: CAR-T Enterocolitis 2

description:
Library name: EC2
10X Genomics


title: CAR-T Enterocolitis 3

description:
Library name: EC3
10X Genomics


title: CAR-T Enterocolitis 1

description:
Library name: EC1
10X Genomics


title: Vehicle-treated MYCN-amplified NB PDX 307

city: Ghent

first: Sarah-Lee

last: Bekaert

state: No state

address: Corneel Heymanslaan 10

country: Belgium

institute: UGent

description: Library name: DNA158501_307_Vehicle

library_source: genomic

data_processing:
Raw WES reads were preprocessed using a in house standard pipeline. Reads were mapped to the human reference genome (hg38) using the SNAP aligner, producing CRAM-formatted files.
CRAM files containing aligned sequencing reads (hg38, SNAP aligner) were converted to BAM format for compatibility with variant calling tools. Whole-exome sequencing achieved an average coverage of 126×.
Somatic variant calling was performed using GATK Mutect2 in tumor-only mode, comparing drug-treated and vehicle samples. Reference databases were used to filter likely germline variants and false positives.
Variant calls from all samples were merged into combined tables. Variants were then quantified by number and type per condition and per sample, using mean allele frequencies to assess variability between treatments.
Assembly: Homo sapiens GRCh38.96
Supplementary files format and content: Tab-delimited text file including merged variant calls across all samples, with per-sample filters and annotation.
Supplementary files format and content: Normalized, filtered per-sample VCF with variant positions, alleles, quality, filter status, and sample genotypes.
Supplementary files format and content: The vcf.gz files contain the compressed variant call format (VCF) data. The corresponding .vcf.gz.csi files are index files generated for each VCF, which enable efficient random access and querying of the compressed VCF files (e.g., for visualization or downstream analysis). The .csi files do not contain additional data beyond indexing information and are provided to facilitate processing of the VCF files.

molecule: genomic DNA

source_name: Tumor tissue

extract_protocol:
Mice were euthanised at a tumor volume of 2000 mm³, genomic DNA was extracted from harvested neuroblastoma PDX tumor tissue using the QIACube automated system (QIAGEN), according to the manufacturer’s instructions.
Exome libraries were constructed from genomic DNA using an Illumina-compatible exome enrichment protocol, including DNA fragmentation, adapter ligation, PCR amplification, and hybrid capture of coding regions according to the manufacturer’s guidelines.

treatment_protocol: Four-week-old female NOD Xenograft Gamma (NXG) mice (Janvier Labs) were acclimatised for 2 weeks prior to treatment. Mice bearing MYCN-amplified neuroblastoma PDX tumors were treated by oral gavage for 21 consecutive days. Merestinib (24 mg/kg) or vehicle was administered in the morning, followed by OKI-1546 (10 mg/kg; OnKure Therapeutics) or vehicle in the afternoon (maximum volume 200 μL). OKI-1546 was prepared fresh daily in 10% DMSO, 20% PEG400, 10% Solutol HS15, and 60% H₂O; merestinib was dissolved in 10% PEG400 and 90% 20% Captisol in MilliQ H₂O. Tumor volume was measured every 3 days.

value: Tumor tissue

value: MYCN-amplified neuroblastoma PDX

value: neuroblast

value: Vehicle


title: Vehicle-treated MYCN-amplified NB PDX 303

description: Library name: DNA158500_303_Vehicle


title: Vehicle-treated MYCN-amplified NB PDX 289

description: Library name: DNA158499_289_Vehicle


title: OKIMer-treated MYCN-amplified NB PDX 308

description: Library name: DNA158498_308_OKIMER

value: Combi Merestinib & OKI-1546


title: OKIMer-treated MYCN-amplified NB PDX 300

description: Library name: DNA158497_300_OKIMER


title: OKIMer-treated MYCN-amplified NB PDX 285

description: Library name: DNA158496_285_OKIMER


title: AB8265

description: Library name: Sample 23

value: PBMCs

value: monocytes


title: AB8264

description: Library name: Sample 22


title: AB7037

description: Library name: Sample 21


title: AB7036

description: Library name: Sample 20


title: AB7035

description: Library name: Sample 19


title: TN D

city: Beer Sheva

first: Shiran

last: Dror

address: Ben-Gurion blvd. 1, Building 39, room 205

institute: Ben-Gurion University of the Negev

description: Library name: TN_D

data_processing:
NeatSeq Flow pipeline (https://doi.org/10.1101/173005)
raw reads were trimmed using TrimGalore (--length 25, -q 25).
Trimmed reads were aligned to the genome using RSEM (Bowtie2)
Assembly: Homo_sapiens.GRCh38
Supplementary files format and content: tab delimited text file including counts, TPM and FPKM per gene for each sample

growth_protocol: flasks were seeded with 500,000 cells incubated (37 °C, 5% CO2) for 6 h.

extract_protocol:
Total RNA was extracted using Direct-zolTM RNA MicroPrep with Tri Reagent® (Zymo Research) from thawed samples
RNA-seq libraries were generated by enrichment of PolyA RNA from total RNA using NEBNext® Poly(A) mRNA Magnetic Isolation Module (NEB, #E7490L). Libraries for sequencing were generated using NEBNext UltraExpress® RNA Library Prep Kit (NEB, #E3330L) following manufacturer protocols.

treatment_protocol: crystals were added to the flasks at a final concentration of 0.1mg/mL

value: breast premalignant

value: TN - Thin bipyramid COD (calcium oxalate dihydrate)


title: TN C

description: Library name: TN_C


title: TN B

description: Library name: TN_B


title: TK D

description: Library name: TK_D

value: TK - Thick bipyramid COD (calcium oxalate dihydrate)


title: TK C

description: Library name: TK_C


title: TK B

description: Library name: TK_B


title: TN A

description: Library name: TN_A


title: SPH D

description: Library name: SPH_D

value: SPH - Spherical COD (calcium oxalate dihydrate)


title: TK A

description: Library name: TK_A


title: SPH C

description: Library name: SPH_C


title: SPH B

description: Library name: SPH_B


title: SPH A

description: Library name: SPH_A


title: DB D

description: Library name: DB_D

value: DB - Dumbbell-like COD (calcium oxalate dihydrate)


title: DB C

description: Library name: DB_C


title: DB A

description: Library name: DB_A


title: DB B

description: Library name: DB_B


title: COM D

description: Library name: COM_D

value: COM (calcium oxalate monohydrate) plates


title: COM C

description: Library name: COM_C


title: COM B

description: Library name: COM_B


title: COM A

description: Library name: COM_A


title: Control G

description: Library name: Control_G

value: Control


title: Control E

description: Library name: Control_E


title: Control D

description: Library name: Control_D


title: LIF+PD_rep3

city: Chicago

first: Bradley

middle: J

last: Merrill

address: 900 S Ashland Ave

institute: University of Illinois at Chicago

description: replicate 3

hyb_protocol: RNA was hybridized to an Illumina Mouse Whole Genome 8-V2 Beadchip microarray.

scan_protocol: Illumina protocol

data_processing: Raw IDAT files were background-corrected using an offset estimated from control probe quantiles. Data were then transformed using variance-stabilizing transformation (vst) and normalized using robust spline normalization (rsn), both via the Lumi R package. For datasets from different array batches, batch correction was applied using the ComBat function from the sva R package. Differential expression analysis was performed using the limma R package with empirical Bayes moderation.

label: biotin

source_name: mouse embryonic stem cells

label_protocol: Illumina protocol

growth_protocol: ESC: cells were grown in N2B27 medium supplemented with 1uM PD0325901, 3uM CHIR99021, and 1000U/mL LIF. EpiLC: cells were grown in N2B27 medium supplemented with 12 ng/mL Fgf2. EpiLC+CH: cells were grown in N2B27 medium supplemented with 12 ng/mL Fgf2 for 3 days and 3uM CHIR99021 were added for the next 24 hours. ContinuedCH : cells were grown in N2B27 medium supplemented with 12 ng/mL Fgf2 and 3uM CHIR99021. LIF+CHIR: cells were grown in N2B27 supplemented with 1000U/mL LIF and 3uM CHIR99021. LIF+PD: cells were grown in N2B27 supplemented with 1000U/mL LIF and 1uM PD0325901. LIF+PD+24hrCH:  cells were grown in N2B27 supplemented with 1000U/mL LIF and 1uM PD0325901 for the first 24 hours and 3uM CHIR99021 for the next 48 hours. PD+CHIR: cells were grown in N2B27 supplemented with 1uM PD0325901 and 3uM CHIR99021.

extract_protocol: Biological triplicates were prepared for RNA isolation with TRIZOL, followed by column   purification with the Qiagen RNeasy kit per manufacturer protocol.

value: mouse embryonic stem cells

value: WT

tag: growth condition

value: LIF+PD


title: Control C

description: Library name: Control_C


title: PD+CH_rep1

description: replicate 1

value: PD+CHIR


title: LIF+PD_24hr+CH_rep3

description: replicate 3


title: Control B

description: Library name: Control_B


title: LIF+PD_rep2

description: replicate 2


title: LIF+PD_24hr+CH_rep1

description: replicate 1


title: WT_Naive_rep3

description: replicate 3

value: ESC


title: Control A

description: Library name: Control_A


title: LIF+PD_rep1

description: replicate 1


title: LIF+CH_rep1

description: replicate 1

value: LIF+CHIR


title: Day 8 rep2

city: Vilnius

first: Kotryna

last: Kvederaviciute

address: Sauletekio av. 7

department: Life Sciences Center

country: Lithuania

institute: Vilnius University

data_processing:
Raw data quality was evaluated using FASTQ (v0.11.9). Adapters, low quality bases and short reads were removed using cutadapt (v4.4). Read starts were corrected using an in-house PERL script.
Cleaned reads were mapped using bwa (0.7.17-r1188) and filtered using samtools (1.12).
CG coverage matrix was generated custom in-house R (4.3.0) script.
Assembly: mm10
Supplementary files format and content: CSV file containing per CpG coverage.

growth_protocol: Naïve E14tg2a Dnmt1wt/wt and Dnmt1wt/N1580A cell lines were grown on 0.15% gelatin-coated 24-well plates at a density of 5x10^4 cells per well in DMEM medium supplemented with 15% fetal bovine serum and 1000 U/mL mLIF, 3 µM CHIR99021 and 1 µM PD0325901 kinase inhibitors. The cellular shift to the “primed” state was promoted by passaging mESC cells at the same density in DMEM media (15% FBS, 1000 U/mL mLIF) for the subsequent 8 days without the presence of 2i. For the mESC ground state transition from naïve to “primed”, embryonic stem E14tg2a Dnmt1wt/wt and Dnmt1wt/N1580A cell lines were grown on 0.15% gelatin-coated 24-well plates at a density of 5x10^4 cells per well for 48h in Dulbecco‘s modified Eagle‘s medium (Gibco) containing 15% fetal bovine serum (Gibco), 1000 U/ml mouse leukemia inhibitory factor (Millipore).

extract_protocol:
Genomic DNA was purified from cell lysates using Zymo Genomic DNA Clean & Concentrator-10 Kit.
Libraries were constructed according to the TOP-seq (Tethered Oligonucleotide-Primed sequencing) protocol (Stasevskij et al., 2017). Briefly, 900 ng of sonicated genomic DNA were end-filled, a 3’-dA mononucleotide extension was added and DNA was ligated to adapters. Ligated DNA was then subjected to Cu(I)-catalyzed cycloaddition reaction in which the alkyne-bearing oligodeoxyribonucleotide with biotin was attached to the azide moiety of the modified DNA. Biotinylated DNA was enriched with streptavidin-coupled magnetic beads and subsequently used in a TOP DNA priming reaction from the attached priming oligodeoxyribonucleotide. The products were amplified and subjected to Ion Proton sequencing.

treatment_protocol: E14TG2a Dnmt1wt/wt and Dnmt1wt/N1580A cells were inoculated with freshly prepared 1 mM ado-6-azide solution in Opti-MEM by electroporation with NEPA21 system (Nepa Gene) using cell culture plate electrode CUY900. Cell poring pulse voltage was set up at 200V and pulse length - 5 ms. gDNA was isolated 3h following the electroporation. For the mESC ground state transition from naïve to “primed”, gDNA was isolated on day 0 (naïve cell state), day 2, day 4 and day 8 of mESC “priming” 3h following the electroporation.

value: Embryonic stem cells

value: Heterozygous Dnmt1 N1580A knock-in


title: LIF+PD_24hr+CH_rep2

description: replicate 2


title: WT_EpiLC_rep3

description: replicate 3

value: EpiLC


title: 3XKO_EpiLC_rep3

description: replicate 3


title: Day 8 rep1


title: 4XKO_EpiLC+CH_rep3

description: replicate 3

value: EpiLC+CH


title: Day 4 rep2


title: 3XKO_Naive_rep3

description: replicate 3


title: KO_EpiLC+CH_rep3

description: replicate 3


title: Day 4 rep1


title: Day 2 rep2


title: WT_continuous_CH_rep3

description: replicate 3

value: ContinuedCH


title: Day 0 rep2


title: Day 0 rep1


title: KO_EpiLC+CH_rep2

description: replicate 2


title: Day 2 rep1


title: Wild type Dnmt1 control rep2

value: Wild type


title: 4XKO_EpiLC+CH_rep2

description: replicate 2


title: 4XKO_EpiLC_rep3

description: replicate 3


title: Wild type Dnmt1 control rep1


title: WT_EpiLC+CH_rep3

description: replicate 3


title: KO_EpiLC_rep3

description: replicate 3


title: Wild type Dnmt1 rep3


title: KO_Naive_rep3

description: replicate 3


title: KO_EpiLC_rep2

description: replicate 2


title: Wild type Dnmt1 rep2


title: Wild type Dnmt1 rep1


title: Heterozygous Dnmt1 N1580A knock-in rep3


title: 3XKO_Naive_rep2

description: replicate 2


title: WT_continuous_CH_rep2

description: replicate 2


title: Heterozygous Dnmt1 N1580A knock-in rep2


title: Heterozygous Dnmt1 N1580A knock-in rep1


title: KO_EpiLC+CH_rep1

description: replicate 1


title: Control F

description: Library name: Control_F

value: breast premalignant


title: 3XKO_naive_rep1

description: replicate 1


title: 203991410080_R03C01_20163903_PFC

type: genomic

city: Exeter

first: Joshua

last: Harvey

state: Devon

address: RILD Building, RD&E, Barrack Road

department: Clinical and Biomedical Sciences

country: United Kingdom

institute: University of Exeter

hyb_protocol: 500 ng DNA from each sample was sodium bisulfite-treated using the Zymo EZ 96 DNA methylation kit (Zymo Research) according to the manufacturer’s standard protocol.

scan_protocol: Samples were assessed using the Illumina Infinium HumanMethylationEPIC BeadChip (Illumina) using a Illumina iScan System (Illumina)

data_processing:
Data was imported using the R package methylumi methylumIDAT function. Data was then pre-processed in the R package wateRmelon using the pfilter and dasen functions.
[ukbbn_betas_normalised.Rdata] wateRmelon processed beta values, dasen quantile normalised

label: Cy3 & Cy5

source_name: Prefrontal cortex

label_protocol: Standard Illumina Protocol

extract_protocol: ~30mg of brain tissue was milled over liquid nitrogen and extracted following the Qiagen AllPrep DNA/RNA/miRNA Universal kit following standard protocol. Samples were pre-checked using nanodrop fluorometer prior to further processing.

value: Prefrontal cortex

tag: regiondescription

tag: plate

tag: centre

value: Newcastle Brain Tissue Resource

value: female

tag: thal

value: FALSE


title: WT_EpiLC_rep2

description: replicate 2

tag: cell type

value: mouse embryonic stem cells


title: 203991410080_R02C01_PD681_PFC

value: Imperial Brain Bank


title: WT_continuous_CH_rep1

description: replicate 1

tag: genotype

value: WT


title: 3XKO_EpiLC_rep2

description: replicate 2


title: 203991410080_R01C01_PD1013_PFC

value: male


title: 203991410079_R07C01_PD579_PFC


title: KO_Naive_rep2

description: replicate 2

value: ESC


title: 203991410079_R05C01_20174952_PFC


title: WT_Naive_rep2

description: replicate 2


title: 203991410079_R03C01_PD683_PFC


title: 203991410079_R02C01_PD822_PFC


title: KO_EpiLC_1

description: replicate 1


title: 203991410079_R01C01_PD336_PFC


title: 203991410122_R04C01_NP12/064_PFC

value: Oxford Brain Bank


title: WT_EpiLC+CH_rep2

description: replicate 2


title: 203991410065_R07C01_PD590_PFC


title: 203991410065_R04C01_20110403_PFC


title: 3XKO_EpiLC+CH_rep3

description: replicate 3


title: 4XKO_EpiLC_rep2

description: replicate 2


title: 203991410065_R03C01_NP16/044_PFC


title: 4XKO_Naive_rep3

description: replicate 3


title: 203991410065_R02C01_PD967_PFC


title: WT_EpiLC_rep1

description: replicate 1


title: 3XKO_EpiLC+CH_rep2

description: replicate 2


title: 4XKO_Naive_rep2

description: replicate 2


title: 203991410065_R01C01_PD430_PFC


title: 203991410052_R07C01_PD834_PFC


title: 203991410052_R04C01_NP13/128_PFC


title: SUB27, Dendritic cells, A/H7N9 vaccine with AS03 adjuvant, Day2

city: Rockville

first: Johannes

last: Goll

state: MD

address: 401 N Washington St

department: Bioinformatics Service Group

institute: The Emmes Company

description:
Library name: SUB27_D2_DNR
SUB27_D2_DNR

data_processing:
Human reference genome assembly (GRCh38), gene models, and associated gene annotation information were obtained from the ENSEMBL database (Version 99). The genomic reference was built by merging all human chromosomes except for X and Y chromosomes (to avoid gender-specific effects). Adapter sequences and low-quality 5′ ending sequences were removed from raw sequencing reads using the Trimmomatic software (Version 0.39). Following adapter removal, sequence reads were aligned to the reference transcriptome/genome using HISAT2 splice-aware sequence aligner (Version 2.2.0).  For each sample, the quality of reference alignments was evaluated using the RSeQC software (Version 3.0.1). Gene expression quantification was conducted on the gene level using Subread v2.0.0 counting mapped paired-reads to obtain fragment counts per gene.
Assembly: GRCh38 ENSEMBL database (Version 99)
Supplementary files format and content: tab-delimited text includes raw counts of each ENSEMBL Gene ID for each Sample

source_name: Dendritic cells

extract_protocol:
Peripheral blood mononuclear cells (PBMC) were recovered from phlebotomy samples and processed immediately. Magnetic sorting (AutoMACS Pro) was used to isolate individual immune cells using microbeads coated with CD15 (PMN), CD19 (B-cells), CD3 (T-cells), CD56 (NK cells), CD11c (dendritic cells), and CD14 (monocytes). During optimization, flow cytometric analysis confirmed >99% purity of each immune cell compartment. RNA was extracted from PBMC using the Promega simplyRNA Cell Kit according to the manufacturer’s protocol.
Polyadenylated RNAs were captured using NEBNext Magnetic Oligo d(T)25 Beads, and the NEBNext mRNA Library Prep Reagent Set for Illumina (New England BioLabs Inc., Ipswich, MA, USA) was used to prepare individually bar-coded libraries as per manufacturer’s recommended protocol. Accurate quantification for sequencing applications was determined using the qPCR-based KAPA Biosystems Library Quantification Kit (Kapa Biosystems, Inc., Woburn, MA, USA).
Paired-end sequencing (25 million, 75-bp, paired-end reads) was performed on an Illumina Novaseq 6000 sequencers (Illumina, Inc., San Diego, CA, USA) as per manufacturer’s recommended protocol.

value: Dendritic cells

tag: treatment

value: A/H7N9 vaccine with AS03 adjuvant

tag: day


title: 203991410052_R02C01_20174926_PFC

tag: tissue


title: 203991410053_R08C01_20174918_PFC


title: 203991410053_R07C01_20185913_PFC


title: 203991410053_R05C01_PD544_PFC


title: 4XKO_EpiLC+CH_rep1

description: replicate 1


title: 3XKO_EpiLC+CH_rep1

description: replicate 1


title: KO_Naive_rep1

description: replicate 1


title: 4XKO_EpiLC_rep1

description: replicate 1

value: EpiLC


title: WT_Naive_rep1

description: replicate 1


title: 203991410053_R04C01_PD269_PFC


title: WT_EpiLC+CH_rep1

description: replicate 1

value: EpiLC+CH


title: KO-2

city: Xi'an

first: dengxu

last: Tan

address: Changlexilu

department: Laboratory Animal Center

institute: Fourth Military Medical  University

description:
Library name: KO-2
knockdown group, replicate biosample 2

data_processing:
CLC Genomics Workbench v 11.0.1
Sequence reads were trimmed for adaptor sequence/low-quality sequence using CLC genomic benchwork (parameter- Quality limit: 0.05)
Trimmed sequence reads were mapped to mm10  using CLC genomic benchwork (parameters- mismath cost: 2 insertion cost: 3 deletion cost: 3 length fraction: 0.8 similarity fraction: 0.8)
Read count extraction and normalization were performed using CLC genomic benchwork
Assembly: mm10
Supplementary files format and content: Excel file includes gene count for each Sample

source_name: pancreatic tumor

extract_protocol:
RNA was extracted from cell culture using TRIzol reagent. Briefly, cell culture were washed with PBS, lysed in TRIzol, and incubated for 5 min. Chloroform (20% volume) was added, followed by vigorous mixing and centrifugation (12,000 ×g, 15 min, 4°C) to separate phases. The aqueous layer was collected, mixed with isopropanol, and centrifuged (12,000 ×g, 10 min) to precipitate RNA. The pellet was washed twice with 75% ethanol, air-dried, and dissolved in RNase-free water. RNA concentration and integrity (RIN >7) were assessed using Nanodrop and Bioanalyzer. Samples were stored at -80°C to prevent degradation. This method ensures high-quality RNA for transcriptomic analyses such as RNA-seq or qPCR.
Total RNA is enriched for small RNAs, followed by 3' and 5' adapter ligation. Reverse transcription generates cDNA, which is then PCR amplified with indexed primers. The final library is size-selected (typically ~150 bp) and validated by Bioanalyzer before sequencing on an Illumina flow cell.

value: pancreatic tumor

tag: cell line

value: CAF

value: MAOA ko

value: MAOA knockout


title: KO-3

description:
Library name: KO-3
knockdown group, replicate biosample 3


title: 203991410053_R02C01_PD957_PFC

value: Prefrontal cortex


title: KO-1

description:
Library name: KO-1
knockdown group, replicate biosample 1


title: 4XKO_Naive_rep1

description: replicate 1


title: 203991410111_R07C01_PDC110_PFC

value: female


title: NC-3

description:
Library name: NC-3
control group, replicate biosample 3

value: wt

value: control


title: 203991410111_R02C01_20030129_PFC

value: Newcastle Brain Tissue Resource

value: FALSE


title: NC-2

description:
Library name: NC-2
control group, replicate biosample 2


title: 203991410111_R01C01_P24/17_PFC

value: QSBB


title: 203991410028_R05C01_P54/13_PFC


title: NC-1

description:
Library name: NC-1
control group, replicate biosample 1


title: AKI_4

city: Palo Alto

first: Avnesh

last: Thakor

state: California

address: 3155 Porter Dr

department: Radiology

institute: Stanford Medicine

description:
Library name: Sampl4
6h_after_reperfusion

data_processing:
Sequenced reads were trimmed for adaptor sequence
Then mapped to mouse genome Mus Musculus using HISTAT
HTSeq was used to generate the raw read counts
DESeq2 was used for differential gene expression analysis
Assembly: mm39
Supplementary files format and content: tab-delimited text file include count values for IRI and therapy samples
Supplementary files format and content: tab-delimited text file include count values for sham surgery samples
Supplementary files format and content: tab-delimited text file include count values for IRI temporal samples

source_name: kidney

growth_protocol: MSCs were cultured in DMEM-low glucose with 10% FBS + 1% Pencillin-strptomycin

extract_protocol:
total RNA was extracted from each replicate using the RNAeasy minikit (qiagen)
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: MSCs were injected immediately following reperfusion during IRI under same anesthesia

value: kidney

value: IRI


title: AKI_3

description:
Library name: Sampl3
6h_after_reperfusion


title: SUB08, Monocytes, A/H7N9 vaccine unadjuvanted, Day30

description:
Library name: SUB08_D30_MNR
SUB08_D30_MNR

source_name: Monocytes

value: Monocytes

value: A/H7N9 vaccine unadjuvanted


title: 203991390053_R08C01_PD233_PFC

value: Imperial Brain Bank


title: AKI_2

description:
Library name: Sampl2
6h_after_reperfusion


title: 203991390053_R06C01_NP17/074_PFC

value: Oxford Brain Bank


title: AKI_1

description:
Library name: Sampl1
6h_after_reperfusion


title: 203991390053_R01C01_C020_PFC


title: 203991390053_R04C01_PD045_PFC

value: male


title: SUB08, T cells, A/H7N9 vaccine unadjuvanted, Day2

description:
Library name: SUB08_D2_TCR
SUB08_D2_TCR

source_name: T cells

value: T cells


title: 203991390089_R07C01_20070009_PFC


title: exp34_W3_memory_mixed_Hashtag_Data

city: Prague

first: Juraj

last: Michalik

address: Vídeňská 1083

country: Czech Republic

institute: Institute of Molecular Genetics of the Czech Academy of Sciences

description: Library name: exp34-W3-CSP

library_source: other

data_processing:
Sequencing was performed on NovaSeq6000 platform.
Base calling and FASTQ generation were performed using Cell Ranger v8.0.1 mkref tool.
The murine reference genome used for read alignment was obtained from Ensembl release 102 and prepared using the mkref tool from 10x Cell Ranger v8.0.1 (Zheng et al., 2017). Count matrices were generated using the count tool from either 10x Cell Ranger v8.0.1 using paired-end sequencing mode.
Subsequent analyses were performed in R v4.5.2 using the Seurat v5.3.0 package (Hao et al., 2024).
Assembly: GRCm38 v102 (Ensembl)
Supplementary files format and content: File containing specification of each hashtag and sample for Well 1 (W1) samples, in CSV format, used by 10X Cell Ranger to quantify each hashtag for each cell.
Supplementary files format and content: File containing specification of each hashtag and sample for Well 2 (W2) samples, in CSV format, used by 10X Cell Ranger to quantify each hashtag for each cell.
Supplementary files format and content: File containing specification of each hashtag and sample for Well 3 (W3) samples, in CSV format, used by 10X Cell Ranger to quantify each hashtag for each cell.
Supplementary files format and content: 10X Cell Ranger output: list of barcodes in TSV format (W1)
Supplementary files format and content: 10X Cell Ranger output: list of genes/features and their type in TSV format (W1)
Supplementary files format and content: 10X Cell Ranger output: sparse matrix quantifying results (W1)
Supplementary files format and content: 10X Cell Ranger output: list of barcodes in TSV format (W2)
Supplementary files format and content: 10X Cell Ranger output: list of genes/features and their type in TSV format (W2)
Supplementary files format and content: 10X Cell Ranger output: sparse matrix quantifying results (W2)
Supplementary files format and content: 10X Cell Ranger output: list of barcodes in TSV format (W3)
Supplementary files format and content: 10X Cell Ranger output: list of genes/features and their type in TSV format (W3)
Supplementary files format and content: 10X Cell Ranger output: sparse matrix quantifying results (W2)
Supplementary files format and content: RDS file containing Seurat object of processed samples from spleen and Tcm/Tn(Tcm) only.
Supplementary files format and content: RDS file containing Seurat object of processed samples from spleen and Tcm/Tn(Tcm) only.
Supplementary files format and content: RDS file containing Seurat object of processed samples from spleen and Tcm/Tn(Tcm) only.
Supplementary files format and content: RDS file containing Seurat object of processed samples from spleen and Tem/Tn(Tem) only.
Library strategy: CITE-seq

molecule: protein

source_name: spleen

growth_protocol: The cells were isolated from OT-I Rag2-/- mice (D3), Vb5 mice (D7/D10). GP33 LCMV antigen-specific memory cells were isolated from WT mice previously infected with LCMV (D7).

extract_protocol:
At indicated time points p.i., the progeny was FACS-isolated from the spleen.
Cells from all experiments were loaded onto a Chromium X Controller (10x Genomics). cDNA libraries were prepared using the Chromium GEM-X Single Cell' 5 Reagent Kits v3 with Feature Barcode technology for CRISPR Screening and Cell Surface Protein (10x Genomics; #PN-1000694, #PN-1000698, #PN-1000699, #PN-1000703, #PN-1000215, #PN-1000250), following the manufacturer's protocol (#CG000736 Rev A).

treatment_protocol: The day after transfer, the mice were infected with Lm-OVA or LCMV.

value: spleen

value: CD8+ T cells

value: Progeny of Tn/Tem/Tcm

value: Lm-OVA/LCMV infection

tag: time

value: Day 3/Day 7/Day 10


title: exp34_W3_memory_mixed_GEX_Data

description: Library name: exp34-W3-GEX

data_processing:
Sequencing was performed on NovaSeq6000 platform.
Base calling and FASTQ generation were performed using Cell Ranger v8.0.1 mkref tool.
The murine reference genome used for read alignment was obtained from Ensembl release 102 and prepared using the mkref tool from 10x Cell Ranger v8.0.1 (Zheng et al., 2017). Count matrices were generated using the count tool from either 10x Cell Ranger v8.0.1 using paired-end sequencing mode.
Subsequent analyses were performed in R v4.5.2 using the Seurat v5.3.0 package (Hao et al., 2024).
Assembly: GRCm38 v102 (Ensembl)
Supplementary files format and content: File containing specification of each hashtag and sample for Well 1 (W1) samples, in CSV format, used by 10X Cell Ranger to quantify each hashtag for each cell.
Supplementary files format and content: File containing specification of each hashtag and sample for Well 2 (W2) samples, in CSV format, used by 10X Cell Ranger to quantify each hashtag for each cell.
Supplementary files format and content: File containing specification of each hashtag and sample for Well 3 (W3) samples, in CSV format, used by 10X Cell Ranger to quantify each hashtag for each cell.
Supplementary files format and content: 10X Cell Ranger output: list of barcodes in TSV format (W1)
Supplementary files format and content: 10X Cell Ranger output: list of genes/features and their type in TSV format (W1)
Supplementary files format and content: 10X Cell Ranger output: sparse matrix quantifying results (W1)
Supplementary files format and content: 10X Cell Ranger output: list of barcodes in TSV format (W2)
Supplementary files format and content: 10X Cell Ranger output: list of genes/features and their type in TSV format (W2)
Supplementary files format and content: 10X Cell Ranger output: sparse matrix quantifying results (W2)
Supplementary files format and content: 10X Cell Ranger output: list of barcodes in TSV format (W3)
Supplementary files format and content: 10X Cell Ranger output: list of genes/features and their type in TSV format (W3)
Supplementary files format and content: 10X Cell Ranger output: sparse matrix quantifying results (W2)
Supplementary files format and content: RDS file containing Seurat object of processed samples from spleen and Tcm/Tn(Tcm) only.
Supplementary files format and content: RDS file containing Seurat object of processed samples from spleen and Tcm/Tn(Tcm) only.
Supplementary files format and content: RDS file containing Seurat object of processed samples from spleen and Tcm/Tn(Tcm) only.
Supplementary files format and content: RDS file containing Seurat object of processed samples from spleen and Tem/Tn(Tem) only.

extract_protocol:
At indicated time points p.i., the progeny was FACS-isolated from the spleen.
Cells from all experiments were loaded onto a Chromium X Controller (10x Genomics). cDNA libraries were prepared using the Chromium GEM-X Single Cell' 5 Reagent Kits v3 with Feature Barcode technology for CRISPR Screening and Cell Surface Protein (10x Genomics; #PN-1000694, #PN-1000698, #PN-1000699, #PN-1000703, #PN-1000215, #PN-1000250), following the manufacturer's protocol (#CG000736 Re


title: 203991390089_R06C01_20050098_PFC

value: Prefrontal cortex


title: SUB08, Neutrophils, A/H7N9 vaccine unadjuvanted, Day30

description:
Library name: SUB08_D30_NER
SUB08_D30_NER

source_name: Neutrophils

value: Neutrophils


title: exp34_W2_memory_mixed_Hashtag_Data

description: Library name: exp34-W2-CSP


title: 203991390089_R04C01_PDC026_PFC

value: female

value: TRUE


title: exp34_W2_memory_mixed_GEX_Data

description: Library name: exp34-W2-GEX


title: 203977090067_R07C01_19900133_PFC

value: Newcastle Brain Tissue Resource

value: FALSE


title: exp34_W1_memory_mixed_Hashtag_Data

description: Library name: exp34-W1-CSP


title: 203977090067_R06C01_C037_PFC


title: exp34_W1_memory_mixed_GEX_Data

description: Library name: exp34-W1-GEX


title: Pooled liver nuclei from young WT, aged WT, aged ADK control, and aged ADK heterozygous mice

city: College Station

first: Chaodong

last: Wu

state: TX

address: 373 Olsen Blvd

department: Nutrition

institute: Texas A&M University

description:
Library name: Liver_aging_pooled_snRNAseq
Four samples were pooled to generate a single 10x Genomics library and were subsequently demultiplexed into four experimental groups.

data_processing:
Sequencing reads were processed using the 10x Genomics Cell Ranger multi pipeline. Reads were assigned to individual samples using their sample-specific Flex probe barcodes, and gene-by-nucleus count matrices were generated for each sample.
Filtered feature-barcode matrices for the four samples were used for downstream quality control, normalization, dimensionality reduction, clustering, and cell-type annotation in Seurat.
Assembly: Mus musculus mm10
Supplementary files format and content: HDF5 files containing 10x Genomics filtered feature-barcode count matrices. Each file contains the sparse gene-by-nucleus count matrix, feature annotations, and nucleus barcode identifiers for one biological sample.

source_name: liver

growth_protocol: Mice were maintained under standard laboratory conditions until the indicated age. Liver tissues were collected from 3-month-old and 18-month-old mice and frozen prior to nuclei isolation.

extract_protocol:
Nuclei were isolated from frozen mouse liver tissue using a nuclei isolation procedure optimized for single-nucleus RNA sequencing. Isolated nuclei were filtered, counted, and assessed for quality before processing.
Single-nucleus gene-expression libraries were prepared using the 10x Genomics Chromium Single Cell Gene Expression Flex workflow according to the manufacturer's instructions. The four samples were labeled with distinct sample-specific probe barcodes, pooled, and sequenced as one multiplexed paired-end library.

treatment_protocol: No pharmacological treatment was applied. Experimental groups were defined by age and genotype.

value: liver

value: liver nuclei

value: mixed genotypes


title: 203977090067_R05C01_PDC034_PFC

value: Imperial Brain Bank


title: 203977090067_R01C01_20110310_PFC


title: exp20_OTI_LmOVA_D6_Hashtag_Data

description: Library name: exp20-CSP

data_processing:
Sequencing was performed on NovaSeq 6000 platform.
Base calling and FASTQ generation were performed using the Illumina BaseSpace GenerateFASTQ workflow v1.37.0.
The murine reference genome used for read alignment was obtained from Ensembl release 102 and prepared using the mkref tool from 10x Cell Ranger v5.0.1 (Zheng et al., 2017). Count matrices were generated using the count tool from either 10x Cell Ranger v5.0.1 using paired-end sequencing mode.
Subsequent analyses were performed in R v4.5.2 using the Seurat v5.3.0 package (Hao et al., 2024).
Assembly: GRCm38 v102 (Ensembl)
Supplementary files format and content: File containing specification of each hashtag and sample, in CSV format, used by 10X Cell Ranger to quantify each hashtag for each cell.
Supplementary files format and content: 10X Cell Ranger output: list of barcodes in TSV format
Supplementary files format and content: 10X Cell Ranger output: list of genes/features and their type in TSV format
Supplementary files format and content: 10X Cell Ranger output: sparse matrix quantifying results
Supplementary files format and content: RDS file containing Seurat object of all processed samples together.
Library strategy: CITE-seq

growth_protocol: The cells were isolated from OT-I Rag2-/- mice. Memory cells were created and memory+naïve cells were transferred into separate congenic hosts in the same numbers.

extract_protocol:
6 days p.i., the progeny was FACS-isolated from the spleen.
Cells from all experiments were loaded onto a Chromium Controller (10x Genomics). cDNA libraries were prepared using the Chromium Next GEM Single Cell 5′ Reagent Kits v2 (Dual Index) with Feature Barcode technology for CRISPR Screening and Cell Surface Protein (10x Genomics; #PN-1000263, #PN-1000286, #PN-1000541, #PN-1000190, #PN-1000215, #PN-1000250), following the manufacturer’s protocol (#CG000511 Rev C).

treatment_protocol: The day after transfer, the mice were infected with Lm-OVA.

value: Progeny of Tn/Tcm/Tem

value: Lm-OVA infection

value: Day 6


title: 203977090074_R07C01_20000020_PFC

value: male


title: exp20_OTI_LmOVA_D6_GEX_Data

description: Library name: exp20-GEX

data_processing:
Sequencing was performed on NovaSeq 6000 platform.
Base calling and FASTQ generation were performed using the Illumina BaseSpace GenerateFASTQ workflow v1.37.0.
The murine reference genome used for read alignment was obtained from Ensembl release 102 and prepared using the mkref tool from 10x Cell Ranger v5.0.1 (Zheng et al., 2017). Count matrices were generated using the count tool from either 10x Cell Ranger v5.0.1 using paired-end sequencing mode.
Subsequent analyses were performed in R v4.5.2 using the Seurat v5.3.0 package (Hao et al., 2024).
Assembly: GRCm38 v102 (Ensembl)
Supplementary files format and content: File containing specification of each hashtag and sample, in CSV format, used by 10X Cell Ranger to quantify each hashtag for each cell.
Supplementary files format and content: 10X Cell Ranger output: list of barcodes in TSV format
Supplementary files format and content: 10X Cell Ranger output: list of genes/features and their type in TSV format
Supplementary files format and content: 10X Cell Ranger output: sparse matrix quantifying results
Supplementary files format and content: RDS file containing Seurat object of all processed samples together.

value: spleen

value: CD8+ T cells


title: 203977090074_R06C01_PDC022_PFC


title: exp12_W2_OTI_LmOVA_W12_Hashtag_Data

description: Library name: exp12-W2-CSP

data_processing:
Sequencing was performed on NovaSeq6000 platform.
Base calling and FASTQ generation were performed using Cell Ranger v5.0.1 mkref tool.
The murine reference genome used for read alignment was obtained from Ensembl release 102 and prepared using the mkref tool from 10x Cell Ranger v5.0.1 (Zheng et al., 2017). Count matrices were generated using the count tool from either 10x Cell Ranger v5.0.1 using paired-end sequencing mode.
Subsequent analyses were performed in R v4.5.2 using the Seurat v5.3.0 package (Hao et al., 2024).
Assembly: GRCm38 v102 (Ensembl)
Supplementary files format and content: File containing specification of each hashtag and sample for Well 1 (W1) samples, in CSV format, used by 10X Cell Ranger to quantify each hashtag for each cell. Analysis was done only on samples from spleen, to keep results comparable with other data used within publication.
Supplementary files format and content: File containing specification of each hashtag and sample for Well 2 (W2) samples, in CSV format, used by 10X Cell Ranger to quantify each hashtag for each cell. Analysis was done only on samples from spleen, to keep results comparable with other data used within publication.
Supplementary files format and content: 10X Cell Ranger output: list of barcodes in TSV format
Supplementary files format and content: 10X Cell Ranger output: list of genes/features and their type in TSV format
Supplementary files format and content: 10X Cell Ranger output: sparse matrix quantifying results
Supplementary files format and content: RDS file containing Seurat object of processed samples from spleen and Tcm/Tn(Tcm) only.
Supplementary files format and content: RDS file containing Seurat object of processed samples from spleen and Tem/Tn(Tem) only.
Library strategy: CITE-seq

source_name: spleen/blood

growth_protocol: The cells were isolated from OT-I Rag2-/- mice. Memory cells were created and co-transferred together with naïve cells in 1:1 ratio to congenic recipients.

extract_protocol:
12 weeks p.i., the progeny was FACS-isolated frrom the spleen and blood.
Cells from all experiments were loaded onto a Chromium Controller (10x Genomics). cDNA libraries were prepared using the Chromium Next GEM Single Cell 5′ Reagent Kits v2 (Dual Index) with Feature Barcode technology for CRISPR Screening and Cell Surface Protein (10x Genomics; #PN-1000263, #PN-1000286, #PN-1000541, #PN-1000190, #PN-1000215, #PN-1000250), following the manufacturer’s protocol (#CG000511 Rev C).

treatment_protocol: The day after re-transfer, the mice were infected with Lm-OVA.

value: spleen/blood

value: Progeny of Tn(Tem)/Tn(Tcm)/Tem/Tcm

value: Week 12


title: 203977090074_R05C01_P69/10_PFC

value: Prefrontal cortex

value: QSBB


title: 203977090074_R04C01_20110837_PFC

value: Newcastle Brain Tissue Resource


title: exp12_W2_OTI_LmOVA_W12_GEX_Data

description:
Library name: exp12-W2-GEX
Blood samples were not used.

data_processing:
Sequencing was performed on NovaSeq6000 platform.
Base calling and FASTQ generation were performed using Cell Ranger v5.0.1 mkref tool.
The murine reference genome used for read alignment was obtained from Ensembl release 102 and prepared using the mkref tool from 10x Cell Ranger v5.0.1 (Zheng et al., 2017). Count matrices were generated using the count tool from either 10x Cell Ranger v5.0.1 using paired-end sequencing mode.
Subsequent analyses were performed in R v4.5.2 using the Seurat v5.3.0 package (Hao et al., 2024).
Assembly: GRCm38 v102 (Ensembl)
Supplementary files format and content: File containing specification of each hashtag and sample for Well 1 (W1) samples, in CSV format, used by 10X Cell Ranger to quantify each hashtag for each cell. Analysis was done only on samples from spleen, to keep results comparable with other data used within publication.
Supplementary files format and content: File containing specification of each hashtag and sample for Well 2 (W2) samples, in CSV format, used by 10X Cell Ranger to quantify each hashtag for each cell. Analysis was done only on samples from spleen, to keep results comparable with other data used within publication.
Supplementary files format and content: 10X Cell Ranger output: list of barcodes in TSV format
Supplementary files format and content: 10X Cell Ranger output: list of genes/features and their type in TSV format
Supplementary files format and content: 10X Cell Ranger output: sparse matrix quantifying results
Supplementary files format and content: RDS file containing Seurat object of processed samples from spleen and Tcm/Tn(Tcm) only.
Supplementary files format and content: RDS file containing Seurat object of processed samples from spleen and Tem/Tn(Tem) only.


title: exp12_W1_OTI_LmOVA_W12_Hashtag_Data

description: Library name: exp12-W1-CSP


title: 203977090074_R02C01_P21/17_PFC

value: FALSE


title: exp12_W1_OTI_LmOVA_W12_GEX_Data

description:
Library name: exp12-W1-GEX
Blood samples were not used.


title: 203977090074_R01C01_20050033_PFC


title: Fgfr1b, TGFb treated, biol rep 3

city: Chapel Hill

first: Shea

middle: N

last: Ricketts

state: NC

address: 111 Mason Farm Road

department: Pathology and Laboratory Medicine

institute: UNC Chapel Hill

description: Library name: Fgfr1btgfb3

data_processing:
Data was assessed for quality with FastQC and aligned to mouse genome using STAR
Transcript expression was inferred using featureCounts
Assembly: mm10
Supplementary files format and content: tab-delimited text file includs TPM values for each sample

source_name: Heart

growth_protocol: Cardiac fibroblasts isolated from wildtype C57BL/6  mice were maintained in DMEM supplemented with 20% fetal bovine serum, 1% nonessential amino acids and 1% penicillin-streptomycin in humidified atmosphere at 37 ºC under 5% CO2

extract_protocol:
RNA was harvested with QIA shredder homogenization (Qiagen #795654) and RNeasy Plus Mini Kit (Qiagen #74134pi). 1.3 ug of total RNA was used for sequencing libraries.
Library preparation was performed by Novogene

treatment_protocol: For FGFR1 knockdown assays, cardiac fibroblasts were treated with lentiviral shFgfr1 to deplete FGFR1 for and treated with lentiviral shNT for control. For FGFR1 overexpression assays, cardiac firboblasts were treated with lentiviral overexpression constructs (Fgfr1a1, Fgfr1a2, or Fgfr1b) and treated with lentiviral LacZ for Control. All lentiviral treatments were supplemented with 8ug/mL of polybrene.

value: Heart

value: Fibroblast

value: Wildtype, Fgfr1b OeX

value: Profibrotic stimulation by TGFb (10 ng/ul)


title: 203973690024_R06C01_PD814_PFC

value: Imperial Brain Bank

value: female


title: 203973690024_R05C01_C075_PFC


title: Fgfr1b, TGFb treated, biol rep 2

description: Library name: Fgfr1btgfb2


title: 203973690024_R04C01_PD359_PFC


title: Fgfr1b, TGFb treated, biol rep 1

description: Library name: Fgfr1btgfb1


title: SUB08, Dendritic cells, A/H7N9 vaccine unadjuvanted, Day36

description:
Library name: SUB08_D36_DNR
SUB08_D36_DNR

value: Dendritic cells

value: A/H7N9 vaccine unadjuvanted


title: Fgfr1b, untreated, biol rep 3

description: Library name: Fgfr1b3

value: Serum


title: 203973690024_R02C01_PD727_PFC

value: male


title: Fgfr1b, untreated, biol rep 2

description: Library name: Fgfr1b2


title: SUB08, T cells, A/H7N9 vaccine unadjuvanted, Day32

description:
Library name: SUB08_D32_TCR
SUB08_D32_TCR

value: T cells


title: 203973690002_R08C01_20174936_PFC


title: Fgfr1b, untreated, biol rep 1

description: Library name: Fgfr1b1


title: 203973690002_R07C01_20150535_PFC


title: Fgfr1a2, TGFb treated, biol rep 3

description: Library name: Fgfr1a2tgfb3

value: Wildtype, Fgfr1a2 OeX


title: 203973690002_R06C01_PD010_PFC


title: Fgfr1a2, TGFb treated, biol rep 2

description: Library name: Fgfr1a2tgfb2


title: 203973690002_R02C01_PDC123_PFC


title: Fgfr1a2, TGFb treated, biol rep 1

description: Library name: Fgfr1a2tgfb1


title: 203991400112_R07C01_19870884_PFC


title: 203991400112_R04C01_P77/17_PFC


title: Fgfr1a2, untreated, biol rep 3

description: Library name: Fgfr1a23


title: 203991390103_R01C01_PD1031_PFC


title: Fgfr1a2, untreated, biol rep 2

description: Library name: Fgfr1a22


title: Fgfr1a2, untreated, biol rep 1

description: Library name: Fgfr1a21


title: 203991390158_R07C01_P14/14_PFC


title: 203991390158_R06C01_PD927_PFC


title: Fgfr1a1, TGFb treated, biol rep 3

description: Library name: Fgfr1a1tgfb3

value: Wildtype, Fgfr1a1 OeX


title: 203991390158_R05C01_PD904_PFC

value: Prefrontal cortex


title: Fgfr1a1, TGFb treated, biol rep 1

description: Library name: Fgfr1a1tgfb1


title: Fgfr1a1, TGFb treated, biol rep 2

description: Library name: Fgfr1a1tgfb2


title: 203991390158_R04C01_20030113_PFC


title: 3XKO_EpiLC_rep1

description: replicate 1

value: mouse embryonic stem cells

value: EpiLC


title: Fgfr1a1, untreated, biol rep 3

description: Library name: Fgfr1a13


title: 203991390158_R01C01_P67/15_PFC

value: QSBB

value: FALSE


title: Fgfr1a1, untreated, biol rep 2

description: Library name: Fgfr1a12

value: Heart

value: Fibroblast


title: 203991390146_R04C01_PD306_PFC


title: Fgfr1a1, untreated, biol rep 1

description: Library name: Fgfr1a11


title: 203991390160_R08C01_19870841_PFC

value: Newcastle Brain Tissue Resource


title: control, LacZ TGFb treated, biol rep 3

description: Library name: LacZtgfb3

value: Wildtype, LacZ

value: Profibrotic stimulation by TGFb (10 ng/ul)


title: 203991390160_R07C01_NP14/073_PFC

value: Oxford Brain Bank


title: 203991390160_R06C01_PD067_PFC

value: Imperial Brain Bank


title: control, LacZ TGFb treated, biol rep 2

description: Library name: LacZtgfb2


title: control, LacZ TGFb treated, biol rep 1

description: Library name: LacZtgfb1


title: 203991390160_R02C01_20196910_PFC


title: control, LacZ untreated, biol rep 3

description: Library name: LacZ3

value: Serum


title: 203991390151_R06C01_P73/15_PFC

value: female


title: control, LacZ untreated, biol rep 2

description: Library name: LacZ2


title: 203991390151_R01C01_C084_PFC


title: control, LacZ untreated, biol rep 1

description: Library name: LacZ1


title: shFgfr1, TGFb, biol rep 3

description: Library name: shFgfr1tgfb3

value: Wildtype, shFgfr1


title: 203973690007_R08C01_P17/16_PFC


title: shFgfr1, TGFb, biol rep 2

description: Library name: shFgfr1tgfb2


title: 203973690007_R07C01_NP16/050_PFC

value: male


title: shFgfr1, TGFb, biol rep 1

description: Library name: shFgfr1tgfb1


title: 203973690007_R02C01_19900338_PFC


title: shFgfr1, untreated, biol rep 3

description: Library name: shFgfr3


title: 203973690007_R01C01_NP16/079_PFC


title: shFgfr1, untreated, biol rep 2

description: Library name: shFgfr2


title: 203973690015_R06C01_20100742_PFC


title: 203973690015_R05C01_PD077_PFC


title: control, shNT TGFb treated, biol rep 3

description: Library name: shNTtgfb3

value: WildType, shNT


title: 203973690015_R02C01_PD060_PFC

value: Prefrontal cortex


title: shFgfr1, untreated, biol rep 1

description: Library name: shFgfr1


title: 203973690015_R01C01_PD093_PFC


title: 203991410139_R07C01_20174907_PFC


title: 203991410064_R04C01_20185907_PFC


title: control, shNT untreated, biol rep 3

description: Library name: shNT3


title: 203991410064_R01C01_PD368_PFC


title: control, shNT untreated, biol rep 1

description: Library name: shNT1


title: 203991410110_R08C01_PD562_PFC


title: combo (anti-human CTLA-4 + anti-mouse FcgRII)

city: Lund

first: Björn

last: Frendeus

state: Skane

address: Ideongatan 1

country: Sweden

institute: BioInvent International

description:
Library name: Sample4
10x Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting anf aggregation were made using the Cell Ranger software v7.0.0 (https://www.10xgenomics.com/support/software/cell-ranger/latest/release-notes/cr-release-notes#v7-0-0)
Assembly: Mouse mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Tumor

extract_protocol:
Tumors from 11 mice/group was harvested and pooled together into 1 sample, in total 4 samples. Harvested tumors were cut into small (2-3 mm) pieces using scalpels. Tissue pieces were enzymatically digested using 0,5 mg/ml Liberase TM (Merck) and 200 kunitz/ml DNAse (Merck) for 2x5 min at 37 degrees with slight vortex in between. Digestion reaction was quenched with 5 mL of RPMI (containing 10% FCS) and cells were filtered through a 70 mm cell-strainer. Viable lymphocytes were isolated using Lympholyte-M Separation Media (Cedarlane) gradients. Lymphocytes were stained with viability dye and CD45 antibody and live CD45+ cells were sorted using a FACS AriaFusion (Becton Dickinson). Cells were counted (NucleoCounter NC-202, ChemoMetec) and fixed according to “10x sample fixation Protocol” from 10x Genomics and kept at -80 °C until analyzed using scRNA- seq.
Viable CD45+ cells were sorted using FACS and samples were fixed using 4% formaldehyde for 20 hours at 4 °C, followed by long-term storage at –80 °C according to ‘10x Genomics’ flex fixation kit recommendations. In short, prior to library preparation, samples were thawed, washed, and hybridized with barcoded probe sets according to the Chromium Next-GEM Flex protocol (10x Genomics). Approximately 10k cells per sample were targeted for capture, and the pooled samples were loaded onto a Chromium X instrument using a Chip Q. The sequencing Libraries were sequenced on an Illumina NovaSeq 600

value: Tumor

value: CD45 positive cells

tag: host strain

value: combo(anti-human CTLA-4 + anti-mouse FcgRII)

tag: batch

value: batch 1


title: control, shNT untreated, biol rep 2

description: Library name: shNT2

value: Heart


title: 203991410066_R08C01_PDC112_PFC

tag: Sex

value: FALSE


title: SUB08, NK cells, A/H7N9 vaccine unadjuvanted, Day29

description:
Library name: SUB08_D29_NKR
SUB08_D29_NKR

source_name: NK cells

value: NK cells

value: A/H7N9 vaccine unadjuvanted


title: isotype control

description:
Library name: Sample1
10x Genomics

value: isotype control


title: E12.5+18h ureter cultures, LiCl treated, repl. #3

description:
Library name: Sample 6
Column name in raw_counts_all_samples.txt: LI_3

data_processing:
Sequencing was performed on an Illumina Illumina NovaSeq 6000 platform using paired-end 150 bp reads. Adapters were trimmed using fastp v0.23. Reads were aligned to GRCm39/Mus_musculus_Ensemble_107 using STAR v2.7. Gene counts were generated using featureCounts v2.0. Differential expression analysis was performed with DESeq2 v1.40.
Assembly: GRCm39/Mus_musculus_Ensemble_107
Supplementary files format and content: tab-delimited text file includes raw counts for each sample
Supplementary files format and content: tab-delimited text files include FPKM values for each sample

source_name: ureter

extract_protocol:
Extraction of total RNA was performed using the QIAGEN RnNeasy micro kit according to the manufacturer’s recommendations. The total RNA samples were sent to Novogene, Munich for quality control, library construction, sequencing and bioinformatics analysis.
Libraries were prepared using Illumina TruSeq Stranded mRNA Library Prep Kit following manufacturer instructions. PolyA-selected RNA was fragmented and reverse transcribed.

treatment_protocol: Ureters were mechanically dissected from E12.5 embryos and cultured on transwell membranes for 18h in culture medium (DMEM/F12 with 1x GlutaMAX, 1x Penicillin/Streptomycin, 1x NEAA, 1x Pyruvate) with or without 15 mM LiCl.

value: ureter

tag: mouse strain

value: NMRI

value: embryonic ureter

value: wildtype

value: 15 mM LiCl

tag: embryonic stage

tag: culture period


title: anti-mouse FcgRII

description:
Library name: Sample3
10x Genomics

value: anti-human CTLA-4


title: E12.5+18h ureter cultures, LiCl treated, repl. #2

description:
Library name: Sample 5
Column name in raw_counts_all_samples.txt: LI_2


title: 203991410066_R03C01_PD021_PFC

tag: regiondescription

value: Imperial Brain Bank

value: male


title: E12.5+18h ureter cultures, LiCl treated, repl. #1

description:
Library name: Sample 4
Column name in raw_counts_all_samples.txt: LI_1


title: 203991410066_R01C01_20030111_PFC

value: Prefrontal cortex

tag: plate

value: Newcastle Brain Tissue Resource


title: E12.5+18h ureter cultures, control, repl. #3

description:
Library name: Sample 3
Column name in raw_counts_all_samples.txt: K_3

value: water


title: 203973690079_R07C01_PDC035_PFC

tag: centre

value: female


title: 203973690079_R06C01_PD082_PFC

tag: thal


title: E12.5+18h ureter cultures, control, repl. #2

description:
Library name: Sample 2
Column name in raw_counts_all_samples.txt: K_2

tag: cell type


title: 203973690079_R05C01_PD109_PFC


title: 203973690079_R04C01_20131187_PFC


title: E12.5+18h ureter cultures, control, repl. #1

description:
Library name: Sample 1
Column name in raw_counts_all_samples.txt: K_1

tag: genotype


title: C57BL/6 mice, kidney, adenine diet & AA, 4

city: Suzhou

first: liwei

last: zhu

state: Jiangsu

address: 77th, Changan South Street

institute: Zhangjiagang TCM Hospital Affiliated to Nanjing University ofChinese Medicine

description: Library name: AA_4

data_processing:
The clustering of the index-coded samples was performed on a cBot Cluster Generation System using TruSeq PE Cluster Kit v3-cBot-HS (Illumia) according to the manufacturer’s instructions. After cluster generation, the library preparations were sequenced on an Illumina Novaseq platform and 150 bp paired-end reads were generated.
Raw data (raw reads) of fastq format were firstly processed through fastp software. In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data. At the same time, Q20, Q30 and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality.
Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using Hisat2 v2.0.5 and paired-end clean reads were aligned to the reference genome using Hisat2 v2.0.5. We selected Hisat2 as the mapping tool for that Hisat2 can generate a database of splice junctions based on the gene model annotation file and thus a better mapping result than other non-splice mapping tools.
featureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene. FPKM, expected number of Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced, considers the effect of sequencing depth and gene length for the reads count at the same time, and is currently the most commonly used method for estimating gene expression levels.
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample
Supplementary files format and content: csv files include FPKM values for each Sample

growth_protocol: Eight-week-old male C57BL/6 mice (20 ± 2 g)

extract_protocol:
Total RNA was used as input material for the RNA sample preparations. Briefly, mRNA was purified from total RNA using poly-T oligo-attached magnetic beads. Fragmentation was carried out using divalent cations under elevated temperature in First Strand Synthesis Reaction Buffer(5X). First strand cDNA was synthesized using random hexamer primer and M-MuLV Reverse Transcriptase(RNase H-). Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and RNase H.
Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. After adenylation of 3’ ends of DNA fragments, Adaptor with hairpin loop structure were ligated to prepare for hybridization. In order to select cDNA fragments of preferentially 370~420 bp in length, the library fragments were purified with AMPure XP system. Then PCR was performed with Phusion High-Fidelity DNA polymerase, Universal PCR primers and Index (X) Primer. At last, PCR products were purified (AMPure XP system) and library quality was assessed on the Agilent Bioanalyzer 2100 system.

treatment_protocol: The CKD model was established by administering adenine-enriched chow for 4 week, AA groups received daily oral gavage of AA, while the control animals were maintained on adenine-free chow. Weeks 5–8, all groups were transitioned to standard diet while AA treatment continued.

value: kidney

tag: strain

tag: treatment

value: adenine diet & AA


title: 203973690079_R02C01_20050022_PFC

tag: tissue

value: FALSE


title: C57BL/6 mice, kidney, adenine diet & AA, 3

description: Library name: AA_3


title: 203973690079_R01C01_PD761_PFC


title: 203973690069_R08C01_20185962_PFC


title: C57BL/6 mice, kidney, adenine diet & AA, 1

description: Library name: AA_1


title: 203968030031_R07C01_P22/12_PFC

value: QSBB


title: 203968030031_R04C01_PD311_PFC


title: C57BL/6 mice, kidney, adenine diet, 4

description: Library name: M_4

value: adenine diet


title: 203968030031_R02C01_PD827_PFC


title: 203968030084_R08C01_P11/11_PFC


title: C57BL/6 mice, kidney, adenine diet, 2

description: Library name: M_2


title: 203968030084_R03C01_19960095_PFC


title: 203968030084_R01C01_20174955_PFC


title: 203968030060_R07C01_PD295_PFC


title: C57BL/6 mice, kidney, normal diet,4

description: Library name: C_4

value: normal diet


title: C57BL/6 mice, kidney, normal diet, 3

description: Library name: C_3


title: 203968030060_R02C01_20160560_PFC


title: C57BL/6 mice, kidney, normal diet, 2

description: Library name: C_2


title: 203968030090_R05C01_PDC126_PFC


title: C57BL/6 mice, kidney, normal diet, 1

description: Library name: C_1


title: 203968030090_R04C01_PD910_PFC


title: Brain immune cells from aged mice, CA, Day 3

city: Durham

first: Vaibhav

last: Jain

state: North Carolina

address: 300 N Duke St

department: Duke Molecular Physiology Institute

institute: Duke University

description:
Library name: A_CA
10X Genomics

data_processing:
The demultiplexing, barcoded processing and gene counting were made using the 10X Cellranger software version 7.1.0
Assembly: mm10-2020-A
Supplementary files format and content: Tab separated barcode, gene and matrix files

source_name: Brain

extract_protocol:
Mice were intubated, anesthetized with isoflurane, and transcardially perfused. Brains were immediately harvested and dissociated mechanically. Immune cells were enriched using Percoll. Cell suspensions were resuspended in FACS buffer and subjected to FACS sorting to collect CD45⁺ cells. The sorted cells were then processed for library preparation and sequencing.
10x Genomics CG000315 Chromium NextGEM Single Cell 3’ Gene Expression v3.1, Dual Index, Rev. E

treatment_protocol: Young and aged mice were subjected to a KCl-mediated mouse model of cardiac arrest and resuscitation. Sham-operated mice underwent the same surgical procedures without the experimental intervention.

value: Brain

value: CD45+ cells

value: Wild-type

value: Cardiac arrest


title: 203968030090_R01C01_PDC029_PFC


title: 203991390061_R08C01_PDC107_PFC


title: Brain immune cells from young mice, CA, Day 3

description:
Library name: Y_CA
10X Genomics


title: Brain immune cells from young mice, Sham, Day 3

description:
Library name: Y_Sham
10X Genomics

value: Sham surgery


title: 203991390061_R04C01_PD102_PFC

value: Imperial Brain Bank


title: 203991390061_R03C01_PD954_PFC


title: C57BL/6J 8-10 weeks female, Colon epithelium, 36dpi, Biological replicate 3

city: Boston

first: Yuko

last: Hasegawa

address: 181 Longwood Ave.

institute: Brigham and Women's Hospital

description:
Library name: ColonEpi-day36-3
ColonEpi_featureCounts.txt

data_processing:
Low-quality bases and the adaptors were trimmed using Trim Galore. The reads were mapped to the mouse reference genome (mm10) using STAR with default parameters, and the gene-level raw read count matrix was obtained using the featureCounts function in the subread using mouse GENCODE annotation M25 (GRCm38.p6)
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes raw counts for each sample

source_name: Colon

extract_protocol:
RNA was harvested by bead-beating the tissue in TRIzol
RNA libraries for RNA-seq were prepared using NEBNext Ultra II Directional RNA Library Prep Kit following manufacturer's protocols

treatment_protocol: Mice were orally gavaged with 5 × 10⁹ Citrobacter rodentium

value: Colon

value: WT

value: Cr infection


title: 203991390118_R07C01_20030103_PFC

data_processing:
Data was imported using the R package methylumi methylumIDAT function. Data was then pre-processed in the R package wateRmelon using the pfilter and dasen functions.
[ukbbn_betas_normalised.Rdata] wateRmelon processed beta values, dasen quantile normalised

value: Prefrontal cortex

value: Newcastle Brain Tissue Resource


title: C57BL/6J 8-10 weeks female, Colon epithelium, 36dpi, Biological replicate 2

description:
Library name: ColonEpi-day36-2
ColonEpi_featureCounts.txt


title: C57BL/6J 8-10 weeks female, Colon epithelium, 36dpi, Biological replicate 1

description:
Library name: ColonEpi-day36-1
ColonEpi_featureCounts.txt


title: 203991390118_R04C01_20110852_PFC

value: male


title: 203991390118_R03C01_PDC092_PFC


title: C57BL/6J 8-10 weeks female, Colon epithelium, 21dpi, Biological replicate 4

description:
Library name: ColonEpi-day21-4
ColonEpi_featureCounts.txt


title: SUB24, T cells, A/H7N9 vaccine unadjuvanted, Day4

description:
Library name: SUB24_D4_TCR
SUB24_D4_TCR

data_processing:
Human reference genome assembly (GRCh38), gene models, and associated gene annotation information were obtained from the ENSEMBL database (Version 99). The genomic reference was built by merging all human chromosomes except for X and Y chromosomes (to avoid gender-specific effects). Adapter sequences and low-quality 5′ ending sequences were removed from raw sequencing reads using the Trimmomatic software (Version 0.39). Following adapter removal, sequence reads were aligned to the reference transcriptome/genome using HISAT2 splice-aware sequence aligner (Version 2.2.0).  For each sample, the quality of reference alignments was evaluated using the RSeQC software (Version 3.0.1). Gene expression quantification was conducted on the gene level using Subread v2.0.0 counting mapped paired-reads to obtain fragment counts per gene.
Assembly: GRCh38 ENSEMBL database (Version 99)
Supplementary files format and content: tab-delimited text includes raw counts of each ENSEMBL Gene ID for each Sample

value: T cells

value: A/H7N9 vaccine unadjuvanted

tag: day


title: SUB25, Dendritic cells, A/H7N9 vaccine unadjuvanted, Day-7

description:
Library name: SUB25_D.7_DNR
SUB25_D.7_DNR

value: Dendritic cells


title: SUB25, B cells, A/H7N9 vaccine unadjuvanted, Day-7

description:
Library name: SUB25_D.7_BCR
SUB25_D.7_BCR

source_name: B cells

value: B cells


title: 203991400161_R08C01_NP15/013_PFC

source_name: Prefrontal cortex

value: Oxford Brain Bank

value: FALSE


title: 203991400161_R07C01_PD1012_PFC

value: female


title: C57BL/6J 8-10 weeks female, Colon epithelium, 21dpi, Biological replicate 2

description:
Library name: ColonEpi-day21-2
ColonEpi_featureCounts.txt

tag: time


title: C57BL/6J 8-10 weeks female, Colon epithelium, 21dpi, Biological replicate 1

description:
Library name: ColonEpi-day21-1
ColonEpi_featureCounts.txt


title: C57BL/6J 8-10 weeks female, Colon epithelium, 17dpi, Biological replicate 4

description:
Library name: ColonEpi-day17-4
ColonEpi_featureCounts.txt


title: C57BL/6J 8-10 weeks female, Colon epithelium, 17dpi, Biological replicate 3

description:
Library name: ColonEpi-day17-3
ColonEpi_featureCounts.txt


title: 203991400161_R05C01_20020045_PFC


title: CST-CREB, NGP, CREB (Input)

city: Washington

first: Yang

last: Yu

state: DC

address: 111 Michigan Ave NW

institute: Children's national hospital

description: Library name: CST-CREB, INPUT

data_processing:
CREB ChIP-seq data from three biological replicates were aligned to the human hg38 genome using Bowtie2, and peaks were called with MACS2 (q < 0.05) using matched input controls.
Gene transcription start sites (TSSs) were annotated based on UCSC refGene annotations hg38, and genes were considered CREB-associated if at least one CREB ChIP-seq peak overlapped a ±50 kb window surrounding the TSS.
Assembly: hg38
Supplementary files format and content: narrowPeak, tsv

source_name: NGP

growth_protocol: NGP cells were maintained in RPMI-1640 supplemented with 20% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
ChIP assays were performed by using a chromatin immunoprecipitation (ChIP) kit (Active Motif).
ChIP-seq libraries were prepared using the KAPA HTP Library Preparation Kit . 4 ng of DNA was used as starting material for input and ip samples. Libraries were amplified on the thermocycler. Post amplification libraries were size selected at 250-450bp in length using Agencourt AMPure XP beads from Beckman Coulter.

treatment_protocol: When cell confluency was 80 to 90%, NGP cells were harvested for ChIP assay.

tag: cell line

value: NGP

value: human neuroblastoma


title: Healthy control 1

city: Kolkata

first: Mitali

last: Chatterjee

state: West Bengal

address: 244B, AJC Bose Road

department: Pharmacology

country: India

institute: Institute of Post Graduate Medical Education & Research, Kolkata

description: Library name: H30

data_processing:
Illumina Novaseq 6000 platform was used for basecalling to generate paired-end reads of 100 bases
Sequenced reads were trimmed for adaptor sequences using CutAdapt, quality trimmed at the 5' and 3′ ends, then mapped to the human genome (hg19/GRCh37) using STAR v2.7.11b
The mapped reads were filtered based on mapping quality using samtools view with parameter -q 10
Raw read counts of genes were generated using HTSeq-count v2.1.2 with parameters -s reverse --nonunique all
Differential expression analysis was carried out using Deseq2
Assembly: hg19/GrCh37
Supplementary files format and content: Tab-delimited text files include raw read counts for all known genes for each sample.

source_name: Healthy control preputial skin from boys undergoing voluntary circumcision

extract_protocol:
Total RNA was isolated using the PureLink RNA Mini Kit following the manufacturer’s instructions. Briefly, tissues were snap-frozen in liquid nitrogen, crushed using a mortar and pestle, and transferred to microcentrifuge tubes containing 1 ml TRIzol reagent. Phase separation was performed using chloroform, and the aqueous phase was collected for further processing. Ethanol was added to facilitate RNA binding, and the sample was applied to an RNeasy Mini spin column, allowing total RNA to bind to the membrane. On-column DNase treatment was performed to remove genomic DNA, followed by washing steps to eliminate contaminants. Finally, high-quality RNA was eluted in 30 µl of nuclease-free water. RNA quality was assessed using the Agilent RNA ScreenTape on the Agilent 2200 TapeStation system, and quantification was performed using a NanoDrop spectrophotometer and Qubit fluorometer (Thermo Scientific).
RNA-seq libraries were prepared from 100 ng of total RNA using the KAPA RNA HyperPrep Kit with RiboErase (HMR) according to the manufacturer’s instructions (KR1351-v2.17). Ribosomal RNA was depleted by hybridization with complementary DNA oligonucleotides followed by RNase H and DNase treatment. The rRNA-depleted RNA was then fragmented using heat and magnesium, and first-strand cDNA synthesis was performed using random priming, followed by second-strand synthesis with A-tailing to generate double-stranded cDNA incorporating dUTP in the second strand. Adapter ligation with 3′ dTMP overhangs was carried out, followed by limited-cycle high-fidelity PCR amplification to produce strand-specific libraries. Library quality was evaluated using High Sensitivity D1000 ScreenTape on the Agilent 2200 TapeStation system, and final library quantification was performed using Real-Time PCR (QuantStudio 7 Flex). Paired-end sequencing (2 × 100 bp or 2 × 150 bp, depending on insert size) was performed on the Illumina NovaSeq 6000 platform.

value: Healthy control preputial skin samples were collected during voluntary circumcision.

tag: age of_onset


title: 203991400161_R03C01_RI95/1012_PFC

extract_protocol: ~30mg of brain tissue was milled over liquid nitrogen and extracted following the Qiagen AllPrep DNA/RNA/miRNA Universal kit following standard protocol. Samples were pre-checked using nanodrop fluorometer prior to further processing.

tag: Sex


title: C57BL/6J 8-10 weeks female, Colon epithelium, 17dpi, Biological replicate 2

description:
Library name: ColonEpi-day17-2
ColonEpi_featureCounts.txt


title: C57BL/6J 8-10 weeks female, Colon epithelium, 17dpi, Biological replicate 1

description:
Library name: ColonEpi-day17-1
ColonEpi_featureCounts.txt


title: 203991400161_R01C01_PD714_PFC

value: Imperial Brain Bank


title: PKDL 3

description: Library name: P708

source_name: Dermal biopsy from patient with PKDL

value: Lesional biopsy from patient with PKDL


title: C57BL/6J 8-10 weeks female, Colon epithelium, 10dpi, Biological replicate 4

description:
Library name: ColonEpi-day10-4
ColonEpi_featureCounts.txt

value: Colon

value: WT


title: 203991400162_R07C01_PD207_PFC

value: Prefrontal cortex