title: Matrigel 3D cultured rLPCs for 14 d (rerepr_6)

city: BOSTON

first: CHANGHEE

last: LEE

state: MA

address: 77 AVENUE LOUIS PASTEUR

department: Genetics

institute: Harvard Medical School

description:
mouse.rds
combined.rds
Matrigel 3D cultured rLPCs for 14 days

data_processing:
All four human samples were multiplexed with mouse and chick samples. The chick data was not presented in this manuscript. Thus, for species demultiplexing, Ensembl release 99 hg38 transcriptome, Ensembl release 98 Gallus gallus-6.0 transcriptome and the filtered Ensembl release 98 mm10 transcriptome was merged using the cellranger mkgtf command to generate human-mouse-chick transcriptome for initial mapping for demultiplexing.
For InDrop preprocessing, sequencing results were demultiplexed by dropTag from dropEst package (Petukhov et al. 2018) and demultiplexed reads were aligned with STAR aligner (Dobin et al. 2013). The aligned reads were split into forward and reverse alignment, since InDrop is directional. The resulting forward and reverse alignment files were quantified using dropEst package including directional UMI correction option (Petukhov et al. 2018) with transcriptome annotation split into forward and reverse direction to avoid mapping of antisense reads.
Sequencing results were demultiplexed by cellranger and aligned using cellranger count (internally by STAR aligner (Dobin et al. 2013)). For the four libraries that needed species demultiplexing, cellular barcodes that had less than 5% of UMI counts from other species were selected for subsequent mapping with the corresponding species transcriptome.
Cellular barcodes with high mitochondrial content (>15%), high hemoglobin gene count (>10%) and low gene counts (<1,200) were filered out. All libraries were subject to doublet detection via Scrublet (Wolock et al. 2019). Batch effect was assessed by simply merging the individual UMI count matrices for clustering and Seurat v3 integration procedure was applied (Stuart, Butler et al. 2019) with 30 dimensions for the individual batches. Further, cell cycle effect, fraction of mitochondrial genes were regressed out. Principal component analysis (PCA) was performed on the integrated, scaled features for dimensional reduction and Uniform Manifold Appxoimation and Projection (UMAP) (McInnes et al. 2018) was used primarily for the cellular embedding coordinates. Leiden algorithm was applied on the shared neighborhood graph with 10 iterations (Seurat default) to derive cluster boundaries (Traag et al. 2019).
Genome_build: For all mouse samples, Ensembl release 98 mm10 transcriptome was used as base transcriptome annotation, with pseudogenes filtered from the GTF file using cellranger mkgtf command . For retroviral infected hyaluronan samples, transgenes for human Lin28a, EGFP (for Prx1GFP transgene) was added to generate custom transcriptome annotation for quantification for reprogrammed cells (mm10.98.hlin28a.gtf.gz). For lentiviral infected Matrigel samples, transgenes for EGFP (for Prx1GFP transgene), rtTA, and human Lin41 as well as PLZF, and 3’UTR sequences of WPRE were added to generate custom transcriptome annotation for quantification for reprogrammed cells (mm10.98.4factor.tdtomato.gtf.gz). The limb progenitor cells were subject to the same transcriptome annotation (yielding zero counts for the transgenes). For human-specific mapping, the filtered hg38 transcriptome with transgenes for EGFP, rtTA, and mouse Prdm16 and mouse Lin28a were added (hg38.4factor.gtf.gz).
Supplementary_files_format_and_content: Seurat (v3.1.5) object with meta information; equivalent text file in market matrix format (MTX) with rownames (features) and colnames (barcodes) as well as meta information in tab-delimited format are included. The whole data is split into mouse-only data (prefix mouse.), human-only data (prefix human.), and for convenience, combined data (prefix combined.) which only contains the matching features and MNN coordinates are provided.

source_name: Non limb fibroblasts cultured in matrigel 3D culture for 14 days with 4-factors

growth_protocol: Non-limb fibroblasts cultured in 2D, Lentivirally-expressed non-limb fibroblasts (reprogrammed cells) in 3D hyaluronan or matrigel growth culture condition, directly harvested embryonic primary mesenchyme

extract_protocol:
For sorting reprogrammed Prx1-GFP or Prx1-tdTomato cells from embryos, a FACS sorter Astrios (Beckman Coulter) or On-chip Sort HSG (On-chip Biotechnologies) was used. After washing with PBS, the cells cultured in the HA-gels or on Matrigel were incubated in TryPLE Express (gibco) for 30 min at 37℃. The cell suspension was pipetted with cut P1000 pipette tips every 10 min, to completely dissociate the cell clusters. The suspension was filtrated by 100 μm Cell strainers (Falcon) and 40 μm Cell strainers (VWR), and cells were pelleted by centrifugation (400 x g for 5 min). The pellets were dissociated by DRAQ5/DAPI in 0.1% BSA/PBS and incubated for 5 min before the sorting. DRAQ5-positive, DAPI-negative cells were sorted for cells on reprogramming at day 2, 4, 8. For HA-gel reprogrammed cells at day 14, additional gating on GFP channel derived GFP-positive and GFP-negative samples. For Matrigel-derived day 14 reprogrammed cells for PZL- as well as PZLL- factors, only GFP-positive cells were collected. DRAQ5-positive, DAPI-negative, Matrigel-derived day 8 cultured E9.5 and E10.5 limb progenitors were collected. The E9.5 cultured limb progenitors were subject to 4-OHT, such that large fraction were tdtomato-positive, but the cells were collected regardless of tdTomato-positivity. DRAQ5-positive, DAPI-negative, tdTomato-positive cells were sorted for the limb mesenchyme cells for E10.5, E11.5 as well as E12.5 cells. For E9.5 limb progenitors, samples were collected without tdTomato gating to maximize yield. InDrop cell capture was processed in Harvard Medical School Single Cell Core. All libraries included about 10-15% of Non-limb fibroblasts to mitigate batch effect. Cells were captured by the Chromium Controller (10X genomics, Biopolymer facility at Harvard Medical School).
single cell RNA libraries were prepared for sequencing using 10X Genomics Chromium V3 protocols and inDrops libraries were prepared by the Harvard Single Cell Core according to the published protocol
scRNA-seq

value: mesenchymal cells

tag: treatment/condition

value: Matrigel 3D culture, DMEM 10% FBS, Chir99021 (3uM), Fgf8 (150ng/ml), Retinoic acid (25nM), SB431542 (5uM), Y-27632 (10uM)

value: 10X v3 scRNA-seq


title: EndoC-bH3_siPDIA6#1_7_batch2

status: Public on Nov 15 2023

type: SRA

city: Cleveland

first: Sisi

last: Lai

state: Ohio

address: 10900 Euclid Avenue, BRB 609A

department: Genetics and Genome Sciences

country: USA

institute: Case Western Reserve University

library_source: transcriptomic

data_processing:
RNA-seq reads were filtered for quality and trimmed for adaptor sequences.
Reads were alighed to reference genome assembly for mouse (mm10) and human (hg19) using HISAT2 with default parameters.
Read count tables were generated with FeatureCounts.
Normalized and differential expression analysis was performed with DESeq2.
Assembly: mm10 and hg19
Supplementary files format and content: Tab-delimited text file with normalized read couns over all genes.

molecule: polyA RNA

organism: Homo sapiens

growth_protocol: MIN6 cells were cultured in high glucose DMEM with 10% heat-inactivated Fetal Bovine Serum (Gibco), 2 mM GlutMAX (Gibco), 1 mM sodium pyruvate, 50 μM β-mercaptoethanol. EndoC-βH3 were cultured in DMEM containing 5.6 mM glucose, 2% fatty acid free BSA fraction V, 10 mM nicotinamide, 5.5 mg/ml transferrin, 6.7 ng/ml sodium selenite, Penicillin (100 units/ml)/ Streptomycin (100 mg/ml). Cells were passaged and seeded onto matrigel- and fibronectin- coated cell culture dishes.

extract_protocol:
Trizol used to extract RNA from MIN6 cells. Quick-RNA™ Microprep Kit used for EndoC-bH3 RNA extraction.
Illumina TruSeq stranded mRNA kit for MIN6. mRNA-seq Lib Prep Kit (ABclonal) used for EndoC-bH3 cells.

tag: cell line

tag: genotype


title: E9.5 limb mesenchymal cells, Matrigel 3D cultured non limb fibroblasts with control infection for 4 d (rererepr_3)

description:
mouse.rds
combined.rds
E9.5 limb mesenchymal cells, Matrigel 3D cultured non limb fibroblasts with control infection for 4 days

molecule: total RNA

organism: Mus musculus

source_name: E9.5 embryonic limb, Matrigel 3D cultured non limb fibroblasts with control infection for 4 days

tag: cell type

value: Directly from embryo, Matrigel 3D culture, DMEM 10% FBS, Chir99021 (3uM), Fgf8 (150ng/ml), Retinoic acid (25nM), SB431542 (5uM), Y-27632 (10uM)


title: sgEts1_1_day 7 1

city: Memphis

first: Hongbo

last: Chi

state: TN

address: 262 Danny Thomas Place

department: Immunology

institute: St Jude Children's Research Hospital

library_source: transcriptomic single cell

data_processing:
The Cell Ranger 6.0 Single-Cell Software Suite (10x Genomics) was implemented to process the  raw sequencing data from the Illumina HiSeq run.
This pipeline performed de-multiplexing,  alignment (mm10), and barcode processing to generate gene-cell matrices used for downstream  analysis.
Assembly: mm10
Supplementary files format and content: cell ranger count matrix for single cells in each sample

source_name: sgRNA transduced OT-I cells

growth_protocol: OT-I cells transduced with indicatd sgRNAs were sorted from B16-OVA tumor after adoptive transfer

extract_protocol:
CD8+ OT-I T cells were sorted from the dual-color transfer system at day 7 post adoptive transfer from B16-OVA tumor and loaded onto  the Chromium Controller according to their respective cell counts to target 9000 single cell GEMs (gel beads in emulsion) per sample.
Libraries were prepared using the Chromium Single Cell 3’ v3 Library and Gel Bead Kit (10x Genomics)

value: sgRNA transduced OT-I cells

tag: transduced

tag: strain


title: Matrigel 3D cultured rLPCs for 14 d (rerepr_5)

source_name: Non limb fibroblasts cultured in matrigel 3D culture for 14 days with 3-factors


title: EndoC-bH3_siPDIA6#2_5_batch1


title: Matrigel 3D cultured non limb fibroblasts with control infection for 14 d (rerepr_2)

description:
mouse.rds
combined.rds
Matrigel 3D cultured non limb fibroblasts with control infection for 14 days

source_name: Non limb fibroblasts cultured in matrigel 3D culture for 14 days


title: "spike for sgEts1_1"_ day 7 2

value: sgNTC (‘spike for sgEts1’)


title: "spike for sgEts1_1"_ day 7 1


title: IM24h_RiboTag IP_4

city: Bonn

first: Reiner

last: Schneider

address: Venusberg-Campus 1

department: Surgery Department

country: Germany

institute: University Clinics Bonn

data_processing:
Library strategy: Ribo-seq
Pipeline: Data was analyzed with Partek Flow software and the publicly available Lexogen pipeline (Lexogen12112017)
Partek Flow Software - Trim adapters - CUTADAPT_1_12 - Version 10.0.21.1116 - Both ends trimmed -Adapter sequences:  AAAAAAAAAAAA,TTTTTTTTTTTT
Partek Flow Software - Pre-alignment QA/QC - Version 10.0.21.1116 - K-mer length 10
Partek Flow Software - Trim adapters - CUTADAPT_1_12 - Version 10.0.21.1116 - 3'-end trimmed -Min overlap length 5 - Min read length 25
Partek Flow Software - Pre-alignment QA/QC - Version 10.0.21.1116 - K-mer length 10
Partek Flow Software - Trim bases - Version 10.0.21.1116 - Trim on quality score Phred 10 - 3'-end timmed - Min read length 20
Partek Flow Software - Pre-alignment QA/QC - Version 10.0.21.1116
Partek Flow Software - Alignment STAR - 2.5.3a - Version 10.0.21.1116
Partek Flow Software - Post-alignment QA/QC - Version 10.0.21.1116
Partek Flow Software - Quantify to annotation model (Partek E/M) - Version 10.0.21.1116
Assembly: mm10 Ensembl Transcripts release 99
Supplementary files format and content: IM3h_RiboTag_Transcript_counts: raw transcript counts RiboTag Naive vs IM3h samples
IM3h_RiboTag_POI_Normalized GSA to Naive: normalized GSA of transcript counts RiboTag IM3h to naive controls
IM24h_RiboTag_Transcript_counts: raw transcript counts RiboTag Naive vs IM24h samples
IM24h_RiboTag_POI_Normalized GSA to Naive: normalized GSA of transcript counts RiboTag IM24h to naive controls
IM72h_RiboTag_Transcript_counts: raw transcript counts RiboTag Naive vs IM72h samples
IM72h_RiboTag_POI_Normalized GSA to Naive: normalized GSA of transcript counts RiboTag IM72h to naive controls
Total RNA_POI_Gene_counts: raw gene counts Total RNA input samples
Total RNA_POI_Transcript_counts: raw transcript counts Total RNA input samples
Total RNA_POI_Normalized GSA to Naive: normalized GSA of transcript counts Total RNA to naive controls

source_name: Small bowel muscularis externa

extract_protocol:
Muscularis externa was prepared from small bowel and subjected to an immunoprecipitation protocol for RiboTag (Leven et al 2021, Application of a RiboTag-based approach to generate and analyze mRNA from enteric neural cells,  https://doi.org/10.1111/nmo.14309). Input samples were generated from total lysate while IP samples underwent the entire precipitation process and were purified afterwards.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Animals underwent abdominal surgery (postoperative ileus model) and were sacrificed after indicated time points

tag: tissue

value: Small bowel muscularis externa

tag: treatment

value: B6 Tg(Sox10-icre/ERT2)388Wdr/J x B6N.129 Rpl22tm1.1Psam/J

tag: fraction

value: RiboTag Pulldown mRNA (IP)


title: Matrigel 3D cultured rLPCs for 4 d (rerepr_1)

description:
mouse.rds
combined.rds
Matrigel 3D cultured rLPCs for 4 days

source_name: Non limb fibroblasts cultured in matrigel 3D culture for 4 days with 3-factors and 4-factors (cultured separately, multiplexed during capture)


title: IM24h_RiboTag IP_3


title: sgRNA Library-transduced OT-I cells  B2S11

description: sgRNA Library-transduced OT-I cells

data_processing:
The Cell Ranger 6.0 Single-Cell Software Suite (10x Genomics) was implemented to process the  raw sequencing data from the Illumina HiSeq run.
This pipeline performed de-multiplexing,  alignment (mm10 and CRISPR library), and barcode processing to generate gene-cell and sgRNA-cell matrices used for downstream  analysis.
Assembly: mm10
Supplementary files format and content: cell ranger gene expression and sgRNA count matrix for single cells in each sample

source_name: sgRNA Library-transduced OT-I cells at day 7 post adoptive transfer from B16-OVA tumor

growth_protocol: OT-I cells transduced with indicatd sgRNA Library were sorted from B16-OVA tumor after adoptive transfer

extract_protocol:
CD8+ OT-I T cells were sorted at day 7 post adoptive transfer from B16-OVA tumor and loaded onto  the Chromium Controller according to their respective cell counts to target 9000 single cell GEMs (gel beads in emulsion) per sample.
Libraries were prepared using the Chromium Single Cell 3’ v3 Library, CRISPR screening library and Gel Bead Kit (10x Genomics)
scRNA-seq and direct capture CRISPR

value: sgRNA Library transduced OT-I cells


title: E10.5 limb mesenchymal cells (mm10_tdtomato_hrepr_1)

description:
mouse.rds
combined.rds
E10.5 limb mesenchymal cells

source_name: E10.5 embryonic limb

value: Directly from embryo


title: sgRNA Library-transduced OT-I cells  B2S12

description: sgRNA Library-transduced OT-I cells


title: EndoC-bH3_siPDIA6#1_4_batch1


title: EndoC-bH3_siPDIA6#2_8_batch2


title: Matrigel 3D cultured rLPCs for 8 d (repr_4)

description:
mouse.rds
combined.rds
Matrigel 3D cultured rLPCs for 8 days

source_name: Non limb fibroblasts cultured in matrigel 3D culture for 8 days with 4-factor expression


title: sgRNA Library-transduced OT-I cells  B2S10

description: sgRNA Library-transduced OT-I cells


title: Matrigel 3D cultured non-limb fibroblast control for 4 d (mm10_hrepr_3)

description:
mouse.rds
combined.rds
Matrigel 3D cultured non-limb fibroblast control for 4 days

source_name: Non limb fibroblasts cultured in matrigel 3D culture for 4 days


title: sgRNA Library-transduced OT-I cells  B2S9

description: sgRNA Library-transduced OT-I cells


title: IM3h_RiboTag IP_3


title: IM24h_RiboTag IP_2


title: IM24h_RiboTag IP_1


title: C_DAA003_7

city: Aurora

first: Neelanjan

last: Mukherjee

state: Colorado

address: 12800 E 19th Ave, RC1-South

department: Biochemistry and Molecular Genetics

institute: CU Anschutz

data_processing:
Raw sequencing FASTQs were processed using the 10X Genomics Space Ranger v1.2.1 pipeline.
Sequences were aligned to the refdata-gex-GRCh38-2020-A transcriptome.
Gene expression counts were quantified using Space Ranger to generate count matrix and Loupe Brower files.
Assembly: hg38
Supplementary files format and content: barcodes.tsv.gz - spatial barcodes
Supplementary files format and content: features.tsv.gz - gene IDs
Supplementary files format and content: matrix.mtx.gz - gene expression count data
Supplementary files format and content: filtered_feature_bc_matrix.h5
Supplementary files format and content: aggr_all.cloupe - loupe exploratory browser file
Supplementary files format and content: summary.json - processsing summary
Supplementary files format and content: tissue_images.tar.gz
Supplementary files format and content: spatial_*.tar.gz - per slice spatial coords and images
Library strategy: Spatial Transcriptomics

source_name: Adrenal Gland

extract_protocol:
Normal adrenal glands were dissected and placed into histidine tryptophan ketoglutarate (HTK) solution. Within 2 hours of receiving the tissue, the gland was cut into sections for fresh frozen tissue and to create OCT blocks for storage. 10-micron sections of OCT blocks were cut and used for H&E to ensure a well-preserved tissue to use in further experiments. Adjacent sections were cut and used for spatial transcriptomics and immunohistochemical analysis. Frozen samples were OCT embedded and sectioned at 10μm on a Cryostar NX70 cryostat (Thermo Fisher Scientific). Capture sections were fixed with methanol, stained with H&E, and imaged on an Evos M7000 (ThermoFisher) with brightfield settings.
Capture sections were permeabilized and processed to generate RNA libraries following the 10x Visium protocol. Libraries were sequenced to a depth of 60,000 read pairs per spot calculated from the image, on a Novaseq6000 (Illumina) sequencer with 151x151 bp runs.

value: Adrenal Gland

tag: Sex

value: Female

tag: age

value: 31 years


title: IM3h_RiboTag IP_4


title: IM3h_RiboTag IP_2


title: sgRNA Library-transduced OT-I cells  B2S8

description: sgRNA Library-transduced OT-I cells


title: B_DAA003_6


title: A_DAA003_4


title: sgRNA Library-transduced OT-I cells  B2S7

description: sgRNA Library-transduced OT-I cells


title: Matrigel 3D cultured E10.5 mouse embryonic limb progenitors for 8 d, Matrigel 3D cultured rLPCs for 8 d (matrigel2)

description:
mouse.rds
combined.rds
Matrigel 3D cultured E10.5 mouse embryonic limb progenitors for 8 days, Matrigel 3D cultured rLPCs for 8 days

source_name: E10.5 mouse embryonic limb progenitors cultured in matrigel 3D culture for 8 days, Non limb fibroblasts cultured in matrigel 3D culture for 8 days with 3-factor expression (cultured separately, two multiplexed)


title: IM3h_RiboTag IP_1


title: Resistant2

city: Hefei

first: Hanyuan

last: Liu

address: Huangshan Road

country: China

institute: University of Science and Technology of China

data_processing:
RNA-seq was performed on the Illumina platform using 150-bp paired-end reads. The reads were mapped to GRCh38 using hisat2 (v2.2.1) and converted the ENSG ID to Gene symbols.
Gene expression was analyzed, and p value < 0.05 in addition with absolute log2FC ≥1 was set as significant.
Assembly: hg38
Supplementary files format and content: tab-delimited text files include reads for each RNA-seq Sample

source_name: Ovarian Cancer

extract_protocol:
Total RNA was extracted by TRIzol reagent (Invitrogen, 15596026) according to the manufacturer’s instructions.
Libraries were constructed by the TruSeq Ribo Profile Library Prep Kit (Illumina, RPHMR12126) according to the manufacturer’s instructions.

value: Ovarian Cancer


title: EndoC-bH3_siNT_3_batch1

value: siNT


title: Naive_RiboTag IP_4

value: Naive


title: Matrigel 3D cultured E9.5 mouse embryonic limb progenitors, 8 d (matrigel1)

description:
mouse.rds
combined.rds
Matrigel 3D cultured E9.5 mouse embryonic limb progenitors, 8 days

source_name: E9.5 mouse embryonic limb progenitors cultured in matrigel 3D culture for 8 days

value: mesenchymal cells


title: D_DAA004_3

value: 71 years


title: Matrigel 3D cultured non-limb fibroblast control for 8 d (mm10_hrepr_4)

description:
mouse.rds
combined.rds
Matrigel 3D cultured non-limb fibroblast control for 8 days

value: Matrigel 3D culture, DMEM 10% FBS, Chir99021 (3uM), Fgf8 (150ng/ml), Retinoic acid (25nM), SB431542 (5uM), Y-27632 (10uM)

value: 10X v3 scRNA-seq


title: MGC803_siCXCR7_3

city: Xinxiang

first: Zhongbo

last: li

state: Henan

institute: Xinxiang medical university

data_processing:
Using BGISEQ-500 sequencing platform
The sequencing data was filtered with SOAPnuke (v1.5.2) by (1) Removing reads containing sequencing adapter; (2) Removing reads whose low-quality base ratio (base quality less than or equal to 5) is more than 20%; (3) Removing reads whose unknown base ('N' base) ratio is more than 5%, afterwards clean reads were obtained and stored in FASTQ format.
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Assembly: GRCh38
Supplementary files format and content: xlsx files include FPKM values for each Sample

source_name: human gastric cancer cell line MGC803

growth_protocol: MGC803 cells were plated in 12-well plates at 30% fusion per well

extract_protocol:
Lysis of cells with Trizol reagent and harvesting of RNA
RNA libraries were prepared for sequencing using BGISEQ-500 protocols

treatment_protocol: MGC803 cells were transfected with siControl or siCXCR7.

value: human gastric cancer cell line


title: scRNA_OR43-PP

city: Chicago

first: Yu

last: Zhao

state: IL

address: 5841 S. Maryland Ave

department: Section of Genetic Medicine, Department of Medicine

institute: The University of Chicago

data_processing:
scRNA-seq gene expression raw sequencing data were processed using the Cell Ranger software v7.0.1and the 10X human transcriptome GRCh38-2020-A as the reference. The expected number of cells were auto-estimated in cellranger.
Assembly: hg38
Supplementary files format and content: Expression matricies divided into matrix, barcode, and feature files.

source_name: pre-pouch ileum

extract_protocol:
Intact mucosal tissues were rinsed in 1.5 ml ice-cold PBS [Thermo Fisher 10010023] six times. Mucosal tissues from the same regions were combined and minced by iris scissors. Minced tissues were transferred to 2 ml fresh chelator solution (HBSS Ca/Mg-Free [Thermo Fisher 14175095], 10 mM EGTA [Fisher Scientific 50-255-956], 10 mM HEPES [Thermo Fisher 15630080], and 10% FBS [Gemini Bio 100-106]). The tissues were incubated at 37°C for 15 minutes with end-over-end rotation, then cooled on ice for 10 minutes. The epithelium was separated from lamina propria by mechanical agitation (shaking 20 times). Visualizing epithelial sheets in the solution, the supernatant was collected and spun down at 300g for 5 minutes at 4°C. The remnant tissue chunks were rinsed in ice-cold PBS and incubated in 2 ml enzyme solution (HBSS Ca/Mg-Free [Thermo Fisher 14175095], 10 mM HEPES [Thermo Fisher 15630080], 200 μg/ml Liberase TM [Millipore Sigma 5401127001] and DNase I [Gold Bio D-301-100]) at 37°C for 20 minutes. The spun-down epithelium was resuspended and incubated in 2 ml TrypLE express [Thermo Fisher 12605010], at 37°C for 5 minutes. Both incubations were applied with end-over-end rotation. Tissues were gently triturated with a P1000 pipette after incubations and no visible tissue chunks remained after trituration. Cells were filtered through a 40 μM cell strainer [Falcon/VWR 21008–949]. After filtration, epithelial cells and cells from lamina propria were combined and spun down at 300 g for 5 minutes at 4°C. Cell pellet from each region were resuspended in 200 μl cold wash buffer (HBSS Ca/Mg-Free [Thermo Fisher 14175095] and 10% FBS [Gemini Bio 100-106]). Cell suspension was then diluted by 2 ml lysis buffer [Miltenyi Biotec 130-094-183] and sat for 3 minutes at room temperature to eliminate red blood cells. Cells in suspensions were spun at 300g for 5 minutes at 4°C. Cell pellets were resuspended in 200 μl suspension buffer (PBS and 0.04% BSA [Miltenyi Biotec 130-091-376]) and assessed for density and viability with Trypan Blue [Thermo Fisher 15250061]. Only cell suspensions with >85% viability were used for downstream single cell assays.
Single cells were loaded chip G per the manufacturer’s protocol for the Chromium Single Cell 3’ Library (V3.1) [10X Genomics 1000121]. In short, single cells were partitioned into Gel Beads in Emulsion (GEMs) in Chromium controller. GEMs were incubated for cell lysis and barcoded reverse transcription, followed by cDNA amplification. The cDNAs were then enzymatically fragmented and indexed. Approximately 8,300 single cells were loaded to a channel with a target recovery for 5,000 cells. Libraries were sequenced on Illumina NovaSeq 6000 platforms.

tag: condition

value: UC-IPAA

value: pre-pouch ileum

tag: pouchitis diagnosis

value: No


title: scRNA_OR48-PP

value: Male


title: Matrigel 3D cultured non limb fibroblasts with control infection for 2 d (mm10_hrepr_1)

description:
mouse.rds
combined.rds
Matrigel 3D cultured non limb fibroblasts with control infection for 2 days

source_name: Non limb fibroblasts cultured in matrigel 3D culture for 2 days


title: Naive_RiboTag IP_2

value: Small bowel muscularis externa

value: B6 Tg(Sox10-icre/ERT2)388Wdr/J x B6N.129 Rpl22tm1.1Psam/J

value: RiboTag Pulldown mRNA (IP)


title: scRNA_OR72-PP


title: Naive_RiboTag IP_3


title: MGC803_siCXCR7_2


title: MGC803_siControl_3

value: siControl


title: scRNA_OR102-PP


title: IM72h_input_4

data_processing:
Pipeline: Data was analyzed with Partek Flow software and the publicly available Lexogen pipeline (Lexogen12112017)
Partek Flow Software - Trim adapters - CUTADAPT_1_12 - Version 10.0.21.1116 - Both ends trimmed -Adapter sequences:  AAAAAAAAAAAA,TTTTTTTTTTTT
Partek Flow Software - Pre-alignment QA/QC - Version 10.0.21.1116 - K-mer length 10
Partek Flow Software - Trim adapters - CUTADAPT_1_12 - Version 10.0.21.1116 - 3'-end trimmed -Min overlap length 5 - Min read length 25
Partek Flow Software - Pre-alignment QA/QC - Version 10.0.21.1116 - K-mer length 10
Partek Flow Software - Trim bases - Version 10.0.21.1116 - Trim on quality score Phred 10 - 3'-end timmed - Min read length 20
Partek Flow Software - Pre-alignment QA/QC - Version 10.0.21.1116
Partek Flow Software - Alignment STAR - 2.5.3a - Version 10.0.21.1116
Partek Flow Software - Post-alignment QA/QC - Version 10.0.21.1116
Partek Flow Software - Quantify to annotation model (Partek E/M) - Version 10.0.21.1116
Assembly: mm10 Ensembl Transcripts release 99
Supplementary files format and content: IM3h_RiboTag_Transcript_counts: raw transcript counts RiboTag Naive vs IM3h samples
IM3h_RiboTag_POI_Normalized GSA to Naive: normalized GSA of transcript counts RiboTag IM3h to naive controls
IM24h_RiboTag_Transcript_counts: raw transcript counts RiboTag Naive vs IM24h samples
IM24h_RiboTag_POI_Normalized GSA to Naive: normalized GSA of transcript counts RiboTag IM24h to naive controls
IM72h_RiboTag_Transcript_counts: raw transcript counts RiboTag Naive vs IM72h samples
IM72h_RiboTag_POI_Normalized GSA to Naive: normalized GSA of transcript counts RiboTag IM72h to naive controls
Total RNA_POI_Gene_counts: raw gene counts Total RNA input samples
Total RNA_POI_Transcript_counts: raw transcript counts Total RNA input samples
Total RNA_POI_Normalized GSA to Naive: normalized GSA of transcript counts Total RNA to naive controls

value: Total RNA (input)


title: Naive_RiboTag IP_1


title: MGC803_siCXCR7_1


title: scRNA_OR109-PP


title: sgRNA Library-transduced OT-I cells  B2S4

description: sgRNA Library-transduced OT-I cells

value: sgRNA Library transduced OT-I cells


title: sgRNA Library-transduced OT-I cells  B2S3

description: sgRNA Library-transduced OT-I cells


title: sgRNA Library-transduced OT-I cells  B2S1

description: sgRNA Library-transduced OT-I cells


title: sgRNA Library-transduced OT-I cells  B2S2

description: sgRNA Library-transduced OT-I cells


title: sgRNA Library-transduced OT-I cells  B2S6

description: sgRNA Library-transduced OT-I cells


title: scRNA_OR101-PP

value: Female


title: MGC803_siControl_2


title: IM72h_input_3


title: scRNA_OR72-POU

source_name: ileal pouch

value: ileal pouch


title: sgRNA Library-transduced OT-I cells  B1S4

description: sgRNA Library-transduced OT-I cells


title: MGC803_siControl_1


title: IM72h_input_2


title: sgRNA Library-transduced OT-I cells  B2S5

description: sgRNA Library-transduced OT-I cells


title: scRNA_OR48-POU


title: sgRNA Library-transduced OT-I cells  B1S3

description: sgRNA Library-transduced OT-I cells


title: IM72h_input_1


title: scRNA_OR43-POU


title: IM24h_input_4


title: scRNA_OR109-POU


title: IM24h_input_3


title: IM24h_input_2


title: scRNA-seq_sgRbpj_1_day 7

source_name: sgRNA-transduced OT-I cells from the dual-color transfer system at day 7 post adoptive transfer from B16-OVA tumor

value: sgRNA transduced OT-I cells


title: ATAC-seq_sgRbpj_Tex_3_day 7

library_source: genomic

data_processing:
Adapter sequences were removed using cutadapt v.1.9
and aligned them to the mouse genome mm10 (GRCm38_68 from Sanger; ftp://ftp-mouse.sanger.ac.uk/ref/GRCm38_68.fa) using the Burrows–Wheeler algorithm32 (version 0.5.9-r26-dev, default parameter)
duplicated reads were then marked with Picard (version 1.65 (1160)) and only non-duplicated reads were kept, using samtools (parameter ‘-q 1 -F 1024’ version 0.1.18 (r982:295))
After adjustment using the Tn5 shift (by which reads were offset by +4 bp for the sense strand and −5 bp for the antisense strand), we separated reads into nucleosome-free, mononucleosome, dinucleosome and trinucleosome by fragment size
performed peak-calling for nucleosome-free reads using MACS2 (version 2.1.0.20150603, default parameters with ‘–extsize 200 –nomodel’, merged by bedtools if within 100 bp) for individual samples
Assembly: mm10
Supplementary files format and content: Consensus peaks and fragment counts for all samples

molecule: genomic DNA

source_name: sgRNA-transduced OT-I cells from the dual-color transfer system at day 7 post adoptive transfer to B16-OVA tumor

growth_protocol: OT-I cells transduced with indicatd sgRNAs were sorted from B16-OVA tumor

extract_protocol:
Cells were lysed in 50 μl ATAC-seq lysis buffer (10 mM Tris-HCl, pH 7.4, 10 mM NaCl, 3 mM MgCl2, 0.1% IGEPAL CA-630 detergent) on ice for 10 min. Resulting nuclei were pelleted at 500g for 10 min at 4 °C. Supernatant was carefully removed with a pipette and discarded. The pellet was resuspended in 50 μl transposase reaction mix (25 μl 2 × TD buffer, 22.5 μl nuclease-free water, 2.5 μl transposase) and incubated for 30 min at 37 °C. After the reaction, the DNA was cleaned up using the Qiagen MinElute kit
The barcoding reaction was run using the NEBNext HiFi kit on the basis of the manufacturer’s instructions and amplified for five cycles


title: ATAC-seq_sgRbpj_Tpex_3_day 7

value: sgRNA-transduced OT-I cells from the dual-color transfer system at day 7 post adoptive transfer to B16-OVA tumor


title: IM24h_input_1


title: scATAC_OR48-PP

data_processing:
scATAC-seq raw sequencing data were processed using the Cell Ranger ATAC 2.0.0, and the 10X human transcriptome GRCh38-2020-A-2.0.0 as the reference. Further filtering was conducted using ArchR(v.1.0.3). Only high quality individual cells are kept for downstream analysis (doublet filter ratio = 2.0, minimum fragments per cell = 2000, minimum TSS enrichment score = 6).
Assembly: hg38
Supplementary files format and content: Fragments files and tabix index of fragments files

extract_protocol:
Intact mucosal tissues were rinsed in 1.5 ml ice-cold PBS [Thermo Fisher 10010023] six times. Mucosal tissues from the same regions were combined and minced by iris scissors. Minced tissues were transferred to 2 ml fresh chelator solution (HBSS Ca/Mg-Free [Thermo Fisher 14175095], 10 mM EGTA [Fisher Scientific 50-255-956], 10 mM HEPES [Thermo Fisher 15630080], and 10% FBS [Gemini Bio 100-106]). The tissues were incubated at 37°C for 15 minutes with end-over-end rotation, then cooled on ice for 10 minutes. The epithelium was separated from lamina propria by mechanical agitation (shaking 20 times). Visualizing epithelial sheets in the solution, the supernatant was collected and spun down at 300g for 5 minutes at 4°C. The remnant tissue chunks were rinsed in ice-cold PBS and incubated in 2 ml enzyme solution (HBSS Ca/Mg-Free [Thermo Fisher 14175095], 10 mM HEPES [Thermo Fisher 15630080], 200 μg/ml Liberase TM [Millipore Sigma 5401127001] and DNase I [Gold Bio D-301-100]) at 37°C for 20 minutes. The spun-down epithelium was resuspended and incubated in 2 ml TrypLE express [Thermo Fisher 12605010], at 37°C for 5 minutes. Both incubations were applied with end-over-end rotation. Tissues were gently triturated with a P1000 pipette after incubations and no visible tissue chunks remained after trituration. Cells were filtered through a 40 μM cell strainer [Falcon/VWR 21008–949]. After filtration, epithelial cells and cells from lamina propria were combined and spun down at 300 g for 5 minutes at 4°C. Cell pellet from each region were resuspended in 200 μl cold wash buffer (HBSS Ca/Mg-Free [Thermo Fisher 14175095] and 10% FBS [Gemini Bio 100-106]). Cell suspension was then diluted by 2 ml lysis buffer [Miltenyi Biotec 130-094-183] and sat for 3 minutes at room temperature to eliminate red blood cells. Cells in suspensions were spun at 300g for 5 minutes at 4°C. Cell pellets were resuspended in 200 μl suspension buffer (PBS and 0.04% BSA [Miltenyi Biotec 130-091-376]) and assessed for density and viability with Trypan Blue [Thermo Fisher 15250061]. Only cell suspensions with >85% viability were used for downstream single cell assays.
Single nuclei were isolated from single cell suspensions following the manufacturer’s protocol for the Chromium Single cell ATAC (v 1.1). Briefly, single nuclei were transposed before loading to chip H. Transposed nuclei were partitioned into GEMS in Chromium controller. GEMs were incubated for barcoding, followed by fragment indexing. Approximately 8,000 single nuclei were transposed and loaded to a channel with a target recovery for 5,000 nuclei. Libraries were sequenced on Illumina NovaSeq 6000 platforms.


title: ATAC-seq_spike for sgRbpj_Tex_3_ day 7


title: scATAC_OR72-PP


title: scRNA_OR101-POU


title: sgRNA Library-transduced OT-I cells  B1S2

description: sgRNA Library-transduced OT-I cells


title: IM3h_input_3

value: B6.Cg-Tg73.12Mvs/J(Gfap-cre)  x B6N.129 Rpl22tm1.1Psam/J


title: sgRNA Library-transduced OT-I cells  B1S1

description: sgRNA Library-transduced OT-I cells


title: IM3h_input_2


title: IM3h_input_1


title: Naive_input_3

value: Naive


title: scATAC_OR109-PP


title: ATAC-seq_spike for sgRbpj_Tpex_3_ day 7


title: scRNA_OR102-POU


title: scRNA-seq_spike for sgRbpj_1_ day 7


title: scATAC_OR102-PP


title: scATAC_OR43-PP


title: Control Skin Mou (OUL25_RET)

type: RNA

city: Paris

first: Pierre

last: de la Grange

address: 29, rue du Faubourg Saint-Jacques

department: Paris Biotech Santé

country: France

institute: GenoSplice technology

hyb_protocol: GeneChip WT hybridization wash and stain protocol from ThermoFisher Scientific was conducted with 5.5µg of labelled cDNA

scan_protocol: Microarrays were scanned with a GCS3000 4G scanner from Affymettrix - ThermoFisher Scientific

data_processing: Data were normalized using Expression Console from Affymetrix (RMA-GENE analysis)

label: biotin

source_name: skin

label_protocol: GeneChip WT Pico protocol from ThermoFisher Scientific was conducted using 10ng of total RNA

growth_protocol: Primary culture medium composed of RPI1640 supplemented with 10% Fetal calf serum

extract_protocol: Qiagen RLT+b-mercaptoethanol

value: skin

tag: sampletype

value: normal skin

tag: localization

value: Ret


title: Control Skin Mou (OUL25_PAP)

value: Pap


title: Naive_input_2

source_name: Small bowel muscularis externa


title: Control Skin Maj (MAJ23_PAP)


title: Keloid EXT Nko Scalp (NKO27_PP)

value: Keloid EXT

value: PP


title: Keloid EXT Nko Scalp (NKO27_PR)

value: PR


title: Control Skin Maj (MAJ23_RET)


title: Control Skin Mou (MOU19_RET)


title: scATAC_OR101-PP

value: UC-IPAA

value: pre-pouch ileum

value: No


title: ATAC-seq_sgRbpj_Tpex_2_day 7


title: Naive_input_1

value: Small bowel muscularis externa

value: Total RNA (input)


title: scATAC_OR72-POU

value: ileal pouch

value: Male


title: ATAC-seq_spike for sgRbpj_Tex_2_ day 7

value: sgRNA-transduced OT-I cells from the dual-color transfer system at day 7 post adoptive transfer to B16-OVA tumor


title: scATAC_OR48-POU


title: Huh7.5 STAT1 K.O.,interferon alpha,24h,input

city: Poznan

first: Hans

last: Bluyssen

address: Uniwersytetu Poznańskiego 6

department: Laboratory of Human Molecular Genetics

country: Poland

institute: Adam Mickiewicz University

data_processing:
Quality assessment of raw reads was performed with FastQC
Alignment to the GRCh38.106 human genome assembly was done with Bowtie2 v2.4.1 and BAM files were sorted by SAMTools v1.6. PCR duplicates were removed using BamUtil v1.0.15
Peaks were called with MACS v2.2.6 with the significance cut-off q-value 0.01 and -nomodel -call-summits options. For peak annotation and motif enrichment (GAS and ISRE) HOMER v4.11 was used
In order to generate STAT1, STAT2, IRF9, pSTAT1 and pSTAT2 binding profiles upon IFN alpha treatment matrices were computed across 4 kb region centered on ChIP-Seq peak summits with deepTools v3.5.0 (reference-point TSS, upstream region 3000 bp, downstream region 1000 bp). Further steps were performed with profileplyr_1.10.0 R package
Data processing steps described above are valid for 2fTGH and ST2-U3C cell lines. Huh7.5 STAT1 K.O. has been processed in the same way as Huh7.5 wild-type cells submitted previously as part of GSE222668 SuperSeries
Assembly: hg38
Supplementary files format and content: narrowPeak for 2fTGH and ST2-U3C cell lines; regionPeak for Huh7.5 STAT1 K.O. (high-confidence peaks obtained after IDR evaluation between biological replicates - optimal output peak set; https://www.encodeproject.org/data-standards/terms/)

source_name: Human hepatocellular carcinoma

growth_protocol: DMEM; 10% fetal bovine serum (FBS); 2mM L-glutamine; 100 IU/ml penicillin,100 µg/ml streptomycin,250 ng/ml amphotericin B. Cells were cultured at 37C at 5% CO2

extract_protocol:
Cells were cross-linked with DSG for 30 min (or 45min for Huh STAT1KO) and then with formaldehyde for 10 min. After fixation chromatin was sonicated with a Diagenode Bioruptor Plus to generate 200–1000 bp fragments
ChIP-Seq libraries were performed using TruSeq ChIP Library Preparation Kit or NEBNext® ChIP-Seq Library Prep Master Mix Set for Illumina. 5-10ng of DNA was used as starting material. Libraries were amplified on the thermocycler. Post amplification libraries were size selected at 200-800bp using gel extraction (TruSeq) or 200bp using Agencourt AMPure XP beads (NEBNext). Libraries were then quantified using Qubit dsDNA HS assay kit and quality was assessed by the Agilent 2100 Bioanalyzer (High Sensitivity DNA Kit).

treatment_protocol: Cells were starved with medium containing 1% FBS and subsequently treated with 1000U/mL of IFN alpha up to 72h

value: Human hepatocellular carcinoma

value: Huh7.5 STAT1 K.O.

tag: chip antibody


title: ATAC-seq_sgRbpj_Tex_2_day 7


title: Control Skin Mou (MOU19_PAP)

value: skin


title: scATAC_OR43-POU

value: Female


title: Huh7.5 STAT1 K.O.,interferon alpha,2h,input


title: Keloid EXT Nko Scalp (NKO27_CP)

value: CP


title: ATAC-seq_sgRbpj_Tex_1_day 7


title: scATAC_OR109-POU


title: ATAC-seq_sgRbpj_Tpex_1_day 7


title: Huh7.5 STAT1 K.O.,untreated,input


title: scATAC_OR102-POU


title: ATAC-seq_spike for sgRbpj_Tex_1_ day 7


title: scATAC_OR101-POU


title: Huh7.5 STAT1 K.O.,interferon alpha,72h,STAT2,rep2


title: Keloid EXT Oss Thorax (OSS69_CP)


title: Keloid EXT Oss Thorax (OSS69_CR)

value: CR


title: Keloid EXT Oss Thorax (OSS69_PP)

value: Keloid EXT


title: ATAC-seq_spike for sgRbpj_Tpex_1_ day 7


title: Keloid EXT Nko Scalp (NKO27_CR)


title: Huh7.5 STAT1 K.O.,interferon alpha,72h,STAT2,rep1


title: Keloid EXT Dua Thorax (DUA21_PR)


title: PB Neutrol, IS, Day 7, P#10

city: Guangzhou

first: Chi Kwan

last: Tsang

address: Building #3, 613 Huangpu avenue west

department: Clinical Neuroscience Institute

institute: Jinan 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 filtering 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. Reads mapping to the reference genome Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using Hisat2 v2.0.5 and paired-end clean reads were aligned to the reference genome using Hisat2 v2.0.5. We selected Hisat2 as the mapping tool for that Hisat2 can generate a database of splice junctions based on the gene model annotation file and thus a better mapping result than other non-splice mapping tools. Quantification of gene expression level feature Counts v1.5.0-p3 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene. 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.
Assembly: hg19
Supplementary files format and content: Processed data file is in tab-delimited text format with the content of raw counts of sequencing reads for each sample.

source_name: Circulatory neutrophils

extract_protocol:
RNA was harvested using RNeasy Plus Kit (Qiagen), and RNA integrity was assessed using the RNA Nano 6000 Assay Kit of the Bioanalyzer 2100 system (Agilent Technologies, CA, USA). Total RNA (1 microgram) was then used for library construction.
Messenger RNAs were purified from total RNA using poly-T oligo-attached magnetic beads. Fragmentation was carried out using divalent cations under elevated temperature in First Strand Synthesis Reaction Buffer(5X). First strand cDNA was synthesized using random hexamer primer and M-MuLV Reverse Transcriptase (RNase H-). Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and RNase H. Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. After adenylation of 3’ ends of DNA fragments, Adaptor with hairpin loop structure were ligated to prepare for hybridization. In order to select cDNA fragments of preferentially 370~420 bp in length, the library fragments were purified with AMPure XP system (Beckman Coulter, Beverly, USA). Then PCR was performed with Phusion High-Fidelity DNA polymerase, Universal PCR primers and Index (X) Primer. At last, PCR products were purified (AMPure XP system) and library quality was assessed on the Agilent Bioanalyzer 2100 system.

value: Circulatory neutrophils

value: TIA

tag: time point


title: sgIkzf1_2_day 7

value: sgRNA transduced OT-I cells


title: Huh7.5 STAT1 K.O.,interferon alpha,24h,STAT2,rep2


title: Huh7.5 STAT1 K.O.,interferon alpha,24h,STAT2,rep1


title: Huh7.5 STAT1 K.O.,interferon alpha,2h,STAT2,rep2


title: spike for sgIkzf1_2_ day 7


title: PB Neutrol, IS, Day 7, P#9


title: PB Neutrol, IS, Day 7, P#8


title: PB Neutrol, IS, Day 7, P#7


title: Keloid EXT Dua Thorax (DUA21_PP)

value: PP


title: spike for sgIkzf1_1_ day 7


title: sgIkzf1_1_day 7


title: Huh7.5 STAT1 K.O.,interferon alpha,2h,STAT2,rep1


title: PB Neutrol, IS, Day 7, P#6


title: R10038

city: 1 Fusionopolis Way, #20-10 Connexis North Tower

first: nicholas

last: ang

country: Singapore

institute: SIgN

data_processing:
FASTQ files were mapped using STAR to  GRCh38 genome build
Gene counts were obtained using featureCounts on GENCODE v26 annotations
Assembly: GRCh38
Supplementary files format and content: gene_count

source_name: cell culture

extract_protocol:
Arcturus PicoPure RNA Isolation kit
Smart-Seq v2 protocol

tag: disease severity

value: hiMicros


title: Keloid EXT Dua Thorax (DUA21_CR)


title: Keloid NOD Kar (KAR25_PR)

value: Keloid NOD

value: PR


title: R10037

address: 1 Fusionopolis Way, #20-10 Connexis North Tower


title: PB Neutrol, IS, Day 7, P#5


title: Keloid EXT Dua Thorax (DUA21_CP)


title: Keloid NOD Kar (KAR25_PP)


title: Keloid NOD Kar (KAR25_CR)


title: Huh7.5 STAT1 K.O.,untreated,STAT2,rep2

tag: cell line


title: Huh7.5 STAT1 K.O.,interferon alpha,72h,pSTAT2,rep2


title: Keloid NOD Kar (KAR25_CP)


title: Huh7.5 STAT1 K.O.,interferon alpha,72h,pSTAT2,rep1


title: R10036


title: Huh7.5 STAT1 K.O.,interferon alpha,24h,pSTAT2,rep2


title: Huh7.5 STAT1 K.O.,untreated,STAT2,rep1


title: R8139

value: hiMacs


title: PB Neutrol, IS, Day 7, P#1


title: PB Neutrol, IS, Day 7, P#3


title: PB Neutrol, IS, Day 7, P#4


title: PB Neutrol, IS, Day 7, P#2


title: R8141


title: R8140


title: 786-0 hypoxia-3

city: Nanjing

last: Zhang

state: China/Jiangsu

address: No. 87 Dingjiaqiao, Gulou District

department: Department of Pathology

institute: School of Medicine, Southeast University

data_processing:
Trimmomatic software (v0.36) was done to obtain data filtering.
The clean reads were then aligned to the reference according to Spliced Transcripts Alignment to a Reference (STAR, v2.5).
The expected number of Fragments Per Kilobase of transcript sequence per Million base pairs sequenced (FPKMs) of reads in every sample were calculated through RSEM (v1.1.17)
The transcripts with |log2(FC) |>1 and p‐adjust < 0.05 were assigned as DEGs, which were analyzed by DESeq2 software (v1.16.1)
Assembly: hg19
Supplementary files format and content: tab-delimited text files include RPKM values for every sample

growth_protocol: DMEM/F-12(1:1) basic (Gibco, USA) with 10% fetal bovine serum (FBS) was used to culture HK-2 cells, while 786-0 cells were cultured in RPMI medium 1640 basic (Gibco, USA) supplied with 10% FBS.

extract_protocol:
Total RNA in all groups were extracted separately with Total RNA Extraction Reagent (Vazyme, Nanjing, China).
NanoPhotometer spectrophotometer (IMPLEN, USA), Qubit 2.0 Fluorometer (Life Technologies, USA), and Bioanalyzer 2100 system (Agilent Technologies, USA) were used to assess RNA purity, concentration as well as integrity respectively. The sequencing libraries were generated and sequenced with the Illumina Hiseq 4000 platform.

treatment_protocol: For hypoxia treatment, HK-2 cells and 786-0 cells were cultured in an atmosphere of 5% CO2, 94% N2 and 1% O2 for 24 h.

value: Epithelial cells

value: Hypoxia

tag: time


title: PB Neutrol, Control, Day 1, P#10

tag: cell type


title: Keloid NOD Cam (CAM31_PR)


title: Keloid NOD Cam (CAM31_PP)


title: 786-0 hypoxia-2


title: Keloid NOD Cam (CAM31_CR)


title: Keloid NOD Cam (CAM31_CP)


title: Keloid NOD Sou (SOU22_PR)


title: PB Neutrol, Control, Day 1, P#9


title: PB Neutrol, Control, Day 1, P#8


title: PB Neutrol, Control, Day 1, P#7


title: Huh7.5 STAT1 K.O.,untreated,pSTAT2,rep2

value: Human hepatocellular carcinoma


title: Keloid NOD Sou (SOU22_PP)


title: Huh7.5 STAT1 K.O.,interferon alpha,2h,pSTAT2,rep1

value: Huh7.5 STAT1 K.O.


title: 786-0 normoxia-3

value: Normoxia


title: Huh7.5 STAT1 K.O.,untreated,pSTAT2,rep1


title: 786-0 hypoxia-1


title: PB Neutrol, Control, Day 1, P#6


title: Huh7.5 STAT1 K.O.,interferon alpha,24h,pSTAT2,rep1


title: Huh7.5 STAT1 K.O.,interferon alpha,2h,pSTAT2,rep2


title: Huh7.5 STAT1 K.O.,interferon alpha,72h,IRF9,rep2


title: PB Neutrol, Control, Day 1, P#5


title: Small intestine T regulatory cells rep2

city: Philadlephia

first: Daniel

last: Beiting

state: Pennsylvania

address: 380 S. University Avenue

institute: University of Pennsylvania

description:
Small intestine T regulatory cells rep2
K14_gut_Treg

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalised using quantile normalisation with IlluminaGUI in R

source_name: small intestine

label_protocol: Biotinylated cRNA were prepared with the Ambion MessageAmp kit for Illumina arrays

extract_protocol: Spleen and small intestine were processed to single cell suspensions. Cells were antibody stained for Flourescence activated cell sorted. Viability dye and antibodies against CD4, CD8, TCRb, and B220 were utilized to sort live TCRb+CD4+CD8-B220-GFP+ Treg cells and  TCRb+CD4+CD8-B220-GFP- T conventional cells. RNA was extracted with Trizol reagent, followed by clean-up and  with QIAGEN RNeasy mini kit before labeling and microarray preparations. Each sample includes cells from multiple mice to reach sufficient intestinal Treg numbers for RNA isolation

value: mixed male and female

tag: genotype

value: K14Aβb, FOXP3GFP

value: 7-14 weeks

value: small intestine


description:
Small intestine T conventional cells rep2
K14_gut_Tcon

tag: strain


title: Small intestine T regulatory cells rep1

description:
Small intestine T regulatory cells rep1
WT_gut_treg

value: MHCII+/-, FOXP3GFP

tag: tissue


title: HK-2 hypoxia-3

value: Tubular epithelial cells

tag: treatment


title: Keloid NOD Sou (SOU22_CR)

value: skin

value: CR


title: Huh7.5 STAT1 K.O.,interferon alpha,24h,IRF9,rep2


title: PB Neutrol, Control, Day 1, P#4

value: Circulatory neutrophils

value: TIA


title: Huh7.5 STAT1 K.O.,interferon alpha,72h,IRF9,rep1


title: Keloid NOD Sou (SOU22_CP)

value: Keloid NOD

value: CP


title: 786-0 normoxia-1

value: Epithelial cells


title: PB Neutrol, Control, Day 1, P#3


title: Huh7.5 STAT1 K.O.,interferon alpha,24h,IRF9,rep1


title: HK-2 hypoxia-1

value: Hypoxia


title: HK-2  normoxia-3


title: HK-2 hypoxia-2


title: Huh7.5 STAT1 K.O.,interferon alpha,2h,IRF9,rep1

value: Human hepatocellular carcinoma


title: PB Neutrol, Control, Day 1, P#1


title: ICGC_MB88

type: genomic

city: Heidelberg

first: Konstantin

last: Okonechnikov

state: Germany

address: Im Neuenheimer Feld 280

department: Pediatric Neurooncology

institute: German Cancer Research Center

description: MBEN sample

hyb_protocol: Illumina protocol

scan_protocol: Illumina iScan System according to the manufacturer's protocol

data_processing:
Bioconductor  package minifi (Version 1.18) using function 'preprocessIllumina' Average beta
MBEN_matrix_processed.tsv represents normalized (preprocessIllumina function) Average Beta

label: Cy5 and Cy3

source_name: Medulloblastoma

label_protocol: Illumina protocol

extract_protocol: Illumina protocol

value: Tumor

tag: tumor class

value: Medulloblastoma

tag: tumor subclass

value: MB SHH INF

tag: m stage

tag: gender

value: M

value: MBEN tumor


title: Huh7.5 STAT1 K.O.,interferon alpha,2h,IRF9,rep2

value: Huh7.5 STAT1 K.O.


title: ATAC-seq_spike for sgRbpj_Tpex_2_ day 7

value: sgRNA-transduced OT-I cells from the dual-color transfer system at day 7 post adoptive transfer to B16-OVA tumor


title: Double KO SAM24409575

city: South San Francisco

first: Benjamin

middle: I

last: Laufer

state: California

address: 1 DNA Way

institute: Genentech

data_processing:
GSNAP was used to align reads to GRCh38.
The HTSeqGenie Bioconductor package was used to count genes.
Gene models were obtained from an internal database.
Assembly: GRCh38
Supplementary files format and content: Tab-delimeted text files with raw counts, width, and rpkm normalized values for each gene.

source_name: Differentiated microglia from the PGP1 iPS cell line (Synthego)

extract_protocol: Truseq Stranded mRNA Kit (Illumina).

value: Double KO

tag: batch

value: B


title: PB Neutrol, Control, Day 1, P#2


description:
Small intestine T conventional cells rep1
WT_gut_Tcon

tag: Sex

value: mixed male and female

value: MHCII+/-, FOXP3GFP

tag: age

value: 7-14 weeks

value: small intestine


title: HK-2  normoxia-2

value: Tubular epithelial cells

value: Normoxia


title: Splenic T regulatory cells rep1

description:
Splenic T regulatory cells rep1
WT_spleen_treg

source_name: spleen

value: spleen


title: HK-2  normoxia-1


title: Splenic T conventional cells rep2

description:
Splenic T conventional cells rep2
K14_spleen_Tcon

value: K14Aβb, FOXP3GFP


title: TMEM106B KO SAM24409574

value: Differentiated microglia from the PGP1 iPS cell line (Synthego)

value: TMEM106B KO


title: Splenic T regulatory cells rep2

description:
Splenic T regulatory cells rep2
K14_spleen_Treg


title: Huh7.5 STAT1 K.O.,interferon alpha,72h,input

value: Human hepatocellular carcinoma

tag: chip antibody


title: ICGC_MB299

description: MBEN sample

value: Tumor

value: Medulloblastoma

value: MB SHH INF

value: M


title: ICGC_MB295

description: MBEN sample

value: MBEN tumor


title: GRN KO SAM24409573

value: GRN KO

value: B


title: ST2-U3C,interferon alpha,72h,phospho-STAT2,rep2

source_name: Human fibrosarcoma

value: Human fibrosarcoma


title: WT SAM24409572

value: WT


title: ST2-U3C,interferon alpha,72h,phospho-STAT2,rep1


title: ST2-U3C,interferon alpha,2h,phospho-STAT2,rep2


title: ICGC_MB263

description: MBEN sample

value: F


title: ICGC_MB287

description: MBEN sample


title: 786-0 normoxia-2

value: Epithelial cells


title: ST2-U3C,interferon alpha,2h,phospho-STAT2,rep1


title: Double KO SAM24409570

value: Double KO

value: A


title: Double KO SAM24409571


title: Double KO SAM24409569


title: ICGC_MB266

description: MBEN sample


title: Splenic T conventional cells rep1

description:
Splenic T conventional cells rep1
WT_spleen_Tcon

value: mixed male and female

value: MHCII+/-, FOXP3GFP

value: 7-14 weeks

value: spleen


title: ST2-U3C,interferon alpha,24h,STAT2,rep2

value: STAT2 (SantaCruz, #sc-839)


title: Huh7.5 STAT1 K.O.,untreated,IRF9,rep2

value: Human hepatocellular carcinoma

value: Huh7.5 STAT1 K.O.


title: ST2-U3C,untreated,phospho-STAT2,rep2


title: ST2-U3C,interferon alpha,24h,STAT2,rep1


title: TMEM106B KO SAM24409568

value: Differentiated microglia from the PGP1 iPS cell line (Synthego)

value: TMEM106B KO


title: Huh7.5 STAT1 K.O.,untreated,IRF9,rep1


title: RNA43

city: Yufu-city

first: Yoshiyuki

last: Tsukamoto

state: Oita

address: hasamacho idaigaoka 1-1

department: Molecular Pathology

country: Japan

institute: Oita university, Faculty of Medicine

hyb_protocol: Gene Expression Hybridization kit was used for hybridization in accordance with the manufacture's instructions (Agilent Technologies).

scan_protocol: Microarray images were obtained by using a laser confocal scanner G2565BA (Agilent Technologies).

data_processing: Feature Extraction software (Agilent Technologies) with the manufacturer’s recommended settings was applied for the microarray image analysis. Analysis of the raw data obtained from Feature Extraction software was performed with GeneSpring GX software(Aglrent). For comparison among multiple arrays, probe set data were median-normalized per chip.

source_name: endoscopic biopsy before neoadjuvant chemotherapy

label_protocol: Cy3-labeled cRNA targets were generated by use of Low input Quick Amp labeling Kit according to manufacture's instructions (Agilent Technologies).

extract_protocol: Total RNA from each biopsy sample was isolated by RNeasy Mini Kit (QIAGEN) in combination with DNase treatment (RNase-Free DNase Set, QIAGEN)

tag: tumor or non-tumor

value: tumor

tag: histologic response based on papers (pmid


title: RNA42


title: RNA41


title: GD80 fetal pig lung sorted LGR5/H2B-GFP positive

city: Raleigh

first: Jorge

last: Piedrahita

state: NORTH CAROLINA

address: 1060 William Moore Drive, BPC Suite 200

institute: North Carolina State University

data_processing:
Salmon Alevin was used for the alignment and quantification.
A Seurat object (v4.1.1) in R was created with 100 minimum cells.
Cells with fewer than less than 5% ribosomal reads and 2000 detected genes were discarded.
Unsupervised clustering of the cells was performed with the shared nearest neighbor (SNN) clustering algorithm implemented in the FindClusters() function in Seurat with a resolution of 0.75.
Assembly: Sus scrofa 11.1
Supplementary files format and content: 10X_alevin_quants_mat_sl1.rds.gz contains Alevin quantified counts.
Supplementary files format and content: Seurat_obj.rds.gz contains the processed Seurat object.

organism: Sus scrofa

source_name: Lung

extract_protocol:
Cells were isolated from lungs of adult or fetal LGR5 pigs. 2-3 cm2 pieces of lung were collected in cold PBS and moved into a sterile hood. Lung tissue was then minced using scissors or razor blade and then washed twice with cold PBS to remove blood and immune cells. Minced tissues were then incubated for 1 hour in a roller incubator at 37℃ in an enzymatic digest buffer containing 10 mg/mL Dispase (Invitrogen), 2 mg/mL DNase I (STEMCELL Technologies), and 5mg/mL (adult) or 2mg/mL (fetal) Collagenase Type II (Sigma). The digestion mixture was then strained using a 70 μM cell strainer and washed with a wash buffer (PBS, 5% FBS, 1% antibiotic-antimycotic) and centrifuged. For adult tissue, pellets were incubated in Red Blood Cell Lysis Buffer (Invitrogen) for 10 minutes at room temperature with gentle agitation. For fluorescent activated cell sorting, cells from porcine lung or dissociated organoids were suspended in MACS buffer (Miltenyi) and incubated with 10μl/ml anti-EpCAM-APC (Thermo Scientific, 17-5791-83) and/or anti-NGFR-PE (eBioscience, 12-9400-41). Propidium iodide was added for dead cell exclusion immediately before fluorescence activated cell sorting (Beckman Coulter MoFlo XPD).
Chromium SIngle Cell 3’ Library & Gel Bead Kit

value: Lung

value: LGR5-H2B-GFP knock-in


title: RNA38


title: ST2-U3C,untreated,phospho-STAT2,rep1

value: Human fibrosarcoma

tag: cell line


title: GRN KO SAM24409565

value: GRN KO

value: B


title: GRN KO SAM24409564


title: RNA39


title: ST2-U3C,untreated,STAT2,rep2


title: ST2-U3C,interferon alpha,2h,IRF9,rep3

value: IRF9 (SantaCruz, #sc-10793)


title: ST2-U3C,interferon alpha,2h,IRF9,rep2


title: ST2-U3C,interferon alpha,24h,IRF9,rep1


title: WT SAM24409560

value: WT

value: A


title: WT SAM24409562


title: WT SAM24409561


title: ST2-U3C,interferon alpha,24h,IRF9,rep3


title: 2fTGH,interferon alpha,2h,STAT2,rep4


title: 2fTGH,interferon alpha,72h,STAT2,rep1


title: ST2-U3C,untreated,STAT2,rep1


title: 2fTGH,interferon alpha,72h,STAT2,rep2


title: ST2-U3C,interferon alpha,2h,IRF9,rep1


title: ST2-U3C,untreated,IRF9,rep3


title: ST2-U3C,untreated,IRF9,rep2


title: 2fTGH,interferon alpha,2h,STAT2,rep3


title: Primary hepatoblastoma cell line 2

city: Cincinnati

first: Rebekah

last: Karns

state: OH

address: 3333 Burnet Ave

department: Gastroenterology, Hepatology, & Nutrition

institute: Cincinnati Children's Hospital Medical Center

description: Hepatoblastoma tumor-derived cell line grown in culture from 3 year old

data_processing:
Sequences were aligned against GRCh38, and Ensembl annotation.  Quality control evaluation of the fastq files was performed using FastQC
Following removal of primers and barcodes, raw reads were processed using kallisto (Pachter lab) which uses pseudoalignment to accurately quantify RNA reads with transcripts per million (TPM) as output.  GRCh38/Hg38 annotations were provided by UCSC.
Prior to analyses, data were log2-transformed and baselined to the overall median.  Only reasonably expressed transcripts (TPM>3 in >20% of samples) were included in differential analyses.
Assembly: GRCh38/Hg38
Supplementary files format and content: tab-delimited file with gene symbol and transcripts per million

growth_protocol: Hepatoblastoma tumor derived cell lines (AB 30, 45, 60, 74, 81) were generated from patient tumor from established xenograft models using basic explant culture.  Experiments were conducted in vitro in monolayer culture from these cell lines and the established liver cancer cell line HepG2 for up to 12 passages. All cells were cultured in Dulbeccos’ Modified Eagle’s Medium (DMEM, Gibco) containing 10% fetal bovine serum (FBS), 1% non-essential amino acids, 1% penicillin/streptomycin, 20 μM Rho kinase inhibitor, Y27632, and incubated at 37°C with 5% CO2

extract_protocol:
Qiagen RNeasy Plus Mini kit was used following manufacturers protocol.
PolyA stranded RNA-Seq was performed using NovaSeq6000 according to manufacturers protocols.

value: Hepatoblastoma-derived cell line


title: RNA36


title: Primary hepatoblastoma cell line 3


title: RNA34


title: RNA35


title: Primary hepatoblastoma cell line 1


title: 2fTGH,interferon alpha,72h,phospho-STAT2


title: RNA33N

value: non-tumor


title: Primary hepatoblastoma cell line 4

description: Hepatoblastoma tumor-derived cell line grown in culture from 4 year old


title: 2fTGH,interferon alpha,24h,STAT2,rep2


title: 2fTGH,interferon alpha,2h,STAT2,rep1


title: RNA37


title: 2fTGH,interferon alpha,24h,STAT2,rep1


title: 2fTGH,interferon alpha,2h,phospho-STAT2


title: Human dermal fibroblast

description: human dermal fibroblasts after one passage in culture from adult skin

value: Dermal fibroblasts


title: 2fTGH,interferon alpha,2h,STAT2,rep2

value: STAT2 (SantaCruz, #sc-839)


title: 2fTGH,interferon alpha,24h,phospho-STAT2


title: Human hepatocyte

description: human hepatocytes isolated from primary human liver

value: Hepatocytes


title: Human liver cancer

description: An immortal cell line from a 15 year old hepatoblastoma patient

value: Liver cancer cell line


title: 2fTGH,untreated,phospho-STAT2


title: 2fTGH,untreated,STAT2,rep2


title: 2fTGH,untreated,STAT2,rep1


title: 2fTGH,interferon alpha,72h,STAT1,rep2

value: STAT1 (SantaCruz, #sc-346)


title: 2fTGH,interferon alpha,72h,STAT1,rep1


title: HK2-Hypoxia_Input

data_processing:
After obtaining sequencing Data (Raw Data), the data should be filtered first to acquire high-quality data (Clean Data) created by FastQC (version 0.11.9).
Reads were then aligned to the reference genome (hg38) via Bowtie2.
Peaks calling and annotation were performed using Hypergeometric Optimization of Motif Enrichment (HOMER)
Annotated files using Excel were created to describe density and distribution plots.
After removing the redundancy from the comparison files, visualization is performed using IGV software
Assembly: hg38
Supplementary files format and content: 1.txt, mapping information of every samples; 2. xls, annotations of peaks among every samples; 3.xls, distributions of peaks among every samples;

source_name: HK-2 cells

growth_protocol: DMEM/F-12(1:1) basic (Gibco, USA) with 10% fetal bovine serum (FBS) were used to culture HK-2 cells

extract_protocol:
Cells were fixed with 1% formaldehyde at room temperature for 10 min and quenched in 2.5 M glycine (1:20) for 5 min. Cell precipitates were collected and at centrifuged with 1200 r/min and at 4 °C for 3min. The collected cell precipitates were then sonicated to generate DNA fragments. Chromatin fragments were immunoprecipitated and incubated at 4 °C overnight using antibodies against HIF-1α (ab243860, Abcam). 50 μl magnetic beads (Protein G) were placed into 1.5ml EP tubes and mixed with chip binding buffer, and the supernatant was not discarded until liquid was transparent. Then, chromatin fragments-antibody mixture was added with magnetic beads and incubated for 4 h at 4 °C. The precipitated DNA was purified using the ChIP DNA Clean Kit.
Chip sequencing was conducted by KeyGEN Bio TECH. Sequencing was performed using VAHTS mRNA-seq V3 Library Prep Kit for Illumina NovaSeq 6000.

treatment_protocol: HK-2 normoxia group were incubated at 37 ℃ in an incubator containing 5% CO2 and 21% O2, while for hypoxia treatment, HK-2 cells were cultured in an atmosphere of 5% CO2, 94% N2 and 1% O2 for 6h at 37 ℃.

value: HK-2 cells

value: Tubular epithelial cells


title: RNA32

value: tumor


title: RNA29N


title: HK2-Normoxia_HIF1α

description:
HK2-Normoxia_HIF1A.mapping.info
HK2-Normoxia_HIF1A_peaks.annotation
HK2-Normoxia_HIF1A_peaks.distribution

value: HIF1α (Abcam, #ab243860)


title: RNA30


title: HK2-Normoxia_Input


title: RNA31


title: 2fTGH,interferon alpha,2h,STAT1,rep3

value: Human fibrosarcoma


title: RNA33


title: 2fTGH,interferon alpha,2h,STAT1,rep1


title: 2fTGH,interferon alpha,2h,STAT1,rep2


title: RNA29


title: 2fTGH,untreated,STAT1,rep2


title: STAT1-STAT2-IRF9-U3C,untreated,rep3

data_processing:
After quality control assessments using FastQC, fastq files were mapped to the Homo sapiens GRCh38/hg38 genome build (release-100) using STAR version 2.7.3a
Read counts were generated using FeatureCounts v1.6.2 with default parameters
For U3C and ST1-ST2-IRF9-U3C Salmon v1.10.2 have been used to count transcript-level abundance estimates with gencode.v43.basic.annotation GTF file
Counts normalization and DEG analysis were performed using the DESeq2 v.1.30.1 package in R version 4.0.3
The Wald Test (for  U3C and ST1-ST2-IRF9-U3C) or likelihood ratio test (LRT; for the rest of the cell lines) was used to identify DEG. Huh7.5 wild-type cells and Huh7.5 STAT1 K.O. data have been submitted previously as part of GSE222668 SuperSeries
Assembly: hg38
Supplementary files format and content: normalized counts in csv format

extract_protocol:
Total RNA was extracted using the GeneMATRIX Universal RNA Purification Kit. 500 ng of purified total RNA was then reverse-transcribed using ThermoFisher Scientific reagents
RNA libraries were prepared in three biological repeats from 1μg of total RNA using NEBNext® Ultra™ or Ultra™ II RNA Library Prep Kit for Illumina® (New England Biolabs, NEB) together with NEBNext Poly(A) mRNA Magnetic Isolation Module (NEB) and NEBNext® Multiplex Oligos for Illumina® (NEB), according to the manufacturer's protocol

treatment_protocol: Cells were starved with medium containing 1% FBS concentration and subsequently treated with 1000U/ml of IFN alpha up to 72h

value: untreated


title: HK2-Hypoxia_HIF1α

description:
HK2-Hypoxia_HIF1A.mapping.info
HK2-Hypoxia_HIF1A_Peaks.annotation
HK2-Hypoxia_HIF1A_peaks.distribution


title: RNA28


title: 2fTGH,untreated,STAT1,rep1


title: 2fTGH,interferon alpha,24h,STAT1,rep2


title: STAT1-STAT2-IRF9-U3C,untreated,rep2


title: STAT1-STAT2-IRF9-U3C,untreated,rep1


title: 2fTGH,interferon alpha,24h,IRF9,rep2


title: RNA27


title: U3C,untreated,rep3


title: U3C,untreated,rep2


title: RNA28N


title: 2fTGH,interferon alpha,72h,IRF9,rep1


title: 2fTGH,interferon alpha,24h,IRF9,rep1


title: U3C,untreated,rep1


title: RNA25


title: 2fTGH,interferon alpha,2h,IRF9,rep1


title: 2fTGH,interferon alpha,2h,IRF9,rep2


title: RNA26


title: RNA25N


title: K562_FLT3_NR_rep2

city: Seoul

first: Jae Seok

last: Roe

address: Yonsei-ro, 50

country: South Korea

institute: Yonsei University

data_processing:
Raw reads were mapped to the reference genome assembly hg19 using STAR mapping tool (Dobin et al, 2013l; PMID: 23104886).
Assembly: hg19
Supplementary files format and content: Differentially expressed genes were analyzed using Cufflinks tools (Trapnell et al, 2012; PMID: 22383036)

source_name: Lymphoblast cells isolated from the bone marrow of a 53-year-old chronic myelogenous leukemia patient

growth_protocol: Above cell lines were cultured in conditions as described in this study.

extract_protocol:
Total RNAs were extracted from ~ 1 million cells using Qiaizol reagent
Libraries were prepared using the NEXTflex Rapid Directional mRNA-seq kit (Cat# NOVA-5138-11; PerkinElmer) according to the manufacturer's instructions.

treatment_protocol: treated with drugs as indicated.

tag: expression vector

value: FLT3 cDNA

value: NR

tag: biological replicate


title: RNA24


title: K562_FLT3_NR_rep3


title: 2fTGH,untreated,IRF9,rep2

value: IRF9 (SantaCruz, #sc-10793)


title: K562_FLT3_NR_rep1


title: 2fTGH,untreated,IRF9,rep1


title: K562_FLT3_IR_rep2

value: IR


title: K562_FLT3_IR_rep3


title: ST2-U3C,interferon alpha,72h,rep1

value: interferon alpha,72h


title: ST2-U3C,interferon alpha,72h,rep2


title: RNA19


title: ST2-U3C,interferon alpha,48h,rep2

value: interferon alpha,48h


title: RNA20


title: K562_FLT3_rep3


title: RNA22


title: RNA21


title: ST2-U3C,interferon alpha,48h,rep1


title: RNA17


title: ST2-U3C,interferon alpha,36h,rep2

value: interferon alpha,36h


title: ST2-U3C,interferon alpha,36h,rep1


title: K562_mock_rep3

value: mock


title: RNA16


title: RNA15


title: K562_FLT3_IR_rep1


title: RNA18


title: K562_mock_rep2


title: ST2-U3C,interferon alpha,24h,rep2

value: interferon alpha,24h


title: XIST 2KD Replicate 4

city: Baltimore

first: Erica

middle: L

last: Darrah

state: Maryland

address: 5200 Eastern Ave.

department: Molecular Rheumatology

institute: Johns Hopkins School of Medicine

data_processing:
Illumina CASAVA performed base-calling of Illumina NovaSeq 6000, 100-base-single-end data producing FASTQ files
Mapping with STAR - 2.7.3a using default parameters
Count quantification in Partek Flow to annotation model (Partek E/M), GRCh38.p13_refseq_v99 transcript counts with default parameters
Partek Flow normalized to FPKM at default parameters, and 1 added to all values to eliminate nulls for zero
FPKMs log2 quantile normalzed with Partek GS v6.6 and 1-way two-tailed t-test run
Assembly: GRCh38.p13
Supplementary files format and content: Format txt, Log2 quantile normalized FPKM

source_name: Tissue Culture ATCC (CRL-1555)

growth_protocol: Cells were grown in Dulbecco's Modified Eagle's Medium (DMEM) (ATCC cat # 30-2002) with 10% Fetal Bovine Serum (FBS), 100 I.U./mL Penicillin, and 100 ug/mL streptomycin

extract_protocol:
Total RNA was isolated from WT A431 cells, pCAS-treated A431 cells, and XIST knockdown A431 cells using RNeasy Mini Kit (Qiagen, cat # 74104) with on-column DNase digestion using the RNase-Free Dnase Set (Qiagen, cat # 79254).
Illumina Stranded Total RNA Prep Ligation with Ribo-Zero Plus with manufacturer's protocol

treatment_protocol: CRISPR-Cas9-mediated knockdown of XIST was performed using the XIST Human Gene Knockout Kit (CRISPR) (Origene, cat # KN412685) according to the manufacturer’s protocol. WT A431 cells (ATCC, cat # CRL-1555) were used as target cells. After the initial round of treatment and serial dilution to generate the cell line XIST KD, another round of treatment with a different gRNA (AGCGCTTTAAGAACTGAAGG) and serial dilution was performed to generate cell line XIST 2KD.

tag: cell type

value: A431 cells

value: CRISPR-Cas9 targeted (2x)

tag: genotype

value: XIST-deficient


title: XIST 2KD Replicate 2


title: ST2-U3C,interferon alpha,24h,rep1

tag: tissue


title: K562_FLT3_rep1

tag: treatment


title: RNA14


title: K562_FLT3_rep2


title: XIST 2KD Replicate 3


title: K562_mock_rep1


title: Hela Scrambled shRNA with PBS replicate 5

city: Montréal

first: Gael

middle: Louis Max

last: Cagnone

state: QC

address: 3175 Chemin de la Côte-Sainte-Catherine

department: The Montreal single-cell Academy

country: Canada

institute: CHU Sainte Justine

data_processing:
RNAseq data were pre-processed using the RNAseq next-flow pipeline(Ewels et al., 2020) with the star_salmon aligner and the salmon pseudo-aligner (reference genome GRCh38).
Gene counts were normalized and scaled to perform differential gene expression analysis between groups using Seurat after regressing for batch effect(Hao et al., 2021).
Assembly: GRCh38
Supplementary files format and content: salmon.merged.gene_counts.tsv

source_name: HeLa cells

growth_protocol: HeLa (CCL-2 ATCC) and A549 (CCL-185 ATCC) were purchased from commercial vendors and maintained according to the manufacturers protocol in DMEM, 10% FBS and 1% Pen/Strep, U-251MG cells were a kind gift from Dr. Hardy’s lab and maintained in EMEM + 2 mM Glutamine + 1% non-essential amino acids + 1 mM Sodium Pyruvate + 10% FBS and 1% Pen/Strep in a humidified incubator with 5% CO2 at 37 °C. Stable cells were generated using appropriate drug selection (G-418, Puromycine) after plasmid transfection or viral transduction, and were maintained in these antibiotic instead of Pen/Strep.

extract_protocol:
Equal number of cells were seeded in 10cm dish and let to grow a density of 70-80% confluency. Lactate was added to the final concentration of 10mM (or equal volume of PBS) and incubated to 6 hours. RNA was extracted with RNeasy mini Kit (Qiagen). Samples were sent to IRIC genomic platform for analysis and sequencing. RNA integrity and quantity was validated with Bioanalyzer and then used for sequencing.
Samples were analyzed with bioanalyzer for quality control and single-end NGS was performed at IRIC genomic platform with Nextseq 500 illumina system.
Samples were sequenced with Nextseq 500 illumina system with a depth of ~35M per sample with single-end 75 cycles. Each sample was sequenced at least in triplicates.

treatment_protocol: A stock concentration of 500 mM lactate (in PBS and pH adjusted to 7.4) was used for cell stimulation and similar volume of PBS as vehicle was used as control. Lentiviral shRNA against HCAR1 targeting 3’UTR regions of the gene (shHCAR1a: GCTTTATTTCAGGCCGAATGA; shHCAR1b: GCTCTGACCTTCTTCAAATCT) and the scrambled shRNA were purchased from GeneCopoeia (Cat# LPP-HSH007585-LVRU6MP-100). Targeting the 3’UTR regions allowed us to use our previous plasmid constructs for rescue experiments.

value: HeLa cells

value: Cervical cancer cells

value: WT - Scrambled shRNA

value: PBS


title: XIST KD Replicate 3

value: CRISPR-Cas9 targeted


title: XIST KD Replicate 2


title: RNA11

value: tumor


title: RNA12


title: RNA09


title: ST2-U3C,interferon alpha,8h,rep2

value: Human fibrosarcoma

value: interferon alpha,8h


title: XIST 2KD Replicate 1


title: Hela Scrambled shRNA with PBS replicate 4


title: ST2-U3C,interferon alpha,2h,rep2

value: interferon alpha,2h


title: RNA10


title: ST2-U3C,interferon alpha,8h,rep1


title: Hela Scrambled shRNA with PBS replicate 3


title: pCAS Replicate 4

value: Scrambled gRNA

value: XIST-sufficient


title: XIST KD Replicate 1


title: Hela Scrambled shRNA with PBS replicate 2


title: pCAS Replicate 3


title: ST2-U3C,interferon alpha,1h,rep2

value: interferon alpha,1h


title: ST2-U3C,interferon alpha,2h,rep1


title: pCAS Replicate 2


title: Hela Scrambled shRNA with PBS replicate 1


title: RNA07


title: ST2-U3C,interferon alpha,1h,rep1


title: RNA05


title: Hela Scrambled shRNA with Lactate replicate 3

value: Lactate


title: pCAS Replicate 1


title: ST2-U3C,untreated,rep2

value: untreated


title: WT Replicate 3

value: A431 cells

value: Untreated


title: ST2-U3C,untreated,rep1


title: Fresh mouse limb progenitors grafted into chick wings for 4 days (2nd batch0

city: BOSTON

first: CHANGHEE

last: LEE

address: 77 AVENUE LOUIS PASTEUR

institute: Harvard Medical School

description:
sample14
xenografted LPCs

data_processing:
For xenograft1-3, sample11-14, matrigel4, all the chick contaminant cells have been filtered out. All remaining MULTI-seq multiplexed libraries (D10, D14, ROUND5, 3F-1, 3F-2, D3 & D4) were also filtered to contain only relevant cellular barcodes that have correct MULTI-seq barcodes called.
Supplementary files format and content: Seurat objects in .RDS format. 20230509_3F_integrated.RDS contains all relevant data for the single cell data figures except Figure 7 and Figure S13. 20230509_4F_integrated.RDS contains all relevant single cell data for Figure S13. 20230503_11_xeno_integrated.rds contains all relevant scRNA-seq data for Figure 7.

organism:
Gallus gallus
Mus musculus

source_name: limb bud

extract_protocol: 10X scRNA-seq v3.1 chemistry

value: limb bud

value: limb mesenchymal cells (differentiated)

value: Prrx1CGE-Ai9 (tdtomato+ cells)

value: wildtype


title: RNA08


title: RNA06


title: WT Replicate 2


title: RNA03


title: RNA35N

value: non-tumor


title: RNA04


title: 2fTGH,interferon alpha,72h,rep3

value: interferon alpha,72h


title: Hela Scrambled shRNA with Lactate replicate 1

value: HeLa cells

value: Cervical cancer cells

value: WT - Scrambled shRNA


title: Remnant GEM beads from sample 14

description:
sample13
xenografted LPCs


title: RNA01

value: tumor


title: WT Replicate 1


title: Remnant GEM beads from sample 11

description:
sample12
xenografted LPCs


title: BT549 cells, F2C

city: Edinburg

first: Megan

middle: Erin

last: Keniry

state: TX

address: 1201 W. University Dr.

department: Biology

institute: UTRGV

data_processing:
Illumina Casava software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to human whole genome Homo Sapiens(GRCh38/hg38) using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Supplementary_files_format_and_content: Tab-delimited text files include FPKM values for each Sample.  Matrix table with raw gene counts for every gene and every sample.

source_name: BT549 cells

growth_protocol: 100,000 BT549 cells were plated onto 10cm dishes.

extract_protocol:
RNA was extracted using Rneasy Qiagen kit as per manufacturer's protocol.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Cells were treated the next day with either DMSO control or 200nM AS1842856 for 48 hours.

value: BT549 cancer cell line


title: Fresh mouse limb progenitors grafted into chick wings for 4 days (1st batch)

description:
sample11
xenografted LPCs


title: Hela Scrambled shRNA with Lactate replicate 2


title: BT549 cells, F2B


title: 2fTGH,interferon alpha,72h,rep1

value: Human fibrosarcoma


title: Hela shHCAR1b+ RNAi δS305A HCAR1 with PBS replicate 1

value: WT - shHCAR1b+ RNAi dS305A HCAR1

value: PBS


title: 2fTGH,interferon alpha,48h,rep3

value: interferon alpha,48h


title: Day 14 rLPC grafted into chick wings for 4 days and dissociated (3rd batch)

description:
xenograft3
xenografted rLPCs

value: reprogrogrammed from fibroblasts


title: BT549 cells, F2A


title: 2fTGH,interferon alpha,48h,rep2


title: Hela shHCAR1b+ RNAi δS305A HCAR1 with PBS replicate 3


title: Hela shHCAR1b+ RNAi δS305A HCAR1 with Lactate replicate 2

value: Lactate


title: Hela shHCAR1b+ RNAi δS305A HCAR1 with Lactate replicate 3


title: BT549 cells, D1C

value: DMSO


title: 2fTGH,interferon alpha,72h,rep2


title: Day 14 rLPC grafted into chick wings for 4 days and dissociated (1st batch)

description:
xenograft1
xenografted rLPCs

value: limb bud

value: limb mesenchymal cells (differentiated)


title: BT549 cells, D1B


title: 2fTGH,interferon alpha,36h,rep3

value: interferon alpha,36h


title: Hela shHCAR1b+ RNAi δS305A HCAR1 with Lactate replicate 1


title: Hela shHCAR1b+ RNAi δS305A HCAR1 with PBS replicate 2


title: Hela shHCAR1 with PBS replicate 5

value: WT - shHCAR1


title: Hela shHCAR1 with PBS replicate 4


title: Stigma, P. pyrifolia, rep1 [SMAA]

city: Jerusalem

first: Yuval

last: Nevo

address: Ein Kerem Campus

country: Israel

institute: The Hebrew University of Jerusalem

description:
processed data columns: A-E, microRNA annotations, including pre-miR name and genomic location; mature miR name, aliases (other mature miRs with the exact same sequence) and sequence; F-K, stigma exudates data, ExAA and ExAS for P. pyrifolia, ExEu for P. communis, ExWG, ExWM and ExWS for P. syriaca; L-Q, stigma tissue data, SMAA and SMAS for P. pyrifolia, SMEu for P. communis, SMWG, SMWM and SMWS for P. syriaca.
SMAA

data_processing:
Trimming raw reads with Cutadapt, v1.1, using a quality threshold of 32, removing adapter and poly-A sequences that were added by the CATS kit, and keeping reads 18 to 28 bases long.
Filtering low quality reads with fastq_quality_filter, FASTX package v0.0.14, using -q 20 and -p 85.
Alignment and counting of microRNAs expression with miRExpress, v2.0, using the ‘Raw_data_parse’, ‘alignmentSIMD’ and ‘analysis’ steps. Reference microRNAs were taken from miRBase, version 22, using all Rosaceae species in the database - Fragaria vesca, fve; Malus domestica, mdm; and Prunus persica, ppe. Alignment allowed up to 7% mismatches and mature microRNA assignment allowed for offset of up to 11 bases and required at least 50% overlap.
Mature microRNAs having the exact same sequence were collapsed to a unique representative, averaging the counts from all its appearances in the dataset.
Identified miRs were further analyzed to find potential targets in the plant A. thaliana, using the web server 'psRNATarget' with default parameters and expectation threshold <=2.5. Enrichment analysis using AgriGO2 was performed on the lists of potential targets in Arabidopsis.
Assembly: miRBase version 22
Supplementary files format and content: raw_counts_all.xlsx: an Excel file with a single header row, followed by a row for each unique mature microRNA in the dataset of Rosaceae miRs from miRBase v22. Columns A-E include miRs annotations; columns F-K include the data for stigma exudates samples; columns L-Q include the data for stigma tissue samples.
Supplementary files format and content: Supporting_dataset_1.docx: details of miRs identified in stigma exudates and tissue, as explained within the file.
Supplementary files format and content: Supporting_dataset_2.xlsx: potential target genes in A. thaliana, as given by 'psRNATarget'. Includes two sheets, one for exudate miRs and one for stigma specific ones.
Supplementary files format and content: Supporting_dataset_3.xlsx: enriched GO terms. Includes two sheets, one for predicted targets of exudate miRs and one for predicted targets of stigma specific miRs.
Supplementary files format and content: Supporting_dataset_4.xlsx: potential target genes of exudate miRs in A. thaliana pollen transcriptome.

organism: Pyrus pyrifolia

source_name: Stigma tissue

extract_protocol:
Stigma lobes were randomly excised from several flowers at 12 hours after anthesis (HAA). Stigma exudates were collected in a nondestructive manner as described earlier (Pusey et al., 2008). RNA was isolated with the cf-RNA isolation  kit, NORGEN BIOTEK, #29600.
Libraries were prepared using CATS Small RNA kit (C05010044), then size selected by 4% agarose gel.

treatment_protocol: Blooming branches were collected at the field during spring 2018 (March-April), immediately placed in water cans and transferred after removing all the open flowers, for overnight acclimation in growth room (day/night cycles of 16 h at 24 °C and 8 h at 18 °C, humidity of 40–60% and white light of 120–130 µmol/m2 sec).

value: Stigma tissue

tag: cultivar

value: Hosui

tag: altitude

tag: sampling time

value: 12 HAA


title: 2fTGH,interferon alpha,36h,rep2


title: Day 14 rLPC grafted into chick wings for 4 days and dissociated (2nd batch)

description:
xenograft2
xenografted rLPCs

value: Prrx1CGE-Ai9 (tdtomato+ cells)


title: Hela shHCAR1 with PBS replicate 3

value: HeLa cells

value: Cervical cancer cells


title: Exudates, P. pyrifolia, rep2 [ExAS]

description:
processed data columns: A-E, microRNA annotations, including pre-miR name and genomic location; mature miR name, aliases (other mature miRs with the exact same sequence) and sequence; F-K, stigma exudates data, ExAA and ExAS for P. pyrifolia, ExEu for P. communis, ExWG, ExWM and ExWS for P. syriaca; L-Q, stigma tissue data, SMAA and SMAS for P. pyrifolia, SMEu for P. communis, SMWG, SMWM and SMWS for P. syriaca.
ExAS

source_name: Stigma exudates

value: Stigma exudates

value: Shinsui


title: 2fTGH,interferon alpha,36h,rep1

value: Human fibrosarcoma


title: Stigma, P. pyrifolia, rep2 [SMAS]

description:
processed data columns: A-E, microRNA annotations, including pre-miR name and genomic location; mature miR name, aliases (other mature miRs with the exact same sequence) and sequence; F-K, stigma exudates data, ExAA and ExAS for P. pyrifolia, ExEu for P. communis, ExWG, ExWM and ExWS for P. syriaca; L-Q, stigma tissue data, SMAA and SMAS for P. pyrifolia, SMEu for P. communis, SMWG, SMWM and SMWS for P. syriaca.
SMAS


title: Exudates, P. pyrifolia, rep1 [ExAA]

description:
processed data columns: A-E, microRNA annotations, including pre-miR name and genomic location; mature miR name, aliases (other mature miRs with the exact same sequence) and sequence; F-K, stigma exudates data, ExAA and ExAS for P. pyrifolia, ExEu for P. communis, ExWG, ExWM and ExWS for P. syriaca; L-Q, stigma tissue data, SMAA and SMAS for P. pyrifolia, SMEu for P. communis, SMWG, SMWM and SMWS for P. syriaca.
ExAA


title: Hela shHCAR1 with PBS replicate 2

value: PBS


title: RNA-seq of cytoplasmic fraction in kdRpb9  replicate2

city: San Diego

first: Yajing

last: Hao

state: CA

address: George Palade Laboratories 9500 Gilman Drive, Room 217

department: Dept. of Cellular and Molecular Medicine

institute: University of California, San Diego

data_processing:
After obtaining raw RNA-Seq data, we first used Trimmomatic to perform sliding window trimming, cutting the average quality once within the 4-bp window falling below 20 and removing the trimmed read if it had a length less than 38. SortMeRNA (Kopylova et al., 2012) was used to filter ribosomal RNAs with default parameters. We mapped the filtered reads to the genome (genome version hg38) using STAR (Dobin et al., 2013) with parameters --outFilterScoreMinOverLread 0.1, --outFilterMatchNminOverLread 0.1, --outFilterMismatchNmax 4 and --outFilterMultimapNmax 8.
After obtaining the mapping files, we removed the duplicate reads using Picard (http://broadinstitute.github.io/picard/) with parameters MarkDuplicates and REMOVE_DUPLICATES = true. We calculated the gene read counts using FeatureCounts (Liao et al., 2014) and converted them to FPKM using the edgeR (Robinson et al., 2010) package in R language. The bigwig files of each RNA-Seq data set from the sense strand and antisense strand were obtained using bamCoverage from DeepTools with a parameter --binSize 1, --ignoreDuplicates, –minMappingQuality 255 and –normalizeUsing CPM.
For the analysis of relative gene abundance and reads signals in different subcellular fractions, we constructed an in-house reference file by combing the genome assembly mm10 with our in-house spike-in sequence (XXX and XXX). The RNA-seq data of each fraction were mapped to the in-house reference and the ratio of reads that mapped to spike-in was also calculated ((reads mapped to spike-in)/(total mappable reads)). The FPKM value of each gene and the bigwig file signals was further normalized by the corresponding ratio of spike-in. We constructed the new Exon and intron annotation files based on the latest ReSeq gene annotation downloaded from UCSC. The SPI value and 3SS ratio were calculated as previously described (Herzel and Neugebauer, 2015).
Genome_build: hg38

source_name: HeLa S3 cell

growth_protocol: Cells were grown in DMEM supplemented with 10% FBS and 1 x penicillin-streptomycin, at 37 °C in a 5% of CO2 incubator. Cells were negative for mycoplasma (tested every three months).

extract_protocol: Each RNA was extracted using Trizol reagent and coupled with Direct-zol RNA Miniprep kit according to the manufacturer’s instructions.

treatment_protocol: The cell fractionation was performed as previously described, with additional modifications. Briefly, 5 x 106 cells were gently trypsinized and collected by centrifugation. the cell pellets were rinsed twice with ice-cold 1 x PBS and then were lysed by ice-cold CE buffer (10 mM HEPES [pH 7.5], 0.1 % NP-40, 1 mM EDTA, 1 mM DTT, 60 mM KCl and 340 mM Sucrose) for 5 min on ice. The supernatant (cytoplasmic fraction) was collected by centrifugation. the nuclei pellets were gently rinsed with ice-cold 1 x PBS/1 mM EDTA then gently resuspended in ice-cold glycerol buffer (20 mM Tris-HCl [pH 7.5], 75 mM NaCl, 0.5 mM EDTA, 0.85 mM DTT and 50% glycerol). Gently mix with equal volume of nuclei lysis buffer (10 mM HEPES [pH 7.5], 1.0% NP-40, 0.2 mM EDTA, 1 mM DTT, 7.5 mM MgCl2, 300 mM NaCl and 1 M urea) and incubated on ice for 3 min, then collect the supernatant (nucleoplasm fraction) by centrifugation. the chromatin pellets were gently rinsed twice with ice-cold 1 x PBS/1 mM EDTA and then dissolved with TRIzol reagents (Invitrogen) for extracting chromatin-associated RNA. The purified chromatin-associated RNA was used for RNA-seq library preparation. RNA-seq libraries were generated using the Illumina TruSeq Stranded Total RNA Library Prep Gold with TruSeq Unique Dual Indexes. Samples were processed following manufacturer’s instructions, except modifying RNA shear time to five minutes. The libraries were multiplexed and sequenced with 100 bp paired end (PE100) to a depth of approximately 30 million reads per library on an Illumina NovaSeq 6000.

tag: fraction

value: cytoplasmic


title: RNA-seq of cytoplasmic fraction in kdRpb9 replicate1


title: RNA-seq of cytoplasmic fraction in kdRpb1  replicate2


title: 2fTGH,interferon alpha,24h,rep1

city: Poznan

last: Bluyssen

address: Uniwersytetu Poznańskiego 6

institute: Adam Mickiewicz University

value: interferon alpha,24h


title: RNA-seq of cytoplasmic fraction in kdRpb1  replicate1


title: BT549 cells, D1A

value: BT549 cancer cell line

value: DMSO


title: Trophozoites, RNAseq_MorcKD_Mel3

city: Sao Paulo

first: Maneesh Kumar

last: Singh

state: SP

address: Av. Prof. Lineu Prestes, 580

country: Brazil

institute: University of Sao Paulo

description:
MS-25-Mel-3
RNAseq of trophozoites stage Plasmodium falciparum PfMORC transgenic knockdown parasite treated with 100nM melatonin for 5 hours

data_processing:
The quality of the RNA-seq libraries was evaluated using the FastQC tool. Next, we used Salmon (V1.9.0) quant with default arguments to quantify the expression of all transcripts in the PlasmoDB release-58 Pfalciparum3D7 genome. The transcript expression was summarized to gene-level expression with tximport 1.22.0. Finally, the gene counts were used to detect differentially expressed genes (DEGs) with DESeq2 (1.34.0). Furthermore, only genes with an >1 log2 fold change and adjusted p value <0.1 were considered significant for further analysis.
Assembly: PlasmoDB release-58 Pfalciparum3D7
Supplementary files format and content: PfMORC_gene_TPM.tsv, sf files

organism: Plasmodium falciparum

source_name: whole organism

growth_protocol: The P. falciparum strains were cultured at 37°C in RPMI 1640 medium supplemented with 0.5% Albumax II (Gibco). Parasites were grown under a 5% CO2, 5% O2, and 90% N2 atmosphere. Cultures were synchronized with 5% sorbitol.

extract_protocol:
Total RNA was extracted following the manufacturer’s protocol, and an RNA cleanup kit (Qiagen) was used to achieve high-purity RNA. The isolated RNA was quantified using a NanoDrop ND-1000 UV/Vis spectrophotometer, and RNA quality was determined using an RNA ScreenTape System (Agilent 2200 TapeStation). Total RNA (10000 ng) from each sample was stabilized in RNAStable (Biomatrica) and sent to the Micromon Genomics facility at Monash University for next-generation sequencing.
RNA samples were prepared using the MGITech RNA Directional Library Prep Kit V2 (Item No. 1000006385), as per the manufacturer's instructions, with the following parameters: input RNA: 50 ng, fragmentation: target of 200 bp-400 bp, 87 °C for 6 mins, adapter clean-up: 200 bp-400 bp and library amplification cycles: 16. Libraries were assessed for quantity using the Invitrogen Qubit and dsDNA HS chemistry (Item No. Q33230) and quality/quality using the Agilent Fragment Analyser 5200 with the HS NGS Fragment Kit (Item No. DNF-473-0500). The libraries were pooled in equimolar concentrations and sequenced using an MGITech DNBSEQ-G400RS sequencing instrument with High-Throughput Sequencing Set (FCL PE100, Item No. 1000016950) chemistry.

treatment_protocol: To induce PfMORC knockdown, tightly synchronized parasites at young trophozoite stage (22hpi) were treated with 2.5 mM glucosamine (GlcN) till next cycle. Parasites at 34hpi were harvested for total RNA extraction and stored in Trizol reagent. For melatonin assay, when majority of parasites reached to 28hpi, 100 nM melatonin was added in culture for 5h and then parasites were harvested and stored in Trizol reagent.

tag: isolate

tag: Stage

value: trophozoites

value: PfMORC-KD

value: 100nM Melatonin

tag: time

value: 5 hours

value: whole organism


title: Trophozoites, RNAseq_MorcKD_Mel2

description:
MS-25-Mel-2
RNAseq of trophozoites stage Plasmodium falciparum PfMORC transgenic knockdown parasite treated with 100nM melatonin for 5 hours


title: 2fTGH,interferon alpha,8h,rep2

first: Hans

value: interferon alpha,8h


title: Hela shHCAR1 with Lactate replicate 5

value: WT - shHCAR1

value: Lactate


title: 2fTGH,interferon alpha,48h,rep1

value: interferon alpha,48h


title: RNA-seq of cytoplasmic fraction in control condition  replicate2

value: control condition


title: Hela shHCAR1 with Lactate replicate 4

value: HeLa cells

value: Cervical cancer cells


title: 2fTGH,interferon alpha,8h,rep1

value: Human fibrosarcoma


title: Trophozoites, RNAseq_MorcKD_Con3

description:
MS-25-Con-3
RNAseq of trophozoites stage Plasmodium falciparum PfMORC transgenic knockdown parasite

value: control


title: Hela shHCAR1 with Lactate replicate 3


title: 2fTGH,interferon alpha,4h,rep2

value: interferon alpha,4h


title: 2fTGH,interferon alpha,24h,rep2

value: interferon alpha,24h


title: RNA-seq of nucleoplasm fraction in kdRpb9 replicate2

value: nucleoplasm


title: Hela shHCAR1 with Lactate replicate 2


title: Hela shHCAR1 with PBS replicate 1

value: PBS


title: Trophozoites, RNAseq_MorcKD_Con2

description:
MS-25-Con-2
RNAseq of trophozoites stage Plasmodium falciparum PfMORC transgenic knockdown parasite

value: trophozoites

value: PfMORC-KD


title: RNA-seq of nucleoplasm fraction in kdRpb9 replicate1


title: 2fTGH,interferon alpha,4h,rep1


title: Trophozoites, RNAseq_MorcKD_Con1

description:
MS-25-Con-1
RNAseq of trophozoites stage Plasmodium falciparum PfMORC transgenic knockdown parasite


title: 2fTGH,interferon alpha,2h,rep2

value: interferon alpha,2h


title: RNA-seq of nucleoplasm fraction in kdRpb1  replicate2


title: Trophozoites, RNAseq_MorcKD_Mel1

description:
MS-25-Mel-1
RNAseq of trophozoites stage Plasmodium falciparum PfMORC transgenic knockdown parasite treated with 100nM melatonin for 5 hours

value: 100nM Melatonin

value: 5 hours

value: whole organism


title: 2fTGH,interferon alpha,1h,rep2

value: interferon alpha,1h


title: RNA-seq of nucleoplasm fraction in control condition  replicate2


title: HeLa, Lactate,Hcar1 C-term flag replicate 1

description:
Sample_C-81_L_A.bw
ChIP_NoLigand_vs_input_peaks.narrowPeak

data_processing:
ChipSeq pipeline from GenPipe V3.01 beta (Bourgey et al., 2019).
module_bwa=mugqic/bwa/0.7.12  module_homer=mugqic/homer/4.9.1  module_java=mugqic/java/openjdk-jdk1.8.0_72  module_macs2=mugqic/MACS2/2.1.1.20160309  module_mugqic_R_packages=mugqic/mugqic_R_packages/1.0.4  module_mugqic_tools=mugqic/mugqic_tools/2.1.9  module_pandoc=mugqic/pandoc/1.15.2  module_perl=mugqic/perl/5.22.1  module_picard=mugqic/picard/2.0.1  module_python=mugqic/python/2.7.13  module_R=mugqic/R_Bioconductor/3.5.0_3.7  module_samtools=mugqic/samtools/1.3.1  module_trimmomatic=mugqic/trimmomatic/0.36  module_weblogo=mugqic/weblogo/3.3  module_deeptools=mugqic/deepTools/2.5.3  #module_sambamba=mugqic/sambamba/0.6.5  module_ucsc=mugqic/ucsc/v346  module_multiqc=mugqic/MultiQC/v1.3dev
Assembly: hg19
Supplementary files format and content: bigWig, narrowPeak (except for Input sample)

extract_protocol:
Chromatin immunoprecipitation (ChIP) was performed using SimpleChIP® Enzymatic Chromatin IP Kit (Cell Signaling) based on manufacturer’s protocol. Briefly, DNA-protein complexes were crosslinked using 1% final concentration of formaldehyde (Sigma) for 10min at RT, and quenched with Glycine (final concentration of 125mM). Cells were then washed with cold PBS + PI cocktail, scraped into conical tubes and centrifuged to remove the supernatant. After isolation, nuclei were treated with micrococcal nuclease to digest the DNA, and then sonicated. Digested chromatin was analyzed by agarose gel. Chromatins were then incubated with immunoprecipitating antibody O/N at 4°C with rotation. Control samples were incubated with IgG antibody. ChIP-grade protein G magnetic beads were added to the IP reactions and incubated for 2h at 4°C with rotation. Beads were then washed with low- to high-salt wash buffers and chromatin was eluted in elution buffer for 30min at 65°C. Chromatins were reverse-crosslinked with NaCl and proteinase K and incubation at 65°C for 2h. DNA was purified with spin columns, and analyzed by qPCR or sent to Next Generation Sequencing.
ChIP-seq. Samples were analyzed with bioanalyzer for quality control and single-end NGS was performed at IRIC genomic platform with Nextseq 500 illumina system.
ChIP-seq. Samples were sequenced with a depth of ~35M per sample with 75 cycles. Both C- and N-terminus flag tagged cells were used for ChIP-seq studies. Two samples from each terminus tagged cells were used for either lactate or vehicle (PBS); in total 4 samples per treatment group, and only shared genes in each group was used for further bioinformatic analysis.

treatment_protocol: A stock concentration of 500 mM lactate (in PBS and pH adjusted to 7.4) was used for cell stimulation and similar volume of PBS as vehicle was used as control.

value: WT

value: Lactate


title: HeLa, Input

value: HeLa cells


title: Trophozoites, RNAseq_MorcWT_Mel2

description:
MS-0-Mel-2
RNAseq of trophozoites stage Plasmodium falciparum PfMORC transgenic wildtype parasite treated with 100nM melatonin for 5 hours


title: 2fTGH,interferon alpha,1h,rep1


title: Trophozoites, RNAseq_MorcWT_Mel3

description:
MS-0-Mel-3
RNAseq of trophozoites stage Plasmodium falciparum PfMORC transgenic wildtype parasite treated with 100nM melatonin for 5 hours