title: 200810877-14

description: study sample


title: 200810831-10

status: Public on Sep 30 2025

type: genomic

city: Miami

first: Lily

last: Wang

address: 1120 NW 14th St

country: USA

institute: University of Miami

description: study sample

hyb_protocol: Bisulfite-converted DNA was amplified, fragmented and hybridized to Illumina MethylationEPIC BeadChip using standard Illumina protocol.

scan_protocol: Standard recommended Illumina scanner setting.

data_processing:
idat files were read using minfi::read.metharray.exp, converted to beta values with minfi::getBeta
beta.csv contains beta values

label: Cy3 and Cy5

molecule: genomic DNA

organism: Homo sapiens

source_name: Blood

label_protocol: Standard Illumina Protocol.

extract_protocol: Bisulfite conversion of genomic DNA from peripheral blood was performed using the EZ DNA methylation kit according to manufacturer's instructions (Zymo Research).

tag: tissue

value: Blood

tag: batch


title: 200810786-09

description: study sample


title: mFibroblast, pbody, PANDORA-seq, rep4

type: SRA

city: Boulder

first: Mika

last: Nevo

state: Colorado

address: 2315 Walnut St

institute: CU Boulder

description: Library name: mFibroblast-pbody_PANDORAseq_4

library_source: transcriptomic

data_processing:
The raw reads were trimmed by performing SPORTS1.1.2 (parameters: sports.pl -M 1 -a -x GUUCAGAGUUCUACAGUCCGACGAUC -y AAGATCGGAAGAGCACACGTCT -l 15 -L 45 -s).
Assembly: mm39 (for mouse), hg38 (for human)
Supplementary files format and content: tab-delimited text files include sequences, length of sequences and sequence counts.

molecule: total RNA

organism: Mus musculus

source_name: Fibroblast

extract_protocol:
Total RNAs were extracted by Trizol (Invitrogen). Then small RNAs sized at 15-50nt were excised from 15% (w/v) urea polyacrylamide gel.
Small RNA libraries were constructed according to NEBNext® Multiplex Small RNA Library Prep Set for Illumina (New England Biolabs).

tag: cell type

value: Fibroblast

tag: fraction

value: Pbody

tag: treatment

value: The 15-50nt RNAs were treated with T4PNK, then AlkB before small RNA library construction.


title: 200810730-09

description: study sample


title: mFibroblast, cytoplasm, PANDORA-seq, rep1

description: Library name: mFibroblast-cyto_PANDORAseq_1

value: Cytoplasm


title: 200810770-12

description: study sample


title: mFibroblast, pbody, PANDORA-seq, rep3

description: Library name: mFibroblast-pbody_PANDORAseq_3


title: 200810931-09

description: study sample


title: 200810727-08

description: study sample


title: 200810711-10

description: study sample


title: 200810723-09

description: study sample


title: 200810923-08

description: study sample


title: mFibroblast, pbody, PANDORA-seq, rep2

description: Library name: mFibroblast-pbody_PANDORAseq_2


title: mFibroblast, pbody, PANDORA-seq, rep1

description: Library name: mFibroblast-pbody_PANDORAseq_1


title: mESC, Naïve, cytoplasm, traditional-seq, rep4

description: Library name: mESC-naive-cyto_traditional_4

source_name: Naive ES cells

value: Naive ES cells

value: The 15-50nt RNAs were sequenced with standard small RNA library construction protocols.


title: 200810686-12

description: study sample


title: 200810688-09

description: study sample


title: 200810674-11

description: study sample


title: mFibroblast, cytoplasm, PANDORA-seq, rep2

description: Library name: mFibroblast-cyto_PANDORAseq_2


title: mESC, Naïve, cytoplasm, traditional-seq, rep2

description: Library name: mESC-naive-cyto_traditional_2


title: mESC, Naïve, pbody, traditional-seq, rep4

description: Library name: mESC-naive-pbody_traditional_4


title: 200810633-12

description: study sample


title: 200810610-13

description: study sample


title: mESC, Naïve, cytoplasm, traditional-seq, rep3

description: Library name: mESC-naive-cyto_traditional_3


title: 200810559-09

description: study sample


title: 200810554-12

description: study sample


title: 200810587-10

description: study sample


title: mESC, primed, cytoplasm, traditional-seq, rep2

description: Library name: mESC-primed-cyto_traditional_2

source_name: Primed ES cells

value: Primed ES cells


title: 200810532-11

description: study sample


title: mESC, primed, cytoplasm, traditional-seq, rep4

description: Library name: mESC-primed-cyto_traditional_4


title: mESC, primed, cytoplasm, traditional-seq, rep1

description: Library name: mESC-primed-cyto_traditional_1


title: 200810531-08

description: study sample


title: 200810510-11

description: study sample


title: 200810465-10

description: study sample


title: mESC, primed, pbody, traditional-seq, rep3

description: Library name: mESC-primed-pbody_traditional_3


title: 200810684-09

description: study sample


title: 200810447-10

description: study sample


title: mESC, primed, pbody, traditional-seq, rep1

description: Library name: mESC-primed-pbody_traditional_1


title: mESC, Naïve, cytoplasm, traditional-seq, rep1

description: Library name: mESC-naive-cyto_traditional_1


title: 200810445-10

description: study sample


title: mESC, Naïve, pbody, traditional-seq, rep3

description: Library name: mESC-naive-pbody_traditional_3


title: 200810422-13

description: study sample


title: 200810590-10

description: study sample


title: mESC, Naïve, pbody, traditional-seq, rep2

description: Library name: mESC-naive-pbody_traditional_2


title: mFibroblast, cytoplasm, traditional-seq, rep3

description: Library name: mFibroblast-cyto_traditional_3


title: mFibroblast, cytoplasm, traditional-seq, rep4

description: Library name: mFibroblast-cyto_traditional_4


title: mESC, Naïve, pbody, traditional-seq, rep1

description: Library name: mESC-naive-pbody_traditional_1


title: 200810402-10

description: study sample


title: mESC, primed, cytoplasm, traditional-seq, rep3

description: Library name: mESC-primed-cyto_traditional_3


title: 200810372-10

description: study sample


title: mFibroblast, cytoplasm, traditional-seq, rep1

description: Library name: mFibroblast-cyto_traditional_1


title: mFibroblast, pbody, traditional-seq, rep3

description: Library name: mFibroblast-pbody_traditional_3


title: 200810338-12

description: study sample


title: 200810326-13

description: study sample


title: mFibroblast, pbody, traditional-seq, rep2

description: Library name: mFibroblast-pbody_traditional_2


title: mESC, primed, pbody, traditional-seq, rep4

description: Library name: mESC-primed-pbody_traditional_4


title: 200810289-12

description: study sample


title: mESC, primed, pbody, traditional-seq, rep2

description: Library name: mESC-primed-pbody_traditional_2


title: 200810267-14

description: study sample


title: 200810239-12

description: study sample


title: mFibroblast, cytoplasm, traditional-seq, rep2

description: Library name: mFibroblast-cyto_traditional_2


title: 200810401-10

description: study sample


title: BWS_patient63

city: Caserta

first: Francesco

last: Cecere

state: Caserta

address: Via A. Vivaldi, n. 43

department: DiStABiF

country: Italy

institute: University of Campania "Luigi Vanvitelli"

hyb_protocol: We performed methylation array analysis on bisulfite-converted PBL DNA of 51 patients and 16 healthy individuals using the Illumina Infinium MethylationEPIC BeadChip 850k v.1 array

scan_protocol: Arrays were imaged using BeadArray Reader (HiScan) and standard recommended Illumina scanner setting

data_processing:
We analyzed and imported the “idat” files using the “champ.load” module of the “ChAMP” R package (v.2.23.1). To normalize and remove batch effects, we applied the “champ.norm” function with the “BMIQ” parameter and the “champ.runCombat” function to correct for slide technical effect.
normalized_matrix.txt.gz: Beta value matrix normalized and corrected for technical effects.

label_protocol: Standard Illumina protocol

extract_protocol: Genomic DNA of patients and their parents were isolated from peripheral blood leukocyte (PBL) by standard salting-out procedure (Miller 1988). DNA concentration was determined using the NanoDrop™ 2000c Spectrophotometer (Thermo Fisher Scientific).

tag: disease state

value: Beckwith-Wiedemann syndrome


title: m2C_shDdx6-83_Pos-2

description:
Library name: 22017FL-26-01-64
202507_m2C.RawCount.mm39.M30.csv

data_processing:
RNA-seq was analyzed by mapping reads using hisat2.1.0150 to the mouse mm39 genome assembly, human hg38 assembly. Gene counts were annotated using featureCounts v1.6.2.
Assembly: hg38, mm39
Supplementary files format and content: raw counts

source_name: Mervl-tdTomato/Zscan4-GFP mESC

extract_protocol:
miRNeasy Micro Kit (QIAGEN)
SNAP-total seq

tag: cell line

value: Mervl-tdTomato/Zscan4-GFP mESC

tag: genotype

value: Pos


title: 18mo mouse, retina, snRNAseq, rep1

city: Irvine

first: Dorota

last: Skowronska-Krawczyk

address: Gavin Herbert Eye Institute

institute: University of California, Irvine

description: Library name: 18mo_mouse_retina_snRNAseq_replicate_1

library_source: transcriptomic single cell

data_processing:
91 bp sequencing reads are generated by Illumina sequencing. Reads are mapped to the genome and counts at features are identified using the Cell Ranger for Single Cell Gene Expression software with default parameters (mkfastq and count functions).
On a per-sample basis, a Seurat data object is created from the Cell Ranger outputs. High quality cellular barcodes are selected using a mixture of both adaptive and selective thresholds. To pass quality control in a standard analysis, a cellular barcode must match all three of the following gene expression criteria: 1. The number of unique molecular identifiers (UMIs) must be within three median absolute deviations (MADs) of the population median 2. The number of expressed genes must be within three MADs of the population median. 3. The percentage of reads mapping to mitochondrial genes must be under 15%.
Marker genes are identified with the Seurat software package on a per cluster basis (FindAllMarkers function). Marker genes are identified using a Wilcoxon rank-sum test between cells in a given cluster versus all other cells, and this test is only performed for genes that are expressed in at least 10% of the cells in the cluster or at least 10% of the cells that are not in the cluster. For a standard analysis, a gene is only considered a marker if it is expressed in more than 10% of the cells in a cluster, has an average log fold change greater than 0.3 when compared to all other cells, and has an adjusted p-value of less than 0.1.
Assembly: mm10
Supplementary files format and content: tab-separated values and matrix files

molecule: nuclear RNA

source_name: retina

extract_protocol:
nuclei were isolated following the Illumina Single Cell Nuclei Isolation
according to the10x single-cell kit Chromium Next GEM Single Cell 3’ Reagent Kits V3.1 ( Dual Index). Specific part number: Chromium Next GEM Single Cell 3ʹ Kit v3.1, 16 rxns PN-1000268

value: retina

value: WT


title: 3mo mouse, retina, snRNAseq, rep3

description: Library name: 3mo_mouse_retina_snRNAseq_replicate_3


title: 3mo mouse, retina, snRNAseq, rep2

description: Library name: 3mo_mouse_retina_snRNAseq_replicate_2


title: 18mo mouse, retina, snRNAseq, rep3

description: Library name: 18mo_mouse_retina_snRNAseq_replicate_3


title: BWS_patient64


title: m2C_shDdx6-83_Pos-1

description:
Library name: 22017FL-26-01-63
202507_m2C.RawCount.mm39.M30.csv


title: 18mo mouse, retina, snRNAseq, rep2

description: Library name: 18mo_mouse_retina_snRNAseq_replicate_2


title: BWS_patient61


title: 3mo mouse, retina, snRNAseq, rep1

description: Library name: 3mo_mouse_retina_snRNAseq_replicate_1


title: BWS_patient60


title: m2C_shDdx6-83_Neg-2

description:
Library name: 22017FL-26-01-62
202507_m2C.RawCount.mm39.M30.csv

value: Neg


title: BWS_patient62


title: m2C_shDdx6-83_Neg-1

description:
Library name: 22017FL-26-01-61
202507_m2C.RawCount.mm39.M30.csv


title: m2C_shDdx6-82_Pos-2

description:
Library name: 22017FL-26-01-60
202507_m2C.RawCount.mm39.M30.csv


title: BWS_patient57


title: 200810287-11

description: study sample


title: BWS_patient56


title: mFibroblast, pbody, traditional-seq, rep1

description: Library name: mFibroblast-pbody_traditional_1


title: m2C_shDdx6-82_Pos-1

description:
Library name: 22017FL-26-01-59
202507_m2C.RawCount.mm39.M30.csv


title: 200810262-09

description: study sample


title: m2C_shDdx6-82_Neg-2

description:
Library name: 22017FL-26-01-58
202507_m2C.RawCount.mm39.M30.csv


title: BWS_patient55


title: m2C_shDdx6-82_Neg-1

description:
Library name: 22017FL-26-01-57
202507_m2C.RawCount.mm39.M30.csv


title: BWS_patient53


title: BWS_patient54


title: m2C_shCTRL_Pos-2

description:
Library name: 22017FL-26-01-56
202507_m2C.RawCount.mm39.M30.csv

value: shCTRL


title: BWS_patient50


title: BWS_patient51


title: BWS_patient52


title: BWS_patient59


title: m2C_shCTRL_Neg-1

description:
Library name: 22017FL-26-01-53
202507_m2C.RawCount.mm39.M30.csv


title: BWS_patient49


title: CLP 6 weeks 5

city: Cologne

first: Simon

last: Geissen

address: Kerpener Strasse 62

country: Germany

institute: University Hospital Cologne

description: Library name: SID164173

data_processing:
Data preprocessing involved using the CellRanger pipeline for demultiplexing, alignment to the murine transcriptome (mm10), and unique molecular identifier (UMI) counting, followed by quality control and normalization steps in the Scanpy (ver. 1.9.6) environment.
Assembly: murine transcriptome (mm10)
Supplementary files format and content: Filtered feature matrices for each sample as created by the CellRanger pipeline.

source_name: heart

extract_protocol:
Single, viable (DAPIlow) and CD45-expressing cardiac leukocytes were sorted for scRNAseq experiments using a BD LSRFortessa.
The cells were processed using the 10x Genomics Chromium Single Cell 3' Library & Gel Bead Kit v3, generating Illumina-compatible libraries that were sequenced on an Illumina NovaSeq 6000 platform.

value: heart

value: CD45+ leukocytes

value: wildtype


title: BWS_patient47

value: Blood


title: BWS_patient48


title: control 6

description: Library name: SID164176


title: BWS_patient58


title: CLP 6 weeks 6

description: Library name: SID164174


title: CLP 6 weeks 4

description: Library name: SID168581


title: BWS_patient44


title: BWS_patient45


title: BWS_patient43


title: CLP 6 weeks 2

description: Library name: SID168579


title: CLP 6 weeks 3

description: Library name: SID168580


title: BWS_patient42


title: CLP 6 weeks 1

description: Library name: SID168578


title: control 4

description: Library name: SID168577


title: BWS_patient41


title: m2C_shCTRL_Neg-2

description:
Library name: 22017FL-26-01-54
202507_m2C.RawCount.mm39.M30.csv


title: m2C_shCTRL_Pos-1

description:
Library name: 22017FL-26-01-55
202507_m2C.RawCount.mm39.M30.csv


title: control 3

description: Library name: SID168576


title: BWS_patient39


title: control 2

description: Library name: SID168575


title: BWS_patient40


title: WT, IRI, male, rep5

city: Los Angeles

first: Shun-Yang

last: Cheng

state: CA

address: 1425 San Pablo St

department: USC Stem cell - Eli and Edythe Broad Center for Regenerative Medicine

institute: University of Southern California

description: Library name: 508

data_processing:
Raw sequence reads underwent pre-processing with fastp (version 0.23.2) to remove low-quality bases (quality score ≤ 20) and discard reads shorter than 20 bp. High-quality reads were then aligned to the mouse genome (mm39, GRCm39) using STAR (version 2.7.0)
Assembly: mm39
Supplementary files format and content: Reads mapped to annotated genomic regions from GENCODE release M28 were quantified with featureCounts (version 2.0.3).

source_name: Kidney

extract_protocol:
Rneasy mini kit (Qiagen)
RNA samples were provided to the Novogene for library construction and sequencing. NovaSeq X Plus Series (PE150), mRNA library preparation (poly A enrichment).

value: Kidney

value: Wildtype

value: NX+IRI


title: BWS_patient37


title: control 1

description: Library name: SID168574


title: WT, IRI, male, rep4

description: Library name: 507


title: BWS_patient38


title: control 5

description: Library name: SID164175


title: BWS_patient35


title: BWS_patient46


title: TG, IRI, male, rep3

description: Library name: 486


title: BWS_patient33


title: TG, IRI, male, rep5

description: Library name: 506


title: BWS_patient36


title: BWS_patient34


title: TG, IRI, male, rep4

description: Library name: 487


title: BWS_patient32


title: BWS_patient31


title: TG, NX, male, rep2

description: Library name: 478

value: Nephrectomy (NX)


title: BWS_patient30


title: TG, IRI, male, rep2

description: Library name: 485


title: WT, IRI,male, rep2

description: Library name: 473


title: WT, IRI, male, rep3

description: Library name: 483


title: BWS_patient28


title: TG, IRI,male, rep1

description: Library name: 472


title: BWS_patient27


title: BWS_patient26


title: WT, IRI, male, rep1

description: Library name: 469


title: BWS_patient25


title: TG, IRI, male

description: Library name: 466


title: WT, IRI, male

description: Library name: 465


title: BWS_patient24


title: WT,NX, male, rep2

description: Library name: 442


title: BWS_patient23


title: BWS_patient22


title: WT, NX, male, rep1

description: Library name: 440


title: BWS_patient19


title: BWS_patient20


title: BWS_patient15


title: WT, NX, male

description: Library name: 437


title: TG, NX, male

description: Library name: 438


title: TG, Female, no-surgery, rep1

description: Library name: 528

value: NO, female


title: TG, NX, male, rep1

description: Library name: 441


title: BWS_patient11


title: BWS_patient10


title: BWS_patient8


title: WT, Female, no-surgery, rep2

description: Library name: 526


title: WT, Female, no-surgery, rep1

description: Library name: 525


title: TG, Female, no-surgery

description: Library name: 527


title: BWS_patient16


title: TG, Female, no-surgery, rep2

description: Library name: 529


title: BWS_patient7


title: WT, Female, no-surgery

description: Library name: 524


title: TG, male, no-surgery, rep1

description: Library name: 522

value: NO, male


title: TG, male, no-surgery, rep2

description: Library name: 523


title: Control40

value: Control


title: Control39


title: Control38


title: TG, male, no-surgery

description: Library name: 521


title: Control37


title: WT, male, no-surgery, rep2

description: Library name: 520


title: Control36


title: WT, male, no-surgery, rep1

description: Library name: 519


title: BWS_patient13

value: Beckwith-Wiedemann syndrome


title: Control35


title: Control34


title: SrfKO2

city: Research Triangle Park

middle: John

last: DeMayo

state: North Carolina

address: 111 T W Alexander Dr

department: DIR

institute: NIEHS

description: Library name: SrfKO2

data_processing:
Raw sequencing data was processed by CellRanger 'count' function (v6.0.0) with the --include-introns setting.
Assembly: mm10
Supplementary files format and content: Cell Ranger output files: barcodes.tsv.gz, features.tsv.gz, matrix.mtx.gz
Supplementary files format and content: table of single-cell annotation info in tab-delimited text format

molecule: polyA RNA

source_name: uterus

extract_protocol:
After dissection and washing in cold PBS, tissues were digested into single cell suspensions by mechanically mincing the tissues then incubating in 0.25% Trypsin-EDTA (Gibco #25200056) for 60 min on ice, 10 min at room temperature, then 50 min at 37oC. Tubes were agitated by hand every 5 minutes, and tissues were broken up by pipetting. Trypsin activity was stopped by adding DMEM/F12 (Gibco #11320033) supplemented with 10% fetal bovine serum (FBS, Gibco #10082147), and cells were pelleted by centrifugation at 450 xg for 10 minutes. Pellets were resuspended in fresh DMEM/F12 with 10% FBS and sequentially filtered through 100 µm, 70 µm, then 30 µm cell strainers. Red blood cells were removed by resuspending with red blood cell lysing buffer (Sigma #R7757) before resuspending in PBS with 0.04% BSA for counting and viability assessment. The cells were counted and examined for viability with AO/PI staining using a Luna FX7 cell counter (Logos Biosystems). Each sample used for sequencing yielded a minimum of 1.6 million cells and was at least 91% viable.
Approximately 16,000 live cells at 1×106 cells/ml concentration were loaded into the Single Cell Chip to generate single cell emulsion in Chromium Controller with Chromium Single Cell 3’ Library & Gel Bead Kit v3.1 (10x Genomics #1000268). Reverse transcription of mRNA and cDNA amplification were carried out following the manufacturer’s instructions. The amplified cDNA was further fragmented to construct NGS libraries.

value: uterus

value: PgrCre/+Srfflox/flox


title: Control33


title: WT, male, no-surgery

description: Library name: 518


title: Control32


title: Ctrl2

description: Library name: Ctrl2

value: Srfflox/flox


title: Control31


title: Control30


title: Liver_AC4

city: Barcelona

first: Francesc

last: Villarroya

state: Barcelona

address: Diagonal 643

department: Biochemistry and Molecular Biomedicine

country: Spain

institute: University of Barcelona

description:
Library name: AW6236
Column name in raw_countsCold.xlsx: Liver_AC4

data_processing:
Adaptor ligation, purification of 100 base-pair cDNA fragments, amplification of these fragments, and library preparation were performed according to the manufacturer’s instructions (Illumina) and sequenced using Illumina NovaSeq 6000 platform at Centro Nacional de Análisis Genómico (Barcelona, Spain).
The sequenced 100-base pair paired-end reads were quality-checked using FastQC, and Quality control alignment. The obtained reads were subsequently aligned to the mouse reference genome (GRCm39) using STAR (2.7.8a) and the number of exon reads for all RefSeq genes were counted using RSEM (1.3.0).
Data analysis of the resulting count matrix was performed in R studio (4.3.1) to determine differentially expressed genes by DESeq application (V1.42.0).
Assembly: GRCm38
Supplementary files format and content: excel file
Supplementary files format and content: raw counts from samples

source_name: Liver

growth_protocol: Mice were housed at 22 °C under a 12-h light cycle  (lights on, from 08.00 am to 08.00 pm) with 50% ±5% relative humidity with free access to water and a standard diet.

extract_protocol:
Total RNA was extracted using a NucleoSpin RNA kit, 2ug of total RNA was used for the construction of seq libraries
Integrity of RNA samples was determined using Qubit RNA IQ Assay (Invitrogen). A purification of 2ug from the obtained mRNA was performed using TruSeq RNA sample prep kit v2 (Illumina). Adaptor ligation, purification of 100 base-pair cDNA fragments, amplification of these fragments, and library preparation were performed according to the manufacturer’s instructions (Illumina) and sequenced

treatment_protocol: Mice were maintained under standard rodent diet (2018, Teklad Diet, Envigo) and put to thermoneutrality (30C) or cold (4C) conditions for 24 hours.

value: Liver

value: Wild-type

value: Cold


title: Liver_AC5

description:
Library name: AW6237
Column name in raw_countsCold.xlsx: Liver_AC5


title: Control29


title: Control28


title: Liver_AC2

description:
Library name: AW6211
Column name in raw_countsCold.xlsx: Liver_AC2


title: Control27


title: Ctrl1

description: Library name: Ctrl1


title: Control26


title: Liver_TN5

description:
Library name: AW6209
Column name in raw_countsCold.xlsx: Liver_TN5

value: Thermoneutrality


title: Control25


title: Liver_AC1

description:
Library name: AW6210
Column name in raw_countsCold.xlsx: Liver_AC1


title: FOXO1-Ab ESR1 E2 R1

description: Library name: Sample2

library_source: genomic

data_processing:
Reads from CUT&RUN were trimmed of adapter sequences using Trim Galore!  Version 0.6.10 with default settings except for specifying Illumina adapter sequences and paired-end validation.
Trimmed sequences were aligned to hg38 genome using bowtie2 (Version 2.5.2).
Alignment files were processed using Picard (http://broadinstitute.github.io/picard; Version 3.2.0) for duplicate removal and samtools (Version 1.18) to filter for reads with MAPQ  5
Assembly: hg38 genome (GCF_000001405.40)
Supplementary files format and content: bigwig files
Library strategy: CUT&Run

source_name: THESC

growth_protocol: CRISPR engineered cells were maintained in DMEM/F-12 supplemented with 10% Fetal Bovine Serum and 4ug/mL Blasticidin. Cells were cultured and grown in a 5% CO2 and 37°C incubator. Cell media was changed every three days and cells were passaged before reaching 90% confluency.

extract_protocol:
Targeted DNA amplicons were isolated using the Epicypher CUTANA Cut&Run Kit Version 3 with antibodies targeting PGR and control antibody IgG.
A total of 550,000 cells per sample were collected in DNA LoBind 1.5mL tubes containing wash buffer. Cells were captured with BioMag Plus Concavalin A beads and incubated with FOXO1 antibody (Cell Signaling Technologies, Cat. No. 2880, clone C29H4; 1:50) or IgG antibody (1:100) supplied by the CUTANA kit overnight at 4°C in antibody incubation buffer. After washing away antibodies, pAG-MNase generated by the NIEHS proteomics core was added and incubated for 30 minutes at room temperature. After washing, CaCl2 was added and incubated for 30 minutes in an aluminum cold block placed in ice. The protein-DNA complexes were released by incubating at 37°C for 10 minutes. DNA was purified using the Qiagen MiniElute PCR Purification Kit. Sequencing libraries were prepared using the NEBNext Ultra II DNA library preparation kit for Illumina  according to the manufacturer’s instructions, with 14 cycles of PCR amplification. The PCR products were quantified using the Qubit dsDNA HS Assay Kit and quality control was performed with Bioanalyzer DNA Analysis. The libraries were sequenced by the NIEHS sequencing core.

treatment_protocol: Cells were treated with 10nM E2 or 0.01% EtOH (vehicle) in OptiMEM with 2% Charcoal Stripped Serumand 1% Penicillin-Streptomycin for 24 hours.

value: THESC

value: Endometrial Stromal Cells

value: ESR1 activated

value: 10nM Estradiol


title: Liver_TN4

description:
Library name: AW6208
Column name in raw_countsCold.xlsx: Liver_TN4


title: Liver_TN2

description:
Library name: AW6206
Column name in raw_countsCold.xlsx: Liver_TN2


title: D_70_8_MInT_M_27

city: Ulm

first: Emil

last: Chteinberg

address: Albert-Einstein-Allee 11

institute: Ulm University Medical Center

description:
HTG EdgeSeq Pan B-Cell Lymphoma Panel
RNA (amplified oligo nucleotide probes)

data_processing:
FASTQ Files using Illumina BaseSpace BCL to FASTQ software version 2.2.0 and Illumina Local Run Manager Software version 2.0.0.
FASTQ Files were analyzed with HTG EdgeSeq Parser software version 5.5 to generate raw counts for a total of 298 genes.
Assembly: Assembly: GRCh38.p13
Supplementary files format and content: raw counts
Supplementary files format and content: log2(Count per million+1)

source_name: Diffuse large B-ell lymphoma

extract_protocol:
Three hundred sixty DLBCLs tissues were processed. Using 5 ¬µm unstained FFPE sections. The optimal amounts of tissue for each HTG EdgeSeq panB Lymphoma assay. The sample preparation as performed according to the manufacturer’s instructions.
Probe_captured FFPE samples for EdgeSeq panB Lymphoma assay were amplified¨ and indexed via polymerase chain reaction (PCR) using the master mix (OneTaq HotStart 2X MasterMix in GC Buffer (New England Biolabs Inc., Ipswich, MA, USA), and indexing primers according to manufacturer’s instructions. The following library cleanup was performed using AMPure XP beads according to manufacturer’s instructions
Targeted mRNA Sequencing using HTG EdgeSeq Pan B_Cell Lymphoma Panel assay

value: Diffuse large B-ell lymphoma

tag: tissue-fixation

value: FFPE

tag: Sex

value: M

tag: age


title: Liver_TN3

description:
Library name: AW6207
Column name in raw_countsCold.xlsx: Liver_TN3


title: SrfKO1

description: Library name: SrfKO1


title: D_70_3_MInT_F_22

value: F


title: D_70_25_MInT_F_23


title: eWAT_AC5

description:
Library name: AW6235
Column name in raw_countsCold.xlsx: eWAT_AC5

source_name: Epididymal white adipose tissue

value: Epididymal white adipose tissue


title: Liver_TN1

description:
Library name: AW6205
Column name in raw_countsCold.xlsx: Liver_TN1


title: D_70_22_MInT_F_33


title: D_70_12_MInT_F_50


title: eWAT_AC3

description:
Library name: AW6202
Column name in raw_countsCold.xlsx: eWAT_AC3


title: eWAT_AC2

description:
Library name: AW6201
Column name in raw_countsCold.xlsx: eWAT_AC2


title: Liver_AC3

description:
Library name: AW6212
Column name in raw_countsCold.xlsx: Liver_AC3


title: eWAT_AC4

description:
Library name: AW6204
Column name in raw_countsCold.xlsx: eWAT_AC4


title: D_70_18_MInT_F_53


title: D_70_1_MInT_F_26


title: eWAT_AC1

description:
Library name: AW6200
Column name in raw_countsCold.xlsx: eWAT_AC1


title: D_58_16_MInT_F_39


title: eWAT_TN5

description:
Library name: AW6199
Column name in raw_countsCold.xlsx: eWAT_TN5


title: D_61_3_MInT_F_54


title: D_58_14_MInT_F_58


title: eWAT_TN3

description:
Library name: AW6197
Column name in raw_countsCold.xlsx: eWAT_TN3


title: eWAT_TN4

description:
Library name: AW6198
Column name in raw_countsCold.xlsx: eWAT_TN4


title: D_43_9_MInT_F_42


title: eWAT_TN2

description:
Library name: AW6196
Column name in raw_countsCold.xlsx: eWAT_TN2


title: D_42_2_MInT_F_32


title: eWAT_TN1

description:
Library name: AW6195
Column name in raw_countsCold.xlsx: eWAT_TN1


title: D_355_11_MInT_M_42


title: iWAT_AC4

description:
Library name: AW6193
Column name in raw_countsCold.xlsx: iWAT_AC4

source_name: Inguinal white adipose tissue

value: Inguinal white adipose tissue


title: iWAT_AC5

description:
Library name: AW6194
Column name in raw_countsCold.xlsx: iWAT_AC5


title: iWAT_AC2

description:
Library name: AW6191
Column name in raw_countsCold.xlsx: iWAT_AC2


title: D_268_5_MInT_M_46

description:
HTG EdgeSeq Pan B-Cell Lymphoma Panel
RNA (amplified oligo nucleotide probes)


title: iWAT_AC3

description:
Library name: AW6192
Column name in raw_countsCold.xlsx: iWAT_AC3


title: D_268_11_MInT_F_50


title: D_268_1_MInT_F_34


title: D_337_5_MInT_F_60


title: D_268_10_MInT_M_48


title: iWAT_AC1

description:
Library name: AW6190
Column name in raw_countsCold.xlsx: iWAT_AC1


title: mFibroblast, pbody, traditional-seq, rep4

description: Library name: mFibroblast-pbody_traditional_4

value: Fibroblast

value: Pbody

value: The 15-50nt RNAs were sequenced with standard small RNA library construction protocols.


title: iWAT_TN5

description:
Library name: AW6189
Column name in raw_countsCold.xlsx: iWAT_TN5


title: D_24_5_MInT_F_48


title: iWAT_TN4

description:
Library name: AW6188
Column name in raw_countsCold.xlsx: iWAT_TN4


title: D_24_1_MInT_M_39


title: D_144_2_MInT_M_45


title: iWAT_TN2

description:
Library name: AW6186
Column name in raw_countsCold.xlsx: iWAT_TN2


title: iWAT_TN3

description:
Library name: AW6187
Column name in raw_countsCold.xlsx: iWAT_TN3


title: D_24_2_MInT_M_33


title: D_113_3_MInT_F_50


title: BAT_AC5

description:
Library name: AW6184
Column name in raw_countsCold.xlsx: BAT_AC5

source_name: Brown adipose tissue

value: Brown adipose tissue


title: iWAT_TN1

description:
Library name: AW6185
Column name in raw_countsCold.xlsx: iWAT_TN1

value: Wild-type


title: D_113_8_MInT_M_47


title: D_107_1_MInT_M_55


title: BAT_AC4

description:
Library name: AW6183
Column name in raw_countsCold.xlsx: BAT_AC4

value: Cold


title: BAT_AC3

description:
Library name: AW6182
Column name in raw_countsCold.xlsx: BAT_AC3


title: D_113_16_MInT_F_20


title: 996_RICOVER_60_F_62


title: 99_RICOVER_60_F_78


title: BAT_AC2

description:
Library name: AW6181
Column name in raw_countsCold.xlsx: BAT_AC2


title: BAT_TN5

description:
Library name: AW6179
Column name in raw_countsCold.xlsx: BAT_TN5

value: Thermoneutrality


title: BAT_AC1

description:
Library name: AW6180
Column name in raw_countsCold.xlsx: BAT_AC1


title: 978_RICOVER_60_M_74


title: BAT_TN4

description:
Library name: AW6178
Column name in raw_countsCold.xlsx: BAT_TN4


title: 977_RICOVER_60_M_77


title: BAT_TN3

description:
Library name: AW6177
Column name in raw_countsCold.xlsx: BAT_TN3


title: 973_RICOVER_60_M_71

description:
HTG EdgeSeq Pan B-Cell Lymphoma Panel
RNA (amplified oligo nucleotide probes)


title: BAT_TN1

description:
Library name: AW6175
Column name in raw_countsCold.xlsx: BAT_TN1


title: neonatal mouse organ of Corti, Bmi1 KO, ATAC-seq

city: SHANGHAI

first: yunzhong

last: zhang

state: SHANGHAI

address: 83 fenyang road, xuhui district

department: Department of ENT Institute and Otorhinolaryngology

country: China

institute: Eye & ENT Hospital of Fudan University

data_processing:
Low-quality bases and adapter sequences were removed, and the data were quality-controlled using FastQC software. The quality-controlled reads were mapped to the reference genome using BWA-MEM software. Peak calling was performed with MACS2. The peaks were annotated by associating them with their nearest gene elements using HOMER software. Functional enrichment analysis of the peak-associated genes was then conducted using databases such as Gene Ontology (GO) and KEGG.
Assembly: mm10
Supplementary files format and content: narrowPeak

source_name: neonatal mouse organ of Corti

extract_protocol:
OCs from WT and Bmi1-/- neonatal mice were dissected separately. Nuclei isolation was performed using lysis buffer containing 10 mM Tris-HCl (pH 7.4), 10 mM NaCl, 3 mM MgCl2, and 0.1% IGEPAL CA-630.
The ATAC-seq library preparation was conducted using the Hyperactive ATAC-Seq Library Prep Kit for Illumina (Vazyme, TD711) following the manufacturer's protocol.

value: neonatal mouse organ of Corti

value: Bmi1 KO


title: neonatal mouse organ of Corti, WT, bio rep 3

data_processing:
Preliminary processing of raw reads was performed using TrimGalore (v0.6.10) for removing adapters and low-quality bases. Trimmed reads for each sample were aligned to the Mus musculus Ensembl mm10 genome (release-110) using HISAT2 (v2.2.1), and aligned reads were summarized with featureCounts (v2.0.6). Differential expression analysis between conditions was performed using the DESeq2 R package (1.34.0), and genes with an adjusted p-value (padj) < 0.05 and log2 fold change > 0.25 were regarded as differentially expressed.
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample

extract_protocol:
Six mouse organ of Corti (OCs) from WT and Bmi1-/- neonatal mice were separately used.  Each OC was carefully extracted from the cochlea with the anlage of the stria vascularis, the modiolus, and the tectorial membrane removed.
Total RNA was extracted with the AllPrep DNA/RNA/Protein Mini kit (QIAGEN). For each genotype we performed three biological replicates. The double-strand cDNA was synthesized from the total RNA LT Sample Prep Kit v2 (Illumina). Illumina adapters were ligated to the cDNA molecules after end repair, and the ligated cDNA was cleaned up with AmpureBeads (Beckman). The library was amplified using 10 cycles of PCR for the enrichment of adapter-ligated fragments, and transcriptome sequencing was carried out with an Illumina-Hiseq2500 system (Illumina).

value: WT


title: neonatal mouse organ of Corti, WT, bio rep 2


title: 93_MegaCHOEP_III_M_60


title: 928_RICOVER_60_M_64


title: neonatal mouse organ of Corti, WT, bio rep 1


title: 910_RICOVER_60_M_75


title: 91_DENSER_F_64


title: 96_DENSER_F_63


title: 911_RICOVER_60_F_67


title: neonatal mouse organ of Corti, WT, ATAC-seq


title: 904_RICOVER_60_M_71


title: 948_RICOVER_60_F_61


title: neonatal mouse organ of Corti, Bmi1 KO, bio rep2


title: neonatal mouse organ of Corti, Bmi1 KO, bio rep3


title: neonatal mouse organ of Corti, Bmi1 KO, bio rep4


title: 90_DENSER_M_72


title: 90_MegaCHOEP_III_M_51


title: neonatal mouse organ of Corti, Bmi1 KO, H3K27me3

data_processing:
Raw ChIP-seq reads were trimmed using the trimmomatic tool [69] and then aligned to the Mus musculus UCSC mm10 genome using Hisat250. Duplicated reads were removed, and only uniquely mapping reads were retained for further analysis. The MACS2 (version 2.1.1) callpeak algorithm was used to identify regions of ChIP-seq enrichment over background. Only differential binding peaks with fold change ≥1.5 and FDR < 0.05 were used for further study. A correlation heatmap based on the affinity scores for ChIP-seq samples was also plotted using the Pheatmap R package with the default settings.
Deeptools was used to normalize all genes of the two sets of data according to the gene length and to calculate the average signal values of all genes at each site within the range of 3 kb from the upstream of transcription start site to 3 kb from the downstream of transcriptional end site (TES). DEGseq and edgeR were used to analyze the differences in peaks between the two groups of data, and Deeptools was used to calculate the signal values of all peaks at each site in the normalized difference peak region, and a heat map was drawn.
Assembly: mm10
Supplementary files format and content: bigWig

extract_protocol:
Twenty OCs from WT and Bmi1-/- neonatal mice were separately harvested and sonicated to shear crosslinked chromatin.
The chromatin extract was then incubated with anti-H3K27me3 (Abcam) overnight at 4°C followed by the addition of Protein A/G Dynabeads (1:1, Invitrogen). Immunoprecipitated complex was eluted from the beads and de-crosslinked, and chromatin was purified using the MinElute PCR Purification Kit (Qiagen). Purified DNA was used to prepare ChIP-seq DNA libraries for Illumina sequencing.


title: neonatal mouse organ of Corti, Bmi1 KO, bio rep1


title: 873_RICOVER_60_M_62


title: neonatal mouse organ of Corti, WT, H3K27me3


title: BAT_TN2

description:
Library name: AW6176
Column name in raw_countsCold.xlsx: BAT_TN2


title: 88_MegaCHOEP_III_F_55


title: 84_DENSER_M_75


title: PABPN1L-1C-rep2

city: Hangzhou

first: Heng-yu

last: Fan

state: Zhejiang

address: Yuhangtang Road

institute: Life Sciences  Institute

data_processing:
*library strategy: S4U-seq
The T-C mutation ratio was detected using SLAMDUNK software
Assembly: mm10
Supplementary files format and content: Tables containing T-C mutation ratios of each sample

source_name: Zygote

extract_protocol:
Each sample contains 50 zygotes collected from mated female mice at 26 h after hCG injection were cultured in KSOM containing 200 μM 4-Thiouridine (S4U) (Sigma; T4509) for 2 h for labeling.
After washing with DNase/RNase-free 0.2% BSA, samples were collected in DNase/RNase-free tubes. Total RNA was extracted using TRIzol reagent, and ribosomal RNA was removed using the rRNA depletion module (Abclonal; RK20348). The alkylation was performed using iodoacetamide (Sigma; I1149). Total RNA after iodoacetamide treatment was used as the input for library construction using the Fast RNA-seq Lib Prep Kit V2 (Abclonal; RK20306). DNA fragments were selected, and the final sequencing libraries were constructed from to 300-400 bp of the amplified cDNA.

value: Zygote


title: 83_MegaCHOEP_III_M_56

value: Diffuse large B-ell lymphoma


title: neonatal mouse organ of Corti, WT, Input


title: 822_RICOVER_60_M_79

value: FFPE


title: 83_DENSER_F_71


title: 79_DENSER_M_67

value: M


title: PABPN1L-1C-rep1


title: 773_RICOVER_60_M_70


title: 74_DENSER_M_77


title: WT-1C-rep1


title: WT-1C-rep2


title: 77_MegaCHOEP_III_F_29

value: F


title: EAP,prostate,VUF11207,14d,rep2

city: Hefei

first: Yi

last: Zhang

address: Jixi Road 218, Shushan District, Hefei City 230022, Anhui Province, People’s Republic of China.

institute: the First Affiliated Hospital of Anhui Medical University

data_processing:
The libraries were sequenced on an llumina Novaseq 6000 platform and 150 bp paired-end reads were generated
Raw reads of fastq format were firstly processed using fastp and the low quality reads were removed to obtain the clean reads.
The clean reads were mapped to the reference genome using HISAT2
FPKM of each gene was calculated and the read counts of each gene were obtained by HTSeq-count.
Assembly: mm10
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

source_name: Prostate

extract_protocol:
Total RNA was extracted using the TRIzol reagent (Invitrogen, CA, USA) according to the manufacturer’s protocol.
The libraries were constructed using VAHTS Universal V6 RNA-seq Library Prep Kit according to the manufacturer’s instructions.

value: Prostate


title: 750_RICOVER_60_M_65


title: 754_RICOVER_60_M_69


title: 706_RICOVER_60_M_70


title: 712_RICOVER_60_M_75


title: 866_RICOVER_60_M_69


title: neonatal mouse organ of Corti, Bmi1 KO, Input


title: 701_RICOVER_60_F_67


title: EAP,prostate,VUF11207,14d,rep1


title: EAP,prostate,DMSO,14d,rep3

value: DMSO(5 mg/kg/d),14d


title: 70_DENSER_F_73


title: WT-2C-rep2


title: 694_RICOVER_60_F_61


title: 704_RICOVER_60_F_68


title: EAP,prostate,VUF11207,14d,rep3


title: EAP,prostate,DMSO,14d,rep1


title: EAP,prostate,DMSO,14d,rep2


title: WT-2C-rep1


title: 69_DENSER_F_72


title: 761_RICOVER_60_F_67


title: 685_RICOVER_60_F_62


title: cko, replicate 2, scRNAseq

city: Guangzhou

first: Xiaoling

state: Guangdong

address: No. 195, West Dongfeng Road

institute: Guangzhou Medical University

description: 10x Genomics single-cell transcriptome sequencing

data_processing:
Raw single-cell RNA-sequencing data were processed using the “cellranger multi” pipeline (10x Genomics Cell Ranger v.7.0.0). This involved demultiplexing the FASTQ files, aligning the reads to the pre-built transcriptome reference (mm10/GRCm38 v2020-A, 10x Genomics) and V(D)J reference (ENSEMBL/GRCm38 v4.0.0, 10x Genomics) specific to mouse, with an input parameter setting of expected cells equal 3,000.
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Subcutaneously inoculated tumor

extract_protocol:
Live tumor infiltrating CD45+ cells were FACS-sorted from Ctrl or Ctcf cKO mice bearing MC38 tumors (3 biological replicates per group).
Single-cell sequencing libraries were prepared using the Chromium Single Cell 5’ Library & Gel Bead Kit and the Chromium Single Cell V(D)J Enrichment Kit (10x Genomics), following the manufacturer’s protocols.

value: Subcutaneously inoculated tumor

value: tumor infiltrating CD45+ cells

value: Ctcf knockout in Tregs


title: 68_DENSER_F_78


title: 665_RICOVER_60_M_61


title: 632_RICOVER_60_M_64


title: 63_DENSER_F_77


title: ctr, replicate 3, scRNAseq

value: Ctcf WT in Tregs


title: ctr, replicate 2, scRNAseq


title: 623_RICOVER_60_M_62


title: ctr, replicate 1, scRNAseq


title: cko, replicate 1, scRNAseq


title: 618_RICOVER_60_M_80


title: 61_DENSER_F_80


title: 597_RICOVER_60_F_65


title: ctr, replicate 1, ATACseq

data_processing:
the quality of the raw data was assessed using FastQC (v0.12.1). The adaptor sequences were trimmed, and low-quality bases were removed using Trim Galore (v0.6.10). Subsequently, the reads were aligned to the mouse reference genome (UCSC mm10) and only uniquely mapped reads (MAPQ > 10) were retained using HISAT2 (v2.2.1). SAMtools v1.7 was used to convert the SAM files to BAM files and to sort the BAM files. PicardMarkDuplicates 2.21.6 was used to remove duplicate reads in the bam files. MACS v.2.1.1 was used for ATAC-seq, CTCF and H3K27ac peak calling. BAM files were then converted to Bigwig files using deepTools (v3.5.4). Motif enrichment analysis was conducted using HOMER. Visualization of signal tracks was performed using IGV and WashU Epigenome Browser.
Assembly: mm10
Supplementary files format and content: bigWig, narrowPeak,matrix files

extract_protocol:
FACS-sorted live Treg cells
A total of 200 ng of RNA was used as input for the SMARTer Stranded Total RNA Sample Prep Kit - HI Mammalian (Clontech), following the manufacturer’s protocol. libraries for ATAC-seq CUT&Tag were following manufacturer's protocols

value: Treg cells from MC38 subcutaneous tumors


title: anti-PD-1, replicate 3,  ATACseq

value: Treg cells from MC42 subcutaneous tumors


title: ctr, replicate 2,  ATACseq

value: Treg cells from MC39 subcutaneous tumors


title: Fiko, replicate 3,ATACseq

source_name: the spleen and lymph nodes

value: the spleen and lymph nodes

value: Treg cells from the spleen and lymph nodes

value: CtcfiKO


title: 59_MegaCHOEP_III_M_60


title: ctr, replicate 3, ATACseq

value: Treg cells from MC40 subcutaneous tumors

value: WT


title: cko, replicate 3, scRNAseq


title: 583_RICOVER_60_F_74

value: Diffuse large B-ell lymphoma

value: FFPE


title: Fiko, replicate 2,ATACseq


title: Fiko, replicate 1,ATACseq


title: 574_RICOVER_60_F_67

value: F


title: 570_RICOVER_60_M_75

value: M


title: 57_DENSER_M_76


title: Fctr, replicate 2,ATACseq

value: Control


title: anti-PD-1, replicate 2,  ATACseq

value: Subcutaneously inoculated tumor

value: Treg cells from MC41 subcutaneous tumors


title: 62_DENSER_F_68


title: 56_DENSER_F_62


title: 6_DENSER_M_79


title: 54_DENSER_F_71


title: Ycko, replicate 3, ATACseq

value: CtcfcKo


title: 522_RICOVER_60_M_62


title: Ycko, replicate 1,ATACseq


title: Yctr, replicate 3, ATACseq

value: CtrlCre


title: Fctr, replicate 3,ATACseq


title: TIP815

city: Oxford

first: Alison

last: Simmons

address: John Radcliffe Hospital/Headley Way

department: The MRC Weatherall Institute of Molecular Medicine

country: United Kingdom

institute: University of Oxford

description: Library name: TIP_815_INFLAMMATORY

data_processing:
Raw reads were processed using 10x Genomics spaceranger pipeline, against hg38 human reference genome
Assembly: hg38
Supplementary files format and content: Zip file contains Spaceranger output raw counts matrices, H&E images, spatial coordinates and image scaling factors
Library strategy: Spatial Transcriptomics

source_name: intestine

extract_protocol:
FFPE tissue sections were cut at 10um thickness with cryostat.
Spatial Transcriptomics gene expression libraries were prepared according to the manufacter's instructions using 10x Visium Spatial Gene Expression Slides and Reagents Kit.

value: intestine

tag: disease

value: CD

tag: fistula type


title: Yctr, replicate 2, ATACseq


title: TIP535_2

description: Library name: TIP535JR_FISTULATING

value: ENTEROCUTANEOUS


title: 506_RICOVER_60_M_70


title: TIP633

description: Library name: TIP_633_JR_HEALTHY

value: HEALTHY


title: Fctr, replicate 1,ATACseq

value: the spleen and lymph nodes

value: Treg cells from the spleen and lymph nodes


title: Yctr, replicate 1,ATACseq


title: TPTMB16 REP4

type: RNA

city: Hamilton

first: Yonghong

last: Wan

state: Ontario

address: 1280 Main St W

department: Medicine

country: Canada

institute: McMaster University

description: Gene expression of memory T cells purified 7 days post-challenge

hyb_protocol: Sample preparation for microarray hybridization was conducted with a GeneChip WT Pico Reagent Kit according to manufacturer instructions.

scan_protocol: Samples were run on a GeneChip Scanner 3000.

data_processing: Probe set signals were SST-RMA-normalized prior to further analysis.

label: biotin

source_name: CD8+ Tetramer+ T cells flow-sorted from secondary lymphoid organs

growth_protocol: Cells were cultured in MEM/F11 containing 10% FBS, 2 mM l-glutamine, 5 ml sodium pyruvate, 5 mL nonessential amino acids, 5 mL vitamin solution, 55 μM 2-mercaptoethanol, 100 U/mL penicillin, and 100 ng/ml streptomycin.

extract_protocol: In any experiment that involved the co-analysis of TP-TM and VP-TM, the memory T cell generation time was normalized to seven days to mitigate age-related influences on cellular senescence induction. Inguinal lymph nodes, and/or spleens were isolated and mechanically dissociated in complete RPMI. Cells were sorted or analyzed based on CD8, gp33 tetramer (gp33H2DbTet) and T cell differentiation marker (CD44, CD62L, CD127, KLRG1) staining.

treatment_protocol: For implantation, trypsinized tumor cells were washed twice with PBS and resuspended in PBS at a concentration of 10^5 cells/30 μL and injected i.d. LCMV-Armstrong was injected i.p. at a concentration of 2x105 pfu/μL

tag: strain

tag: tumor stage

value: 7d B16-gp33 tumor-bearing mice


title: TIP559

description: Library name: TIP_559_FISTULATING_1

value: ILEOCOLIC


title: Ycko, replicate 2, ATACseq


title: 497_RICOVER_60_M_75

value: Diffuse large B-ell lymphoma


title: TIP535_1

description: Library name: TIP_535_FISTULATING


title: TIP522

description: Library name: TIP_522_HEALTHY


title: TPTMMC38 REP2

label_protocol: Sample preparation for microarray hybridization was conducted with a GeneChip WT Pico Reagent Kit according to manufacturer instructions.

value: 7d MC38-gp33 tumor-bearing mice


title: 52_MegaCHOEP_III_M_32

value: FFPE


title: TPTMB16 REP3


title: 496_RICOVER_60_M_66

value: M


title: 508_RICOVER_60_F_69

value: F


title: TIP473JR

description: Library name: TIP_473_JR_FISTULATING


title: TPTMMC38 REP3


title: VPTM REP3

value: 7d LCMV-Armstrong infected mice


title: GFP-negative 11

city: Madrid

first: Alfonso

last: Gutiérrez-Adán

address: Av. Puerta de Hierro 28

department: Animal Reproduction

institute: INIA

data_processing:
Raw reads were trimmed using Trimmomatic, then aligned to the reference genome using HISAT2
Assembly and quantification was performed by StringTie.
Gffcompare and RNAsamba were used to annotate novel transcripts and predict coding potential
Assembly: Mus musculus mm39
Supplementary files format and content: Ctab files contain coverage data per transcript for each sample obtained by StringTie

source_name: Sertoli

extract_protocol:
Total RNA was isolated using TRIzol reagent and treated with Dnase for 1 h.
Library preparation includes rRNA removal and dUTP method for strand-specific library

value: Sertoli

tag: phenotype

value: Non-green


title: TPTMB16 REP1


title: GI7738JR

description: Library name: GI_7738_JR_STRICTURING


title: TPTMMC38 REP1


title: VPTM REP2


title: TPTMMC38 REP4


title: TPTMB16 REP2


title: VPTM REP1


title: GI7595

description: Library name: GI_7595_STRICTURING


title: GI7051

description: Library name: GI_7051_INFLAMMATORY


title: 49_DENSER_M_69


title: GFP-negative M


title: GI6968

description: Library name: GI_6968_HEALTHY


title: GFP-positive 7

value: Green


title: 47_DENSER_M_74


title: 469_RICOVER_60_M_77


title: 17451/20

description: Library name: FISTULATING_JR_5

value: intestine

value: ILEOCAECAL


title: 31183/22

description: Library name: FISTULATING_JR_4

value: CD

value: ILEAL


title: 451_RICOVER_60_M_78


title: 51343/21

description: Library name: FISTULATING_JR_2


title: 35259/13

description: Library name: FISTULATING_JR_1B

value: ILEAL-SIGMOID


title: GFP-positive 2


title: 449_MegaCHOEP_obs_M_60


title: JR37317_21

description: Library name: C4

value: ILEOCEACAL


title: BAY10460320/JR2029122

description: Library name: C3

value: ILEOCAECAL/PERIANAL


title: JR23234_23

description: Library name: B12

value: PERIANAL


title: 448_MegaCHOEP_obs_F_55

value: Diffuse large B-ell lymphoma


title: JR18076_22

description: Library name: C1

value: ANAL


title: 447_MegaCHOEP_obs_M_45

value: FFPE


title: BAY10533820

description: Library name: C2

value: TRANS-SPHINCTERIC


title: GFP-negative 9


title: progenitor exhausted_4

city: Paris

first: Elodie

last: Segura

address: 156 rue de Vaugirard

department: INSERM U1151

country: France

institute: INSERM

data_processing:
Quality of RNA-seq data was assessed using FastQC (v0.11.9). Reads were aligned to the transcriptome using STAR.
Assembly: mm10
Supplementary files format and content: raw count matrix (csv file)

source_name: tumor

extract_protocol:
Total RNA was extracted using the Total RNA purification kit (Norgen) according to the manufacturer’s protocol. cDNA was generated using the SMART-Seq v4 kit (Takara) according to the manufacturer’s protocol.
The integrity of the DNA was confirmed in BioAnalyzer using High Sensitivity DNA kit (Agilent Technologies) (8 < RIN). Libraries were prepared according to Illumina's instructions accompanying the Nextera XT DNA Library Prep Kit (Illumina).
Sequencing was performed in 2 sequencing unit of NovaSeq 6000 (Illumina) (100-nt-length reads, paired end).

treatment_protocol: Mice were inoculated subcutaneously with 5x105 MCA101-OVA fibrosarcoma cells at day 0. When tumors reached 80-100 mm3, mice were treated intra-peritoneally with 200 micro-g anti-PD1. Tumors were analyzed 24h later.

value: tumor

value: WT

value: anti-PD1 therapy


title: JR7907_23

description: Library name: B10

value: COLONIC


title: 446_MegaCHOEP_obs_M_54

value: M


title: 439_MegaCHOEP_obs_F_29

value: F


title: JR15707_22/JR43196

description: Library name: B9

value: intestine


title: TIP525

description: Library name: A12

value: HEALTHY


title: JR47926_22

description: Library name: B11

value: CD

value: ENTEROCUTANEOUS


title: GFP-positive 4

value: Sertoli

value: Green


title: effector_3

value: KO


title: JR50621

description: Library name: A10

value: DIVERTICULAR


title: 48715

description: Library name: A9

value: ENTEROCOLIC


title: GI6966

description: Library name: GI_6966_INFLAMMATORY


title: JR51747

description: Library name: A8


title: effector_1


title: 436_MegaCHOEP_obs_F_46

value: Diffuse large B-ell lymphoma

value: FFPE


title: JR45695

description: Library name: A7

value: PERIANAL


title: effector_2

value: tumor


title: effector_4

value: WT

value: anti-PD1 therapy


title: progenitor exhausted_3


title: 429_MegaCHOEP_obs_F_41


title: progenitor exhausted_1


title: JR115964

description: Library name: A6

value: ILEOCOLIC


title: 9174_22

description: Library name: A4


title: JR8610

description: Library name: A5


title: 42_MegaCHOEP_III_M_43

value: M


title: 94350_21

description: Library name: A3

value: intestine

value: ILEOCEACAL


title: Healthy control

city: New Haven

first: Andrés

last: Hidalgo

address: 10 Amistad Street

institute: Yale University

description: Fresh frozen Spatial transcriptome sequencing

data_processing:
Raw sequencing data were processed using the 10x Genomics Space Ranger v1.3.0 pipeline to generate FASTQ files
Sequences were aligned to mm10 genome to gene expression count using Space Ranger's default settings
Assembly: mm10
Supplementary files format and content: barcodes.tsv.gz:  list of spatial barcodes
Supplementary files format and content: features.tsv.gz:  list of gene IDs
Supplementary files format and content: matrix.mtx.gz:  gene expresion count data in Matrix Market Exchange Format
Supplementary files format and content: aligned_fiducials.jpg.gz:  aligned fiducials of the tissue image
Supplementary files format and content: detected_tissue_image.jpg.gz:  image of tissue and spots
Supplementary files format and content: scalefactors_json.json.gz:  scalefactors in json format
Supplementary files format and content: tissue_hires_image.png.gz:  hi-res image of tissue
Supplementary files format and content: tissue_lowres_image.png.gz:  low-res image of tissue
Supplementary files format and content: tissue_positions_list.csv.gz:  list of spatial barcodes and the coordinates specifying spots

source_name: lung

growth_protocol: All experiments were performed on 6–24-week-old C57BL/6 background mice. Chow and water were available ad libitum

extract_protocol:
For the generation of spatial transcriptomes tissues were first permeabilized. Afterward, tissues were lysed, and reverse transcription was performed followed by second strand synthesis and cDNA denaturation. Spatially barcoded, full length cDNAs were amplified. Finally, sequencing of GEX libraries was carried out.
Full length cDNAs were amplified by PCR for 16 and 17 cycles, depending on the initial concentration previously determined by qPCR. Indexed sequencing libraries were generated via End Repair, A-tailing, adaptor ligation and sample index PCR. Size distribution and concentration of full-length GEX libraries were verified on an Agilent Bioanalyzer High Sensitivity chip (Agilent)

value: lung

value: Male


title: progenitor exhausted_2


title: 414_MegaCHOEP_obs_F_48

value: F


title: 22635_21

description: Library name: A2

value: JEJUNAL


title: JR18170

description: Library name: A11


title: 41_DENSER_M_71


title: 113385_21

description: Library name: A1

value: CD

value: COLOCUTANEOUS


title: Lewis Lung Cancer, 2

value: intravenous injection of Lewis Lung Carcinoma (LLC)


title: Rpl22-/-Mll-AF9 Cd11b+Gr1+ splenocytes replicate 2

city: Philadelphia

first: David

last: Wiest

address: 333 Cottman Ave

institute: Fox Chase Cancer Center

description: Library name: KO-2

data_processing:
adapters were trimmed using trimmomatic, transcripts were mapped independent of reference using Salmon
Assembly: GRCm39
Supplementary files format and content: csv

source_name: Spleen

extract_protocol:
macherey nagel nucleozol
Manufacturer protocol Illumina mRNA stranded kit

value: Spleen

value: primary


title: Rpl22-/-Mll-AF9 Cd11b+Gr1+ splenocytes replicate 3

description: Library name: KO-3


title: Lewis Lung Cancer, 1


title: 434_MegaCHOEP_obs_F_58

value: Diffuse large B-ell lymphoma

value: FFPE


title: Rpl22-/-Mll-AF9 Cd11b+Gr1+ splenocytes replicate 1

description: Library name: KO-1


title: 408_RICOVER_60_F_69


title: Rpl22+/+Mll-AF9 Cd11b+Gr1+ splenocytes replicate 3

description: Library name: WT-3


title: p2 utricle, gentamycin control, CUT&Tag, IgG control

data_processing:
The CUT&Tag data analysis was performed as previously described following the Bench top CUT&Tag V.3 protocol. Briefly, raw reads were first processed through in-house perl scripts. In this step, clean data were obtained by removing reads containing adapters, reads containing ploy-N, and low-quality reads from the raw data. Based on the high-quality clean data, paired-end reads were aligned to the mm10 reference genome using the Bowtie2 program (v2.5.1). For spike-in normalization, reads were aligned to the E. coli genome for generating the scaling factor. Peaks were called using SEACR (v1.3), and the peaks were annotated by ChIPseeker (v1.36.0) and analyzed by deepTools (v3.5.3). Differential peak analysis was carried out using edgeR based on the counts of reads, and genomic data was visualized using the Integrative Genomics Viewer (v2.16).
Assembly: mm10
Supplementary files format and content: bigWig
Library strategy: CUT&Tag

source_name: mouse inner ear utricle explants

extract_protocol:
Accutase was used for cell detachment and tissue dissociation of the utricle explants for 15–20 min at 37°C with gentle trituration every 5 min (50 times with a 200 µl low‐retention pipette). Lysates containing a total of 10,000 cells were obatined
Lysates containing a total of 10,000 cells were incubated at room temperature with concanavalin A-coated magnetic beads for 10 minutes and then with the primary antibody against c-Fos (1:50 dilution; ab25949, Abcam) or IgG control antibody (normal rabbit IgG: Millipore cat. No. 12-370) overnight at 4°C, with secondary antibodies (1:100 dilution; anti-rabbit IgG antibody, goat monoclonal: Millipore AP132) for 2 h, and then with pA/G-Tn5 adapter complex for 1 h. DNAs were extracted using a DNA purification kit containing selection beads (Yeasen, 12601ES03), and a fixed amount of E. coli DNA was added for spike-in calibration. Libraries were prepared using the Hieff NGS Tagment Index Kit for Illumina (96 index) (Yeasen, 12610ES96), and the size distribution of the libraries was determined using an Agilent 4200 TapeStation. Paired-end 150 bp sequencing was carried out on a NovaSeq 6000 platform following the manufacturer’s instructions.

value: mouse inner ear utricle explants

value: WT

value: gentamycin


title: Rpl22+/+Mll-AF9 Cd11b+Gr1+ splenocytes replicate 2

description: Library name: WT-2


title: Rpl22+/+Mll-AF9 Cd11b+Gr1+ splenocytes replicate 1

description: Library name: WT-1


title: Neutrophils heterogeneity in mice under rewilding conditions rhapsody transcriptome

description: Library name: rewilded

data_processing:
Rhapsody processing pipeline
Assembly: GRCm39
Supplementary files format and content: Seurat r object containing the raw counts and metadata

source_name: Mouse tissues and blood (multiplexed)

growth_protocol: For the rewilding experiments, C57BL6 littermate of mice were generated from multiple breeding pairs and randomly assigned to either remain in the institutional vivarium (laboratory mice; Rutgers University ) or released into the outdoor enclosures (rewilded mice) to control for the microbiota at the onset of the experiment.

extract_protocol:
For the generation of single-cell whole-transcriptomes we used a BD Rhapsody system according to manufacture instructions. 60,000 sorted live cells were loaded into a Rhapsody Single Cell Analysis System cartridge. Cell capture and cDNA synthesis were performed according to manufacturer’s instructions; cells were isolated into nanowells by gravity, then cells lysed and mRNA, AbSeq oligos and Sample tags oligos were released and captured by beads present in the nanowells.
Indexed libraries were prepared for whole transcriptome analysis and Sample Tag demultiplexing following manufacturer’s instructions. The average size of the libraries was calculated using the 2100 Bioanalyzer (Agilent) and the concentration was determined using the Qubit fluorometer (Thermofisher). Finally, libraries were combined and sequenced together in a paired end run (60x42) using a NextSeq 2000 system (Illumina) and a P2 flowcell. Output files were processed with NextSeq 1000/2000 Control Software Suite v1.4.1. FastQ files for each sample were obtained using BCL Convert v3.6.3 software (Illumina).

treatment_protocol: For the generation of single-cell whole-transcriptomes, neutrophils were sorted in BD FACS Aria Fusion sorter as DAPI-CD11b+Ly6G+ cells and loaded into a BD Rhapsody cartridge

value: Mouse tissues and blood (multiplexed)

value: Leukocyte

value: male

tag: library type

value: mRNA


title: 397_RICOVER_60_M_61

source_name: Diffuse large B-ell lymphoma

value: M


title: p2 utricle, gentamycin+BMP4+DAPT, CUT&Tag

tag: tissue


title: Flu

value: lung

value: Male

value: 100 PFU of the virus strain A/PR8/34 (H1N1) were administered intra-nasally


title: 394_MegaCHOEP_obs_F_55

value: F


title: Neutrophils in clonal hemaptopoiesis rhapsody transcriptome

description: Library name: cDNA

source_name: Blood, bone marrow and lung

growth_protocol: All experiments were performed on 3-4months-old C57BL/6 male mice. Chow and water were available ad libitum.

extract_protocol:
For the generation of single-cell whole-transcriptomes we used a BD Rhapsody system according to manufacture instructions. 60,000 sorted live cells were loaded into a Rhapsody Single Cell Analysis System cartridge. Cell capture and cDNA synthesis were performed according to manufacturer’s instructions; cells were isolated into nanowells by gravity, then cells lysed and mRNA, AbSeq oligos and Sample tags oligos were released and captured by beads present in the nanowells.
Two separated indexed libraries were prepared for whole transcriptome analysis and Sample Tag demultiplexing following manufacturer’s instructions. The average size of the libraries was calculated using the 2100 Bioanalyzer (Agilent) and the concentration was determined using the Qubit fluorometer (Thermofisher). Finally, libraries were combined and sequenced together in a paired end run (60x42) using a NextSeq 2000 system (Illumina) and a P2 flowcell. Output files were processed with NextSeq 1000/2000 Control Software Suite v1.4.1. FastQ files for each sample were obtained using BCL Convert v3.6.3 software (Illumina).

treatment_protocol: For the generation of single-cell whole-transcriptomes,  cell suspensions from blood, bone marrow and lung were sorted in BD FACS Aria Fusion sorter as DAPI- CD45.1+ OR CD45.2+ CD11b+Ly6G+ cells and loaded into a BD Rhapsody cartridge

value: Blood, bone marrow and lung

value: JAXBoy PtprcK302E and C57BL6 Chimera


title: Neutrophils in clonal hemaptopoiesis rhapsody sample tags

description: Library name: tags

value: Rhapsody tags


title: 389_MegaCHOEP_obs_M_54

extract_protocol:
Three hundred sixty DLBCLs tissues were processed. Using 5 ¬µm unstained FFPE sections. The optimal amounts of tissue for each HTG EdgeSeq panB Lymphoma assay. The sample preparation as performed according to the manufacturer’s instructions.
Probe_captured FFPE samples for EdgeSeq panB Lymphoma assay were amplified¨ and indexed via polymerase chain reaction (PCR) using the master mix (OneTaq HotStart 2X MasterMix in GC Buffer (New England Biolabs Inc., Ipswich, MA, USA), and indexing primers according to manufacturer’s instructions. The following library cleanup was performed using AMPure XP beads according to manufacturer’s instructions
Targeted mRNA Sequencing using HTG EdgeSeq Pan B_Cell Lymphoma Panel assay

value: Diffuse large B-ell lymphoma


title: p2 utricle, gentamycin+BMP4, CUT&Tag


title: Neutrophils heterogeneity in germ free mice and BHLHE40 deficient mice rhapsody transcriptome

description: Library name: cDNA

source_name: Mouse tissues and blood

growth_protocol: C57BL/6  Mrp8 CRE+ BHLHE40 Floxed mice and  C57BL/6 control mice were used Chow and water were available ad libitum. In addition,  8-week old male Germ-free mice (C57Bl/6) were kindly provided by Noah Palm’s Lab (Yale University). In brief, Germ-free C57BL/6 mice were bred and maintained under sterile conditions in flexible film isolators (Class Biologically Clean) in the Palm laboratory Gnotobiotic Facility at Yale School of Medicine. Mice were housed in a temperature- and humidity-controlled room under a dark–light cycle of 12 h–12 h.

value: Mouse tissues and blood

value: pooled male and female


title: Neutrophils heterogeneity in BALB/c and C57BL6 rhapsody sample tags

description: Library name: tags

growth_protocol: All experiments were performed on 7–16-week-old C57BL/6 or BALB/C mice. Chow and water were available ad libitum.

value: WT


title: Neutrophils heterogeneity in BALB/c and C57BL6 rhapsody transcriptome

description: Library name: cDNA


title: 392_MegaCHOEP_obs_M_58

value: FFPE


title: 384_RICOVER_60_M_66


title: p2 utricle, gentamycin+BMP4+DAPT, bio rep3

source_name: mouse inner ear utricle

growth_protocol: P2 mouse utricles were quickly removed from the temporal bone, and the tectorial membrane was peeled off under sterile conditions. The otoconia were removed and the utricles were attached to coverslips pre-coated with CellTak (BD Biosciences) and placed in 4-well Petri dishes. Whole organs were cultured in serum-free media consisting of DMEM/F12 (1:1; Invitrogen), N2 (1:100 dilution, Invitrogen), B27 (1:50 dilution, Invitrogen), and ampicillin (50 ng/ml; Sigma) at 37°C with 5% CO2.

extract_protocol:
Each group of 12 utricles was separately used for extracting total RNA with the AllPrep DNA/RNA/Protein Mini kit (QIAGEN).
Sequencing libraries were generated using the NEBNext Ultra RNA Library Prep Kit for Illumina (NEB, USA) following the manufacturer’s recommendations, and index codes were added to attribute sequences to each sample.

value: mouse inner ear utricle


title: 386_MegaCHOEP_obs_F_52


title: p2 utricle, gentamycin+BMP4+DAPT, bio rep2


title: p2 utricle, gentamycin+BMP4+DAPT, bio rep1


title: p2 utricle, gentamycin control, CUT&Tag

value: mouse inner ear utricle explants

value: gentamycin


title: Hypoxia 1

city: Edinburgh

first: Manuel

middle: Alejandro

last: Sanchez Garcia

state: Midlothian

address: 4 Little France Drive

institute: University of Edinburgh

description: Library name: H3K4me3-4

data_processing:
The quality of FASTQ files was assess by FastQC program
After trimming adapter sequences, the reads were aligned to mouse genome mm10 by BWA
Peaks were called by MACS2 program
Bigwig files were generated by MACS2 and visualized with IGV or genome browser
Assembly: mm10
Supplementary files format and content: Bigwig
Library strategy: CUT&Run

source_name: Bone marrow GMP

extract_protocol:
Bone marrow tissue was harvested and filtered through a 40 micrometer cell trainer to obtain a cell suspension. A red blood cell lysis step (Biolegend) was used prior to staining with a mix of antibodies that identifies GMP. The samples were sorted with a BD FACSAria Fusion cell sorter by using DAPI to gate dead cells out and obtain a highly pure GMP population. Cells were fixed with 0.1 % PFA for 2 min at room temperature and cross-linking stopped by adding glycine solution (Cell Signaling) and incubating for 5 min.
Cut&Run libraries as per manufacturer’s guidelines (Cell Signaling Technology). Briefly, the cells were thawed and bound with Concanavalin A beads. After cell permeabilization by digitonin, anti-H3K4me3 antibody (Cell Signaling) was added to the samples and incubated for 2 h at 4 degrees. After removing unbound antibodies by washing, the samples were mixed with pAG-MNase and incubated for 1 h at 4 degrees. After washing, pAG-MNase was activated by adding calcium chloride. DNA was digested for 30 min at 4 degrees and the digestion reaction was stopped by ETDA. DNA fragments were collected by column-based DNA purification. DNA sequencing libraries were prepared by HAKA HyperPrep kit.

value: Bone marrow GMP

value: Hypoxia


title: Hypoxia + LPS 1

description: Library name: H3K4me3-7

value: Hypoxia + LPS


title: Hypoxia + LPS 3

description: Library name: H3K4me3-9


title: Hypoxia 3

description: Library name: H3K4me3-6


title: 38_DENSER_M_73

data_processing:
FASTQ Files using Illumina BaseSpace BCL to FASTQ software version 2.2.0 and Illumina Local Run Manager Software version 2.0.0.
FASTQ Files were analyzed with HTG EdgeSeq Parser software version 5.5 to generate raw counts for a total of 298 genes.
Assembly: Assembly: GRCh38.p13
Supplementary files format and content: raw counts
Supplementary files format and content: log2(Count per million+1)

value: M


title: Hypoxia 2

description: Library name: H3K4me3-5


title: Hypoxia + LPS 2

description: Library name: H3K4me3-8


title: 378_MegaCHOEP_obs_F_55


title: Normoxia 3

description: Library name: H3K4me3-3

value: Normoxia


title: Normoxia 2

description: Library name: H3K4me3-2


title: p2 utricle, gentamycin+BMP4, bio rep3


title: Normoxia 1

description: Library name: H3K4me3-1


title: p2 utricle, gentamycin+BMP4, bio rep2


title: Subcutanious BRCA2 mutated tumor treated with Gem/Cis followed by placebo maintenance therapy, Sample 5

first: John

middle: C

last: McVey

state: Pennsylvania

address: 3400 Spruce st

institute: University of Pennsylvania

description:
Library name: Sample 14
S26GC

data_processing:
DESeq2 (v1.32.0) was used for gene expression normalization and differential gene expression analysis across groups.
Assembly: Reads were mapped to the GRCm38/mm10 genome using the Base-Space Suite (Illumina).
Supplementary files format and content: CSV file including raw counts from every sample
Supplementary files format and content: CSV file including raw counts per sample

source_name: Tumor

growth_protocol: 1x106 cells were implanted subcutaneously into the flank of each mouse. Sex-matched eight- to twelve-week-old mice were block randomized in an unblinded manner.

extract_protocol:
Total RNA extracted using the RNeasy FFPE kit (Qiagen) from multiple 5μm serial sections cut from FFPE tissues
3' mRNA-seq libraries were generated from100 ng of DNase I–treated total RNA using the QuantSeq FWD Library Preparation Kit (Hexogen) according to the manufacturer’s directions.

treatment_protocol: Gemcitabine (120 mg/kg) suspended in PBS and cisplatin (4 mg/kg) suspended in 0.9% sodium chloride were administered by intra-peritoneal (i.p.) injection weekly. Olaparib (50 mg/kg) suspended in 4% DMSO, 30% PEG300 and 66% ddH2O was administered daily by i.p. injection.

value: Tumor

value: KPCB.c1 tumor cell line

value: Pancreatic cancer

value: Placebo maintenance

tag: batch

value: Day of death


title: 38_MegaCHOEP_III_M_24

tag: cell type

value: Diffuse large B-ell lymphoma


title: Subcutanious BRCA2 mutated tumor treated with Gem/Cis followed by placebo maintenance therapy, Sample 4

description:
Library name: Sample 13
S25GC


title: p2 utricle, gentamycin+BMP4, bio rep1

data_processing:
Preliminary processing of raw reads was performed using TrimGalore (v0.6.10) for removing adapters and low-quality bases. Trimmed reads for each sample were aligned to the Mus musculus Ensembl mm10 genome (release-110) using HISAT2 (v2.2.1), and aligned reads were summarized with featureCounts (v2.0.6). Differential expression analysis between conditions was performed using the DESeq2 R package (1.34.0), and genes with an adjusted p-value (padj) < 0.05 and log2 fold change > 0.25 were regarded as differentially expressed.
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample


title: p2 utricle, gentamycin control, bio rep3


title: Subcutanious BRCA2 mutated tumor treated with Gem/Cis followed by placebo maintenance therapy, Sample 3

description:
Library name: Sample 12
S23GC


title: 377_MegaCHOEP_obs_F_39

value: F


title: 375_MegaCHOEP_obs_F_52


title: Subcutanious BRCA2 mutated tumor treated with Gem/Cis followed by placebo maintenance therapy, Sample 1

description:
Library name: Sample 10
S21GC


title: p2 utricle, gentamycin control, bio rep2

value: WT


title: 373_RICOVER_60_F_67

value: FFPE


title: 372_MegaCHOEP_obs_F_53


title: Subcutanious BRCA2 mutated tumor treated with Gem/Cis followed by Olaparib maintenance therapy, Sample 9

description:
Library name: Sample 9
S20O

value: Olaparib maintenance


title: Subcutanious BRCA2 mutated tumor treated with Gem/Cis followed by Olaparib maintenance therapy, Sample 8

description:
Library name: Sample 8
S19O


title: Subcutanious BRCA2 mutated tumor treated with Gem/Cis followed by Olaparib maintenance therapy, Sample 7

description:
Library name: Sample 7
S18O


title: p2 utricle, gentamycin control, bio rep1

value: mouse inner ear utricle


title: Subcutanious BRCA2 mutated tumor treated with Gem/Cis followed by Olaparib maintenance therapy, Sample 5

description:
Library name: Sample 5
S16O


title: 369_RICOVER_60_M_62


title: Subcutanious BRCA2 mutated tumor treated with Gem/Cis followed by Olaparib maintenance therapy, Sample 6

description:
Library name: Sample 6
S17O


title: Subcutanious BRCA2 mutated tumor treated with Gem/Cis followed by Olaparib maintenance therapy, Sample 3

description:
Library name: Sample 3
S14O


title: Subcutanious BRCA2 mutated tumor treated with Gem/Cis followed by Olaparib maintenance therapy, Sample 4

description:
Library name: Sample 4
S15O


title: cite_seq

library_source: other

data_processing:
Fastq files were generated using 'bcl2fastq' conversion software (version 2.20) from Illumina with specific sample indexes corresponding to each sample
Resulting data was then imported and processed into Seurat object using Seurat and Signac R packages
Assembly: mm10
Supplementary files format and content: seurat object containg peaks, RNA counts and CITE-seq per cell

molecule: other

source_name: mixed sample (non-demultiplexed)

extract_protocol:
Mice -   DIG permeabilization –  The pooled cell suspension is washed, resuspended in 100ul of cold DIG lysis buffer, and incubated for 5min on ice. 1ml of cold DIG wash buffer is then added to the suspension and spun down for 5min at 500g. The pellet is resuspended in 100ul of 1x Nuclei buffer (2000207, 10X Genomics) supplemented with 1mM DTT (10708984001, Sigma) and 2U/l RNAse inhibitor (3335399001, Roche), at a final concentration of 3,400 cells/ul.
The library was prepared following the CG000338_ChromiumNextGEM_Multiome_ATAC_GEX_User_Guide_RevE user guide.The sequencing has been performed on a NovaSeq instrument, HiSeq paired-end 150 bp, 75 million reads.

value: mixed sample (non-demultiplexed)

value: FACS neutrophils (CD11b+Ly6G+)

tag: chip antibody

value: TotalSeq_A0301 (spleen - ACCCACCAGTAAGAC) / TotalSeq_A0302 (bone marrow - GGTCGAGAGCATTCA) / TotalSeq_A0303 (blood - CTTGCCGCATGTCAT) / TotalSeq_A0310 (lung - CCGATTGTAACAGAC)


title: gex


title: 361_RICOVER_60_M_69


title: atac


title: Subcutanious BRCA2 mutated tumor treated with Gem/Cis followed by Olaparib maintenance therapy, Sample 2

description:
Library name: Sample 2
S13O

tag: treatment


title: Subcutanious BRCA2 mutated tumor Olaparib treated, sample 5

description:
Library name: Sample 13
S23791O

value: Olaparib

value: Day 25


title: Subcutanious BRCA2 mutated tumor treated with Gem/Cis followed by Olaparib maintenance therapy, Sample 1

description:
Library name: Sample 1
S12O


title: 355_RICOVER_60_F_73


title: Subcutanious BRCA2 mutated tumor Olaparib treated, sample 4

description:
Library name: Sample 12
S23787O


title: Subcutanious BRCA2 mutated tumor Olaparib treated, sample 3

description:
Library name: Sample 11
S23786O


title: 346_MegaCHOEP_III_F_38


title: Subcutanious BRCA2 mutated tumor Olaparib treated, sample 2

description:
Library name: Sample 10
S23684O


title: tgfb_bhe

description: Leukocytes from multiple tissues and blood were collected from  8-10 week old wild type and TGgfb_DN mice

data_processing:
Rhapsody processing pipeline
Assembly: GRCm38
Supplementary files format and content: Seurat r object containing raw counts and metadata

extract_protocol:
For the generation of single-cell whole-transcriptomes we used a BD Rhapsody system according to manufacture instructions. 60,000 sorted live cells were loaded into a Rhapsody Single Cell Analysis System cartridge. Cell capture and cDNA synthesis were performed according to manufacturer’s instructions; cells were isolated into nanowells by gravity, then cells lysed and mRNA, AbSeq oligos and Sample tags oligos were released and captured by beads present in the nanowells
Two separated indexed libraries were prepared for whole transcriptome analysis and Sample Tag demultiplexing following manufacturer’s instructions. The average size of the libraries was calculated using the 2100 Bioanalyzer (Agilent) and the concentration was determined using the Qubit fluorometer (Thermofisher). Finally, libraries were combined and sequenced together in a paired end run (60x42) using a NextSeq 2000 system (Illumina) and a P2 flowcell. Output files were processed with NextSeq 1000/2000 Control Software Suite v1.4.1. FastQ files for each sample were obtained using BCL Convert v3.6.3 software (Illumina).

treatment_protocol: For the generation of single-cell whole-transcriptomess tissues were dissected and dissociated into a single-cell suspension by enzyme digestion. Cell strainer-filtered single-cell solution were sorted in BD Aria Cell Sorter as DAPI-CD11b+Ly6G+ cells and loaded into a BD Rhapsody cartridge

value: WT, TgfbRIIDN or Mrp8CRE+; TgfbRII Flox/Flox


title: Subcutanious BRCA2 mutated tumor Olaparib treated, sample 1

description:
Library name: Sample 9
S23683O

value: Tumor


title: 344_MegaCHOEP_III_M_47

value: M


title: inVitro

description: Bone marrow leukocytes treated in vitro for 24, 48 and 72h

value: Multiple in vitro treatments:Conditioned medium Pancreatic cancer, Conditioned medium lung cancer, LPS (5ng/ml), TNFa (5ng/ml), GMCSF (10ng/ml), GCSF (10ng/ml), TGFB (10ng/ml), IFNB (10ng/ml)


title: 34_DENSER_M_76


title: Subcutanious BRCA2 mutated tumor Gem/Cis treated, sample 3

description:
Library name: Sample 7
S23785CG

value: KPCB.c1 tumor cell line

value: Pancreatic cancer

value: Gem/Cis


title: Subcutanious BRCA2 mutated tumor Gem/Cis treated, sample 2

description:
Library name: Sample 6
S23676CG


title: Subcutanious BRCA2 mutated tumor Gem/Cis treated, sample 4

description:
Library name: Sample 8
S23826CG


title: 37_DENSER_M_77

value: Diffuse large B-ell lymphoma


title: interferon

description: Leukocytes isolated from blood and multiples tissues from naïve and zymosan-treated mice

value: WT, IfnarDN or Mrp8CRE+; Ifnar Flox/Flox

value: Peritonitis:Mice were injected intraperitoneally with zymosan (1mg)


title: Subcutanious BRCA2 mutated tumor Gem/Cis treated, sample 1

description:
Library name: Sample 5
S23673CG


title: mESC, naive, cytoplasm, PANDORA-seq, rep2

city: Boulder

first: Mika

last: Nevo

address: 2315 Walnut St

institute: CU Boulder

description: Cytoplasm

data_processing:
The raw reads were trimmed by performing SPORTS1.1.2 (parameters: sports.pl -M 1 -a -x GUUCAGAGUUCUACAGUCCGACGAUC -y AAGATCGGAAGAGCACACGTCT -l 15 -L 45 -s).
Assembly: mm39 (for mouse), hg38 (for human)
Supplementary files format and content: tab-delimited text files include sequences, length of sequences and sequence counts.

source_name: Naive ES cells

extract_protocol:
Total RNAs were extracted by Trizol (Invitrogen). Then small RNAs sized at 15-50nt were excised from 15% (w/v) urea polyacrylamide gel.
Small RNA libraries were constructed according to NEBNext® Multiplex Small RNA Library Prep Set for Illumina (New England Biolabs).

value: Naive ES cells

value: The 15-50nt RNAs were treated with T4PNK, then AlkB before cDNA library construction.


title: 333_RICOVER_60_M_73

value: FFPE


title: 336_RICOVER_60_M_71


title: mESC, naive, cytoplasm, PANDORA-seq, rep1

description: Cytoplasm


title: Subcutanious BRCA2 mutated tumor untreated, sample 4

description:
Library name: Sample 4
S23789C

value: Untreated


title: Subcutanious BRCA2 mutated tumor untreated, sample 3

description:
Library name: Sample 3
S23788C


title: Subcutanious BRCA2 mutated tumor untreated, sample 1

description:
Library name: Sample 1
S23672C


title: timestamp

description: Multiple samples including leukocytes isolated from the blood and tissues of WT, cancer bearing-mice, and LPS-treated mice at different timepoints after tamoxifen administration

value: mixed sample (non-demultiplexed)

value: Multiple treatments:LLC:intravenous injection of Lewis Lung Carcinoma (LLC); 400ng of LPS i.v. and samples harvested 24h, 36H and 72H after Tamoxifen administration (2mg)


title: YO2

description: Leukocytes from multiple tissues and blood were collected from  8-10 week old and 20 month old C57BL6 females


title: Subcutanious BRCA2 mutated tumor untreated, sample 2

description:
Library name: Sample 2
S23675C

value: Day 25


title: YO1


title: mESC, naive, pbody, PANDORA-seq, rep2

description: Pbody


title: 33_DENSER_F_65

value: F


title: non_steady1

description: Leukocytes isolated from blood and placenta of E.17.5 pregnant females; from blood and lung of E17.5 Embryos, from the pancreas of pancreatic tumor and pancreatitis, from the brain after stroke  and from meninges and blood

value: Multiple treatments:Pancreatic_tumor:100000 tumor cells from the pancreatic adenocarcinoma FC1242 cell line were injected in the pancreas; Acute_Pancreatitis:intraperitoneal injections of 50 µg/kg of cerulein every hour for a total of 7 administrations; Stroke:Mice were subjected to permanent focal cerebral ischemia (middle cerebral artery occlusion - pMCAO) through the distal occlusion of middle cerebral artery


title: jb2

description: Leukocytes from multiple tissues and blood were collected from  8-10 week old wild type and Cxcr4_DN mice

value: WT, JunBDN or Mrp8CRE+; JunB Flox/Flox


title: 323_RICOVER_60_M_80

value: M


title: non_steady2

description: Leukocytes isolated from lungs with flu and fibrosis; breast tumours; ischemic hearts; inflammed peritoneum (zymosan) and blood

value: Multiple treatments:Peritonitis:Mice were injected intraperitoneally with zymosan (1mg); Breast cancer:Mice were implanted orthotopically with 500000 E0771 breast cancer cells; Flu:100 PFU of the virus strain A/PR8/34 (H1N1) were administered intra-nasally; Liver_DDC:Mice were fed a 0.1% of 3,5-diethoxycarbonyl-1,4-dihydrocollidine (DDC)-supplemented diet for 3 weeks; AMI:The left anterior descending artery (LAD) was ligated with a nylon suture for 45 min; Bleomycin:We administered 1 mg/Kg of bleomycin sulphate into the tracheal lumen;


title: mESC, naive, cytoplasm, traditional-seq, rep2

description: Cytoplasm

value: The 15-50nt RNAs were sequenced with standard protocols.


title: jb1

description: Leukocytes isolated from  bone marrow and lungs  from WT and JunbDN naïve and  tumor-bearing mice. Bone marrow control leukocytes were also included

value: intravenous injection of Lewis Lung Carcinoma (LLC)


title: mESC, naive, cytoplasm, traditional-seq, rep1

description: Cytoplasm


title: diagnostic2

description: Multiple samples including leukocytes isolated from the blood and lung of cancer bearing-mice at different timepoints of disease progression;  blood leukocytes from mice infected with Aureus, Candida, blood leukocytes from mice fed with High fat diet orfrom mice with ceacal puncture

value: C57BL6 and Apoe-/- mice

value: Multiple treatments:LLC:intravenous injection of Lewis Lung Carcinoma (LLC); Blood Aureus:Mice were intravenously infected with 1 with 2.5 × 107 CFU of Staphylococcus aureus (RNU4220 strain); Blood_Candida:Mice were intravenously infected with 1.5x105 C. albicans conidia (SC5314 strain); Blood_CLP:A 23-gauge needle was then used to puncture both walls of the distal end of the cecum, and a small drop of faeces was extruded through the perforation; ApoE-/- were fed for 6 weeks with a control or high-fat diet (HFD, 10.7% total fat, 0.75% cholesterol.


title: 320_RICOVER_60_F_71

value: Diffuse large B-ell lymphoma


title: diagnostic1

description: Blood Leukocytes from mice with flu, colitis and liver injury. In addition, leukocytes from the ischemic muscle HLI at different timepoints, leukocytes from the liver after DDC diet from control and CXCR4_DN mice and from Piezo1-/- mic are included.

value: WT, Cxcr4DN or Mrp8CRE+; Cxcr4 Flox/Flox; LysMCRE+ Piezo1 Flox/Flox

value: Multiple treatments:HLI:Both the proximal end of the femoral artery and the distal portion of the saphenous artery were ligated; DDC:mice were fed a 0.1% of 3,5-diethoxycarbonyl-1,4-dihydrocollidine (DDC)-supplemented diet for 3 weeks;  Flu:100 PFU of the virus strain A/PR8/34 (H1N1) were administered intra-nasally; DSS:ice received for 9 days water with 1.5% Dextran Sulphate Sodium (DSS)


title: 32_DENSER_F_71

description:
HTG EdgeSeq Pan B-Cell Lymphoma Panel
RNA (amplified oligo nucleotide probes)

value: FFPE


title: Cxcr4

value: WT, Cxcr4DN or Mrp8CRE+; Cxcr4 Flox/Flox


title: mESC, naive, pbody, traditional-seq, rep2

description: Pbody

value: Naive ES cells


title: E14 Kidney LPD replicate 2

city: Clayton

first: Kieran

last: Short

address: 19 Innovation Walk

country: Australia

institute: Monash University

description: 10X Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v3 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
For E14.5 data, samples were sequenced with a paired-end single index configuration by Illumina NextSeq 2000. Cell Ranger version 5.0 (10x Genomics) was used to map raw data to references of gex-mm10-2020-A.
For the P0 snRNAseq data - 10X Genomics Cell Ranger 3 was used to process the NPD_19-5_19-8, NPD_24-3_24_2, LPD_5_4_5-2 and LPD_014-6_014 samples as above, with the exception of mapping using pre-mRNA transcripts based on mm10.
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: E14.5 embryonic kidney

extract_protocol:
For the E14.5 samples - two groups of kidneys five E14.5 kidneys, from 2 different females, per diet were pooled together and processed to obtain single-cell suspension. Approximately 10k single cells (per sample) were emulsified with Single Cell 3’ V3 beads (10X Genomics) and libraries generated on a 10X Chromium instrument. For the P0 samples - one snap frozen male and one snap frozen female kidney were placed in a cold Kimble dounce homogeniser and gentle nuclear extraction was performed using a nuclear lysis buffer (Sigma) dosed with RNAse inhibitors while grinding the kidneys. After homogenisation, nuclei were pelleted at 300 x g for 3 minutes, supernatant aspirated and resuspended in phosphate buffered saline containing RNAse inhibitors, centrifuged once more, aspirated, resuspended in PBS containing RNAseq inhibitor. Nuclei were stained with DAPI and flow sorted to enrich nuclei and remove any remaining particulates. Nuclei were finally processed by emulsion with 10X Genomics 3' V3 beads, and library generation on a 10X chromium instrument.
Library was performed according to the manufacter’s instructions (single cell 3’ v3 protocol, 10x Genomics). Briefly, kidney cells or nuclei were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead-in-emulsion (GEM). The RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA, which contains an Ilumina R1 primer sequence, Unique Molecular Identifier (UMI) and the 10x Barcode. The pooled barcoded cDNA was then cleaned up with Silane DynaBeads, amplified by PCR and the apropiated sized fragments were selected with SPRIselect reagent for subsequent library construction. During the library construction Ilumina R2 primer sequence, paired-end constructs with P5 and P7 sequences and a sample index were added.

treatment_protocol: Female and Males CD1 or C57BL6 mice were placed on low protein diet (6-8%) or Normal protein (20%) diet for 3 weeks before mating and maintaned on diet on diet during gestation. At E14.5 the embryos were dissected and the embryonic kidneys processed for single-cell RNA sequencing and E19.5 or P0 kidneys were dissected, snap frozen, and processed for single-nuclear RNA sequencing.

value: E14.5 embryonic kidney

value: pooled male and female

value: WT

value: 6% Low Protein Diet


title: 313_MegaCHOEP_III_F_48

value: F


title: 327_MegaCHOEP_III_F_42


title: mESC, naive, pbody, traditional-seq, rep1

description: Pbody


title: 312_SMARTER_M_70

value: M


title: E14 Kidney NPD replicate 2

description: 10X Genomics

value: 20% Normal Protein Diet


title: E14 Kidney LPD replicate 1

description: 10X Genomics


title: E14 Kidney NPD replicate 1

description: 10X Genomics


title: mESC, naive, pbody, PANDORA-seq, rep1

description: Pbody

value: The 15-50nt RNAs were treated with T4PNK, then AlkB before cDNA library construction.


title: U-2 OS Lunapark KO replicate 1

city: Ashburn

first: Jennifer

last: Lippincott-Schawrtz

state: VA

address: 19700 Helix Dr

institute: HHMI

description:
Library name: U2OS_LNPKO_rep1
Lunapark knockout U-2 OS cells, replicate 1

data_processing:
Adapters trimmed with Cutadapt v2.10.
Reads aligned with STAR v2.7.5c to GRCh38.
Gene counts generated using STARsolo.
Differential expression analyzed using DESeq2 (Matlab implementation).
Assembly: Homo sapiens GRCh38 (Ensembl).
Supplementary files format and content: Tab-delimited count matrices per sample; DESeq2 normalized counts and differential expression tables.

source_name: cultured cells

growth_protocol: U-2 OS cells cultured in phenol red–free DMEM supplemented with 10% FBS, 2 mM L-glutamine, and antibiotics at 37 °C and 5% CO₂

extract_protocol:
Total RNA extracted using Trizol (Invitrogen) followed by purification and QC using Agilent Bioanalyzer
cDNA synthesis from 1 ng total RNA using barcoded polyT primer and template-switch oligo. Libraries prepared with modified Nextera XT protocol and dual indexing

treatment_protocol: Lunapark knockout generated by CRISPR/Cas9 using Synthego sgRNAs and SpCas9 electroporation. Control cells received no editing

value: cultured cells

value: U-2 OS

value: osteocarcinoma

value: LNPK KO


title: U-2 OS Lunapark KO replicate 3

description:
Library name: U2OS_LNPKO_rep3
Lunapark knockout U-2 OS cells, replicate 3


title: U-2 OS Lunapark KO replicate 2

description:
Library name: U2OS_LNPKO_rep2
Lunapark knockout U-2 OS cells, replicate 2


title: 311_SMARTER_M_64

value: Diffuse large B-ell lymphoma


title: 311_RICOVER_60_M_62


title: Methamphetamine, replicate4, scRNAseq

first: Hai

last: Qiu

state: Guangdong province

address: 1023 Satai South Road, Jingxi Street

department: Institute of forensic medicine

institute: southern medical university

description: 10x Genomics

data_processing:
The raw sequencing data was precessed by Fastp firstly (Chen, Zhou et al. 2018) to trim primer sequence and low quality bases.
Processing  sample demultiplexing, barcode processing, single cell 3' gene counting and aggretion, generating feature-barcode matrices by Cell Ranger v7.0(https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: hippocampus

extract_protocol:
After harvested from mice,hippocampal tissues were washed in ice-cold RPMI1640 and dissociated using Tissue Dissociation Reagent A (Seekone K01301-30) from SeekGene as instructions. DNase Ⅰ (Sigma 9003-98-9) treatment was optional according to the viscosity of the homogenate. Cell count and viability was estimated using fluorescence Cell Analyzer (Countstar® Rigel S2) with AO/PI reagent after removal erythrocytes (Solarbio R1010) and then debris and dead cells removal was decided to be performed or not (Miltenyi 130-109-398/130-090-101). Finally fresh cells were washed twice in the RPMI1640 and then resuspended at 1×106 cells per ml in 1×PBS and 0.04% bovine serum albumin.
Single-cell RNA-Seq libraries were prepared using Chromium Next GEM Single Cell 3ʹ Reagent Kits v3.1 (10x Genomics Catalog No.1000268). Briefly, appropriate number of cells were mixed with reverse transcription reagent and then loaded to the sample well in Chromium Next GEM Chip G. Subsequently Gel Beads and Partitioning Oil were dispensed into corresponding wells separately in chip. After emulsion droplet generation reverse transcription were performed at 53℃for 45 minutes and inactivated at 85℃ for 5 minutes. Next, cDNA was purified from broken droplet and amplified in PCR reaction. The amplified cDNA product was then cleaned, fragmented, end repaired, A-tailed and ligated to sequencing adaptor. Finally, the indexed PCR were performed to amplified the DNA representing 3’ polyA part of expressing genes which also contained Cell Bar code and Unique Molecular Index. The indexed sequencing libraries were cleanup with SPRI beads, quantified by quantitative PCR (KAPA Biosystems KK4824) and then sequenced on illumina NovaSeq 6000 with PE150 read length or DNBSEQ-T7 platform with PE150 read length.

value: hippocampus

value: 18 weeks old

value: male

value: widetype

value: Methamphetamine, 10mg/kg for 28days, intraperitoneal injection


title: U-2 OS control replicate 3

description:
Library name: U2OS_CTRL_rep3
Control U-2 OS cells, replicate 3


title: Methamphetamine, replicate3, scRNAseq

description: 10x Genomics


title: U-2 OS control replicate 2

description:
Library name: U2OS_CTRL_rep2
Control U-2 OS cells, replicate 2


title: U-2 OS control replicate 1

description:
Library name: U2OS_CTRL_rep1
Control U-2 OS cells, replicate 1


title: 310_SMARTER_F_74

first: Emil

address: Albert-Einstein-Allee 11

institute: Ulm University Medical Center

value: FFPE


title: Methamphetamine, replicate2, scRNAseq

description: 10x Genomics


title: 308_SMARTER_F_66


title: 310_MegaCHOEP_III_M_55


title: Methamphetamine, replicate1, scRNAseq

description: 10x Genomics


title: Saline, replicate5, scRNAseq

description: 10x Genomics

value: Saline, equal volume to methamphetamine for 32days, intraperitoneal injection


title: RNA-Seq J17

city: Rochester

first: Aditya

last: Bhagwate

state: MN

address: 200 1st Street SW

institute: Mayo Clinic

description: Library name: J17

data_processing:
Reads were aligned using STAR
Expression counts were generated using featureCounts
Assembly: hg38
Supplementary files format and content: Gene count matrrix(.tsv)

source_name: jejunum

growth_protocol: Enteroids were cultured in Expansion Medium (EM, Advanced DMEM/F12, 1x B-27 supplement, 1 mM N-acetylcysteine, 50 ng/mL EGF, 500 nM A83-01, 10 µM SB 202190, 100 µg/mL Primocin, 50% v/v Wnt3A conditioned media, 15% v/v Rspondin-1 conditioned media, 10% v/v Noggin conditioned media).

extract_protocol:
Total RNA was extracted using an RNeasy Micro Kit (Qiagen).
RNA libraries were prepared using Illumina TruSeq RNA Library Preparation Kit v2.

treatment_protocol: Eneroids were plated on permeable tissue culture supports, cultured in EM until confluent, and then induced to differentiate for 5 d in Differentiation Medium (DM, same formulation as EM but lacking Wnt3A, Rspondin-1, A83-01, and SB 2020190).

value: jejunum

value: intestinal organoid (enteroid)

value: intestinal epithelia

value: obese


title: RNA-Seq J12

description: Library name: J12


title: RNA-Seq J4

description: Library name: J4

value: obese, hyperabsorptive


title: RNA-Seq J20

description: Library name: J20


title: Methamphetamine, replicate5, scRNAseq

description: 10x Genomics


title: RNA-Seq J21

description: Library name: J21


title: RNA-Seq J23

description: Library name: J23

value: lean


title: RNA-Seq J2

description: Library name: J2


title: 302_MegaCHOEP_III_F_36

last: Chteinberg

value: F


title: Saline, replicate4, scRNAseq

description: 10x Genomics

value: Saline, equal volume to methamphetamine for 31days, intraperitoneal injection


title: RNA-Seq J11

description: Library name: J11


title: Saline, replicate3, scRNAseq

description: 10x Genomics

value: Saline, equal volume to methamphetamine for 30days, intraperitoneal injection


title: 308_MegaCHOEP_III_F_56

value: Diffuse large B-ell lymphoma


title: RNA-Seq J1

description: Library name: J1


title: ATAC-Seq J20

description: Library name: J20

data_processing:
Paired end reads were aligned using BWA
Reads were filtered to uniquely mapping read pairs
Peaks were called using MACS2 (q<0.01)
Assembly: hg38
Supplementary files format and content: peak files (narrowPeak)

extract_protocol:
Enteroid monolayers were washed with PBS and treated with Accutase at 25 °C for approximately 20 min to detach cells. The single cell suspension was collected in a low-binding microcentrifuge tube, washed, counted, and ~50,000 cells were resuspended in 100 µL Anti-Freezing Buffer (Advanced DMEM/F12, 10% v/v FBS, 10% DMSO) and stored at -80 °C prior to DNA extraction. After thawing, nuclei were extracted...
Cryopreserved cells were thawed, washed with PBS, and prepared following the Omni-ATAC approach (Corces MR et al, Nat Methods 2017, 14:959). Libraries were purified by AMPure XP magnetic beads with double size selection (0.55x and 1.35x), and size distribution determined by High Sensitivity NGS Fragment analysis kit.


title: 301_MegaCHOEP_III_M_53

value: M


title: 300_MegaCHOEP_III_F_50