title: CD4T_0h-H2AZ-cKO_rep2

status: Public on Aug 10 2026

first: Mingzhao

address: 15 Da Tun Rd, Chaoyang District

department: Key Laboratory of Infection and Immunity

institute: Institute of Biophysics, Chinese Academy of Sciences

description:
Library name: CD4T_0h-H2AZ-cKO-2
24h-cKO-2
CD4T_0-24h_WTvsH2AZ-cKO_fpkm.txt

data_processing:
Trim Galore (v0.6.7) and Trimmomatic (v0.39) was used to remove the low quality reads (parametrs- --quality 20 --stringency 3)
Bowtie2 (v2.5.1) was used to align reads to the mouse genome
Assembly: mm10
Supplementary files format and content: tab delimited text files includes FPKM values for each sample

source_name: spleen

growth_protocol: T cells were maintained in 1640 supplemented with 10% fetal bovine serum (BI), 10mM Hepes (Gibco), 1% NEAA (Gibco), 1% penicillin/streptomycin (Gibco), 50uM β-Mercaptoethanol (Gibco) and antibiotics in humidified atmosphere with 5% CO2 at 37℃.

extract_protocol:
Total RNA was extracted from 1 × 10⁶ naïve or activated T cells using TRIzol reagent (Invitrogen, 15596018).
RNA-seq libraries were constructed with the NEBNext Ultra II RNA Library Prep Kit for Illumina (NEB, E7770L) following manufacturer's protocols.

treatment_protocol: T cells were inoculated with or without 2 µg/ml coated anti-CD3 antibody and 2 µg/ml soluble anti-CD28 antibody.

value: spleen

value: naive CD4 T cell

value: unstimulated


title: Thymus_DMSOforDex_KO_rep4

status: Public on Aug 07 2026

type: SRA

city: Hangzhou

first: Xiaoping

last: Han

state: Zhejiang

address: Yuhangtang Road 866

department: Center for Stem Cell and Regenerative Medicine

country: China

institute: Zhejiang University School of Medicine

description:
Library name: Thymus_DMSOforDex_KO_rep4_RNA-seq
Dex versus DMSO in KO mice (10 tissues)
RNAseq_KO_Dex_vs_DMSO_count.txt.gz

library_source: transcriptomic

data_processing:
Adapters in FASTQ files were trimmed using cutadapt with the following command “cutadapt -a CTGTCTCTTATACACATCT -A CTGTCTCTTATACACATCT -j 0 -O 16 -m 20”.
The trimmed reads were then aligned to mm10 or hg38 using STAR (v2.7.10a).
Read counts were generated using featureCounts.
Assembly: mm10
Supplementary files format and content: Tab-delimited text files including raw count values for individual samples.

molecule: polyA RNA

organism: Mus musculus

source_name: Thymus

extract_protocol:
For the pituitary and spinal cord, subsequent procedures were directly performed after samples were removed. The bone marrow was isolated from femur and tibia bones. Muscles were removed and both ends of bones were carefully trimmed. The bone marrow cavity was flushed 2–3 times with DPBS to collect most of the cells. Tubes were then centrifuged at 300 g for 5 min at 4°C to collect cell pellets. For the stomach, intestine, and bladder, their luminal content was cleaned up before frozen in dry ice. Other tissues were directly frozen once removed. Frozen tissues were ground in liquid nitrogen. The ground powder was used for subsequent library construction and can be stored at −80°C.
Total RNA was isolated using the FastPure Cell/Tissue Total RNA Isolation Kit V2 (Vazyme). The extracted RNA was used for reverse transcription. Following the reaction, a PCR amplification program was performed. Purification was then conducted using 0.9× of VAHTS DNA Clean Beads. TruePrep DNA Library Prep Kit for MGI (Vazyme) was used for sequencing library construction.

tag: tissue

value: Thymus

tag: genotype

value: Mecp2 KO

tag: strain

tag: Sex

value: Male

tag: age

value: 1.5 months

tag: mouse id


title: Milk fat globule_day 4_high insulin resistance_biol rep 7

city: Oxford

first: Fadil

middle: M

last: Hannan

state: Oxfordshire

address: Level 3, Women's Centre, John Radcliffe Hospital

department: Nuffield Department of Women's and Reproductive Health

country: United Kingdom

institute: University of Oxford

description:
Library name: MFG055
MFG055

library_source: other

data_processing:
The sequencing libraries were multiplexed and loaded on an Illumina NovaSeq 6000 instrument. Samples were sequenced using a 2x150 paired-end (PE) configuration. Image analysis and base calling were conducted on instrument, and raw sequence data were converted into FASTQ files and demultiplexed using Illumina bcl2fastq program version 2.20.
Assembly: HC11: mm9, NCBI Build 37. MCF-12A and MFG: human (hg19, GRCh37).
Supplementary files format and content: CSV files containing raw counts data for each sample; one counts file per dataset.

molecule: other

organism: Homo sapiens

source_name: Breastmilk-derived milk fat globules

extract_protocol:
HC11 and MCF-12A RNA was extracted using the RNeasy mini plus kit (Qiagen). MFG RNA was extracted using the RNeasy plus universal kit (Qiagen).
HC11 and MCF-12A RNA sequencing libraries were prepared using the NEBNext Ultra II RNA Library Prep Kit for Illumina following manufacturer’s instructions (NEB, Ipswich, MA, USA). MFG RNA libraries were prepared using rRNA depletion followed by NEBNext Ultra II RNA Library Prep Kit for Illumina according to the manufacturer’s recommendations.

tag: cell type

value: Breastmilk-derived milk fat globules

value: WT

value: High


title: Thymus_DMSOforDex_KO_rep2

description:
Library name: Thymus_DMSOforDex_KO_rep2_RNA-seq
Dex versus DMSO in KO mice (10 tissues)
RNAseq_KO_Dex_vs_DMSO_count.txt.gz


title: Milk fat globule_day 4_high insulin resistance_biol rep 6

description:
Library name: MFG054
MFG054


title: Thymus_DMSOforDex_KO_rep1

description:
Library name: Thymus_DMSOforDex_KO_rep1_RNA-seq
Dex versus DMSO in KO mice (10 tissues)
RNAseq_KO_Dex_vs_DMSO_count.txt.gz


title: Milk fat globule_day 4_high insulin resistance_biol rep 4

description:
Library name: MFG052
MFG052


title: Thymus_Dex_KO_rep3

description:
Library name: Thymus_Dex_KO_rep3_RNA-seq
Dex versus DMSO in KO mice (10 tissues)
RNAseq_KO_Dex_vs_DMSO_count.txt.gz


title: Milk fat globule_day 4_high insulin resistance_biol rep 3

description:
Library name: MFG051
MFG051


title: Thymus_Dex_KO_rep2

description:
Library name: Thymus_Dex_KO_rep2_RNA-seq
Dex versus DMSO in KO mice (10 tissues)
RNAseq_KO_Dex_vs_DMSO_count.txt.gz


title: Milk fat globule_day 4_high insulin resistance_biol rep 2

description:
Library name: MFG050
MFG050


title: Telencephalon_DMSOforDex_KO_rep5

description:
Library name: Telencephalon_DMSOforDex_KO_rep5_RNA-seq
Dex versus DMSO in KO mice (10 tissues)
RNAseq_KO_Dex_vs_DMSO_count.txt.gz

source_name: Telencephalon

value: Telencephalon


title: Milk fat globule_day 4_high insulin resistance_biol rep 8

description:
Library name: MFG056
MFG056


title: Telencephalon_DMSOforDex_KO_rep4

description:
Library name: Telencephalon_DMSOforDex_KO_rep4_RNA-seq
Dex versus DMSO in KO mice (10 tissues)
RNAseq_KO_Dex_vs_DMSO_count.txt.gz


title: Milk fat globule_day 4_high insulin resistance_biol rep 1

description:
Library name: MFG049
MFG049


title: Telencephalon_DMSOforDex_KO_rep3

description:
Library name: Telencephalon_DMSOforDex_KO_rep3_RNA-seq
Dex versus DMSO in KO mice (10 tissues)
RNAseq_KO_Dex_vs_DMSO_count.txt.gz


title: Milk fat globule_day 3_low insulin resistance_biol rep 5

description:
Library name: MFG048
MFG048

value: Low


title: Milk fat globule_day 3_low insulin resistance_biol rep 4

description:
Library name: MFG047
MFG047


title: Milk fat globule_day 3_low insulin resistance_biol rep 3

description:
Library name: MFG046
MFG046


title: Telencephalon_DMSOforDex_KO_rep1

description:
Library name: Telencephalon_DMSOforDex_KO_rep1_RNA-seq
Dex versus DMSO in KO mice (10 tissues)
RNAseq_KO_Dex_vs_DMSO_count.txt.gz


title: Milk fat globule_day 3_low insulin resistance_biol rep 2

description:
Library name: MFG045
MFG045


title: Milk fat globule_day 4_medium insulin resistance_biol rep 4

description:
Library name: MFG065
MFG065

value: Medium


title: Male, Saline, IgG antibody, Replicate 5

city: New York

first: Molly

middle: S

last: Estill

state: NY

address: 1 Gustave L. Levy Place

department: Neuroscience

country: USA

institute: Mount Sinai School of Medicine

description: Library name: M-sal-igg-5

library_source: genomic

data_processing:
The NGS-Data-Charmer pipeline was used for preprocessing, QC, and alignment of the dataset (https://github.com/shenlab-sinai/NGS-Data-Charmer). Peak calling was performed using MACS on deduplicated alignments (parameters: -f BAMPE -g mm -B -q 0.01), using IgG as background.
Assembly: mm10
Supplementary files format and content: Peak calls are provided as Narrowpeak files, generated by MACS.
Library strategy: CUT&Run

molecule: genomic DNA

source_name: Nucleus accumbens

extract_protocol:
Nuclei were equally split for IGG and E2F3a and Cut&Run was performed using IGG (CellSignaling #2729; 1:100) or E2F3a (MilliporeSigma #HPA065012, 1:50) antibodies. DNA fragments were eluted by incubating the samples at 37˚C for 30 min with 500 RPM mixing (Eppendorf, Thermomixer). The samples were centrifuged at 16,000 RCF for 5 min at 4˚C and the supernatant was reserved for DNA clean-up via phenol-chloroform precipitation.
Sequencing libraries were prepared using the NEBNext® Ultra™ II DNA Library Prep Kit for Illumina® (E7645, New England BioLabs) with NEBNext® Multiplex Oligos for Illumina® (Dual Index Primers Set 1) (E7600S, New England BioLabs) with modifications.

treatment_protocol: Female and male mice were injected (i.p.) with saline or cocaine (20 mg/kg) for 7 consecutive days in their home-cages before brain collection for CUT&RUNseq. Nuclei were isolated from frozen tissue of bilateral  12G punches of the Nucleus accumbens) .

value: Nucleus accumbens

tag: antibody

value: IGG

value: Wildtype C57BL/6J

tag: treatment

value: coc


title: Telencephalon_DMSOforDex_KO_rep2

description:
Library name: Telencephalon_DMSOforDex_KO_rep2_RNA-seq
Dex versus DMSO in KO mice (10 tissues)
RNAseq_KO_Dex_vs_DMSO_count.txt.gz


title: CytoMix 10_T8 rep2

city: Lausanne

first: Aline

last: Roch

address: EPFL Innovation Park Building L

country: Switzerland

institute: DOPPL SA

description: Library name: S92

data_processing:
Aligned to hg19 genome using bowtie2 in --sensitive-local mode
Peak calling using epic
Assembly: hg19
Supplementary files format and content: csv files include raw counts for each sample

molecule: total RNA

source_name: small intestine

extract_protocol:
Each well of the Gri3D® platform was collected individually on day T-2 or day T-8. 4 wells of the same condition were collected separately and analyzed as quadruplicates for transcriptome profiling. Samples were lysed using LBE lysis buffer (C39467, Beckman Coulter) and vortexed for 1 min. Lysates were stored at –80°C before performing RNA extraction and subsequent analysis. Total RNA was extracted from human organoid tissues using the Agencourt RNAdvance Tissue Kit (A32649, Beckman Coulter), following the manufacturer’s protocol. Tissue disruption and lysis were carried out using the FastPrep-24™ instrument (MP Biomedicals) at a speed setting of 6.0 for two cycles of 1 minute each. A total of 400 µL of lysate was processed per sample, and RNA was eluted in 50 µL of nuclease-free water. RNA concentration was quantified using the Quant-iT™ RiboGreen RNA Assay Kit (R11490, Invitrogen) on a SpectraMax® F1 Microplate Reader (Molecular Devices). Integrity was assessed with the Fragment Analyzer 96-capillary system (Agilent Technologies) using the Standard Sensitivity RNA Analysis Kit (DNF-471-0500). We consistently obtained high-quality RNA from all organoid samples, with an average yield of 0.36 µg per sample. Notably, all samples achieved an RNA integrity number (RIN) value of 10, indicating excellent RNA integrity.
A total of 300 ng of RNA per sample was used to generate sequencing libraries with the Illumina Stranded mRNA Library Prep Kit, following the manufacturer's protocol. The workflow includes a bead-based mRNA capture, followed by fragmentation, first- and second-strand synthesis, end repair, 3’ adenylation, and indexed linker ligation steps. The adapter-ligated cDNA library fragments were next enriched by PCR using 13 cycles of amplification. From the extracted total RNA, 90 individual barcoded stranded mRNASeq libraries were successfully prepared with an average yield of 35.4 ng/µL. Two equimolar pools of 78 and 12 unique dual (UD) indexed libraries were sequenced paired-end (PE) with 59 bases each read on four individual P3 100 NextSeq 2000 flow cells. The first dark cycle was introduced to the sequencing run to improve the flow-cell cluster detection. 5.0 billion PE reads passing the chastity filter (>Q30) were generated, with an average of 46.2 million reads per sample with a standard deviation of 11.8 million reads (26%).

treatment_protocol: On day 4, cytokines were introduced to the organoids to initiate Phase 1 of epithelial barrier disruption (T-0). Organoids were stimulated with CytoMix, a pro-inflammatory cytokine cocktail comprising TNF-α (300-01A, Thermo Fisher Scientific), IL-1β (200-01B, Thermo Fisher Scientific), and IFN-γ (300-02, Thermo Fisher Scientific), each administered at final concentrations of 5, 10, 20, or 50 ng/mL. In parallel, IFN-γ was applied as a single agent at identical concentrations. Cytokines were reconstituted at 100 µg/mL in PBS (10010056, Thermo Fisher Scientific) supplemented with 0.1% bovine serum albumin (BSA; 15260-037, Thermo Fisher Scientific). CytoMix was removed, and the cultures were washed by performing two successive medium replacements, marking the onset of the Phase 2 post-treatment recovery period (T–2). As part of the prevention protocol, organoids cultured in Gri3D® platform for 72 hours (day 3) were supplemented with the bioactive compounds’ dexamethasone (DEX - 1 µM; D4902, Sigma-Aldrich), niacinamide (NAM - 0.5 mM; 0429449, DSM-Firmenich), and β-hydroxybutyrate (BHB - 1 mM; 3HB-Mg, Osaka Gas). Following cytokine withdrawal and medium washout, bioactives were reintroduced into the culture at the same concentration on day T-2 and subsequently replenished at identical concentrations on days T-4 and T-6.

value: small intestine

tag: cell line

value: primary intestinal epithelial cells

value: TNF-α 10 ng/mL, IL-1β 10 ng/mL, IFN-γ 10 ng/mL

tag: time

value: day 8 post cytokine treatment


title: Milk fat globule_day 3_medium insulin resistance_biol rep 12

description:
Library name: MFG043
MFG043


title: Telencephalon_Dex_KO_rep4

description:
Library name: Telencephalon_Dex_KO_rep4_RNA-seq
Dex versus DMSO in KO mice (10 tissues)
RNAseq_KO_Dex_vs_DMSO_count.txt.gz

value: Mecp2 KO


title: Telencephalon_Dex_KO_rep5

description:
Library name: Telencephalon_Dex_KO_rep5_RNA-seq
Dex versus DMSO in KO mice (10 tissues)
RNAseq_KO_Dex_vs_DMSO_count.txt.gz

value: Male


title: Milk fat globule_day 3_medium insulin resistance_biol rep 11

description:
Library name: MFG042
MFG042


title: Telencephalon_Dex_KO_rep3

description:
Library name: Telencephalon_Dex_KO_rep3_RNA-seq
Dex versus DMSO in KO mice (10 tissues)
RNAseq_KO_Dex_vs_DMSO_count.txt.gz

value: 1.5 months


title: Milk fat globule_day 4_high insulin resistance_biol rep 12

description:
Library name: MFG060
MFG060

value: Breastmilk-derived milk fat globules


title: WhiteFat_Dex_KO_rep4

description:
Library name: WhiteFat_Dex_KO_rep4_RNA-seq
Dex versus DMSO in KO mice (10 tissues)
RNAseq_KO_Dex_vs_DMSO_count.txt.gz

source_name: WhiteFat

value: WhiteFat


title: Telencephalon_Dex_KO_rep2

description:
Library name: Telencephalon_Dex_KO_rep2_RNA-seq
Dex versus DMSO in KO mice (10 tissues)
RNAseq_KO_Dex_vs_DMSO_count.txt.gz


title: WhiteFat_Dex_KO_rep2

description:
Library name: WhiteFat_Dex_KO_rep2_RNA-seq
Dex versus DMSO in KO mice (10 tissues)
RNAseq_KO_Dex_vs_DMSO_count.txt.gz


title: Milk fat globule_day 3_medium insulin resistance_biol rep 10

description:
Library name: MFG041
MFG041

value: WT


title: Spleen_DMSOforDex_KO_rep5

description:
Library name: Spleen_DMSOforDex_KO_rep5_RNA-seq
Dex versus DMSO in KO mice (10 tissues)
RNAseq_KO_Dex_vs_DMSO_count.txt.gz

source_name: Spleen

value: Spleen


title: Milk fat globule_day 3_low insulin resistance_biol rep 1

description:
Library name: MFG044
MFG044

value: Low


title: Milk fat globule_day 3_medium insulin resistance_biol rep 9

description:
Library name: MFG040
MFG040

value: Medium


title: Spleen_DMSOforDex_KO_rep4

description:
Library name: Spleen_DMSOforDex_KO_rep4_RNA-seq
Dex versus DMSO in KO mice (10 tissues)
RNAseq_KO_Dex_vs_DMSO_count.txt.gz


title: mammary epithelial cells, Luminal HR-

city: Memphis

first: Jiyang

last: Yu

state: TN

address: 262 Danny Thomas Pl

department: Department of Computational Biology

institute: St Jude Children's Research Hospital

description: Library name: MG3_scATAC

library_source: genomic single cell

data_processing:
Read processing including demultiplexing, barcode assignment, and UMI quantification was performed by the Cell Ranger atac analysis pipeline.
Assembly: mm10
Supplementary files format and content: Cellranger output

source_name: tissue: mammary gland

extract_protocol:
The 3rd and 4th mammary glands were dissected from female mice, pooled, and minced followed by enzymatic digestion in DMEM/F12 media containing 2 mg/ml Collagenase A (Roche #11088793001) and 100 U/ml Hyaluronidase (Sigma #H3506) for 2 hours at 37°C. . Flow-sorted single cells were captured with the 10×Genomics Chromium Controller (10×Genomics).
Libraries were prepared with Epi ATAC v1.1 by 10X Genomics and sequenced on NextSeq 500 systems (Illumina).

value: tissue:mammary gland

value: Luminal HR-


title: mammary epithelial cell, Procr+

description: Library name: MG2_scATAC

value: Procr+


title: mammary epithelial cells, Luminal HR+

description: Library name: MG4_scATAC

value: Luminal HR+


title: Milk fat globule_day 3_medium insulin resistance_biol rep 8

description:
Library name: MFG039
MFG039


title: mammary epithelial cells, Basal

description: Library name: MG1_scATAC

value: Basal


title: Thymus_DMSOforDex_KO_rep3

description:
Library name: Thymus_DMSOforDex_KO_rep3_RNA-seq
Dex versus DMSO in KO mice (10 tissues)
RNAseq_KO_Dex_vs_DMSO_count.txt.gz

value: Thymus


title: Spleen_DMSOforDex_KO_rep3

description:
Library name: Spleen_DMSOforDex_KO_rep3_RNA-seq
Dex versus DMSO in KO mice (10 tissues)
RNAseq_KO_Dex_vs_DMSO_count.txt.gz


title: PRWT, PRKO, pooled input

city: Adelaide

first: Thao

last: Dinh

state: South Australia

address: North Terrace

country: Australia

institute: University of Adelaide

description: Library name: PRWT_KO_pooled_input

data_processing:
Genomic alignment using bowtie2 (version 2.4.5) against the mm10 genome build
Peak calling using MACS2 against input (params -f BAM -g 1.87e9 -B -p 10e-10 --nomodel
Assembly: mm10
Supplementary files format and content: bigwig

source_name: ovary

growth_protocol: 21 day mice

extract_protocol:
Lysates were clarified from sonicated nuclei and protein-DNA complexe were isolated with antibody.
Illumina sequencing libraries were prepared from ChIP and pooled input DNA by the standard consecutive enzymatic steps of end-polishing, dA-addition, adaptor ligation. After PCR purification, DNA libraries were quantified and sequenced.

treatment_protocol: mice were injected with 5 IU eCG, after 44h mice were either humanely killed (0h post-hCG) or injected with 5 IU hCG (6h post-hCG). hCG-injecte mice were humanely killed 6 h post-treatment. All mice were dissected and ovaries were punctured for granulosa cell collection.

value: ovary

value: ovarian granulosa cells

value: WT+KO

value: 6h post-hCG


title: Milk fat globule_day 3_medium insulin resistance_biol rep 7

description:
Library name: MFG038
MFG038


title: PRKO, GR

description: Library name: PRKO_GR

value: KO


title: Spleen_DMSOforDex_KO_rep2

description:
Library name: Spleen_DMSOforDex_KO_rep2_RNA-seq
Dex versus DMSO in KO mice (10 tissues)
RNAseq_KO_Dex_vs_DMSO_count.txt.gz

value: Mecp2 KO

value: Male

value: 1.5 months


title: PRWT, GR

description: Library name: PRWT_GR

value: WT


title: Milk fat globule_day 3_medium insulin resistance_biol rep 6

description:
Library name: MFG037
MFG037

value: Breastmilk-derived milk fat globules


title: pooled input

data_processing:
Genomic alignment using bowtie2 (version 2.4.5) against the mm10 genome build
Peak calling using MACS2 against input (params -f BAM -g 1.87e9 -B -p 10e-10 --nomodel
Assembly: mm10

growth_protocol: 21 days old mice

value: CBA x C57BL/6 F1

value: granulosa cells

value: wildtype

value: mixed


title: Spleen_DMSOforDex_KO_rep1

description:
Library name: Spleen_DMSOforDex_KO_rep1_RNA-seq
Dex versus DMSO in KO mice (10 tissues)
RNAseq_KO_Dex_vs_DMSO_count.txt.gz

value: Spleen


title: Milk fat globule_day 4_high insulin resistance_biol rep 5

description:
Library name: MFG053
MFG053

value: High


title: PMSG, H3K27ac

value: 0h post-hCG

value: #39133 (Active Motif)


title: hCG, GR, rep2

value: ovary

value: sc-8992 (Santa Cruz Biotechnology)


title: Milk fat globule_day 3_medium insulin resistance_biol rep 5

description:
Library name: MFG036
MFG036

value: Medium


title: Thymus_Dex_KO_rep5

description:
Library name: Thymus_Dex_KO_rep5_RNA-seq
Dex versus DMSO in KO mice (10 tissues)
RNAseq_KO_Dex_vs_DMSO_count.txt.gz

value: Thymus


title: Spleen_Dex_KO_rep5

description:
Library name: Spleen_Dex_KO_rep5_RNA-seq
Dex versus DMSO in KO mice (10 tissues)
RNAseq_KO_Dex_vs_DMSO_count.txt.gz

value: Mecp2 KO


title: Milk fat globule_day 3_medium insulin resistance_biol rep 4

description:
Library name: MFG035
MFG035


title: hCG, GR, rep1

value: 6h post-hCG


title: PMSG, GR, rep2


title: Milk fat globule_day 3_medium insulin resistance_biol rep 3

description:
Library name: MFG034
MFG034


title: Spleen_Dex_KO_rep4

description:
Library name: Spleen_Dex_KO_rep4_RNA-seq
Dex versus DMSO in KO mice (10 tissues)
RNAseq_KO_Dex_vs_DMSO_count.txt.gz

value: Male

value: 1.5 months


title: PMSG, GR, rep1


title: Spleen_Dex_KO_rep3

description:
Library name: Spleen_Dex_KO_rep3_RNA-seq
Dex versus DMSO in KO mice (10 tissues)
RNAseq_KO_Dex_vs_DMSO_count.txt.gz


title: AR pooled input, rep1 rep2


title: Milk fat globule_day 3_medium insulin resistance_biol rep 2

description:
Library name: MFG033
MFG033

value: Breastmilk-derived milk fat globules

value: WT


title: AR pooled input, rep3 rep4

value: granulosa cells


title: PGRKO, hCG, AR, rep4

value: PGRKO

value: #39781 (Active Motif)


title: Spleen_Dex_KO_rep2

description:
Library name: Spleen_Dex_KO_rep2_RNA-seq
Dex versus DMSO in KO mice (10 tissues)
RNAseq_KO_Dex_vs_DMSO_count.txt.gz

value: Spleen


title: PGRKO, hCG, AR, rep3


title: Milk fat globule_day 3_medium insulin resistance_biol rep 1

description:
Library name: MFG032
MFG032


title: Muscle_DMSOforDex_KO_rep5

description:
Library name: Muscle_DMSOforDex_KO_rep5_RNA-seq
Dex versus DMSO in KO mice (10 tissues)
RNAseq_KO_Dex_vs_DMSO_count.txt.gz

source_name: Muscle

value: Muscle


title: PGRKO, hCG, AR, rep1


title: PGRKO, hCG, AR, rep2


title: PGRWT, hCG, AR, rep3

value: wildtype


title: Milk fat globule_day 3_high insulin resistance_biol rep 12

description:
Library name: MFG031
MFG031

value: High


title: Muscle_DMSOforDex_KO_rep4

description:
Library name: Muscle_DMSOforDex_KO_rep4_RNA-seq
Dex versus DMSO in KO mice (10 tissues)
RNAseq_KO_Dex_vs_DMSO_count.txt.gz


title: PGRWT, hCG, AR, rep4

value: ovary


title: Milk fat globule_day 3_high insulin resistance_biol rep 11

description:
Library name: MFG030
MFG030


title: PGRWT, hCG, AR, rep2


title: Muscle_DMSOforDex_KO_rep3

description:
Library name: Muscle_DMSOforDex_KO_rep3_RNA-seq
Dex versus DMSO in KO mice (10 tissues)
RNAseq_KO_Dex_vs_DMSO_count.txt.gz


title: PGRWT, hCG, AR, rep1


title: Milk fat globule_day 3_high insulin resistance_biol rep 10

description:
Library name: MFG029
MFG029


title: PGRWT, PMSG, AR, rep4

value: 0h post-hCG


title: Muscle_DMSOforDex_KO_rep2

description:
Library name: Muscle_DMSOforDex_KO_rep2_RNA-seq
Dex versus DMSO in KO mice (10 tissues)
RNAseq_KO_Dex_vs_DMSO_count.txt.gz


title: Milk fat globule_day 3_high insulin resistance_biol rep 9

description:
Library name: MFG028
MFG028


title: PGRWT, PMSG, AR, rep2


title: Muscle_DMSOforDex_KO_rep1

description:
Library name: Muscle_DMSOforDex_KO_rep1_RNA-seq
Dex versus DMSO in KO mice (10 tissues)
RNAseq_KO_Dex_vs_DMSO_count.txt.gz


title: PGRWT, PMSG, AR, rep3


title: PGRWT, PMSG, AR, rep1


title: Melanocyte siSCR Input

city: Urbana

first: Jun

last: Song

email: songj@illinois.edu, jssong137@gmail.com

state: IL

address: 1110 West Green Street, MC 704

institute: University of Illinois, Urbana-Champaign

data_processing:
Alignment to genome (hg19)
Deduplication of aligned reads
Peak calling using Macs2 (narrow peak option for MITF, broad peak option for H3K27ac)
Genome_build: hg19
Supplementary_files_format_and_content: narrowPeak and broadPeak files of ChIP-seq peaks

source_name: Melanocyte siSCR

growth_protocol: We isolated human primary melanocytes from neonatal foreskin and cultured with TIVA medium (F-10 with 7.5% FBS, 50 ng/mL TPA, 225 μM IBMX, 1 μM Na3VO4, and 1 mM dbcAMP (Sigma)) in 150 mm tissue culture plates.

extract_protocol:
~50-60 million primary cultured melanocytes were fixed in 1% formaldehyde for 10 minutes at room temperature, followed by addition of glycine to 0.125 M. Crosslinked cells were centrifuged at 430 rcf for 5 minutes at 4º C and pellets snap frozen in liquid Nitrogen and stored at -80 ºC before use. Thawed crosslinked cells were incubated in lysis buffer (50 Mm Tris-HCL (pH 8.0), 1% SDS, and 10 Mm EDTA with complete mini protease inhibitor cocktail tablet (Roche Diagnostics)) on ice for 30 minutes. Cells were then passed through a 26 gauge needle 5-6 times, followed by centrifugation at 5000 rpm for 10 minutes at 4º C, and resuspension in lysis buffer. Cells were sonicated at 4º C using the Bioruptor (Diagenode) for 80 minutes (cycles of 30 second high power output pulse, followed by 1.5 minute pause) to achieve an average chromatin length of 200-500 bp. Samples were then centrifuged at 14,000 rpm for 10 minutes at 4ºC and the sonicated chromatin supernatant was utilized for ChIP reactions.
15 ug of sonicated chromatin was precleared with salmon sperm/BSA blocked Protein A and G Sepharose beads (Amersham ) in 10 mM Tris-HCl (pH 8.0), 1% Triton X-100, 0.1% deoxycholate, 0.1% SDS, 90 mM NaCl, 2 mM EDTA with Complete-Mini PIC tablet (EDTA Free; Roche diagnostics) at 4º C for 2 hours on a rotator. 5 ug of Histone H3K27ac antibody (Active Motif catalog #39133) was added for the ChIP reaction and rotated at 4º C overnight.  Protein sepharose beads were washed twice with 20 mM Tris-HCl (pH 8.0), 0.1% SDS, 1% Triton X-100, 2m M EDTA, and 150 mM NaCl, followed by a final wash with  20 mM Tris-HCl (pH 8.0),  0.1% SDS, 1% Triton X-100, 2 mM EDTA, and 500 mM NaCl. Elution and reverse-crosslinking was performed by incubating protein Sepharose beads in elution buffer (100 mM NaHCO3 and 1% SDS) with 0.05 ug/ul RNAse (Roche diagnostics), and 0.3 M NaCl in a thermomixer at 68º C for 2 hours. 0.1 mg/ml proteinase K was then added, followed by an additional 15 minutes of 68º C incubation. Eluted DNA was purified using the QIAquick PCR purification kit.  Illumina sequencing library construction was performed using the NEBNext ChIP-Seq Library Prep Reagent Set for Illumina as per manufacturer’s protocol, except DNA cleanup with Qiaquick PCR purification or Minelute PCR purification kits, adaptor ligated DNA size selection using a 2% agarose gel, the use of custom index adapters, and 18 cycles of PCR amplification. Multiplexed libraries were sequenced using 75 bp single-end sequencing chemistry using an Illumina HiSeq 2000.

treatment_protocol: We transfected siRNAs (control (Dharmacon Cat. D-001206-14-05) or against MITF (Dharmacon Cat. M-008674-00-0005)) with lipidoid (Proc Natl Acad Sci USA 107, 1864-1869 (2010)) and incubated 72 hours.

value: Melanocyte

tag: chip antibody


title: Muscle_Dex_KO_rep5

description:
Library name: Muscle_Dex_KO_rep5_RNA-seq
Dex versus DMSO in KO mice (10 tissues)
RNAseq_KO_Dex_vs_DMSO_count.txt.gz


title: Milk fat globule_day 3_high insulin resistance_biol rep 8

description:
Library name: MFG027
MFG027


title: Melanocyte siSCR H3K27ac ChIP


title: Milk fat globule_day 3_high insulin resistance_biol rep 7

description:
Library name: MFG026
MFG026


title: Melanocyte siMITF Input

source_name: Melanocyte siMITF


title: Muscle_Dex_KO_rep4

description:
Library name: Muscle_Dex_KO_rep4_RNA-seq
Dex versus DMSO in KO mice (10 tissues)
RNAseq_KO_Dex_vs_DMSO_count.txt.gz


title: Melanocyte siMITF H3K27ac ChIP


title: Milk fat globule_day 3_high insulin resistance_biol rep 6

description:
Library name: MFG025
MFG025


title: mammary epithelial cells h3

library_source: transcriptomic single cell

data_processing:
Read processing including demultiplexing, barcode assignment, and UMI quantification was performed by the Cell Ranger analysis pipeline.
This pipeline performed de-multiplexing, alignment (hg38), and barcode processing to generate gene-cell matrices used for downstream analysis.
Assembly: GRCh38
Supplementary files format and content: cell ranger count matrix for single cells in each sample

source_name: mammary gland

extract_protocol:
Fresh tissue was obtained from mastectomy surgeries via the Biorepository Core at Mount Sinaiaccording to an approved protocol. Samples were dissociated according to a published method (Shehata and Stingl, 2017). Briefly, the tissue was minced and enzymatically digested in DMEM/F12 media containing 2 mg/ml Collagenase A (Roche #11088793001), 100 U/ml Hyaluronidase (Sigma #H3506), 2% BSA,5 μg/ml insulin, 50 μg/ml gentamycin, and 10mM HEPES overnight at 37°C. The samples were enriched for epithelial cells via centrifugation at 200xg for 5 minutes.
Library preparation was performed with Chromium Single Cell Gene Expression 3′ Kits (10x Genomics)

value: mammary gland


title: Muscle_Dex_KO_rep3

description:
Library name: Muscle_Dex_KO_rep3_RNA-seq
Dex versus DMSO in KO mice (10 tissues)
RNAseq_KO_Dex_vs_DMSO_count.txt.gz

value: Mecp2 KO


title: Muscle_Dex_KO_rep2

description:
Library name: Muscle_Dex_KO_rep2_RNA-seq
Dex versus DMSO in KO mice (10 tissues)
RNAseq_KO_Dex_vs_DMSO_count.txt.gz


title: mammary epithelial  Procr+ cells H4


title: Milk fat globule_day 3_high insulin resistance_biol rep 5

description:
Library name: MFG024
MFG024


title: mammary epithelial cells H1


title: mammary epithelial  Procr+ cells H2


title: Milk fat globule_day 3_high insulin resistance_biol rep 4

description:
Library name: MFG023
MFG023


title: TS+SAHA NOR Hippocampal neurons, replicate 3, RNA-seq

first: Cesar

last: Sierra

address: SV 2513 (Bâtiment SV)

department: SV

institute: EPFL

description: Library name: 82R

data_processing:
Reads were then aligned using STAR (v.2.5.2a) to reference genome (mm10) and quantified using Rsubreads (v.1.26)
Assembly: mm10
Supplementary files format and content: tab-delimited text contains normalized (log2 transformed) reads per gene for each sample

molecule: nuclear RNA

source_name: Hippocampus

extract_protocol:
200,000 nuclei were FANS-sorted sorted directly in RLT Buffer for purification using the RNeasy Micro Kit (Qiagen #74004)
SMARTer Stranded Total RNA-Seq Kit v2 from ribo-depleted total RNA

value: Hippocampus

value: Neurons

value: TS

value: SAHA

tag: batch


title: LymphNode_DMSOforDex_KO_rep5

description:
Library name: LymphNode_DMSOforDex_KO_rep5_RNA-seq
Dex versus DMSO in KO mice (10 tissues)
RNAseq_KO_Dex_vs_DMSO_count.txt.gz

source_name: LymphNode

value: LymphNode

value: Male

value: 1.5 months


title: TS+SAHA NOR Hippocampal neurons, replicate 2, RNA-seq

description: Library name: 38R


title: Milk fat globule_day 3_high insulin resistance_biol rep 3

description:
Library name: MFG022
MFG022

value: Breastmilk-derived milk fat globules

value: WT


title: TS+SAHA NOR Hippocampal neurons, replicate 1, RNA-seq

description: Library name: 25R


title: TS NOR Hippocampal neurons, replicate 4, RNA-seq

description: Library name: 35R

value: Vehicle


title: LymphNode_DMSOforDex_KO_rep4

description:
Library name: LymphNode_DMSOforDex_KO_rep4_RNA-seq
Dex versus DMSO in KO mice (10 tissues)
RNAseq_KO_Dex_vs_DMSO_count.txt.gz


title: Milk fat globule_day 3_high insulin resistance_biol rep 2

description:
Library name: MFG021
MFG021


title: TS NOR Hippocampal neurons, replicate 3, RNA-seq

description: Library name: 33R


title: TS NOR Hippocampal neurons, replicate 2, RNA-seq

description: Library name: 30R


title: LymphNode_DMSOforDex_KO_rep3

description:
Library name: LymphNode_DMSOforDex_KO_rep3_RNA-seq
Dex versus DMSO in KO mice (10 tissues)
RNAseq_KO_Dex_vs_DMSO_count.txt.gz


title: TS NOR Hippocampal neurons, replicate 1, RNA-seq

description: Library name: 26R


title: Milk fat globule_day 3_high insulin resistance_biol rep 1

description:
Library name: MFG020
MFG020


title: LymphNode_DMSOforDex_KO_rep2

description:
Library name: LymphNode_DMSOforDex_KO_rep2_RNA-seq
Dex versus DMSO in KO mice (10 tissues)
RNAseq_KO_Dex_vs_DMSO_count.txt.gz


title: WT NOR Hippocampal neurons, replicate 4, RNA-seq

description: Library name: 31R


title: WT NOR Hippocampal neurons, replicate 3, RNA-seq

description: Library name: 13R


title: Milk fat globule_day 2_medium insulin resistance_biol rep 7

description:
Library name: MFG019
MFG019

value: Medium


title: Milk fat globule_day 2_medium insulin resistance_biol rep 6

description:
Library name: MFG018
MFG018


title: WT NOR Hippocampal neurons, replicate 2, RNA-seq

description: Library name: 12R


title: WT NOR Hippocampal neurons, replicate 1, RNA-seq

description: Library name: 11R


title: TS naive Hippocampal neurons, replicate 3, RNA-seq

description: Library name: 28R


title: Milk fat globule_day 2_medium insulin resistance_biol rep 5

description:
Library name: MFG017
MFG017


title: LymphNode_Dex_KO_rep5

description:
Library name: LymphNode_Dex_KO_rep5_RNA-seq
Dex versus DMSO in KO mice (10 tissues)
RNAseq_KO_Dex_vs_DMSO_count.txt.gz


title: LymphNode_DMSOforDex_KO_rep1

description:
Library name: LymphNode_DMSOforDex_KO_rep1_RNA-seq
Dex versus DMSO in KO mice (10 tissues)
RNAseq_KO_Dex_vs_DMSO_count.txt.gz


title: TS naive Hippocampal neurons, replicate 2, RNA-seq

description: Library name: 27R


title: LymphNode_Dex_KO_rep4

description:
Library name: LymphNode_Dex_KO_rep4_RNA-seq
Dex versus DMSO in KO mice (10 tissues)
RNAseq_KO_Dex_vs_DMSO_count.txt.gz


title: TS naive Hippocampal neurons, replicate 1, RNA-seq

description: Library name: 19R


title: Milk fat globule_day 2_medium insulin resistance_biol rep 4

description:
Library name: MFG016
MFG016


title: WT naive Hippocampal neurons, replicate 2, RNA-seq

description: Library name: 37R


title: WT naive Hippocampal neurons, replicate 1, RNA-seq

description: Library name: 36R


title: LymphNode_Dex_KO_rep3

description:
Library name: LymphNode_Dex_KO_rep3_RNA-seq
Dex versus DMSO in KO mice (10 tissues)
RNAseq_KO_Dex_vs_DMSO_count.txt.gz


title: Milk fat globule_day 2_medium insulin resistance_biol rep 3

description:
Library name: MFG015
MFG015


title: TS+SAHA NOR Hippocampal neurons, replicate 3, ATAC-seq

description: Library name: 16A

data_processing:
After trimming adaptors, 50 bp paired-end reads were aligned using bowtie2 (v.2.2.6) to the mouse reference genome (GRCm38/mm10). Duplicated reads were removed using Picardtools (v.2.17) and only paired reads with very high mapping quality (MAPQ score > 30) were used for further analysis. In order to account for the triplicated region in Ts65Dn, reads mapping to this region were divided by 1.5 in trisomic samples. ATAC-seq peak regions of each sample were called using MACS2 with parameters -q 0.05 --nomodel --extsize 200 --broad. Regions listed in the ENCODE Blacklist were excluded from called peaks.
Following this preprocessing step, ATACseqQC package47 was employed to perform Quality Control of each individual sample. Low quality samples (fraction of reads in peaks, FRiP < 0.1) were discarded for downstream analyses.
Assembly: mm10
Supplementary files format and content: bigwig

extract_protocol:
50,000 FANS-sorted nuclei were pelleted at 4 °C, 1,000 × g for 7 min
Nuclei were resuspended in 50 μl of transposition mix (25μL buffer + 22.5μL H2O + 2.5μL Tn5) and gently pipetted to resuspend the nuclei. Transposition reaction was incubated at 37ºC for 45 min in a thermomixer with shaking at 1000 r.p.m. The transposed DNA was purified using GenElute PCR Clean-up (Sigma; #NA1020). To reduce PCR-induced biases during library preparation, after the first 5 PCR cycles, 10% of the sample was monitored with SYBR-green qPCR for 20 cycles to calculate the 25% of saturation per sample (every sample needed more than 7 PCR cycles in total). Final libraries and purification were performed by two-side size selection using magnetic beads.


title: TS+SAHA NOR Hippocampal neurons, replicate 1, ATAC-seq

description: Library name: 25A


title: TS+SAHA NOR Hippocampal neurons, replicate 2, ATAC-seq

description: Library name: 38A


title: LymphNode_Dex_KO_rep2

description:
Library name: LymphNode_Dex_KO_rep2_RNA-seq
Dex versus DMSO in KO mice (10 tissues)
RNAseq_KO_Dex_vs_DMSO_count.txt.gz


title: Milk fat globule_day 2_medium insulin resistance_biol rep 2

description:
Library name: MFG014
MFG014


title: Lung_DMSOforDex_KO_rep5

description:
Library name: Lung_DMSOforDex_KO_rep5_RNA-seq
Dex versus DMSO in KO mice (10 tissues)
RNAseq_KO_Dex_vs_DMSO_count.txt.gz

source_name: Lung

value: Lung


title: TS NOR Hippocampal neurons, replicate 5, ATAC-seq

description: Library name: 35A


title: TS NOR Hippocampal neurons, replicate 4, ATAC-seq

description: Library name: 34A


title: Milk fat globule_day 2_medium insulin resistance_biol rep 1

description:
Library name: MFG013
MFG013


title: Lung_DMSOforDex_KO_rep4

description:
Library name: Lung_DMSOforDex_KO_rep4_RNA-seq
Dex versus DMSO in KO mice (10 tissues)
RNAseq_KO_Dex_vs_DMSO_count.txt.gz


title: TS NOR Hippocampal neurons, replicate 3, ATAC-seq

description: Library name: 33A


title: Milk fat globule_day 2_low insulin resistance_biol rep 8

description:
Library name: MFG012
MFG012

value: Low


title: Milk fat globule_day 2_low insulin resistance_biol rep 7

description:
Library name: MFG011
MFG011


title: Lung_DMSOforDex_KO_rep3

description:
Library name: Lung_DMSOforDex_KO_rep3_RNA-seq
Dex versus DMSO in KO mice (10 tissues)
RNAseq_KO_Dex_vs_DMSO_count.txt.gz


title: TS NOR Hippocampal neurons, replicate 1, ATAC-seq

description: Library name: 26A


title: WT NOR Hippocampal neurons, replicate 4, ATAC-seq

description: Library name: 31A


title: Lung_DMSOforDex_KO_rep2

description:
Library name: Lung_DMSOforDex_KO_rep2_RNA-seq
Dex versus DMSO in KO mice (10 tissues)
RNAseq_KO_Dex_vs_DMSO_count.txt.gz


title: Milk fat globule_day 5_medium insulin resistance_biol rep 1

description:
Library name: MFG096
MFG096


title: NETseq_RelA*_purF_Rep1

city: Madison

first: Michael

last: Wolfe

state: WI

address: 1300 University Ave

institute: University of Wisconsin-Madison

description: Library name: RL3937_NETseq_Rep1

data_processing:
NET-seq data were processed using standard tools and scaled for quantitative comparison across samples based on the number of B. subtilis spike-in reads that mapped uniquely to B. subtilis genome. Adapters, linker, and control oligos potentially contaminating each sample were trimmed from raw reads using cutadapt (v3.4) (10.14806/ej.17.1.200). Reads with a minimum length of 15 nt were mapped to the MG1655 genome (NC_000913.3) using Bowtie (v1.3.0) allowing one mismatch and allowing random assignment of reads mapping to multiple loci based on alignment stratum (Bowtie options --best -a -M 1 -v 1) (10.1038/nmeth.1923). Alignments for all samples, except those derived from E. coli RL3938, were converted to BAM and BED files using samtools (v1.16.1) and bedtools (v2.30.0) (10.1093/bioinformatics/btp352 (PMID: 19505943); 10.1093/bioinformatics/btq033 (PMID: 20110278)) . To bring mapped reads from RL3938 into parity with those of the other strains, alignments were randomly down-sampled to 30% of mapped reads using samtools (option -s 10.3) prior to conversion to BED files. The specific 3′-end counts for each genome position were determined using bedtools (options -d -strand - -5 [plus strand] or -d -strand + -5 [minus strand]). To scale read count between samples, the 3′-end counts mapped to each genome position were scaled to total read counts per ten million and multiplied by the B. subtilis-unique scaling factor.
NET-seq scaling factors: To determine the scaling factor for each sample, we first identified specific regions in the B. subtilis genome (Accession: NC_000964.3) to which E. coli reads did not map (Bsu-unique regions) using an E. coli-only NET-seq dataset (10.1093/nar/gkae209). We mapped reads from the E. coli-only NET-seq library to a combined E. coli MG1655 and B. subtilis strain 168 genome file using Bowtie with options to suppress reads that map to multiple loci and allowing no mismatches (options –best -a -m 1 -v 0). After conversion to BAM and BED files, total locus coverage (read coverage not 3′-end coverage) was determined for the B. subtilis str 168 genome. We then generated a BED table of regions with zero coverage (i.e., regions of the B. subtilis genome to which E. coli-only reads did not map) to detect B. subtilis-unique reads present in E. coli NET-seq samples containing a B. subtilis spike-in. To determine the number of B. subtilis-unique reads in each sample with B. subtilis spike-ins, we followed the same NET-seq processing pipeline used to generate the table of B. subtilis unique loci above but used Bedtools to count 3′-end coverage for both B. subtilis unique reads and reads mapping to both B. subtilis and E. coli (i.e., not mapping to the B. subtilis unique loci). To determine the B. subtilis-unique scaling factor for each sample, the fraction of B. subtilis-unique reads was calculated as the B. subtilis-unique counts divided by the total number of reads mapping to E. coli and B. subtilis loci (Table Sa). The smallest B. subtilis-unique fraction was identified among the set of samples to be compared, and this number was divided by the B. subtilis-unique fraction for each sample to obtain the B. subtilis-unique scaling fraction. The scaling fraction was converted to a scaling factor by multiplying it by 107 divided by the total reads mapped to E. coli. The scaling factor was then used to generate scaled reads per 107 reads for each sample. For most analyses, the average of the two scaled reads per genome position was used.
Assembly: U00096.3 and AL009126.3
Supplementary files format and content: Spike-in scaled NETseq wig coverage files

organism: Escherichia coli

growth_protocol: A single colony was inoculated into MOPS EZ rich defined medium with 0.2% (w/v) glucose (RDM, Teknova) for overnight growth at 37 °C. A 2.5-mL portion of the overnight culture was inoculated into 0.85 L RDM supplemented with ampicillin (100 µg/mL) to maintain plasmids pALS13 or pALS14. The cultures were grown in Fernbach flasks on an orbital shaker at 200 rpm and 37 °C until cell density reached early log-phase (apparent OD600 ~0.39 +/– 0.02). RelA expression was then induced by addition of IPTG to 1 mM with continued shaking at 37 °C. After 5 minutes of induction, cells for GTP quantitation were removed and rapidly filtered (described in detail below). FLAG-tagged RNAP B. subtilis cells (strain RL3116) were then added as spike-in, 50 mL samples were removed for ChIP, and the remaining culture for NET-Seq analysis was rapidly filtered through a 0.45 µ cellulose filter, quickly scraped from the filter with a spatula, and plunged into liquid nitrogen before storage at –80 °C as described previously (Churchman et al. 2012). Cells for ChIP were immediately mixed with sodium phosphate (pH 7.6, 10 mM final) and formaldehyde (1% final) and incubated at 37 °C for crosslinking as described previously, (Hustmyer et al. 2022) followed by quenching with glycine (100 mM final) for 30 min at 4 °C. The crosslinked cells were then centrifuged, washed multiple times with phosphate-buffered saline (PBS; 137 mM NaCl, 2.7 KCl, 10 mM Na2HPO4, 1.8 mM KH2PO4), and stored at –80 °C. Biological triplicate samples were collected for each strain or experimental condition. B. subtilis cells were added from pre-measured and stored aliquots to E. coli cultures immediately before harvest at a ratio of 3.3% B. subtilis-to-E. coli cells as calculated from a pre-determined relationship between apparent OD600 and colony-forming units for each E. coli strain grown in RDM. Aliquots of B. subtilis RL3116 cells at measured cell densities were prepared from late log–phase cultures that were cooled on ice, mixed with cold glycerol to a final concentration of 15% glycerol, flash-frozen in liquid nitrogen, and stored at –80°C. Prior to adding B. subtilis cells to the E. coli cultures, aliquots were thawed in ice water and stored on ice.

extract_protocol:
Nascent RNA was purified as described previously (Larson et al. 2014) with slight modifications. Frozen cells harvested from 0.5 L cell culture were combined with frozen lysis buffer (20 mM Tris-HCl, pH 8.0, 0.4% Triton-X 100, 0.1% NP-40), 100 mM NH4Cl, 10 mM MnCl2, 1x EDTA-free cOmplete Mini protease inhibitor cocktail (Roche)), and 50U/mL RNasin [Promega, N211B]). The mixture was subjected to six rounds of milling at 15 Hz for 3 min in a Retsch MM400 Mixer Mill using 50 ml canisters pre-cooled in liquid nitrogen and 25 mm stainless steel balls. The lysate volume was adjusted to 5.5 mL of lysis buffer by gentle addition of cold lysis buffer and RQ1 DNase I (Promega, 0.054 U/mL) was added followed by incubation for 20 min on ice. The reaction was quenched with EDTA (25 mM final) to release ribosomes from the transcripts and chelate Mg2+ to inactivate RNAP. The lysate was then clarified at 4 °C by centrifugation at 25,000 xg for 10 min and incubated with 0.5 mL anti-FLAG M2 affinity resin (Sigma-Aldrich) for 3 h at 4 °C to isolate RNAP-nascent transcript complexes. The resin was washed four times with lysis buffer with 100 mM NH4Cl, 300 mM KCl, 1 mM EDTA, and 50 U/mL RNasin. ECs were eluted with 600 µL lysis buffer with 2 mg/mL FLAG peptide (Sigma-Aldrich), 100mM NH4Cl, 1mM EDTA, and 50U/mL RNasin. Nascent RNA was extracted from the eluate with miRNeasy Mini Kit (Qiagen) following manufacturer’s instructions. The nascent RNA sample was further purified by an additional overnight isopropanol-GlycoBlue precipitation at -20 °C, dissolved in DEPC-treated water, and stored at –80°C.
NET-seq library preparation was performed as described previously (Larson et al. 2014) with minor changes to use custom adaptors compatible with sequencing using Illumina NovaSeq 6000. An adaptor oligo (14047) was adenylated using a NEB 5´ DNA Adenylation kit (by incubating 6 µM of the oligo with 80 µM ATP, 6 µM Mth RNA ligase (NEB), and 25% (v/v) PEG 8000 in 1X NEB Buffer 1 at 65 °C for 4 hours, inactivated at 85 °C for 5 min, and then and precipitated overnight at -20°C with isopropanol. Precipitated nascent RNA (1 µg per sample) was then ligated to the 5 adenylated adaptor oligo in triplicate reactions using a T4 RNA Ligase 2, truncated (T4 Rnl2tr) kit (NEB) with 10% DMSO, 22% PEG8000, 3 µM adenylated DNA linker, T4 Rnl2tr [14.7U/µL], RNasin [2U/µL], and 1x T4 RNA Ligase Reaction Buffer). These ligation reactions were incubated for 4 hrs at 37°C and the RNA ligase was inactivated with Proteinase K (0.04U/µL) (NEB, P8107).  The ligated material was then subjected to cDNA synthesis (1 h) and cDNA circularization reactions (3 h) using CircLigase (Lucigen) as described previously (Larson et al. 2014; Bao et al. 2024). Circularized cDNA libraries were PCR amplified as previously described 10 with Q5 DNA polymerase (NEB) using PCR conditions recommended by the manufacturer and dual-indexed primers for the NovaSeq6000 (Illumina) sequencing platform. Library concentration and size distribution were determined using an Agilent TapeStation 4150 before 150-nt paired-end sequencing on an Illumina NovaSeq 6000 instrument (sequencing performed by the University of Wisconsin-Madison Biotechnology Center).

value: RL3000 rpoC::3XFLAG yja::kan pALS13


title: WT NOR Hippocampal neurons, replicate 3, ATAC-seq

description: Library name: 13A


title: ChIPseqInput_RelA*_purF-_site1_Rep1

description: Library name: RL3941_ChIPInput_Rep1

data_processing:
ChIP-seq data was processed as described previously Hustmyer et al. mBio (2022) and reproduced and modified here. Read quality control was performed using fastqc (https://www.bioinformatics.babraham.ac.uk/projects/fastqc/) and MultiQC (10.1093/bioinformatics/btw354). All ChIP-seq analysis were performed using an open-source-software-based ChIP-seq pipeline (https://github.com/mikewolfe/ChIPseq_pipeline). The pipeline manages computational jobs using Snakemake (https://doi.org/10.12688/f1000research.29032.2) and maintains the relationship between samples and their metadata using peppy (https://doi.org/10.1093/gigascience/giab077). Paired- and single-end reads were trimmed of adapter sequences using CutAdapt (10.14806/ej.17.1.200) with parameters ‘-a AGATCGGAAGAGCACACGTCTGAACTCCAGTCA -A AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT’. Quality trimming was performed using trimmomatic (10.1093/bioinformatics/btu170) with parameters "LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15". The reads were aligned to the E. coli (Genbank accession: U00096.3) and B. sub (Genbank accession: AL009126.3) chromosomes using bowtie2 (10.1038/nmeth.1923) with parameters "-- end-to-end --very-sensitive --phred33". Raw read coverage was calculated using deepTools (10.1093/nar/gkw257) with the parameters "--binSize 5 --samFlagInclude 67 --extendReads". The raw coverage counts were first scaled by multiplying the raw coverage by a spike-in based scaling factor determined as described in Bonhoure et al. Genome Research 2014 (10.1101/gr.168260.113). Briefly, a background subtracted fragment count is determined in the spike-in fragments by taking the raw fragment counts across the B. sub chromosome AL009126.3 for paired extracted and input samples, dividing the read fragments by the total number of B. sub read fragments per million for each sample and then determining a background subtracted fragment count as follows: w_i = max(0,z_i-βx_i) Where, w_i is the background subtracted fragment count per position i, z_i is the fragment counts in the extracted sample, x_i is the fragment counts in the paired input sample, and β is a regression-based scale factor determined by linear regression with regions outside the full coding region of all genes plus an additional 300 bp upstream of each gene. The average enrichment for a given sample, k, is then calculated using the background subtracted fragment count per position j in each coding region plus an additional 300 bp upstream for each gene as follows: η_k=mean(w_j)  Finally, the spike-in based scaling factor for each sample k is determined as follows: S_k=η_k-(∑_(i=1)^n η_i )/n Where n is the total number of samples to be scaled together. This spike-in factor is then applied to the non-spike in fragments mapping to the E. coli genome by taking the raw fragment counts and first scaling by the total number of fragments per million that mapped to the E. coli genome per sample and then scaling by the spike-in scale factor S_k described above.  After initial scaling, all ChIP traces were copy-number corrected to account for changes in DNA content between the two genotypes as described in the input correction section below.
NET-seq scaling factors: To determine the scaling factor for each sample, we first identified specific regions in the B. subtilis genome (Accession: NC_000964.3) to which E. coli reads did not map (Bsu-unique regions) using an E. coli-only NET-seq dataset (10.1093/nar/gkae209). We mapped reads from the E. coli-only NET-seq library to a combined E. coli MG1655 and B. subtilis strain 168 genome file using Bowtie with options to suppress reads that map to multiple loci and allowing no mismatches (options –best -a -m 1 -v 0). After conversion to BAM and BED files, total locus coverage (read coverage not 3′-end coverage) was determined for the B. subtilis str 168 genome. We then generated a BED table of regions with zero coverage (i.e., regions of the B. subtilis genome to which E. coli-only reads did not map) to detect B. subtilis-unique reads present in E. coli NET-seq samples containing a B. subtilis spike-in. To determine the number of B. subtilis-unique reads in each sample with B. subtilis spike-ins, we followed the same NET-seq processing pipeline used to generate the table of B. subtilis unique loci above but used Bedtools to count 3′-end coverage for both B. subtilis unique reads and reads mapping to both B. subtilis and E. coli (i.e., not mapping to the B. subtilis unique loci). To determine the B. subtilis-unique scaling factor for each sample, the fraction of B. subtilis-unique reads was calculated as the B. subtilis-unique counts divided by the total number of reads mapping to E. coli and B. subtilis loci (Table Sa). The smallest B. subtilis-unique fraction was identified among the set of samples to be compared, and this number was divided by the B. subtilis-unique fraction for each sample to obtain the B. subtilis-unique scaling fraction. The scaling fraction was converted to a scaling factor by multiplying it by 107 divided by the total reads mapped to E. coli. The scaling factor was then used to generate scaled reads per 107 reads for each sample. For most analyses, the average of the two scaled reads per genome position was used.
Assembly: U00096.3 and AL009126.3
Supplementary files format and content: Spike-in scaled NETseq and ChIP-seq coverage wig files

extract_protocol:
ChIP-seq was performed as previously described (Hustmyer et al. 2022; Mooney et al. 2009). A cell pellet corresponding to 50 mL of crosslinked E. coli culture was mixed with separately formaldehyde-crosslinked B. subtilis RL3116 cells (using a volume of B. subtilis cells equivalent to 1% of the E. coli cells) and used for each IP reaction. Immunoprecipitation was performed as described (Hustmyer et al. 2022) using an antibody against the beta subunit of RNAP or the FLAG tag on the C-terminal end of the beta prime subunit.
Paired-end libraries were prepared using NEBNext Ultra II DNA library reagents according to the manufacturer’s protocols and sequenced on Illumina NovaSeq 6000.

value: RL3000 delrpoZ[del2-5] rpoC[R362A, R417A, K615A]::3XFLAG yja::cat pALS13 purF[R45A]


title: WT NOR Hippocampal neurons, replicate 2, ATAC-seq

description: Library name: 12A


title: Milk fat globule_day 2_low insulin resistance_biol rep 6

description:
Library name: MFG010
MFG010


title: Milk fat globule_day 5_high insulin resistance_biol rep 8

description:
Library name: MFG093
MFG093

value: High


title: Milk fat globule_day 5_high insulin resistance_biol rep 4

description:
Library name: MFG089
MFG089


title: Lung_DMSOforDex_KO_rep1

description:
Library name: Lung_DMSOforDex_KO_rep1_RNA-seq
Dex versus DMSO in KO mice (10 tissues)
RNAseq_KO_Dex_vs_DMSO_count.txt.gz

value: Mecp2 KO


title: ChIPseqInput_RelA*_purF-_Rep2

description: Library name: RL3939_ChIPInput_Rep2


title: WT NOR Hippocampal neurons, replicate 1, ATAC-seq

description: Library name: 11A

value: Hippocampus


title: Milk fat globule_day 2_low insulin resistance_biol rep 5

description:
Library name: MFG009
MFG009


title: TS naive Hippocampal neurons, replicate 2, ATAC-seq

description: Library name: 28A

value: Neurons


title: Lung_Dex_KO_rep5

description:
Library name: Lung_Dex_KO_rep5_RNA-seq
Dex versus DMSO in KO mice (10 tissues)
RNAseq_KO_Dex_vs_DMSO_count.txt.gz


title: WT naive Hippocampal neurons, replicate 2, ATAC-seq

description: Library name: 37A


title: TS naive Hippocampal neurons, replicate 1, ATAC-seq

description: Library name: 27A

value: TS


title: WT naive Hippocampal neurons, replicate 1, ATAC-seq

description: Library name: 36A


title: Milk fat globule_day 2_low insulin resistance_biol rep 4

description:
Library name: MFG008
MFG008


title: Lung_Dex_KO_rep4

description:
Library name: Lung_Dex_KO_rep4_RNA-seq
Dex versus DMSO in KO mice (10 tissues)
RNAseq_KO_Dex_vs_DMSO_count.txt.gz


title: IM3_S6

city: Philadelphia

first: Ronald

last: DeMatteo

state: PA

address: 3400 Spruce St

department: Department of Surgery

institute: University of Pennsylvania

description:
Library name: IM3_S6
IM3_S6 in DVC_GDT_counts.xlsx processed file

data_processing:
Raw counts filtered an normalized
Assembly: GRCm38
Supplementary files format and content: Normalized count matrix

source_name: Gastrointestinal stromal tumor

extract_protocol:
RNeasy Mini Kit (Qiagen)
Libraries constructed accoriding to TrueSeq library preparation guidelines

value: Gastrointestinal stromal tumor

value: Imatinib


title: Milk fat globule_day 2_low insulin resistance_biol rep 3

description:
Library name: MFG007
MFG007


title: Milk fat globule_day 2_low insulin resistance_biol rep 2

description:
Library name: MFG006
MFG006


title: IM2_S5

description:
Library name: IM2_S5
IM2_S5 in DVC_GDT_counts.xlsx processed file


title: Lung_Dex_KO_rep3

description:
Library name: Lung_Dex_KO_rep3_RNA-seq
Dex versus DMSO in KO mice (10 tissues)
RNAseq_KO_Dex_vs_DMSO_count.txt.gz

value: Male


title: IM1_S4

description:
Library name: IM1_S4
IM1_S4 in DVC_GDT_counts.xlsx processed file


title: Lung_Dex_KO_rep2

description:
Library name: Lung_Dex_KO_rep2_RNA-seq
Dex versus DMSO in KO mice (10 tissues)
RNAseq_KO_Dex_vs_DMSO_count.txt.gz

value: 1.5 months


title: Milk fat globule_day 2_low insulin resistance_biol rep 1

description:
Library name: MFG005
MFG005

value: Breastmilk-derived milk fat globules


title: Veh-3_S3

description:
Library name: Veh-3_S3
Veh.3_S3 in DVC_GDT_counts.xlsx processed file


title: Veh-2_S2

description:
Library name: Veh-2_S2
Veh.2_S2 in DVC_GDT_counts.xlsx processed file


title: Heart_DMSOforDex_KO_rep5

description:
Library name: Heart_DMSOforDex_KO_rep5_RNA-seq
Dex versus DMSO in KO mice (10 tissues)
RNAseq_KO_Dex_vs_DMSO_count.txt.gz

source_name: Heart

value: Heart


title: Veh-1_S1

description:
Library name: Veh-1_S1
Veh.1_S1 in DVC_GDT_counts.xlsx processed file

value: Vehicle


title: Milk fat globule_day 2_high insulin resistance_biol rep 4

description:
Library name: MFG004
MFG004

source_name: Breastmilk-derived milk fat globules

value: WT


title: mammary epithelial Procr+ cells [MaSC_O]

data_processing:
Read processing including demultiplexing, barcode assignment, and UMI quantification was performed by the Cell Ranger analysis pipeline.
This pipeline performed de-multiplexing, alignment (mm10), and barcode processing to generate gene-cell matrices used for downstream analysis.
Assembly: mm10
Supplementary files format and content: cell ranger count matrix for single cells in each sample

extract_protocol:
The 3rd and 4th mammary glands were dissected from female mice, pooled, and minced followed by enzymatic digestion in DMEM/F12 media containing 2 mg/ml Collagenase A (Roche #11088793001) and 100 U/ml Hyaluronidase (Sigma #H3506) for 2 hours at 37°C.
Library preparation was performed with Chromium Single Cell Gene Expression 3′ Kits (10x Genomics)

value: tissue:mammary gland


title: Heart_DMSOforDex_KO_rep4

description:
Library name: Heart_DMSOforDex_KO_rep4_RNA-seq
Dex versus DMSO in KO mice (10 tissues)
RNAseq_KO_Dex_vs_DMSO_count.txt.gz


title: Milk fat globule_day 2_high insulin resistance_biol rep 3

description:
Library name: MFG003
MFG003


title: mammary epithelial Procr+ cells [MaSC_E]


title: mammary epithelial Procr+ cells [MaSC_D]


title: Heart_DMSOforDex_KO_rep3

description:
Library name: Heart_DMSOforDex_KO_rep3_RNA-seq
Dex versus DMSO in KO mice (10 tissues)
RNAseq_KO_Dex_vs_DMSO_count.txt.gz


title: mammary epithelial Procr+ cells [MaSC_Y]


title: Milk fat globule_day 2_high insulin resistance_biol rep 2

description:
Library name: MFG002
MFG002


title: mammary epithelial cells [unsort_O]


title: Heart_DMSOforDex_KO_rep2

description:
Library name: Heart_DMSOforDex_KO_rep2_RNA-seq
Dex versus DMSO in KO mice (10 tissues)
RNAseq_KO_Dex_vs_DMSO_count.txt.gz


title: mammary epithelial cells [unsort_E2]


title: Milk fat globule_day 2_high insulin resistance_biol rep 1

description:
Library name: MFG001
MFG001


title: mammary epithelial cells [unsort_E1]


title: mammary epithelial cells [unsort_D]


title: Heart_DMSOforDex_KO_rep1

description:
Library name: Heart_DMSOforDex_KO_rep1_RNA-seq
Dex versus DMSO in KO mice (10 tissues)
RNAseq_KO_Dex_vs_DMSO_count.txt.gz


title: Akt knockdown,100nM insulin, 4h, biol rep 5

description:
Library name: AKT4H5
AKT4H5

value: Mammary epithelial cell

value: Akt knockdown

value: 100nM insulin


title: Akt knockdown,100nM insulin, 4h, biol rep 4

description:
Library name: AKT4H4
AKT4H4


title: Heart_Dex_KO_rep5

description:
Library name: Heart_Dex_KO_rep5_RNA-seq
Dex versus DMSO in KO mice (10 tissues)
RNAseq_KO_Dex_vs_DMSO_count.txt.gz


title: Multiome, H3K27M-mutant gliomas, ASCL1-KO, GEX

first: Alan

last: Jiao

state: MA

address: Old Road Campus Research Building

institute: Ludwig Institute for Cancer Research, Oxford University

description: Library name: BT245_Day6_DM_ASCL1KO_RNA

data_processing:
Count matrices were generated by mapping reads to hg38 using CellRanger-ARC (v2.0.0) and SAMtools (v1.18). Downstream processing was performed in Seurat v5
Assembly: hg38
Supplementary files format and content: Cellranger output files: barcodes.tsv.gz, features.tsv.gz, matrix.mtx.gz

extract_protocol:
Control and ASCL1-KO BT245 cells were collected at Day 6 in DM. ~4,000 nuclei per sample were loaded onto the Chromium X (10X Genomics).
Gel beads in emulsion (GEMs) were processed for single-nuclear RNA+ATAC-seq according to the manufacturer’s protocol (Chromium Next GEM Single Cell Multiome ATAC + Gene Expression Rev F) using 7 cycles for cDNA amplification and 11 cycles for library amplification.

value: glioma

value: serum differentiation


title: Multiome, H3K27M-mutant gliomas, ASCL1-KO, ATAC

description: Library name: BT245_Day6_DM_ASCL1KO_ATAC


title: mammary epithelial cells [unsort_Y]


title: Multiome, H3K27M-mutant gliomas, control, ATAC

description: Library name: BT245_Day6_DM_Control_ATAC


title: Heart_Dex_KO_rep4

description:
Library name: Heart_Dex_KO_rep4_RNA-seq
Dex versus DMSO in KO mice (10 tissues)
RNAseq_KO_Dex_vs_DMSO_count.txt.gz

value: Mecp2 KO


title: Akt knockdown,100nM insulin, 4h, biol rep 3

description:
Library name: AKT4H3
AKT4H3


title: Multiome, H3K27M-mutant gliomas, control, GEX

description: Library name: BT245_Day6_DM_Control_RNA


title: Heart_Dex_KO_rep3

description:
Library name: Heart_Dex_KO_rep3_RNA-seq
Dex versus DMSO in KO mice (10 tissues)
RNAseq_KO_Dex_vs_DMSO_count.txt.gz


title: 2D10, Treated, Ser5-P

city: Beer Sheva

first: Praveenkumar

last: Murugavelu

address: David Ben Gurion Blvd

country: Israel

institute: Ben Gurion University

description: Library name: 2D10_Treated_Ser5-P

data_processing:
Raw FASTQ files were trimmed using Trim Galore (v0.4.5) and quality-checked with FastQC (v0.12.0). Paired-end reads were aligned to the human genome (hg38) and E. coli spike-in genome using BWA (v0.7.12).
PCR duplicates were removed and BAM files were coordinate-sorted using SAMtools. Spike-in–based normalization between samples and IgG controls was performed using a custom scaling script and applied during bigWig generation with deepTools bamCoverage (v1.5.91).
Reads mapping to ENCODE blacklisted regions and off-chromosome locations were removed using BedClip (v377) and Bedtools (v2.30.0), and final bigWig files were generated using bedGraphToBigWig. Peak calling was performed using SEACR.
Assembly: hg38
Supplementary files format and content: bigWig
Library strategy: Cut&Run

source_name: Blood

extract_protocol:
2D10 cells were treated with SR4835 drug for 2hours and washed with 1XPBS. After 24hours, cells were collected for CUT&RUN according to EpiCypher CUTANA™ Protocol.
CUT&RUN was performed using the EpiCypher CUTANA™ protocol. Nuclei were bound to ConA beads, incubated with antibody against RNA polymerase II CTD (general), followed by pA-MNase digestion. Released DNA fragments were purified, libraries prepared.

value: Blood

value: 2D10 (Jurkat)

value: T cell

value: SR4835 (CDK12/Cyclin K Inhibitor)


title: Akt knockdown,100nM insulin, 4h, biol rep 2

description:
Library name: AKT4H2
AKT4H2


title: 2D10, Treated, Ser2-P

description: Library name: 2D10_Treated_Ser2-P


title: 2D10, Treated, Pol ll

description: Library name: 2D10_Treated_Pol ll


title: BoneMarrow_DMSOforDex_KO_rep5

description:
Library name: BoneMarrow_DMSOforDex_KO_rep5_RNA-seq
Dex versus DMSO in KO mice (10 tissues)
RNAseq_KO_Dex_vs_DMSO_count.txt.gz

data_processing:
Adapters in FASTQ files were trimmed using cutadapt with the following command “cutadapt -a CTGTCTCTTATACACATCT -A CTGTCTCTTATACACATCT -j 0 -O 16 -m 20”.
The trimmed reads were then aligned to mm10 or hg38 using STAR (v2.7.10a).
Read counts were generated using featureCounts.
Assembly: mm10
Supplementary files format and content: Tab-delimited text files including raw count values for individual samples.

source_name: BoneMarrow

value: BoneMarrow

value: Male


title: 2D10, Treated, H3K27ac

description: Library name: 2D10_Treated_H3K27ac


title: 100nM insulin, 8h, biol rep 5

description:
Library name: 100nM8H5
100nM8H5

data_processing:
The sequencing libraries were multiplexed and loaded on an Illumina NovaSeq 6000 instrument. Samples were sequenced using a 2x150 paired-end (PE) configuration. Image analysis and base calling were conducted on instrument, and raw sequence data were converted into FASTQ files and demultiplexed using Illumina bcl2fastq program version 2.20.
Assembly: HC11: mm9, NCBI Build 37. MCF-12A and MFG: human (hg19, GRCh37).
Supplementary files format and content: CSV files containing raw counts data for each sample; one counts file per dataset.


title: 2D10, Treated, H3K4me3

description: Library name: 2D10_Treated_H3K4me3


title: BoneMarrow_DMSOforDex_KO_rep4

description:
Library name: BoneMarrow_DMSOforDex_KO_rep4_RNA-seq
Dex versus DMSO in KO mice (10 tissues)
RNAseq_KO_Dex_vs_DMSO_count.txt.gz

value: 1.5 months


title: Akt knockdown,100nM insulin, 4h, biol rep 1

description:
Library name: AKT4H1
AKT4H1


title: 2D10, Untreated, Ser5-P

description: Library name: 2D10_Untreated_Ser5-P


title: 2D10, Untreated, Ser2-P

description: Library name: 2D10_Untreated_Ser2-P


title: BoneMarrow_DMSOforDex_KO_rep3

description:
Library name: BoneMarrow_DMSOforDex_KO_rep3_RNA-seq
Dex versus DMSO in KO mice (10 tissues)
RNAseq_KO_Dex_vs_DMSO_count.txt.gz


title: 100nM insulin, 8h, biol rep 4

description:
Library name: 100nM8H4
100nM8H4


title: 2D10, Untreated, Pol II

description: Library name: 2D10_Untreated_Pol II


title: 2D10, Untreated, H3K27ac

description: Library name: 2D10_Untreated_H3K27ac


title: 2D10, Untreated, H3K4me3

description: Library name: 2D10_Untreated_H3K4me3


title: 100nM insulin, 8h, biol rep 3

description:
Library name: 100nM8H3
100nM8H3


title: 2D10, Treated, CDK9

description: Library name: 2D10_Treated_CDK9

data_processing:
Assembly: hg38
Supplementary files format and content: bigwig
Raw FASTQ files were trimmed using Trim Galore (v0.4.5) and quality-checked with FastQC (v0.12.0). Paired-end reads were aligned to the human genome (hg38) and E. coli spike-in genome using BWA (v0.7.12). PCR duplicates were removed and BAM files were coordinate-sorted using SAMtools. Spike-in-based normalization between samples and IgG controls was performed using a custom scaling script and applied during bigWig generation with deepTools bamCoverage (v1.5.91). Reads mapping to ENCODE blacklisted regions and off-chromosome locations were removed using BedClip (v377) and Bedtools (v2.30.0), and final bigWig files were generated using bedGraphToBigWig. Peak calling was performed using SEACR.

extract_protocol:
Infected cells were treated with SR4835 for 2hrs and wash with 1xPBS. After 24hours, Cells were then collected and centrifuged at 1200 RPM for 5 mins. Cells were fixed with 1% formaldehyde for 10 minutes. After cell lysis, chromatin was sonicated using a ultrasonicator (Covaris)
ChIP DNA (1 µg per sample) was used for library preparation using the NEBNext Ultra II DNA Library Prep Kit for Illumina (New England Biolabs), following the manufacturer’s instructions. Briefly, DNA ends were repaired and A-tailed, Illumina-compatible adapters were ligated, and adaptor-ligated DNA was PCR-amplified. Libraries were purified using SPRI beads and size-selected to obtain fragments corresponding to an average insert size of ~200 bp (final library size ~300–350 bp including adapters). Library quality and size distribution were assessed using an Agilent Bioanalyzer prior to sequencing on an Illumina platform.


title: BoneMarrow_DMSOforDex_KO_rep2

description:
Library name: BoneMarrow_DMSOforDex_KO_rep2_RNA-seq
Dex versus DMSO in KO mice (10 tissues)
RNAseq_KO_Dex_vs_DMSO_count.txt.gz

extract_protocol:
For the pituitary and spinal cord, subsequent procedures were directly performed after samples were removed. The bone marrow was isolated from femur and tibia bones. Muscles were removed and both ends of bones were carefully trimmed. The bone marrow cavity was flushed 2–3 times with DPBS to collect most of the cells. Tubes were then centrifuged at 300 g for 5 min at 4°C to collect cell pellets. For the stomach, intestine, and bladder, their luminal content was cleaned up before frozen in dry ice. Other tissues were directly frozen once removed. Frozen tissues were ground in liquid nitrogen. The ground powder was used for subsequent library construction and can be stored at −80°C.
Total RNA was isolated using the FastPure Cell/Tissue Total RNA Isolation Kit V2 (Vazyme). The extracted RNA was used for reverse transcription. Following the reaction, a PCR amplification program was performed. Purification was then conducted using 0.9× of VAHTS DNA Clean Beads. TruePrep DNA Library Prep Kit for MGI (Vazyme) was used for sequencing library construction.


title: 100nM insulin, 8h, biol rep 2

description:
Library name: 100nM8H2
100nM8H2

extract_protocol:
HC11 and MCF-12A RNA was extracted using the RNeasy mini plus kit (Qiagen). MFG RNA was extracted using the RNeasy plus universal kit (Qiagen).
HC11 and MCF-12A RNA sequencing libraries were prepared using the NEBNext Ultra II RNA Library Prep Kit for Illumina following manufacturer’s instructions (NEB, Ipswich, MA, USA). MFG RNA libraries were prepared using rRNA depletion followed by NEBNext Ultra II RNA Library Prep Kit for Illumina according to the manufacturer’s recommendations.


title: BoneMarrow_DMSOforDex_KO_rep1

description:
Library name: BoneMarrow_DMSOforDex_KO_rep1_RNA-seq
Dex versus DMSO in KO mice (10 tissues)
RNAseq_KO_Dex_vs_DMSO_count.txt.gz


title: Sample 4 Treated

description: Library name: Replica#4 Treated-4

data_processing:
Quality Control was conducted by evaluating the quality of the FASTQ files using 'Fastqc' (v0.12.1).
Subsequently, the samples underwent quality trimming via the 'Fastp' software (v0.23.3).
To identify potential contaminations, 'fastq-screen' software was applied.
Read alignment involved aligning the reads to the Human GRCh38 genome (Ensembl release 110) using 'STAR' software (v2.7.10b).
Read assignments to coding regions were determined using the 'SubRead' package ('FeatureCounts' v2.0.6).
Assembly: Finally, BAM files were sorted using ‘samtools’. Differential expression analysis was conducted in the R4 environment utilizing the 'DESeq2' R-package (v2.40.1).
Supplementary files format and content: PCA was performed to evaluate data dispersion, revealing a batch effect among samples collected on different dates.
Supplementary files format and content: tab-delimited text files include total counts values for each gene in each Sample. A correction was implemented in the DESeq2 model to minimize this batch effect. Finally, the indicated groups were compared (without including the control in the model), identifying 90 DEGs. The selected cutoff values were an adjusted p-value <0.05 and a fold-change > 1.5. For enrichment analysis, the DAVID program was employed to identify enriched pathways and terms associated with the selected genes

source_name: blood

extract_protocol:
2D10 cells were treated with SR4835 for 6hrs. Cells were then centrifuged at 1200 RPM for 5 mins and incubated in 500µl Fenozol. Total RNA was purified according to Fenozol manual.
RNA-seq

value: blood


title: 100nM insulin, 8h, biol rep 1

description:
Library name: 100nM8H1
100nM8H1


title: 2D10, Untreated, CDK9

description: Library name: 2D10_Untreated_CDK9


title: Sample 3 Treated

description: Library name: Replica#3 Treated-3


title: BoneMarrow_Dex_KO_rep5

description:
Library name: BoneMarrow_Dex_KO_rep5_RNA-seq
Dex versus DMSO in KO mice (10 tissues)
RNAseq_KO_Dex_vs_DMSO_count.txt.gz


title: 100nM insulin, 4h, biol rep 5

description:
Library name: 100nM4H5
100nM4H5


title: Sample 2 Treated

description: Library name: Replica#2 Treated-2


title: BoneMarrow_Dex_KO_rep4

description:
Library name: BoneMarrow_Dex_KO_rep4_RNA-seq
Dex versus DMSO in KO mice (10 tissues)
RNAseq_KO_Dex_vs_DMSO_count.txt.gz


title: Sample 1 Treated

description: Library name: Replica#1 Treated-1


title: Sample 4 Untreated

description: Library name: Replica#4 Untreated-4


title: 100nM insulin, 4h, biol rep 4

description:
Library name: 100nM4H4
100nM4H4


title: Sample 3 Untreated

description: Library name: Replica#3 Untreated-3


title: BoneMarrow_Dex_KO_rep3

description:
Library name: BoneMarrow_Dex_KO_rep3_RNA-seq
Dex versus DMSO in KO mice (10 tissues)
RNAseq_KO_Dex_vs_DMSO_count.txt.gz


title: Sample 2 Untreated

description: Library name: Replica#2 Untreated-2


title: 100nM insulin, 4h, biol rep 3

description:
Library name: 100nM4H3
100nM4H3


title: Peripheral B cells, ACPA-positive non-converter, post, BCR-seq, PN5B

city: Stanford

first: Mengrui

last: Zhang

state: CA

address: 291 Campus Drive

department: Division of Immunology and Rheumatology

institute: Stanford University

description:
Library name: PN5B_BCR
10x Genomics Chromium BCR V(D)J library; Cell Ranger filtered contig annotations

data_processing:
GEX FASTQ files were processed with 10x Genomics Cell Ranger to generate filtered feature-barcode count matrices (barcodes.tsv.gz, features.tsv.gz, matrix.mtx.gz) aligned to the human GRCh38 reference transcriptome.
CITE-seq/ADT libraries were processed to UMI count matrices (barcodes.tsv.gz, features.tsv.gz, matrix.mtx.gz) for antibody-derived tags; antibody feature definitions are provided in feature_README.txt.
BCR V(D)J FASTQ files were processed with 10x Genomics Cell Ranger VDJ to generate filtered contig FASTA and filtered_contig_annotations.csv files.
Processed files were assigned unique sample-specific filenames for GEO deposition while retaining Cell Ranger file contents.
Assembly: GRCh38
Supplementary files format and content: For each GEX sample: Cell Ranger filtered feature-barcode matrix Market Exchange (MEX) files (*_GEX_barcodes.tsv.gz, *_GEX_features.tsv.gz, *_GEX_matrix.mtx.gz) containing UMI counts for gene expression features. For each CITE-seq sample: ADT UMI count MEX files (*_CITE_barcodes.tsv.gz, *_CITE_features.tsv.gz, *_CITE_matrix.mtx.gz). For each BCR sample: Cell Ranger filtered_contig_annotations.csv and filtered_contig.fasta. Supplementary feature_README.txt maps ADT barcodes to antibody names.
Supplementary files format and content: Matrix Market files store sparse cell-by-feature UMI counts; features are Ensembl gene IDs (GEX) or antibody-derived tags (CITE). BCR annotation CSV includes contig-level V(D)J calls and cell barcodes.
Library strategy: BCR-Seq

source_name: peripheral blood

growth_protocol: Not applicable (ex vivo peripheral blood B cells; no cell culture growth protocol).

extract_protocol:
Peripheral blood was collected and B cells were enriched for single-cell multiomics profiling. Gene expression, surface protein (ADT), and BCR V(D)J libraries were prepared using 10x Genomics Chromium workflows according to the manufacturer protocols.
Single-cell gene expression, CITE-seq/ADT, and BCR V(D)J libraries were constructed with the 10x Genomics Chromium platform and sequenced on an Illumina NovaSeq X Plus instrument.

treatment_protocol: No experimental treatment was applied. Samples are paired longitudinal peripheral blood draws (pre and post) from healthy controls, ACPA-positive non-converters, and ACPA-positive individuals who converted to clinical rheumatoid arthritis.

value: peripheral blood

tag: disease state

value: ACPA-positive non-converter

value: B cells

value: female

tag: timepoint

value: post

tag: subject group

value: non-converter


title: Sample 1 Untreated

description: Library name: Replica#1 Untreated-1


title: 100nM insulin, 4h, biol rep 2

description:
Library name: 100nM4H2
100nM4H2

value: Mammary epithelial cell

value: WT

value: 100nM insulin


title: BoneMarrow_Dex_KO_rep2

description:
Library name: BoneMarrow_Dex_KO_rep2_RNA-seq
Dex versus DMSO in KO mice (10 tissues)
RNAseq_KO_Dex_vs_DMSO_count.txt.gz

value: Mecp2 KO


title: Peripheral B cells, ACPA-positive non-converter, post, CITE-seq, PN5B

description:
Library name: PN5B_CITE
Antibody-derived tag (ADT) surface protein library; UMI count matrix

data_processing:
GEX FASTQ files were processed with 10x Genomics Cell Ranger to generate filtered feature-barcode count matrices (barcodes.tsv.gz, features.tsv.gz, matrix.mtx.gz) aligned to the human GRCh38 reference transcriptome.
CITE-seq/ADT libraries were processed to UMI count matrices (barcodes.tsv.gz, features.tsv.gz, matrix.mtx.gz) for antibody-derived tags; antibody feature definitions are provided in feature_README.txt.
BCR V(D)J FASTQ files were processed with 10x Genomics Cell Ranger VDJ to generate filtered contig FASTA and filtered_contig_annotations.csv files.
Processed files were assigned unique sample-specific filenames for GEO deposition while retaining Cell Ranger file contents.
Assembly: GRCh38
Supplementary files format and content: For each GEX sample: Cell Ranger filtered feature-barcode matrix Market Exchange (MEX) files (*_GEX_barcodes.tsv.gz, *_GEX_features.tsv.gz, *_GEX_matrix.mtx.gz) containing UMI counts for gene expression features. For each CITE-seq sample: ADT UMI count MEX files (*_CITE_barcodes.tsv.gz, *_CITE_features.tsv.gz, *_CITE_matrix.mtx.gz). For each BCR sample: Cell Ranger filtered_contig_annotations.csv and filtered_contig.fasta. Supplementary feature_README.txt maps ADT barcodes to antibody names.
Supplementary files format and content: Matrix Market files store sparse cell-by-feature UMI counts; features are Ensembl gene IDs (GEX) or antibody-derived tags (CITE). BCR annotation CSV includes contig-level V(D)J calls and cell barcodes.
Library strategy: CITE-seq

molecule: protein


title: Peripheral B cells, ACPA-positive non-converter, post, scRNA-seq, PN5B

description:
Library name: PN5B_GEX
10x Genomics Chromium gene expression library; Cell Ranger filtered feature-barcode matrix

data_processing:
GEX FASTQ files were processed with 10x Genomics Cell Ranger to generate filtered feature-barcode count matrices (barcodes.tsv.gz, features.tsv.gz, matrix.mtx.gz) aligned to the human GRCh38 reference transcriptome.
CITE-seq/ADT libraries were processed to UMI count matrices (barcodes.tsv.gz, features.tsv.gz, matrix.mtx.gz) for antibody-derived tags; antibody feature definitions are provided in feature_README.txt.
BCR V(D)J FASTQ files were processed with 10x Genomics Cell Ranger VDJ to generate filtered contig FASTA and filtered_contig_annotations.csv files.
Processed files were assigned unique sample-specific filenames for GEO deposition while retaining Cell Ranger file contents.
Assembly: GRCh38
Supplementary files format and content: For each GEX sample: Cell Ranger filtered feature-barcode matrix Market Exchange (MEX) files (*_GEX_barcodes.tsv.gz, *_GEX_features.tsv.gz, *_GEX_matrix.mtx.gz) containing UMI counts for gene expression features. For each CITE-seq sample: ADT UMI count MEX files (*_CITE_barcodes.tsv.gz, *_CITE_features.tsv.gz, *_CITE_matrix.mtx.gz). For each BCR sample: Cell Ranger filtered_contig_annotations.csv and filtered_contig.fasta. Supplementary feature_README.txt maps ADT barcodes to antibody names.
Supplementary files format and content: Matrix Market files store sparse cell-by-feature UMI counts; features are Ensembl gene IDs (GEX) or antibody-derived tags (CITE). BCR annotation CSV includes contig-level V(D)J calls and cell barcodes.


title: Peripheral B cells, ACPA-positive non-converter, pre, BCR-seq, PN5A

description:
Library name: PN5A_BCR
10x Genomics Chromium BCR V(D)J library; Cell Ranger filtered contig annotations

value: pre


title: Bone_DMSOforDex_KO_rep5

description:
Library name: Bone_DMSOforDex_KO_rep5_RNA-seq
Dex versus DMSO in KO mice (10 tissues)
RNAseq_KO_Dex_vs_DMSO_count.txt.gz

source_name: Bone

value: Bone


title: 100nM insulin, 4h, biol rep 1

description:
Library name: 100nM4H1
100nM4H1


title: Bone_DMSOforDex_KO_rep4

description:
Library name: Bone_DMSOforDex_KO_rep4_RNA-seq
Dex versus DMSO in KO mice (10 tissues)
RNAseq_KO_Dex_vs_DMSO_count.txt.gz


title: Peripheral B cells, ACPA-positive non-converter, pre, CITE-seq, PN5A

description:
Library name: PN5A_CITE
Antibody-derived tag (ADT) surface protein library; UMI count matrix


title: 100nM insulin, 1h, biol rep 5

description:
Library name: 100nM1H5
100nM1H5


title: Peripheral B cells, ACPA-positive non-converter, pre, scRNA-seq, PN5A

description:
Library name: PN5A_GEX
10x Genomics Chromium gene expression library; Cell Ranger filtered feature-barcode matrix


title: Bone_DMSOforDex_KO_rep3

description:
Library name: Bone_DMSOforDex_KO_rep3_RNA-seq
Dex versus DMSO in KO mice (10 tissues)
RNAseq_KO_Dex_vs_DMSO_count.txt.gz


title: Peripheral B cells, ACPA-positive non-converter, post, BCR-seq, PN4B

description:
Library name: PN4B_BCR
10x Genomics Chromium BCR V(D)J library; Cell Ranger filtered contig annotations


title: 100nM insulin, 1h, biol rep 4

description:
Library name: 100nM1H4
100nM1H4


title: Peripheral B cells, ACPA-positive non-converter, post, scRNA-seq, PN4B

description:
Library name: PN4B_GEX
10x Genomics Chromium gene expression library; Cell Ranger filtered feature-barcode matrix


title: 100nM insulin, 1h, biol rep 3

description:
Library name: 100nM1H3
100nM1H3


title: Peripheral B cells, ACPA-positive non-converter, post, CITE-seq, PN4B

description:
Library name: PN4B_CITE
Antibody-derived tag (ADT) surface protein library; UMI count matrix


title: Bone_DMSOforDex_KO_rep2

description:
Library name: Bone_DMSOforDex_KO_rep2_RNA-seq
Dex versus DMSO in KO mice (10 tissues)
RNAseq_KO_Dex_vs_DMSO_count.txt.gz


title: Peripheral B cells, ACPA-positive non-converter, pre, BCR-seq, PN4A

description:
Library name: PN4A_BCR
10x Genomics Chromium BCR V(D)J library; Cell Ranger filtered contig annotations


title: Bone_DMSOforDex_KO_rep1

description:
Library name: Bone_DMSOforDex_KO_rep1_RNA-seq
Dex versus DMSO in KO mice (10 tissues)
RNAseq_KO_Dex_vs_DMSO_count.txt.gz


title: 100nM insulin, 1h, biol rep 2

description:
Library name: 100nM1H2
100nM1H2


title: Bone_Dex_KO_rep5

description:
Library name: Bone_Dex_KO_rep5_RNA-seq
Dex versus DMSO in KO mice (10 tissues)
RNAseq_KO_Dex_vs_DMSO_count.txt.gz


title: Peripheral B cells, ACPA-positive non-converter, pre, scRNA-seq, PN4A

description:
Library name: PN4A_GEX
10x Genomics Chromium gene expression library; Cell Ranger filtered feature-barcode matrix


title: Peripheral B cells, ACPA-positive non-converter, post, BCR-seq, PN3B

description:
Library name: PN3B_BCR
10x Genomics Chromium BCR V(D)J library; Cell Ranger filtered contig annotations


title: Peripheral B cells, ACPA-positive non-converter, pre, CITE-seq, PN4A

description:
Library name: PN4A_CITE
Antibody-derived tag (ADT) surface protein library; UMI count matrix


title: 100nM insulin, 1h, biol rep 1

description:
Library name: 100nM1H1
100nM1H1


title: Bone_Dex_KO_rep4

description:
Library name: Bone_Dex_KO_rep4_RNA-seq
Dex versus DMSO in KO mice (10 tissues)
RNAseq_KO_Dex_vs_DMSO_count.txt.gz


title: Peripheral B cells, ACPA-positive non-converter, post, CITE-seq, PN3B

description:
Library name: PN3B_CITE
Antibody-derived tag (ADT) surface protein library; UMI count matrix


title: Peripheral B cells, ACPA-positive non-converter, post, scRNA-seq, PN3B

description:
Library name: PN3B_GEX
10x Genomics Chromium gene expression library; Cell Ranger filtered feature-barcode matrix


title: Peripheral B cells, ACPA-positive non-converter, pre, BCR-seq, PN3A

description:
Library name: PN3A_BCR
10x Genomics Chromium BCR V(D)J library; Cell Ranger filtered contig annotations


title: Bone_Dex_KO_rep3

description:
Library name: Bone_Dex_KO_rep3_RNA-seq
Dex versus DMSO in KO mice (10 tissues)
RNAseq_KO_Dex_vs_DMSO_count.txt.gz


title: Peripheral B cells, ACPA-positive non-converter, pre, CITE-seq, PN3A

description:
Library name: PN3A_CITE
Antibody-derived tag (ADT) surface protein library; UMI count matrix


title: 10nM insulin, 8h, biol rep 4

description:
Library name: 10nM8H4
10nM8H4

value: 10nM insulin


title: Bone_Dex_KO_rep2

description:
Library name: Bone_Dex_KO_rep2_RNA-seq
Dex versus DMSO in KO mice (10 tissues)
RNAseq_KO_Dex_vs_DMSO_count.txt.gz


title: Peripheral B cells, ACPA-positive non-converter, pre, scRNA-seq, PN3A

description:
Library name: PN3A_GEX
10x Genomics Chromium gene expression library; Cell Ranger filtered feature-barcode matrix


title: Peripheral B cells, ACPA-positive non-converter, post, BCR-seq, PN2B

description:
Library name: PN2B_BCR
10x Genomics Chromium BCR V(D)J library; Cell Ranger filtered contig annotations


title: 10nM insulin, 8h, biol rep 3

description:
Library name: 10nM8H3
10nM8H3


title: Peripheral B cells, ACPA-positive non-converter, post, CITE-seq, PN2B

description:
Library name: PN2B_CITE
Antibody-derived tag (ADT) surface protein library; UMI count matrix


title: 10nM insulin, 8h, biol rep 5

description:
Library name: 10nM8H5
10nM8H5


title: Peripheral B cells, ACPA-positive non-converter, post, scRNA-seq, PN2B

description:
Library name: PN2B_GEX
10x Genomics Chromium gene expression library; Cell Ranger filtered feature-barcode matrix


title: 10nM insulin, 8h, biol rep 2

description:
Library name: 10nM8H2
10nM8H2


title: WhiteFat_DMSOforDex_WT_rep4

description:
Library name: WhiteFat_DMSOforDex_WT_rep4_RNA-seq
Dex versus DMSO in WT mice (four tissues)
RNAseq_WT_Dex_vs_DMSO_count.txt.gz

source_name: WhiteFat

value: WhiteFat

value: 2 months


title: Peripheral B cells, ACPA-positive non-converter, pre, BCR-seq, PN2A

description:
Library name: PN2A_BCR
10x Genomics Chromium BCR V(D)J library; Cell Ranger filtered contig annotations


title: WhiteFat_DMSOforDex_WT_rep3

description:
Library name: WhiteFat_DMSOforDex_WT_rep3_RNA-seq
Dex versus DMSO in WT mice (four tissues)
RNAseq_WT_Dex_vs_DMSO_count.txt.gz

value: Male


title: Peripheral B cells, ACPA-positive non-converter, pre, CITE-seq, PN2A

description:
Library name: PN2A_CITE
Antibody-derived tag (ADT) surface protein library; UMI count matrix


title: 10nM insulin, 8h, biol rep 1

description:
Library name: 10nM8H1
10nM8H1


title: WhiteFat_DMSOforDex_WT_rep2

description:
Library name: WhiteFat_DMSOforDex_WT_rep2_RNA-seq
Dex versus DMSO in WT mice (four tissues)
RNAseq_WT_Dex_vs_DMSO_count.txt.gz


title: Peripheral B cells, ACPA-positive non-converter, pre, scRNA-seq, PN2A

description:
Library name: PN2A_GEX
10x Genomics Chromium gene expression library; Cell Ranger filtered feature-barcode matrix


title: 10nM insulin, 4h, biol rep 5

description:
Library name: 10nM4H5
10nM4H5


title: WhiteFat_Dex_WT_rep4

description:
Library name: WhiteFat_Dex_WT_rep4_RNA-seq
Dex versus DMSO in WT mice (four tissues)
RNAseq_WT_Dex_vs_DMSO_count.txt.gz


title: Peripheral B cells, ACPA-positive non-converter, post, BCR-seq, PN1B

description:
Library name: PN1B_BCR
10x Genomics Chromium BCR V(D)J library; Cell Ranger filtered contig annotations


title: Peripheral B cells, ACPA-positive non-converter, post, scRNA-seq, PN1B

description:
Library name: PN1B_GEX
10x Genomics Chromium gene expression library; Cell Ranger filtered feature-barcode matrix


title: Peripheral B cells, ACPA-positive non-converter, post, CITE-seq, PN1B

description:
Library name: PN1B_CITE
Antibody-derived tag (ADT) surface protein library; UMI count matrix


title: 10nM insulin, 4h, biol rep 4

description:
Library name: 10nM4H4
10nM4H4


title: Peripheral B cells, ACPA-positive non-converter, pre, BCR-seq, PN1A

description:
Library name: PN1A_BCR
10x Genomics Chromium BCR V(D)J library; Cell Ranger filtered contig annotations


title: WhiteFat_Dex_WT_rep3

description:
Library name: WhiteFat_Dex_WT_rep3_RNA-seq
Dex versus DMSO in WT mice (four tissues)
RNAseq_WT_Dex_vs_DMSO_count.txt.gz


title: Peripheral B cells, ACPA-positive non-converter, pre, CITE-seq, PN1A

description:
Library name: PN1A_CITE
Antibody-derived tag (ADT) surface protein library; UMI count matrix


title: 10nM insulin, 4h, biol rep 3

description:
Library name: 10nM4H3
10nM4H3


title: Peripheral B cells, ACPA-positive non-converter, pre, scRNA-seq, PN1A

description:
Library name: PN1A_GEX
10x Genomics Chromium gene expression library; Cell Ranger filtered feature-barcode matrix


title: WhiteFat_Dex_WT_rep2

description:
Library name: WhiteFat_Dex_WT_rep2_RNA-seq
Dex versus DMSO in WT mice (four tissues)
RNAseq_WT_Dex_vs_DMSO_count.txt.gz


title: Peripheral B cells, ACPA-positive converter to clinical RA, post, BCR-seq, PC5B

description:
Library name: PC5B_BCR
10x Genomics Chromium BCR V(D)J library; Cell Ranger filtered contig annotations

value: ACPA-positive converter to clinical RA

value: converter


title: 10nM insulin, 4h, biol rep 2

description:
Library name: 10nM4H2
10nM4H2


title: WhiteFat_Dex_WT_rep1

description:
Library name: WhiteFat_Dex_WT_rep1_RNA-seq
Dex versus DMSO in WT mice (four tissues)
RNAseq_WT_Dex_vs_DMSO_count.txt.gz


title: Peripheral B cells, ACPA-positive converter to clinical RA, post, CITE-seq, PC5B

description:
Library name: PC5B_CITE
Antibody-derived tag (ADT) surface protein library; UMI count matrix

value: peripheral blood


title: Peripheral B cells, ACPA-positive converter to clinical RA, post, scRNA-seq, PC5B

description:
Library name: PC5B_GEX
10x Genomics Chromium gene expression library; Cell Ranger filtered feature-barcode matrix

value: B cells


title: 10nM insulin, 4h, biol rep 1

description:
Library name: 10nM4H1
10nM4H1


title: Peripheral B cells, ACPA-positive converter to clinical RA, pre, BCR-seq, PC5A

description:
Library name: PC5A_BCR
10x Genomics Chromium BCR V(D)J library; Cell Ranger filtered contig annotations

value: female


title: Peripheral B cells, ACPA-positive converter to clinical RA, pre, CITE-seq, PC5A

description:
Library name: PC5A_CITE
Antibody-derived tag (ADT) surface protein library; UMI count matrix


title: Peripheral B cells, ACPA-positive converter to clinical RA, pre, scRNA-seq, PC5A

description:
Library name: PC5A_GEX
10x Genomics Chromium gene expression library; Cell Ranger filtered feature-barcode matrix


title: 10nM insulin, 1h, biol rep 3

description:
Library name: 10nM1H5
10nM1H5


title: Thymus_DMSOforDex_WT_rep4

description:
Library name: Thymus_DMSOforDex_WT_rep4_RNA-seq
Dex versus DMSO in WT mice (four tissues)
RNAseq_WT_Dex_vs_DMSO_count.txt.gz

source_name: Thymus

value: Thymus


title: Thymus_DMSOforDex_WT_rep3

description:
Library name: Thymus_DMSOforDex_WT_rep3_RNA-seq
Dex versus DMSO in WT mice (four tissues)
RNAseq_WT_Dex_vs_DMSO_count.txt.gz


title: 10nM insulin, 1h, biol rep 2

description:
Library name: 10nM1H4
10nM1H4


title: Peripheral B cells, ACPA-positive converter to clinical RA, post, BCR-seq, PC4B

description:
Library name: PC4B_BCR
10x Genomics Chromium BCR V(D)J library; Cell Ranger filtered contig annotations

value: post


title: Peripheral B cells, ACPA-positive converter to clinical RA, post, CITE-seq, PC4B

description:
Library name: PC4B_CITE
Antibody-derived tag (ADT) surface protein library; UMI count matrix


title: Thymus_DMSOforDex_WT_rep2

description:
Library name: Thymus_DMSOforDex_WT_rep2_RNA-seq
Dex versus DMSO in WT mice (four tissues)
RNAseq_WT_Dex_vs_DMSO_count.txt.gz


title: 10nM insulin, 1h, biol rep 1

description:
Library name: 10nM1H1
10nM1H1

value: Mammary epithelial cell


title: Thymus_DMSOforDex_WT_rep1

description:
Library name: Thymus_DMSOforDex_WT_rep1_RNA-seq
Dex versus DMSO in WT mice (four tissues)
RNAseq_WT_Dex_vs_DMSO_count.txt.gz

value: WT


title: Peripheral B cells, ACPA-positive converter to clinical RA, pre, BCR-seq, PC4A

description:
Library name: PC4A_BCR
10x Genomics Chromium BCR V(D)J library; Cell Ranger filtered contig annotations


title: Akt knockdown, 0nM insulin, biol rep 5

description:
Library name: AKTCTRL5
AKTCTRL5

value: Akt knockdown

value: 0nM insulin control


title: Thymus_Dex_WT_rep4

description:
Library name: Thymus_Dex_WT_rep4_RNA-seq
Dex versus DMSO in WT mice (four tissues)
RNAseq_WT_Dex_vs_DMSO_count.txt.gz


title: Peripheral B cells, ACPA-positive converter to clinical RA, pre, CITE-seq, PC4A

description:
Library name: PC4A_CITE
Antibody-derived tag (ADT) surface protein library; UMI count matrix

value: pre


title: Peripheral B cells, ACPA-positive converter to clinical RA, pre, scRNA-seq, PC4A

description:
Library name: PC4A_GEX
10x Genomics Chromium gene expression library; Cell Ranger filtered feature-barcode matrix


title: Akt knockdown, 0nM insulin, biol rep 4

description:
Library name: AKTCTRL4
AKTCTRL4


title: Peripheral B cells, ACPA-positive converter to clinical RA, post, BCR-seq, PC3B

description:
Library name: PC3B_BCR
10x Genomics Chromium BCR V(D)J library; Cell Ranger filtered contig annotations


title: Thymus_Dex_WT_rep3

description:
Library name: Thymus_Dex_WT_rep3_RNA-seq
Dex versus DMSO in WT mice (four tissues)
RNAseq_WT_Dex_vs_DMSO_count.txt.gz


title: Peripheral B cells, ACPA-positive converter to clinical RA, post, CITE-seq, PC3B

description:
Library name: PC3B_CITE
Antibody-derived tag (ADT) surface protein library; UMI count matrix


title: Peripheral B cells, ACPA-positive converter to clinical RA, post, scRNA-seq, PC3B

description:
Library name: PC3B_GEX
10x Genomics Chromium gene expression library; Cell Ranger filtered feature-barcode matrix


title: Akt knockdown, 0nM insulin, biol rep 3

description:
Library name: AKTCTRL3
AKTCTRL3


title: Peripheral B cells, ACPA-positive converter to clinical RA, pre, BCR-seq, PC3A

description:
Library name: PC3A_BCR
10x Genomics Chromium BCR V(D)J library; Cell Ranger filtered contig annotations


title: Thymus_Dex_WT_rep2

description:
Library name: Thymus_Dex_WT_rep2_RNA-seq
Dex versus DMSO in WT mice (four tissues)
RNAseq_WT_Dex_vs_DMSO_count.txt.gz


title: TS NOR Hippocampal neurons, replicate 2, ATAC-seq

description: Library name: 30A

value: Hippocampus

value: Neurons

value: TS


title: Akt knockdown, 0nM insulin, biol rep 2

description:
Library name: AKTCTRL2
AKTCTRL2


title: Peripheral B cells, ACPA-positive converter to clinical RA, pre, CITE-seq, PC3A

description:
Library name: PC3A_CITE
Antibody-derived tag (ADT) surface protein library; UMI count matrix


title: Peripheral B cells, ACPA-positive converter to clinical RA, pre, scRNA-seq, PC3A

description:
Library name: PC3A_GEX
10x Genomics Chromium gene expression library; Cell Ranger filtered feature-barcode matrix


title: Akt knockdown, 0nM insulin, biol rep 1

description:
Library name: AKTCTRL1
AKTCTRL1


title: Peripheral B cells, ACPA-positive converter to clinical RA, post, BCR-seq, PC2B

description:
Library name: PC2B_BCR
10x Genomics Chromium BCR V(D)J library; Cell Ranger filtered contig annotations


title: Muscle_DMSOforDex_WT_rep4

description:
Library name: Muscle_DMSOforDex_WT_rep4_RNA-seq
Dex versus DMSO in WT mice (four tissues)
RNAseq_WT_Dex_vs_DMSO_count.txt.gz

source_name: Muscle

value: Muscle

value: 2 months


title: Thymus_Dex_WT_rep1

description:
Library name: Thymus_Dex_WT_rep1_RNA-seq
Dex versus DMSO in WT mice (four tissues)
RNAseq_WT_Dex_vs_DMSO_count.txt.gz

value: Male


title: Peripheral B cells, ACPA-positive converter to clinical RA, post, CITE-seq, PC2B

description:
Library name: PC2B_CITE
Antibody-derived tag (ADT) surface protein library; UMI count matrix

value: ACPA-positive converter to clinical RA

value: converter


title: Peripheral B cells, ACPA-positive converter to clinical RA, pre, BCR-seq, PC2A

description:
Library name: PC2A_BCR
10x Genomics Chromium BCR V(D)J library; Cell Ranger filtered contig annotations

value: peripheral blood

value: B cells


title: WT 0nM insulin control, biol rep 5

description:
Library name: WTCTRL5
WTCTRL5


title: Muscle_DMSOforDex_WT_rep3

description:
Library name: Muscle_DMSOforDex_WT_rep3_RNA-seq
Dex versus DMSO in WT mice (four tissues)
RNAseq_WT_Dex_vs_DMSO_count.txt.gz


title: Peripheral B cells, ACPA-positive converter to clinical RA, pre, CITE-seq, PC2A

description:
Library name: PC2A_CITE
Antibody-derived tag (ADT) surface protein library; UMI count matrix

value: female


title: WT 0nM insulin control, biol rep 4

description:
Library name: WTCTRL4
WTCTRL4


title: Peripheral B cells, ACPA-positive converter to clinical RA, pre, scRNA-seq, PC2A

description:
Library name: PC2A_GEX
10x Genomics Chromium gene expression library; Cell Ranger filtered feature-barcode matrix


title: Muscle_DMSOforDex_WT_rep2

description:
Library name: Muscle_DMSOforDex_WT_rep2_RNA-seq
Dex versus DMSO in WT mice (four tissues)
RNAseq_WT_Dex_vs_DMSO_count.txt.gz


title: Peripheral B cells, ACPA-positive converter to clinical RA, post, BCR-seq, PC1B

description:
Library name: PC1B_BCR
10x Genomics Chromium BCR V(D)J library; Cell Ranger filtered contig annotations

value: post


title: Peripheral B cells, ACPA-positive converter to clinical RA, post, scRNA-seq, PC2B

description:
Library name: PC2B_GEX
10x Genomics Chromium gene expression library; Cell Ranger filtered feature-barcode matrix


title: WT 0nM insulin control, biol rep 3

description:
Library name: WTCTRL3
WTCTRL3

value: Mammary epithelial cell


title: Peripheral B cells, ACPA-positive converter to clinical RA, post, CITE-seq, PC1B

description:
Library name: PC1B_CITE
Antibody-derived tag (ADT) surface protein library; UMI count matrix


title: Muscle_Dex_WT_rep4

description:
Library name: Muscle_Dex_WT_rep4_RNA-seq
Dex versus DMSO in WT mice (four tissues)
RNAseq_WT_Dex_vs_DMSO_count.txt.gz

value: WT


title: WT 0nM insulin control, biol rep 2

description:
Library name: WTCTRL2
WTCTRL2


title: Peripheral B cells, ACPA-positive converter to clinical RA, pre, BCR-seq, PC1A

description:
Library name: PC1A_BCR
10x Genomics Chromium BCR V(D)J library; Cell Ranger filtered contig annotations