title: SMC19, Solid (S) component

description:
Library name: SMC19_S
Column name in raw counts in all_Samples.txt : SMC19_S_counts


title: IC-21-siControl-2

status: Public on Aug 27 2025

type: SRA

city: Bethesda

first: Haiming

last: Cao

state: MD

address: 9000 Rockville Pike

department: NHLBI

country: USA

institute: NIH

library_source: transcriptomic

data_processing:
The original FASTQ read files were trimmed and cleaned using fastp, then quality analysis was performed using FastQC
The trimmed fastq files were aligned by HISAT2 to human GENCODE v38 genome reference.
The aligned reads were calculated by featureCounts and differential expression genes (DEGs) were analyzed by R package DESeq2/3.1.0
Assembly: GENCODE v38
Supplementary files format and content: tab-delimited text files include TPM (Transcripts Per Million) for each sample

molecule: total RNA

organism: Mus musculus

source_name: IC-21 cell line

extract_protocol:
The RNAs that have been extracted by Trizol were purified using the MagMAX RNA extraction kit (Thermo Fisher Scientific, Cat.AM1830).
RNA libraries were prepared for sequencing using standard Illumina kit and protocols; strand-specific

tag: strain

tag: treatment

value: LPS

tag: cell type

value: IC-21 cell line


title: SK_4VIC_B10, calcitriol, time 2

city: Birmingham

first: Changde

last: Cheng

state: AL

address: 1824 6th Ave S, Wallace Tumor Institute 520A

department: Medicine

institute: University of Alabama at Birmingham

description: Library name: SK_4VIC_B10

data_processing:
Bulk RNA data were processed using  WARDEN workflow for the analysis of RNA-Seq differential expression (McLeod et al., 2021).
Assembly: GRCh37
Supplementary files format and content: expression_matrix.txt

organism: Homo sapiens

source_name: Blood

extract_protocol:
Lysate from 1000 cells was processed by the Immunological Genome Project protocol (www.immgen.org): final sort of 1,000 cells directly into 5ɥl lysis buffer (TCL Buffer (Qiagen) with 1% 2-Mercaptoethanol). After sort vortex, keep on ice for 5 minutes, give a quick spin. Freeze on dry ice.
Follow Genome Project protocol (www.immgen.org): 5 ul of the lysates are used for each sample for Smart-seq2 library construction, prepared as previously described (Picelli et al., 2013; Picelli et al., 2014) with slight modifications. Briefly, total RNA was captured and purified on RNAClean XP beads (Beckman Coulter). Polyadenylated mRNA was then selected using an anchored oligo(dT) primer (5′–AAGCAGTGGTATCAACGCAGAGTACT30VN-3′) and converted to cDNA via reverse transcription. First strand cDNA was subjected to limited PCR amplification followed by Tn5 transposon based fragmentation using the Nextera XT DNA Library Preparation Kit (Illumina). Samples were then PCR amplified for 12 cycles using barcoded primers such that each sample carries a specific combination of eight base Illumina P5 and P7 barcodes and pooled together prior to sequencing. Smart-seq paired-end sequencing is performed on an Illumina NextSeq500 (two full NextSeq runs per batch of 96 samples, for 10M raw reads/sample on average) using 2 x 38bp reads with no further trimming.

tag: tissue

value: Blood

value: CD14 Monocyte

value: calcitriol

tag: time (day)


title: SK_4VIC_C04, calcitriol, time 2

description: Library name: SK_4VIC_C04


title: IC-21-siControl-1


title: SMC19, Ground-glass (GG) component

city: Seoul

first: Sang-Won

last: Um

address: 81 Irwon-ro

department: Division of Pulmonary and Critical Care Medicine, Department of Medicine, Samsung Medical Center

country: South Korea

institute: Sungkyunkwan University School of Medicine

description:
Library name: SMC19_GG
Column name in raw counts in all_Samples.txt : SMC19_GG_counts

data_processing:
For bulk RNA sequencing, reads were trimmed for adapter sequences and aligned to the hg38 genome using STAR aligner. Gene quantification was performed using RSEM.
For single-cell RNA sequencing, raw data were processed using Cell Ranger, including demultiplexing, barcode processing, and gene counting. Reads were aligned to the hg38 genome.
For spatial transcriptomics, raw sequencing data were processed using Space Ranger, aligned to hg38, and gene expression matrices were generated.
Assembly: hg38
Supplementary files format and content: tab-delimited text file includes raw counts for each Samples
Supplementary files format and content: tab-delimited text files of barcodes, features and matrix files
Supplementary files format and content: tab-delimited text files of barcodes, features, matrix and coordinate spot files, hi-/low resolution image file, cropped image file

source_name: Lung

extract_protocol:
Total RNA were extracted from FFPE tissue samples using the Qiagen AllPrep DNA/RNA Mini Kit (Qiagen, Germany) according to the manufacturer’s instructions. For scRNA seq, fresh tumor and  normal lung tissues were enzymatically dissociated using Miltenyi Tumor Dissociation Kit in combination with the GentleMACS Dissociator (Miltenyi Biotec). Single-cell suspensions were filtered through a 40 μm cell strainer, and cell viability (>85%) was confirmed using Trypan Blue staining and the Countess II Automated Cell Counter (Thermo Fisher). Live cells were enriched using Dead Cell Removal Kit (Miltenyi Biotec).
Total RNA sequencing libraries were prepared using the TruSeq Stranded Total RNA Library Preparation Kit (Illumina). Sequencing was performed on an Illumina HiSeq 4000 system in 150-bp paired-end mode. Single-cell libraries were constructed using the 10X Genomics Chromium Single Cell 3’ v2 Kit. Following cell capture and cDNA synthesis, cDNA amplification and library preparation were performed according to the 10X Genomics protocol. For spatial transcriptomic analysis, 10X Genomics Visium Spatial Gene Expression Slides & Reagent Kit was used according to the manufacturer’s protocol

tag: individuals

value: Lung


title: Duodenum,wide type,rep4

city: Beijing

first: Yang

middle: yang

last: Ge

state: Beijing

address: No. 2 Yabao Road

department: Department of Medical Genetics

country: China

institute: Capital Institute of Pediatrics

data_processing:
Index of the reference genome was built using Hisat2 v2.0.5 and paired-end clean reads were aligned to the reference genome using Hisat2 v2.0.5.
featureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene.
Assembly: Mus Musculus(GRCm38/mm10)
Supplementary files format and content: tab delimited text file includes FPKM values for each sample

source_name: Duodenum

extract_protocol:
RNA was extracted from duodenal tissues of Zeb2+/+ and Zeb2+/- mice
Messenger RNA was purified from total RNA using poly-T oligo attached magnetic beads. After fragmentation, the first strand cDNA was synthesized using random hexamer primers. Then the second strand cDNA was synthesized using dUTP, instead of dTTP. The directional library was ready after end repair, A-tailing, adapter ligation, size selection, USER enzyme digestion, amplification, and purification.

value: Duodenum

tag: genotype

value: WT


title: Macrophage-Mut-SMIM30-OE-3

source_name: Peritoneal Macrophage

value: Peritoneal Macrophage


title: Duodenum,wide type,rep3


title: AD2

city: xiamen

first: zuoxing

last: wu

address: No. 4221, Xiangan Road, Xiangan District, Xiamen

institute: xiamen university

data_processing:
CLC Genomics Workbench y 11 .0.1
Assembly: GRCm39.107
Supplementary files format and content: Excel file includes raw counts for each Sample
Supplementary files format and content: Excel file includes RPKM values for each Sample

source_name: Dorsal root ganglion

extract_protocol:
Total RNA was extracted from cultured cells or tissues using Trizol (Invitrogen, 15596026), as directed by the manufacturer.
RNA was harvested using Rneasy mini plus kit (Qiagen)1.5 ug of total RNA was used for the construction of sequencing libraries

value: Dorsal root ganglion

tag: cell line

value: neruro

value: sensory neruro


title: SK_4VIC_B09, calcitriol, time 0

description: Library name: SK_4VIC_B09


title: Macrophage-Mut-SMIM30-OE-2


title: SMC19, Distant normal (DN) lung region

description:
Library name: SMC19_DN
Column name in raw counts in all_Samples.txt : SMC19_DN_counts


title: SMC18, Solid (S) component

description:
Library name: SMC18_S
Column name in raw counts in all_Samples.txt : SMC18_S_counts


title: IC-21-siSMIM30-2


title: WT4


title: Duodenum,wide type,rep1


title: SK_4VIC_B07, calcifediol, time 0

description: Library name: SK_4VIC_B07

value: calcifediol


title: SMC18, Ground-glass (GG) component

description:
Library name: SMC18_GG
Column name in raw counts in all_Samples.txt : SMC18_GG_counts


title: Macrophage-Mut-SMIM30-OE-1


title: SMC18, Distant normal (DN) lung region

description:
Library name: SMC18_DN
Column name in raw counts in all_Samples.txt : SMC18_DN_counts


title: WT3


title: SK_4VIC_B06, placebo, time 2

description: Library name: SK_4VIC_B06

value: placebo


title: SK_4VIC_B11, calcifediol, time 0

description: Library name: SK_4VIC_B11


title: Macrophage-Mut-Control-3


title: WT2


title: AD3


title: SK_4VIC_B05, placebo, time 0

description: Library name: SK_4VIC_B05


title: SMC13, Solid (S) component

description:
Library name: SMC13_S
Column name in raw counts in all_Samples.txt : SMC13_S_counts


title: SK_4VIC_B04, placebo, time 2

description: Library name: SK_4VIC_B04


title: WT1


title: SMC13, Ground-glass (GG) component

description:
Library name: SMC13_GG
Column name in raw counts in all_Samples.txt : SMC13_GG_counts


title: AD1


title: SK_4VIC_B08, calcifediol, time 2

description: Library name: SK_4VIC_B08


title: P75-KO3


title: SK_4VIC_B03, placebo, time 0

description: Library name: SK_4VIC_B03


title: SMC13, Distant normal (DN) lung region

description:
Library name: SMC13_DN
Column name in raw counts in all_Samples.txt : SMC13_DN_counts


title: Macrophage-Mut-3


title: P75-KO2


title: SK_4VIC_B02, placebo, time 2

description: Library name: SK_4VIC_B02


title: Macrophage-Mut-2


title: SMC11, Solid (S) component

description:
Library name: SMC11_S
Column name in raw counts in all_Samples.txt : SMC11_S_counts


title: P75-KO1


title: SMC11, Ground-glass (GG) component

description:
Library name: SMC11_GG
Column name in raw counts in all_Samples.txt : SMC11_GG_counts


title: SK_4VIC_B01, placebo, time 0

description: Library name: SK_4VIC_B01


title: P75-WT3


title: Macrophage-Mut-1


title: SMC11, Distant normal (DN) lung region

description:
Library name: SMC11_DN
Column name in raw counts in all_Samples.txt : SMC11_DN_counts


title: SK_4VIC_A12, calcitriol, time 2

description: Library name: SK_4VIC_A12


title: P75-WT2


title: Macrophage-WT-3


title: Macrophage-WT-2


title: SMC08, Solid (S) component

description:
Library name: SMC08_S
Column name in raw counts in all_Samples.txt : SMC08_S_counts


title: SK_4VIC_A10, calcitriol, time 2

description: Library name: SK_4VIC_A10


title: Macrophage-Mut-Control-1


title: SMC08, Ground-glass (GG) component

description:
Library name: SMC08_GG
Column name in raw counts in all_Samples.txt : SMC08_GG_counts


title: Macrophage-Mut-Control-2


title: Macrophage-WT-1


title: TAC_RFP_cells

first: Xiaoyi

last: Wang

address: No.167, Beilishi Road, Xicheng District, 100037

department: Department of Cardiovascular Surgery, Fuwai Hospital

institute: Fuwai Hospital, National Center for Cardiovascular Diseases

description: one sample from mice left atrium

data_processing:
Alignment, filtering, barcode counting, and UMI counting were performed with cellranger count module to generate feature-barcode matrix and determine clusters (Cell Ranger software v6.0.1)
Assembly: GRCh38 for human data; mm10 for mice data
Supplementary files format and content: Matrix table with raw gene counts for every gene and every cell

molecule: polyA RNA

source_name: left atrium

extract_protocol:
Using single cell 3 'Library and Gel Bead Kit V3 (10x Genomics, 1000075) and Chromium Single Cell B Chip Kit (10x Genomics, 1000074), the cell suspension (300-600 living cells per microliter determined by Count Star) was loaded onto the Chromium single cell controller (10x Genomics) to generate single-cell gel beads in the emulsion according to the manufacturer’s protocol. Captured cells were lysed and the released RNA were barcoded through reverse transcription in individual GEMs. Reverse transcription was performed on a S1000TM Touch Thermal Cycler (Bio Rad) at 53°C for 45 min, followed by 85°C for 5 min, and hold at 4°C. The cDNA was generated and then amplified, and quality assessed using an Agilent 4200
According to the manufacture’s introduction, Single-cell RNA-seq libraries were constructed using Single Cell 3’ Library andGel Bead Kit V3. The libraries were finally sequenced using an Illumina Novaseq6000 sequencer with a sequencing depth of at least 100,000 reads per cell with pair-end 150 bp (PE150) reading strategy

treatment_protocol: C57BL/6 C57BL/6 J Cdh5-CreERT2/RFP  mice were performed transverse aortic constriction or sham surgery at 10-12 weeks

value: left atrium

tag: age

value: 20 weeks

value: transverse aortic constriction


title: Sham_RFP_cells

description: one sample from mice left atrium

value: sham surgery with transverse aortic constriction


title: BATF3_WT_LPS_Rep2[CUT_Tag]

city: San Antonio

first: Hui

last: Yan

state: TX

address: 7703 Floyd Curl Dr.

department: MIMG

institute: UTHSCSA

library_source: genomic

data_processing:
After Cut&Tag reads were aligned to the mouse genome (GRCm38/mm10) by Bowtie2 with the default parameters, mapped reads in bam files were masked using Samtools to generate bed files.
Peaks were identified by MACS2 without building the shifting model and set extension size at 200 bp, and further annotated by annotatePeaks.pl (–d option) in HOMER.
For each gene, the sum of peak scores in the region within 10 Kb of the TSS was calculated using a custom Python script.
Assembly: mm10
Supplementary files format and content: bigWig file from combined narrow peak files of revalent samples
Library strategy: CUT&Tag

molecule: genomic DNA

source_name: B cell

extract_protocol:
Follow instruction from manual of CUT&Tag-IT Assay kit (Active Motif, #53160)
Illumina-compatible index primers

value: B cell

value: LPS


title: SK_4VIC_A08, calcifediol, time 2

description: Library name: SK_4VIC_A08

value: Blood

value: CD14 Monocyte


title: SK_4VIC_A09, calcitriol, time 0

description: Library name: SK_4VIC_A09

value: calcitriol


title: SMC06, Solid (S) component

description:
Library name: SMC06_S
Column name in raw counts in all_Samples.txt : SMC06_S_counts

value: Lung


title: SMC08, Distant normal (DN) lung region

description:
Library name: SMC08_DN
Column name in raw counts in all_Samples.txt : SMC08_DN_counts


title: BATF3_WT_LPS_Rep1[CUT_Tag]

value: WT


title: SK_4VIC_A06, placebo, time 2

description: Library name: SK_4VIC_A06


title: BATF3_WT_LA21_Rep1[CUT_Tag]


title: SMC06, Ground-glass (GG) component

description:
Library name: SMC06_GG
Column name in raw counts in all_Samples.txt : SMC06_GG_counts


title: SK_4VIC_A07, calcifediol, time 0

description: Library name: SK_4VIC_A07


title: SMC06, Distant normal (DN) lung region

description:
Library name: SMC06_DN
Column name in raw counts in all_Samples.txt : SMC06_DN_counts


title: BATF3_WT_LA21_Rep2[CUT_Tag]


title: SK_4VIC_A11, calcitriol, time 0

description: Library name: SK_4VIC_A11


title: AO_18h_2

city: a

first: Li

last: Xiaoli

address: a

institute: YNU University

description: Library name: Sample 11

data_processing:
Date was analyzed using OmicShare tools (https://www.omicshare.com/).
Assembly: HiSat2 and StringTie
Supplementary files format and content: xls file includes tpm value for each sample

organism: Orbilia oligospora

source_name: hypha

extract_protocol:
Total RNA was extracted from tissue samples, the concentration and purity of the extracted RNA were detected by Nanodrop2000, RNA integrity was detected by agarose gel electrophoresis, and RIN value was determined by Agilent2100. A single library construction requires that the total amount of RNA is ≥1ug, the concentration is ≥35ng/μL, OD260/280 is 1.8 - 2.2, and OD260/230≥1.0.
The libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: The WT and ΔAoopy2 mutant strains were pre-cultured in liquid TG medium at 28ºC for 48 h. Next, mycelia were transferred to the WA medium, a low-nutrient environment, to induce trap formation. Approximately 1000 nematodes were added to each well. Mycelial samples were harvested immediately before nematode addition (0 h post-induction) and 18 h post-induction.

value: hypha

value: Fungal hyphae cells

value: wild type

value: Trap induction with nematode


title: SK_4VIC_E04, calcitriol, time 2

description: Library name: SK_4VIC_E04


title: SK_4VIC_A05, placebo, time 0

description: Library name: SK_4VIC_A05


title: BATF3_WT_A21_Rep2[CUT_Tag]


title: P75-WT1

value: Dorsal root ganglion

value: neruro

value: sensory neruro


title: AO_0h_3

description: Library name: Sample 9

growth_protocol: The WT and ΔAoopy2 mutant strains were pre-cultured in liquid TG medium at 28ºC for 48 h

value: no treatment


title: AO_18h_3

description: Library name: Sample 12


title: SK_4VIC_A04, calcitriol, time 2

description: Library name: SK_4VIC_A04


title: H1341-NU7441-2, 5days

city: New York

first: BiNGS

last: Core

address: 1470 Madison Ave

institute: Icahn School of Medicine at Mount Sinai

description: RNA sequencing

data_processing:
Salmon to quantfiy counts, DESeq2 for count norrmalization
Median Rations Normlaization
Assembly: hg38
Supplementary files format and content: salmon_gene_counts_normalized.csv

source_name: Immortalized Cell lines derived from Small Cell Lung Cancer patients

extract_protocol:
Cells were grown in RPMI 1640 media supplemented with 10% FBS, 1% pen-strep. And 1X Glutamax, in 37 degree C, 90% Humidity and 5% carbon-di-oxide. 2 X 10^6 cells were plated 24 hours before treatment and then were treated with either DMSO or 4µM NU7441.
Sequencing libraries were clustered on one flowcell lane and then loaded on the Illumina HiSeq instrument (4000 or equivalent) according to manufacturer’s instructions. Samples were sequenced using a 2x150bp paired end (PE) configuration. Image analysis and base calling were conducted by the HiSeq Control Software (HCS). Raw sequence data (.bcl files) was converted into fastq files and de-multiplexed using Illumina's bcl2fastq 2.17 software. One mismatch was allowed for index sequence identification.

treatment_protocol: Total RNA was extracted using the RNeasy Plus Universal mini kit following manufacturer’s instructions (Qiagen, Hilden, Germany). RNA sequencing libraries were prepared using the NEBNext Ultra II RNA Library Prep Kit for Illumina following manufacturer’s instructions (NEB, Ipswich, MA, USA). RNA samples and sequencing libraries were validated on the Agilent TapeStation (Agilent Technologies, Palo Alto, CA, USA), and quantified by using Qubit 2.0 Fluorometer (Invitrogen, Carlsbad, CA) as well as by quantitative PCR (KAPA Biosystems, Wilmington, MA, USA).

value: SCLC cells


title: BATF3_WT_A21_Rep1[CUT_Tag]


title: AO_18h_1

description: Library name: Sample 10


title: BATF3_KO_LA21_Rep2[CUT_Tag]

value: Batf3 knockout


title: H1341-NU7441-1, 5days

description: RNA sequencing

growth_protocol: Cells were grown in RPMI 1640 media supplemented with 10% FBS, 1% pen-strep. And 1X Glutamax, in 37 degree C, 90% Humidity and 5% carbon-di-oxide

value: Immortalized Cell lines derived from Small Cell Lung Cancer patients


title: AO_0h_1

description: Library name: Sample 7


title: Opy2_18h_3

description: Library name: Sample 6

value: mutant strain


title: SK_4VIC_A02, calcifediol, time 2

description: Library name: SK_4VIC_A02

value: Blood

value: calcifediol


title: SK_4VIC_A03, calcitriol, time 0

description: Library name: SK_4VIC_A03

value: CD14 Monocyte

value: calcitriol


title: H1341-Control-3, 5days

description: RNA sequencing

value: WT


title: BATF3_KO_LA21_Rep1[CUT_Tag]

value: B cell


title: AO_0h_2

description: Library name: Sample 8

value: hypha

value: Fungal hyphae cells


title: SK_4VIC_A01, calcifediol, time 0

description: Library name: SK_4VIC_A01


title: H3K27me3_LPS_Rep2[CUT_Tag]

data_processing:
After CUT&Tag reads were aligned to the mouse genome (GRCm38/mm10) by Bowtie2 with the default parameters, mapped reads in bam files were masked using Samtools to generate bed files.
Peaks were identified by MACS2 without building the shifting model and set extension size at 200 bp, and further annotated by annotatePeaks.pl (–d option) in HOMER.
For each gene, the sum of peak scores in the region within 10 Kb of the TSS was calculated using a custom Python script.
Assembly: mm10
Supplementary files format and content: bigWig file from combined narrow peak files of revalent samples
Library strategy: CUT&Tag

value: LPS


title: H1341-Control-2, 5days

description: RNA sequencing

value: DMSO


title: Opy2_18h_2

description: Library name: Sample 5

value: Trap induction with nematode


title: SK_4VIB_H10, placebo, time 2

description: Library name: SK_4VIB_H10

value: placebo


title: H3K27me3_LPS_Rep1[CUT_Tag]


title: Opy2_18h_1

description: Library name: Sample 4


title: H1341-Control-1, 5days

description: RNA sequencing


title: H1341-NU7441-3, 5days

description: RNA sequencing


title: SK_4VIB_H09, placebo, time 0

description: Library name: SK_4VIB_H09


title: H3K27me3_LA21_Rep2[CUT_Tag]


title: H720-NU7441-3, 5days

description: RNA sequencing


title: Opy2_0h_3

description: Library name: Sample 3

value: no treatment


title: H3K27me3_LA21_Rep1[CUT_Tag]


title: SK_4VIB_H08, calcitriol, time 2

description: Library name: SK_4VIB_H08


title: SK_4VIB_H07, calcitriol, time 0

description: Library name: SK_4VIB_H07


title: H720-NU7441-2, 5days

description: RNA sequencing

value: SCLC cells


title: Opy2_0h_2

description: Library name: Sample 2


title: H3K27ac_LPS_Rep2[CUT_Tag]


title: H720-NU7441-1, 5days

description: RNA sequencing


title: SK_4VIB_H06, calcifediol, time 2

description: Library name: SK_4VIB_H06


title: Opy2_0h_1

description: Library name: Sample 1


title: H3K27ac_LPS_Rep1[CUT_Tag]


title: AD-bMSC, Knockout-Library, day30, Replicate 3, Amplicon-seq

city: Rehovot

first: Roni

last: Rak

address: Herzl 229

department: Animal Science

country: Israel

institute: Agriculture Research Organization

data_processing:
Raw fastq files were quality filtered followed by sgRNA abundance counting using MaGeCK count function
Ranking and scoring of sgRNA and genes by enrichment/depletion was performed using MaGeck test function
Comparison and validation of ranking and scoring of genes compared to the DepMap database
Genes were clustered based on their temporal expression profile of change in sgRNA abundance over time
Identified clusters were analysed for over-represented gene ontology terms using gProfiler
Assembly: ARS-UCD1.2
Supplementary files format and content: comma-sepearted txt file contains raw reads by sample and gene
Library strategy: CRISPR sgRNA-seq

organism: Bos taurus

source_name: Bovine subcutaneous adipose derived mesenchymal stem cells

growth_protocol: Post-transduction, cells were passaged every 5 days, seeding 3.5e3 cells/cm2

extract_protocol:
Total DNA was extracted from 5x10^5 cells using QuickExtract reagent (Lucigen) followed by two consecutive PCR to amplify sgRNA amplicon
Extracted genomic DNA was amplified and added unique sample adapters, followed by SPRI-beads size selection and a second PCR adding NGS adapters, followed by a second SPRI-beads size selection

treatment_protocol: Cells were transduced with both Cas9 and CRISPR-knockout library, and were passaged for 30 days

value: CRISPR-KO Library

value: Proliferation

tag: sequencing batch

tag: time

value: day 30


title: H720-Control-2, 5days

description: RNA sequencing

value: Immortalized Cell lines derived from Small Cell Lung Cancer patients


title: H720-Control-3, 5days

description: RNA sequencing


title: H3K27ac_LA21_Rep2[CUT_Tag]


title: SK_4VIB_H05, calcifediol, time 0

description: Library name: SK_4VIB_H05

value: Blood

value: calcifediol


title: AD-bMSC, Knockout-Library, day30, Replicate 2, Amplicon-seq

value: Bovine subcutaneous adipose derived mesenchymal stem cells


title: H3K27ac_LA21_Rep1[CUT_Tag]

value: WT


title: SK_4VIB_H04, placebo, time 2

description: Library name: SK_4VIB_H04

value: CD14 Monocyte


title: RELA_nil_Rep1[ChIP_Seq]

data_processing:
After ChIP-seq reads were aligned to the mouse genome (GRCm38/mm10) by Bowtie2 with the default parameters, mapped reads in bam files were masked using Samtools to generate bed files.
Peaks were identified by MACS2 without building the shifting model and set extension size at 200 bp, and further annotated by annotatePeaks.pl (–d option) in HOMER.
BigWig files were convered from sorted bam file.
Assembly: mm10
Supplementary files format and content: bigWig file from combined narrow peak files of revalent samples

extract_protocol:
B cells were treated with disuccinimidyl glutarate for 30 m and then washing with cold PBS before chromatin crosslinking by 1% formaldehyde in PBS at 25°C for 10 m.  Chromatin was sonicated to yield approximately 200–600-bp DNA fragments, pre-cleared with agarose beads conjugated with protein A (ThermoFisher) and then incubated with a polyclonal rabbit Ab to NF-kB p65. After incubation overnight, immune complexes were isolated using agarose-beads conjugated with protein A, washed and eluted in buffer.  Eluates were incubated at 65°C for 4 h to reverse formaldehyde crosslinks. DNA was purified using a QIAquick PCR purification column (Qiagen).
Illumina-compatible index primers

value: B cell


title: H446-NU7441-3, 5days

description: RNA sequencing


title: SK_4VIB_H03, placebo, time 0

description: Library name: SK_4VIB_H03


title: AD-bMSC, Knockout-Library, day24, Replicate 3, Amplicon-seq

value: day 24


title: SK_4VIB_H02, calcifediol, time 2

description: Library name: SK_4VIB_H02


title: AD-bMSC, Knockout-Library, day30, Replicate 1, Amplicon-seq


title: H446-NU7441-2, 5days

description: RNA sequencing


title: RELA_LPS_Rep1[ChIP_Seq]

value: LPS


title: RELA_LC21_Rep3[ChIP_Seq]


title: AD-bMSC, Knockout-Library, day24, Replicate 1, Amplicon-seq


title: SK_4VIB_G12, calcitriol, time 2

description: Library name: SK_4VIB_G12

value: calcitriol


title: H446-NU7441-1, 5days

description: RNA sequencing


title: SK_4VIB_H01, calcifediol, time 0

description: Library name: SK_4VIB_H01


title: RELA_LC21_Rep2[ChIP_Seq]


title: H446-Control-3, 5days

description: RNA sequencing

value: DMSO


title: AD-bMSC, Knockout-Library, day16, Replicate 3, Amplicon-seq

value: day 16


title: SK_4VIB_G11, calcitriol, time 0

description: Library name: SK_4VIB_G11


title: RELA_LC21_Rep1[ChIP_Seq]


title: AD-bMSC, Knockout-Library, day16, Replicate 2, Amplicon-seq


title: H720-Control-1, 5days

description: RNA sequencing


title: H446-Control-2, 5days

description: RNA sequencing


title: SK_4VIB_G10, placebo, time 2

description: Library name: SK_4VIB_G10

value: placebo


title: H446-Control-1, 5days

description: RNA sequencing

value: SCLC cells


title: AD-bMSC, Knockout-Library, day16, Replicate 1, Amplicon-seq

value: CRISPR-KO Library


title: H196-NU7441-3, 5days

description: RNA sequencing


title: Input_LPS_Rep1[ChIP_Seq]


title: SK_4VIB_G09, placebo, time 0

description: Library name: SK_4VIB_G09


title: Input_nil_Rep1[ChIP_Seq]


title: AD-bMSC, Knockout-Library, day7, Replicate 3, Amplicon-seq

value: Proliferation

value: day 7


title: SK_4VIB_G08, calcitriol, time 2

description: Library name: SK_4VIB_G08


title: Input_LC21_Rep1[ChIP_Seq]


title: AD-bMSC, Knockout-Library, day24, Replicate 2, Amplicon-seq


title: BATF3_WT_LPS_Rep4[ATAC_Seq]

data_processing:
After ATAC-Seq reads were aligned to the mouse genome (GRCm38/mm10) by Bowtie2 with the default parameters, mapped reads in bam files were masked using Samtools to generate bed files.
Peaks were identified by MACS2 without building the shifting model and set extension size at 200 bp, and further annotated by annotatePeaks.pl (–d option) in HOMER.
For each gene, the sum of peak scores in the region within 10 Kb of the TSS was calculated using a custom Python script.  These values were averaged across the three ATAC-seq replicates for each experimental condition.
Bigwig files were convered from bam file.
Assembly: mm10
Supplementary files format and content: All processed data presented in bigwig format.

growth_protocol: Cells were cultured in RPMI 1640 with 10% of FBS plus 1% antibiotics and 50 uM beta-mercaptoethanol

extract_protocol:
Follow instruction from manual of TransNGSTn5 DNA Library Prep Kit for Illumina® (for 50 ng DNA, #KP101-02)
Follow instruction from manual of TransNGSTn5 Index Kit for Illumina®

treatment_protocol: B cells from Batf3 wildtype and knockout mice were stimulated with either LPS or LPS plus anti-CD40 and IL-21 (LA21)


title: SK_4VIB_G07, calcitriol, time 0

description: Library name: SK_4VIB_G07


title: AD-bMSC, Knockout-Library, day7, Replicate 2, Amplicon-seq


title: H196-NU7441-1, 5days

description: RNA sequencing

value: Immortalized Cell lines derived from Small Cell Lung Cancer patients


title: H196-NU7441-2, 5days

description: RNA sequencing


title: AD-bMSC, Knockout-Library, day7, Replicate 1, Amplicon-seq


title: SK_4VIB_G06, calcifediol, time 2

description: Library name: SK_4VIB_G06

value: Blood


title: BATF3_WT_LPS_Rep3[ATAC_Seq]


title: H196-Control-3, 5days

description: RNA sequencing


title: SK_4VIB_G05, calcifediol, time 0

description: Library name: SK_4VIB_G05

value: calcifediol


title: H196-Control-2, 5days

description: RNA sequencing


title: BATF3_WT_LPS_Rep2[ATAC_Seq]


title: AD-bMSC, Knockout-Library, day3, Replicate 3, Amplicon-seq

value: Bovine subcutaneous adipose derived mesenchymal stem cells

value: day 3


title: AD-bMSC, Knockout-Library, day3, Replicate 2, Amplicon-seq


title: SK_4VIB_G04, placebo, time 2

description: Library name: SK_4VIB_G04

value: CD14 Monocyte


title: H196-Control-1, 5days

description: RNA sequencing

value: WT


title: BATF3_WT_LPS_Rep1[ATAC_Seq]

value: B cell


title: BATF3_WT_LA21_Rep4[ATAC_Seq]


title: AD-bMSC, Knockout-Library, day3, Replicate 1, Amplicon-seq


title: AD-bMSC, Knockout-Library, Late Term Screen, Day 100, Replicate 3, Amplicon-seq

value: day 100


title: H146-NU7441-2, 5days

description: RNA sequencing


title: BATF3_WT_LA21_Rep3[ATAC_Seq]


title: H146-NU7441-3, 5days

description: RNA sequencing


title: AD-bMSC, Knockout-Library, Late Term Screen, Day 100, Replicate 2, Amplicon-seq


title: SK_4VIB_G01, calcitriol, time 0

description: Library name: SK_4VIB_G01

value: calcitriol


title: SK_4VIB_G02, calcitriol, time 2

description: Library name: SK_4VIB_G02


title: BATF3_WT_LA21_Rep2[ATAC_Seq]


title: AD-bMSC, Knockout-Library, Late Term Screen, Day 100, Replicate 1, Amplicon-seq


title: SK_4VIB_F12, calcitriol, time 2

description: Library name: SK_4VIB_F12


title: H146-Control-3, 5days

description: RNA sequencing

value: DMSO


title: H146-NU7441-1, 5days

description: RNA sequencing


title: AD-bMSC, Knockout-Library, Late Term Screen, Day 70, Replicate 3, Amplicon-seq

value: day 70


title: BATF3_KO_LPS_Rep4[ATAC_Seq]

value: Batf3 knockout

value: LPS


title: SK_4VIB_F11, calcitriol, time 0

description: Library name: SK_4VIB_F11


title: BATF3_WT_LA21_Rep1[ATAC_Seq]


title: SK_4VIB_F10, calcifediol, time 2

description: Library name: SK_4VIB_F10


title: BATF3_KO_LPS_Rep3[ATAC_Seq]


title: AD-bMSC, Knockout-Library, Late Term Screen, Day 70, Replicate 1, Amplicon-seq

value: CRISPR-KO Library


title: SK_4VIB_F09, calcifediol, time 0

description: Library name: SK_4VIB_F09


title: BATF3_KO_LPS_Rep2[ATAC_Seq]


title: SK_4VIB_G03, placebo, time 0

description: Library name: SK_4VIB_G03

value: placebo


title: H146-Control-2, 5days

description: RNA sequencing

value: SCLC cells


title: H146-Control-1, 5days

description: RNA sequencing

value: Immortalized Cell lines derived from Small Cell Lung Cancer patients


title: AD-bMSC, Knockout-Library, Late Term Screen, Day 70, Replicate 2, Amplicon-seq

value: Proliferation


title: AD-bMSC, Knockout-Library, Late Term Screen, Day 50, Replicate 3, Amplicon-seq

value: day 50


title: SK_4VIB_F08, calcifediol, time 2

description: Library name: SK_4VIB_F08

value: Blood

value: calcifediol


title: DMS114-NU7441-2, 5days

description: RNA sequencing


title: BATF3_KO_LA21_Rep4[ATAC_Seq]


title: AD-bMSC, Knockout-Library, Late Term Screen, Day 50, Replicate 2, Amplicon-seq

value: Bovine subcutaneous adipose derived mesenchymal stem cells


title: SK_4VIB_F07, calcifediol, time 0

description: Library name: SK_4VIB_F07

value: CD14 Monocyte


title: DMS114-NU7441-1, 5days

description: RNA sequencing

value: WT


title: AD-bMSC, Knockout-Library, Late Term Screen, Day 50, Replicate 1, Amplicon-seq


title: SK_4VIB_F06, placebo, time 2

description: Library name: SK_4VIB_F06


title: DMS114-Control-3, 5days

description: RNA sequencing


title: AD-bMSC, Knockout-Library, Late Term Screen, Day 15, Replicate 3, Amplicon-seq

value: day 15


title: SK_4VIB_F05, placebo, time 0

description: Library name: SK_4VIB_F05


title: BATF3_KO_LA21_Rep2[ATAC_Seq]

value: B cell


title: AD-bMSC, Knockout-Library, Late Term Screen, Day 15, Replicate 2, Amplicon-seq


title: SK_4VIB_F04, placebo, time 2

description: Library name: SK_4VIB_F04


title: DMS114-Control-1, 5days

description: RNA sequencing

value: DMSO


title: BATF3_KO_LA21_Rep1[ATAC_Seq]


title: AD-bMSC, Knockout-Library, Late Term Screen, Day 15, Replicate 1, Amplicon-seq


title: SK_4VIB_F03, placebo, time 0

description: Library name: SK_4VIB_F03


title: DMS114-NU7441-3, 5days

description: RNA sequencing


title: WT_Nil_Rep3[ATAC_Seq]

data_processing:
After ATAC-Seq reads were aligned to the mouse genome (GRCm38/mm10) by Bowtie2 with the default parameters, mapped reads in bam files were masked using Samtools to generate bed files.
Peaks were identified by MACS2 without building the shifting model and set extension size at 200 bp, and further annotated by annotatePeaks.pl (–d option) in HOMER.
For each gene, the sum of peak scores in the region within 10 Kb of the TSS was calculated using a custom Python script.  These values were averaged across the three ATAC-seq replicates for each experimental condition.
Assembly: mm10
Supplementary files format and content: ATAC_Seq_WT_B_cells_Different_Stimuli.csv


title: SK_4VIB_F02, calcitriol, time 2

description: Library name: SK_4VIB_F02

value: calcitriol


title: Person Living with HIV and have had latent TB (PWH 30)

type: genomic

city: Kampala

first: Joseph

middle: Baruch

last: Baluku

address: Mulago Hill Rd

country: Uganda

institute: Makerere University Lung Institute

hyb_protocol: Bisulphite converted DNA was amplified, fragemented and hybridized to human Infinium MethylationEPICv2 using standard Illumina protocol

scan_protocol: Arrays were imaged using BeadArray Reader (iScan system) with standard recommended illumina scanner setting

data_processing:
Minfi Packagein R environment (v4.4.1)
[processed value definition] Average Beta (linked as supplementary file on Series record)

label: Cy3, Cy5

source_name: Plasma

label_protocol: Standard Illumina Protocol

extract_protocol: Genomic DNA was extracted from the blood using the QIAamp DNA Blood Mini Kit (QIAGEN) according to standard instructions

value: Plasma

tag: sample group

value: LatentTB

tag: Sex

value: Female

tag: ever been diagnosed with tb

value: No

tag: igra results

value: Positive

tag: previous tb infection

value: Yes


title: BATF3_KO_LPS_Rep1[ATAC_Seq]

value: Batf3 knockout

value: LPS


title: Person Living with HIV and have had active TB (PWH 29)

value: ActiveTB

value: Male

value: Negative


title: SK_4VIB_F01, calcitriol, time 0

description: Library name: SK_4VIB_F01

value: Blood

value: CD14 Monocyte


title: immortalized brown adipocytes D7 (iBAT), FGF8-treated

city: Freising

first: Katharina

last: Küllmer

state: Bavaria

address: Gregor-Mendel Straße 2

country: Germany

institute: Technical University of Munich

description: Library name: Sample 6

data_processing:
Alignmet was done using the Galaxy Europe Server. Before, reads got trimmed using TrimGalore. Mapping was done using HISAT2.
Assembly: mm39
Supplementary files format and content: countmatrix as txt file

source_name: iBAT

growth_protocol: Primary white preadipocytes (iWAT) were maintained in high-glucose DMEM medium supplemented with 20% fetal bovine serum (FBS) and antibiotics in humidified atmosphere at 5% CO2 and 37°C.

extract_protocol:
RNA was extracted using the Promega Kit (SV Total RNA Isolation System )
Library preparation was performed using the Illumina Kit following the instructions.

treatment_protocol: Cells were treated upon 70-80% confluency with 5.5 nM FGF1, 2, 4, 8, or 9 or left untreated.

value: iBAT

value: immortalized cells (stromal vascular fraction)

value: brown adipocytes

value: Bl6N, wild-type


title: immortalized brown adipocytes D3 (iBAT), FGF8-treated

description: Library name: Sample 5


title: Person Living with HIV and have had no TB (PWH 28)

value: Plasma


title: WT_Nil_Rep2[ATAC_Seq]

value: B cell

value: WT


title: immortalized brown preadipocytes D0 (iBAT), FGF8-treated

description: Library name: Sample 4

value: brown preadipocytes


title: SK_4VIB_E12, calcifediol, time 2

description: Library name: SK_4VIB_E12

value: calcifediol


title: WT_LPS_Rep3[ATAC_Seq]


title: BATF3_KO_LA21_Rep3[ATAC_Seq]


title: DMS114-Control-2, 5days

description: RNA sequencing

value: Immortalized Cell lines derived from Small Cell Lung Cancer patients

value: SCLC cells

value: DMSO


title: SK_4VIB_E11, calcifediol, time 0

description: Library name: SK_4VIB_E11


title: Person Living with HIV and have had latent TB (PWH 27)

value: LatentTB

value: Female

value: No

value: Positive

value: Yes


title: immortalized brown adipocytes D7 (iBAT), untreated

description: Library name: Sample 3

value: iBAT

value: untreated


title: WT_LPS_Rep2[ATAC_Seq]

value: LPS


title: immortalized brown adipocytes D3 (iBAT), untreated

description: Library name: Sample 2

value: immortalized cells (stromal vascular fraction)

value: brown adipocytes

value: Bl6N, wild-type


title: Person Living with HIV and have had no TB (PWH 26)

value: Plasma

value: Negative


title: SK_4VIB_E10, calcifediol, time 2

description: Library name: SK_4VIB_E10

value: Blood

value: CD14 Monocyte

value: calcifediol


title: immortalized brown preadipocytes D0 (iBAT), untreated

description: Library name: Sample 1

value: brown preadipocytes


title: WT_LPS_Rep1[ATAC_Seq]

value: B cell

value: WT


title: Person Living with HIV and have had active TB (PWH 25)

value: ActiveTB

value: Male


title: SK_4VIB_E09, calcifediol, time 0

description: Library name: SK_4VIB_E09


title: WT_LC21_Rep3[ATAC_Seq]


title: Person Living with HIV and have had latent TB (PWH 24)

value: LatentTB

value: Female

value: No

value: Positive

value: Yes


title: Person Living with HIV and have had latent TB (PWH 23)


title: WT_LC21_Rep2[ATAC_Seq]


title: SK_4VIB_E08, placebo, time 2

description: Library name: SK_4VIB_E08

value: placebo


title: Modified Sm-RIP human extract, mouse polyA-RNA, +ATP, stringent washing 2 (hxmras2)

city: Cleveland

first: Anton

middle: James

last: Blatnik III

state: Ohio

address: 2109 Adelbert Road

institute: Case Western Reserve University

description:
Library name: hxmras2
RNA enriched by Y12-RIP from human S3-iNPC cytoplasmic extract incubated with mouse NSC-34 polyA-RNA and ATP under stringent washing conditions

data_processing:
Adapter sequences were trimmed using Cutadapt. Reads were aligned to both the human GRCh38 and mouse GRCm39 genome assemblies, separately, (Esnembl release 100) using STAR. Reads were counted using FeatureCounts from the subread package, using the fractional argument for reads mapped to multiple loci. The standard use of FeatureCounts is supplied in the '_Sm_counts_master_' files. Additionally, FeatuerCounts was supplied a Simplified Annotation File containing only intronic coordinates and was used to provide count information for intronic reads and is supplied in the '_Sm_counts2intron_master_' processed data files. Unix commands were used combine the counts for each sample into a single master sheet used as an input for Deseq2.
Wald-test comparisons of the FeatureCounts outputs were performed using Deseq2 in RStudio (version 2023.12.1+402) on an Apple 2023 MacBook Pro running macOS Sonoma 14.6.1. For all comparisons, the adjusted p-values from Deseq2 were used. Principal component analysis was performed on the top 1000 genes to ensure proper clustering of samples. Custom R scripts were then written to analyze the data presented within this manuscript and are available upon request.
Assembly: GRCh38, GRCm39
Supplementary files format and content:
Modified FeaturesCount output file for alignment of all samples to human GRCh38 or mouse GRCm39. This file contains a single column of the assigned counts for each sample library and was used as the input for Deseq2.
'2023_n3_Sm_counts2intron_master_human.txt' for GSM8548423-25, GSM8548429-31, GSM8548438-40, and GSM8548444-46
'2023_n3_Sm_counts2intron_master_mouse.txt' for GSM8548426-28, GSM8548432-37, GSM8548441-43

molecule: cytoplasmic RNA

source_name: S3-iNPC, NSC-34

growth_protocol: Neural stem cell NSC-34 cells were cultured in 12% FBS DMEM supplemented with L-glutamine and PenStrep (12% FBS Atlanta S11550, 10% PenStrep/L-Glutamine Gibco 10378-016, DMEM Gibco 11960077) under 37 °C,  5% CO2 in normoxic conditions. Cells were routinely passaged every 2-3 days by washing twice with Phosphate Buffered Saline lacking divalent cations, and then treating with 0.05% Trypsin-EDTA (Gibco 25300054). S3 fibroblasts were induced to a neural progenitor cell fate as described by Meyer et al (79). To culture neural progenitor cell S3-iNPCs, dishes were coated with fibronectin (Millipore FC010-10MG) and cells were cultured in DMEM/F12+ Glutamax (Gibco 10565-042) supplemented with 10% N2 (Gibco 17502-048), 10% B27 (Gibco 17504-044), 10% Anti-Anti (Gibco 15270-62), and 20 ng/mL FGF2 ( Peprotech 100-18B), under 37 °C, 5% CO2 in normoxic conditions. Cells were routinely passaged every 2-3 days by washing twice with PBS lacking divalent cations and treating with StemPro Accutase (ThermoFisher A1110501).

extract_protocol:
Cytoplasmic cell extracts were generated by scraping and collecting NSC-34 or S3-iNPC cells in cold phosphate buffered saline containing only monovalent cations. Cells were pelleted by centrifugation 400 x g for 4 min. Cells were resuspended in digitoxin lysis buffer (20 mM Tris pH 8, 50 mM KCl, 0.5 MgCl2, 1x eComplete, 200 units/mL RNase-OUT, 50 ug/mL digitonin, in DEPC-treated water) and incubated on ice for a few minutes. Lysates were passaged 6 times through a 27 gauge needle with syringe then centrifuged at 1,500 x g for 1 minute at 4 °C. Supernatant was measured and transferred to a new microfuge tube and supplemented with NP-40 to achieve 0.01% final concentration. Lysates were then centrifuged at 4,000 x g for 15 minutes at 4 °C. Supernatants were then aliquoted into microfuge tubes and frozen in liquid nitrogen.
Three replicates of the four conditions for both species combinations were used to generate sequencing libraries, using 50 ng of captured RNA as input for the Takara SMARTer Stranded Total RNA-Seq Kit v3-Pico Input Mammalian (Takara 634451) or Takara SMARTer Stranded Total RNA-Seq Kit v2-Pico Input Mammalian (Takara 634411).

treatment_protocol: Oligo-dT isolation of polyA-RNA - Four 15 cm dishes of NSC-34 or S3-iNPC cell were washed thrice with PBS lacking divalent cations and treated with 8 mL TRIzol Reagent (Invitrogen 15596026) per 15 cm dish. TRIzol samples were pooled and a large scale total RNA isolation and precipitation was performed following manufacturer’s instructions. After purification, isolated RNA was treated with 200 units of Turbo DNase (Invitrogen AM2239) and incubated at 37 °C for 30 minutes with gentle rotation at 350 rpm in Eppendorf Thermomixer R. DNase was removed by phenol:chloroform extraction. RNA was precipitated with 1.5 M final concentration of LiCl and 100% ethanol, centrifuged at > 18,000 x g for 15 minutes. RNA was resupsended in 1 mL nuclease-free water and quantified using Qubit RNA Broad Range Assay (Invitrogen Q10211). PolyA-RNA was isolated using Dynabeads mRNA Purification Kit (Invitrogen 61006). Oligo-dT beads were reused post-polyA-RNA elution to isolate the magnitude of polyA-RNA required for modified Sm-ring assembly reaction and sequencing conditions. After isolation, polyA-RNA was quantified using Qubit RNA Broad Range Assay (Invitrogen Q10211) and RNA integrity (RIN) was quantified by TapeStation analysis performed by the Ohio State Comprehensive Cancer Center Genomics Core to determine removal of polyA-minus RNAs. For Sm-RIP and modified Sm-ring assembly RIPs, Protein-A DynaBeads (Invitrogen 10001D) were aliquoted 8.6 µL/rxn and washed three times in PBS + 0.1% NP-40. 1.6 µg/rxn Y12 antibody (Novus Biologicals NB600-546) was conjugated to Protein-A DynaBeads by incubating in PBS + 0.1% NP-40 for 1 hour at 4 °C with rotation. Beads were washed 3 more times with PBS + 0.1% NP-40, then three times with RSB-500 + 0.1% NP-40 (RSB-500: 10 mM Tris pH 7.4, 500 mM NaCl, 2.5 mM MgCl2). Beads were finally resuspended in 120 µL/rxn RSB-500 + 0.1% NP-40 supplemented with 2 mg/mL heparin. Sm-ring assembly reactions were scaled up to 250 µg human S3-iNPC and 438 µg mouse NSC-34 total protein cytoplasmic extract, supplemented with 4 µg polyA-RNA (RIN 5-6), and incubated for 1 hour at 30 °C with shake at 750 rpm in the presence or absence of ATP (1 unit/µL RNAse-OUT, 0.25 ug/uL yeast tRNA, 0.01% NP-40, 2.5 mM ATP, 20 mM Tris pH 8, 50 mM KCl, 0.5 MgCl2). Assembly reactions were immunoprecipitated with 120 µL/rxn Y12-conjugated dynabeads, incubated for 1 hour at 30 °C with shaking at 750 rpm. Beads were washed 8 times with RSB-500 + 0.1% NP-40, utilizing magnets to sequester beads. 50 ng of capture RNA was used as input for library preparation including three replicates of four conditions: 1) polyA-RNA only, 2) anti-Sm-RIP, 3) Modified Sm-RIP in which human extract was incubated with mouse polyA-RNA in the absence of ATP (and vice versa), and 4) Modified Sm-RIP in which human extract was incubated with mouse polyA-RNA and ATP (and vice versa). Libraries were prepped following Takara SMARTer Stranded Total RNA-Seq Kit v3-Pico Input Mammalian (Takara 634451) Kit, and sequenced using the NOVA-Seq platform, 150 base-pair paired-end reads. For samples hb, hy, hxmrs, and hxmras: extracts were treated with 2 M urea and 5 mg/mL for 15 min prior to Sm-antibody incubation and the concentration of NaCl in the wash buffer was increased to 1 M. Libraries for hc, hb, hy, hxmrs, and hxmras samples were prepped using the Takara SMARTer Stranded Total RNA-Seq Kit v2-Pico Input Mammalian (Takara 634411) Kit, and sequenced on the Nova-Seq X platform, 150 base-pair paired-end reads by the Case Western Reserve University Genomics Core.

value: S3-iNPC, NSC-34

value: Induced neural progenitor cell, Neural stem cell-like hybridoma

value: wild-type

value: anti-Sm-RNA immunoprecipitation


title: WT_Nil_Rep1[ATAC_Seq]


title: SK_4VIB_E07, placebo, time 0

description: Library name: SK_4VIB_E07

value: Blood

value: CD14 Monocyte


title: Person Living with HIV and have had no TB (PWH 22)

value: Plasma

value: Negative


title: WT_LC21_Rep1[ATAC_Seq]

value: B cell

value: WT


title: Modified Sm-RIP human extract, mouse polyA-RNA, +ATP, stringent washing 1 (hxmras1)

description:
Library name: hxmras1
RNA enriched by Y12-RIP from human S3-iNPC cytoplasmic extract incubated with mouse NSC-34 polyA-RNA and ATP under stringent washing conditions


title: SK_4VIB_E06, calcifediol, time 2

description: Library name: SK_4VIB_E06

value: calcifediol


title: Modified Sm-RIP human extract, mouse polyA-RNA, stringent washing 3 (hxmrs3)

description:
Library name: hxmrs3
RNA enriched by Y12-RIP from human S3-iNPC cytoplasmic extract incubated with mouse NSC-34 polyA-RNA under stringent washing conditions


title: WT_LC_Rep3[ATAC_Seq]

value: LC


title: Person Living with HIV and have had active TB (PWH 21)

value: ActiveTB

value: Female


title: SK_4VIB_E05, calcifediol, time 0

description: Library name: SK_4VIB_E05


title: Modified Sm-RIP human extract, mouse polyA-RNA, stringent washing 2 (hxmrs2)

description:
Library name: hxmrs2
RNA enriched by Y12-RIP from human S3-iNPC cytoplasmic extract incubated with mouse NSC-34 polyA-RNA under stringent washing conditions


title: Person Living with HIV and have had active TB (PWH 20)

value: Positive


title: SK_4VIB_E04, placebo, time 2

description: Library name: SK_4VIB_E04


title: Person Living with HIV and have had latent TB (PWH 19)

value: LatentTB

value: Male

value: No

value: Yes


title: WT_LC_Rep1[ATAC_Seq]


title: WT_LC_Rep2[ATAC_Seq]


title: SK_4VIB_E03, placebo, time 0

description: Library name: SK_4VIB_E03

value: placebo


title: WT_CD154_Rep3[ATAC_Seq]


title: Person Living with HIV and have had active TB (PWH 18)


title: Modified Sm-RIP human extract, mouse polyA-RNA, +ATP, stringent washing 3 (hxmras3)

description:
Library name: hxmras3
RNA enriched by Y12-RIP from human S3-iNPC cytoplasmic extract incubated with mouse NSC-34 polyA-RNA and ATP under stringent washing conditions

value: S3-iNPC, NSC-34

value: Induced neural progenitor cell, Neural stem cell-like hybridoma

value: wild-type

value: anti-Sm-RNA immunoprecipitation


title: PL19-45-liver,oncogene induced primary HCC tumor model, treated with antibody

city: SAN DIEGO

first: Yichun

last: Ji

state: ca

address: 9500 Gilman drive BRFII Room1220 Bay C #0864

department: PATHOLOGY

institute: UCSD

description:
Library name: V350274934_L03_PL19-45.fq.tabular
column name in Yichun_count_all.txt

data_processing:
Gene-level raw counts were obtained using HTSeq-count (v0.13.5) with the "union" mode for feature assignment
Cufflinks (v2.2.1) was used to calculate FPKM (Fragments Per Kilobase of transcript per Million mapped reads) values for transcript-level quantification
.DESeq2 v3.20. Volcano plots were generated using the Enhanced Volcano (v1.11.3) package in R.
Assembly: Trim Galore (v0.6.7)
Supplementary files format and content: raw count txt for each sample
Supplementary files format and content: txt file include  FPKM values for each sample

source_name: liver

growth_protocol: 7 weeks wild-type C57BL/6J mice were purchased from Jackson Laboratory,have an adapted feed for one week

extract_protocol:
liver immune cells RNA was extracted using the RNeasy Plus Micro Kit (74034; Qiagen)
RNA-seq libraries were prepared with the Illumina TruSeq v2 Kit according to the manufacturer’s instructio

treatment_protocol: 200ug αPD-L1,4mg/kgPolyIC and 5mg/kg αVEGF-A  were administered via intraperitoneal injection at 200 μg every other day for six doses respectively

value: liver

value: immune cells

value: PolyIC+anti PD-L1

tag: batch


title: Person Living with HIV and have had no TB (PWH 17)

value: Plasma

value: Negative


title: P11-45-liver,oncogene induced primary HCC tumor model, treated with antibody

description:
Library name: V350274934_L02_P11-45.fq.tabular
column name in Yichun_count_all.txt

value: WT


title: SK_4VIB_E01, calcitriol, time 0

description: Library name: SK_4VIB_E01

data_processing:
Bulk RNA data were processed using  WARDEN workflow for the analysis of RNA-Seq differential expression (McLeod et al., 2021).
Assembly: GRCh37
Supplementary files format and content: expression_matrix.txt

value: Blood

value: CD14 Monocyte

value: calcitriol


title: WT_CD154_Rep1[ATAC_Seq]

value: B cell


title: Person Living with HIV and have had latent TB (PWH 16)

value: LatentTB

value: Male

value: No

value: Positive


title: SK_4VIB_D12, calcifediol, time 2

description: Library name: SK_4VIB_D12

value: calcifediol


title: A12,Teosinte,rep3

city: Shenyang

first: Wei

last: Xue

state: Liaoning

address: 120 Dongling Rd,Shenhe District

department: College of Agronomy

institute: Shenyang Agricultural University

description: Library name: T6

data_processing:
Raw sequencing reads (~42.6 million per sample on average) were processed with fastq software to remove adapters, poly-Ns, and low-quality reads, yielding ~40.6 million clean reads per sample. Q20, Q30, and GC content were calculated, and downstream analyses were performed using high-quality clean data. The W22 reference genome and annotation files (Zm-W22-REFERENCE-NRGENE-2.0) were downloaded from MaizeGDB (https://download.maizegdb.org/). Genome indexing and read alignment were conducted with Hisat2 v2.0.5. Differential gene expression was analyzed using the DESeq2 R package (v1.20.0), with genes having adjusted P-v alues <=0.05 and fold change >1 defined as differentially expressed.
Assembly: Zm-W22-REFERENCE-NRGENE-2.0
Supplementary files format and content: Comma-Separated Values file includes raw counts for each Sample

organism: Zea mays

source_name: V6-V9 immature ears(a pool of at least 50 immature ears)

extract_protocol:
Total RNA was extracted following the standard TRIzol protocol (Invitrogen, Carlsbad, CA) as described by Lemmon (Lemmon et al., 2014, 10.1371/journal.pgen.1004745).
Transcriptome library preparation and sequencing were performed by Novogene Co., Ltd. (Beijing, China). Briefly, polyadenylated mRNAs were enriched using Oligo(dT) magnetic beads and randomly fragmented in NEB Fragmentation Buffer containing divalent cations (Parkhomchuk et al., 2009). First-strand cDNA synthesis was carried out using random oligonucleotide primers and M-MuLV reverse transcriptase, followed by second-strand synthesis using DNA polymerase I and dNTPs after RNaseH digestion. Purified double-stranded cDNA underwent end-repair, A-tailing, and adapter ligation. Fragments of approximately 370–420 bp were selected using AMPure XP beads, PCR-amplified, and further purified to finalize the libraries.

value: NIRILs(nearly isogenic recombinant inbred lines) A12

value: IM,SPM

value: qKRN5.04b teosinte

value: samples collected under standard growth conditions

value: Same batch


title: PL19-3-liver,oncogene induced primary HCC tumor model, treated with antibody

description:
Library name: V350274934_L03_PL19-3.fq.tabular
column name in Yichun_count_all.txt

value: liver

value: immune cells

value: PolyIC+anti PD-L1


title: SK_4VIB_D11, calcifediol, time 0

description: Library name: SK_4VIB_D11

value: Blood


title: Person Living with HIV and have had no TB (PWH 15)

value: Plasma

value: Negative


title: P2-3-liver,oncogene induced primary HCC tumor model, treated with antibody

description:
Library name: V350274934_L03_P2-3.fq.tabular
column name in Yichun_count_all.txt

value: WT


title: SK_4VIB_D10, placebo, time 2

description: Library name: SK_4VIB_D10

value: CD14 Monocyte

value: placebo


title: A12,Teosinte,rep1

description: Library name: T3

value: V6-V9 immature ears(a pool of at least 50 immature ears)


title: Modified Sm-RIP human extract, mouse polyA-RNA, stringent washing 1 (hxmrs1)

description:
Library name: hxmrs1
RNA enriched by Y12-RIP from human S3-iNPC cytoplasmic extract incubated with mouse NSC-34 polyA-RNA under stringent washing conditions

value: S3-iNPC, NSC-34

value: Induced neural progenitor cell, Neural stem cell-like hybridoma

value: wild-type

value: anti-Sm-RNA immunoprecipitation


title: Person Living with HIV and have had no TB (PWH 13)

value: Female

value: No


title: P111-3-liver,oncogene induced primary HCC tumor model, treated with antibody

description:
Library name: V350274934_L02_P11-3.fq.tabular
column name in Yichun_count_all.txt


title: Person Living with HIV and have had latent TB (PWH 12)

value: LatentTB

value: Male

value: Positive

value: Yes


title: SK_4VIB_D09, placebo, time 0

description: Library name: SK_4VIB_D09

value: Blood


title: B46,Maize,rep3

description: Library name: M4

value: NIRILs(nearly isogenic recombinant inbred lines) B46

value: IM,SPM

value: qKRN5.04b maize

value: samples collected under standard growth conditions

value: Same batch


title: SK_4VIB_D08, calcitriol, time 2

description: Library name: SK_4VIB_D08

value: CD14 Monocyte

value: calcitriol


title: PL19-8-liver,oncogene induced primary HCC tumor model, treated with antibody

description:
Library name: V350274934_L03_PL19-8.fq.tabular
column name in Yichun_count_all.txt

value: liver

value: immune cells

value: WT

value: PolyIC+anti PD-L1


title: SK_4VIB_E02, calcitriol, time 2

description: Library name: SK_4VIB_E02


title: B46,Maize,rep2

description: Library name: M2

value: V6-V9 immature ears(a pool of at least 50 immature ears)


title: P2-8-liver,oncogene induced primary HCC tumor model, treated with antibody

description:
Library name: V350274934_L02_P2-8.fq.tabular
column name in Yichun_count_all.txt


title: Person Living with HIV and have had latent TB (PWH 11)

value: Plasma

value: LatentTB

value: Female

value: No


title: WT_CD154_Rep2[ATAC_Seq]

value: B cell


title: P2-45-liver,oncogene induced primary HCC tumor model, treated with antibody

description:
Library name: V350274934_L02_P2-45.fq.tabular
column name in Yichun_count_all.txt


title: B46,Maize,rep1

description: Library name: M1

value: NIRILs(nearly isogenic recombinant inbred lines) B46


title: SK_4VIB_D07, calcitriol, time 0

description: Library name: SK_4VIB_D07

value: Blood


title: P11-8-liver,oncogene induced primary HCC tumor model, treated with antibody

description:
Library name: V350274934_L02_P11-8.fq.tabular
column name in Yichun_count_all.txt


title: SK_4VIB_D06, calcitriol, time 2

description: Library name: SK_4VIB_D06


title: Person Living with HIV and have had active TB (PWH 10)

value: ActiveTB

value: Yes

value: Negative


title: OS myobudles,tomatidine-treated, Day 21 replicate 3

city: Orlando

first: Siobhan

last: Malany

state: FL

address: 6550 Sanger Rd

department: Department of Cellular and Systems Pharmacology

institute: UF Research and Academic Center at Lake Nona

description: Library name: 12-OS-Estim-Tom-MP20-Chip-10

data_processing:
Bases called with Illumina sequencing machine (Novaseq X); files contain raw reads
Assembly: GRch38
Supplementary files format and content: tab-delimited matrix file, containing non-normalized FPKM values for all genes in all samples

source_name: muscle

growth_protocol: Injectable hydrogel mixtures (3.3 mg/mL rat tail collagen I, and 22% (v/v) Matrigel) were combined with YA- and OS-derived CD56+ enriched myoblasts. The cell-laden hydrogels were injected into the PDMS chips to a final cell density of 15 and 20 million cells/mL for YA- and OS-derived cells, respectively. Cells were allowed to polymerize at 37°C for 60 min and seeding ports were sealed using polylactic acid (PLA, Makerbot, Brooklyn, NY) plugs. Chips were perfused with degassed Skeletal Muscle Growth media supplemented with 0.1 mg/ml Primocin (InvivoGen, San Diego, CA) at a constant flow rate of 1 mL/h at 37°C and 5% CO2.

extract_protocol:
RNA was harvested using Quiagen kit. Illumina TruSeq RNA Sample Prep Kit (Cat#) was used with 0.5 ug of total RNA for the construction of sequencing libraries.
Sample quality was assessed using the Agilent TapeStation 4200 (Agilent Technologies, Inc). 250 ng of total RNA was used for library construction using NEB Ultra II Directional RNA-seq library preparation kit for Illumina according to manufacturer's protocol. First, 100 ng of total RNA was used for mRNA isolated using the NEBNext Poly(A) mRNA Magnetic Isolation Module (New England Biolabs, catalog # E7490). Then followed by RNA library construction with the NEBNext Ultra II Directional RNA Library Prep Kit (New England Biolabs, catalog #E7760) according to the manufacturer's user guide. Briefly, RNA was fragmented in NEBNext First Strand Synthesis Buffer via incubation at 94 °C for the desired time. This step was followed by first-strand cDNA synthesis using reverse transcriptase and random hexamer primer.  Synthesis of ds-cDNA was performed using the 2nd strand master mix provided in the kit, followed by end-repair and adaptor ligation.  At this point, Illumina adaptors were ligated to the sample.  Finally, each library (uniquely barcoded) was enriched by 12 cycles of amplification, and purified with Agencourt AMPure beads (Beckman Coulter, catalog # A63881). 15 barcoded libraries were sized on the TapeStation 4200 and quantified with the Qubit® 2.0 Fluorometer. Finally, Barcoded libraries were pooled equimolarly for sequencing simultaneously for NovaSeq

value: muscle

value: Enriched CD56+ myoblasts

value: Wild type ( cell line)

value: OS treated ( EStim)


title: C18-45-liver,RAS/MYC HTVi induce tumor model without treatment

description:
Library name: V350274934_L02_C18-45.fq.tabular
column name in Yichun_count_all.txt

value: liver

value: immune cells

value: WT

value: no


title: Person Living with HIV and have had active TB (PWH 9)

value: Plasma

value: Male


title: Person Living with HIV and have had no TB (PWH 14)

value: No


title: OS myobudles,tomatidine-treated, Day 21 replicate 2

description: Library name: 11-OS-Estim-Tom-MP17-Chip-14


title: Person Living with HIV and have had no TB (PWH 8)

value: Female


title: A12,Teosinte,rep2

description: Library name: T5

value: V6-V9 immature ears(a pool of at least 50 immature ears)

value: NIRILs(nearly isogenic recombinant inbred lines) A12

value: IM,SPM

value: qKRN5.04b teosinte

value: samples collected under standard growth conditions

value: Same batch


title: SK_4VIB_D04, placebo, time 2

description: Library name: SK_4VIB_D04

extract_protocol:
Lysate from 1000 cells was processed by the Immunological Genome Project protocol (www.immgen.org): final sort of 1,000 cells directly into 5ɥl lysis buffer (TCL Buffer (Qiagen) with 1% 2-Mercaptoethanol). After sort vortex, keep on ice for 5 minutes, give a quick spin. Freeze on dry ice.
Follow Genome Project protocol (www.immgen.org): 5 ul of the lysates are used for each sample for Smart-seq2 library construction, prepared as previously described (Picelli et al., 2013; Picelli et al., 2014) with slight modifications. Briefly, total RNA was captured and purified on RNAClean XP beads (Beckman Coulter). Polyadenylated mRNA was then selected using an anchored oligo(dT) primer (5′–AAGCAGTGGTATCAACGCAGAGTACT30VN-3′) and converted to cDNA via reverse transcription. First strand cDNA was subjected to limited PCR amplification followed by Tn5 transposon based fragmentation using the Nextera XT DNA Library Preparation Kit (Illumina). Samples were then PCR amplified for 12 cycles using barcoded primers such that each sample carries a specific combination of eight base Illumina P5 and P7 barcodes and pooled together prior to sequencing. Smart-seq paired-end sequencing is performed on an Illumina NextSeq500 (two full NextSeq runs per batch of 96 samples, for 10M raw reads/sample on average) using 2 x 38bp reads with no further trimming.

value: Blood

value: CD14 Monocyte

value: placebo


title: OS myobudles,tomatidine-treated, Day 21 replicate 1

description: Library name: 10-OS-Estim-Tom-MP17-Chip-2

value: muscle

value: Enriched CD56+ myoblasts

value: Wild type ( cell line)

value: OS treated ( EStim)


title: Person Living with HIV and have had latent TB (PWH 6)

value: Plasma

value: LatentTB

value: Positive

value: Yes


title: CV6-3-liver,RAS/MYC HTVi induce tumor model without treatment

description:
Library name: V350274934_L03_CV6-3.fq.tabular
column name in Yichun_count_all.txt

value: liver

value: immune cells

value: WT

value: no


title: SK_4VIB_D03, placebo, time 0

description: Library name: SK_4VIB_D03


title: C1-45-liver,RAS/MYC HTVi induce tumor model without treatment

description:
Library name: V350274934_L02_C1-45.fq.tabular
column name in Yichun_count_all.txt


title: C18-3-liver,RAS/MYC HTVi induce tumor model without treatment

description:
Library name: V350274934_L02_C18-3.fq.tabular
column name in Yichun_count_all.txt


title: OS myobudles, control, Day 21 replicate 1

description: Library name: 7-OS-Estim-MP17-Chip-4

value: OS control ( EStim)


title: SK_4VIB_D01, calcifediol, time 0

description: Library name: SK_4VIB_D01

value: calcifediol


title: OS myobudles, control, Day 21 replicate 3

description: Library name: 9-OS-Estim-MP20-Chip-9


title: Person Living with HIV and have had active TB (PWH 4)

value: ActiveTB

value: Male


title: YA myobudles, tomatidine-treated, Day 21 replicate 3

description: Library name: 6-YA-Estim-Tom-MP20-Chip-6

value: YA treated ( EStim)


title: SK_4VIB_C12, placebo, time 2

description: Library name: SK_4VIB_C12

value: Blood

value: CD14 Monocyte

value: placebo


title: Person Living with HIV and have had latent TB (PWH 3)

value: Female

value: No


title: SK_4VIB_D05, calcitriol, time 0

description: Library name: SK_4VIB_D05

value: calcitriol


title: C5-3-liver,RAS/MYC HTVi induce tumor model without treatment

description:
Library name: V350274934_L02_C5-3.fq.tabular
column name in Yichun_count_all.txt


title: SK_4VIB_C11, placebo, time 0

description: Library name: SK_4VIB_C11


title: YA myobudles, tomatidine-treated, Day 21 replicate 2

description: Library name: 5-YA-Estim-Tom-MP20-Chip-5

value: muscle

value: Enriched CD56+ myoblasts

value: Wild type ( cell line)


title: C5-45-liver,RAS/MYC HTVi induce tumor model without treatment

description:
Library name: V350274934_L03_C5-45.fq.tabular
column name in Yichun_count_all.txt

value: liver

value: immune cells


title: SK_4VIB_C10, calcitriol, time 2

description: Library name: SK_4VIB_C10


title: Person Living with HIV and have had no TB (PWH 1)

value: Plasma

value: Negative


title: C5-8-liver,RAS/MYC HTVi induce tumor model without treatment

description:
Library name: V350274934_L02_C5-8.fq.tabular
column name in Yichun_count_all.txt

value: WT

value: no


title: YA myobudles, tomatidine-treated, Day 21 replicate 1

description: Library name: 4-YA-Estim-Tom-MP20-Chip-4


title: C1-8-liver,RAS/MYC HTVi induce tumor model without treatment

description:
Library name: V350274934_L03_C1-8.fq.tabular
column name in Yichun_count_all.txt


title: Person Living with HIV and have had no TB (PWH 7)

value: Male


title: OS myobudles, control, Day 21 replicate 2

description: Library name: 8-OS-Estim-MP17-Chip-6

value: OS control ( EStim)


title: SK_4VIB_C09, calcitriol, time 0

description: Library name: SK_4VIB_C09

value: Blood


title: SK_4VIB_D02, calcifediol, time 2

description: Library name: SK_4VIB_D02

value: CD14 Monocyte

value: calcifediol


title: Person Living with HIV and have had active TB (PWH 5)

value: ActiveTB

value: Female

value: Yes

value: Positive


title: Muscle_Mut_4

description: Library name: Sample 32

data_processing:
The original FASTQ files were aligned using salmon to a transcriptome reference created using GENCODE vM34
Gene level counts were generated using pytximport and differentially expressed genes were computed using pydeseq2
Assembly: GENCODE vM34
Supplementary files format and content: tab-delimited text files include TPMs for each sample. The TPMs are  transcript level abundance estimates from salmon that can be used to generate estimate gene counts for gene level analysis

source_name: Muscle

extract_protocol:
The RNA was extractedusing the MagMAX™-96 Total RNA Isolation Kit (Invitrogen) by the Kingfisher Duo Prime Purification
RNA libraries were prepared for sequencing using standard Illumina kit and protocols; strand-specific

value: Muscle

tag: strain

value: Mut


title: SK_4VIB_C08, calcitriol, time 2

description: Library name: SK_4VIB_C08

source_name: Blood

tag: treatment

value: calcitriol


title: YA myobudles, control, Day 21 replicate 2

description: Library name: 2-YA-Estim-MP20-Chip-1

value: muscle

value: Enriched CD56+ myoblasts

value: Wild type ( cell line)

value: YA control ( EStim)


title: acites_lavage_samples_HTO

city: Dallas

first: Siyuan

last: Zhang

address: 6001 Forest Park Rd

department: Department of Pathology

institute: UT Southwestern Medical Center

description:
Library name: Ascites_HTO
10x Genomics

library_source: other

data_processing:
Raw fastq files generated from the sequencing runs (mRNA, HTO, LARRY outputs) were processed through the 10x Genomics CellRanger pipeline to generate count matrices. Custom python scripts were used for LARRY barcode extraction, error correction, and processing.
Assembly: mm10
Supplementary files format and content: Tab separated files and matrix files
Library strategy: CITE-seq

molecule: protein

source_name: peritoneal lavage

extract_protocol:
Cell suspensions from omentums were prepared by mechanical dissociation, followed by enyzmatic digestion using collagenase and DNAse I. The single cell suspension was then sorted for ZombieRed negative live cells. For ascital fluid, RBC lysis was performed along with several 1xPBS washes. Samples were subjected to FcR block, followed by HTO staining.
3x libraries from each lane are sequenced separately on a NovaSeq X machine. Transcriptome library preparation was conducted according to the Chromium Next GEM Single Cell 3’ Reagents Kits v3.1 with Feature Barcoding technology kit manual. Hashtag libraries were prepared using the standard CITE-seq protocol (https://citeseq.files.wordpress.com/2019/02/cite- seq_and_hashing_protocol_190213.pdf). LARRY barcode libraries were constructed using a custom nested PCR protocol followed by indexing.

value: peritoneal lavage

tag: cell type

value: tumor, stroma, immune

value: B6, female


title: Muscle_Mut_3

first: Haiming

last: Cao

address: 9000 Rockville Pike

institute: NIH

description: Library name: Sample 31

tag: tissue


title: Muscle_Mut_2

description: Library name: Sample 30


title: YA myobudles, control, Day 21 replicate 1

description: Library name: 1-YA-Estim-MP17-Chip-4


title: Person Living with HIV and have had active TB (PWH 2)

value: Plasma

value: Male

value: Negative


title: SK_4VIB_C07, calcitriol, time 0

first: Changde

last: Cheng

address: 1824 6th Ave S, Wallace Tumor Institute 520A

institute: University of Alabama at Birmingham

description: Library name: SK_4VIB_C07

value: Blood

value: CD14 Monocyte

tag: time (day)


title: C18-8-liver,RAS/MYC HTVi induce tumor model without treatment

description:
Library name: V350274934_L03_C18-8.fq.tabular
column name in Yichun_count_all.txt

value: liver

value: immune cells

value: WT

value: no


title: SK_4VIB_C06, calcifediol, time 2

description: Library name: SK_4VIB_C06

value: calcifediol


title: omentum_samples_LARRY

description:
Library name: Omentum_LARRY
10x Genomics

molecule: other

source_name: omentum

value: omentum


title: acites_lavage_samples_transcriptome

description:
Library name: Ascites_mRNA
10x Genomics


title: Human Y12 Sm-RIP, stringent washing 3 (hys3)

description:
Library name: hys3
RNA enriched by Y12-RIP from human S3-iNPC under stringent washing conditions and detected by random priming

value: Induced neural progenitor cell

value: wild-type

value: anti-Sm-RNA immunoprecipitation


title: SK_4VIB_C05, calcifediol, time 0

description: Library name: SK_4VIB_C05


title: SK_4VIB_C04, calcitriol, time 2

description: Library name: SK_4VIB_C04

value: calcitriol


title: Muscle_WT_4

description: Library name: Sample 28

value: Muscle


title: omentum_samples_HTO

description:
Library name: Omentum_HTO
10x Genomics

value: tumor, stroma, immune

value: B6, female


title: Muscle_Mut_1

description: Library name: Sample 29

value: Mut


title: Human Y12 Sm-RIP, stringent washing 1 (hys1)

description:
Library name: hys1
RNA enriched by Y12-RIP from human S3-iNPC under stringent washing conditions and detected by random priming


title: Muscle_WT_3

description: Library name: Sample 27


title: omentum_samples_transcriptome

description:
Library name: Omentum_mRNA
10x Genomics


title: YA myobudles, control, Day 21 replicate 3

description: Library name: 3-YA-Estim-MP20-Chip-2

value: muscle

value: Enriched CD56+ myoblasts

value: Wild type ( cell line)

value: YA control ( EStim)


title: SK_4VIB_C03, calcitriol, time 0

description: Library name: SK_4VIB_C03

value: Blood

value: CD14 Monocyte


title: LIG20-3

last: xiaojiaoyang

address: Bei jing shi chao yang qu bei san huan dong lu 11

institute: Beijing University of Chinese Medicine

description: Library name: Sample 9

data_processing:
Raw reads of fastq format were firstly processed using fastp and the low qulity reads were removed to obtain the clean reads.
The reference genome using HISAT2 v2.1.0.
Difference expression analysis was performed using the DESeq2.
Assembly: GRCm39
Supplementary files format and content: tab-delimited text files include FPKM values Sample

extract_protocol:
Total RNA was isolated using TRIzol reagent (Invitrogen, CA, USA) according to the manufacturer's protocol.Then, RNA puritied and quantificated by NanoDrop 2000 spectrophotometer (Thermo Scientific, USA).
RNA libraries for RNA-seq were prepared using VAHTS Universal V6 RNA-seq Library Prep Kit according to the manufacturer's instructions.

value: liver


title: Human SmB Sm-RIP, stringent washing 2 (hbs2)

description:
Library name: hbs2
RNA enriched by SmB-RIP from human S3-iNPC under stringent washing conditions and detected by random priming


title: acties_lavage_samples_LARRY

description:
Library name: Ascites_LARRY
10x Genomics

value: peritoneal lavage


title: SK_4VIB_C02, placebo, time 2

description: Library name: SK_4VIB_C02

value: placebo


title: Muscle_WT_1

description: Library name: Sample 25

value: WT


title: Human SmB Sm-RIP, stringent washing 3 (hbs3)

description:
Library name: hbs3
RNA enriched by SmB-RIP from human S3-iNPC under stringent washing conditions and detected by random priming

value: Induced neural progenitor cell

value: wild-type


title: Human SmB Sm-RIP, stringent washing 1 (hbs1)

description:
Library name: hbs1
RNA enriched by SmB-RIP from human S3-iNPC under stringent washing conditions and detected by random priming

value: anti-Sm-RNA immunoprecipitation


title: SK_4VIB_C01, placebo, time 0

description: Library name: SK_4VIB_C01


title: LIG20-1

description: Library name: Sample 7


title: SK_4VIB_B12, calcifediol, time 2

description: Library name: SK_4VIB_B12

value: calcifediol


title: Human Y12 Sm-RIP, stringent washing 2 (hys2)

description:
Library name: hys2
RNA enriched by Y12-RIP from human S3-iNPC under stringent washing conditions and detected by random priming


title: LIG20-2

description: Library name: Sample 8


title: BDL-3

description: Library name: Sample 6


title: Human cytoplasmic RNA 2 (hc2)

description:
Library name: hc2
Cytoplasmic RNA isolated from human S3-iNPC

value: Cytoplasmic fraction


title: Liver_Mut_2

description: Library name: Sample 22

source_name: Liver

value: Liver


title: SK_4VIB_B11, calcifediol, time 0

description: Library name: SK_4VIB_B11


title: Liver_Mut_4

description: Library name: Sample 24

value: Mut


title: BDL-2

description: Library name: Sample 5


title: BDL-1

description: Library name: Sample 4


title: SK_4VIB_B10, placebo, time 2

description: Library name: SK_4VIB_B10


title: SK_4VIB_B09, placebo, time 0

description: Library name: SK_4VIB_B09


title: Liver_WT_4

description: Library name: Sample 20


title: Liver_Mut_1

description: Library name: Sample 21


title: Human cytoplasmic RNA 1 (hc1)

description:
Library name: hc1
Cytoplasmic RNA isolated from human S3-iNPC


title: Muscle_WT_2

description: Library name: Sample 26

value: Muscle


title: sham-3

description: Library name: Sample 3


title: SK_4VIB_B08, calcitriol, time 2

description: Library name: SK_4VIB_B08

value: calcitriol


title: sham-2

description: Library name: Sample 2


title: Liver_WT_3

description: Library name: Sample 19


title: SK_4VIB_B07, calcitriol, time 0

description: Library name: SK_4VIB_B07


title: PV MSCs_monoculture_2_1

city: LONDON

first: Giuseppe

middle: Alessandro

last: D'Agostino

state: ENGLAND

address: 1 Midland Road

country: United Kingdom

institute: The Francis Crick Institute

description:
Library name: PV MSCs_2_1
Polycythemia Vera MSC monoculture from donor 6, replicate 1

data_processing:
FASTQ files were trimmed using TrimGalore v. 0.6.0 to remove adapters.
Trimmed FASTQ files were aligned to the Homo sapiens genome using the GRCh38 reference genome.
A pre-built Salmon reference which uses selective alignment was downloaded from Refgenie and Salmon 1.9.0 was used to quantify the sequencing reads using default paired-end parameters.
Assembly: GRCh38 Ensembl Salmon index with selective alignment downloaded from RefGenie (asset 2230c535660fb4774114bfa966a62f823fdb6d21acf138d4)
Supplementary files format and content: quant.sf transcript-level quantifications by Salmon

source_name: Bone Marrow derived

extract_protocol:
RNA was extracted using an RNA purification kit (Zymo Research, US).
~10 ng of RNA/sample were used for library preparation using NEBNext Ultra II Directional PolyA mRNA kit (New England Biolabs, US), following manufacturer’s instructions.

value: Bone Marrow derived

value: Mesenchymal stromal cells


title: PV MSCs_monoculture_1_2

description:
Library name: PV MSCs_1_2
Polycythemia Vera MSC monoculture from donor 5, replicate 2


title: Liver_WT_2

city: Bethesda

description: Library name: Sample 18


title: sham-1

description: Library name: Sample 1


title: SK_4VIB_B06, calcifediol, time 2

city: Birmingham

description: Library name: SK_4VIB_B06

value: Blood


title: Human cytoplasmic RNA 3 (hc3)

description:
Library name: hc3
Cytoplasmic RNA isolated from human S3-iNPC


title: Liver_WT_1

description: Library name: Sample 17


title: PV MSCs_monoculture_1_1

description:
Library name: PV MSCs_1_1
Polycythemia Vera MSC monoculture from donor 5, replicate 1


title: myotubes, Nrip1KO, IgG, rep1

city: Philadelphia

first: Daniel

last: Kelly

state: PA

address: 3400 Civic Center Blvd

department: Penn Cardiovascular Institute

institute: University of Pennsylvania

description: Library name: sample_8

data_processing:
Reads were aligned to the reference genome using BWA-MEM2 (v2.2.1)
Broad peak calling was performed using HOMER (v4.11)
To identify differentially acetylated regions between control and KO samples, HOMER was used with a ≥2-fold change cutoff for peak intensity differences
bigWig files for vizualization were created with HOMER’s makeUCSCfile
Assembly: mm10
Supplementary files format and content: bigWig files for individual samples
Supplementary files format and content: BED files with differentially acetylated regions in Nrip1 KO
Library strategy: CUT&Run

source_name: Primary skeletal muscle

growth_protocol: Primary myoblasts were cultured in growth media (80% Ham's F-10, 20% FBS, 10 ng/mL EGF, 1 µg/mL insulin solution, 0.39 µg/mL dexamethasone, 1x pen/strep). Myoblasts were differentiated in differentiation medium (low glucose DMEM, 2% horse serum, 1x pen/strep) for four days.

extract_protocol:
Nuclei were isolated from myotubes utilizing the nuclei extraction protocol (CUT&TAG Kit Version 1 by EpiCypher) and proceeded to the CUTANA™ ChIC/CUT&RUN Kit Version 4 protocol (EpiCypher, New England Biolabs) following manufacturer’s instructions.
CUT&RUN libraries were constructed using CUTANA™ CUT&RUN Library Prep Kit (EpiCypher, New England Biolabs). 5 ng of DNA was utilized for library construction. To barcode samples, unique combinations of i5 and i7 indexing primers were used to amplify during PCR.

value: Primary skeletal muscle

value: myotubes

tag: antibody

value: CUTANA IgG Negative Control Antibody for CUT&RUN and CUT&Tag, SKU:13-0042, EpiCypher


title: ET MSCs_monoculture_2_2

description:
Library name: ET MSCs_2_2
Essential Thrombocythemia MSC monoculture from donor 4, replicate 2


title: SK_4VIB_B05, calcifediol, time 0

description: Library name: SK_4VIB_B05

value: CD14 Monocyte


title: SK_4VIB_B04, placebo, time 2

description: Library name: SK_4VIB_B04

value: placebo


title: ET MSCs_monoculture_2_1

description:
Library name: ET MSCs_2_1
Essential Thrombocythemia MSC monoculture from donor 4, replicate 1


title: myotubes, Ctrl, H3K27Ac, rep1

description: Library name: sample_7

tag: genotype

value: Ctrl

value: Anti-Histone H3 (acetyl K27), Abcam, ab4729


title: PV MSCs_monoculture_2_2

description:
Library name: PV MSCs_2_2
Polycythemia Vera MSC monoculture from donor 6, replicate 2


title: Heart_Mut_3

description: Library name: Sample 15

source_name: Heart

value: Heart


title: Heart_Mut_2

description: Library name: Sample 14


title: myotubes, Ctrl, H3K27Ac, rep2

description: Library name: sample_6


title: SK_4VIB_B02, calcifediol, time 2

description: Library name: SK_4VIB_B02

value: calcifediol


title: SK_4VIB_B03, placebo, time 0

description: Library name: SK_4VIB_B03


title: ET MSCs_monoculture_1_2

description:
Library name: ET MSCs_1_2
Essential Thrombocythemia MSC monoculture from donor 3, replicate 2


title: ET MSCs_monoculture_1_1

description:
Library name: ET MSCs_1_1
Essential Thrombocythemia MSC monoculture from donor 3, replicate 1


title: Heart_Mut_1

description: Library name: Sample 13


title: myotubes, Ctrl, IgG, rep1

description: Library name: sample_5


title: myotubes, Nrip1KO, IgG, rep2

description: Library name: sample_4


title: HD MSCs_monoculture_2_2

description:
Library name: HD MSCs_2_2
Healthy MSC monoculture from donor 2, replicate 2


title: Heart_WT_4

description: Library name: Sample 12

value: WT


title: SK_4VIB_B01, calcifediol, time 0

description: Library name: SK_4VIB_B01


title: myotubes, Ctrl, IgG, rep2

description: Library name: sample_3


title: SK_4VIB_A12, calcitriol, time 2

description: Library name: SK_4VIB_A12


title: HD MSCs_monoculture_2_1

description:
Library name: HD MSCs_2_1
Healthy MSC monoculture from donor 2, replicate 1


title: Heart_WT_3

description: Library name: Sample 11


title: SK_4VIB_A11, calcitriol, time 0

description: Library name: SK_4VIB_A11


title: myotubes, Nrip1KO, H3K27Ac, rep2

description: Library name: sample_2


title: Heart_WT_2

description: Library name: Sample 10


title: Heart_Mut_4

description: Library name: Sample 16


title: HD MSCs_monoculture_1_2

description:
Library name: HD MSCs_1_2
Healthy MSC monoculture from donor 1, replicate 2


title: myotubes, Nrip1KO, H3K27Ac, rep1

description: Library name: sample_1


title: SK_4VIB_A10, calcifediol, time 2

description: Library name: SK_4VIB_A10


title: HD MSCs_monoculture_1_1

description:
Library name: HD MSCs_1_1
Healthy MSC monoculture from donor 1, replicate 1


title: SK_4VIB_A09, calcifediol, time 0

description: Library name: SK_4VIB_A09


title: BAT_Mut_4

description: Library name: Sample 8

source_name: Brown Adipose

value: Brown Adipose


title: Modified Sm-RIP mouse extract, human polyA-RNA, +ATP 3 (mxhra3)

description:
RNA enriched by Sm-RIP from mouse NSC-34 cytoplasmic extract incubated with human iNPC polyA-RNA and ATP
2023_n3_Sm_counts_master_human.txt
2023_n3_Sm_counts_master_mouse.txt
F4U45

source_name: NSC-34, S3-iNPC

extract_protocol:
Cytoplasmic cell extracts were generated by scraping and collecting NSC-34 or S3-iNPC cells in cold phosphate buffered saline containing only monovalent cations. Cells were pelleted by centrifugation 400 x g for 4 min. Cells were resuspended in digitoxin lysis buffer (20 mM Tris pH 8, 50 mM KCl, 0.5 MgCl2, 1x eComplete, 200 units/mL RNase-OUT, 50 ug/mL digitonin, in DEPC-treated water) and incubated on ice for a few minutes. Lysates were passaged 6 times through a 27 gauge needle with syringe then centrifuged at 1,500 x g for 1 minute at 4 °C. Supernatant was measured and transferred to a new microfuge tube and supplemented with NP-40 to achieve 0.01% final concentration. Lysates were then centrifuged at 4,000 x g for 15 minutes at 4 °C. Supernatants were then aliquoted into microfuge tubes and frozen in liquid nitrogen.
Three replicates of the four conditions for both species combinations were used to generate sequencing libraries, using 50 ng of captured RNA as input for the Takara SMARTer Stranded Total RNA-Seq Kit v3-Pico Input Mammalian (Takara 634451)

treatment_protocol: Oligo-dT isolation of polyA-RNA - Four 15 cm dishes of NSC-34 or S3-iNPC cell were washed thrice with PBS lacking divalent cations and treated with 8 mL TRIzol Reagent (Invitrogen 15596026) per 15 cm dish. TRIzol samples were pooled and a large scale total RNA isolation and precipitation was performed following manufacturer’s instructions. After purification, isolated RNA was treated with 200 units of Turbo DNase (Invitrogen AM2239) and incubated at 37 °C for 30 minutes with gentle rotation at 350 rpm in Eppendorf Thermomixer R. DNase was removed by phenol:chloroform extraction. RNA was precipitated with 1.5 M final concentration of LiCl and 100% ethanol, centrifuged at > 18,000 x g for 15 minutes. RNA was resupsended in 1 mL nuclease-free water and quantified using Qubit RNA Broad Range Assay (Invitrogen Q10211). PolyA-RNA was isolated using Dynabeads mRNA Purification Kit (Invitrogen 61006). Oligo-dT beads were reused post-polyA-RNA elution to isolate the magnitude of polyA-RNA required for modified Sm-ring assembly reaction and sequencing conditions. After isolation, polyA-RNA was quantified using Qubit RNA Broad Range Assay (Invitrogen Q10211) and RNA integrity (RIN) was quantified by TapeStation analysis performed by the Ohio State Comrpehensive Cancer Center Genomics Core to determine removal of polyA-minus RNAs. For Sm-RIP and modified Sm-ring assembly RIPs, Protein-A DynaBeads (Invitrogen 10001D) were aliquoted 8.6 µL/rxn and washed three times in PBS + 0.1% NP-40. 1.6 µg/rxn Y12 antibody (Novus Biologicals NB600-546) was conjugated to Protein-A DynaBeads by incubating in PBS + 0.1% NP-40 for 1 hour at 4 °C with rotation. Beads were washed 3 more times with PBS + 0.1% NP-40, then three times with RSB-500 + 0.1% NP-40 (RSB-500: 10 mM Tris pH 7.4, 500 mM NaCl, 2.5 mM MgCl2). Beads were finally resuspended in 120 µL/rxn RSB-500 + 0.1% NP-40 supplemented with 2 mg/mL heparin. Sm-ring assembly reactions were scaled up to 250 µg human S3-iNPC and 438 µg mouse NSC-34 total protein cytoplasmic extract, supplemented with 4 µg polyA-RNA (RIN 5-6), and incubated for 1 hour at 30 °C with shake at 750 rpm in the presence or absence of ATP (1 unit/µL RNAse-OUT, 0.25 ug/uL yeast tRNA, 0.01% NP-40, 2.5 mM ATP, 20 mM Tris pH 8, 50 mM KCl, 0.5 MgCl2). Assembly reactions were immunoprecipitated with 120 µL/rxn Y12-conjugated dynabeads, incubated for 1 hour at 30 °C with shaking at 750 rpm. Beads were washed 8 times with RSB-500 + 0.1% NP-40, utilizing magnets to sequester beads. 50 ng of capture RNA was used as input for library preparation including three replicates of four conditions: 1) polyA-RNA only, 2) anti-Sm-RIP, 3) Modified Sm-RIP in which human extract was incubated with mouse polyA-RNA in the absence of ATP (and vice versa), and 4) Modified Sm-RIP in which human extract was incubated with mouse polyA-RNA and ATP (and vice versa). Libraries were pr3pped following = Takara SMARTer Stranded Total RNA-Seq Kit v3-Pico Input Mammalian (Takara 634451) Kit, and sequenced using the NOVA-Seq platform, 150 base-pair paired-end reads.

tag: cell line

value: NSC-34, S3-iNPC

value: Neural stem cell-like hybridoma, Induced neural progenitor cell

value: wild-type

value: anti-Sm-RNA immunoprecipitation


title: Heart_WT_1

description: Library name: Sample 9


title: SK_4VIB_A08, calcitriol, time 2

description: Library name: SK_4VIB_A08

value: calcitriol


title: DKO 5X Enterololin Biol Rep 3, 4h

city: Hamilton

first: Denise

middle: Buquiran

last: Catacutan

state: Ontario

address: 1280 Main Street West

department: Biochemistry and Biomedical Sciences

country: Canada

institute: McMaster University

description: Library name: Sample 12

data_processing:
Paired-end sequence data in FASTQ files were processed with FASTQC v.0.12.0 and trimmed with Trimmomatic v.0.3975 to remove Truseq adaptor sequences
mRNA abundances were then quantified as transcripts per million using the kallisto (version 0.44.0) ‘quant’ function, and parameter ‘-b 100’ with paired-end reads.
All downstream analysis were performed using R (version 4.3.0). Expression differences between enterololin-treated samples and non-treated controls were quantified using the DeSeq2 pipeline (version 1.40.2).
We defined the cut-off of log2(FC) ≥ 1.5 and padj ≤ 0.01 to identify differentially expressed genes.
Assembly: Paired-end sequence data in FASTQ format were aligned to CP009273.1 (E. coli BW25113).
Supplementary files format and content: Tab-separated values file includes target id, estimated counts, and TPM

organism: Escherichia coli BW25113

growth_protocol: E. coli BW25113 ∆bamB∆tolC cells were grown overnight in 3 ml LB medium at 37°C with shaking at 200 RPM. Cells were diluted 1:10,000 into 50 ml fresh LB and grown to mid-log (~107 CFU ml-1) at 37°C with shaking at 200 RPM.

extract_protocol:
After the required durations of incubation post-treatment, 2 ml samples were collected and pelleted by centrifugation at 0˚C for 5 min at 21,300 × g. RNA extraction and rRNA depletion were performed by Genewiz.
cDNA library construction and sequencing for these samples were performed by Genewiz.

treatment_protocol: At mid-log, cultures were supplemented with 5× MIC enterololin or no drug and grown for an additional 2 h or 4 h

value: bamB and tolC double knockout

value: 5X MIC enterololin


title: BAT_Mut_3

description: Library name: Sample 7

value: Mut


title: SK_4VIB_A07, calcitriol, time 0

description: Library name: SK_4VIB_A07

value: Blood


title: BAT_Mut_2

description: Library name: Sample 6


title: DKO 5X Enterololin Biol Rep 1, 4h

description: Library name: Sample 10


title: Modified Sm-RIP mouse extract, human polyA-RNA 3 (mxhr3)

description:
RNA enriched by Sm-RIP from mouse NSC-34 cytoplasmic extract incubated with human iNPC polyA-RNA
2023_n3_Sm_counts_master_human.txt
2023_n3_Sm_counts_master_mouse.txt
E4U42


title: Modified Sm-RIP mouse extract, human polyA-RNA, +ATP 1 (mxhra1)

description:
RNA enriched by Sm-RIP from mouse NSC-34 cytoplasmic extract incubated with human iNPC polyA-RNA and ATP
2023_n3_Sm_counts_master_human.txt
2023_n3_Sm_counts_master_mouse.txt
F1U43


title: DKO 5X Enterololin Biol Rep 2, 2h

description: Library name: Sample 8


title: SK_4VIB_A05, placebo, time 0

description: Library name: SK_4VIB_A05

value: CD14 Monocyte


title: Modified Sm-RIP mouse extract, human polyA-RNA, +ATP 2 (mxhra2)

description:
RNA enriched by Sm-RIP from mouse NSC-34 cytoplasmic extract incubated with human iNPC polyA-RNA and ATP
2023_n3_Sm_counts_master_human.txt
2023_n3_Sm_counts_master_mouse.txt
F3U44


title: DKO 5X Enterololin Biol Rep 3, 2h

description: Library name: Sample 9


title: Modified Sm-RIP mouse extract, human polyA-RNA 2 (mxhr2)

description:
RNA enriched by Sm-RIP from mouse NSC-34 cytoplasmic extract incubated with human iNPC polyA-RNA
2023_n3_Sm_counts_master_human.txt
2023_n3_Sm_counts_master_mouse.txt
E3U41


title: BAT_WT_4

description: Library name: Sample 4


title: DKO 5X Enterololin Biol Rep 1, 2h

description: Library name: Sample 7


title: BAT_Mut_1

description: Library name: Sample 5


title: SK_4VIB_A04, placebo, time 2

description: Library name: SK_4VIB_A04

value: placebo


title: Modified Sm-RIP mouse extract, human polyA-RNA 1 (mxhr1)

description:
RNA enriched by Sm-RIP from mouse NSC-34 cytoplasmic extract incubated with human iNPC polyA-RNA
2023_n3_Sm_counts_master_human.txt
2023_n3_Sm_counts_master_mouse.txt
E1U40


title: DKO Control Biol Rep 3, 4h

description: Library name: Sample 6

value: no drug


title: BAT_WT_3

description: Library name: Sample 3


title: SK_4VIB_A03, placebo, time 0

description: Library name: SK_4VIB_A03


title: DKO 5X Enterololin Biol Rep 2, 4h

description: Library name: Sample 11


title: Human Sm-RIP 3 (hx3)

description:
RNA enriched by Sm-RIP from human S3-iNPC and detected by random priming
2023_n3_Sm_counts_master_human.txt
2023_n3_Sm_counts_master_mouse.txt
A4U27

value: Induced neural progenitor cell


title: BAT_WT_2

description: Library name: Sample 2


title: BAT_WT_1

description: Library name: Sample 1


title: Human Sm-RIP 2 (hx2)

description:
RNA enriched by Sm-RIP from human S3-iNPC and detected by random priming
2023_n3_Sm_counts_master_human.txt
2023_n3_Sm_counts_master_mouse.txt
A3U26


title: SK_4VIB_A02, calcifediol, time 2

description: Library name: SK_4VIB_A02


title: DKO Control Biol Rep 2, 4h

description: Library name: Sample 5


title: SK_4VIB_A01, calcifediol, time 0

description: Library name: SK_4VIB_A01


title: DKO Control Biol Rep 1, 4h

description: Library name: Sample 4


title: Human Sm-RIP 1 (hx1)

description:
RNA enriched by Sm-RIP from human S3-iNPC and detected by random priming
2023_n3_Sm_counts_master_human.txt
2023_n3_Sm_counts_master_mouse.txt
A2U25


title: SK_4VIB_A06, placebo, time 2

description: Library name: SK_4VIB_A06


title: DKO Control Biol Rep 3, 2h

description: Library name: Sample 3


title: Modified Sm-RIP human extract, mouse polyA-RNA, +ATP 3 (hxmra3)

description:
RNA enriched by Sm-RIP from human S3-iNPC cytoplasmic extract incubated with mouse NSC-34 polyA-RNA and ATP
2023_n3_Sm_counts_master_human.txt
2023_n3_Sm_counts_master_mouse.txt
C4U33

value: S3-iNPC, NSC-34

value: Induced neural progenitor cell, Neural stem cell-like hybridoma


title: Org_17 liver spheroids Insphero

city: Los Angeles

first: Ana

middle: C

last: Maretti-Mira

state: CA

address: 1450 Biggy Street, NRT 3514

institute: USC

description: 10X Genomics

library_source: transcriptomic single cell

data_processing:
Raw data processing: Cell by gene count matrices were generated by processing FASTQ files using the Cell Ranger count (version 5.0.1, 10X Genomics) pipeline with the GRCh38 (version refdata-gex-GRCh38-2020-A, 10X Genomics) human genome reference for each sample.
Gene expression data were processed using the R package Seurat (version 4) [PMID: 29608179].
Assembly: GRCh38
Supplementary files format and content: Tab-separated values files and matrix files

source_name: liver spheroids Insphero

growth_protocol: 7 days in low glucose media (media obtained from InSphero)

extract_protocol:
Not extracted, spheroids cells were dissociated for 15min using Trypsin, at 37˚C. Dead cells were removed using Dead Cell Removal Kit (Miltenyi Biotec). Viable cells were particioned using 10x Chromium Controller and kit 3' v3.1.
Library was performed according to the manufacter’s instructions

treatment_protocol: PFAS replenished every 2-3 days with media change

value: liver spheroids Insphero

value: PFOS


title: Human polyA-RNA 3 (hr3)

description:
polyA-RNA enriched by oligo-dT purification isolated from human S3-iNPC
2023_n3_Sm_counts_master_human.txt
2023_n3_Sm_counts_master_mouse.txt
H3U48

value: oligo-dT purified


title: Modified Sm-RIP human extract, mouse polyA-RNA, +ATP 2 (hxmra2)

description:
RNA enriched by Sm-RIP from human S3-iNPC cytoplasmic extract incubated with mouse NSC-34 polyA-RNA and ATP
2023_n3_Sm_counts_master_human.txt
2023_n3_Sm_counts_master_mouse.txt
C2U32


title: Human polyA-RNA 2 (hr2)

description:
polyA-RNA enriched by oligo-dT purification isolated from human S3-iNPC
2023_n3_Sm_counts_master_human.txt
2023_n3_Sm_counts_master_mouse.txt
H2U47


title: Modified Sm-RIP human extract, mouse polyA-RNA, +ATP 1 (hxmra1)

description:
RNA enriched by Sm-RIP from human S3-iNPC cytoplasmic extract incubated with mouse NSC-34 polyA-RNA and ATP
2023_n3_Sm_counts_master_human.txt
2023_n3_Sm_counts_master_mouse.txt
C1U31


title: Org_16 liver spheroids Insphero

description: 10X Genomics

value: DMSO


title: DKO Control Biol Rep 1, 2h

description: Library name: Sample 1


title: Org_14 liver spheroids Insphero

description: 10X Genomics

value: PFNA


title: Modified Sm-RIP human extract, mouse polyA-RNA 3 (hxmr3)

description:
RNA enriched by Sm-RIP from human S3-iNPC cytoplasmic extract incubated with mouse NSC-34 polyA-RNA
2023_n3_Sm_counts_master_human.txt
2023_n3_Sm_counts_master_mouse.txt
B4U30

value: wild-type

value: anti-Sm-RNA immunoprecipitation


title: Human polyA-RNA 1 (hr1)

description:
polyA-RNA enriched by oligo-dT purification isolated from human S3-iNPC
2023_n3_Sm_counts_master_human.txt
2023_n3_Sm_counts_master_mouse.txt
H1U46


title: DKO Control Biol Rep 2, 2h

description: Library name: Sample 2

value: bamB and tolC double knockout


title: Org_13 liver spheroids Insphero

description: 10X Genomics


title: Modified Sm-RIP human extract, mouse polyA-RNA 2 (hxmr2)

description:
RNA enriched by Sm-RIP from human S3-iNPC cytoplasmic extract incubated with mouse NSC-34 polyA-RNA
2023_n3_Sm_counts_master_human.txt
2023_n3_Sm_counts_master_mouse.txt
B2U29