title: Elderly TNBC_5

value: Elderly

tag: subtype

tag: current age

tag: age at biobank entrance

tag: age at dx

tag: cid code

tag: clinical stage

tag: tumor relapse

tag: os

tag: os.time (days)

tag: Sex

value: Female

tag: race

value: White

tag: bmi

value: Overweight

tag: physical activity

tag: cigarrette use

value: In the past

tag: alcohol use

value: Never

tag: cancer family history

tag: mitotic index

tag: histologic grade

tag: estrogen receptor

value: Negative

tag: progesterone receptor

tag: her2 (ihc)

value: 0 (Negative)

tag: t

tag: n

tag: m

tag: neoadjuvant treatment


title: A-B-plasmid-library-Gecko

status: Public on Sep 25 2023

type: SRA

city: Bordeaux

first: Amandine

last: Crombe

address: 229 cours de l'Argonne

country: France

institute: Institut Bergonié

library_source: genomic

data_processing:
The entire genomic DNA was sequenced by Nucleus Biotech. SgRNA was amplified, and Next-Generation Sequencing (NGS) was performed on the Illumina NextSeq platform, targeting 60 million reads.
Supplementary files format and content: tab-delimited text file with CrispR cloud fold change results
Supplementary files format and content: Excel file with RIGER fold change results
Supplementary files format and content: Excel file with RIGER calculations
Supplementary files format and content: tab-delimited text file with Mageck fold change results

molecule: genomic DNA

organism: synthetic construct

source_name: not cell (plasmid)

growth_protocol: Cells were cultured in RPMI medium 1640 (Sigma Life Technologies, Saint Louis, MO) supplemented with 10% fetal calf serum (Dutscher, France)  at 37 °C with 5% CO2

extract_protocol: Genomic DNA was extracted using the DNeasy Blood and Tissue kit (Qiagen ID: 69504) following the manufacturer's protocol

treatment_protocol: Cells were treated by DMSO or  by 40µM of AZD7648 during 72h.

tag: cell type

value: not cell (plasmid)


title: CTL_WAT-1 251486841797_1_1

type: RNA

city: RTP

first: NIEHS

last: Microarray Core

state: NC

address: 111 T.W. Alexander Drive

department: DIR

country: USA

institute: NIEHS

description:
CTL_WAT-1
Gene expression from control white adipose tissue

hyb_protocol: For each sample, 1.65ug of Cy3 labeled cRNAs were fragmented and hybridized for 17 hours in a rotating hybridization oven.

scan_protocol: Slides were washed and then scanned with an Agilent Scanner.

data_processing: The Agilent Feature Extraction Software performed error modeling, adjusting for additive and multiplicative noise

molecule: total RNA

organism: Mus musculus

source_name: White Adipose Tissue

label_protocol: Starting with 500ng of total RNA, Cy3 labeled cRNA was produced according to manufacturer’s protocol.

extract_protocol: RNA was prepared using the Qiagen RNeasy Kit for total RNA isolation

tag: tissue

value: adipose tissue

tag: Sex


title: MTN_51

city: Philadelphia

first: Junhyong

last: Kim

state: PA

address: 433 S University Avenue

department: Biology

institute: University of Pennsylvania

description: MTN, 3 Weeks, Batch 2

library_source: transcriptomic single cell

data_processing:
Basecalling was done with bcl2fastq v2.17. Reads were trimmed for adapters, low quality base calls, and poly-A sequence using both in-house software and cutadapt v2.10 (Martin, Marcel. 2011), and then mapped to the mouse genome (mm10) using STAR v2.7.2d (Dobin et al. 2013). Uniquely mapped reads were used for gene quantification using VERSE v0.1.4 with parameters "-s 0 -z 3 --nonemptyModified" (Zhu et al. 2016)
Assembly: mm10
Supplementary files format and content: Tab-separated values files; gene counts

source_name: Brainstem

extract_protocol:
DPA and MTN neurons were labeled with 1,1'-Dioctadecyl-3,3,3',3'-tetramethylindocarbocyanine perchlorate (DiI) from the maxillary first molars of C57BL/6  mouse, then isolated in acute culture from the TG tissues and from brainstem slices, respectively. Afterwards, they were manually collected using a glass micropipette containing RNase inhibitor; each neuron was also photographed prior to collection, and the images were used for cell body area (μm2) measurements using ImageJ software.
Neurons were individually digested and reverse-transcribed into non-stranded cDNA using poly-T primers. The resulting cDNA was amplified using SMART-Seq v4 Ultra Low Input RNA kit according to the manufacturer’s instructions, but with the following modifications: 1) ERCC RNA Spike-In controls were added at the cell lysis step 2) 18 PCR cycles were performed to amplify cDNA libraries. The libraries were diluted accordingly and used to make DNA sequencing libraries by following the Nextera XT DNA Library Preparation Kit protocol. Library size distribution and quality were measured using Agilent's BioAnalyzer High Sensitivity DNA assay prior to sequencing.

value: Mesencephalic Trigeminal Nucleus (MTN) Neurons

value: Brainstem

tag: strain

tag: age

value: 3 weeks old


title: AdipoKO_BAT-4 251486841535_1_2

description:
AdipoKO_BAT-4
Gene expression from brown adipose tissue GR knockout mice

source_name: Brown Adipose Tissue

value: Adipose tissue

value: Male


title: MTN_49

description: MTN, 3 Weeks, Batch 2


title: AdipoKO_BAT-3 251486841535_1_1

description:
AdipoKO_BAT-3
Gene expression from brown adipose tissue GR knockout mice


title: AdipoKO_BAT-2 251486841534_1_4

description:
AdipoKO_BAT-2
Gene expression from brown adipose tissue GR knockout mice


title: AdipoKO_BAT-1 251486841534_1_3

description:
AdipoKO_BAT-1
Gene expression from brown adipose tissue GR knockout mice


title: NCOR2-013 OE THP-1 macrphages, TM, rep3

city: Nanning

first: Wudi

last: Wei

address: 22nd Shuangyong Road

country: China

institute: Guangxi Medical University

library_source: transcriptomic

data_processing:
CLC Genomics Workbench v 11.0.1
Sequence reads were trimmed for adaptor sequence/low-quality sequence using CLC genomic benchwork (parameter- Quality limit: 0.05)
Trimmed sequence reads were mapped to GrCM37 using CLC genomic benchwork (parameters- mismath cost: 2 insertion cost: 3 deletion cost: 3 length fraction: 0.8 similarity fraction: 0.8)
Read count extraction and normalization were performed using CLC genomic benchwork
Assembly: GrCM37
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

organism: Homo sapiens

source_name: THP1 macrophage

growth_protocol: THP-1 macrophages were maintained in DMEM supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen). 1.3 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacturer's protocols.

treatment_protocol: The human NCOR2-013 overexpression THP-1 macrophages were challenged with T. marneffei spores (MOI = 10) for 24h

tag: cell line

value: THP1 macrophage

value: peripheral blood monocyte

tag: genotype

value: NCOR2-013 overexpression

tag: treatment

value: T. marneffei infection

tag: time

value: 24 hours


title: NCOR2-013 OE THP-1 macrphages, TM, rep2


title: NCOR2-013 OE THP-1 macrphages, TM, rep1


title: Young Luminal HER2_2

city: Sao Paulo

first: Alexis Germán

last: Murillo Carrasco

email: agmurilloc@gmail.com, agmurilloc@usp.br

state: Sao Paulo

address: Av. Dr. Arnaldo 251, Sao Paulo

country: Brazil

institute: ICESP

description: vesicular miRNA from 1mL of plasma were loaded into the platform.

hyb_protocol: miRNAv3 NanoString® cartridges (NanoString® Technologies, cat. CSO-MIR3-12) were loaded with the mix per sample and sealed.

scan_protocol: For data collection, we transferred samples to an nCounter® Digital Analyzer device (NanoString® Technologies).

data_processing:
miRNA expression data were analyzed in the nSolver™ Data Analysis v.4.0 software (NanoString® Tech.) with the default protocol by the manufacturer. For cf-miRNA, we normalize the expression of human miRNAs by the geometric mean of all negative (negative normalization) and positive (positive normalization) probes. Then, we used the top 15 more stable regions to normalize the content set data.
Data were exported in comma-separated value (*.csv) format for further analysis.

label: miRNA reported and capture probes

source_name: plasma (Evs)

label_protocol: All miRNA concentrated per each sample were hybridized for 16.5 hours with molecular barcoding for 827 experimentally validated human miRNAs (from miRBase v21) using the nCounter Master Mix (NanoString® Technologies, cat. NAA-AKIT-012).

extract_protocol: Using 1mL of human plasma, we isolated extracellular vesicles using the qEV Izon columns. Then, we isolated vesicular miRNA following the instructions of the miRNeasy Serum/plasma kit (cat. 217184, Qiagen).

value: Young

tag: subtype

value: Luminal HER2

tag: current age

tag: age at biobank entrance

tag: age at dx

tag: cid code

tag: clinical stage

value: II

tag: tumor relapse

value: No

tag: os

value: Alive

tag: os.time (days)

value: Female

tag: race

value: Brown

tag: bmi

value: Eutrophic

tag: physical activity

value: With regularity

tag: drug use

tag: cigarrette use

tag: alcohol use

tag: cancer family history

tag: previous surgeries

value: Yes

tag: diabetes mellitus

tag: hbp

tag: dpoc

tag: gastritis

tag: first kindgree (cancer cases)

tag: first kindgree (breast/ovarian cancer cases)

tag: menopause status

tag: tubular grade

tag: nuclear grade

tag: mitotic index

tag: histologic grade

value: Positive

tag: her2 (fish)


title: Young Luminal HER2_1

tag: subtype

tag: current age

tag: age at biobank entrance

tag: age at dx

tag: cid code

tag: clinical stage

value: IV

tag: tumor relapse

tag: os

tag: os.time (days)

tag: Sex

tag: race

value: Others

tag: bmi

tag: physical activity

tag: drug use

value: Never

tag: estrogen receptor

tag: progesterone receptor

tag: t

tag: n

tag: m

tag: neoadjuvant treatment


title: CTL_BAT-2 251486841478_1_4

description:
CTL_BAT-2
Gene expression from brown adipose tissue control

tag: tissue

value: Adipose tissue

value: Male


title: CTL_BAT-3 251486841534_1_1

description:
CTL_BAT-3
Gene expression from brown adipose tissue control


title: Young Luminal B6

tag: subtype

value: Luminal B

tag: current age

tag: age at biobank entrance

tag: age at dx

tag: cid code

value: III

value: Obese

tag: cigarrette use

tag: alcohol use

value: In the past

tag: cancer family history

tag: previous surgeries

tag: diabetes mellitus

tag: hbp

tag: dpoc

tag: gastritis

tag: first kindgree (cancer cases)

tag: first kindgree (breast/ovarian cancer cases)

tag: menopause status

tag: tubular grade

tag: nuclear grade

tag: mitotic index

tag: histologic grade

tag: her2 (fish)

value: Negative


title: CTL_BAT-4 251486841534_1_2

description:
CTL_BAT-4
Gene expression from brown adipose tissue control

tag: tissue

tag: Sex


title: CTL_BAT-1 251486841478_1_3

description:
CTL_BAT-1
Gene expression from brown adipose tissue control


title: MTN_50

description: MTN, 3 Weeks, Batch 2

tag: cell type

value: Mesencephalic Trigeminal Nucleus (MTN) Neurons

value: Brainstem

tag: strain

tag: age

value: 3 weeks old


title: Young Luminal HER2_3

value: Young

tag: subtype

value: Luminal HER2

tag: current age

tag: age at biobank entrance

tag: age at dx

tag: cid code

tag: clinical stage

value: II

tag: tumor relapse

value: No

tag: os

value: Alive

tag: os.time (days)

value: Female

tag: race

value: Black

tag: bmi

tag: physical activity

tag: drug use

tag: cigarrette use

tag: alcohol use

tag: cancer family history

tag: previous surgeries

tag: diabetes mellitus

tag: estrogen receptor

tag: progesterone receptor

tag: t

tag: n

tag: m

tag: neoadjuvant treatment


title: NC THP-1 macrophages, TM, rep3

tag: cell line

value: THP1 macrophage

tag: cell type

value: peripheral blood monocyte

tag: genotype

value: WT

tag: treatment

value: T. marneffei infection

tag: time

value: 24 hours


title: MTN_45

description: MTN, 3 Weeks, Batch 2

tag: tissue

tag: strain

tag: age


title: Young Luminal B5

tag: subtype

value: Luminal B

tag: current age

tag: age at biobank entrance

tag: age at dx

tag: cid code

tag: clinical stage

value: III

tag: tumor relapse

tag: os

tag: os.time (days)

tag: Sex

tag: race

value: White

tag: bmi

value: Overweight

tag: physical activity

tag: drug use

tag: cigarrette use

value: In the past

tag: alcohol use

value: Never

tag: cancer family history

value: Yes

tag: hbp

tag: dpoc

tag: gastritis

tag: first kindgree (cancer cases)

tag: first kindgree (breast/ovarian cancer cases)

tag: menopause status

tag: tubular grade

tag: nuclear grade

tag: mitotic index

tag: histologic grade

value: Positive

tag: her2 (ihc)

value: 0 (Negative)


title: Young Luminal B4

value: Young

tag: subtype

tag: current age

tag: age at biobank entrance

tag: age at dx

tag: cid code

tag: clinical stage

tag: tumor relapse

value: No

tag: os

value: Alive

tag: os.time (days)

tag: Sex

tag: race

value: Others

tag: bmi

value: Eutrophic

tag: previous surgeries

tag: diabetes mellitus

tag: estrogen receptor

tag: progesterone receptor

tag: her2 (fish)

value: Suspicious

tag: t

tag: n

tag: m

tag: neoadjuvant treatment


title: MTN_44

description: MTN, 3 Weeks, Batch 2

tag: cell type

value: Mesencephalic Trigeminal Nucleus (MTN) Neurons

tag: tissue

value: Brainstem

tag: strain

tag: age

value: 3 weeks old


title: MTN_48

description: MTN, 3 Weeks, Batch 2


title: NC THP-1 macrophages, TM, rep1

tag: cell line

value: THP1 macrophage

value: peripheral blood monocyte

tag: genotype

value: WT

tag: treatment

value: T. marneffei infection

tag: time

value: 24 hours


title: AdipoKO_WAT-4 251486841478_1_2

description:
AdipoKO_WAT-4
Gene expression from white adipose tissue GR knockout mice

value: Adipose tissue

tag: Sex

value: Male


title: Young Luminal B2

tag: subtype

value: Luminal B

tag: current age

tag: age at biobank entrance

tag: age at dx

tag: cid code

tag: clinical stage

value: I

tag: tumor relapse

tag: os

tag: os.time (days)

value: Female

tag: race

value: Black

tag: bmi

tag: physical activity

value: With regularity

tag: cigarrette use

value: In the past

tag: alcohol use

tag: cancer family history

value: Yes

tag: previous surgeries

tag: diabetes mellitus

tag: hbp

tag: dpoc

tag: gastritis

tag: first kindgree (cancer cases)

tag: first kindgree (breast/ovarian cancer cases)

tag: menopause status

tag: tubular grade

tag: nuclear grade

tag: mitotic index

tag: histologic grade

value: Positive

tag: her2 (ihc)

value: 0 (Negative)


title: MTN_43

description: MTN, 3 Weeks, Batch 2

tag: cell type

value: Mesencephalic Trigeminal Nucleus (MTN) Neurons

tag: tissue

value: Brainstem

tag: strain

tag: age

value: 3 weeks old


title: MTN_42

description: MTN, 3 Weeks, Batch 2


title: Young Luminal B3

value: Young

tag: subtype

tag: current age

tag: age at biobank entrance

tag: age at dx

tag: cid code

tag: clinical stage

value: III

tag: tumor relapse

tag: os

value: Death

tag: os.time (days)

tag: Sex

tag: race

value: Brown

tag: bmi

value: Eutrophic

tag: physical activity

value: Frequently

tag: drug use

value: No

tag: cigarrette use

tag: alcohol use

value: Still in use

tag: cancer family history

tag: previous surgeries

tag: estrogen receptor

tag: progesterone receptor

value: Negative

tag: t

tag: n

tag: m

tag: neoadjuvant treatment


title: MTN_46

description: MTN, 3 Weeks, Batch 2

tag: cell type

tag: tissue

tag: strain

tag: age


title: CC10Cre-_Inf_lung_5

city: Riverside

first: Meera

last: Nair

state: CA

address: 243 SOM Research 3401 Watkins Drive

institute: UC Riverside

description:
50ng of total RNA was hybridized using the Mouse Immunology probeset from Nanstring which includes 561 target genes and 15 internal reference genes.
SAMPLE 3

hyb_protocol: Lysates were hybridized to  Nanostring MouseImmunology probes sets overnight per the manufacterers protocol.

scan_protocol: Samples were loaded onto the nanostring cartridge and read using the Nanostring nCounter Sprint.

data_processing: Data was processed using Rosalind Bio, where normalization and background subtraction were performed.

source_name: lung homogenate

growth_protocol: Lung from CC10 Cre- or CC10 Cre+ mice was homogenized into a singel cell suspension, around 1M cells were separated for RNA isolation.

extract_protocol: From around 1M cells, total RNA was isolated using the Promega SV Total RNA Isolation System  kit , cat. no, Z3105.

tag: genotype

value: CC10 Cre-

tag: infection status

value: day 30 post N. Brasiliensis infection


title: CC10Cre+_Inf_lung_1

description:
50ng of total RNA was hybridized using the Mouse Immunology probeset from Nanstring which includes 561 target genes and 15 internal reference genes.
SAMPLE 4

value: CC10 Cre+


title: NC THP-1 macrophages, TM, rep2

tag: cell line

value: THP1 macrophage

value: peripheral blood monocyte

value: WT

tag: treatment

value: T. marneffei infection

tag: time

value: 24 hours


title: Mx1-Cre; p53mut NrasG12D ; moribund, sample 4 [Mx1RG-C2102]

city: Madison

first: Jing

last: Zhang

state: Wisconsin

address: 7453 WI Institutes for Medical Research, 1111 Highland Ave

department: University of Wisconsin Carbone Cancer Center

institute: University of Wisconsin-Madison

description: NPmut 4

data_processing:
Reads from each sample were aligned to the Mus musculus GRCm38.p6 genome using STAR v2.6.1d 15
During alignment, the first three nucleotides (the switching oligonucleotides) were clipped from each read as recommended by Takara Bio USA/Clontech.
Reads that aligned to the sense strand of genes within the Gencode release M24 genome annotation were then counted.
Read counts for each sample were then imported into R v3.6.1 (https://www.R-project.org/) and normalized using DESeq2 v1.26.0 16.
Wald tests within DESeq2 were conducted to assess differential gene expression between groups and the ashr method was used to shrink log2 fold-change values
Assembly: Mus musculus GRCm38.p6 genome
Supplementary files format and content: comma separated values file includes raw counts for each sample

source_name: Bone marrow

extract_protocol:
Total RNAs were isolated from 50,000 sorted Lin- cKit+ bone marrow cells of age-matched control (n=3), p53R172H/+ (n=3), NrasG12D/+ (n=3) and moribund NPmut (n=4) mice using RNeasy Micro Kit (Qiagen).
RNA-Seq libraries were prepared using SMARTer® Stranded Total RNA-Seq Kit v1 - Pico Input Mammalian (Takara Bio USA/Clontech) using manufacturer's protocols

treatment_protocol: To induce Mx1-Cre expression, ~6 weeks old mice were injected intraperitoneally (i.p.) with 100 μg of polyinosinic-polycytidylic acid (pI-pC; GE Healthcare) every other day for three times

value: Bone marrow

value: Lin- cKit + BM cells


title: Young Luminal B1

value: Young

tag: subtype

value: Luminal B

tag: current age

tag: age at biobank entrance

tag: age at dx

tag: cid code

tag: clinical stage

value: II

tag: tumor relapse

tag: os

value: Alive

tag: os.time (days)

tag: Sex

value: Female

tag: race

value: Black

tag: bmi

value: Obese

tag: physical activity

value: With regularity

tag: cigarrette use

value: Never

tag: alcohol use

tag: cancer family history

value: Yes

tag: diabetes mellitus

tag: hbp

tag: dpoc

tag: gastritis

tag: first kindgree (cancer cases)

tag: first kindgree (breast/ovarian cancer cases)

tag: menopause status

tag: tubular grade

tag: nuclear grade

tag: mitotic index

tag: histologic grade

value: Positive

tag: her2 (ihc)

value: 0 (Negative)


title: Mx1-Cre; p53mut NrasG12D ; moribund, sample 1 [Mx1RG-C2153]

description: NPmut 1

tag: tissue

tag: cell type

tag: genotype

tag: treatment


title: Mx1-Cre; p53mut NrasG12D ; moribund, sample 2 [Mx1RG-C2154]

description: NPmut 2


title: AdipoKO_WAT-2 251486841477_1_4

description:
AdipoKO_WAT-2
Gene expression from white adipose tissue GR knockout mice

value: Adipose tissue

tag: Sex

value: Male


title: MTN_40

description: MTN, 3 Weeks, Batch 2

value: Mesencephalic Trigeminal Nucleus (MTN) Neurons

value: Brainstem

tag: strain

tag: age

value: 3 weeks old


title: Mx1-Cre; NrasG12D ; pI:pC treated, age-matched control 3 [Mx1G-C2427]

description: Nras G12D 3

value: Bone marrow

value: Lin- cKit + BM cells

value: Mx1-Cre; Nras G21D/+


title: CTL_WAT-4 251486841477_1_2

description:
CTL_WAT-4
Gene expression from white adipose tissue control


title: MTN_41

description: MTN, 3 Weeks, Batch 2


title: Young Luminal A4

value: Young

tag: subtype

value: Luminal A

tag: age at biobank entrance

tag: age at dx

tag: cid code

tag: clinical stage

value: II

tag: tumor relapse

value: No

tag: race

value: White

value: Overweight

tag: physical activity

tag: drug use

tag: cigarrette use

tag: alcohol use

tag: cancer family history

tag: previous surgeries

tag: diabetes mellitus

tag: hbp

tag: dpoc

tag: estrogen receptor

tag: progesterone receptor


title: AdipoKO_WAT-1 251486841477_1_3

description:
AdipoKO_WAT-1
Gene expression from white adipose tissue GR knockout mice

tag: tissue

tag: Sex


title: Mx1-Cre; p53mut NrasG12D ; moribund, sample 3 [Mx1RG-C2514]

description: NPmut 3

tag: cell type

tag: genotype

tag: treatment


title: Young Luminal A3

tag: subtype

tag: current age

tag: age at biobank entrance

tag: age at dx

tag: cid code

tag: clinical stage

tag: tumor relapse

tag: os

value: Alive

tag: os.time (days)

value: Female

tag: race

tag: bmi

value: In the past

value: Never

tag: gastritis

tag: first kindgree (cancer cases)

tag: first kindgree (breast/ovarian cancer cases)

tag: menopause status

tag: tubular grade

tag: nuclear grade

tag: mitotic index

tag: histologic grade

tag: her2 (ihc)

tag: t

tag: n

tag: m

tag: neoadjuvant treatment


title: MTN_39

description: MTN, 3 Weeks, Batch 2

tag: cell type

tag: tissue

tag: strain

tag: age


title: MTN_38

description: MTN, 3 Weeks, Batch 1


title: Mx1-Cre; NrasG12D ; pI:pC treated, age-matched control 2 [Mx1G-C2422]

description: Nras G12D 2

tag: genotype

tag: treatment


title: Young Luminal A2

tag: subtype

tag: current age

tag: age at biobank entrance

tag: age at dx

tag: cid code

tag: clinical stage

value: IV

tag: tumor relapse

value: Yes

tag: os

tag: os.time (days)

tag: Sex

tag: race

tag: bmi

tag: physical activity

tag: drug use

tag: cigarrette use

tag: alcohol use

tag: cancer family history

tag: previous surgeries

tag: diabetes mellitus

tag: hbp

tag: dpoc

tag: gastritis

tag: first kindgree (cancer cases)

tag: first kindgree (breast/ovarian cancer cases)

tag: estrogen receptor

value: Positive

tag: progesterone receptor

value: 0 (Negative)


title: Mx1-Cre; NrasG12D ; pI:pC treated, age-matched control 1 [Mx1G-C2419]

description: Nras G12D 1

tag: tissue

value: Bone marrow

tag: cell type

tag: genotype

tag: treatment


title: AdipoKO_WAT-3 251486841478_1_1

description:
AdipoKO_WAT-3
Gene expression from white adipose tissue GR knockout mice

value: Adipose tissue

tag: Sex

value: Male


title: CTL_WAT-2 251486841432_1_4

description:
CTL_WAT-2
Gene expression from white adipose tissue control


title: CTL_WAT-3 251486841477_1_1

description:
CTL_WAT-3
Gene expression from white adipose tissue control


title: Mx1-Cre; p53mut ; pI:pC treated, age-matched control 3 [Mx1R-C2517]

description: p53 mut 3

value: Lin- cKit + BM cells


title: Young Luminal A1

value: Young

tag: subtype

value: Luminal A

tag: current age

tag: age at biobank entrance

tag: age at dx

tag: cid code

tag: clinical stage

tag: tumor relapse

tag: os

tag: os.time (days)

tag: race

tag: bmi

value: Eutrophic

tag: physical activity

tag: drug use

tag: cigarrette use

value: Still in use

tag: menopause status

tag: tubular grade

tag: nuclear grade

tag: mitotic index

tag: histologic grade

tag: her2 (ihc)

tag: t

tag: n

tag: m

tag: neoadjuvant treatment


title: MTN_37

description: MTN, 3 Weeks, Batch 1

tag: cell type

value: Mesencephalic Trigeminal Nucleus (MTN) Neurons

tag: tissue

value: Brainstem

tag: strain

tag: age

value: 3 weeks old


title: Triple-negative subtype S4

description: 65 ng of miRNA were loaded into the platform.

source_name: plasma

label_protocol: ~65 ng of cf-miRNA were hybridized for 16.5 hours with molecular barcoding for 827 experimentally validated human miRNAs (from miRBase v21) using the nCounter Master Mix (NanoString® Technologies, cat. NAA-AKIT-012).

tag: subtype

value: TRIPLE-NEGATIVE

value: Elderly (diagnosed after 40yo)


title: Triple-negative subtype S3


title: Mx1-Cre; p53mut ; pI:pC treated, age-matched control 2 [Mx1R-C2485]

description: p53 mut 2

tag: genotype

tag: treatment


title: Mx1-Cre; p53mut ; pI:pC treated, age-matched control 1 [Mx1R-C2431]

description: p53 mut 1


title: MTN_34

description: MTN, 3 Weeks, Batch 1


title: Mx1-Cre; pI:pC treated, age-matched control 3 [Mx1-C2484]

description: Control 3


title: Triple-negative subtype S1

value: Young (diagnosed before 40yo)


title: MTN_33

description: MTN, 3 Weeks, Batch 1


title: Mx1-Cre; pI:pC treated, age-matched control 2 [Mx1-C2482]

description: Control 2


title: Luminal HER2 subtype S2

value: LUMINAL HER2


title: MTN_32

description: MTN, 3 Weeks, Batch 1


title: Mx1-Cre; pI:pC treated, age-matched control 1 [Mx1-C2478]

description: Control 1


title: MTN_36

description: MTN, 3 Weeks, Batch 1


title: Luminal HER2 subtype S1


title: Luminal B subtype S2

value: LUMINAL B


title: NT331_MeOH-3FA_SS-LB_F

city: Leiden

first: Remus

last: Dame

state: Zuid-Holland

address: Einsteinweg 55

department: Leiden Institute of Chemistry

country: Netherlands

institute: Leiden University

description: Escherichia coli MG1655 ΔendA cells at exponential phase in low-salt LB medium (0.08 M NaCl), at OD600 = ~1.0, treated with 5.0 M NaCl to a final concentration of 0.3 M NaCl, cells incubated for 10 minutes; Treated with 80% methanol then fixed with 3% formaldehyde (Sigma-Aldrich) in 1X HS-PBS; Ligation performed with insoluble fraction of fixed, digested chromatin; Restriction digestion performed with PsuI (ThermoFisher)

data_processing:
According to the protocol described in Hofmann, A., & Heermann, D. W. (2018). Processing and Analysis of Hi-C Data on Bacteria. In Bacterial Chromatin (pp. 19-31). Humana Press, New York, NY.
Assembly: NC_000913.3
Supplementary files format and content: Processed data files are provided as *.hic files that can be read using the open-source Juicebox software (RRID:SCR_021172) designed by the Lieberman-Aiden lab.
Supplementary files format and content: The processed data files are heat maps that show the porbability of interaction between chromosomal loci

organism: Escherichia coli str. K-12 substr. MG1655

source_name: bacterial cells in culture, in LB medium

extract_protocol:
According to the protocol described in PMID: 30109602
KAPA HyperPlus library preparation kit according to the protocol described in PMID: 30109602

tag: accession number

value: MG1655 {delta}endA

value: treated with 80% methanol followed by fixed with 3% formaldehyde, exponential culture in low-salt LB medium subjected to a hyperosmotic shock, fractionated


title: MG1655 ΔendA, fixed with 7% formaldehyde, non-fractionated

description: Escherichia coli MG1655 ΔendA cells at exponential phase (OD600 = ~1.0) in LB medium; Fixed with 7% formaldehyde (Sigma-Aldrich) in 1X PBS; Ligation was performed without enriching for the insoluble fraction of fixed, digested chromatin; Restriction digestion performed with HpaII (NEB)

data_processing:
According to the protocol described in Hofmann, A., & Heermann, D. W. (2018). Processing and Analysis of Hi-C Data on Bacteria. In Bacterial Chromatin (pp. 19-31). Humana Press, New York, NY.
Assembly: NC_000913.3
Supplementary files format and content: Processed data is provided as a NT331_7FA_NF.txt file that shows the source data for plotting the heatmap provided in the NT331_7FA_NF.png file.
Supplementary files format and content: The processed data files are heat maps that show the porbability of interaction between chromosomal loci

source_name: bacterial cells

extract_protocol:
According to the protocol described in Crémazy, F. G., Rashid, F. Z. M., Haycocks, J. R., Lamberte, L. E., Grainger, D. C., & Dame, R. T. (2018). Determination of the 3D genome organization of bacteria using Hi-C. In Bacterial Chromatin (pp. 3-18). Humana Press, New York, NY. Minor modifications were included: the restriction digestion ends of HpaII-digested chromatin was not filled in with biotin-labelled nucleotides, and NGS library preparation was performed directly after reverse cross-linking and library purification (all intervening steps were skipped).
KAPA HyperPlus library preparation kit according to the protocol described in Crémazy, F. G., Rashid, F. Z. M., Haycocks, J. R., Lamberte, L. E., Grainger, D. C., & Dame, R. T. (2018). Determination of the 3D genome organization of bacteria using Hi-C. In Bacterial Chromatin (pp. 3-18). Humana Press, New York, NY. Minor modifications were included: biotin-labelled ligation junctions were not present in the library, hence, the step describing the enrichment of biotin-labelled ligation junctions was not performed.

value: bacterial cells

value: MG1655 [delta]endA

value: bacterial cells in culture, in LB medium


title: MTN_30

description: MTN, 3 Weeks, Batch 1


title: MTN_31

description: MTN, 3 Weeks, Batch 1


title: MTN_35

description: MTN, 3 Weeks, Batch 1


title: KO DEN + PB 3

description: Gene expression in mouse liver

data_processing: Data was obtained using the Agilent Feature Extraction software (v12), using the 1-color defaults for all parameters. The Agilent Feature Extraction Software performed error modeling, adjusting for additive and multiplicative noise.

source_name: Liver, Gadd45β KO, DEN + PB, replicate 3

label_protocol: Starting with 500ng of total RNA, Cy3 labeled cRNA was produced following the manufacturer’s protocol.

extract_protocol: RNA was isolated using Trizol reagent then purified with Rneasy mini kit.

treatment_protocol: Wild type C57BL/6J and Gadd45β KO mice were treated with diethylnitrosamine (DEN) at 5 weeks of age (90 mg/kg body weight). Mice were kept between 7 to 57 weeks old with phenobarbital (PB, 0.5 g/l) in drinking water. WT DEN, WT DEN +PB, KO DEN, and KO DEN + PB groups.  4 mice for each group

tag: gender

value: male

value: 57 weeks

value: Liver

value: Gadd45b KO

value: DEN + PB


title: Triple-negative subtype S2


title: Luminal B subtype S1


title: MTN_29

description: MTN, 3 Weeks, Batch 1

value: Mesencephalic Trigeminal Nucleus (MTN) Neurons

value: Brainstem


title: KO DEN 4

description: Gene expression in mouse liver

source_name: Liver, Gadd45β KO, DEN, replicate 4

value: DEN


title: KO DEN + PB 2

description: Gene expression in mouse liver

source_name: Liver, Gadd45β KO, DEN + PB, replicate 2


title: CTL_WAT-1 251486841432_1_3

description:
CTL_WAT-1
Gene expression from white adipose tissue control

value: Adipose tissue

tag: Sex

value: Male


title: HER2 subtype S3

value: Young (diagnosed before 40yo)


title: MTN_28

description: MTN, 3 Weeks, Batch 1

value: 3 weeks old


title: KO DEN 2

description: Gene expression in mouse liver

source_name: Liver, Gadd45β KO, DEN, replicate 2


title: KO DEN + PB 4

description: Gene expression in mouse liver

source_name: Liver, Gadd45β KO, DEN + PB, replicate 4


title: NT331_MeOH-3FA_HS-LB_F

description: Escherichia coli MG1655 ΔendA cells at exponential phase (OD600 = ~1.0) in high-salt LB medium (0.3 M NaCl); Treated with 80% methanol then fixed with 3% formaldehyde (Sigma-Aldrich) in 1X HS-PBS; Ligation performed with insoluble fraction of fixed, digested chromatin; Restriction digestion performed with PsuI (ThermoFisher)

value: MG1655 {delta}endA

value: treated with 80% methanol followed by fixed with 3% formaldehyde, exponential culture in high-salt LB medium, fractionated


title: NT331_MeOH-3FA_LB-e_F

description: Escherichia coli MG1655 ΔendA cells at exponential phase (OD600 = ~1.0) in LB medium; Treated with 80% methanol then fixed with 3% formaldehyde (Sigma-Aldrich) in 1X PBS; Ligation performed with insoluble fraction of fixed, digested chromatin; Restriction digestion performed with PsuI (ThermoFisher)

value: treated with 80% methanol followed by fixed with 3% formaldehyde, exponential culture in LB medium, fractionated


title: KO DEN 3

description: Gene expression in mouse liver

source_name: Liver, Gadd45β KO, DEN, replicate 3


title: HER2 subtype S2


title: KO DEN + PB 1

description: Gene expression in mouse liver

source_name: Liver, Gadd45β KO, DEN + PB, replicate 1


title: HER2 subtype S1

value: Elderly (diagnosed after 40yo)


title: NT331_MeOH_NF

description: Escherichia coli MG1655 ΔendA cells at exponential phase (OD600 = ~1.0) in LB medium; Treated with 80% methanol; Ligation was performed without enriching for the insoluble fraction of fixed, digested chromatin; Restriction digestion performed with PsuI (ThermoFisher)

value: bacterial cells in culture, in LB medium

value: treated with 80% methanol, non-fractionated


title: NT331_MeOH_F

description: Escherichia coli MG1655 ΔendA cells at exponential phase (OD600 = ~1.0) in LB medium; Treated with 80% methanol; Ligation performed with insoluble fraction of fixed, digested chromatin; Restriction digestion performed with PsuI (ThermoFisher)

value: treated with 80% methanol, fractionated


title: KO DEN 1

description: Gene expression in mouse liver

source_name: Liver, Gadd45β KO, DEN, replicate 1

value: male

value: 57 weeks

value: Liver


title: MTN_27

description: MTN, 3 Weeks, Batch 1

source_name: Brainstem

value: Mesencephalic Trigeminal Nucleus (MTN) Neurons


title: Luminal A subtype S1

value: LUMINAL A


title: NT331_3FA-MeOH_NF

description: Escherichia coli MG1655 ΔendA cells at exponential phase (OD600 = ~1.0) in LB medium; Fixed with 3% formaldehyde (Sigma-Aldrich) in 1X PBS followed by treatment with 80% methanol; Ligation was performed without enriching for the insoluble fraction of fixed, digested chromatin; Restriction digestion performed with PsuI (ThermoFisher)

value: fixed with 3% formaldehyde followed by treatment with 80% methanol, non-fractionated


title: MTN_24

description: MTN, 3 Weeks, Batch 1

value: Brainstem


title: MTN_23

description: MTN, 3 Weeks, Batch 1


title: WT DEN + PB 4

description: Gene expression in mouse liver

source_name: Liver, wild type, DEN + PB, replicate 4

value: WT

value: DEN + PB


title: OPL2_rep2

city: Kyoto

first: Eriko

last: Kage-Nakadai

state: Kyoto

address: 53 Kawahara-cho, Shogoin, Sakyo-ku

country: Japan

institute: Koyto Univ.

data_processing:
Illumina Real-Time Analysis (RTA) software used for basecalling.
The raw reads were trimmed and quality-filtered using the Trim Galore! (ver. 0.6.5), Trimmomatic (ver. 0.39) and cutadapt (ver. 2.7) software. Clean reads were aligned versus the N2 Caenorhabditis elegans reference genome ce11 (WBcel235.98) using STAR (ver. 2.7.2b).
The read count of gene features was performed with the featureCounts tool (ver. 1.6.4)
Supplementary files format and content: ce11
Supplementary files format and content: tab-delimited text files include featureCount values for each sample

organism: Caenorhabditis elegans

source_name: Whole

extract_protocol:
Approximately 200 worms in each group were collected and soaked in RNAlater solution (Qiagen). Total RNA was isolated using the RNeasy Lipid Tissue kit (Qiagen).
mRNAs were purified using the NEBNext Poly(A) mRNA Magnetic Isolation Module. Libraries were prepared using the SMARTer® Stranded Total RNA-Seq Kit (Clontech)

treatment_protocol: Three-day-old worms were cultured for five days on mNGM plates covered with OP50 (control-fed group) or a mixture of OP50 and Lactococcus lactis NBRC 100923 or 12007.

value: Whole

tag: cell line

value: Bristol N2

value: hermaphrodite

value: wild-type

value: feeding OP50+LL 12007

tag: time

value: three-day-old


title: NT331_3FA-MeOH_F

description: Escherichia coli MG1655 ΔendA cells at exponential phase (OD600 = ~1.0) in LB medium; Fixed with 3% formaldehyde (Sigma-Aldrich) in 1X PBS followed by treatment with 80% methanol; Ligation performed with insoluble fraction of fixed, digested chromatin; Restriction digestion performed with PsuI (ThermoFisher)

value: MG1655 {delta}endA

value: bacterial cells in culture, in LB medium

value: fixed with 3% formaldehyde followed by treatment with 80% methanol, fractionated


title: MTN_22

description: MTN, 3 Weeks, Batch 1

value: 3 weeks old


title: WT DEN + PB 2

description: Gene expression in mouse liver

source_name: Liver, wild type, DEN + PB, replicate 2

value: male

value: 57 weeks

value: Liver


title: OPL2_rep1


title: NT331_3FA_NF

description: Escherichia coli MG1655 ΔendA cells at exponential phase (OD600 = ~1.0) in LB medium; Fixed with 3% formaldehyde (Sigma-Aldrich) in 1X PBS; Ligation was performed without enriching for the insoluble fraction of fixed, digested chromatin; Restriction digestion performed with PsuI (ThermoFisher)

value: fixed with 3% formaldehyde, non-fractionated


title: OPL1_rep2

value: feeding OP50+LL 100923


title: WT DEN + PB 3

description: Gene expression in mouse liver

source_name: Liver, wild type, DEN + PB, replicate 3

value: WT


title: KO_Inf_CD11c_3

description:
SAMPLE 6
50ng of total RNA was hybridized using the Mouse Immunology probeset from Nanstring which includes 561 target genes and 15 internal reference genes.

hyb_protocol: Lysates were hybridized to  Nanostring Mouse Myeloid Innate Immunity probes sets overnight per the manufacterers protocol.

scan_protocol: Samples were loaded onto the nanostring cartrisge and read using the Nanostring nCounter Sprint.

source_name: bead-enriched CD11c+ cells from lung homogenate

growth_protocol: Lung from WT or KO mice was homogenized into a singel cell suspension, CD11c-positive cells were bead enriched using Miltenyi MACS cell separation per manufacterers protocol.

extract_protocol: Whole cell lysates were directly added to the nanostring hybridization step using 5,000 cells per manufacterers protocol.

value: KO:Retnla-/-,td tomato

value: day 7 post N. Brasiliensis infection


title: WT DEN 4

description: Gene expression in mouse liver

source_name: Liver, wild type, DEN, replicate 4

value: DEN


title: WT DEN + PB 1

description: Gene expression in mouse liver

source_name: Liver, wild type, DEN + PB, replicate 1

value: DEN + PB


title: MTN_25

description: MTN, 3 Weeks, Batch 1

value: Mesencephalic Trigeminal Nucleus (MTN) Neurons

value: Brainstem


title: WT DEN 3

description: Gene expression in mouse liver

source_name: Liver, wild type, DEN, replicate 3


title: WT DEN 1

description: Gene expression in mouse liver

source_name: Liver, wild type, DEN, replicate 1


title: MTN_21

description: MTN, 3 Weeks, Batch 1


title: OPL1_rep1

value: Whole

value: Bristol N2

value: hermaphrodite

value: wild-type

value: three-day-old


title: NT331_3FA_F

description: Escherichia coli MG1655 ΔendA cells at exponential phase (OD600 = ~1.0) in LB medium; Fixed with 3% formaldehyde (Sigma-Aldrich) in 1X PBS; Ligation performed with insoluble fraction of fixed, digested chromatin; Restriction digestion performed with PsuI (ThermoFisher)

source_name: bacterial cells in culture, in LB medium

value: MG1655 {delta}endA

value: fixed with 3% formaldehyde, fractionated


title: WT DEN 2

description: Gene expression in mouse liver

source_name: Liver, wild type, DEN, replicate 2

value: male

value: 57 weeks

value: Liver


title: KO_Inf_CD11c_2

description:
SAMPLE 5
50ng of total RNA was hybridized using the Mouse Immunology probeset from Nanstring which includes 561 target genes and 15 internal reference genes.


title: MTN_20

description: MTN, 3 Weeks, Batch 1

value: 3 weeks old


title: OP50_rep2

value: feeding OP50


title: KO_Inf_CD11c_1

description:
SAMPLE 4
50ng of total RNA was hybridized using the Mouse Immunology probeset from Nanstring which includes 561 target genes and 15 internal reference genes.

value: KO:Retnla-/-,td tomato

value: day 7 post N. Brasiliensis infection


title: MTN_19

description: MTN, 3 Weeks, Batch 1


title: OP50_rep1


title: WT_Inf_CD11c_3

description:
SAMPLE 3
50ng of total RNA was hybridized using the Mouse Immunology probeset from Nanstring which includes 561 target genes and 15 internal reference genes.

value: WT


title: MTN_18

description: MTN, 3 Weeks, Batch 1

value: Mesencephalic Trigeminal Nucleus (MTN) Neurons


title: S4N

city: Bethesda

first: Joseph

middle: M

last: Ziegelbauer

state: MD

address: 10 Center Dr. 6N110

institute: NIH / National Cancer Institute

data_processing:
The reads from the FASTQ files (reads are generated by HiSeq Illumina 4000 and NovaSeq 6000) were trimmed of Illumina adapters using cutadapt  with default parameter except for --q 10 and --minimum-length 25.  We generated a ‘combined genome reference’ by catenating the human reference genome (GRCh38) and KSHV reference genome (NC009333).   The reads (average 45.9 million reads per sample) were aligned to the combined genome reference using STAR (version 2.7.8a). The transcriptome bam files created by STAR was used to estimate the read counts and Transcript per million (TPM) values at the gene level using RSEM v1.3.2. The GENCODE v30 reference gene annotation (GTF) combined with the KSHV gene annotation were used for annotation using STAR and RSEM.
Assembly: Human GRCh38 with KSHV (NC009333)
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample

source_name: Skin

extract_protocol:
Tissues were stored in RNAlater and lysed with Trizol. Tissues were homogenized and extracted for total RNA with Direct-Zol Miniprep kit (Zymo) with DNase-treatment.
Ribosomal RNA was removed, and sequencing libraries were prepared using NEBnext Ultra Low Input Total RNA with rRNA Depletion Prep (NEB).

tag: infection status

value: normal


title: S3T

value: KS lesion


title: P31

city: China Tianjin

first: Liu

last: Jinming

address: Nankai University Biological Station, Nankai District

department: School of Life Sciences

institute: Nankai University

data_processing: none provided

source_name: colorectal cancer

extract_protocol: none provided

value: colorectal cancer

value: organoids

value: cancer stem cell


title: WT_Inf_CD11c_2

description:
SAMPLE 2
50ng of total RNA was hybridized using the Mouse Immunology probeset from Nanstring which includes 561 target genes and 15 internal reference genes.


title: MTN_17

description: MTN, 3 Weeks, Batch 1

value: Brainstem


title: MTN_16

description: MTN, 3 Weeks, Batch 1


title: S3N


title: WT_Inf_CD11c_1

description:
SAMPLE 1
50ng of total RNA was hybridized using the Mouse Immunology probeset from Nanstring which includes 561 target genes and 15 internal reference genes.


title: S2T


title: P29


title: S4T


title: S2N


title: MTN_15

description: MTN, 3 Weeks, Batch 1


title: KMS11_GNE781

city: Atlanta

first: Benjamin

middle: G

last: Barwick

state: GA

address: 1365 Clifton Rd. NE WCI-C 4th Floor Benches 36-37

department: Hematology and Medical Oncology

institute: Emory University

data_processing:
FASTQ files were quality trimmed with TrimGalore! (v0.6.4) and CutAdapt (v2.5)
Quality and adapter trimmed FASTQ files were mapped to the GRCh38 reference genome using bowtie2 (v2.3.5.1)
Putative PCR duplicate reads were marked in BAM files using Samtools (v1.10)
Regions of chromatin accessibility were identified in each sample using MACS2 (v2.1.1.20160309)
The union of all accessible regions was determined and reads mapping to these regions for each sample was assessed using the ‘summarizeOverlaps’ function of the GenomicAlignments package (v1.30.0) in R (v4.1.2)
Regions that overlapped ENCODE blacklisted regions were removed.
Assembly: GRCh38 reference genome (GRCh38.d1.vd1.fa)
Supplementary files format and content: MACS2_q_0.01.union.annot.clean.cts: Raw read counts for each sample in regions of chromatin accessibility
Supplementary files format and content: MACS2_q_0.01.union.annot.clean.rppm.cov: Read per peak per million normalized reads for each sample in each chromatin accessible region

source_name: multiple myeloma

growth_protocol: RPMI 1640 supplemented with 5% FBS and 1X glutamineGlutaMAX (Gibco), without antibiotics

extract_protocol:
Nuclei isolation, transposition and DNA sequencing library preparations were performed using the protocol from Buenrostro et al. (Nature Methods 2013, PMID: 24097267)
Nuclei were tagmented with the Nextera DNA Library Prep kit (Illumina REF15028212) followed by PCR amplified, then cleaned using SPRI bead purification.

treatment_protocol: Cells were treated with 200 nM pomalidomide, 40 nM GNE-781, both, or an equivalent amount of DMSO for 48 hours

value: multiple myeloma


title: P27


title: P26


title: KMS11_Pom

value: 200 nM POM


title: MTN_14

description: MTN, 3 Weeks, Batch 1


title: P30


title: S1T


title: KMS11_ctrl

value: DMSO


title: MTN_13

description: MTN, 3 Weeks, Batch 1


title: P25


title: MTN_12

description: MTN, 3 Weeks, Batch 1


title: S1N


title: P24


title: G2T

source_name: GI


title: JJN3_GNE781


title: KMS11_Pom_GNE781

value: 200 nM POM + 40 nM GNE-781


title: P23


title: G2N


title: JJN3_Pom


title: MTN_11

description: MTN, 3 Weeks, Batch 1


title: MTN_09

description: MTN, 3 Weeks, Batch 1


title: JJN3_ctrl


title: G1T


title: P20


title: MTN_10

description: MTN, 3 Weeks, Batch 1


title: G1N


title: P8


title: MTN_07

description: MTN, 3 Weeks, Batch 1


title: P16


title: MTN_06

description: MTN, 3 Weeks, Batch 1


title: JJN3_Pom_GNE781


title: P37


title: Muscle, rAAV, VEGF-B+Pro-MSTN

city: Jyväskylä

first: Riikka

last: Kivelä

address: Rautpohjankatu 8

country: Finland

institute: University of Jyväskylä

description: 10x Genomics

data_processing:
Data filtering: UMI count < 500; gene count < 500; mitochondrial content > 10% or < 0.5%; ribosomal content < 5%; hemoglobin content > 1%; complexity score < 0.8; genes expressed in <10 cells; exclude genes with zero UMI counts; all multiplets.
Regressing cell cycle, normalization and variance stabilization using SCTRANSFORM.
Data dimmensionality reduction using PCA and UMAP
Cluster (cell type) identificadion using PCA (21 components)

source_name: TA muscle (four muscles pooled)

growth_protocol: Animals were housed under standard conditions with free access to food and water.

extract_protocol:
For single-cell RNA sequencing mononuclear cells of TA muscle were isolated and multinucleated muscle fibers were filtered out. Four TA muscles of each study group were pooled for the analysis. The tissue digestion and single-cell isolation process, including tissue mincing, collagenase digestion and filtration was conducted as previously described by us (K. A. Hemanthakumar, S. Fang, A. Anisimov, M. I. Mayranpaa, E. Mervaala, R. Kivela, Cardiovascular disease risk factors induce mesenchymal features and senescence in mouse cardiac endothelial cells. Elife 10, (2021).). Prior to scRNAseq, the cell viability was determined using an automated cell counter (Luna, Logos Biosystems).
The Chromium Single Cell 3’RNAseq run and library preparation were done using the Chromium Next GEM Single Cell 3’ Reagent Kit v3.1 chemistry according to the manufacter’s instructions.

treatment_protocol: 11-14 weeks old male mice (n=2 per group= 4 TA muscles) were injected under anesthesia with recombinant Adeno-Associated Viral Vectors (rAAV) (total 6 x 10^10 VP in 30 µl) intramuscularly in both tibialis anterior (TA) muscles according to the study group and were sacrificed after 2 weeks for single-cell RNA sequencing.

value: tibialis anterior muscle

value: Male

value: 11-14 weeks old

value: rAAV-VEGF-B+Pro-MSTN

value: TA muscle (four muscles pooled)

value: mononuclear cells


title: Muscle, rAAV, Pro-MSTN

description: 10x Genomics

value: rAAV-Pro-MSTN


title: P36


title: MTN_05

description: MTN, 3 Weeks, Batch 1

source_name: Brainstem

value: Mesencephalic Trigeminal Nucleus (MTN) Neurons

value: 3 weeks old


title: P21

value: colorectal cancer


title: MTN_04

description: MTN, 3 Weeks, Batch 1


title: Donor_I_Vd1_PD1_pos

city: London

first: Shraddha

last: Kamdar

address: Guys Hospital,Great Maze Pond, London Bridge

department: Peter Gorer Department of Immunobiology

country: United Kingdom

institute: King’s College London

description: ~13336 lysed cells in 8ul RLT buffer was hybridised to the nCounter panel at 65 degrees overnight.

hyb_protocol: 8 ul of lysed cells (except sample Donor_A_Vd1_PD1_pos where 4ul was run)  were hybridised at 65 degrees celcius overnight to NanoString's human nCounter Immune exhaustion panel

scan_protocol: Hybridized samples were processed on an nCounter prep station (NanoString Technologies) following manufacturer's instructions.

data_processing: Data were collected on an nCounter digital analyzer (NanoString Technologies), following manufacturer’s instructions. Using nSolver 4.0 (NanoString Technologies), raw counts were scaled based on the geometric mean of all positive control probes. Gene expression normalization (normalised counts) was performed relative to the geometric mean of all housekeeping genes included in the panel. The lower limit of detection was set at a normalised count of 20 which encompassed all negative control reference probes.

source_name: Human abdominal skin

growth_protocol: Cultured human skin cells expanded for a total of 6 weeks in human IL-2 and IL15:  3mm punch biopsies obtained from discarded  abdominal skin following elective plastic/reconstructive surgery were placed on tantalum coated grids and cultured in medium supplemented with human IL-2 and IL-15 for 3 weeks(Grid isolation). The cells were then taken 'off the grids' and cultured for a further 3 weeks in  medium supplemented with human IL-2 and IL-15 (expansion phase).

extract_protocol: Cells were stained with a live dead exclusion dye and human antibodies specific for PD-1, CD3, TCRab, Vd1, CD8a and Pan gd. PD-1+ and PD-1-  CD8 ab T cell and Vd1+ gd T cells were FACS sorted and lysed in RLT lysis buffer

tag: individual

value: Female

tag: cell sort and lysis

value: Following culture, cell population indicated in column A was FACS sorted and lysed in RLT at a concentration of ~1667 cells/ul


title: MTN_08

description: MTN, 3 Weeks, Batch 1

value: Brainstem


title: T-ALL _IA-15 (RNA-seq)

city: New York

first: Javier

last: Rodriguez Hernaez

state: New York

address: East 30th Street. 8th Floor

institute: NYU Langone Health

data_processing:
Read alignment: STAR aligner version 2.5.0c was used to map reads against the reference genome hg19. Only uniquely mapping reads were kept (specific parameters: --trim5p=13, --outFilterMultimapNmax 1, --outFilterMismatchNoverLmax 0.05)
Deduplication: Duplicated reads were excluded using picard-tools version 2.6.0.
Read counting: Reads were counted on a stranded gene-basis within annotated exons downloaded from Ensembl Genes V75 using the ngsutils tool bamutils count (special paramters: -uniq, -multiple complete, -library RF).
Normalization: edgeR version 3.14.0 was used to normalize read counts per sample and genes were filtered for counts-per-million > 1. CDS length from Ensembl Genes V75 was used to calculate FPKM values for filtered genes.
Assembly: hg19
Supplementary files format and content: tab delimited text file containing FPKM values for each sample

source_name: peripheral blood

extract_protocol:
RNA was extracted using the RNEasy micro kit following manufacturer's guidelines
RNA libraries for RNA-seq were prepared using Truseq library prep protocol with ribodepletion (Ribo-zero) step

value: peripheral blood

value: T-ALL


title: ETP-ALL_IA-06 (RNA-seq)

value: ETP-ALL


title: Donor_I_CD8_PD1_neg


title: Donor_H_Vd1_PD1_pos

source_name: Human breast skin


title: 2-cell embryos, ChIP-Seq, rep1

city: Zhengzhou

first: Lin-Li

last: Yang

state: Henan

address: No. 1, Jianshe East Road, Erqi District

department: department of obstetrics and gynecology

institute: The First Affiliated Hospital of Zhengzhou University

data_processing:
The original image data obtained by sequencing was converted into sequencing data through Base Calling, that is, FASTQ format, and the most original sequencing data file was obtained.
Bowtie2 was then used to filter out low-quality reads and compare them with MM10. SAMtools was used to remove data with low comparison rates, and Picard was used to remove PCR repeats.
To visualize the H3K4me3 signal in the IGV Genome Browser, the genome was divided into 50 nucleotide Windows and the RPKM for each window was calculated using DeepTools' bamCoverage function.
Assembly: GRCm39
Supplementary files format and content: bigWig, narrow peak

source_name: embryos

growth_protocol: The embryos were cultured in KSOM in vitro.

extract_protocol:
1. Cells were collected and counted at room temperature. 2. Take the required number of cells and centrifuge them in a 1.5ml EP tube at a low speed of 2,500 rpm(600 × g) at room temperature for 5 min, then discard the supernatant. 3. Add 100 μl pre-cooled NE Buffer（TD903，Vazyme） to each sample, gently blow the suspended cells with a pipette, and incubate on ice for 10 min. 4. Centrifuge at 2500rpm (600 × g) at low speed for 5 min at room temperature and discard the supernatant. 5. 100μl Wash Buffer was added to each sample.
CHIP-seq libraries were prepared using the Hyperactive Universal CUT&Tag Assay Kit for Illumina(TD903，Vazyme).

treatment_protocol: The transcript of siAcox1 group  were deleted by small-interfering-RNA(siRNA) microinjection into mouse zygotes.

value: embryos

tag: chip antibody

value: wild type

value: embryonic development


title: 2-cell embryos, ChIP-Seq, rep2


title: 2-cell embryos, siAcox1 injection, ChIP-Seq, rep1

value: gene knockdown


title: Muscle, rAAV, VEGF-B

description: 10x Genomics

value: tibialis anterior muscle

value: Male

value: 11-14 weeks old

value: rAAV-VEGF-B


title: Donor_H_Vd1_PD1_neg


title: 2-cell embryos, siAcox1 injection, ChIP-Seq, rep2


title: T-ALL_p22 (RNA-seq)

source_name: bone marrow aspirate

value: bone marrow aspirate


title: DPA_96

description: DPA

source_name: Trigeminal Ganglion

extract_protocol:
DPA and MTN neurons were labeled with 1,1'-Dioctadecyl-3,3,3',3'-tetramethylindocarbocyanine perchlorate (DiI) from the maxillary first molars of C57BL/6  mouse, then isolated in acute culture from the TG tissues and from brainstem slices, respectively. Afterwards, they were manually collected using a glass micropipette containing RNase inhibitor; each neuron was also photographed prior to collection, and the images were used for cell body area (μm2) measurements using ImageJ software.
Neurons were individually digested and reverse-transcribed into non-stranded cDNA using poly-T primers. The resulting cDNA was amplified using SMART-Seq v4 Ultra Low Input RNA kit according to the manufacturer’s instructions, but with the following modifications: 1) ERCC RNA Spike-In controls were added at the cell lysis step 2) 18 PCR cycles were performed to amplify cDNA libraries. The libraries were diluted accordingly and used to make DNA sequencing libraries by following the Nextera XT DNA Library Preparation Kit protocol. Library size distribution and quality were measured using Agilent's BioAnalyzer High Sensitivity DNA assay prior to sequencing.

value: Dental Primary Afferent (DPA) Neurons

value: Trigeminal Ganglion

value: 7 weeks old


title: Donor_I_Vd1_PD1_neg

value: Female

value: Following culture, cell population indicated in column A was FACS sorted and lysed in RLT at a concentration of ~1667 cells/ul


title: T-ALL_p21 (RNA-seq)


title: MTN_01

description: MTN, 3 Weeks, Batch 1

value: Mesencephalic Trigeminal Nucleus (MTN) Neurons

value: Brainstem

value: 3 weeks old


title: DPA_95

description: DPA


title: Muscle, rAAV, CTRL

description: 10x Genomics

value: rAAV-CTRL

value: TA muscle (four muscles pooled)

value: mononuclear cells


title: Donor_H_CD8_PD1_pos

description: ~9104 lysed cells in 8ul RLT buffer was hybridised to the nCounter panel at 65 degrees overnight.

value: Following culture, cell population indicated in column A was FACS sorted and lysed in RLT at a concentration of ~1138 cells/ul


title: Donor_H_CD8_PD1_neg


title: DPA_93

description: DPA


title: MTN_03

description: MTN, 3 Weeks, Batch 1


title: Donor_G_Vd1_PD1_neg


title: RBFOX2 size matched input (SMI) Rep2

city: Aurora

first: Nicole

middle: D

last: Moss

address: 1775 Aurora Ct

institute: University of Colorado

data_processing:
library strategy: eCLIP-Seq
Library complexity was determined using preseq v3.1.1 before analysis. Resulting sequences were analyzed using an adapted pipeline following the original eCLIP analysis pipeline (Van Nostrand et al., 2016).
Assembly: mm10
Supplementary files format and content: Normalized peaks called by clipper.

growth_protocol: Mouse insulinoma cells (MIN6) (Miyazaki et al., 1990) were maintained using standard techniques, 37ºC in 5% CO2 and passaged every 7 days. Cells were cultured in Dulbecco’s modified eagle’s medium (DMEM) with 10% FBS and 1% Penicillin-Streptomycin.

extract_protocol:
Samples were prepared using eCLIPse Bioinnovations RBP-eCLIP kit and protocol (RBP-eCLIP Protocol v1.01R, #ECK001)
Library was prepared forlling instructions from eCLIPse Bioinnovations RBP-eCLIP kit and protocol (RBP-eCLIP Protocol v1.01R, #ECK001)

treatment_protocol: MIN6 cells were grown to 70% confluence in 15cm dishes. Cells were then UV crosslinked twice on ice at 150 mJ/cm2 using Stratagene UV Stratalinker 2400.

value: insulinoma

tag: eclip antibody

value: anti-RBFOX2 rabbit polyclonal antibody (Bethyl, A300-864A)


title: T-ALL_p20 (RNA-seq)

tag: cell type

value: T-ALL


title: T-ALL_p19 (RNA-seq)

tag: tissue


title: RBFOX2 eCLIP Rep2


title: IgG size matched input (SMI) Rep2

value: anti-IgG rabbit antibody (Chemicon, PG64 25050057)


title: DPA_92

description: DPA

data_processing:
Basecalling was done with bcl2fastq v2.17. Reads were trimmed for adapters, low quality base calls, and poly-A sequence using both in-house software and cutadapt v2.10 (Martin, Marcel. 2011), and then mapped to the mouse genome (mm10) using STAR v2.7.2d (Dobin et al. 2013). Uniquely mapped reads were used for gene quantification using VERSE v0.1.4 with parameters "-s 0 -z 3 --nonemptyModified" (Zhu et al. 2016)
Assembly: mm10
Supplementary files format and content: Tab-separated values files; gene counts

tag: strain


title: ETP-ALL_p18 (RNA-seq)

value: bone marrow aspirate

value: ETP-ALL


title: ETP-ALL_p17 (RNA-seq)


title: DPA_91

description: DPA

value: Dental Primary Afferent (DPA) Neurons

value: Trigeminal Ganglion

tag: age


title: DPA_89

description: DPA

value: 7 weeks old


title: RBFOX2 size matched input (SMI) Rep1


title: RBFOX2 eCLIP Rep1


title: ETP-ALL_p16 (RNA-seq)


title: Donor_F_Vd1_PD1_pos

description: ~16000 lysed cells in 8ul RLT buffer was hybridised to the nCounter panel at 65 degrees overnight.

value: Female

value: Following culture, cell population indicated in column A was FACS sorted and lysed in RLT at a concentration of ~2000 cells/ul


title: IgG eCLIP Rep2


title: IgG size matched input (SMI) Rep1


title: Donor_F_Vd1_PD1_neg


title: T-ALL_p14 (RNA-seq)

source_name: Pleural fluid

value: Pleural fluid


title: DPA_90

description: DPA


title: Donor_E_Vd1_PD1_pos


title: Donor_F_CD8_PD1_neg


title: DPA_88

description: DPA


title: IgG eCLIP Rep1


title: Donor_E_CD8_PD1_pos


title: T-ALL_p13 (RNA-seq)


title: DPA_86

description: DPA


title: T-ALL_p12 (RNA-seq)


title: ETP-ALL_p15 (RNA-seq)

value: peripheral blood


title: Donor_D_Vd1_PD1_pos


title: P0_HP_Rnf2_cKO_rep2

city: wuhan

first: zhao

last: chen

state: Hubei

address: shuiguohu

department: BIOLOGY

institute: wuhan university

data_processing:
Sequence reads were trimmed for adaptor sequence/low-quality sequence using Cutadapt (parameter: )
Trimmed sequence reads were mapped to UCSC genome GrCM38/mm10 using STAR (parameters: default)
The gene expression level was calculated by Cufflinks (version 2.2.1, http://cole-trapnell-lab.github.io/ cufflinks) and normalized by fragments per kilobase of bin per million mapped reads (FPKM).
Principal component analysis (PCA) of the quality control matrices was employed to determine the presence of RNA-Seq sample outliers.
Differentially expressed genes are defined by DESeq2 as ones with the p value less than 0.05.
Assembly: mm10
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

source_name: Hippocampus

extract_protocol:
RNA isolation was performed using the RNAiso Plus (TAKARA) according to manufacturer’s instructions.
RNA libraries for RNA-seq were prepared using NEBNext® Ultra™ II RNA Library Prep Kit for Illumina® following manufacturer's protocols.

treatment_protocol: Cortex were collected from P0 Kdm2b-ctrl and Kdm2b-cKO mice; hippocampus tissues  were collected from P0 Rnf2-ctrl and Rnf2-cKO mice.

value: postnatal Day 0

value: Hippocampus


title: P0_HP_Rnf2_cKO_rep1


title: MTN_26

description: MTN, 3 Weeks, Batch 1

value: Mesencephalic Trigeminal Nucleus (MTN) Neurons

value: Brainstem

value: 3 weeks old


title: DPA_85

description: DPA


title: T-ALL_p11 (RNA-seq)


title: P0_HP_Rnf2_Ctrl_rep2

value: Rnf2fl/+ or Rnf2fl/fl


title: DPA_84

description: DPA


title: DPA_87

description: DPA


title: T-ALL_p10 (RNA-seq)

source_name: pleural fluid

value: pleural fluid

value: T-ALL


title: T-ALL_p09 (RNA-seq)


title: P0_Cortex_Kdm2b_cKO_rep2

source_name: Cortex

value: cKO

value: Cortex


title: Donor_D_CD8_PD1_pos


title: T-ALL_p08 (RNA-seq)

value: bone marrow aspirate


title: Donor_D_Vd1_PD1_neg


title: DPA_83

description: DPA

value: Dental Primary Afferent (DPA) Neurons

value: Trigeminal Ganglion


title: Donor_D_CD8_PD1_neg

value: Female


title: DPA_81

description: DPA

value: 7 weeks old


title: T-ALL_p07 (RNA-seq)

source_name: unknown

value: unknown


title: Donor_E_CD8_PD1_neg

value: Following culture, cell population indicated in column A was FACS sorted and lysed in RLT at a concentration of ~2000 cells/ul


title: P0_Cortex_Kdm2b_cKO_rep1

value: postnatal Day 0


title: P0_HP_Rnf2_Ctrl_rep1

value: Hippocampus


title: Donor_C_Vd1_PD1_neg

description:
Donor_C_Vd1_PD1_neg
~13576 lysed cells in 8ul RLT buffer was hybridized to the nCounter panel at 65 degrees overnight.

hyb_protocol: 8 ul of lysed cells (except sample RFD02_Vd1_PD1_pos where 4ul was run)  were hybridized at 65 degrees Celsius overnight to NanoString's human nCounter Immune exhaustion panel NanoString's human immune exhaustion panel run on the nCounter Max platform

data_processing: Data were collected on an nCounter digital analyzer (NanoString Technologies), following manufacturer’s instructions. Using nSolver 4.0 (NanoString Technologies), raw counts were scaled based on the geometric mean of all positive control probes. Gene expression normalization (normalized counts) was performed relative to the geometric mean of all housekeeping genes included in the panel. The lower limit of detection was set at a normalized count of 20 which encompassed all negative control reference probes.

extract_protocol: Following culture, cell population was stained with a live dead exclusion dye and human antibodies specific for PD-1, CD3, TCRab, Vd1, CD8a and Pan gd. PD-1+ and PD-1-  CD8 ab T cell and Vd1+ gd T cells were FACS sorted and lysed in RLT lysis buffer at an approximate concentration of 1660 cells/ul except Donor_A_CD8_PD1_pos which was lysed in RLT buffer at ~958 cells/ul

value: Donor C

value: Following culture, cell population indicated in column A was FACS sorted and lysed in RLT at a concentration of ~1670 cells/ul


title: P0_Cortex_Kdm2b_Ctrl_rep2

value: Kdm2bfl/+ or Kdm2bfl/fl

value: Ctrl


title: DPA_80

description: DPA


title: Donor_C_CD8_PD1_pos

description:
Donor_C_CD8_PD1_pos
~12920 lysed cells in 8ul RLT buffer was hybridized to the nCounter panel at 65 degrees overnight.

value: Following culture, cell population indicated in column A was FACS sorted and lysed in RLT at a concentration of ~1615 cells/ul


title: T-ALL_p06 (RNA-seq)

value: T-ALL


title: T-ALL_p05 (RNA-seq)

value: peripheral blood


title: DPA_78

description: DPA


title: DPA_79

description: DPA


title: P0_Cortex_Kdm2b_Ctrl_rep1

value: Cortex


title: ETP-ALL_p04 (RNA-seq)

value: bone marrow aspirate

value: ETP-ALL


title: DPA_76

description: DPA

value: Dental Primary Afferent (DPA) Neurons

value: Trigeminal Ganglion


title: T-ALL_p03 (RNA-seq)


title: Neurosphere, cKO, rep2

data_processing:
Sequence reads were trimmed for adaptor sequence/low-quality sequence using Cutadapt (parameter: )
Trimmed sequence reads were mapped to UCSC genome GrCM38/mm10 using STAR (parameters: default)
The gene expression level was calculated by Cufflinks (version 2.2.1, http://cole-trapnell-lab.github.io/ cufflinks) and normalized by fragments per kilobase of bin per million mapped reads (FPKM).
Principal component analysis (PCA) of the quality control matrices was employed to determine the presence of RNA-Seq sample outliers.
Differentially expressed genes are defined by DESeq2 as ones with the p value less than 0.05.
Assembly: mm10
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

source_name: NPC

growth_protocol: Ctrl and cKO mice hippocampal neural progenitor cells (NPCs) were enriched from P0 mouse hippocampi, cultured on ultra-low-attachment plates and maintained in indicated culture media (DMEM/F12, Life Technologies) containing N2 and B27 supplements (1×, Life Technologies), 1mM Na-pyruvate, 1 mM N-acetyl-L-cysteine (NAC), human recombinant FGF2, and EGF (20 ng/mL each; Life Technologies) with 5% CO2 at 37C

treatment_protocol: Hippocampus tissues were collected from P0 ctrl and cKO mice, NPCs were enriched from P0 mouse hippocampi.

value: NPC

value: cKO


title: Neurosphere, cKO, rep1


title: DPA_82

description: DPA

value: 7 weeks old


title: Donor_B_Vd1_PD1_pos

description:
Donor_B_Vd1_PD1_pos
~13340 lysed cells in 8ul RLT buffer was hybridized to the nCounter panel at 65 degrees overnight.

value: Donor B

value: Female

value: Following culture, cell population indicated in column A was FACS sorted and lysed in RLT at a concentration of ~1660 cells/ul


title: Donor_C_Vd1_PD1_pos

description:
Donor_C_Vd1_PD1_pos
~13536 lysed cells in 8ul RLT buffer was hybridized to the nCounter panel at 65 degrees overnight.

value: Donor C

value: Following culture, cell population indicated in column A was FACS sorted and lysed in RLT at a concentration of ~1690 cells/ul


title: Donor_B_Vd1_PD1_neg

description:
Donor_B_Vd1_PD1_neg
~13336 lysed cells in 8ul RLT buffer was hybridized to the nCounter panel at 65 degrees overnight.


title: T-ALL_p01 (RNA-seq)


title: DPA_75

description: DPA


title: DPA_74

description: DPA


title: T-ALL_p02 (RNA-seq)


title: Donor_B_CD8_PD1_pos

description:
Donor_B_CD8_PD1_pos
~13248 lysed cells in 8ul RLT buffer was hybridized to the nCounter panel at 65 degrees overnight.


title: Neurosphere, Ctrl, rep1

value: Kdm2bfl/+ or Kdm2bfl/fl

value: Ctrl

value: postnatal Day 0


title: Hippocampus, cKO, rep3

value: Hippocampus


title: Donor_B_CD8_PD1_neg

description:
Donor_B_CD8_PD1_neg
~13336 lysed cells in 8ul RLT buffer was hybridized to the nCounter panel at 65 degrees overnight.


title: CUTLL3, rep1 (RNA-seq)


title: Donor_A_Vd1_PD1_pos

description:
Donor_A_Vd1_PD1_pos
~6400 lysed cells in 4ul RLT buffer was hybridized to the nCounter panel at 65 degrees overnight.

value: Donor A

value: Following culture, cell population indicated in column A was FACS sorted and lysed in RLT at a concentration of ~1600 cells/ul


title: Loucy, rep4 (RNA-seq)

source_name: Loucy

value: Loucy

value: ETP-ALL

value: DMSO


title: Hippocampus, cKO, rep1


title: Hippocampus, cKO, rep2


title: DPA_72

description: DPA

value: Dental Primary Afferent (DPA) Neurons

value: Trigeminal Ganglion


title: Donor_A_Vd1_PD1_neg

description:
Donor_A_Vd1_PD1_neg
~13336 lysed cells in 8ul RLT buffer was hybridized to the nCounter panel at 65 degrees overnight.


title: DPA_70

description: DPA

value: 7 weeks old


title: Loucy, rep3 (RNA-seq)


title: Hippocampus, Ctrl, rep3


title: DPA_69

description: DPA


title: NT331_MeOH-3FA_LS-LB_F

description: Escherichia coli MG1655 ΔendA cells at exponential phase (OD600 = ~1.0) in low-salt LB medium (0.08 M NaCl); Treated with 80% methanol then fixed with 3% formaldehyde (Sigma-Aldrich) in 1X LS-PBS; Ligation performed with insoluble fraction of fixed, digested chromatin; Restriction digestion performed with PsuI (ThermoFisher)

source_name: bacterial cells in culture, in LB medium

value: MG1655 {delta}endA

value: treated with 80% methanol followed by fixed with 3% formaldehyde, exponential culture in low-salt LB medium, fractionated


title: Loucy, rep2 (RNA-seq)


title: Donor_A_CD8_PD1_neg

description:
Donor_A_CD8_PD1_neg
~13336 lysed cells in 8ul RLT buffer was hybridized to the nCounter panel at 65 degrees overnight.

value: Female

value: Following culture, cell population indicated in column A was FACS sorted and lysed in RLT at a concentration of ~1660 cells/ul


title: Hippocampus, Ctrl, rep2


title: DPA_68

description: DPA


title: Neurosphere, Ctrl, rep2

value: NPC


title: DPA_73

description: DPA


title: Donor_G_CD8_PD1_neg

value: Following culture, cell population indicated in column A was FACS sorted and lysed in RLT at a concentration of ~1667 cells/ul


title: Loucy, rep1 (RNA-seq)


title: DPA_67

description: DPA


title: Hippocampus, Ctrl, rep1

value: Kdm2bfl/+ or Kdm2bfl/fl

value: Ctrl


title: P0-Neurosphere_Ctrl-Input_rep2

description: Neurosphere, Ctrl, Input, rep2

data_processing:
All P0 hippocampus and neurosphere ChIP-seq data were detected and remove adaptors using Cutadapt.
ChIP-seq reads were aligned to the UCSC mm10 genome using Bowtie version 2.4.5.
To create ChIP-seq coverage plots, the locations of the mapped ChIP-seq reads were extended to 10 bp to represent sequenced fragments, renormalized (Reads Per Kilobase per Million mapped reads, rpkm) and reformatted in the bigWig file format.
Regions of peaks were called using the SICER software package, with the input genomic DNA as a background control.
Assembly: UCSC mm10
Supplementary files format and content: sicer call Peak bed file (except for Input sample)

source_name: Neurosphere

extract_protocol:
Cells were fixed with 1% formaldehyde for 10 minutes. After digested by micrococcal nuclease, cell lysis was sonicated in EP tubes with power output 100 W, 5 min, 0.5 s on, 0.5 s off on ice.
ChIP-seq libraries were constructed by VAHTS Universal DNA Library Prep Kit for Illumina V3 (Vazyme ND607). 5 ng of DNA was used as starting material for input and ip samples. Libraries were amplified using 10 cycles on the thermocycler. Post amplification libraries were size selected at about 300 bp in length using VAHTS DNA Clean Beads (Vazyme N411). The concentration and quality of DNA was measured with an Agilent 2100 Bioanalyzer.

value: Neurosphere


title: DPA_65

description: DPA


title: P0-Neurosphere_Ctrl-Input_rep1

description: Neurosphere, Ctrl, Input, rep1


title: Donor_A_CD8_PD1_pos

description:
Donor_A_CD8_PD1_pos
~7664 lysed cells in 8ul RLT buffer was hybridized to the nCounter panel at 65 degrees overnight.

value: Donor A

value: Following culture, cell population indicated in column A was FACS sorted and lysed in RLT at a concentration of ~958 cells/ul


title: DPA_64

description: DPA


title: P0-Neurosphere_Ctrl-H3K36me2_rep1

description: Neurosphere, H3K36me2, rep1


title: DPA_63

description: DPA


title: Blood-NK-WTM-CGC063

city: Paris

first: Nicolas

last: Huot

address: 28, rue du Dr Roux

institute: Institut Pasteur

hyb_protocol: Seventy microliters of hybridization buffer was added to the reporter code set to make a master mixture. 2,1µl of proteinase K were added. Eight microliters of this master mixture was then incubated in separate tubes with 5µl of the lysate's sample and 2 ul of the capture code set. This hybridization mixture was incubated at 65°C for 18 hours. The hybridization mixture bind to Cartridge with a NanoString Prepstation.

scan_protocol: The cartridgenCounter™ Analysis System allows then to collect image and count barcodes.

data_processing:
Raw counts were normalized to geometric mean counts of the synthetic positive controls included on the codeset. nCAAM and the geNorm algorithm was used to normalize each dataset by taking the five most stable housekeeping genes across samples and using it on all datasets.
Data were analyzed by ROSALIND® (https://rosalind.bio/), with a HyperScale architecture developed by ROSALIND, Inc. (San Diego, CA). Read Distribution percentages, violin plots, identity heatmaps, and sample MDS plots were generated as part of the QC step. Normalization, fold changes and p-values were calculated using criteria provided by Nanostring. ROSALIND® follows the nCounter® Advanced Analysis protocol of dividing counts within a lane by the geometric mean of the normalizer probes from the same lane. Housekeeping probes to be used for normalization are selected based on the geNorm algorithm as implemented in the NormqPCR R library.

organism: Macaca fascicularis

source_name: Peripheral blood mononuclear cells

label_protocol: The system uses molecular “barcodes” and single molecule imaging to detect and count hundreds of unique transcripts in a single reaction.

growth_protocol: Simian NKG2a/c+ NK cells were isolated to a purity exceeding 90% from both BALF and blood samples using positive selection with antibody-coated magnetic beads from Miltenyi Biotec.To achieve this, we utilized the anti-NKG2A PE-conjugated monoclonal antibody (clone Z199, Beckman Coulter Life Sciences, USA). All steps of cell staining and selection were executed in strict accordance with the supplier's instructions.

extract_protocol: The cells were resuspended in 30µl of RLT buffer with beta-mercaptoethanol (Qiagen) following the Nanostring protocols recommendation for cell Lysate (MAN-10051-05).

value: NKG2a/c+ NK cells

tag: viral status

value: >461 days post infection with the wild type Wuhan strain


title: Blood-NK-WTM-CGC025


title: DPA_62

city: Philadelphia

first: Junhyong

last: Kim

address: 433 S University Avenue

institute: University of Pennsylvania

description: DPA


title: Blood-NK-WTM-CGD001


title: Blood-NK-WTM-CGB105


title: P0-Neurosphere_Ctrl-H3K27me3_rep1

description: Neurosphere, H3K27me3, rep1

tag: genotype


title: Blood-NK-WTM-CGB090


title: Blood-NK-WTM-CGB065


title: DPA_61

description: DPA


title: DPA_60

description: DPA


title: Blood-NK-WTM-CGB063


title: Blood-NK-WTM-CGB060


title: DPA_66

description: DPA


title: DPA_58

description: DPA


title: P0-Neurosphere_Ctrl-H2AK119Ub1_rep1

description: Neurosphere, H2AK119Ub1, rep1

tag: treatment


title: Blood-NK-WTM-CGB048


title: P0-Neurosphere_cKO-Input_rep2

description: Neurosphere, cKO, Input, rep2

value: cKO


title: DPA_57

description: DPA

value: Dental Primary Afferent (DPA) Neurons


title: P0-Neurosphere_Ctrl-H3K36me2_rep2

description: Neurosphere, H3K36me2, rep2


title: Blood-NK-WTM-CGA036


title: P0-Neurosphere_cKO-Input_rep1

description: Neurosphere, cKO, Input, rep1


title: DPA_55

description: DPA

value: Trigeminal Ganglion


title: P0-Neurosphere_cKO-H3K36me2_rep2

description: Neurosphere, H3K36me2, rep2


title: P0-Neurosphere_Ctrl-H3K27me3_rep2

description: Neurosphere, H3K27me3, rep2


title: DPA_52

description: DPA

value: 7 weeks old


title: Blood-NK-WTM-CFL103


title: DPA_53

description: DPA


title: Blood-NK-WTM-CU494


title: P0-Neurosphere_cKO-H3K27me3_rep2

description: Neurosphere, H3K27me3, rep2


title: P0-Neurosphere_Ctrl-H2AK119Ub1_rep2

description: Neurosphere, H2AK119Ub1, rep2


title: P0-Neurosphere_cKO-H3K36me2_rep1

description: Neurosphere, H3K36me2, rep1


title: DPA_50

description: DPA


title: DPA_49

description: DPA


title: DPA_48

description: DPA


title: P0-Neurosphere_cKO-H3K27me3_rep1

description: Neurosphere, H3K27me3, rep1


title: P0-Neurosphere_cKO-H2AK119Ub1_rep1

description: Neurosphere, H2AK119Ub1, rep1


title: IB111 cell line, GSK595 10 days, rep3

city: Bordeaux

first: Amandine

last: Crombe

address: 229 cours de l'Argonne

institute: Institut Bergonié

data_processing:
reads with low quality bases at 5’ and 3’ were trimmed using the Sickle package (Phred cut off 20, max trim size 30 nc)
The SeqPrep package was used to remove sequencing adaptors from raw reads
An home-made python script was developed that split those merged reads into new non-overlapping R1 and R2 paired-end reads
Curated reads were aligned using TOPHAT2 (based on aka BOWTIE2) on both the UCSC hg19 reference genome and transcriptome
post-alignment quality control of aligned reads by removing reads with mapping scores lower than 20 using Samtools (5). PCR duplicate reads were identified and removed using Picard MarkDuplicates (https://broadinstitute.github.io). Read counts were generated performed using the Python module HTSeq
Transcript count data were normalized according the VOOM method
The RNAseq differential gene expression between groups of samples was performed using the statistical t-test from the R package LIMMA
We defined the significantly up- or down-regulated transcripts using an FDR threshold of 0.05. The fold-change used to further filter the differential gene expression was set to a minimum value of 2
Assembly: hg19
Supplementary files format and content: tab-delimited text file of raw counts matrix
Supplementary files format and content: tab delimited text file of diffenrential expression results

growth_protocol: IB111 cells were maintained in RPMI medium 1640 GlutaMAX Supplement in the presence of 10% fetal bovine serum and 1% penicillin/streptomycin at 37°C in a humidified atmosphere containing 5% CO2

extract_protocol:
RNA was extracted using an RNeasy Plus Mini Kit (Qiagen). The purity and concentration of the isolated RNA were determined with a NanoDrop spectrophotometer, and capillary electrophoresis using a Bioanalyzer 2100 was carried out to determine the RNA integrity number (RIN).
RNA libraries were prepared using NEBNext® Ultra™ II mRNA-Seq library kit paired-end 100x2 read protocol

treatment_protocol: IB111 cells were untreated or treated with GSK595 at the IC50 every 3 days for 10 days

value: dedifferentiated liposarcoma

value: WT

value: GSK595 IC50 10 days


title: BALF-NK-WTM-CFL103

source_name: Bronchoalveolar lavage fluids


title: BALF-NK-WTM-CGB060


title: BALF-NK-WTM-CGB063


title: P0-Hippocampus_Ctrl-Input_rep2

description: Hippocampus, Ctrl, Input, rep2

value: Hippocampus


title: DPA_47

description: DPA


title: DPA_46

description: DPA


title: IB111 cell line, GSK595 10 days, rep2


title: BALF-NK-WTM-CGD001


title: BALF-NK-WTM-CGC063


title: BALF-NK-WTM-CU494


title: BALF-NK-WTM-CGB105


title: IB111 cell line, GSK595 10 days, rep1


title: Donor_C_CD8_PD1_neg

description:
Donor_C_CD8_PD1_neg
~13336 lysed cells in 8ul RLT buffer was hybridized to the nCounter panel at 65 degrees overnight.

source_name: Human abdominal skin

value: Donor C

value: Female

value: Following culture, cell population indicated in column A was FACS sorted and lysed in RLT at a concentration of ~1660 cells/ul


title: BALF-NK-WTM-CGC025


title: DPA_44

description: DPA


title: P0-Hippocampus_Ctrl-Input_rep1

description: Hippocampus, Ctrl, Input, rep1

value: Kdm2bfl/+ or Kdm2bfl/fl

value: Ctrl


title: P0-Hippocampus_Ctrl_H3K36me2_rep2

description: Hippocampus, H3K36me2, rep2


title: DPA_45

description: DPA


title: P0-Neurosphere_cKO-H2AK119Ub1_rep2

description: Neurosphere, H2AK119Ub1, rep2

value: Neurosphere


title: IB111 cell line, Control, rep3

value: Vehicle


title: P0-Hippocampus_Ctrl_H3K36me2_rep1

description: Hippocampus, H3K36me2, rep1


title: BALF-NK-WTM-CGB090

value: NKG2a/c+ NK cells


title: IB111 cell line, Control, rep2


title: DPA_42

description: DPA


title: DPA_41

description: DPA


title: IB111 cell line, Control, rep1


title: P0-Hippocampus_Ctrl_H3K36me2_Input_rep1

description: Hippocampus, Ctrl, H3K36me2, Input, rep1


title: P0-Hippocampus_Ctrl-H3K27me3_rep2

description: Hippocampus, H3K27me3, rep2


title: PM2.5_nasal epithelial cell 3

city: Shanghai

first: Hai

last: Lin

state: Shanghai

address: No. 600, Yishan Road, Xuhui District

institute: Shanghai Sixth People's Hospital Affiliated to Shanghai Jiao Tong University School of Medicine

data_processing:
Raw reads were filtered with Seqtk to remove adaptor sequence and low-quality sequence.
Genome mapping was performed by "splices mapping" algorithm in Hista2 (version:2.0.4).
Annotation genome used was GRCh38.p4 (hg38).
Assembly: mm10
Supplementary files format and content: tab-delimited text files include count and RPKM values for each Sample

source_name: nasal epithelial cell

growth_protocol: HNEC were collected by means of epithelial scrapings of uncinate process (UP) from three subjects without chronic rhinosinusitis undergoing skull base surgery with a Rhinoprobe (Arlington Scientific, Springville, Utah) during surgery and were cultured under air-liquid interface (ALI) conditions.

extract_protocol:
RNA was extracted using MagBeads Total RNA Extraction Kit（Cat#T02-096) following manufacturer's protocols.
RNA libraries for RNA-seq were prepared using VAHTS Universal V6 RNA-seq Library Prep Kit for Illumina® following manufacturer's protocols.

treatment_protocol: Cells were treated with 2mL 100 μg/ml PM2.5 or same amount of normal culture medium for 24h.

value: nasal epithelial cell


title: PM2.5_nasal epithelial cell 2


title: DPA_39

description: DPA


title: DPA_37

description: DPA


title: PM2.5_nasal epithelial cell 1


title: P0-Hippocampus_Ctrl-H3K27me3_rep1

description: Hippocampus, H3K27me3, rep1


title: BALF-NK-WTM-CGA036

value: >461 days post infection with the wild type Wuhan strain


title: BALF-NK-WTM-CGB048


title: P0-Hippocampus_Ctrl-H2AK119ub1_rep2

description: Hippocampus, H2AK119ub1, rep2


title: DPA_36

description: DPA

value: Dental Primary Afferent (DPA) Neurons


title: BALF-NK-HC-DD7737

value: Healthy Control


title: P0-Hippocampus_Ctrl_H3K36me2_Input_rep2

description: Hippocampus, Ctrl, H3K36me2, Input, rep2


title: P0-Hippocampus_cKO-Input_rep2

description: Hippocampus, cKO, Input, rep2

value: cKO


title: DPA_35

description: DPA

value: Trigeminal Ganglion

value: 7 weeks old


title: BALF-NK-WTM-CGB065


title: Control_nasal epithelial cell 2

value: Control


title: BALF-NK-WTM-DB331


title: DPA_34

description: DPA


title: BALF-NK-WTM-CGC058


title: Control_nasal epithelial cell 1


title: BALF-NK-WTM-CGC026


title: P0-Hippocampus_Ctrl-H2AK119ub1_rep1

description: Hippocampus, H2AK119ub1, rep1

value: Hippocampus


title: DPA_40

description: DPA


title: P0-Hippocampus_cKO-Input_rep1

description: Hippocampus, cKO, Input, rep1


title: S10T

source_name: Skin

value: KS lesion


title: DPA_33

description: DPA


title: BALF-NK-WTM-CGB063


title: DPA_32

description: DPA


title: P0-Hippocampus_cKO_H3K36me2_rep2


title: S10N

value: normal


title: DPA_31

description: DPA


title: Control_nasal epithelial cell 3


title: S9T


title: P0-Hippocampus_cKO_H3K36me2_rep1


title: DPA_30

description: DPA


title: P0-Hippocampus_cKO_H3K36me2_Input_rep2

description: Hippocampus, H3K36me2, Input, rep2


title: BALF-NK-WTM-CGB105


title: BALF-NK-WTM-CGB060


title: P0-Hippocampus_cKO_H3K36me2_Input_rep1

description: Hippocampus, H3K36me2, Input, rep1


title: BALF-NK-WTM-CFL103


title: DPA_29

description: DPA


title: S8N


title: DPA_28

description: DPA


title: P0-Hippocampus_cKO-H3K27me3_rep2

description: Hippocampus, H3K27me3, rep2


title: S8T


title: P0-Hippocampus_cKO-H3K27me3_rep1

description: Hippocampus, H3K27me3, rep1


title: BALF-NK-WTM-CGA036


title: S7T


title: BALF-NK-WTM-CGB048


title: BALF-NK-HC-2NS18


title: P0-Hippocampus_cKO-H2AK119ub1_rep2

description: Hippocampus, H2AK119ub1, rep2


title: DPA_26

description: DPA


title: BALF-NK-WTM-CGB065


title: S7N


title: DPA_24

description: DPA


title: P0-Hippocampus_cKO-H2AK119ub1_rep1

description: Hippocampus, H2AK119ub1, rep1


title: S6T


title: S9N


title: BALF-NK-WTM-CGC025


title: S6N


title: DPA_23

description: DPA


title: Hippocampus, ATAC, Ctrl, rep2

data_processing:
P0 hippocampus ATAC-seq raw data were trimmed by Cutadapt with parameters -u 3 -u -75 -U 3 -U -75 -m 30 and then aligned to mouse mm10 genome using Bowtie2 (-X 2000 --very-sensitive).
We removed mitochondrial reads after alignment using Samtools.
Then, we filtered reads to remove exact copies of DNA fragments that arise during PCR using Picard’s MarkDuplicates (version 2.26.4) software.
We adjusted the shift read alignment using alignmentSieve.
peaks were called by Macs2 (version 2.2.7.1) with parameters -f BAMPE --nomodel --keep-dup all --shift -100 --extsize 200 -g mm --cutoff-analysis -B.
Assembly: UCSC mm10
Supplementary files format and content: narrowPeak

source_name: neural progenitor cells (NPCs)

growth_protocol: Hippocampus tissues were collected from P0 ctrl and cKO mice.

extract_protocol:
P0 hippocampi were dissected. and gently homogenized in cold nuclear isolation buffer (10 mM Tris-HCl, pH 7.4, 10 mM NaCl, 3 mM MgCl2, 0.1% Igepal CA-630). The nuclei are collected by centrifugal precipitation.
ATAC-seq libraries were constructed by TruePrep DNA Library Prep Kit V2 for Illumina (Vazyme TD501).
50,000 nuclei were put into the tagmentation reaction for each sample (performed with 30 min incubation time at 37°C). Immediately following the tagmentation, we purified DNA fragments using VAHTS DNA Clean Beads (2X). We took purified DNA fragments and added Illumina i5+i7 adapters with unique index to individual samples by PCR reaction (PCR program: 72°C for 3 min, 98°C for 30 s, 98°C for 15 s, 60°C for 30 s, 72°C for 30 s, repeat 3-5 for 13 cycles, 72°C for 5 min, and hold at 4°C). Generated libraries were purified using VAHTS DNA Clean Beads (1.2X). For multiplexing, libraries with different barcode were mixed together with equal molar quantities by considering appropriate sequencing depth (about 50 million reads per library). Libraries were sequenced by Illumina Nova-seq 6000 platform with pair-end reads of 150 bp.

value: neural progenitor cells (NPCs)

value: postnatal Day 0


title: DPA_25

description: DPA


title: S5T

data_processing:
The reads from the FASTQ files (reads are generated by HiSeq Illumina 4000 and NovaSeq 6000) were trimmed of Illumina adapters using cutadapt  with default parameter except for --q 10 and --minimum-length 25.  We generated a ‘combined genome reference’ by catenating the human reference genome (GRCh38) and KSHV reference genome (NC009333).   The reads (average 45.9 million reads per sample) were aligned to the combined genome reference using STAR (version 2.7.8a). The transcriptome bam files created by STAR was used to estimate the read counts and Transcript per million (TPM) values at the gene level using RSEM v1.3.2. The GENCODE v30 reference gene annotation (GTF) combined with the KSHV gene annotation were used for annotation using STAR and RSEM.
Assembly: Human GRCh38 with KSHV (NC009333)
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample


title: Hippocampus, ATAC, Ctrl, rep1

value: Kdm2bfl/+ or Kdm2bfl/fl

value: Ctrl


title: DPA_22

description: DPA


title: DPA_21

description: DPA


title: BALF-NK-WTM-CGC063


title: Hippocampus, ATAC, cKO, rep2


title: BALF-NK-WTM-CGB090


title: Rbfox2-mutant 8wk mouse islets [828]

data_processing:
Sequence reads were trimmed for adaptor sequence/low-quality sequence using cutadapt
Trimmed sequence reads were mapped to mm10 using STAR Aligner
Read count was determined using featureCounts
Assembly: mm10
Supplementary files format and content: txt file containing read counts for each sample, rMATS splicing analysis Rbfox2_islet_rMATs.csv

molecule: polyA RNA

source_name: islets

growth_protocol: Experiments in this study were conducted on 8-week-old adult male and female mice. Islets were collected from Pdx1:CRE; Rbfox2 fl/fl mutant mice and Rbfox2 fl/fl non-cre control mice and rested overnight before RNA extraction.

extract_protocol:
Total RNA was extracted using the RNEasy Plus Mini Kit (Qiagen).
Libraries were prepared using Universal Plus™ mRNA-Seq library preparation kit with NuQuant

value: M

value: islets

value: Pdx1:CRE; Rbfox2 fl/fl

value: mutant


title: Hippocampus, ATAC, cKO, rep1


title: G12T

source_name: GI

extract_protocol:
Tissues were stored in RNAlater and lysed with Trizol. Tissues were homogenized and extracted for total RNA with Direct-Zol Miniprep kit (Zymo) with DNase-treatment.
Ribosomal RNA was removed, and sequencing libraries were prepared using NEBnext Ultra Low Input Total RNA with rRNA Depletion Prep (NEB).


title: G12N


title: DPA_18

description: DPA

source_name: Trigeminal Ganglion

value: Dental Primary Afferent (DPA) Neurons


title: DPA_19

description: DPA


title: BALF-NK-WTM-CGD001

value: NKG2a/c+ NK cells

value: >461 days post infection with the wild type Wuhan strain


title: DPA_17

description: DPA

value: Trigeminal Ganglion


title: BALF-NK-WTM-CU494


title: Rbfox2-mutant 8wk mouse islets [827]


title: G11T


title: BALF-NK-HC-DD240

value: Healthy Control


title: BALF-NK-HC-DD130


title: BALF-NK-HC-IPU18


title: DPA_16

description: DPA

value: 7 weeks old


title: Rbfox2-mutant 8wk mouse islets [825]

value: F


title: G11N


title: S5N


title: BALF-MP-OM-CDH10

growth_protocol: Macrophages were isolated from BALF samples using a positive selection strategy. We employed the anti-CD64 PE-conjugated monoclonal antibody (clone 10.1, BD Bioscience, USA) for this purpose.To reveal the isolated macrophages, anti-PE microbeads from Miltenyi Biotec (USA) were utilized. These macrophages were cultured for 8h.

extract_protocol: After the incubation, the cells were resuspended in 30µl of RLT buffer with beta-mercaptoethanol (Qiagen) following the Nanostring protocols recommendation for cell Lysate (MAN-10051-05).

value: CD64+ macrophages

value: >221 days post infection with the Omicron BA.2 variant


title: non-cre control 8wk mouse islets [826]

value: Rbfox2 fl/fl

value: control


title: G10T

value: KS lesion


title: DPA_15

description: DPA


title: non-cre control 8wk mouse islets [824]


title: G10N

value: normal


title: BALF-MP-WTM-CGB060

value: >221 days post infection with the wild type Wuhan strain


title: BALF-MP-HC-DC884


title: BALF-MP-OM-DD442


title: G9T


title: MIN6 treated with Rbfox2 siRNA, rep4

data_processing:
Sequence reads were trimmed for adaptor sequence/low-quality sequence using cutadapt
Trimmed sequence reads were mapped to mm10 using STAR Aligner
Read count was determined using featureCounts
Assembly: mm10
Supplementary files format and content: rMATS splicing anlysis, Rbfox2_KD_rMATs.csv

treatment_protocol: MIN6 cells were grown to 70% confluence in 6 well plates then transfected with 150pmol of 4 pooled siRNAs targeting Rbfox2 exons or a pool of 4 scramble using RNAi. MAX (Thermo) per manufacturer instructions. Cells were harvested after 48 hours and Rbfox2 knockdown.

value: insulinoma

value: Rbfox2-siRNA Treated

value: siRNA


title: DPA_13

description: DPA

value: Dental Primary Afferent (DPA) Neurons


title: DPA_11

description: DPA


title: G8T


title: MIN6 treated with Rbfox2 siRNA, rep3


title: MIN6 treated with Rbfox2 siRNA, rep2


title: G8N


title: DPA_10

description: DPA


title: MIN6 treated with Rbfox2 siRNA, rep1


title: DPA_09

description: DPA


title: BALF-MP-WTM-CGC125


title: BALF-MP-OM-DA076


title: G7T


title: BALF-MP-HC-DF380


title: DPA_06

description: DPA


title: DPA_14

description: DPA


title: non-cre control 8wk mouse islets [822]

value: M

value: islets


title: BALF-MP-WTM-CGB090


title: MIN6 treated with NT siRNA, rep4

value: NT siRNA Treated


title: MIN6 treated with NT siRNA, rep3


title: BALF-MP-HC-DF987

value: Healthy Control


title: DPA_12

description: DPA

value: Trigeminal Ganglion

value: 7 weeks old


title: G6T


title: BALF-MP-WTM-CFL103

value: CD64+ macrophages


title: G9N


title: DPA_05

description: DPA


title: MIN6 treated with NT siRNA, rep2


title: DPA_04

description: DPA


title: G6N


title: DPA_03

description: DPA


title: HSCs, WT, biol rep 3

city: Lund

first: Alexandra

last: Rundberg Nilsson

address: Klinikgatan 26

department: Experimental Hematology

country: Sweden

institute: Lund University

description:
NexteraXT
WT_4

data_processing:
RNA Galaxy workbench 2.0
Sequence reads were trimmed for adaptor sequence/low-quality sequence using Trim Galore!
Trimmed sequence reads were mapped to mm39.ncbiRefSeq using HISAT2
Read count extraction and normalization were performed using RNA Galaxy workbench
Assembly: mm39
Supplementary files format and content: tab-delimited text files include normalized counts for each Sample

source_name: Bone marrow

extract_protocol:
RNA was harvested using Single Cell RNA Purification Kit (Norgen Biotek Corp)
RNA libraries for RNA-seq were prepared using SMART-Seq v4 Ultra Low Input RNA Kit (Takara Bio USA, Inc) following manufacturer's protocols.

value: Bone marrow

value: hematopoietic stem cells

value: WT

value: untreated

value: 8 weeks old


title: G7N

value: normal


title: G5N


title: DPA_02

description: DPA


title: HSCs, WT, biol rep 2

description:
NexteraXT
WT_3


title: DPA_01

description: DPA


title: G4T

value: KS lesion


title: BALF-MP-HC-DF983


title: BALF-MP-OM-DF749

value: >221 days post infection with the Omicron BA.2 variant


title: HSCs, WT, biol rep 1

description:
NexteraXT
WT_2


title: G4N


title: BALF-MP-OM-DF711


title: BALF-MP-HC-DF549


title: BALF-MP-OM-DF630


title: G3T


title: Adult astrocytes (50-60 dpe)_biol rep4

city: Portland

first: Taylor

middle: Reagan

last: Jay

email: taylor.jay@case.edu, jayta@ohsu.edu

state: OR

address: 3181 Sam Jackson Park Rd.

department: Vollum Institute

institute: Oregon Health & Science University

library_source: other

data_processing:
Fastq files were assembled using bcl2fastq
Assembly: Drosophila melanogaster BDGP6 references genome
Supplementary files format and content: Gene read counts table with all samples compiled (.csv)
Library strategy: Ribosomal RNA depletion

molecule: other

organism: Drosophila melanogaster

source_name: RNA pulled down from tagged ribosomes in astrocytes

growth_protocol: Flies were maintained on standard corn agar food with molasses

extract_protocol:
For adult flies, heads were removed by freezing and vortexing the animals; for pupal samples, head tissue was obtained by cutting the anterior third of the pupae with a razor blade
TruSeq Stranded ribosomal reduction protocol

tag: sample type

value: mixed males and females, pooled from 200 fly heads

value: astrocytes

value: elav-Gal80, alrm-Gal4, UAS-EGFP-L10a


title: Adult astrocytes (50-60 dpe)_biol rep2

value: RNA pulled down from tagged ribosomes in astrocytes


title: G3N


title: Adult astrocytes (50-60 dpe)_biol rep3


title: MIN6 treated with NT siRNA, rep1

value: insulinoma

value: NT siRNA Treated

value: siRNA


title: G5T


title: HSCs, IRF1 KO, biol rep 1

description:
NexteraXT
IRF1_KO_2

value: IRF1 KO


title: HSCs, IRF1 KO, biol rep 2

description:
NexteraXT
IRF1_KO_3


title: Adult astrocytes (50-60 dpe)_biol rep1


title: Darier Patient 7, lesion skin biopsy

city: Lausanne

first: Emmanuella

last: Guenova-Hoetzenecker

state: Vaud

address: 49 rue Bugnon

department: Dermatology

country: Switzerland

institute: CHUV

data_processing:
Raw sequencing reads were subjected to demultiplexing and aligned to the human reference genome (refdata-gex-GRCh38-2020-A) using the cellranger count tool with default parameters.
Assembly: hg38
Supplementary files format and content: Tab-separated files and matrix files.

extract_protocol:
Slow-frozen skin biopsies were washed with RPMI 1640 medium (Gibco, 61870- 010), supplemented with 10% Gold FBS (PAA Laboratories, A15-151). The skin  biopsies were then minced and transferred in 1mL of Liberase (Roche,  5401119001, final concentration 0.5 mg/mL diluted with PBS without Ca and Mg)  to digest the tissues. The mixture was incubated for 1 hour at 37°C and the tube  was manually inverted every 15 minutes. Afterwards, 100 μl of 0.05% trypsin was added to the mixture and incubated at 37°C for additional 15 minutes. The tissue remnants were removed by using 70μm cell strainer. The cells were washed with  MACS buffer (PBS, 0.5% BSA and 2mM EDTA) and then stained with SYTOX Red  (ThermoFisher, S34859) and Hoechst 33342 (ThermoFisher, H3570) for cell  viability assessment. The stained cells were suspended in MACS buffer and single living cells (SYTOX Red-negative and Hoechst 33342-positive) were sorted by  FACS sorter (BD FACSAris-II SORP) at Flow Cytometry Facility of UNIL.  scRNA-seq processing
Single-cell mRNA capture and sequencing were performed immediately by the  Lausanne Genomic Technologies Facility (GTF) of UNIL using the Chromium Next  GEM Single Cell 5’ GEM kit (10x Genimics) following the manufacturer’s protocol.

value: Skin

tag: disease state

value: Darier disease

value: patient 7


title: BALF-MP-OM-CDH017

value: CD64+ macrophages


title: Adult astrocytes (10-12 dpe)_biol rep3


title: Darier Patient 4, lesion skin biopsy

value: patient 4


title: BALF-MP-OM-CDH012


title: Darier Patient 3, lesion skin biopsy

value: patient 3