title: liver_ATAC_172_l1_s2

first: Karen

institute: University of North Carolina at Chapel Hill

extract_protocol:
We pulverized 50-mg pieces of frozen human liver tissue in liquid nitrogen using a Cell Crusher (CellCrusher), homogenized the tissue powder in ice-cold nuclei isolation buffer (NIB: 20 mM Tris-HCl, 50 mM EDTA, 5 mM spermidine, 0.15 mM spermine, 0.1% mercaptoethanol, 40% glycerol [pH 7.5]) using a 1-mL dounce for 40 strokes, and rotated for 5 min at 4°C. We filtered the solution through a Miracloth (Calbiochem), centrifuged at 1,100 × g for 10 min at 4°C, washed the pellet with 250 μL NIB containing 0.5% Triton-X, centrifuged at 500 × g for 5 min at 4°C, and resuspended the pellet in 250 μL of resuspension buffer (10 mM Tris-HCl, 10 mM NaCl, 3 mM MgCl2 [pH 7.4]). After counting isolated nuclei, we pelleted 50,000 nuclei at 500 × g for 5 min at 4°C
We prepared ATAC-seq libraries using the omni-ATAC protocol with 5 ul Tn5 transposase per reaction, cleaned the transposase reaction and final libraries with Zymo DNA Clean and Concentrator (D4029), visualized and quantified the libraries using a TapeStation, and sequenced 150-bp paired-end reads on either an Illumina HiSeq 4000 or HiSeq X ten.

value: liver tissue


title: LCDC cell type, cells alone, replicate 4

status: Public on Feb 01 2025

type: SRA

city: Los Angeles

first: Giorgia

last: Del Vecchio

address: 610 Charles E Young Dr S, Room 5146

country: USA

institute: University of California Los Angeles

library_source: transcriptomic

data_processing:
Raw reads were quality checked using FastQC v.0.11.9.
Sequence reads were trimmed for adaptors sequence and low quality reads using trimmomatic
Trimmed sequence reads were mapped to the human genome version GRCh38/hg38 using STAR v.2.7.9a keeping unique alignments and those with up to 4 mismatches
Counts were generated using the quantMode GeneCounts option in STAR that counts the number of reads per gene while mapping
Assembly: GRCh38/hg38
Supplementary files format and content: tab-delimited txt file with Ensembl gene ID and raw counts for each sample

molecule: total RNA

organism: Homo sapiens

source_name: Langerhans cell-derived Dendritic Cell

extract_protocol:
RNA from stimulated mDC, moDC, and LCDC was isolated using Quick-RNA Microprep kit.
RNA concentration and quality were determined using TapeStation  and sequencing libraries were prepared using the KAPA mRNA HyperPrep kit following manufacturer's protocol.

tag: cell line

value: Langerhans cell-derived Dendritic Cell

tag: treatment

value: cells alone


title: liver_ATAC_172_l1_s1

city: Chapel Hill

middle: L

last: Mohlke

state: NC

address: 120 Mason Farm Road

department: Genetics

description:
Sample titles are in the format liver_ATAC_[sampleID]_[libraryID]_[sequencingRun]. Note that resequenced libraries were run at a later date and were sometimes on a different sequencer than the original sequencing run, so resequenced libraries are listed as separate samples.
172_peaks.narrowPeak.gz
172_scaled.bw

library_source: genomic

data_processing:
Raw sequence reads were trimmed for adapters and low quality bases using cutadapt with parameters -q 20 --minimum-length 36. Reads were aligned to the GRCh38 version of the genome using bowtie2 with parameters --minins 36 --maxins 1000 --no-mixed --no-discordant --no-unal. Reads overlapping ENCODE exclusion regions were removed with BEDTools pairToBed. Reads on primary nuclear chromosomes (chr 1-22, X, Y) with mapq > 20 were selected with samtools. Duplicate alignments were removed using picard MarkDuplicates.
We converted BAM files to BED files using BEDTools and called peaks on each ATAC-seq library separately using MACS2 with parameters -q 0.05 –nomodel –shift -100 –extsize 200 –keep-dup all.
For each individual, we merged the BAM files of the high-quality libraries and removed duplicates using Picard MarkDuplicates because some libraries for the same donor represent re-sequencing of the same library preparation. We then called peaks on merged libraries per individual using the same procedure that we used for single libraries. We merged peaks across individuals using BEDTools and retained merged peaks found in at least 7 individuals (5% of 138). Merging peaks across individuals can result in wide peak boundaries and concatenation of multiple nearby accessible chromatin regions into one peak. Therefore, we developed a procedure to refine the boundaries of the merged peaks found in at least 7 individuals. We first calculated the number of individuals that had a peak overlapping each base of each merged peak, which we define as coverage, using BEDTools coverage. We converted the output of BEDTools coverage into a matrix of coverage values with peak IDs as rows and peak bases as columns. For each peak, we identified all local minima in coverage; peaks that contain only one peak should have only two local minima, whereas peaks containing multiple sub-peaks will have 3 or more local minima. To prevent classifying small fluctuations in coverage as sub-peaks, we only retained adjacent pairs of minima if the distance between them was at least 200 basepairs (bp) and if the maximum coverage between them was both greater than 7 and greater than twice the maximum of the two minima. To define consensus peak boundaries, we identified the position between the two local minima with maximum coverage and extended in both directions until we reached the outermost positions that had half of the maximum coverage. This is similar to the full width at half maximum procedure used to identify boundaries of DNase peaks in ENCODE.
Assembly: GRCh38
Supplementary files format and content: The bigWig (.bw) files contain ATAC-seq signal normalized by reads per million.
Supplementary files format and content: The narrowPeak files contain peaks called on individual donors and are in standard narrowPeak format from macs2. The consensus peaks bed file contains the genomic coordinates of the consensus peaks in bed4 format, with columns chr, start, stop, and peakID.

molecule: genomic DNA

source_name: liver tissue

tag: tissue


title: N4 10x Multiome - GEX

city: Providence

first: Alexander

last: Fleischmann

state: RI

address: 185 meeting street

department: Neuroscience

institute: Brown University

description: 10x Multiome - GEX

library_source: transcriptomic single cell

data_processing:
The generated FASTQ files were processed with Cell Ranger ARC (v2.0.0) for Multiome ATAC + Gene expression experiments and with Cell Ranger (v6.0.0) for Single Cell 3' v3.1 experiments (10x Genomics).
Assembly: Reads were aligned to the mouse (Mus musculus) pre-mRNA reference genome (cellranger-arc-mm10-2020-A-2.0.0)
Supplementary files format and content: Matrix files

molecule: polyA RNA

organism: Mus musculus

source_name: SSp - C57Bl/6 mice (lab mice)

extract_protocol:
Each biological replicate was minced separately and placed into a tube containing cold Nuclei PURE Lysis Buffer and 10% Triton X-100 (Sigma, NUC201-1KT). The minced tissue was transferred into a 7 ml ice-cold tissue grinder (Sigma, D9063), homogenized up and down 20-25 times, and filtered on ice through cell strainers of 100μm, 70μm and 40 μm (Pluriselect, 43-10040). RNasin Plus diluted 1/200 (Promega, N2611) was added in all solutions.
Single -nuclei isolation for multiome sequencing experiments: After centrifuging at 500 rpm for 5 min at 4°C, the supernatant was aspirated and gently resuspended in 100 μl of a cold lysis solution containing Nuclei PURE Lysis Buffer, 10% Triton X-100, 0.01% of digitonin (ThermoFisher, BN2006), and 1% nuclease-free UltraPure™ BSA (ThermoFisher, AM2616). After 1 minute of incubation, 200 μl of cold 1X Nuclei Buffer (10x Genomics, 2000153/2000207) was added, the suspension was filtered again with a 40 μm cell strainer, centrifuged at 500 rpm for 5 min at 4°C, and gently resuspended into a final volume of 50 μl of cold 1X Nuclei Buffer.
Single -nuclei isolation for RNA sequencing experiments: After centrifuging at 500 rpm for 5 min at 4°C, the supernatant was aspirated and gently resuspended in 400 μl of a cold wash solution containing 1X Hanks’ Balanced Salt Solution HBSS and 1% nuclease-free UltraPure™ BSA. This step was repeated for a total of two times, and nuclei were resuspended into a final volume of 50 μl of cold wash solution.
Single-nuclei libraries were generated using the Single Cell Multiome ATAC + Gene Expression kit (10x Genomics, PN-1000283). Manufacturer’s instructions were followed for Tn5-based transposition, cell capture, barcoding, reverse transcription, cDNA amplification, and ATAC and RNA libraries construction. For wild-derived mice, 4 of 6 biological replicates for aPir, 1 of 4 for pPir, and 1 of 2 for SSp were processed using the Single Cell 3' Reagent Kits v3.1 dual index (10x Genomics, PN-1000268). Final libraries (40 libraries from gene expression and 32 libraries from ATAC experiments) were evaluated for quality and quantified using the Qubit fluorometer. The fragment size distribution was evaluated by Agilent TapeStation 2200 (Agilent Technologies). Libraries were further evaluated for proper incorporation of the Illumina adaptors on the Roche LightCycler 480 using the Roche Kapa library quant assay according to manufacturer’s protocol.

value: primary somatosensory cortex

tag: strain

value: C57Bl/6 mice (lab mice)


title: Lymphedema3

city: Daegu

first: Bo-Yoon

last: Park

address: 170 Hyeonchung-ro

country: South Korea

institute: Yeungnam University

data_processing:
Illumina bcl2fastq2-v2.20.0 software used for basecalling.
Trimmomatic program is used to remove adapter sequences and bases with base quality lower than three from the ends. Also using sliding window method, bases of reads that does not qualify for window size 4, and mean quality 15 are trimmed. Afterwards, reads with length shorter than 36bp are dropped to produce trimmed data.
Sequenced reads were mapped to GRCh38 whole genome by using HISAT2 version 2.1.0 with parameter -p 20 -dta --rna-strandness RF --novel-splicesite-outfile -x -1 -2
Fragment Per Kilobase of exon per Megabase of library size (FPKM) were calculated by using StringTie version 2.1.3b, with parameter --rf -p 20 -l -o -G -A -C -e
Assembly: mm10_NCBI_108
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

source_name: Subcutaneous fat

extract_protocol:
Fat issue was flash frozen on dry ice and RNA was harvested using Trizol reagent. The TruSeq Stranded mRNA Library Prep Kit was used with 1 ug of total RNA to construct the sequencing library.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Subcutaneous fat


title: 10^9 cells per gram of soil 12 weeks C

city: Richland

first: Ryan

last: McClure

state: Washington

address: 11829272 Battelle for the US DOE, 790 6th Street

department: Microbiology

institute: Pacific Northwest National Laboratory

description: 10^9 Samples Processed Data File

data_processing:
Raw reads were aligned to the genomes of the eight members of MSC-2 using the Burrows Wheeler Aligner
Resulting SAM files were used with GTF files of the eight members of MSC-2 to obtian counts using HTSeq
Raw count files were normalized using DESeq2
Assembly: https://data.pnnl.gov/group/nodes/dataset/33234
Supplementary files format and content: Processed data files are text .csv files with raw counts for each gene for each sample. One processed data file contains all data for samples inoculated with 10^8 cells per gram of soil (10_8_Samples_Processed_Data_File). The other contains all data for samples inoculated with 10^9 cells per gram of soil (10_9_Samples_Processed_Data_File)

organism:
Sinorhizobium meliloti
Rhodococcus sp. (in: high G+C Gram-positive bacteria)
Ensifer adhaerens
Sphingopyxis sp.
Dyadobacter sp.
Neorhizobium tomejilense
Variovorax beijingensis

source_name: MSC-2 Species (Streptomyces sp001905665, Neorhizobium tomejilense, a Dyadobacter sp., a Sphingopyxis sp., Ensifer adhaerens, Variovorax beijingensis, Sinorhizobium meliloti and Rhodococcus sp003130705)

growth_protocol: MSC-2 community members were grown in R2A media prior to inoculation into soil. Soil was incubated at 20C at Kennedy Space Center before tubes from each timepoint were frozen at -80C

extract_protocol:
RNA was extracted from 2 g portions of soil using the Quick-RNA Fecal/Soil Microbe Microprep kit (ZYMO REsearch, Irvine, CA).
NEBNext®Ultra™II Directional RNA Library Prep Kit for Illumina

treatment_protocol: Time was the only treatment here.  MSC-2 community members were incubated in soil with chitin as a major carbon source

tag: dilution

value: 10^9 cells per gram of soil

tag: time

value: 12 weeks

tag: replicate

value: C


title: N1 10x Multiome - GEX

description: 10x Multiome - GEX


title: Lymphedema2


title: alveolarbone2

city: Beijing

first: Jiayi

last: Wang

state: Beijing

address: No.22 Zhongguancun south Rd., Haidian district, Beijing, China

country: China

institute: Peking university school and hospital of stomatology

description: Library name: Sample2

data_processing:
Raw reads were processed to generate a gene expression matrix. Low-quality reads were removed using FastQC (v.0.11.9) and Fastp (v1).
The cell barcodes and unique molecular identifiers (UMIs) were extracted after trimming poly-A tails and adaptor sequences.
Reads were then mapped to the reference genome GRCh38, while gene and UMI counts were acquired. The number of UMIs per gene per cell was calculated by grouping the genes and UMIs based on the cell barcode. Expression matrix files was generated and used for further analysis.
The above procedure was integrated into CeleScope (https://github.com/singleron-RD/CeleScope, v2.1.0), which was utilized for analysis.
Assembly: mm10
Supplementary files format and content: tsv.gz, mtx.gz, barcodes, featues and matrix of sequencing data.

source_name: Alveolar bone

extract_protocol:
Alveolar bone within 1mm of the extraction socket was immediately collected and cleansed with ice-cold PBS containing 1% FBS. Alveolar bone was pooled from 6 mice per group. Tissue was minced into 1–2 mm size and digested with 2 ml GEXSCOPE® Bone Tissue Dissociation Solution for 60min at 37℃. Samples were then filtered and centrifuged. Single-cell suspensions were obtained after removal of red cells with 2 mL GEXSCOPE® red blood cell lysis buﬀer  at 25°C for 10 min and later analyzed using scRNAseq.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Healthy C57BL/6J mice (6-8 weeks old) weighing 20-25g were used. A nickel-titanium coil spring was attached to the maxillary right first molar and maxillary incisors via a 0.020-inch stainless steel ligature in order to provide mesial orthodontic force on the first molar. The constant force was maintained at 25g. For the control group, no force was applied after spring attachment.

value: Alveolar bone


title: 10^9 cells per gram of soil 8 weeks E

description: 10^9 Samples Processed Data File

value: 8 weeks

value: E


title: Lymphedema1


title: liver_ATAC_162_l3_s1

description:
Sample titles are in the format liver_ATAC_[sampleID]_[libraryID]_[sequencingRun]. Note that resequenced libraries were run at a later date and were sometimes on a different sequencer than the original sequencing run, so resequenced libraries are listed as separate samples.
162_peaks.narrowPeak.gz
162_scaled.bw


title: 10^9 cells per gram of soil 8 weeks D

description: 10^9 Samples Processed Data File

value: D


title: liver_ATAC_162_l2_s1


title: liver_ATAC_162_l1_s2


title: T7 10x Multiome - ATAC

description: 10x Multiome - ATAC

source_name: AI - C57Bl/6 mice (lab mice)

value: agranular insular cortex


title: Control5


title: 10^9 cells per gram of soil 8 weeks B

description: 10^9 Samples Processed Data File

value: B


title: T7 10x Multiome - GEX

description: 10x Multiome - GEX


title: liver_ATAC_162_l1_s1


title: 10^9 cells per gram of soil 4 weeks E

description: 10^9 Samples Processed Data File

value: 4 weeks


title: T6 10x Multiome - ATAC

description: 10x Multiome - ATAC


title: Control3


title: liver_ATAC_122_l1_s2

description:
Sample titles are in the format liver_ATAC_[sampleID]_[libraryID]_[sequencingRun]. Note that resequenced libraries were run at a later date and were sometimes on a different sequencer than the original sequencing run, so resequenced libraries are listed as separate samples.
122_peaks.narrowPeak.gz
122_scaled.bw


title: 10^9 cells per gram of soil 4 weeks D

description: 10^9 Samples Processed Data File


title: N1 10x Multiome - ATAC

description: 10x Multiome - ATAC


title: APEX2-PCNT-EGFP, BP labeling, pre-enrichment, rep3

first: Gang

address: 5th, Yiheyuan Road, Beijing

institute: Peking University

description: Column name: PCNT_Input_rep3

data_processing:
The sequencing reads for each library were aligned against the human genome assembly GRCh38 (hg38) that was downloaded from Ensembl project using HISAT2 (v2.1.0).
Then the results of alignments were sorted by read names. The read counts of each gene were measured with matching gene annotation (v.87) from Ensembl by HTSeq v0.6.1, using the option “-stranded no” .
Assembly: GRCh38 (hg38)
Supplementary files format and content: tab-delimited txt file contains counts of all genes from HEK293T cell lines stably expressing APEX2-NES or APEX2-PCNT-EGFP

growth_protocol: HEK293T cells were cultured in Dulbecco’s Modified Eagle’s Medium (DMEM, Gibco, C11995500BT) supplemented with 10% fetal bovine serum (FBS, Gibco, 10099141). All the cell lines were maintained at 37°C under 5% CO2.

extract_protocol:
Cells were lysed by the addition of TRIzol reagent (Invitrogen, 15596018). After homogenizing via pipetting, total RNAs was extracted via addition of chloroform, isopropanol precipitation, ethanol washing, and air dry according to manufacturer’s protocol. The extracted RNAs were further digested via DNase I (NEB, M0303) at 37°C for 30 min. The reaction mix were purified via RNA Clean & Concentrator kit (Zymo, R1018). Fragment Analyzer (Agilent) was used to analyze the integrity of purified RNAs. Only samples of RQN > 9.0 were subjected to downstream affinity purification. 10 mL purified RNA was set as Input sample. The remained RNAs were subjected to affinity purification, and set as Enrich or Control samples.
Input, Enrich, and Control samples from each biological replicate experiment were subjected to library construction by NEBNext Ultra II RNA Library Prep Kit for Illumina (NEB, E7770) with Poly(A) mRNA Magnetic Isolation Module (NEB, E7490) according to manufacturer’s instructions.

treatment_protocol: HEK293T cells stably expressing APEX2-NES or APEX2-PCNT-EGFP at 80-90% confluency were pre-treated with 100 mM s6G in complete medium for 5 hours before incubation with 0.5 mM BP probe for 30 min at 37°C under 5% CO2. Biotinylation was initiated by addition of 1 mM H2O2 for 1 min. To halt the APEX2 labeling, cells were treated with the quencher solution containing 10 mM sodium ascorbate, 5 mM Trolox, and 10 mM sodium azide for 2 min.

tag: cell type

tag: genotype

value: Stably expressing APEX2-PCNT-EGFP

value: Treated with 100 uM s6G for 5 hours


title: Control2


title: LCDC cell type, cells alone

value: Langerhans cell-derived Dendritic Cell


title: APEX2-PCNT-EGFP, BP labeling, pre-enrichment, rep2

description: Column name: PCNT_Input_rep2


title: Control1


title: 10^9 cells per gram of soil 4 weeks C

description: 10^9 Samples Processed Data File


title: T5 10x Multiome - GEX

description: 10x Multiome - GEX


title: T5 10x Multiome - ATAC

description: 10x Multiome - ATAC


title: 10^9 cells per gram of soil 0 weeks C

description: 10^9 Samples Processed Data File

value: 0 weeks


title: APEX2-PCNT-EGFP, BP labeling, post-enrichment, rep3

description: Column name: PCNT_Enrich_rep3


title: 10^9 cells per gram of soil 0 weeks E

description: 10^9 Samples Processed Data File


title: hCSF1_5xFAD_PILRAKO_rep2

city: South San Francisco

first: David

last: Tatarakis

email: tatarakis@dnli.com, genomics@dnli.com

state: California

address: 161 Oyster Point Blvd

department: Discovery Genomics

institute: Denali Therapeutics

description: 10X Genomics

data_processing:
Demultiplexed fastqs were mapped to a hybrid mouse/human genome using Cell Ranger v 7.0.1
Assembly: mm10/GRCh38
Supplementary files format and content: Tab separated values files and matrix files

source_name: Brain

extract_protocol:
Brains were manually homogenized using a 7mL Dounce homogenizer by adding 4 mL of RPMI 1640 and performing 10 strokes with the “loose” pestle followed by 10 strokes with the “tight” pestle. Samples were then run through a pre-soaked 70uM filter then the filter was washed with 10mL of RPMI 1640. The sample was pelleted by centrifugation and myelin was removed by resuspension in 8L of 30% Percoll overlaid with 2 mL of 1X DPBS centrifuged at 400xg for 20 minutes with acceleration set to 0 and brake set to 4. The myelin band and supernatant were discarded, and cell pellets were resuspended in 70μL MACS buffer (0.5% bovine serum albumin in 1X DPBS) + 30μL Mouse Cell Removal beads (Miltenyi) and incubated at 4°C for 15 minutes. Magnetically labeled mouse cells were separated using LS columns and the MidiMACs separator (Miltenyi) while the unlabeled human cells were collected in the flow through.
scRNA-seq library preparation was performed according to the 10X Genomics Chromium Single-cell 3′ Reagents kit v3.1 user guide except that sample volumes containing 26,500 cells were loaded onto the 10X Genomics flow cell to capture ≈10,000 total microglia.

value: Brain

value: iPSC

value: Microglia

tag: age


title: 10^9 cells per gram of soil 0 weeks B

description: 10^9 Samples Processed Data File

value: 10^9 cells per gram of soil


title: APEX2-PCNT-EGFP, BP labeling, pre-enrichment, rep1

description: Column name: PCNT_Input_rep1


title: APEX2-PCNT-EGFP, BP labeling, post-enrichment, rep2

description: Column name: PCNT_Enrich_rep2


title: T4 10x Multiome - GEX

description: 10x Multiome - GEX

value: C57Bl/6 mice (lab mice)


title: hCSF1_5xFAD_PILRAKO_rep1

description: 10X Genomics


title: Control4

value: Subcutaneous fat


title: 10^8 cells per gram of soil 12 weeks E

value: 10^8 cells per gram of soil

value: 12 weeks


title: T1 10x Multiome - ATAC

description: 10x Multiome - ATAC


title: T6 10x Multiome - GEX

description: 10x Multiome - GEX


title: hCSF1_PILRAKO_rep4

description: 10X Genomics


title: T1 10x Multiome - GEX

description: 10x Multiome - GEX


title: hCSF1_PILRAKO_rep3

description: 10X Genomics


title: 10^8 cells per gram of soil 12 weeks B


title: 10^8 cells per gram of soil 12 weeks A

value: A


title: APEX2-PCNT-EGFP, omit probe, post-enrichment, rep3

description: Column name: PCNT_Control_rep3


title: P6W 10x Single Cell 3' v3.1

description: 10x Single Cell 3' v3.1

source_name: pPir - wild-derived mice

value: posterior piriform cortex

value: wild-derived mice


title: 10^8 cells per gram of soil 8 weeks D

value: 8 weeks

value: D


title: APEX2-NES, BP labeling, pre-enrichment, rep3

description: Column name: NES_Input_rep3

value: Stably expressing APEX2-NES


title: hCSF1_PILRAKO_rep2

description: 10X Genomics


title: hCSF1_PILRAKO_rep1

description: 10X Genomics


title: P5W 10x Single Cell 3' v3.1

description: 10x Single Cell 3' v3.1


title: 10^8 cells per gram of soil 8 weeks C

value: C


title: P4W 10x Single Cell 3' v3.1

description: 10x Single Cell 3' v3.1


title: APEX2-PCNT-EGFP, omit probe, post-enrichment, rep2

description: Column name: PCNT_Control_rep2

value: Stably expressing APEX2-PCNT-EGFP

value: Treated with 100 uM s6G for 5 hours


title: APEX2-NES, BP labeling, pre-enrichment, rep2

description: Column name: NES_Input_rep2


title: T4 10x Multiome - ATAC

description: 10x Multiome - ATAC

value: agranular insular cortex


title: hCSF1_5xFAD_rep4

description: 10X Genomics

value: Brain

value: iPSC


title: APEX2-NES, BP labeling, pre-enrichment, rep1

description: Column name: NES_Input_rep1


title: hCSF1_5xFAD_PILRAKO_rep3

description: 10X Genomics

value: Microglia


title: APEX2-PCNT-EGFP, BP labeling, post-enrichment, rep1

description: Column name: PCNT_Enrich_rep1


title: 10^8 cells per gram of soil 4 weeks E

value: 4 weeks

value: E


title: P1W 10x Multiome - GEX

description: 10x Multiome - GEX


title: APEX2-NES, BP labeling, post-enrichment, rep3

description: Column name: NES_Enrich_rep3


title: 10^8 cells per gram of soil 4 weeks C

value: 10^8 cells per gram of soil


title: P11 10x Multiome - ATAC

description: 10x Multiome - ATAC

source_name: pPir - C57Bl/6 mice (lab mice)

value: C57Bl/6 mice (lab mice)


title: APEX2-NES, BP labeling, post-enrichment, rep2

description: Column name: NES_Enrich_rep2


title: P11 10x Multiome - GEX

description: 10x Multiome - GEX


title: APEX2-NES, BP labeling, post-enrichment, rep1

description: Column name: NES_Enrich_rep1


title: hCSF1_5xFAD_rep1

description: 10X Genomics


title: hCSF1_rep4

description: 10X Genomics


title: P10 10x Multiome - ATAC

description: 10x Multiome - ATAC


title: 10^8 cells per gram of soil 8 weeks B

value: B


title: 10^8 cells per gram of soil 0 weeks B

value: 0 weeks


title: HCT116, PDS-treat 3

city: Guangzhou

first: Huichuan

last: Yu

state: Guangdong

address: 26 Yuancun Erheng Road

institute: Sun Yat-sen University

data_processing:
Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts. In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data. At the same time, Q20, Q30 and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality.
Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using STAR and paired-end clean reads were aligned to the reference genome using STAR (v2.5.1b). STAR used the method of Maximal Mappable Prefix(MMP) which can generate a precise mapping result for junction reads.
HTSeq v0.6.0 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene. FPKM, expected number of Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced, considers the effect of sequencing depth and gene length for the reads count at the same time, and is currently the most commonly used method for estimating gene expression levels.
Differential expression analysis of two conditions/groups (two biological replicates per condition) was performed using the DESeq2 R package (1.10.1). DESeq2 provide statistical routines for determining differential expression in digital gene expression data using a model based on the negative binomial distribution. The resulting P-values were adjusted using the Benjamini and Hochberg’s approach for controlling the false discovery rate . Genes with an adjusted P-value <0.05 found by DESeq2 were assigned as differentially expressed.
Alternative Splicing is an important mechanism for regulate the expression of genes and the variable of protein. rMATS(3.2.1) software was used to analysis the ASevent.
Genome_build: GRCh38 for HCT116 and Rnor_6.0 for NP
Supplementary_files_format_and_content: xls files include FPKM values for each Sample

source_name: HCT116 cells

growth_protocol: All cell lines were either purchased from ATCC or provided by Shanghai Institutes for Biological Sciences, which had their identity confirmed by DNA genotyping and cultured according to manufacturer’s protocol.

extract_protocol:
RNA was isolated from cells of each group using RNeasy mini kit (Qiagen) according to manufacturer’s protocol.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: The cells were treated by 50 mM PDS for 24 hours.

tag: passages

value: PDS


title: hCSF1_rep3

description: 10X Genomics


title: P10 10x Multiome - GEX

description: 10x Multiome - GEX

value: posterior piriform cortex


title: 10^8 cells per gram of soil 0 weeks C


title: P1W 10x Multiome - ATAC

description: 10x Multiome - ATAC

value: wild-derived mice


title: hCSF1_rep2

description: 10X Genomics


title: HCT116, PDS-treat 2


title: P9 10x Multiome - ATAC

description: 10x Multiome - ATAC


title: TBX5-3

type: protein

city: Boston

first: Martha

middle: L.

last: Bulyk

state: MA

address: 77 Avenue Louis Pasteur, Rm 468

department: Division of Genetics

institute: Brigham and Women's Hospital

hyb_protocol: First, microarrays were double stranded by on-slide primer extension. The primer extension mixture contains Cy3-conjugated dUTP, which allows for the relative quantification of double-stranded DNA across the array as reflected by Cy3 intensity at each probe. For the TBX5 arrays, PBM double-stranding was performed as previously described (Berger and Bulyk 2009; Berger 2006) using a Thermo Fisher Sequenase (785001KT). Following its discontinuation by the manufacturer, for CREB1 arrays, double stranding was performed using the Cytiva Thermo Sequenase polymerase (E790000Y) using 3x polymerase but otherwise following the manufacturer's protocol. Double-stranded microarrays were pre-wet in standard phosphate buffered saline (PBS) (10mM PO43-, 137 mM NaCl, 2.7 mMKCl, pH7.4) / 0.01% Triton-X 100 for 5 minutes. PBS / 2% (wt/vol) nonfat dried milk (Sigma) was applied to individual chambers of an eight-chamber gasket cover slip in a steel hybridization chamber (Agilent), and the assembled microarray was incubated for 1 hour at room temperature. Microarrays were then washed once with PBS / 0.1% (vol/vol) Tween-20 for 5 min and once with PBS / 0.01% (vol/vol) Triton X-100 for 2 min. Proteins were diluted in a 75 µL reaction (per array chamber), comprised of 48.8 µL of protein binding mixture (PBS / 2% (wt/vol) milk, 51.3 ng/μl salmon testes DNA (Sigma), 0.2 μg/μl bovine serum albumin (New England Biolabs)) and 26.2 µL of each protein diluted in nuclease-free water. CREB1 isoforms were assayed at 400 nM final concentration and TBX5 isoforms were assayed at 750 nM final concentration. Protein mixtures were applied to individual chambers of an eight-chamber gasket cover slip in a steel hybridization chamber (Agilent), and the assembled microarrays were incubated for 1 hour at room temperature. Microarrays were again washed once with PBS/ 0.5% (vol/vol) Tween-20 for 3 min, and then once with PBS / 0.01% (vol/vol) Triton X-100 for 2 minutes. Alexa-488-conjugated rabbit polyclonal anti-GST antibody (Invitrogen) was diluted to 50μg/ml in PBS / 2% (wt/vol) milk and pre-incubated for 1 hour in the dark at room temperature. The antibody dilution was then applied to individual chambers of an eight-chamber gasket cover slip in a steel hybridization chamber (Agilent), and the assembled microarrays were incubated for 30 minutes at room temperature. Microarrays were washed twice with PBS / 0.05% (vol/vol) Tween-20 for 3 min each, and once in PBS for 2 min. After each incubation step, microarrays and coverslips were disassembled in a staining dish filled with the first wash solution. All washes were performed in Coplin jars at room temperature on an orbital shaker at 125 rpm. Following each series of washes, microarrays were rinsed in PBS and slowly de-wet to ensure uniform drying and removal of all liquid droplets and detergent from the DNA surface.

scan_protocol: PBMs were scanned in a GenePix 4400A microarray scanner. At least 3 scans were taken for each slide at different photomultiplier tube (PMT) gain settings. For each isoform replicate, an optimal scan was selected, corresponding to the PMT gain with the lowest proportions of both over-saturated probes (over-saturated probes are defined here as having intensity levels of >215.5; the signal is completely saturated at 216 = 65,536 intensity levels) and under-saturated probes (defined as intensity levels < 25) across all chambers in the allelic replicate. In this dataset, this always corresponded to a PMT gain of 500.

data_processing: PBM pre-processing was performed using the upbm data analysis pipeline as described in Kock et al. 2023. To map gpr files to probes, the upbm command gpr2PBMExperiment function is used with the parameter probes=pbm_8x60k_v1, which automatically loads the required mappings. These mappings are also included in this GEO submission as a txt file. To pre-process PBMs, probe intensities are background-subtracted, Cy3-normalized (to account for any biases resulting from double-stranding the array), and spatially de-biased. Cy3 normalization is performed using the command cy3FitEmpirical with the parameter refpe=refcy3_8x60k_v1, which automatically loads the Cy3 reference intensities used in the model. These reference intensities are also included in this GEO submission as a txt file. Reference isoforms then served as “anchors” for cross-array normalization for each gene. PBM inference to determine differentially bound DNA 8-mers was then performed using the upbm pipeline, which tests for a difference in the aggregated 8-mer affinity scores against a null hypothesis of zero. Importantly, summarization from the raw probe data to the 8-mer level is performed by running the upbm inference pipeline; these processed 8-mer values are what is included as processed data here.

molecule: protein

source_name: IVT protein

label_protocol: Arrays were incubated with an Alexa-488-conjugated rabbit polyclonal anti-GST antibody (Invitrogen A-11131).

extract_protocol: Full-length CREB1 isoforms were cloned into the PURExpress expression vector pDEST15 and full-length TBX5 isoforms were cloned into the mammalian IVT expression vector pT7CFE1-NHis-GST, both of which confer an N-terminal GST tag. N-terminal GST-CREB1 isoform fusions were then expressed using the PURExpress In Vitro Protein Synthesis Kit (NEB) per the manufacturer's protocol, with the exception of an addition of 1.5 µL of extra tRNA mix (NEB). N-terminal GST-TBX5 isoform fusions were expressed using the 1-Step Human Coupled IVT Kit (NEB) per the manufacturer's protocol.

tag: isoform

value: alternative


title: hCSF1_rep1

description: 10X Genomics


title: HCT116, control 3

value: control


title: 10^8 cells per gram of soil 0 weeks A

value: A


title: P8 10x Multiome - ATAC

description: 10x Multiome - ATAC


title: P9 10x Multiome - GEX

description: 10x Multiome - GEX


title: hCSF1_5xFAD_rep3

description: 10X Genomics


title: HCT116, control 2


title: KO_48_3

city: Cleveland

first: Ernest

middle: R

last: Chan

state: OH

address: 10900 Euclid Ave, Robbins E211

department: PQHS

institute: CWRU

data_processing:
Illumina reads were mapped to reference genome using STAR Aligner program.
The expression levels of genes were determined using Cufflinks and presented as FPKM
Differential expression analysis was done using Cuffdiff
Assembly: GRCh38
Supplementary files format and content: FPKM for all samples and genes

growth_protocol: Cells grown on 60mm cell culture treated dishes in DMEM media with 10% FBS, 1% L-glutamine, 1% penicillin-streptomycin, and 1% non-essential aminio acids in a 5% CO2-humidified chamber at 37 degrees Celcius

extract_protocol:
RNeasy Plus Mini Kit (Qiagen)
RNA-Seq libraries were generated using the Illumina mRNA TruSEQ Directional library kit and sequenced using an Illumina NovaSeq 6000

treatment_protocol: Cells were plated on day -1. On day 0, half of the plates were harvested for RNA, and the other half treated with 800 microM palmitic acid. On day 1, the palmitic acid-treated plates were harvested for RNA.

value: hepatoma

value: ABHD6 KO

value: 800 microM palmitic acid


title: 10^8 cells per gram of soil 4 weeks A


title: KO_48_2


title: TBX5-2


title: TBX5-REF

value: reference


title: HCT116, control 1


title: KO_48_1


title: CREB1-ALT


title: P7 10x Multiome - ATAC

description: 10x Multiome - ATAC


title: KO_48_0


title: WT_48_3

value: WT


title: CREB1-REF


title: 4796, AMLN, zalfermin + semaglutide

city: Oxford

first: Maria

last: Dermit

state: Oxfordshire

country: United Kingdom

institute: Novo nordisk research centre oxford

data_processing:
Adaptor trimming with Trim Galore! (v. 0.6.4_dev)
Alignement with Salmon (v. 1.9.0)
Gene levels counts obtained with tximeta (v. 1.10.0)
Assembly: GRCm38, release M23
Supplementary files format and content: text file with gene-level count values for each sample

source_name: liver

extract_protocol:
Lysis of tissue was performed using a MP FastPrep system. Briefly, 15-20 mg liver biopsy was homogenized and used for RNA extraction on NucleoSpin Plus RNA columns (Macherey-Nagel) as recommended by the supplier. The quantity of the RNA was assessed using a NanoDrop 2000 spectrophotometer (ThermoScientific). The purified RNA was stored at -80c
NeoPrep™ Library Prep System

value: liver

tag: diet

value: AMLN

value: zalfermin + semaglutide


title: HCT116, PDS-treat 1


title: P6 10x Multiome - GEX

description: 10x Multiome - GEX

value: C57Bl/6 mice (lab mice)


title: 4640, AMLN, zalfermin + semaglutide


title: hCSF1_5xFAD_rep2

description: 10X Genomics

value: Brain

value: iPSC

value: Microglia


title: WT_48_2


title: P5 10x Multiome - ATAC

description: 10x Multiome - ATAC

value: posterior piriform cortex


title: 4651, AMLN, zalfermin + semaglutide


title: P8 10x Multiome - GEX

description: 10x Multiome - GEX


title: P5 10x Multiome - GEX

description: 10x Multiome - GEX


title: 4417, AMLN, zalfermin + semaglutide


title: WT_48_0


title: P4 10x Multiome - ATAC

description: 10x Multiome - ATAC


title: 4406, AMLN, zalfermin + semaglutide


title: 4428, AMLN, zalfermin + semaglutide


title: P7 10x Multiome - GEX

description: 10x Multiome - GEX


title: P4 10x Multiome - GEX

description: 10x Multiome - GEX


title: 4351, AMLN, zalfermin + semaglutide


title: P6 10x Multiome - ATAC

description: 10x Multiome - ATAC


title: 4785, AMLN, zalfermin + semaglutide


title: KO_24_1


title: P2 10x Multiome - ATAC

description: 10x Multiome - ATAC


title: P2 10x Multiome - GEX

description: 10x Multiome - GEX


title: KO_24_0


title: WT_48_1


title: KO_24_3


title: 24h_HCl_PA_rep4

type: RNA

city: Giessen

first: Jochen

last: Wilhelm

state: Hessen

address: Aulweg 132

department: Institute for Lung Health

country: Germany

institute: Justus-Liebig University Giessen

hyb_protocol: 2 µg of the labeled cDNA were subjected to hybridization. The cDNA was not fragmented before hybridization. Hybridization was performed following the Agilent protocol at 65°C over-night in an in-situ hybridization oven with slides mounted in Agilent hybridization chambers. Slides were rotated with 2 rpm.

scan_protocol: Slides were scanned using the InnoScan 900 scanner (Innopsys, Carbonne France) at 2 µm/pixel resolution and analyzed with Mapix 8.2.5

data_processing: Raw data was further processed using R (http://www.R-project.org) and limma (Ritchie, M.E., Phipson, B., Wu, D., Hu, Y., Law, C.W., Shi, W., and Smyth, G.K. (2015). limma powers differential expression analyses for RNA-sequencing and microarray studies. NAR 43(7), e47). Background correction was performed with the normexp model using negative control spots and and offset of 1. Spot intensities were quantile normalized between arrays.

source_name: alveolar macrophages

label_protocol: Purified total RNA was amplified using the Ovation PicoSL WTA System V2 kit (NuGEN Technologies, Bemmel, Netherlands). Per sample, 2 µg amplified cDNA was Cy-labeled using the SureTag DNA labeling kit (Agilent, Waldbronn, Germany)

growth_protocol: Animals were grown under standard conditions.

extract_protocol: QIAgen RNeasy Micro Kit

treatment_protocol: Animals were intubated and 50 ul of 0.1N HCl was instilled intratracheally, controls received sham-treatment and the same volume of NaCl 0,9% i.t.. After the indicated time points (24, 96hrs and 7 days) mice were euthanized (nr. 1-16), or infected with Pseudomonas aeruginosa for 3 hours, and bronchoalveolar lavage was performed. Subsequently we stained the cells and sorted live resident alveolar macrophages, defined as 7-AAD-neg, CD45-pos, Ly6G-neg, CD11c-pos, and Siglec-F-pos, directly into RLT-lysis buffer.

value: alveolar macrophages

tag: hcl treatment

value: treated

tag: infection

value: P. aeruginosa


title: Control_rep4

value: none (control)

value: no


title: Control_PA_rep4


title: WT_24_3

value: hepatoma


title: 8d_HCl_PA_rep4


title: 4784, AMLN, semaglutide_low


title: 4650, AMLN, semaglutide_low


title: 96h_HCl_rep4


title: 24h_HCl_rep4


title: KO_24_2

value: ABHD6 KO

value: 800 microM palmitic acid


title: 8d_HCl_rep4


title: P1 10x Multiome - ATAC

description: 10x Multiome - ATAC


title: 96h_HCl_PA_rep4


title: P1 10x Multiome - GEX

description: 10x Multiome - GEX


title: 24h_HCl_PA_rep3


title: 4639, AMLN, semaglutide_low


title: WT_24_2

value: WT


title: 4416, AMLN, semaglutide_low

value: liver


title: KO_0_3

value: basal media


title: 96h_HCl_PA_rep3


title: 4427, AMLN, semaglutide_low

value: AMLN


title: Control_rep3


title: 4795, AMLN, semaglutide_low


title: WT_24_1


title: WT_24_0


title: 4350, AMLN, semaglutide_low


title: 4405, AMLN, semaglutide_low


title: A5W 10x Single Cell 3' v3.1

description: 10x Single Cell 3' v3.1

source_name: aPir - wild-derived mice

value: anterior piriform cortex

value: wild-derived mice


title: A3W 10x Single Cell 3' v3.1

description: 10x Single Cell 3' v3.1


title: 4783, AMLN, semaglutide_high


title: KO_0_1


title: A2W 10x Multiome - GEX

description: 10x Multiome - GEX


title: KO_0_2


title: A4W 10x Single Cell 3' v3.1

description: 10x Single Cell 3' v3.1


title: A6W 10x Single Cell 3' v3.1

description: 10x Single Cell 3' v3.1


title: Control_PA_rep3


title: A2W 10x Multiome - ATAC

description: 10x Multiome - ATAC


title: KO_0_0


title: 8d_HCl_PA_rep3


title: 4426, AMLN, semaglutide_high


title: WT_0_1


title: 96h_HCl_PA_rep2


title: WT_0_0


title: 4897, AMLN, semaglutide_high


title: 24h_HCl_rep3


title: A1W 10x Multiome - ATAC

description: 10x Multiome - ATAC


title: WT_0_2


title: A1W 10x Multiome - GEX

description: 10x Multiome - GEX


title: A11 10x Multiome - ATAC

description: 10x Multiome - ATAC

source_name: aPir - C57Bl/6 mice (lab mice)

value: C57Bl/6 mice (lab mice)


title: 8d_HCl_rep3


title: 96h_HCl_rep2


title: 4638, AMLN, semaglutide_high


title: 4404, AMLN, semaglutide_high


title: 96h_HCl_rep3


title: 4649, AMLN, semaglutide_high


title: Patient 4, timepoint 5, scBCR-seq

city: Suwon

first: Seung-Jun

last: Paek

address: Worldcup-ro

department: Department of Physiology

institute: Ajou University School of Medicine

description:
P4_5_scBCR
10x Genomics

data_processing:
10x Genomics Cell Ranger (version 6.0.0) was used for sequencing reads mapping against the GRCh38 human reference genome, UMI counting and cell filtering. A reference genome was applied from 10X Genomics.
Assembly: GRCh38
Supplementary files format and content: Tab-separated values and matrix files (scRNA gene expression)
Supplementary files format and content: Commna--separated values and matrix files (TCR, BCR clonotypes)

source_name: Peripheral blood mononuclear cell

extract_protocol:
Frozen cells were resuspended using 1xPBS solution and then filtered through a 40 µm filter. A small portion of the cell solution was mixed with AOPI and placed on a cell counting slide to check the viability (LUNA-FL™ Automated Fluorescence Cell Counter). Cells with viability over 70% were used for sequencing.
scRNA-seq: Chromium Next GEM Single Cell 5’ Kit v2 and Chromium Next GEM Chip K Single Cell Kit were used to generate barcoded 5’ single cell library (10X Genomics Chromium Instrument). Each cDNA library that passed the quality control (Agilent Bioanalyzer) was sequenced on an Illumina NovaSeq6000 and NextSeq500.
scV(D)J-seq: TCR and BCR sequencing was performed using cDNA synthesized by the nested-PCR enrichment method. TCR and BCR libraries were generated using the Chromium Single Cell Human TCR and BCR Amplification Kit (10X Genomics), and each library was checked for quality control (Agilent Bioanalyzer) before sequencing.

value: Peripheral blood mononuclear cell

tag: Sex

value: Female

tag: disease state

value: Before flare


title: WT_0_3

tag: cell line


title: 8d_HCl_rep2

value: alveolar macrophages

value: treated


title: A10 10x Multiome - GEX

description: 10x Multiome - GEX


title: 4415, AMLN, semaglutide_high

tag: treatment


title: A11 10x Multiome - GEX

description: 10x Multiome - GEX

tag: tissue


title: Patient 4, timepoint 6, scBCR-seq

description:
P4_6_scBCR
10x Genomics

value: Flare


title: 24h_HCl_rep2

value: no


title: A10 10x Multiome - ATAC

description: 10x Multiome - ATAC

tag: strain


title: 8d_HCl_PA_rep2

value: P. aeruginosa


title: 4349, AMLN, semaglutide_high


title: Patient 4, timepoint 3, scBCR-seq

description:
P4_3_scBCR
10x Genomics


title: Patient 4, timepoint 4, scBCR-seq

description:
P4_4_scBCR
10x Genomics

value: Remission


title: 4793, AMLN, zalfermin_low


title: Patient 4, timepoint 2, scBCR-seq

description:
P4_2_scBCR
10x Genomics


title: Control_rep2

value: none (control)


title: A6 10x Multiome - ATAC

description: 10x Multiome - ATAC


title: A9 10x Multiome - ATAC

description: 10x Multiome - ATAC


title: 4892, AMLN, zalfermin_low


title: Patient 4, timepoint 1, scBCR-seq

description:
P4_1_scBCR
10x Genomics


title: A9 10x Multiome - GEX

description: 10x Multiome - GEX


title: A6 10x Multiome - GEX

description: 10x Multiome - GEX


title: 4648, AMLN, zalfermin_low


title: 4782, AMLN, zalfermin_low


title: Patient 3, timepoint 6, scBCR-seq

description:
P3_6_scBCR
10x Genomics


title: Patient 3, timepoint 5, scBCR-seq

description:
P3_5_scBCR
10x Genomics


title: A4 10x Multiome - ATAC

description: 10x Multiome - ATAC


title: 4637, AMLN, zalfermin_low


title: 96h_HCl_PA_rep1


title: Control_PA_rep2


title: 4425, AMLN, zalfermin_low


title: Patient 3, timepoint 4, scBCR-seq

description:
P3_4_scBCR
10x Genomics


title: A3 10x Multiome - ATAC

description: 10x Multiome - ATAC


title: 8d_HCl_PA_rep1


title: 4414, AMLN, zalfermin_low


title: Patient 3, timepoint 3, scBCR-seq

description:
P3_3_scBCR
10x Genomics


title: Control_PA_rep1


title: 4403, AMLN, zalfermin_low


title: A3 10x Multiome - GEX

description: 10x Multiome - GEX


title: Patient 3, timepoint 2, scBCR-seq

description:
P3_2_scBCR
10x Genomics


title: 96h_HCl_rep1


title: A2 10x Multiome - ATAC

description: 10x Multiome - ATAC


title: 4896, AMLN, zalfermin_high


title: Patient 3, timepoint 1, scBCR-seq

description:
P3_1_scBCR
10x Genomics


title: 4781, AMLN, zalfermin_high


title: A2 10x Multiome - GEX

description: 10x Multiome - GEX


title: Control_rep1


title: Patient 2, timepoint 2, scBCR-seq

description:
P2_2_scBCR
10x Genomics


title: 8d_HCl_rep1


title: IgG_lef_4

city: Wuhan

first: Rong

last: Huang

address: Zhang Zhidong Road

institute: Renmin Hospital of Wuhan University

description:
Library name: Sample 12
F0288

data_processing:
After cluster generation with TruSeq PE Cluster Kit v3-cBot-HS (Illumina), the library preparations were sequenced on an Illumina HiSeq platform, and paired-end reads were generated
The high-quality clean data were aligned to a mouse genome (mm10) with HISAT2
Low-quality reads were removed with FASTX-Toolkit
Differentially expressed gene (DEG) analysis between the two groups was conducted with the DESeq2 R package
RNA-seq and subsequent analyses were performed by Novogene (Beijing, China).
Assembly: mm10
Supplementary files format and content: processed data.xls

source_name: Heart

extract_protocol:
Total RNA was extracted with TriZol, and RNA degradation and potential contamination were determined with 1% agarose gels.
Library construction was performed with a NEBNext® UltraTM RNA Library Prep Kit Illumina® (NEB, USA) with 3 µg RNA per sample following the manufacturer’s recommendations. Library quality was evaluated with  DNBSEQ-T7 system.

value: Heart


title: IgG_lef_3

description:
Library name: Sample 11
A4098


title: 24h_HCl_rep1


title: Patient 2, timepoint 1, scBCR-seq

description:
P2_1_scBCR
10x Genomics


title: A1 10x Multiome - ATAC

description: 10x Multiome - ATAC


title: A4 10x Multiome - GEX

description: 10x Multiome - GEX


title: 4647, AMLN, zalfermin_high

value: liver


title: Patient 1, timepoint 3, scBCR-seq

description:
P1_3_scBCR
10x Genomics

value: Male


title: IgG_lef_2

description:
Library name: Sample 10
A4097


title: A0 10x Multiome - ATAC

description: 10x Multiome - ATAC


title: 4636, AMLN, zalfermin_high

value: AMLN


title: IgG_lef_1

description:
Library name: Sample 9
A4083


title: Patient 1, timepoint 2, scBCR-seq

description:
P1_2_scBCR
10x Genomics


title: aPD1_veh_4

description:
Library name: Sample 8
A4079


title: A0 10x Multiome - GEX

description: 10x Multiome - GEX

value: anterior piriform cortex


title: Patient 1, timepoint 1, scBCR-seq

description:
P1_1_scBCR
10x Genomics


title: Cryo

city: Taichung

first: Chi-Ying

last: Lee

address: No.30-6, Sec. 1, Changping Rd., Beitun Dist., Taichung 406, Taiwan

country: Taiwan

institute: Taiwan IVF center, Lee's women's hospital

data_processing:
CLC Genomics Workbench v  10.0.1
Sequence reads were trimmed for adaptor sequence/low-quality sequence using CLC genomic benchwork (parameter- Quality limit: 0.05)
Trimmed sequence reads were mapped to GrCM38/mm10 using CLC genomic benchwork (parameters- mismath cost: 2 insertion cost: 3 deletion cost: 3 length fraction: 0.8 similarity fraction: 0.8)
Read count extraction and normalization were performed using CLC genomic benchwork
Assembly: Mus musculus GRCm38
Supplementary files format and content: tab-delimited files include FPKM values for each Sample

source_name: embryo

growth_protocol: Superovulation was induced in 6–8-week-old virgin mice of the B6CBF1 strain throughintraperitoneal injection of pregnant mare serum gonadotrophin (Sigma Chemical Co., St Louis, MO, USA) followed 48h later by injection with 5 IU of human chorionic gonadotrophin(Serono, Rome, Italy).

extract_protocol:
Samples of1 µLwere taken to construct a library using the Ovation SoLo RNA-Seq library preparation kit (NuGEN #0501-32)
Samples of1 µLwere taken to construct a library using the Ovation SoLo RNA-Seq library preparation kit (NuGEN #0501-32)

treatment_protocol: Embryo vitrification was performed using a Cryotech Vitrification Kit (Cryotech, Japan)according to the manufacturer’s instructions and the protocol described by Gutnisky et al

value: embryo

value: Embryo transfer with vitrification and warming


title: 4658, AMLN, zalfermin_high


title: 24h_HCl_PA_rep1


title: 4424, AMLN, zalfermin_high


title: Patient 4, timepoint 6, scTCR-seq

description:
P4_6_scTCR
10x Genomics

value: Peripheral blood mononuclear cell


title: aPD1_veh_3

description:
Library name: Sample 7
A4078


title: A1 10x Multiome - GEX

description: 10x Multiome - GEX

value: C57Bl/6 mice (lab mice)


title: 4347, AMLN, zalfermin_high


title: Fresh

value: Embryo transfer without vitrification and warming


title: aPD1_veh_1

description:
Library name: Sample 5
A4072


title: CD24_CD29_rep2

city: New York

first: Matthew

last: Greenblatt

state: NY

address: 1161 York Ave APT 1a

department: Pathology and Laboratory Medicine

institute: WEILL CORNELL MEDICAL COLLEGE

data_processing:
Illumina bcl2fastq2 v2.20 was used for basecalling.
The sequenced reads were cleaned by trimming adapter sequences using cutadapt v2.10, and were aligned to the mouse reference genome (GRCm38) using BWA v0.7.17.
The A, C, G, T bases at each position across the mitochondrial genome were counted and calculated for all possible mutations. High-confidence mutations were then extracted and hierarchical clustering was performed.
Genome_build: mm10
Supplementary_files_format_and_content: plain text files storing per-base coverage and counts on non-reference alleles

source_name: Femur

extract_protocol:
3 month old PolG mouse femurs were isolated, subjected to mechanical and enzymatic digestion, different skeletal cell subsets were then isolated by FACS.
Cells were spun down, lysed and tagmented using Tn5 enzyme (Illumina Tag DNA Enzyme & Buffer Small Kit, 20034197). The tagmented DNA samples were purified using the MinElute PCR kit (Qiagen, cat no 28004) and eluted with 20 μl of ddH2O. ATAC-Seq libraries were prepared and samples were sequenced on an Illumina NovaSeq6000 sequencer with paired-end 100 bps.

value: Skeletal cells

value: PolG D257A/D257A

value: 3 months


title: CD29_rep2


title: Patient 4, timepoint 5, scTCR-seq

description:
P4_5_scTCR
10x Genomics

value: Female

value: Before flare


title: 5006, AMLN, Vehicle

value: NASHVehicle


title: Patient 4, timepoint 4, scTCR-seq

description:
P4_4_scTCR
10x Genomics

value: Remission


title: 4895, AMLN, Vehicle


title: Patient 4, timepoint 3, scTCR-seq

description:
P4_3_scTCR
10x Genomics

value: Flare


title: CD24_rep2


title: aPD1_lef_4

description:
Library name: Sample 4
A4069

value: Heart


title: 4413, AMLN, zalfermin_high

value: liver


title: 4780, AMLN, Vehicle

value: AMLN


title: Patient 4, timepoint 2, scTCR-seq

description:
P4_2_scTCR
10x Genomics


title: aPD1_lef_3

description:
Library name: Sample 3
A4067


title: 4657, AMLN, Vehicle


title: aPD1_lef_2

description:
Library name: Sample 2
A4065


title: Patient 4, timepoint 1, scTCR-seq

description:
P4_1_scTCR
10x Genomics


title: Thy_6C3_rep2


title: 24h_HCl_PA_rep2

value: alveolar macrophages

value: treated

value: P. aeruginosa


title: 4646, AMLN, Vehicle


title: Patient 3, timepoint 6, scTCR-seq

description:
P3_6_scTCR
10x Genomics

value: Peripheral blood mononuclear cell


title: aPD1_veh_2

description:
Library name: Sample 6
A4076


title: 6C3_rep2


title: 4635, AMLN, Vehicle


title: aPD1_lef_1

description:
Library name: Sample 1
A4064


title: Thy_rep2


title: Patient 3, timepoint 5, scTCR-seq

description:
P3_5_scTCR
10x Genomics


title: DOX-induced-MC38-Teton-CXC14 cell2 fq1

city: Shanghai

first: Jingjing

last: Li

address: 800 Dongchuan Rd.

department: School of Pharmacy

institute: Shanghai Jiao Tong University

data_processing:
The software fastp1 was used to remove the splice sequence and filter out low-quality, N-base (indicating that base information could not be determined) to obtain high-quality clean data
Using STAR2 comparison software (, the transcriptome sequencing data (clean data) is compared to the reference genome(mm39), and the results are compared for evaluation and quality control
The StringTie25 software v 2.0.4 was used to quantify the gene expression level, and the FPKM and TPM methods were used to standardize the expression level
Assembly: mm39
Supplementary files format and content: The file format is an expression matrix, where the rows are genes and the columns are samples

growth_protocol: MC38 cells (ATCC CRL-2639) were cultured in DMEM medium supplemented with 10% FBS. Cells were maintained in a humidified incubator at 37°C with 5% CO2 and 80% humidity.

extract_protocol:
Total RNA was extracted from 10 cm dishes of cells or 0.1 g of tumor tissue using column purification column purification (TAKARA, 9767).
Hieff NGS® Ultima Dual-mode mRNA Library Prep Kit for Illumina® (Cat#12301, Yeasen Biotechnology (Shanghai) Co., Ltd., Shnghai, China)

treatment_protocol: when cell grew to 20% fluence, doxycycline was added into the medium to the end concentration of 1 ug/mL. the control group was added with equal volum of solvent (PBS) , the cells were cultured 72 hours, and harvest with TRIzol solution.

value: colon cancer cell

value: DOX-induced


title: CD45_rep2

value: Skeletal cells


title: DOX-induced-MC38-Teton-CXC14 cell1 fq1


title: 4423, AMLN, Vehicle


title: Patient 3, timepoint 3, scTCR-seq

description:
P3_3_scTCR
10x Genomics


title: Patient 3, timepoint 4, scTCR-seq

description:
P3_4_scTCR
10x Genomics


title: 4346, AMLN, Vehicle


title: Patient 3, timepoint 2, scTCR-seq

description:
P3_2_scTCR
10x Genomics


title: Con MC38-Teton-CXC14 cell1 fq1

value: Untreat


title: CD29_rep1

value: PolG D257A/D257A

value: 3 months


title: 5005, CHOW,Vehicle

value: CHOW

value: ChowVehicle


title: CD105_rep2


title: 5004, CHOW,Vehicle


title: Patient 3, timepoint 1, scTCR-seq

description:
P3_1_scTCR
10x Genomics

value: Female

value: Before flare


title: Inulin Tm_5

city: Frederiksberg C

first: Andrew

last: Williams

address: Dyrlægevej 100

country: Denmark

institute: University of Copenhagen

description: Library name: Inulin Tm 5

data_processing:
Adaptor sequences and low quality reads removed
Mapped to Mus Musculus (mm10) using HISAT
DEG assessed using DeSeq2
Assembly: mm10
Supplementary files format and content: excel file with count data and FPKM for each sample.

source_name: Intestinal epithelium

extract_protocol:
Total RNA was extracted using mRNAeasy kits (Qiagen)
Standard BGI Protocol

value: Intestinal epithelium


title: CD24_rep1


title: CD24_CD29_rep1


title: 4801, CHOW,Vehicle

value: liver


title: CD105_rep1


title: Inulin Tm_4

description: Library name: Inulin Tm 4


title: Patient 2, timepoint 2, scTCR-seq

description:
P2_2_scTCR
10x Genomics

value: Flare


title: Patient 2, timepoint 1, scTCR-seq

description:
P2_1_scTCR
10x Genomics


title: 4790, CHOW,Vehicle


title: Inulin Tm_3

description: Library name: Inulin Tm 3


title: 4779, CHOW,Vehicle


title: Thy_6C3_rep1


title: Patient 1, timepoint 3, scTCR-seq

description:
P1_3_scTCR
10x Genomics

value: Male

value: Remission


title: Con MC38-Teton-CXC14 cell2 fq1


title: Inulin Tm_2

description: Library name: Inulin Tm 2


title: 4656, CHOW,Vehicle


title: Inulin Tm_1

description: Library name: Inulin Tm 1


title: Tm_5

description: Library name: Tm 5


title: Patient 1, timepoint 2, scTCR-seq

description:
P1_2_scTCR
10x Genomics


title: 4433, CHOW,Vehicle


title: Patient 4, timepoint 6, scRNA-seq

description:
P4_6_scRNA
10x Genomics


title: Tm_4

description: Library name: Tm 4


title: Thy_rep1


title: CD45_rep1


title: RNA-seq_CD24_CD29_HFD_rep4

description: Mice treated with diet for 4 weeks

data_processing:
Illumina bcl2fastq2 v2.20 was used for basecalling.
Sequenced reads were trimmed for low-quality bases and for adapter sequences using cutadapt; then mapped to the mouse mm10 reference genome using STAR v2.5.2b.
Raw read counts were extracted using HTSeq-count v0.11.2.
Differential expression analysis was performed using DESeq2 v1.26.0.
Genome_build: mm10
Supplementary_files_format_and_content: txt file storing read counts per gene per sample

extract_protocol:
Femurs were isolated from mice, subjected to mechanical and enzymatic digestion, CD24+CD29+ skeletal stem cells were then isolated by FACS. RNA was extracted from lysed cells using the RNeasy plus microkit from Qiagen (Cat #74034)
cDNA libraries were generated using SMART-Seq v4 Ultra low input RNA plus Nextera XT DNA sample preparation kit and sequenced on an Illumina Nova Seq 6000 sequencer (pair end 50)

treatment_protocol: 3-month-old mice were fed with control low fat diet (LFD,10% fat) or high fat diet (HFD, 60% fat) for 4 weeks

value: Skeletal stem cell of bone

value: High Fat diet


title: 12 dpi, replicate B

city: Galveston

first: Jacquelyn

last: Turcinovic

state: TX

address: Galveston National Laboratory, 301 University Blvd.

department: Microbiology and Immunology

institute: University of Texas Medical Branch

description: 10X Genomics, Chromium Next GEM Single Cell 3' GEM, Library & Gel Bead Kit v3.8

data_processing:
Sequencing data was processed via 10X Genomics Cell Ranger 6.0.2 . A custom reference was built from the combined human (GRCh38, Ensembl 101), mouse (GRCm38, Ensembl 101), and SARS-CoV-2 (NC_045512.2) genomes. FASTQ files were generated from raw Illumina BCL files using cellranger mkfastq. FASTQ files were aligned to the custom reference and quantified with cellranger count.
Assembly: GRCh38, GRCm38, and NC_045512.2
Supplementary files format and content: Tab-separated values files and matrix files.

source_name: Fetal lung xenograft

extract_protocol:
Fetal lung xenografts were processed as previously described (Kenney et al (2022) Cell Reports). Briefly, lung tissues were placed in a 60 mm dish, minced using a disposable scalpel, then transferred into a 15 mL conical tube containing 3 mL of digestion buffer (HBSS minus Ca2+, Mg2+, and phenol red, 0.5 mg/mL Liberase TM, 1 mg/mL DNase I) and incubated at 37°C for 30 min with agitation every 10 min. After digestion, tissue was passed through a 70 μm strainer on a 50 mL tube, mashed using the plunger of a 3 mL syringe and washed twice with 1 mL FACS buffer. Cell suspension was centrifuged at 300 x g for 5 minutes at 4°C, suspended in 1 mL of ACK lysing buffer, and incubated for 2 min at room temperature.  After incubation, lysis was quenched with 12 mL of FACS buffer, cell suspension was centrifuged at 300 x g for 5 min at 4°C, and the cell pellet was suspended in 1 mL of FACS buffer prior to downstream processing.Cells were frozen down in a 90% FBS (Bio-Techne, R&D systems) 10% DMSO solution (ThermoFisher Scientific) and kept at -80°C.
Four to five days following freezing, cells were thawed, and viability was assessed using Trypan blue (Fisher Scientific). Samples with ≥90% viability were then processed using the Chromium Next GEM Single Cell 3' GEM, Library & Gel Bead Kit v3.1, as per manufacturer instructions, and single cell barcoding was performed using a Chromium instrument (10x genomics) located in the NEIDL BSL-3. Reverse transcription of RNAs was performed in the BSL-3 using a thermocycler (Applied Biosciences), and cDNA was then removed from containment. Full-length, barcoded cDNAs were then amplified by PCR to generate sufficient mass for library construction. Enzyme fragmentation, A tailing, adaptor ligation and PCR were then performed at the Boston University single-cell sequencing core to obtain final libraries containing P5 and P7 primers used in Illumina bridge amplification. Size distribution and molarity of resulting cDNA libraries were assessed via Bioanalyzer High Sensitivity DNA Assay (Agilent Technologies, USA). All cDNA libraries were sequenced on an Illumina NextSeq 500 instrument at the Boston University microarray and sequencing core according to Illumina and 10x Genomics guidelines with 1.4-1.8pM input and 1% PhiX control library spike-in (Illumina, USA).

value: Fetal lung xenograft

value: BLT-L

value: Infected, 12 dpi


title: RNA-seq_CD24_CD29_HFD_rep3

description: Mice treated with diet for 4 weeks


title: Patient 4, timepoint 5, scRNA-seq

description:
P4_5_scRNA
10x Genomics

value: Peripheral blood mononuclear cell


title: RNA-seq_CD24_CD29_HFD_rep2

description: Mice treated with diet for 4 weeks


title: Tm_2

description: Library name: Tm 2


title: 2 dpi, replicate B

description: 10X Genomics, Chromium Next GEM Single Cell 3' GEM, Library & Gel Bead Kit v3.6

value: Infected, 2 dpi


title: 12 dpi, replicate A

description: 10X Genomics, Chromium Next GEM Single Cell 3' GEM, Library & Gel Bead Kit v3.7


title: Patient 4, timepoint 3, scRNA-seq

description:
P4_3_scRNA
10x Genomics


title: 6C3_rep1

value: Skeletal cells

value: PolG D257A/D257A

value: 3 months


title: RNA-seq_CD24_CD29_LFD_rep4

description: Mice treated with diet for 4 weeks

value: Low fat diet


title: Tm_1

description: Library name: Tm 1


title: 2 dpi, replicate A

description: 10X Genomics, Chromium Next GEM Single Cell 3' GEM, Library & Gel Bead Kit v3.5


title: Inulin_5

description: Library name: Inulin 5


title: RNA-seq_CD24_CD29_LFD_rep3

description: Mice treated with diet for 4 weeks


title: Patient 4, timepoint 1, scRNA-seq

description:
P4_1_scRNA
10x Genomics

value: Female


title: 4411, CHOW,Vehicle

value: CHOW

value: ChowVehicle


title: Naïve, replicate D

description: 10X Genomics, Chromium Next GEM Single Cell 3' GEM, Library & Gel Bead Kit v3.4

value: Uninfected


title: Naïve, replicate B

description: 10X Genomics, Chromium Next GEM Single Cell 3' GEM, Library & Gel Bead Kit v3.2


title: Patient 3, timepoint 6, scRNA-seq

description:
P3_6_scRNA
10x Genomics


title: Naïve, replicate C

description: 10X Genomics, Chromium Next GEM Single Cell 3' GEM, Library & Gel Bead Kit v3.3


title: Inulin_3

description: Library name: Inulin 3

value: Intestinal epithelium


title: RNA-seq_CD24_CD29_LFD_rep1

description: Mice treated with diet for 4 weeks


title: Tm_3

description: Library name: Tm 3


title: Patient 3, timepoint 5, scRNA-seq

description:
P3_5_scRNA
10x Genomics

value: Flare


title: Patient 4, timepoint 4, scRNA-seq

description:
P4_4_scRNA
10x Genomics

value: Remission


title: Patient 3, timepoint 4, scRNA-seq

description:
P3_4_scRNA
10x Genomics

value: Before flare


title: DOX-induced-Tumor-Teton-CXC14 cell4 fq1

data_processing:
The software fastp1 was used to remove the splice sequence and filter out low-quality, N-base (indicating that base information could not be determined) to obtain high-quality clean data
We used HISAT to align the clean reads to the reference genome. The alignment results are shown as follows.
We used Bowtie2 to align the clean reads to the reference genes.
The StringTie25 software v 2.0.4 was used to quantify the gene expression level, and the FPKM and TPM methods were used to standardize the expression level
Assembly: GCF_000001635.26_GRCm38.p6
Supplementary files format and content: The file format is an expression matrix, where the rows are genes and the columns are samples

source_name: subcutaneous tumor

growth_protocol: 7-week-old male mice were used for tumorigenesis. The tumor cells were cultured in complete medium until confluent (80-90%), digested with pancreatin, washed twice with HBSS, resuspended in PBS and adjusted to a density of 10^7/mL. Using a 1 mL syringe, the tumor cells were injected subcutaneously at the armpit, with 100 uL of cell suspension (containing 106 cells) injected into each mouse.

extract_protocol:
Total RNA was extracted from  0.1 g of tumor tissue using column purification column purification (TAKARA, 9767).
Hieff NGS® Ultima Dual-mode mRNA Library Prep Kit for Illumina® (Cat#12301, Yeasen Biotechnology (Shanghai) Co., Ltd., Shnghai, China)

treatment_protocol: When the MC38-TetOn-CXCL14 subcutaneous tumor grows to 300mm^3, mice are given drinking water containing 1mg/mL DOX for 3 days. After 3 days, the mice are sacrificed by cervical dislocation, and tumor tissues are excised.

value: subcutaneous tumor

value: colon cancer

value: DOX-induced


title: Inulin_2

description: Library name: Inulin 2


title: Naïve, replicate A

description: 10X Genomics, Chromium Next GEM Single Cell 3' GEM, Library & Gel Bead Kit v3.1

value: Fetal lung xenograft

value: BLT-L


title: DOX-induced-Tumor-Teton-CXC14 cell2 fq1


title: Het Immune, replicate 1, scRNAseq

first: Single Cell

last: Sequencing Core

address: 72 E. Concord St

institute: BU Single Cell Sequencing Core

description: 10x Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v3.1.0 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: mm10
Supplementary files format and content: Comma separated values of log-normalized counts and cell cluster assignment for each cell

source_name: lung

extract_protocol:
Cell concentration and viability of mouse samples were measured using the Countess II instrument and ranged from 8 – 9 x 105 cells/mL with ~95% viability (Thermofisher Scientific, USA). Cell samples were input into 10x Genomics Single Cell 3′ v3 workflow and processed according to the manufacturer’s instructions for a targeted recovery of 8000 cells (10X Genomics, USA). Resulting cDNA libraries were sequenced on an Illumina NextSeq 500 instrument with 1.8pM input and 1% PhiX control library spike-in (Illumina, USA).
scRNA-seq libraries were generated in BU DOM Single Cell sequencing core facility and sequenced by BU Microarray and Sequencing Resource Core Facility according to 10x Genomics protocol

value: lung

value: Wildtype

value: 4 weeks Sp19 i.t.


title: Control_5

description: Library name: Control 5


title: Patient 4, timepoint 2, scRNA-seq

description:
P4_2_scRNA
10x Genomics

value: Peripheral blood mononuclear cell


title: Naïve, replicate 1, scRNAseq

description: 10x Genomics

value: Saline i.t.


title: Inulin_1

description: Library name: Inulin 1


title: Control_4

description: Library name: Control 4


title: Patient 3, timepoint 3, scRNA-seq

description:
P3_3_scRNA
10x Genomics

value: Female


title: DOX-induced-Tumor-Teton-CXC14 cell1 fq1


title: Sp3, replicate 1, scRNAseq

description: 10x Genomics

value: 24 hours Sp3 i.t.


title: Control_3

description: Library name: Control 3


title: Con tumor-Teton-CXC14 cell4 fq1

value: Untreat


title: Inulin_4

description: Library name: Inulin 4

value: Intestinal epithelium


title: Patient 3, timepoint 1, scRNA-seq

description:
P3_1_scRNA
10x Genomics


title: DOX-induced-Tumor-Teton-CXC14 cell3 fq1


title: RNA-seq_CD24_CD29_LFD_rep2

description: Mice treated with diet for 4 weeks

value: Skeletal stem cell of bone

value: Low fat diet


title: Patient 2, timepoint 2, scRNA-seq

description:
P2_2_scRNA
10x Genomics

value: Flare


title: Con tumor-Teton-CXC14 cell3 fq1

value: subcutaneous tumor


title: Control_2

description: Library name: Control 2


title: Con tumor-Teton-CXC14 cell2 fq1

value: colon cancer


title: Con tumor-Teton-CXC14 cell1 fq1


title: Mouse #557, sample B, naive

data_processing:
Raw FASTQ files were quality-checked with FastQC v0.11.7.
Reads were aligned to the combined human (GRCh38, Ensembl 101) mouse (GRCm38, Ensembl 101), and SARS-CoV-2 (NC_045512.2) genomes with STAR v2.7.1a.
Aligned reads were quantified with featureCounts v1.6.2.
Assembly: GRCh38, GRCm38, and NC_045512.2
Supplementary files format and content: Tab-delimited file contains raw counts for each sample

extract_protocol:
During necropsy a piece of fLX tissue was placed in 600 μL of RNAlater (MilliporeSigma: #R0901500ML) and stored at −80°C until analysis. For RNA extraction, 20–30 mg of tissue was weighed out, placed into a 2 mL tube with 600 μL of RLT buffer with 1% β–mercaptoethanol and a 5 mm stainless steel bead (Qiagen, Hilden, Germany: #69989), then dissociated using a Qiagen TissueLyser II (Qiagen) with the following cycle: two min dissociation at 1800 oscillations/min, one min rest, two min dissociation at 1800 oscillations/min. Dissociated tissues were centrifuged at 13,000 rpm for 10 min at room temperature and cleared supernatant was transferred to a new 1.5 mL eppendorf tube. RNA extractions were performed using a Qiagen RNeasy Plus Mini Kit (Qiagen: #74134), according to the manufacturer’s instructions (Qiagen: #79256). RNA was eluted in 30 μL of RNase/DNase free water and quantified by Nanodrop.
Total RNA was sent to BGI genomics (Hong Kong, China) for polyA-selected library preparation and sequencing (Pair-ends, 100 bp, 20M reads per sample).

value: Uninfected


title: Patient 1, timepoint 3, scRNA-seq

description:
P1_3_scRNA
10x Genomics

value: Male

value: Remission


title: siRNA_4

city: Nagoya

first: Junfeng

last: Chen

state: 23 - 愛知県

address: Nagoya University

country: Japan

institute: Nagoya University

data_processing:
Bowtie2 (version 1.2.3) was used to map the clean reads to our custom reference transcriptome.
Gene expression was quantified using the RSEM program (version 1.3.3).
Assembly: Mmul_10
Supplementary files format and content: Excel file includes FPKM values for each sample.

organism: Macaca mulatta

source_name: Rhesus macaque fibroblast cells

growth_protocol: Macaque fibroblast cells were maintained in high glucose DMEM supplemented with 12% FBS, 100 U/ml penicillin and 100μg/ml streptomycin (ThermoFisher Scientific) at 37 °C with 5% CO2.

extract_protocol:
Total RNA was prepared using the RNeasy Lipid Tissue Mini Kit (Qiagen).
mRNA was first purified from the total RNA using poly-T oligo-attached magnetic beads and then fragmented, after which cDNA synthesis was performed. Then the synthesized cDNA was used for the preparation of PE100 strand specific sequencing libraries. Strand-specific RNA-seq

treatment_protocol: NC group was transfected with 40 pmoles negative control siRNA and siRNA group was transfected with 80 pmoles siRNA containing equal amounts of GABPA and GABPB1 siRNAs.

value: sample co-transfected with GABPA and GABPB1 siRNAs

value: fibroblast cells


title: Patient 2, timepoint 1, scRNA-seq

description:
P2_1_scRNA
10x Genomics

value: Before flare


title: Patient 3, timepoint 2, scRNA-seq

description:
P3_2_scRNA
10x Genomics

value: Peripheral blood mononuclear cell


title: siRNA_2


title: siRNA_3


title: Mouse #585, sample B, naive

value: Fetal lung xenograft

value: BLT-L


title: Patient 1, timepoint 1, scRNA-seq

description:
P1_1_scRNA
10x Genomics


title: 30 wt oca

city: Utrecht

first: Saskia

middle: van

last: Mil

address: Universiteitsweg 100

department: Center for Molecular Medicine

country: Netherlands

institute: UMC Utrecht

data_processing:
Quality control was doen with FastQC (v0.11.8)
TrimGalore (v0.6.5) was used to trim reads based on quality and adapter presence after which FastQC was used to check the resulting quality.
rRNA reads were filtered out using SortMeRNA (v 4.3.3)
Reads were aligned to the reference genome using the STAR (v. 2.73a) aligner
QC on the mapped files was done using Sambamba (v0.7.0), RSeQC (v3.0.1) and PreSeq (v2.0.3)
Assembly: Readcounts were generated using the Subread Featurecounts module (v2.0.0) and normalization using edgeR (v 3.28).
Supplementary files format and content: Hs_GRCh38_gatk_sorted.fasta
Supplementary files format and content: tab-delimited text file containing the raw data counts

source_name: colon

extract_protocol:
RNA was isolated using the Macherey-Nagel Nucleospin RNA isolation kit.
Libraries were prepared using the TruSeq stranded mRNA polyA kit

treatment_protocol: Organoids were lentivirally transduced with either FXRa3, FXRa4 or GFP and treated with either DMSO or obeticholic acid (OCA) for 3 days.

value: colon

value: WT

value: oca


title: siRNA_1


title: Mouse #585, sample A, naive


title: 29 wt dmso

value: dmso


title: NC_4

value: control sample transfected with negative control siRNA


title: Mouse #583, 12 dpi

value: Infected, 12 dpi


title: Patient 1, timepoint 1, scTCR-seq

description:
P1_1_scTCR
10x Genomics


title: Control_1

description: Library name: Control 1

value: Intestinal epithelium


title: NC_3


title: Mouse #579, 2 dpi

value: Infected, 2 dpi


title: Patient 1, timepoint 2, scRNA-seq

description:
P1_2_scRNA
10x Genomics

value: Flare


title: Mouse #578, 12 dpi


title: 27 tpo AKPS fxra4 oca

value: TPO AKPS


title: S-IECs of Nfat5IEC-KO mouse_2

city: Seoul

first: Bong-Ki

last: Hong

address: 222 Banpo-daero, Seocho-gu

department: School of Medicine

institute: Catholic University of Korea

description: Gene expression data of small intestinal epithelial cells from Nfat5IEC-KO mouse

hyb_protocol: The labeled DNA targets were hybridized to the Affymetrix GeneChip Mouse Gene 2.0 ST array (Affymetrix).

scan_protocol: GeneChips were scanned using the GCS3000 Scanner (Affymetrix).

data_processing:
The data were analyzed using the Transcriptome Analysis Console (TAC) software version 4.0.0 (Thermo Fisher Scientific) along with the mouse reference genome (MoGene-2_0-st-v1.na36.mm10.transcript.csv).
affymetrix-algorithm-name = rma-bg.quant-norm.pm-only.med-polish
affymetrix-algorithm-version = 1.0

label: biotin

source_name: S-IECs of Nfat5IEC-KO mouse

label_protocol: Biotinylated cDNA were prepared according to the GeneChip Whole Transcriptome PLUS Reagent Kit (Affymetrix) from  total RNA.

growth_protocol: The small intestine (ileum) and colon epithelail cell were isolated by using EDTA for 30 min at RT.

extract_protocol: RNeasy Mini Kit (Qiagen) extraction of total RNA was performed according to the manufacturer's instructions.

treatment_protocol: No treatment.

value: Small intestinal epithelial cells

value: 11 weeks old


title: L-IECs of Nfat5IEC-KO mouse_1

description: Gene expression data of large intestinal epithelial cells from Nfat5IEC-KO mouse

source_name: L-IECs of Nfat5IEC-KO mouse

value: Large intestinal epithelial cells


title: 26 tpo AKPS fxra4 oca


title: L-IECs of Nfat5fl/fl mouse_3

description: Gene expression data of large intestinal epithelial cells from Nfat5fl/fl mouse

source_name: L-IECs of Nfat5fl/fl mouse


title: S-IECs of Nfat5IEC-KO mouse_1


title: S-IECs of Nfat5IEC-KO mouse_3


title: L-IECs of Nfat5IEC-KO mouse_2


title: L-IECs of Nfat5IEC-KO mouse_3


title: L-IECs of Nfat5fl/fl mouse_2


title: 25 tpo AKPS fxra4 dmso


title: Mouse #577, sample A, naive

value: Uninfected


title: S-IECs of Nfat5fl/fl mouse_3

description: Gene expression data of small intestinal epithelial cells from Nfat5fl/fl mouse

source_name: S-IECs of Nfat5fl/fl mouse


title: Mouse #576, 2 dpi


title: 28 tpo AKPS fxra4 oca


title: S-IECs of Nfat5fl/fl mouse_2


title: L-IECs of Nfat5fl/fl mouse_1


title: Mouse #572, 2 dpi


title: Komagataella phaffii GS115, BMMY+1% Maltose medium, 48h, rep2

city: Xi’an

first: yin

middle: xing

last: wang

address: beilin

institute: northwest

description:
Different carbon source
M2_FPKM

data_processing:
The raw image data files from high-throughput sequencing are transformed into raw sequenced sequence data (RawData) by CASAVA/Basecall_T7_GPU_1.2.0.26_Centos Base Calling analysis.
Reads with adapters were removed, reads containing N (N means that the base information cannot be determined, remove more than 10 N in a read), low quality reads (reads with Qphred <= 30 with more than 50% of the entire read length), and short (read length less than 100 removals) reads were removed. GC content and Q30 calculations were also performed on the clean data.
Indexing of the reference genome was constructed using Hisat2 (2.2.1) and paired-end Clean Reads were sequenced against the reference genome using Hisat2.
Quantitative gene expression analysis was performed using StringTie software.
Assembly: ASM2700v1
Supplementary files format and content: FPKM.LIST

organism: Komagataella phaffii GS115

source_name: yeast cells

extract_protocol:
RNA was harvested using the Universal RNA Extraction Kit.
RNA libraries for RNA-seq are prepared according to Hieff NGS mRNA Isolation Master Kit.

value: yeast cells

value: BMMY+1% Maltose medium


title: Komagataella phaffii GS115, BMMY+1% Maltose medium, 48h, rep3

description:
Different carbon source
M3_FPKM


title: 24 tpo AKPS fxra4 dmso


title: Mouse #571, 12 dpi

value: Fetal lung xenograft

value: BLT-L


title: NC_2

value: fibroblast cells


title: 23 tpo AKPS fxra4 dmso

value: colon


title: Th17-Fsk

city: San Diego

first: Ezra

last: Wiater

state: CA

address: 10010 N Torrey Pines Rd

department: PBL

institute: Salk Institute For Biological Studies

data_processing:
MiSeq Generation of fastq files
tophat2 alignment
cuffdiff alignment
Genome_build: mm10
Supplementary_files_format_and_content: .diff file from cuffdiff comparing two samples

source_name: Primary mouse spleenic CD4+ T cells

growth_protocol: Mouse Diet

extract_protocol:
total RNA extracted with Qiagen Rneasy kit
polyA RNA isolated and library prepared with NEBnext Ultra kit

treatment_protocol: Tissue Extraction

value: wildtype

value: Th17-differentiated splenic CD4+T cells

value: 1  hour Forskolin treatment


title: NC_1

value: control sample transfected with negative control siRNA


title: S-IECs of Nfat5fl/fl mouse_1


title: 22 tpo AKPS fxra3 oca

value: oca


title: Mouse #570, 2 dpi

value: Infected, 2 dpi


title: Komagataella phaffii GS115, BMMY medium, 48h, rep3

description:
Different carbon source
C3_FPKM

value: WT

value: BMMY medium


title: 21 tpo AKPS fxra3 oca

value: TPO AKPS


title: 20 tpo AKPS fxra3 oca


title: multiplexed CSF cells8

city: Bethesda

first: Shinji

last: Ashdia

state: MD

address: 10 Center Drive

department: NIAID

institute: NIH

description: Library name: LIB_05923

data_processing:
In single cell RNA-seq data analysis, each raw data was counted, and QC was checked by Cellranger ver.7.0 (10X Genomics). Doublet cells were excluded by using DoubletFinder ver.2.0 and protein library from CITE-seq was denoised by using dsb package.
Assembly: human reference genome (hg38)
Supplementary files format and content: Tab-separated values (TSV) file, Indicate that the file contains processed data, such as gene expression matrices, cell metadata,generated by the 10x Cell Ranger pipeline.

molecule: cytoplasmic RNA

source_name: CSF cells

extract_protocol:
CSF was collected on ice and processed according to a written standard operating procedure by investigators blinded to diagnoses, clinical, and imaging outcomes. Aliquots were assigned alphanumeric identifiers and centrifuged for 10 minutes at 300g at 4°C within 30 minutes of collection.
The pelleted CSF cells were processed by flow cytometry or processed for single cell RNA sequencing. Fresh CSF cells were collected as described in sample processing. Cells were labelled with 79 Totalseq B antibodies (Biolegend, USA) and washed with PBS with 1% Bovine Serum Albumin (Thermo Fisher Scientific, USA). Labeled cells were fixed by using fixed RNA feature barcode kit (10x Genomics, USA) and stored at -80 degree.  Cellular indexing of transcriptomes and epitopes by sequencing (CITE-seq) method was used to analyze transcriptome and surface protein information based on  single-cell readout. After probe hybridization, gene expression library and surface protein library were constructed by using Chromium Next GEM Single cell 3` LT Reagent kits v3.1 (Dual index) (10X Genomics, USA) following the protocol (CG000400). Single-cell fixed RNA libraries and single-cell feature barcode libraries were sequenced  on a NextSeq 2000 P3 28 cycle + 90 cycle asymmetrical run.  Demultiplexing yielded over 27 million reads per sample when allowing for 1 mismatch per index adapter.

tag: sample id

value: CSF cells

value: Multiple sclerosis


title: Komagataella phaffii GS115, BMMY medium, 48h, rep2

description:
Different carbon source
C2_FPKM

value: yeast cells

tag: time


title: Komagataella phaffii GS115, BMMY medium, 48h, rep1

description:
Different carbon source
C1_FPKM


title: mixed sample (all 24 different samples)

city: Munich

first: Marion

last: Subklewe

address: Feodor-Lynen Straße 25

institute: LMU - Gene Center Munich

data_processing:
Demultiplexing: zUMIs (The demultiplexing is part of the zUMIs-pipeline and during the work-flow there is no generation of individual fastq-files for the different samples. This is why we did not upload individual fastq files for each sample.)
Filtering: fqfilter (zUMIs)
Mapping: STAR (zUMIs)
Counting: Rsubread (zUMIs)
Analysis: DESeq
Assembly: GRCh38
Supplementary files format and content: csv-file; barcodes for every sample
Supplementary files format and content: csv-file; readcount-matrix DEseq output

source_name: mixed sample (primary, HL60)

growth_protocol: Co-cultures of healthy donor T cells (n = 3) and HL-60 cells were set up using 1.5 × 105 T cells per condition and an E:T ratio of 1:10.

extract_protocol:
Cells were stained in PBS containing AquaLive/Dead (Invitrogen) and antibodies against CD2 and CD33. Both the effector cells (CD2+, CD33-) and target cell (CD33+, CD2-) populations were sorted by flow cytometry at the Flow Cytometry Facility (Gene Center, LMU) using a BD FACSAria Fusion cell sorter. Following sorting, 1000 cells per sample were directly lysed in RLT lysis buffer containing 0.04 M DTT and 1% Triton X-100 before storage at –80°C for at least 1 day. Samples were thawed and digested with 1 μL of 20 mg/mL proteinase K per 50μL of sample, then incubated for 10 minutes at 50°C followed by heat inactivation for 10minutes at 80°C. After digestion, RNA was extracted with SPRI beads (prepared from SpeedBeads and PEG 8000). Pooling beads were mixed at a 1:1 ratio, and a standard clean-up process was followed. Samples were eluted in 17 μL of H2O.
For low-input bulk sequencing of T cells, a Beckman Coulter RNAdvance Viral Reagent Kit (cat. C63510) was used according to the manufacturer's protocol. After cleanup, a DNAse I digest was performed. This was followed by the standard mcSCRB-seq v.3 protocol with the following modifications: the amount of water in RT master mix was reduced by 1 μL per sample to facilitate the higher template volume; no molecular crowding agent was used; barcoded oligo(dT) primers were added together with RT master mix; the number of pre-amplification cycles was reduced to 18. Library preparation was finalized using the Nextera XT DNA Library Preparation Kit according to the manufacturer’s instructions. Then, samples were sequenced at the NGS Core Facility (MPI of Biochemistry, Martinsried, Germany) using a NextSeq 1000 system (Illumina). FASTQC3 was used for initial quality control. FASTQ demultiplexing, QC, mapping, and gene counting were performed with zUMIs4 and human genome GRCh38 5 was used as the reference.
low-input bulk RNAseq (adapted from a scRNAseq protocol)

treatment_protocol: Cells were treated with 5 ng/ml AMG330 or c-BiTE in the absence or presence of cGAMP (40 µg/ml) for 8 hours at 37°C and 5% CO2.

tag: individual

value: mixed sample (Do1, Do2, Do3)

value: mixed sample (primary, HL60)

value: mixed sample (T cells, HL60)

value: mixed sample (Bite, Bite+cGAMP, c-Bite, c-Bite+cGAMP)


title: Mouse #569, 12 dpi

value: Fetal lung xenograft

value: BLT-L

value: Infected, 12 dpi


title: cytotoxic Macrophage_3

city: SHENZHEN

first: Yixun

last: Su

state: GUANGDONG

address: 628 Zhenyuan Road

institute: The Seventh Affiliated Hospital, Sun Yat-sen University

data_processing:
Raw reads were passed through adapter filtration and process for potential rRNA contaminants clearance
The clean data were then aligned to GRCm38 for genome reference
Normalization of gene expression was performed by transferring the read counts to FPKM values, and both the read counts and FPKM values were used in visualization
Assembly: GRCm38
Supplementary files format and content: csv file includes baseMean, log2Foldchange, lfcSE, p-value, and adjusted p-value as WT vs. APC KO for OPC samples
Supplementary files format and content: excel files includes TPM, FPKM, Read Count and Normalized Read Count for each sample

source_name: Spinal cord

extract_protocol:
RNA was extracted from the isolated cells by Trizol (Thermo, Cat No. 15596026) according to the manufacturer’s protocol
All EASY-RNAseq libraries were sequenced through the Illumina HiSeq platform with a 150-bp pair-end model.

value: Spinal cord

tag: cell type

value: FACS-isolated cytotoxic macrogphage

value: EAE model


title: 18 tpo AKPS fxra3 dmso

value: colon

value: dmso


title: 19 tpo AKPS fxra3 dmso


title: cytotoxic Macrophage_2

tag: genotype


title: sorted bacteria, 16S-high, rep3

city: Rehovot

first: Roi

last: Avraham

address: Herzl St 234

country: Israel

institute: Weizmann Institute of Science

description:
sorted_positive_biol_rep3
UMI_counts.csv
DEseq2_analysis.csv

data_processing:
*library strategy: Tn-seq
R1 was used to extract reads mapping to the transposon region by searching for the sequence "AGATGTGTATAAGAGACAG"
Filtered reads were trimmed of the transposon region, and mapped by STAR.
Multimappers were excluded.
R2, containing a random sonication point, was used as UMI to collapse PCR duplicates. R1 was used to identify the disrupted gene.
The so-obtained counts were used as input for DESeq2 enrichment analysis.
Assembly: ASM2216v1
Supplementary files format and content: comma-separated file including UMI counts per gene
Supplementary files format and content: comma-separated file including DESeq2 enrichment analysis, where log2FC indicates the enrichment of the 16S-high subpopulation versus the 16S-low

organism: Salmonella enterica subsp. enterica serovar Typhimurium str. 14028S

growth_protocol: Bacteria were grown in LB to the transition phase (OD~1.5-2).

extract_protocol:
Genomic DNA was extracted with DNeasy Blood & Tissue, following the instructions for gram-negative bacteria.
DNA was extracted from 5 million sorted bacteria using DNeasy Blood & Tissue (Qiagen, 69504) following manufacturer’s instructions, with an overnight proteinase K digestion step (which also serves as PFA de-crosslinker), and resuspension in 200 µl of resuspension buffer. DNA (∼ 20 ng per sample) was processed as previously described (Schwartzman et al., Nature Methods 2016), with few modifications. Briefly, DNA was sonicated at 4◦C (program: 6 cycles of 30 s on, 60 s off) on a Bioruptor Plus (Diagenode), achieving a size distribution between 200-1000 nucleotides (nt), with 450 nt average size. The sonicated DNA was end-repaired for 30 minutes at 20◦C in 200 µl final volume containing 1x end-repair buffer and 10 µl of end-repair mix (NEB, E6050L). The reaction was cleaned in 2x Ampure XP Beads (Beckman Coulter, A63881) and eluted in 37.5 µl. A-tailing was performed 20 min at 37◦C in 50 µl final volume, containing 1x NEBuffer 2 (NEB, B7002S), 1 mM ATP, and 125U of Klenow fragment (NEB, M0212M). The reaction was cleaned in 2x Ampure XP Beads (Beckman Coulter, A63881) and eluted in 44 µl. DNA was then dephosphorylated overnight at 37◦C in 50 µl final volume, containing 1x rCutSmart buffer (NEB, B6004S), and 5U of quick CIP (NEB, M0525L). The day after, the reaction was heat-inactivated for 2 minutes at 80◦C, cleaned in 2x Ampure XP Beads (Beckman Coulter, A63881), and eluted in 18 µl. The DNA template was ligated for 20 min at 25C in 50 µl final volume, containing 0.22 µM Illumina-compatible forked indexed adapters, 1x buffer, and 5 µl of quick ligase (NEB M2200L). To release the non-ligated strand of the adaptor, DNA was denatured at 96◦C for 5 min, cleaned with 0.8x Ampure XP beads (Beckman Coulter, A63881), and eluted in 30 µl. Two PCR reactions were used for TIS library construction. The first PCR reaction was performed in triplicate in 25 µl final volume containing 0.5 µM TN bait primer 1, 0.5 µM Illumina enrichment primer, 1x KAPA HiFi HotStart ReadyMix (Roche, KK2601) and 10 µl DNA template. PCR program: 60s 98◦C, 15 cycles of 15s 98◦C, 20s 68◦C, 60s 72◦C, and final extension of 60s 72◦C. Following the first PCR reaction, the amplified DNA from the three reactions was pooled and cleaned with 1x Ampure XP beads (Beckman Coulter, A63881), and the eluate was used as a template in the second PCR reaction. Conditions for the second PCR reaction were identical to the first, with the following differences: reaction was performed in a single 50 µl reaction and TN bait primer mix 2 consisted in a mix of staggered nested primers. Libraries were quantified with NEBNext Library Quant Kit for Illumina (NEB, E7630L) and sequenced on a Novaseq machine with the following settings: R1=85, I1=8, and R2=37.

treatment_protocol: Bacteria were fixed in 3.7% PFA, permeabilized in 70% ethanol, and stained with a probe against 16S rRNA.

value: Bacteria were fixed, stained for 16S rRNA, and sorted by FACS according to their 16S levels


title: sorted bacteria, 16S-high, rep2

description:
sorted_positive_biol_rep2
UMI_counts.csv
DEseq2_analysis.csv


title: sorted bacteria, 16S-high, rep1

description:
sorted_positive_biol_rep1
UMI_counts.csv
DEseq2_analysis.csv


title: multiplexed CSF cells6

description: Library name: LIB_05921


title: cytotoxic Macrophage_1


title: multiplexed CSF cells5

description: Library name: LIB_05920


title: Komagataella phaffii GS115, BMMY+1% Maltose medium, 48h, rep1

description:
Different carbon source
M1_FPKM

value: WT

value: BMMY+1% Maltose medium


title: sorted bacteria, 16S-low, rep3

description:
sorted_negative_biol_rep3
UMI_counts.csv
DEseq2_analysis.csv


title: multiplexed CSF cells4

description: Library name: LIB_05919

value: CSF cells

value: Multiple sclerosis


title: Th1

value: FACS-isolated Th1 cell


title: A3_Donor07_Neut

city: Atlanta

first: Rafick-Pierre

last: Sekaly

state: GA

address: 1750 Haygood Drive

department: Pathology

institute: Emory University

description:
Library name: D7
Neut

data_processing:
FASTQ files were uploaded, processed and aggregated using the CellRanger v6.0.1 on the 10X Genomics Cloud
The Seurat v4 package in R was used to clean the data and filter the count matrix.
Doublet cells were removed using the DoubletFinder package in R
Cell annotation was performed with SingleR, using the MonacoImmuneData reference atlas from the celldex package
The Seurat v4 package was also used for dimensional reduction, unbiased clustering and differential gene expresission (using the MAST function) analyses.
Assembly: GRCh38/hg38
Supplementary files format and content: 10x Genomics Cell Ranger Output: features.tsv.gz, matrix.mtx.gz, barcodes.tsv.gz

molecule: nuclear RNA

source_name: Lymph nodes

extract_protocol:
To prepare lymph node mononuclear cells (LNMCs) for 10x single-cell RNA sequencing, lymph node tissue was mechanically and enzymatically dissociating to obtain a single-cell suspension. Next, mononuclear cells were isolated using density gradient centrifugation, the cells were filtered using 10x's protocol and highly viable cells were used for single-cell RNA-sequencing.
Library preparation was performed following the manufacturer’s instructions (10x Genomics, Single Cell 3’ v3 protocol). Briefly, cells were resuspended in the master mix and loaded with partitioning oil and gel beads into the microfluidic chip to form gel bead-in-emulsion (GEM) droplets. Poly-A RNA from cell lysates within each GEM was reverse transcribed into cDNA. Illumina's paired-end  library constructs containing P5 and P7 sequences, along with a sample index, were generated and sequenced on BGISEQ 500.

value: Lymph nodes

value: Lymph node cells


title: 16 tpo AKPS gfp oca

value: TPO AKPS

value: oca


title: Th17-con

value: wildtype

value: Th17-differentiated splenic CD4+T cells

value: untreated


title: A10_Donor09_NonNeut

description:
Library name: D9
NonNeut


title: 15 tpo AKPS gfp oca


title: sorted bacteria, 16S-low, rep2

description:
sorted_negative_biol_rep2
UMI_counts.csv
DEseq2_analysis.csv


title: multiplexed CSF cells2

description: Library name: LIB_05917


title: 13 tpo AKPS gfp dmso


title: multiplexed CSF cells3

description: Library name: LIB_05918


title: sorted bacteria, 16S-low, rep1

description:
sorted_negative_biol_rep1
UMI_counts.csv
DEseq2_analysis.csv


title: multiplexed CSF cells7

description: Library name: LIB_05922


title: Human MN shTDP43 Soma Rep3

city: Aurora

last: Taliaferro

state: CO

department: Biochemistry and Molecular Genetics

institute: University of Colorado Anschutz Medical Campus

description: Library name: HumanMN_ShTDP43soma6

data_processing:
Adapters were trimmed using Cutadapt
Transcript abundances were calculated using salmon
Gene-level abundances were calculated using tximport
Assembly: mm10, hg38
Supplementary files format and content: Salmon-calculated transcript abundances

source_name: Human iPS motor neuron

growth_protocol: CAD cells were grown in DMEM/F12. N2A cells were grown in DMEM. Both were supplemented with 10% FBS. To differentiate cells, FBS was removed.

extract_protocol:
RNA was extracted with Zymo Quick RNA microprep kits
Libraries were constructed using Kapa RNA Hyperprep kits

treatment_protocol: To induce TDP-43 loss, 2 ug / mL doxycycline was added for 48 hrs

value: Human iPS motor neuron

value: TDP-43 shRNA

tag: compartment

value: soma


title: 14 tpo AKPS gfp oca

value: colon


title: 12 tpo AKPS gfp dmso

value: dmso


title: A6_Donor04_NonNeut

description:
Library name: D4
NonNeut


title: A5_Donor05_Neut

description:
Library name: D5
Neut


title: A2_Donor03_Neut

description:
Library name: D3
Neut


title: Human MN shTDP43 Soma Rep2

description: Library name: HumanMN_ShTDP43soma5


title: CSF cells, RR-MS4

description: Library name: LIB_03636


title: 10 tpo AKPS oca


title: Human MN shTDP43 Soma Rep1

description: Library name: HumanMN_ShTDP43soma4


title: A8_Donor02_NonNeut

description:
Library name: D2
NonNeut


title: Human MN shTDP43 Neurite Rep3

description: Library name: HumanMN_ShTDP43neurite6

value: neurite


title: 17 tpo AKPS fxra3 dmso


title: A4_Donor06_Neut

description:
Library name: D6
Neut


title: 9 tpo AKPS oca


title: CSF cells, PP-MS4

description: Library name: LIB_03404


title: multiplexed CSF cells1

description: Library name: LIB_05916


title: 8 tpo AKPS oca


title: Human MN shTDP43 Neurite Rep2

description: Library name: HumanMN_ShTDP43neurite5


title: CSF cells, PP-MS3

description: Library name: LIB_02385


title: 17-AAG/SPDL1-sgRNA2 #4

city: London

first: Chi

last: Zhang

address: 15 Cotswold Road

department: Division of Cancer Therapeutics

institute: The Institute of Cancer Research

description: 17-AAG/SPDL1-sgRNA2-treated replicate#4

data_processing:
Raw reads were aligned to GRCh38 genome assembly and GENCODE GRCh38.p13 annotation using STAR programme, followed by processing of the resultant file using SAMtools.
Read counting on genomic features was carried out using Rsubread, and the R package DESeq2 was used to perform statistic-based quantifications.
Genome_build: GRCh38
Supplementary_files_format_and_content: Excel table with quantification results, generated by DESeq2

source_name: H2228 Cell line

growth_protocol: NCI-H2228 [H2228] (ATCC, CRL-5935) cells were cultured in RPMI medium (Sigma-Aldrich) supplemented with 10% FBS (PAN Biotech).

extract_protocol:
Total RNA from T-47D cells were extracted using MagNA pure 96 instrument (Roche), and RNA integrity number was measured by BioAnalyzer 2100 (Agilent).
RNA libraries were constructed and sequenced by BGI using poly-dT enrichment in conjunction with DNB technology on BGISEQ-500 instrument.
RNA-seq, non-strand-specific and pair-ended.

treatment_protocol: Cas9-expressing H2228 cells were constructed with pLEX_311-Cas9v2 vector and lentiviral helper plasmids and selected using puromycin. Non-targeting and SPDL1-targeting sgRNA  were purchased with Sigma Aldrich (TRCN0000135058, TRCN0000135059, TRCN0000160944, TRCN0000164576). CRISPR KO cells were treated with DMSO or 6 nM tanespimycin (Selleckchem) for 10 d prior to mRNA extractions.

tag: crispr sgrna

value: SPDL1-targeting, sgRNA2

tag: drug treatments

value: tanespimycin


title: Human MN shTDP43 Neurite Rep1

description: Library name: HumanMN_ShTDP43neurite4


title: Human MN shCtrl Soma Rep3

description: Library name: HumanMN_ShSCRsoma6

value: scramble shRNA


title: A9_Donor01_NonNeut

description:
Library name: D1
NonNeut


title: 17-AAG/SPDL1-sgRNA2 #3

description: 17-AAG/SPDL1-sgRNA2-treated replicate#3


title: CSF cells, HD3

description: Library name: LIB_02384

value: CSF cells

value: Multiple sclerosis