title: Phase I 7C × Phase II 7C, 34 day_rep3

description:
First_E06_N43_T5_7_CCGACC
ControlAcclimation_gene_count_geo.csv


title: 1W-2mm10_asis

status: Public on Nov 06 2024

type: SRA

city: Cambridge

first: Baohong

last: Zhang

state: MA

address: 225 Binney St

country: USA

institute: Biogen Inc.

library_source: transcriptomic single cell

data_processing:
FASTQ files were generated from Illumina bcl files using CellRanger mkfastq. CellRanger count was used to identify UMI and cell barcodes
Assembly: mm10
Supplementary files format and content: h5,  filter UMI and raw UMI

molecule: total RNA

organism: Mus musculus

source_name: Brain

growth_protocol: Age 6-8 weeks-old male mice were used for the cuprizone model study. Research animals were housed under specific-pathogen-free conditions in an AAALAC accredited facility according to an approved institutional animal care and use committee (IACUC) protocol with a 12 hr - 12 hr light - dark cycle and environmental conditions controlled at 21°C and 40–60% humidity.

extract_protocol:
At 4 (CPZ) and 6 weeks (Control and Recovery), mice were euthanized by carbon dioxide (CO2) inhalation, and their brains were subsequently dissected. Each brain was sagittally cut into left and right hemispheres. One hemisphere was then further divided into three coronal segments, which were embedded in OCT for snRNA-seq.
snRNA-seq was performed using the 10X Genomics Chromium Next GEM Single Cell 3' Kit v3.1 (PN1000268), Chromium Next GEM Chip G (PN1000127), and Dual Index Kit TT Set A (PN1000215). Nuclei suspensions were loaded onto the 10X Chromium instrument with the aim of recovering 5000 nuclei per sample.
Libraries were sequenced on an Illumina NovaSeq 6000 S4 flowcell using paired-end sequencing with the following parameters: Read1-28bp, i7-10bp, i5-10bp, Read2-90bp.

treatment_protocol: In the cuprizone (CPZ) group, male mice aged 6-8 weeks were administered a 0.3% Cuprizone diet for 4 weeks to induce demyelination in the brain (n = 3). In the recovery group, mice were administered CPZ diet for 4-weeks and then switched to a control diet for an additional 2 weeks (n = 3). In the control group, mice received the control diet throughout the entire 6-week study period (n = 4).

tag: tissue

value: Brain

tag: genotype

tag: treatment

value: Control


title: Cortex E15.5 C57BL/6 Kat6b Knock Out, rep 1

city: Parkville

first: Alexandra

last: Garnham

state: Victoria

address: 1G Royal Parade

country: Australia

institute: Walter and Eliza Hall Institute of Medical Research

description: Samples were sequenced (NextSeq500, Illumina) to give 66 bp paired end reads.

library_source: transcriptomic

data_processing:
Base calling and quality scoring was performed by Illumina Real-Time Analysis (v2) software. FASTQ file generation and de-multiplexing was performed by bcl2fastq conversion software (v2.15.0.4).
Reads were aligned to the mouse genome by Rsubread version 1.24.1
Read counts were summarized by Entrez Gene ID using the Rsubread's featureCounts function and Rsubread's built-in NCBI annotation.
Assembly: mm10
Supplementary files format and content: tab-delimited text files (tsv). Columns represent Entrez Gene Id, Gene Symbol, total gene length (total base count of all exons) and the number of reads mapping to that gene.

source_name: Cortex

extract_protocol:
Total RNA was collected from cultured NSPCs, E12.5 dorsal telencephalon or E15.5 cortex tissue using a kit (RNeasy mini kit, Qiagen, 74104) according to the manufacturer’s instructions and including the optional DNase I digest step.
500 ng to 1 µg total RNA was used to generate sequencing libraries using a kit (TruSeq RNA prep kit v2, Illumina, RS-122-2002) according to the manufacturer’s instructions.

tag: mouse background

tag: gestation

value: Cortex

tag: mouse litter

tag: embryo number

value: Kat6b KO

tag: replicate

tag: sequencing batch


title: D559 BCR library 1

city: New York

first: Alex

last: George

state: NY

address: 960 Broadway, 2nd Floor, Room 203AC

institute: Columbia University

description:
5' mRNA library: read1 file contains cell barcode and UMI; read2 file contains transcript.
filtered_contig_annotations.BCR.txt.gz

data_processing:
scRNA-seq reads were analyzed by pseudoalignment using kallisto v0.46.2 (GRCh38 with Gencode v24 annotation) and bustools v0.40.0. CITE-seq and hashtag barcodes were demultiplexed and extracted using DropSeqPipeline8 (https://github.com/simslab/DropSeqPipeline8). GEX count matrix was filtered for cell barcodes with >1000 molecules/cell. These cell barcodes were used to filter ADT hashtag/CITE-seq count matrix from DropSeq8. Hashtags were demultiplexed on filtered HTO/ADT count matrix using the HashSolo (https://github.com/calico/solo/blob/master/solo/hashsolo.py) implementation in ScanPy (https://github.com/scverse/scanpy, scanpy.external.pp.hashsolo function) where prior cell frequency arguments for HashSolo function were based on theoretical doublet rate in 5’v2 HT 10x chip based on cell input (e.g. 0.08 doublet rate, 0.01 negative, 0.91 singlet rate, for 20k cell input).
Immune receptor libraries (TCR and BCR) were aligned using Cell Ranger 7.0.1 (vdj function) using reference vdj_GRCh38_alts_ensembl-7.0.0.
A mitochondrial gene filter was applied for any cells above a 95% confidence interval for MT pseudo-alignment rate on a per library basis. A hemoglobin gene filter was applied to all libraries for cells > 0.01 pseudo-alignment rate for HB genes.
MultiModal Classifier Hierarchy (MMOCHI, https://github.com/donnafarberlab/MMoCHi), which is trained using events selected by thresholding of user-defined marker genes and proteins, was implemented to define immune cell subsets across sites. MMOCHI classification legend: (CD4N = Naive CD4 T cell, CD4Treg = CD4 Regulatory T cell, CD4CM = Central Memory CD4 T Cell, CD4EM = Effector Memory CD4 T cell, CD8EM = Effector Memory CD8 T cell, CD8N = Naive CD8 T Cell, CD8CM = Central Memory CD8 T Cells, B_cell_N = Naive B Cells, B_cell_Innate_M = Innate Memory B Cells (IgD+CD27+), B_cell_CD27-IgD- =  CD27-IgD- B cells, Plasma_cluster = Plasma Cells identified by GEX clustering, Myeloid_cluster = Myeloid Cells identified by GEX clustering, NK_Cluster = NK Cells identified by GEX clustering). Memory B cell classifications are subtyped by receptor isotype.
Assembly: GRCh38/Ensembl93
Supplementary files format and content: GEX and ADT libraries: tab-delimited text files with cell-identifying barcodes, hashtags, donor, tissue site, MMOCHI immune cell classification, stimulation condition (w/ applicable sort information), and count matrix
Supplementary files format and content: TCR and BCR libraries: tab-delimited text files with cell-identifying barcodes, immune receptor chain, VDJ genes, cdr3 amino acid sequence, cdr3 nucleotide sequence, raw clonotype id and other alignment statistics/metadata outputted from CellRanger.
Library strategy: CITE-seq (Cellular Indexing of Transcriptomes and Epitopes by sequencing)

molecule: polyA RNA

organism: Homo sapiens

source_name: various

extract_protocol:
Organ donor samples in saline or University of Wisconsin solution were placed on ice, transported to the laboratory, and processed within 2 to 4 hours of procurement. Single cell suspensions were obtained from blood, bone marrow, spleen, lungs, and associated lymph nodes (LN) using mechanical and enzymatic digestion as previously described (Nat Med 22, 72-77. 10.1038/nm.4008). Blood and bone marrow samples were diluted with wash buffer (PBS (Corning, cat #20-030-CV) + 2mM EDTA (Corning, cat #46-034-CI) + 5% FBS (GeminiBio, cat #100-106)), and mononuclear cells were isolated by density centrifugation using Ficoll-Paque PLUS (GE Healthcare, catalog no. 17-1440-03). Lymph nodes were isolated by dissection from the mesentery of the small and large intestine, the tracheobronchial tree of the lung, and inguinal fat. Tissue samples were first mechanically disrupted with scissors. Isolated LNs and lung were then placed into digestion media (IMDM + Collagenase D 1mg/mL (Millipore Sigma cat# 11088882001) and + DNAse 0.1mg/mL (Millipore Sigma cat# DN25-5G)) on a shaker at 37C for 30 minutes followed by addition of 0.5M EDTA (pH 8.0). Digested LNs and lung as well as mechanically disrupted spleen were then pushed through 100m filters and washed with buffers. The samples then underwent density centrifugation as above to isolate live leukocytes. For healthy blood samples, we obtained peripheral blood from a consenting, healthy volunteers by venous puncture. Peripheral blood mononuclear cells (PBMCs) were isolated using Ficoll-Paque PLUS, following manufacturer's protocols for density gradient centrifugation. Single cell mononuclear suspensions isolated from blood and tissue samples prepared as above were plated in 96 well U-bottom plates (1X10^6 cells per well) in 200uL of complete media (RPMI (Corning, catalog no. 10-040-CM), 10% inactivated human AB serum (Gemini, catalog no. 507533010) and penicillin-streptomycin-glutamate (Thermo Fisher Scientific, catalog no. 10378016)) and incubated overnight at 37C in 5% CO2. The next day, the wells were split (5x10^5 cells per well) and topped up with complete media to 200uL. Cells were then blocked for 15 minutes with anti-CD40 monoclonal antibody (0.5g/mL) (Miltenyi Biotec, catalog no. 130-094-133). Subsequently, a SARS-CoV-2 Spike Megapool (S MP) (1g/mL), designed and synthesized as previously described (Cell 181, 1489-1501 e1415. 10.1016/j.cell.2020.05.015), was added to the cell culture for 24 hours. The S MP consists of 253 15-mer peptides overlapping by 10 residues and covering the entire S protein. As controls, additional cells were stimulated with an equimolar amount of DMSO, or a combination of 3 Influenza peptide Mega pools at 1g/mL (CD4 HA, CD4 Other, and CD8), synthesized as previously described (Curr Protoc. 2023 Nov;3(11):e934. doi: 10.1002/cpz1.934.). Following 24-hour stimulation, each tissue and stimulation condition combination for a particular donor was combined, treated with 10uL each of Trustain FcX (BioLegend) and FcR Blocking Reagent (Miltenyi) at 4C for 10 minutes, and then incubated with 2 uL (1 ug) of a unique TotalSeq-C anti-human DNA-barcoded hashtag for 30 minutes at 4C and washed 3 times with FACS buffer) as described. Subsequently all peptide-stimulated samples from a single donor were combined and all DMSO-stimulated samples from a single donor were combined. These samples were stained with BV421 labeled full length Spike protein and a panel of fluorescently labeled antibodies and washed as described above. These samples were sorted using the BD FACSAria III Cell Sorter. Peptide-stimulated samples were sorted for AIM+ CD4 T cells (Live, CD45+, CD19-, CD3+, CD4+, OX40 & 4-1BB++), AIM+ CD8 T cells (Live, CD45+, CD19-, CD3+, CD8+, CD25 & 4-1BB++), and Spike B cells (Live, CD45+, CD19+, CD3-, Spike-BV421+). DMSO-stimulated cells were sorted for AIM-CD4 T cells (Live, CD45+, CD19-, CD3+, CD4+, OX40 & 4-1BB--), AIM-CD8 T cells (Live, CD45+, CD19-, CD3+, CD8+, CD25 & 4-1BB--), and Total B cells (Live, CD45+, CD19+, CD3-, Spike-BV421-). Each sample of sorted cells was counted, and for each donor, a fraction of AIM-CD4 T, AIM-CD8 T, and Total B cells were spiked into the AIM+CD4+T, AIM+CD8+T, and Spike B cell samples to reach ~80K cells for per donor to have adequate cell numbers to manipulate for CITE-seq staining and have sufficient cell numbers after washing for input into 10x microfluidics chip (e.g. spike in cells to achieve 80k cells, yielding ~50k out post-wash for 33.3k cell requirement to achieve 20k cell capture on chip). The samples were then stained with TotalSeq C Human Universal Cocktail V1.0 and washed 3 times with FACS buffer by centrifugation or with a Curiox HT2000 Laminar Wash System (Curiox, 5 uL/sec speed, 27 cycles, 50 uL loading volume). The resultant stained cells (33.3K) were resuspended in 10x genomics recommended loading buffer (1X DPBS w/ 0.04% BSA) for loading into 10x Genomics single sequencing workflows with a target of 20K cell captured per lane on chip. To investigate the role of Tregs in the AIM assay, we performed CD25 depletion on our single cell LLN suspension from D616 prior to the above peptide stimulation and sorting protocols. For depletion, single cell suspensions were pre-incubated with 10uL each of Trustain FcX (BioLegend, catalog no. 422322) and FcR Blocking Reagent (Miltenyi, catalog no. 130-059-901) at 4C for 10 minutes followed by addition of 10uL of biotinylated anti-CD25 for 30 minutes on ice and washed with FACS buffer three times. Washed BioMag Plus Streptavidin Beads (BangsLabs catalog no. BP628) were resuspended in 100uL of FACS buffer and incubated with the single cell suspension at room temperature for 5 minutes. 1.5mL of DPBS was added to the tube and placed on the EasySep magnet (STEMCELL Technologies catalog no. 18000) for 5 minutes. The supernatant was collected and set aside. The remaining beads were combined with DPBS and placed back on the magnet for an additional 5 minutes prior to collecting the supernatant and combining with the supernatant from the first separation. This sample was then plated at 1X10^6 cells per well in 96-well U bottom plates for in vitro peptide stimulations as above. DMSO control, SARS or Flu peptide stimulated, and CD25 depleted SARS or Flu stimulated were FACS sorted with AIM+ gates described above. SARS or Flu peptide stimulated CD4 T cells were also sorted using an altenative AIM+ gating strategy (Live, CD45+, CD19-, CD3+, CD4+, OX40 & CD40LG) while maintaining original CD8 gating strategy. Stimulated and sorted single cell-suspensions were loaded onto a 5v2 high throughput (HT) Chromium Next GEM Single Cell Chip N (10x Genomics) for co-encapsulation with barcoded GelBeads with a target capture of 20-30k cells per sample.
Organ donor samples: Captured mRNA was reverse transcribed to cDNA, amplified, and converted to libraries using the Chromium Next GEM Single Cell 5 HT Reagent kit v2 (10X genomics) protocol and recommended reagents with a 5 Feature Barcode kit (10x genomics) for antibody-derived tag amplification, a Chromium Single Cell Human TCR Amplification kit (10x Genomics) for targeted TCR amplification, and a Chromium Single Cell Human BCR Amplification kit (10x Genomics) for targeted BCR amplification. The scRNA-seq gene expression (GEX) libraries, antibody derived tag (ADT) CITE-seq/hashtag libraries, scTCR-seq and, scBCR-seq libraries were sequenced on S4 flow cells (ADT, GEX libraries pooled together and TCR/BCR libraries pooled on independent flow cell lanes) with an Illumina NovaSeq 6000 (~2.5 billion, 2 x 100-bp, reads per lane). The scTCR-seq and sc-BCRseq libraries for D561 and D574 were sequenced with a 150-cycle high-output kit on an Illumina NextSeq 550 (read 1: 26 bp; read 2: 114 bp; index read 1: 10 bp; index read 2: 10 bp). Hashtag IDs for D534,D559,D561,D564,D568,D574: (HTO1: Donor blood AIM+ SARS, HTO2: Donor blood AIM+ Flu, HTO3: Donor blood AIM- DMSO control, HTO4: Donor bone marrow AIM+ SARS, HTO5: Donor bone marrow AIM+ Flu, HTO6: Donor bone marrow AIM- DMSO control, HTO7: Donor spleen AIM+ SARS, HTO8: Donor spleen AIM+ Flu, HTO9: Donor spleen AIM- DMSO control, HTO10: Donor lung AIM+ SARS, HTO12: Donor lung AIM+ Flu, HTO13: Donor lung AIM- DMSO control, HTO14: Donor lung lymph node AIM+ SARS, HTO15: Donor lung lymph node AIM+ Flu, HTO16: Donor lung lymph node AIM- DMSO control). For D561D564 library, only LNG sample is from D564, all other tissues are from D561. (BLD = blood, BM = bone marrow, SPL = spleen, LNG = lung, LLN = lung lymph node, CITE-seq = cellular indexing of transcriptomes and epitopes).
Healthy blood samples: Captured mRNA was reverse transcribed to cDNA, amplified, and converted to libraries using the Chromium Next GEM Single Cell 5 HT Reagent kit v2 (10X genomics) protocol and recommended reagents with a 5 Feature Barcode kit (10x genomics) for antibody-derived tag amplification, a Chromium Single Cell Human TCR Amplification kit (10x Genomics) for targeted TCR amplification, and a Chromium Single Cell Human BCR Amplification kit (10x Genomics) for targeted BCR amplification. The scRNA-seq gene expression (GEX) libraries, antibody derived tag (ADT) CITE-seq/hashtag libraries, scTCR-seq and, scBCR-seq libraries were sequenced on S4 flow cells (ADT, GEX libraries pooled together and TCR/BCR libraries pooled on independent flow cell lanes) with an Illumina NovaSeq 6000 (~2.5 billion, 2 x 100-bp, reads per lane).  Hashtag IDs for healthy blood donors FLD032,FLD040,FLD015,FLD041,FLD029,FLD030: (HTO1: Donor 1 blood AIM+ SARS, HTO2: Donor 1 blood AIM+ Flu, HTO3: Donor 1 blood AIM- DMSO control, HTO4: Donor 2 blood AIM+ SARS, HTO5: Donor 2 blood AIM+ Flu, HTO6: Donor 2 blood AIM- DMSO control, HTO7: Donor 3 blood AIM+ SARS, HTO2: Donor 3 blood AIM+ Flu, HTO3: Donor 3 blood AIM- DMSO control). Donors 1-3 in hashtag IDs correspond to FLD-prefixed donors in corresponding order in library ID. (BLD = blood, BM = bone marrow, SPL = spleen, LNG = lung, LLN = lung lymph node, CITE-seq = cellular indexing of transcriptomes and epitopes).
Donor 616: Captured mRNA was reverse transcribed to cDNA, amplified, and converted to libraries using the Chromium Next GEM Single Cell 5 HT Reagent kit v2 (10X genomics) protocol and recommended reagents with a 5 Feature Barcode kit (10x genomics) for antibody-derived tag amplification. The scRNA-seq gene expression (GEX) libraries and antibody derived tag (ADT) CITE-seq/hashtag libraries libraries were sequenced on S4 flow cells (ADT, GEX libraries pooled together on independent flow cell lanes) with an Illumina NovaSeq 6000 (~2.5 billion, 2 x 100-bp, reads per lane). Hashtag IDs for D616: (HTOs 1,3,4,5,6,7: Donor 616 LLN AIM- DMSO control, HTO8: Donor 616 LLN AIM+ Flu peptide stimulation, HTO9: Donor 616 LLN AIM+ SARS peptide stimulation, HTO13: Donor 616 LLN CD25 depletion AIM+ Flu peptide stimulation, HTO14: Donor 616 LLN CD25 depletion AIM+ SARS peptide stimulation, HTO10: Donor 616 LLN CD40LG+/OX40+ alternate CD4 AIM+ gate Flu peptide stimulation, HTO12: Donor 616 LLN CD40LG+/OX40+ alternate CD4 AIM+ gate SARS peptide stimulation).  (BLD = blood, BM = bone marrow, SPL = spleen, LNG = lung, LLN = lung lymph node, CITE-seq = cellular indexing of transcriptomes and epitopes).

value: various

tag: cell type

value: mononuclear cells (MNCs)

tag: library type

value: mRNA


title: Phase I 7C × Phase II 7C, 20 day_rep1

city: Geneva

first: Hongrui

last: Wang

address: 630 W. North Street

department: School of Integrative Plant Science, Horticulture section

institute: Cornell University

description:
First_E05_N35_T3_7_CGCCTG
ControlAcclimation_gene_count_geo.csv

data_processing:
FastQC for quality control
BBDuk for removing adaptors and poly-A following the pipeline suggested by the manufacturer (https://www.lexogen.com/quantseq-data-analysis/)
STAR for gene level quantification using ‘-quantMode GeneCounts’
Low count gene filterig based on 'total gene count greater than sample number'
DESeq2 for variance stabilization transformation and gene expression normalization
WGCNA for gene co-expression analysis, noise gene filtering, module eigengene visualization and contrast generation
GSEA for pathway enrichment analysis
Assembly: Vitis vinifera 12X.v2 genome with VCost.v3 annotation
Supplementary files format and content: One matrix table with raw gene counts for every gene and every sample without any filtering

organism: Vitis vinifera

source_name: bud

extract_protocol:
Total RNA was extracted using SpectrumTM Plant Total RNA Kit (Sigma Aldrich, St Louis, MO, USA) following the protocol suggested by the manufacturer
Libraries were constructed with Lexogen QuantSeq 3’mRNA-Seq Prep Kit (Lexogen, Greenland, NH, USA) following standard practices as a service provided by Cornell University Institute of Genomic Diversity (Ithaca, NY, USA). Sequencing of the libraries was accomplished using NextSeq500 (Illumina, Inc., San Diego, CA, USA) with 95 samples per lane at Cornell University Institute of Biotechnology (Ithaca, NY, USA). The read length was 85 bp.

value: bud

tag: cultivar

value: Cabernet Sauvignon

tag: time in_treatment_(day)

tag: phase

value: Phase I

tag: phase i_treatment_(°c)

tag: phase ii_treatment_(°c)

tag: replication


title: 7G-1mm10_asis

tag: tissue


title: Phase I 22C × Phase II 22C, 20 day_rep2

description:
First_E12_N90_T3_22_ATGGCG
ControlAcclimation_gene_count_geo.csv


title: D559 GEX library 1

description:
5' mRNA library: read1 file contains cell barcode and UMI; read2 file contains transcript.
D559.GEX.matrix.txt.gz


title: 7H-1mm10_asis

tag: genotype


title: 7W-1mm10_asis

tag: treatment


title: D559 GEX library 2


title: Dorsal telencephalon E12.5 FVBxBALB/c Wild Type, rep 1

source_name: Dorsal telencephalon

tag: mouse background

value: FVBxBALB/c

value: Dorsal telencephalon

value: WT


title: 7G-2mm10_asis


title: Cortex E15.5 C57BL/6 Wild Type, rep 4

tag: gestation


title: D559 ADT library 2

description:
Antibody-derived oligonucleotide and Cell Hashing library: read1 file contains cell barcode and UMI; read2 file contains Antibody/Hashtag Derived Tag reads. Antibodies/tags: TotalSeq-C Human Universal Cocktail,TotalSeq-C0251,TotalSeq-C0252,TotalSeq-C0253,TotalSeq-C0254,TotalSeq-C0255,TotalSeq-C0256,TotalSeq-C0257,TotalSeq-C0258,TotalSeq-C0259,TotalSeq-C0260,TotalSeq-C0262,TotalSeq-C0263,TotalSeq-C0264,TotalSeq-C0265,TotalSeq-C0276.
D559.ADT.matrix.txt.gz

library_source: other

molecule: protein

value: ADT/HTO

tag: adt/hto

value: Antibodies/tags:TotalSeq-C Human Universal Cocktail v1.0,TotalSeq-C0251 anti-human HTO1,TotalSeq-C0252 anti-human HTO2,TotalSeq-C0253 anti-human HTO3,TotalSeq-C0254 anti-human HTO4,TotalSeq-C0255 anti-human HTO5,TotalSeq-C0256 anti-human HTO6,TotalSeq-C0257 anti-human HTO7,TotalSeq-C0258 anti-human HTO8,TotalSeq-C0259 anti-human HTO9,TotalSeq-C0260 anti-human HTO10,TotalSeq-C0262 anti-human HTO12,TotalSeq-C0263 anti-human HTO13,TotalSeq-C0264 anti-human HTO14,TotalSeq-C0265 anti-human HTO15,TotalSeq-C0276 anti-human HTO16. Hashtag IDs for D534,D559,D561,D564,D568,D574:(HTO1:Donor blood AIM+ SARS, HTO2:Donor blood AIM+ Flu, HTO3:Donor blood AIM- DMSO control, HTO4:Donor bone marrow AIM+ SARS, HTO5:Donor bone marrow AIM+ Flu, HTO6:Donor bone marrow AIM- DMSO control, HTO7:Donor spleen AIM+ SARS, HTO8:Donor spleen AIM+ Flu, HTO9:Donor spleen AIM- DMSO control, HTO10:Donor lung AIM+ SARS, HTO12:Donor lung AIM+ Flu, HTO13:Donor lung AIM- DMSO control, HTO14:Donor lung lymph node AIM+ SARS, HTO15:Donor lung lymph node AIM+ Flu, HTO16:Donor lung lymph node AIM- DMSO control). For D561D564 library, only LNG sample is from D564, all other tissues are from D561. (BLD = blood, BM = bone marrow, SPL = spleen, LNG = lung, LLN = lung lymph node, CITE-seq = cellular indexing of transcriptomes and epitopes).


title: D559 ADT library 1


title: Cortex E15.5 C57BL/6 Wild Type, rep 1

tag: mouse litter

tag: embryo number


title: 4W-2mm10_asis


title: D559 BCR library 2


title: Phase I 2C × Phase II 2C, 7 day_rep2

description:
First_E01_N3_T1_2_AGGCAT
ControlAcclimation_gene_count_geo.csv


title: Phase I 11C × Phase II 11C, 41 day_rep3

description:
First_D10_N73_T6_11_ACGTCT
ControlAcclimation_gene_count_geo.csv

value: Phase II


title: Phase I 2C × Phase II 2C, 26 day_rep1

description:
First_E02_N11_T4_2_ACCTAC
ControlAcclimation_gene_count_geo.csv


title: Cortex E15.5 C57BL/6 Wild Type, rep 3

tag: replicate

tag: sequencing batch


title: Phase I 22C × Phase II 22C, 20 day_rep1

description:
First_D12_N89_T3_22_GACATC
ControlAcclimation_gene_count_geo.csv


title: D534 TCR library 2

description:
5' mRNA library: read1 file contains cell barcode and UMI; read2 file contains transcript.
filtered_contig_annotations.TCR.txt.gz

tag: cell type

tag: library type


title: Phase I 2C × Phase II 2C, 41 day_rep3

description:
First_E03_N19b_T6_2_TGGATT
ControlAcclimation_gene_count_geo.csv

tag: cultivar

tag: time in_treatment_(day)


title: Cortex E15.5 C57BL/6 Wild Type, rep 5


title: 4G-2mm10_asis


title: Cortex E15.5 C57BL/6 Wild Type, rep 2


title: D534 TCR library 1


title: Dorsal telencephalon E12.5 C57BL/6 Kat6b Knock Out, rep 4


title: 4W-1mm10_asis


title: 4G-1mm10_asis


title: D534 BCR library 2


title: Phase I 11C × Phase II 11C, 7 day_rep3

description:
First_D08_N58_T1_11_CTCCAT
ControlAcclimation_gene_count_geo.csv

tag: phase

tag: phase i_treatment_(°c)


title: Phase I 11C × Phase II 11C, 26 day_rep2

description:
First_D09_N66_T4_11_GTCAGG
ControlAcclimation_gene_count_geo.csv

tag: phase ii_treatment_(°c)

tag: replication


title: D534 BCR library 1

tag: tissue


title: EAE_CD3, HTO-derived cDNA

city: Suita

first: Daisuke

last: Motooka

state: Osaka

address: 3-1, Yamadaoka

country: Japan

institute: NGS core facility, Research Institute for Microbial Diseases, Osaka University

description:
Hashtag oligonucleotide (HTO)
EAE_CD3_5DE_genematrix.csv
features.tsv.gz

data_processing:
Sequencing was performed on NovaSeq 6000 platform in a 28+91 base paired-end mode.
Illumina RTA3 v3.4.4 software was used for base calling.
Generated reads were input into the cellranger pipeline (Cell Ranger v.5.0.0, 10x Genomics) for UMI counting for each gene (or tag sequence)-cell (barcode) combination.
Assembly: refdata-gex-mm10-2020-A
Supplementary files format and content: EAE_CD3_5DE_genematrix.csv: comma-delimited text file including UMI counts for all cells detected
Supplementary files format and content: features.tsv.gz: gzipped tab-delimited text file consisted of features (gene and tag) information

source_name: spleen, brain

extract_protocol:
Sinlge cell droplets were generated by 10x Genomics Chromium Controller, and cDNAs with UMIs were generated at single-cell level.
The single cell libraries were prepared following the protocol outlined in the Chromium Next GEM Single Cell 5' Reagent Kits v2 User Guide.

value: spleen, brain

tag: strain

tag: treatment

value: EAE


title: 4H-1mm10_asis

value: Brain

tag: genotype

value: Control


title: Dorsal telencephalon E12.5 C57BL/6 Wild Type, rep 4

tag: mouse background

tag: gestation


title: Dorsal telencephalon E12.5 C57BL/6 Kat6b Knock Out, rep 1

tag: mouse litter

tag: embryo number

value: Kat6b KO


title: Phase I 7C × Phase II 7C, 34 day_rep2

description:
First_D06_N42_T5_7_TCTTAA
ControlAcclimation_gene_count_geo.csv


title: D534 GEX library 2

description:
5' mRNA library: read1 file contains cell barcode and UMI; read2 file contains transcript.
D534.GEX.matrix.txt.gz

value: various


title: Dorsal telencephalon E12.5 C57BL/6 Wild Type, rep 3

description: Samples were sequenced (NextSeq500, Illumina) to give 66 bp paired end reads.

tag: replicate

tag: sequencing batch


title: D534 GEX library 1

tag: cell type

value: mononuclear cells (MNCs)

tag: library type


title: Phase I 7C × Phase II 7C, 13 day_rep3

description:
First_D05_N34_T2_7_TGCTAT
ControlAcclimation_gene_count_geo.csv

tag: cultivar

tag: time in_treatment_(day)


title: Dorsal telencephalon E12.5 C57BL/6 Wild Type, rep 1


title: EAE_CD4IFNGKO_CD3, HTO-derived cDNA

description:
Hashtag oligonucleotide (HTO)
EAE_CD4IFNGKO_CD3_5DE_genematrix.csv
features.tsv.gz

data_processing:
Sequencing was performed on NovaSeq 6000 platform in a 28+91 base paired-end mode.
Illumina RTA3 v3.4.4 software was used for base calling.
Generated reads were input into the cellranger pipeline (Cell Ranger v.5.0.0, 10x Genomics) for UMI counting for each gene (or tag sequence)-cell (barcode) combination.
Assembly: refdata-gex-mm10-2020-A
Supplementary files format and content: EAE_CD4IFNGKO_CD3_5DE_genematrix.csv: comma-delimited text file including UMI counts for all cells detected
Supplementary files format and content: features.tsv.gz: gzipped tab-delimited text file consisted of features (gene and tag) information

source_name: brain

value: brain

value: Ifng fl/fl, CD4-Cre/ Ifng fl/fl


title: Phase I 2C × Phase II 2C, 41 day_rep2

description:
First_D03_N18_T6_2_CACACT
ControlAcclimation_gene_count_geo.csv

value: bud

value: Cabernet Sauvignon

tag: phase

tag: phase i_treatment_(°c)


title: D534 ADT library 2

description:
Antibody-derived oligonucleotide and Cell Hashing library: read1 file contains cell barcode and UMI; read2 file contains Antibody/Hashtag Derived Tag reads. Antibodies/tags: TotalSeq-C Human Universal Cocktail,TotalSeq-C0251,TotalSeq-C0252,TotalSeq-C0253,TotalSeq-C0254,TotalSeq-C0255,TotalSeq-C0256,TotalSeq-C0257,TotalSeq-C0258,TotalSeq-C0259,TotalSeq-C0260,TotalSeq-C0262,TotalSeq-C0263,TotalSeq-C0264,TotalSeq-C0265,TotalSeq-C0276.
D534.ADT.matrix.txt.gz

tag: adt/hto


title: D534 ADT library 1

tag: tissue


title: Fvb/BalbC Kat6b Knock Out, rep 6

source_name: Neural stem cell

growth_protocol: Neural stem and progenitor cells (NSPCs) were derived from E12.5 dorsal telencephalon and cultured as free-floating neurosphere colonies as described (Rietze et al. 2001) in neurosphere medium [DMEM/F12 (Gibco, 12500-062), 5 mM HEPES (Sigma, H-4034), 13.4 mM NaHCO3 (Sigma, G-7021), 100 U/ml penicillin-streptomycin (Gibco, 15140-122), 25 g/ml Insulin (Sigma, I-6634), 60 M putrescine dihydrochloride (Sigma, P-5780), 100 g/ml apo-transferrin (Sigma, T-2252), 30 nM selenium sodium salt (Sigma S-9133), 20 nM progesterone (Sigma, P-6149), 0.2% BSA (Sigma, A-3311), 20 ng/ml EGF (Neurocult, 78006.1) and 10 ng/ml FGF (Neurocult, 78003)] at 37oC and 5% CO2. Neurospheres were dissociated using Accutase (Gibco, A1110501) in a 37oC water bath for 4 min, counted using an automated cell counter (Countess, ThermoFisher) and replated at 10,000 cells/cm2.

treatment_protocol: Cells were grown under proliferation conditions in neurosphere medium [DMEM/F12 (Gibco, 12500-062), 5 mM HEPES (Sigma, H-4034), 13.4 mM NaHCO3 (Sigma, G-7021), 100 U/ml penicillin-streptomycin (Gibco, 15140-122), 25 g/ml Insulin (Sigma, I-6634), 60 M putrescine dihydrochloride (Sigma, P-5780), 100 g/ml apo-transferrin (Sigma, T-2252), 30 nM selenium sodium salt (Sigma S-9133), 20 nM progesterone (Sigma, P-6149), 0.2% BSA (Sigma, A-3311), 20 ng/ml EGF (Neurocult, 78006.1) and 10 ng/ml FGF (Neurocult, 78003)] at 37oC and 5% CO2.

value: Neural stem cell

value: FvB/BalbC

value: Kat6b Tg


title: Phase I 2C × Phase II 2C, 20 day_rep3

description:
First_D02_N10_T3_2_GACGAT
ControlAcclimation_gene_count_geo.csv

value: Phase I

tag: phase ii_treatment_(°c)

tag: replication


title: Fvb/BalbC Kat6b Knock Out, rep 4

tag: genotype


title: Control si BMDM-2

city: Shanghai

first: Xingguang

last: Liu

address: Xiangyin road 800

department: National Key Laboratory of Immunity & Inflammation

country: China

institute: Naval medical university

data_processing:
For each sample, RNA-seq clean reads were obtained that mapped to Genome mm10 using HISAT2 (hierarchical indexing for spliced alignment of transcripts) v2.0.477. Sequencing read counts were calculated using Stringtie (v.1.3.0). Then expression levels from different samples were normalized by the Trimmed Mean of M values (TMM) method. The normalized expression levels of different samples were converted to FPKM (Fragments Per Kilobase of transcript per Million mapped fragments).
The edgeR package of R was used to analyze the difference between intergroup gene expression, the P-values were calculated, and the multiple hypothesis test was performed. The P-value threshold was determined by controlling the FDR (False Discovery Rate) with the Benjamini algorithm. The corrected P-value is called the q-value. Differentially expressed genes (DEGs) were defined as transcripts with a fold change in expression level (according to the FPKM value) greater than 2.0 and a q-value less than 0.05.
GO enrichment analysis was performed with the clusterProfiler package of R and the enrichment criteria including a q-value < 0.05. Heatmaps of specific genes were generated using the pheatmap package of R. PCA analysis was visualized using the scatterplot3d package of R.
Assembly: mm10
Supplementary files format and content: excel file inclues raw counts and PFKM value for every sample

source_name: bone marrow

extract_protocol:
Total RNA was isolated using RNeasy mini kit (Qiagen, Germany). Strand-specific libraries were prepared using the TruSeq Stranded Total RNA Sample Preparation kit (Illumina, USA) following the manufacturer’s instructions.
Library construction was perfromed following the steps of mRNA isolation, fragmentation, first strand cDNA synthesis, second strand cDNA synthesis, end repair, adding A at the 3 'end, connecting connectors, enrichment, using VAHTS Universal V6 RNA-seq Library Prep Kit for Illumina® (Vazyme), AHTS® mRNA Capure Beads (Human/Mouse/Rat) (Vazyme), VAHTS DNA Clean Beads (Vazyme), Qubit™ dsDNA HS Assay Kit (Invitrogen) and Agilent High Sensitivity DNA Kit (Aligent).

value: bone marrow

value: Mouse primary bone marrow-derived macrophages

tag: strain

tag: treatment

value: Control siRNA transfection and LPS treatment


title: CC_input

first: zhennan

last: zhao

address: Fenyang Road 83

institute: Fudan university EENT

data_processing:
Adaptor-trimming and low quality reads removing by cutadapt software (v1.9.3)
For lncRNA:The high quality reads were aligned to the human reference genome (UCSC hg19) with hisat2 software (v2.0.4).
cuffdiff software (v2.2.1, part of cufflinks) was used to get the FPKM as the expression profiles of LncRNA, and fold change and p-value were calculated based on FPKM, differentially expressed LncRNA were identified.
Assembly: hg19
Supplementary files format and content: excel format with RNA expression

source_name: anterior lens capsule

extract_protocol:
RNA was extracted using trizol reagent
RNA libraries were constructed by using NEBNext® Ultra™ II Directional RNA Library Prep Kit (New England Biolabs, Inc., Massachusetts,USA)

value: anterior lens capsule

tag: disease state

value: sporadic congenital cataract (CC)

tag: rip antibody

value: none (input)


title: Control si BMDM-1


title: ARC-2_input

value: age-related cataract(ARC)


title: Fvb/BalbC Kat6b Knock Out, rep 5

tag: mouse background

tag: mouse litter

tag: embryo number


title: Phase I 2C × Phase II 2C, 7 day_rep1

description:
First_D01_N2_T1_2_AGTTGA
ControlAcclimation_gene_count_geo.csv


title: Phase I 7C × Phase II 7C, 69 day_rep1

description:
First_D07_N50_T8_7_CCGCAA
ControlAcclimation_gene_count_geo.csv

value: Phase II


title: Acly-E14si BMDM-2

tag: cell type

value: Acly-E14 siRNA transfection and LPS treatment


title: Phase I 22C × Phase II 22C, 13 day_rep3

description:
First_C12_N88_T2_22_ATGAAC
ControlAcclimation_gene_count_geo.csv

tag: cultivar


title: Fvb/BalbC Kat6b Knock Out, rep 3


title: Dorsal telencephalon E12.5 C57BL/6 Kat6b Knock Out, rep 3

tag: gestation

value: Dorsal telencephalon

value: Kat6b KO

tag: replicate

tag: sequencing batch


title: ARC-1_input


title: Phase I 11C × Phase II 11C, 41 day_rep2

description:
First_C10_N72_T6_11_ACCGTG
ControlAcclimation_gene_count_geo.csv

value: bud

tag: time in_treatment_(day)

tag: phase

tag: phase i_treatment_(°c)


title: Acly-E14si BMDM-1

tag: tissue


title: Fvb/BalbC Kat6b Knock Out, rep 2

tag: genotype


title: EAE_CD3, mRNA-derived cDNA

description:
poly A RNA
EAE_CD3_5DE_genematrix.csv
features.tsv.gz

value: spleen, brain

tag: strain

value: EAE


title: CC_IP


title: EAE_CD4IFNGKO_CD3, mRNA-derived cDNA

description:
poly A RNA
EAE_CD4IFNGKO_CD3_5DE_genematrix.csv
features.tsv.gz

value: brain

value: Ifng fl/fl, CD4-Cre/ Ifng fl/fl

tag: treatment


title: Phase I 11C × Phase II 11C, 26 day_rep1

description:
First_C09_N65_T4_11_TGTGCA
ControlAcclimation_gene_count_geo.csv

value: Cabernet Sauvignon

value: Phase I

tag: phase ii_treatment_(°c)

tag: replication


title: Phase I 11C × Phase II 11C, 7 day_rep2

description:
First_C08_N57b_T1_11_CGTCGC
ControlAcclimation_gene_count_geo.csv


title: ARC-1_IP

tag: disease state

tag: rip antibody


title: BMDM-RIP-Input

data_processing:
Because the interrupted fragment of RIP-seq is usually small, some sequenced reads contain junction sequences. After pruning, the joint sequence was removed. If the length of the remaining reads after pruning was long enough, it could still be used for subsequent analysis. The original reads were pruned to produce clean reads for subsequent analysis.
BWA (Burrows Wheeler Aligner) was used to aligned clean reads to reference genomes mm10. MACS2 software (threshold: qvalue=0.05) was used for peak calling analysis, and the number, width and distribution of peaks were statistically analyzed, and peak related genes were screened out.
The enrichment factor can also be called signal Value, which represents the digital display of the peak signal in the process of calling peak. The larger the value, the more reads enriched to the peak. The concentration ratio of peaks is used as an index to calculate the number of peaks. HOMER software was used for identification of the motifs on RNAs in protein-binding peaks.
Assembly: mm10
Supplementary files format and content: bw file that includes RNA information

source_name: BMDM

extract_protocol:
RIP-seq was performed using Magna RIP™ RNA-Binding Protein Immunoprecipitation Kit (Millipore), according to the product instructions. Briefly, 1x10^7 macrophages were harvested and re-suspended in RIP Lysis Buffer. Rbm25-binding RNA was immunoprecipitated by antibody against Rbm25 (Bethyl) and then purified for use.
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, NEBNext Adaptor with hairpin loop structure were ligated to prepare for hybridization. In order to select cDNA fragments of preferentially 150~200 bp in length, the library fragments were purified with AMPure XP system (Beckman Coulter, Beverly, USA). Then 3 µl USER Enzyme (NEB, USA) was used with size-selected, adaptor-ligated cDNA at 37°C for 15 min followed by 5 min at 95 °C before PCR. 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.

tag: cell line

value: Mouse primary bone marrow-derived macrophages

value: RIP lysate


title: Fvb/BalbC Kat6b Knock Out, rep 1

tag: cell type

value: Neural stem cell

tag: mouse background

value: FvB/BalbC

tag: mouse litter

tag: embryo number

value: Kat6b Tg


title: ARC-2_IP

value: anterior lens capsule

value: age-related cataract(ARC)


title: WT BMDM-LPS 8h

value: bone marrow

value: BMDM

value: WT

value: LPS(100ng/ml) for 8h


title: Fvb/BalbC Wild type, rep 1


title: Rbm25-deficient BMDM-LPS 8h


title: Phase I 7C × Phase II 7C, 34 day_rep1

description:
First_C06_N41_T5_7_CCAATT
ControlAcclimation_gene_count_geo.csv

value: bud

tag: cultivar

value: Phase II


title: C57Bl/6 Kat6b Knock Out, rep 4

value: Kat6b KO


title: WT BMDM-LPS 2h

value: LPS(100ng/ml) for 2h


title: LEO1 KO TT-seq rep2

first: Aiwei

last: Wu

state: Shanghai

address: 800 Dongchuan Road

department: School of Life Sciences and Biotechnology

institute: Shanghai Jiao Tong University

data_processing:
Raw reads were trimmed for adaptor sequence and low-complexity or low-quality sequence were filtered using fastp v0.13.1 with default parameters. Reads were aligned using STAR v2.7.9a.
To create scaled, strand-specific BigWig files for TT-seq data, SAMtools was used to split each target BAM file into mappable reads to either plus or minus strand, and bamCoverage function of deepTools was used to convert each strand-specific BAM file to a scaled BigWig file.
Genome_build: Hg38 and sacCer3 for human TT-seq read mapping. Mm10 and sacCer3 for mouser TT-seq read mapping.
Supplementary_files_format_and_content: Normalized read count (in 50-bp bins) for human TT-seq data. For mouse TT-seq, they were also scaled by scale factors calculated from spike-in gene count matrix.

source_name: K562 cell line

growth_protocol: Human cells K562 were cultured in 90% DMEM + 10% FBS+ 2% Penicillin/Streptomycin + 2 mM L-Glutamine.

extract_protocol:
Total RNA was extracted using TRNzol according to the manufacturer’s instructions; 1 μg 4-thiouracil (4TU) labeled S. cerevisiae BY4741 RNA was added to 100 μg total human RNA as spike-in; After fragmentation, biotinylation of 4sU-labeled RNA, purification of biotinylated RNA with Dynabeads M-280 streptavidin and rRNA depletion.
Strand-specific RNA-seq libraries were constructed as previously described (Zhong et al., 2011).
TT-seq

treatment_protocol: 35 million cells were used for each experiment; cells were transferred to fresh antibiotics-free medium and cultured for 1 hour before 4-thiouridine (4sU) treatment.

value: LEO1 knockout


title: Phase I 2C × Phase II 2C, 69 day_rep3

description:
First_C04_N25_T8_2_GTTACC
ControlAcclimation_gene_count_geo.csv

value: Cabernet Sauvignon

tag: time in_treatment_(day)


title: C57Bl/6 Kat6b Knock Out, rep 3


title: Rbm25-deficient BMDM-LPS 2h

value: Mouse primary bone marrow-derived macrophages


title: Phase I 7C × Phase II 7C, 55 day_rep3

description:
First_C07_N49_T7_7_TTCGAG
ControlAcclimation_gene_count_geo.csv

tag: phase


title: LEO1 KO TT-seq rep1


title: control for PAF1 data TT-seq rep2

value: control


title: C57Bl/6 Kat6b Knock Out, rep 2

description: Samples were sequenced (NextSeq500, Illumina) to give 66 bp paired end reads.

value: Neural stem cell


title: Fvb/BalbC Wild type, rep 2

value: FvB/BalbC


title: BMDM-RIP-Rbm25

value: RIP lysate anti-Rbm25


title: Rbm25-deficient BMDM-LPS 0h

value: LPS(100ng/ml) for 0h


title: C57Bl/6 Wild Type, rep 4


title: Phase I 2C × Phase II 2C, 20 day_rep2

description:
First_C02_N9b_T3_2_GCGCTG
ControlAcclimation_gene_count_geo.csv

value: Phase I

tag: phase i_treatment_(°c)


title: Pre-treatment_rep3

description:
First_C01_N1c_T0__ACAACG
ControlAcclimation_gene_count_geo.csv

tag: tissue

value: Pre-experiment


title: LEO1 KO RNA-seq rep3

description: K562.Ctrl_and_LEO1_KO.fragment_count_table.txt

data_processing:
Raw reads were trimmed for adaptor sequence and low-complexity or low-quality sequence were filtered using fastp v0.13.1 with default parameters. RNA-seq read were aligned using hisat2 v2.1.0 with parameter --rna-strandness RF.
Read/fragment count were obtained using featureCounts v1.6.1.
Genome_build: Hg38 for RNA-seq in human cells and mm10 for RNA-seq in mouse.
Supplementary_files_format_and_content: Tab-delimited text files include read/fragment count values of genes for each sample.

extract_protocol:
RNA was extracted from cells using RNeasy Plus Mini Kit (Qiagen, cat. no. 74134) and Quick-RNA MiniPrep Kit (Zymo Research, cat. no. R1054)
the Illumina TruSeq RNA Library preparation protocol: PolyA RNA is captured by oligodT beads and fragmented when eluted from the beads. The first-strand cDNA was synthesized by reverse transcriptase using dNTP, whereas the second-strand cDNA was generated using a dUTP mix . After end-repair, dA-tailing and adapter ligation, the dUTP-containing second strand is digested by uracil DNA glycosylase, rendering it unamplifiable in the subsequent PCR step. Hence the resulting library contains only PCR product of the first-strand cDNA. And then, the barcoded DNA was amplified by 15-cycle PCR.  Libraries were sequenced on Illumina Genome Analyzer II, HiSeq 2000, or HiSeq 2500.
ssRNAseq

tag: genotype


title: control for PAF1 data TT-seq rep1


title: BisMapR D1Pas1-KO 3

city: Bethesda

first: Heejin

last: Choi

state: Maryland

address: 50 South drive, Building 50, Room 3131

department: NIDDK

institute: NIH

description: R-loops

data_processing:
Fastq files of technical replicates were concatenated when applicable.
Fastq files were preprocessed with cutadapt (v3.4).
RNA-seq data were analyzed using piPipes rna pipeline (v1.1.0).
Small-RNA data were analyzed using piPipes small pipeline (v1.1.0).
R-loop data were analysed following the BisMapR methods (Wulfridge & Sarma, 2021,  eLife 10:e65146).
Assembly: mm10/Gencode M25
Supplementary files format and content: tab-delimited text files of eXpress estimated number of fragments for each sample
Library strategy: BisMapR-seq

source_name: Testis

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen). 2.0 ug of total RNA was used for the construction of sequencing libraries.
RNA and BisMapR libraries were prepared using NEB protocols. Small RNA libraries were prepared using the QIAseq miRNA Library Kit for small RNA-seq.

treatment_protocol: To enrich the piRNA population for the small RNA-seq, b-oxidization was subjected to a total of 20 ug of RNA.

value: Testis

value: male germ cell

value: KO

value: spermatocytes


title: C57Bl/6 Wild Type, rep 2

value: WT


title: PNUTS KO TT-seq rep1

value: PNUTS knockout


title: Phase I 22C × Phase II 22C, 13 day_rep2

description:
First_B12_N87_T2_22_TCGAGG
ControlAcclimation_gene_count_geo.csv

value: bud


title: Phase I 7C × Phase II 7C, 13 day_rep2

description:
First_C05_N33b_T2_7_CTCTCG
ControlAcclimation_gene_count_geo.csv


title: BisMapR D1Pas1-KO 2

description: R-loops


title: LEO1 KO RNA-seq rep2

value: LEO1 knockout


title: Phase I 11C × Phase II 11C, 69 day_rep2

description:
First_B11_N79_T8_11_AGATAG
ControlAcclimation_gene_count_geo.csv

value: Cabernet Sauvignon

value: Phase II


title: C57Bl/6 Wild Type, rep 1


title: Wild type chondrocytes with TNFa

city: Farmington

first: Ernesto

last: Canalis

state: CT

address: 263 Farmington Avenue

department: Orthopaedic Surgery

institute: UConn Health

description: 10x Genomics

data_processing:
Demultiplexing, barcode processing, gene counting, and aggregation made using CellRanger software v.7.0.1 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: mm10-2020-A
Supplementary files format and content: .h5 filtered features, matrix, barcoded files
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Chondrocyte

growth_protocol: Plated wt cells on tissue culture treated plates.

extract_protocol:
Trypsinize lifted and proceed to single cell protocol.
A 10x genomics kit for library construction.

treatment_protocol: 2hr serum deprivation, overnight TNFa treated.

value: Chondrocyte

value: Wild type

tag: age

value: 3-4 day old

value: TNFa


title: LEO1 KO RNA-seq rep1


title: Wild type chondrocytes

description: 10x Genomics

tag: treatment

value: no treatment


title: Phase I 11C × Phase II 11C, 20 day_rep2

description:
First_B09_N64_T3_11_ACCAGT
ControlAcclimation_gene_count_geo.csv

value: Phase I

tag: phase ii_treatment_(°c)


title: PNUTS KO TT-seq rep2


title: Phase I 11C × Phase II 11C, 7 day_rep1

description:
First_B08_N56_T1_11_GGCTGC
ControlAcclimation_gene_count_geo.csv

tag: replication


title: BisMapR D1Pas1-KI 3

description: R-loops

value: KI


title: Wild type chondrocytes treated with TNFa, biological rep 4

data_processing:
Raw reads were trimmed with Sickle, with a quality threshold of 30 and length threshold of 45, following that the trimmed reads were mapped to Mus Musculus genome (GRCm38) with HISAT2 .
The resulting SAM files then converted into BAM format using samtools, and the PCR duplicates were removed using PICARD (http://broadinstitute.github.io/picard/).
The counts were generated against the features with htseq-count.
The differential expression of genes between conditions was evaluated using DESeq2.
Covariates were introduced in the DESeq2 analysis to increase the accuracy of results, and genes showing less than 10 counts across the compared samples were excluded from the analysis.
Genes with a false discovery rate (FDR) < 0.05 were considered significant and used in the downstream analysis.
Assembly: Mus Musculus genome (GRCm39 ensembl release 105)
Supplementary files format and content: COUNTS File (*.counts) and counts

extract_protocol:
Cells were lifted and the RNA extracted using Qiagen Rneasy Mini Kit.
Total RNA samples were prepared for mRNA-Sequencing using the Illumina TruSeq Stranded mRNA Sample Preparation kit following the manufacturer’s protocol (Illumina, San Diego, CA).
Libraries were validated for length and adapter dimer removal using the Agilent TapeStation 4200 D1000 High Sensitivity assay (Agilent Technologies), and then they were quantified and normalized using the dsDNA High Sensitivity Assay for Qubit 3.0 (Thermo Fisher Scientific).
Sample libraries were prepared for Illumina sequencing by denaturing and diluting the libraries per manufacturer’s protocol (Illumina).
All samples were pooled into one sequencing pool, equally normalized, and run as one sample pool across the Illumina NextSeq 500 using version 2.5 chemistry.
Target read depth was achieved for each sample with paired end 75bp reads.

treatment_protocol: 2hr serum deprivation, 6hr TNFa treated.


title: control for PAF1 data RNA-seq rep6

value: control


title: control for PAF1 data RNA-seq rep5


title: Phase I 7C × Phase II 7C, 55 day_rep2

description:
First_B07_N48b_T7_7_CCTAAG
ControlAcclimation_gene_count_geo.csv


title: BisMapR D1Pas1-KI 2

description: R-loops

value: Testis

value: male germ cell


title: BisMapR D1Pas1-KI 1

description: R-loops

value: spermatocytes


title: C57Bl/6 Kat6b Knock Out, rep 1

value: Neural stem cell

value: Kat6b KO


title: Phase I 2C × Phase II 2C, 41 day_rep1

description:
First_C03_N17_T6_2_CAAGCA
ControlAcclimation_gene_count_geo.csv

value: bud


title: Wild type chondrocytes treated with TNFa, biological rep 3


title: WT BMDM-LPS 0h

value: bone marrow

value: BMDM

value: Mouse primary bone marrow-derived macrophages

value: WT

value: LPS(100ng/ml) for 0h


title: D1Pas1 P18 KO 3

data_processing:
Fastq files of technical replicates were concatenated when applicable.
Fastq files were preprocessed with cutadapt (v3.4).
RNA-seq data were analyzed using piPipes rna pipeline (v1.1.0).
Small-RNA data were analyzed using piPipes small pipeline (v1.1.0).
R-loop data were analysed following the BisMapR methods (Wulfridge & Sarma, 2021,  eLife 10:e65146).
Assembly: mm10/Gencode M25
Supplementary files format and content: tab-delimited text files of eXpress estimated number of fragments for each sample

value: KO

value: post-natal day 18


title: Phase I 7C × Phase II 7C, 13 day_rep1

description:
First_B05_N32_T2_7_GATCAC
ControlAcclimation_gene_count_geo.csv

value: Cabernet Sauvignon


title: PNUTS KO RNA-seq rep3

description: K562.Ctrl_and_PNUTS_KO.fragment_count_table.txt

value: PNUTS knockout


title: Phase I 7C × Phase II 7C, 26 day_rep2

description:
First_B06_N40_T4_7_CGCGGA
ControlAcclimation_gene_count_geo.csv

value: Phase I


title: PNUTS KO RNA-seq rep2


title: Wild type chondrocytes treated with TNFa, biological rep 1

value: Chondrocyte

value: Wild type

value: 3-4 day old

value: TNFa


title: BisMapR D1Pas1-KO 1

description: R-loops

value: Testis

value: male germ cell

value: spermatocytes


title: Wild type chondrocytes treated with TNFa, biological rep 2


title: D1Pas1 P18 KO 1


title: Wild type chondrocytes, biological rep 4

value: no treatment


title: Phase I 2C × Phase II 2C, 34 day_rep2

description:
First_B03_N16_T5_2_AACGCC
ControlAcclimation_gene_count_geo.csv

value: bud

value: Phase II


title: control for PAF1 data RNA-seq rep3

value: control


title: Wild type chondrocytes, biological rep 3


title: D1Pas1 P18 WT control 3

value: WT


title: Phase I 2C × Phase II 2C, 20 day_rep1

description:
First_B02_N8_T3_2_CGGTTA
ControlAcclimation_gene_count_geo.csv


title: control for PAF1 data RNA-seq rep2


title: Wild type chondrocytes, biological rep 2


title: control for PAF1 data RNA-seq rep4


title: Wild type chondrocytes, biological rep 1


title: D1Pas1 P18 WT control 2


title: Phase I 22C × Phase II 22C, 13 day_rep1

description:
First_A12_N86_T2_22_GCCACA
ControlAcclimation_gene_count_geo.csv


title: Pre-treatment_rep2

description:
First_B01_N1b_T0__GAACCT
ControlAcclimation_gene_count_geo.csv

value: Pre-experiment


title: D1Pas1 P18 WT control 1

value: post-natal day 18


title: control for PAF1 data RNA-seq rep1


title: LEO1 rescue PNUTS CUT&Tag rep2

description: LEO1_WT2_for_LEO1_rescue.PNUTS.CUTTag.bw

library_source: genomic

data_processing:
Raw reads were trimmed for adaptor sequence and low-complexity or low-quality sequence were filtered using fastp v0.13.1 with default parameters, and subsequently aligned using bowtie2 v2.3.4.1.
Normalized aboundency in each 50-bp genomic bin were generated into bigWig file using deepTools bamCoverage command with parameter --normalizeUsing CPM.
Genome_build: Hg38 for human K562 cells, mm10 for mouse.
Supplementary_files_format_and_content: BigWig files contains normalized read count (CPM, in 50-bp bins) for merged replicates.

molecule: genomic DNA

extract_protocol:
CUT&Tag experiments were performed as previously described with minor modifications(Kaya-Okur, H.S. et al. ). Briefly, 100,000 cells were used for each experiment. Cells were bound to Concanavalin A-coated beads without fixation and chromatin opening. After primary and secondary antibodies binding, pA-Tn5 transposome binding, and tagmentation, DNA was extracted by PCI.
Library was construct by PCR, NEB Phusion(M0530L) was used as protocol.
CUT&Tag

value: LEO1 rescue

value: LEO1 knockout

tag: antibody

value: PNUTS


title: D1Pas1 P18 KO 2

value: KO


title: Phase I 11C × Phase II 11C, 69 day_rep1

description:
First_A11_N78_T8_11_ATAAGA
ControlAcclimation_gene_count_geo.csv

value: Cabernet Sauvignon


title: D1Pas1 P14 KO 3

value: post-natal day 14


title: PNX-7D-LECs-mm10-rep3

city: Milwaukee

first: Akiko

last: Mammoto

state: WI

address: 8701 Watertown Plank rd

institute: Medical College of Wisconsin

data_processing:
Genome alignment and expression count (STAR) were performed using Basepair.
Genome_build: mm10
Supplementary_files_format_and_content: Expression count txt files include Transcript ID, Gene Symbol, Expression Count, Fragments Per Kilobase Million (FPKM), and Transcripts Per Kilobase Million (TPM) for each sample.

source_name: Lung

extract_protocol:
Mouse lung endothelial cells were isolated from C57BL6 mouse lungs (8 week old, male) using anti-CD31 conjugated magnetic beads. RNA was extracted using QIAGEN RNeasy mini kit (Cat# 74104). 1 ug of total RNA as used for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: RNA was collected from endothelial cells isolated from mouse lungs 7 days after PNX and sham-operated mouse lungs

tag: strain

value: lung

value: endothelial cell

value: pneumonectomy 7days

value: 8 week old


title: Phase I 2C × Phase II 2C, 69 day_rep2

description:
First_B04_N24_T8_2_CAGATG
ControlAcclimation_gene_count_geo.csv


title: D1Pas1 P14 KO 2

value: Testis

value: male germ cell


title: LEO1 rescue PNUTS CUT&Tag rep1


title: D1Pas1 P14 KO 1


title: LEO1 KO PNUTS CUT&Tag rep4


title: PNX-7D-LECs-mm10-rep1 [re-used]

description: This is duplicated sample record of GSM4664030 for the convenient retrieval of the complete raw data from SRA


title: PNUTS KO RNA-seq rep1

value: PNUTS knockout


title: Phase I 11C × Phase II 11C, 20 day_rep1

description:
First_A09_N63_T3_11_AATGAA
ControlAcclimation_gene_count_geo.csv

value: bud

value: Phase I


title: Phase I 11C × Phase II 11C, 41 day_rep1

description:
First_A10_N71_T6_11_GATTGT
ControlAcclimation_gene_count_geo.csv

value: Phase II


title: D1Pas1 P14 WT control 3

value: WT


title: Sham-LECs-mm10-rep3

value: sham operated


title: Phase I 7C × Phase II 7C, 55 day_rep1

description:
First_A07_N47_T7_7_AATAGC
ControlAcclimation_gene_count_geo.csv


title: D1Pas1 P14 WT control 2


title: LEO1 KO PNUTS CUT&Tag rep3

value: LEO1 knockout


title: Phase I 7C × Phase II 7C, 26 day_rep1

description:
First_A06_N39_T4_7_CGCAAC
ControlAcclimation_gene_count_geo.csv


title: D1Pas1 P14 WT control 1


title: Sham-LECs-mm10-rep2 [re-used]

description: This is duplicated sample record of GSM4664029 for the convenient retrieval of the complete raw data from SRA


title: Sham-LECs-mm10-rep1 [re-used]

description: This is duplicated sample record of GSM4664028 for the convenient retrieval of the complete raw data from SRA


title: NLRP3-/-MSCs,LPS,Day3

city: Guangzhou

first: Jingrou

last: Chen

address: Zhongshan 2nd Road, Yuexiu District

institute: Sun Yat-Sen University

data_processing:
Reads obtained from the sequencing machines includes raw reads containing adapters or low quality bases which will affect the following assembly and analysis. Thus, to get high quality clean reads, reads were further filtered by Cutadapt (https://cutadapt.readthedocs.io/en/stable/, version:cutadapt-1.9).
We aligned reads of all samples to the Rhododendron reference genome using HISAT2 (https://daehwankimlab.github.io/hisat2/, version:hisat2-2.0.4) package, which initially remove a portion of the reads based on quality information accompanying each read and then maps the reads to the reference genome. HISAT2 allows multiple alignments per read (up to 20 by default) and a maximum of two mismatch when mapping the reads to the reference. HISAT2 build a database of potential splice junctions and confirms these by comparing the previously unmapped reads against the database of putative junctions.
The mapped reads of each sample were assembled using StringTie (http://ccb.jhu.edu/software/stringtie/, version:stringtie-1.3.4d) with default parameters. Then, all transcriptomes from all samples were merged to reconstruct a comprehensive transcriptome using gffcompare software (http://ccb.jhu.edu/software/stringtie/gffcompare.shtml, version:gffcompare-0.9.8). After the final transcriptome was generated, StringTie and ballgown (http://www.bioconductor.org/packages/release/bioc/html/ballgown.html) were used to estimate the expression levels of all transcripts and perform expression abundance for mRNAs by calculating FPKM (fragment per kilobase of transcript per million mapped reads) value.
Assembly: GRCm38
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

source_name: marrow

growth_protocol: MSCs were flushed out and collected from the femur, then cultured in low glucose DMEM supplemented with 10% fetal bovine serum, non-essential amino acids, 2-Mercaptoethanol, and penicillin-streptomycin (all from Gibco), cultured in a 37 °C incubator with 5% CO2.

extract_protocol:
Total RNA was extracted using Trizol reagent (thermofisher, 15596018) following the manufacturer's procedure. The total RNA quantity and purity were analysis of Bioanalyzer 2100 and RNA 6000 Nano LabChip Kit (Agilent, CA, USA, 5067-1511) , high-quality RNA samples with RIN number > 7.0 were used to construct sequencing library.
mRNA was purified from total RNA (5ug) using Dynabeads Oligo (dT) (Thermo Fisher, CA, USA) with two rounds of purification. Following purification, the mRNA was fragmented into short fragments using divalent cations under elevated temperature (Magnesium RNA Fragmentation Module (NEB, cat.e6150, USA) under 94℃ 5-7min). Then the cleaved RNA fragments were reverse-transcribed to create the cDNA by SuperScript™ II Reverse Transcriptase (Invitrogen, cat. 1896649, USA), which were next used to synthesise U-labeled second-stranded DNAs with E. coli DNA polymerase I (NEB, cat.m0209, USA), RNase H (NEB, cat.m0297, USA) and dUTP Solution (Thermo Fisher, cat.R0133, USA). An A-base was then added to the blunt ends of each strand, preparing them for ligation to the indexed adapters. Each adapter contained a T-base overhang for ligating the adapter to the A-tailed fragmented DNA. Dual-index adapters were ligated to the fragments, and size selection was performed with AMPureXP beads. After the heat-labile UDG enzyme (NEB, cat.m0280, USA) treatment of the U-labeled second-stranded DNAs, the ligated products were amplified with PCR by the following conditions: initial denaturation at 95℃ for 3 min; 8 cycles of denaturation at 98℃ for 15 sec, annealing at 60℃ for 15 sec, and extension at 72℃ for 30 sec; and then final extension at 72℃ for 5 min. The average insert size for the final cDNA librarys were 300±50 bp.

treatment_protocol: WT and KO MSCs were stimulated with/without 3 μg/mL LPS (Sigma) for 24 h.

value: marrow

value: NLRP3 knockout

value: LPS

value: Day 1


title: control for PAF1 data PNUTS CUT&Tag rep3

value: control

value: PNUTS


title: LEO1 rescue LEO1 CUT&Tag rep2

value: LEO1 rescue


title: Phase I 2C × Phase II 2C, 69 day_rep1

description:
First_A04_N23_T8_2_AAGACA
ControlAcclimation_gene_count_geo.csv

value: Cabernet Sauvignon


title: HEK293T cell line, siControl, rep3

city: Seoul

first: Seungbok

last: Lee

address: 101, Daehak-ro, Jongno-gu

department: Department of Genomic Medicine

country: South Korea

institute: Seoul National University Hospital

data_processing:
STAR 2-pass mapping
RSEM
Assembly: GRCh38
Supplementary files format and content: Raw count

source_name: cell line

extract_protocol:
TRIzol reagent
TruSeq Stranded Total RNA Ribo-Zero H/M/R kit

value: cell line

tag: cell line

value: siControl


title: NLRP3-/-MSCs,LPS,Day2

tag: cell type


title: Phase I 7C × Phase II 7C, 7 day_rep1

description:
First_A05_N31_T1_7_TAATCG
ControlAcclimation_gene_count_geo.csv


title: LEO1 rescue LEO1 CUT&Tag rep1


title: HEK293T cell line, siControl, rep2


title: LEO1 KO LEO1 CUT&Tag rep2


title: Phase I 2C × Phase II 2C, 34 day_rep1

description:
First_A03_N15b_T5_2_CGAAGG
ControlAcclimation_gene_count_geo.csv


title: HEK293T cell line, siControl, rep1


title: PNX-7D-LECs-mm10-rep2 [re-used]

description: This is duplicated sample record of GSM4664031 for the convenient retrieval of the complete raw data from SRA

value: lung

value: endothelial cell

value: pneumonectomy 7days

value: 8 week old


title: control for PAF1 data PNUTS CUT&Tag rep4


title: Phase I 2C × Phase II 2C, 13 day_rep1

description:
First_A02_N7_T2_2_GGTGAG
ControlAcclimation_gene_count_geo.csv

value: bud

value: Phase I


title: Pre-treatment_rep1

description:
First_A01_N1_T0__ACATTA
ControlAcclimation_gene_count_geo.csv

value: Pre-experiment


title: NLRP3-/-MSCs,LPS,Day1

value: marrow


title: LEO1 KO LEO1 CUT&Tag rep1

value: LEO1 knockout


title: WT MSCs,LPS, Day2

value: WT

value: LPS


title: HEK293T cell line, siBRF2, rep3


title: control for PAF1 data LEO1 CUT&Tag rep2

value: control


title: HEK293T cell line, siBRF2, rep2


title: WT MSCs,LPS, Day1

value: Day 1


title: 1 hour OFF/AM + 15µM FeCl3_3

city: Vancouver

first: James

last: Kronstad

state: BC

address: 2185 E Mall

department: Mircobiology and Immunology

country: Canada

institute: University of British Columbia

data_processing:
illumina hiseq was used for basecalling
Sequenced reads were trimmed for adapter content using BBDuk and parameters ktrim=r k=23 mink=11
Trimmed sequences were then aligned (and genes counted) to the Ustilago maydis genome (version 521 v2.0) via STAR version 2.7.6a with parameters   --runMode alignReads --twopassMode Basic --quantMode GeneCounts --outSAMtype BAM Unsorted --outSAMunmapped Within
Counts were normalized during differential expression analysis via DESeq2’s median of ratios from Anders, S., & Huber, W. (2010).
Assembly: Ustilago maydis 521 v2.0
Supplementary files format and content: Matrix table with normalized expression (DESeq2) information for each gene and every sample

organism: Mycosarcoma maydis

growth_protocol: All strains were grown in ON/NM media for 24 hours at 30℃ then starved in OFF/AM for 24 hours at 30℃ then transferred into the different treatments

extract_protocol:
Cells were flash frozen with liquid nitrogen and RNA was extracted using the Rneasy mini kit by QIAGEN protocol for yeast (mechanical disruption) followed by treatment with Dnase I (TURBO DNA-free™ Kit).
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Treatment was carried out for 1 hour in ON/NM or OFF/AM or OFF + 15µM hemin or OFF + 15µM FeCl3

value: 1 hour OFF/AM + 15uM FeCl3


title: control for PAF1 data LEO1 CUT&Tag rep1


title: 1 hour OFF/AM + 15µM FeCl3_2


title: IL6_KO_CVI_S4

first: Kory

middle: R

last: Johnson

state: MD

address: 10/3B01, 9000 Rockville Pike

department: DIR IT & Bioinformatics

institute: NINDS/NIH

description: 10x Genomics

data_processing:
Post sequencing, the 10x Genomics "cellranger" tool suite (v6.0.1) was used to generate expression counts per known gene (refdata-gex-mm10-2020-A) per sample.
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

growth_protocol: All mice used in this study were handled in accordance with the guidelines established by the NIH Animal Care and Use Committee and the recommendations of AAALAC for the Care and Use of Laboratory Animals. The animal study protocol was approved by the NINDS Animal Care and Use Committee. Mice were bred and maintained within individually ventilated cages in the specific pathogen-free animal facilities at the NIH.

extract_protocol:
IL-6 Wild type (WT, +/+) and IL-6 Knock-out (KO, -/-) mice that were either uninjured (control) or at day 6 post-CVI were anesthetized and perfused using ice cold PBS. Control and CVI-damaged brain tissue was collected using a 4mm biopsy punch (Fisher Scientific; cat#12-460-410). Single cells were dissociated from the punch biopsied brain tissue using a multi tissue dissociation kit 1 (Miltenyi Biotec; cat#130-110-201). After myelin removal using myelin removal beads (Miltenyi Biotec; cat#130-096-733), CD11b+ myeloid cells were positively selected using CD11b microbeads (Miltenyi Biotec; cat#130-093-636). Cell viability and counting were assessed using Acridine orange. Single cell samples in PBS containing 0.05% BSA with viabilities of >80% were used for sequencing.
cDNA libraries were prepared from single-cell suspensions following the 10x Genomics 3′ v3 protocol (www.10xgenomics.com) and sequenced on NovaSeq (www.illumina.com) with aim to generate 150M reads/sample for 4,000 cells/sample.

treatment_protocol: Mice were subjected to either cerebrovascular injury (CVI) or sham surgery (Ctrl). Briefly, 8- to 12-week-old mice were anesthetized using a cocktail of ketamine (85mg per kg), xylazine (13mg per kg), and acepromazine (2 mg per kg) in PBS and placed on hot pads to maintain body temperature throughout the surgery and during the recovery phase. Following an incision over the midline of the scalp, the skull was exposed, and a metal bracket was glued onto the skull, leaving a circular area of the skull exposed, the center of which was 3 mm posterior to bregma and 2.5 mm from the sagittal suture. A cranial window (2 × 3 mm) was carefully thinned to ~30-35μm (mild CVI) or ~20–25μm (severe CVI). Afterward, microspheres (Optison, Perflutren Protein-Type A, GE Healthcare) were injected intravenously (i.v.) via retro-orbital injection (1 μl per gram body weight), and a drop of artificial cerebrospinal fluid (Harvard Apparatus; cat# 597316) was placed over the cranial window. Low-intensity pulsed ultrasound was then applied at 1 MHz with a peak negative pressure of ~200 kPa (2.2 W cm−2), a burst length of 1 ms, 10% duty cycle and a 5-s (mild CVI) or 10-s (severe CVI) exposure to the thinned skull using a Sonicator 740x (Mettler Electronics) with a 5-cm2 dual frequency applicator. After closure of the incision using wound clips (Roboz; cat#RS-9255) and a wound clipper (Roboz; cat#RS-9250), mice were provided with 1ml prewarmed saline (i.v.) and diet gel during the post-surgery recovery period.

value: brain

value: CD11b+ myeloid cells

value: 6 Days Post Cerebrovascular Injury (CVI)


title: MCF7, ATF6α overexpression for 9 hours, rep2

city: Incheon

first: So-Hyun

last: Bae

state: Yeonsu-gu

address: 119, Academy-ro

department: Division of Life Sciences, College of Life Sciences and Bioengineering

institute: Incheon National University

data_processing:
Quality assessment of raw sequences was performed by FastQC (v.0.11.9)
Low-quality and adapter sequences were eliminated with trimgalore (v.0.6.5-1) before the analysis.
The remaining sequences were aligned to the human GRCh38 reference genome using the 2-pass method of STAR (v2.7.3a)
Sequence reads were assigned to genes and the count table was generated by featureCounts (v.2.0.0)
Assembly: hg38
Supplementary files format and content: tab-delimited text files include RNA-seq counts for each Sample

source_name: Breast; Mammary gland

growth_protocol: Human breast cancer MCF-7 cells were obtained from the Korean Cell Line Bank (Seoul, Korea) and cultured in DMEM supplemented with 10% FBS (Gibco) and 1% Anti-Anti (antibiotic-antimycotic) (Gibco). Cells were grown at 37°C in a humidified atmosphere of 5% CO2 and frequently tested for mycoplasma infection using a mycoplasma detection kit (iNtRON, Korea).

extract_protocol:
RNA quantification was achieved with the ND-2000 Spectrophotometer (Thermo Inc., DE, USA).
RNA libraries for RNA-seq were prepared using NEBNext Ultra II Directional RNA-Seq Kit (NEB Inc., UK)

treatment_protocol: To examine the genes involved in significant expression changes through ATF6a ectopic expression in MCF-7 cells, the p3´Flag-ATF6 plasmid (Addgene) was transfected into MCF-7 cells, which were plated in 100 mm culture dishes (SPL Life Sciences, Korea) at 1 ´ 106 cells/dish and grown for 24 hrs, using Lipofectamine 2000 (Invitrogen). For the whole transcriptome sequencing from MCF-7cells overexpressing ATF6a (MCF-7/ATF6a) at three distinct time points (baseline, 6 hrs, and 9 hrs), MCF-7/ATF6a cells were harvested at 0, 6, and 9 hours after ATF6a overexpression.

value: Breast; Mammary gland

value: epithelial cell

value: ATF6alpha overexpression for 9 hours


title: MCF7, ATF6α overexpression for 9 hours, rep1


title: LEO1 rescue ser2p CUT&Tag rep2

description: LEO1_WT2_for_LEO1_rescue.ser2p.CUTTag.bw

value: LEO1 rescue


title: LEO1 rescue ser2p CUT&Tag rep1


title: MCF7, ATF6α overexpression for 6 hours, rep2

value: ATF6alpha overexpression for 6 hours


title: IL6_KO_Ctrl_S3

description: 10x Genomics

value: 6 Days Post Sham Surgery (Ctrl)


title: 1 hour OFF/AM + 15µM hemin_3

value: 1 hour OFF/AM + 15uM hemin


title: 1 hour OFF/AM + 15µM hemin_2


title: 1 hour OFF/AM + 15µM FeCl3_1


title: WT_Ctrl_S1

description: 10x Genomics


title: WT MSCs,LPS, Day3

value: marrow


title: control for PAF1 data ser2p CUT&Tag rep5


title: 1 hour OFF/AM_3

value: 1 hour OFF/AM


title: LEO1 KO ser2p CUT&Tag rep3

value: LEO1 knockout


title: Paf1 cKO TT-seq rep2

source_name: DP thymocytes


title: 1 hour OFF/AM + 15µM hemin_1


title: MCF7, ATF6α overexpression for 6 hours, rep1

value: WT


title: Paf1 cKO TT-seq rep1


title: MCF7, non-ATF6α overexpression, rep1

value: non-ATF6alpha overexpression


title: 1 hour OFF/AM_2


title: control for PAF1 data ser2p CUT&Tag rep4

value: control


title: HEK293T cell line, siBRF2, rep1

value: cell line


title: Paf1 WT TT-seq rep2


title: LEO1 KO TOX4 CUT&Tag rep2


title: Group J, O2-01, 2psi, 3 day, D6, S64

city: Minneapolis

first: Philippa

last: Kennedy

state: Minnesota

address: 425 East River Parkway, Rm 660A

department: Medicine

institute: University of Minnesota

data_processing:
The overall quality of sequencing reads was evaluated using FastQC (v.0.11.9).
Sequence alignments to the reference human genome (GRCh38) were performed using HISAT2 (v2.0.4).
Read count was generated using featureCounts, differential expression analysis between normoxia and different O2 groups were performed using DESeq2, genes were considered significantly differentially expressed when the absolute log2 fold change > 1 and padj < 0.05.
Gene Ontology and KEGG pathway enrichment analysis were done using the g:Profiler – a web server for functional enrichment analysis (https://biit.cs.ut.ee/gprofiler/).
Assembly: hg19
Supplementary files format and content: comma separated text file contains raw counts for each Sample

source_name: blood

growth_protocol: Healthy donor blood was processed to obtain peripheral blood mononuclear cells using density gradient Ficoll-Paque (GE Healthcare, Cat. No. GE17-5442-03). PBMCs were processed fresh using EasySep Human NK Cell Enrichment Kit (STEMCELL Technologies, Cat. No:19055). NK cells were cultured in RPMI (Gibco Cat. No. 2240-089) + 10% fetal bovine serum (Gibco Cat. No. 26140079) + 100 U/mL Penicillin and Streptomycin (Gibco Cat. No. 15140122) supplemented with 1 ng/mL IL-15 (R&D Systems). 300,000 NK cells/well were placed in 96-well U-bottom plates and media was replaced on day 4 of culture when harvesting on day 7.

extract_protocol:
Total RNA was extracted by RNeasy Plus mini kit (Qiagen, Valencia, CA, USA), RNA quality was evaluated by analysis of the RNA integrity number determined using a 2100 bioanalyzer (Agilent RNA 6000 Nano Kit, Agilent Technologies, Santa Clara, CA, USA).
0.5μg total RNA was used for library prep with TruSeq Stranded mRNA Library Prep Kit (Illumina) according to the manufacturer’s instructions. Validation of the library preparations was performed on an Agilent Bioanalyzer using the high sensitivity DNA kit (5067-4626, Agilent Technologies).

treatment_protocol:
NK cells were lysed after 1, 3 or 7 days in culture
NK cells were cultured in a standard humidified incubator (20% O2, 5% CO2, 37℃, atmospheric pressure) or AVATAR System (Xcell Biosciences) incubator imitating blood (12% O2, 5% CO2, 37℃, + 2 pounds per square inch ‘psi’), bone marrow (5% O2, 5% CO2, 37℃, + 0.6 psi), low pressure tumor (1% O2, 5% CO2, 37℃, + 0.3 psi) or high pressure tumor (1% O2, 5% CO2, 37℃, + 2 psi).

value: blood

value: NK cells

tag: oxygen

tag: pressure

tag: time

value: 3 day


title: 1 hour OFF/AM_1


title: Paf1 WT TT-seq rep1


title: WT_CVI_S2

description: 10x Genomics

value: brain

value: CD11b+ myeloid cells

value: 6 Days Post Cerebrovascular Injury (CVI)


title: LEO1 KO ser2p CUT&Tag rep4


title: Group I, O2-01, 0-3psi, 3 day, D6, S63


title: LEO1 KO TOX4 CUT&Tag rep1


title: 1 hour ON/NM _3

value: 1 hour ON/NM


title: Paf1 cKO RNA-seq rep3

description: mouse_DP_thymocytes.Paf1_WT_and_Paf1_cKO.fragment_count_table.txt


title: Group H, O2-05, 0-6psi, 3 day, D6, S62


title: Paf1 cKO RNA-seq rep2


title: 1 hour ON/NM _2


title: 1 hour ON/NM_1


title: MCF7, non-ATF6α overexpression, rep2

value: Breast; Mammary gland

value: epithelial cell


title: Paf1 cKO RNA-seq rep1


title: Group F, O2-20, 0psi, 3 day, D6, S60


title: Paf1 WT RNA-seq rep3


title: AVE0991-3

city: nanjing

first: Rui

last: Duan

address: Yanshan road 139

institute: Nanjing First hospital

data_processing:
Samples were sequenced using the NovaSeq platform (Illumina) to generate 150bp paired-end reads. STAR-v2.7.7a was performed to map clean reads to the reference genome. Normalization of mapped reads and differencial analysis of lncRNAs were performed using DESeq2-v1.10.1. Parameters |log2(fold change)| ≥1 and P-value < 0.05 was defined significantly differentially expressed lncRNAs
Assembly: mm9

organism: Mus

source_name: right SNpc tissues

extract_protocol:
Total RNA was extracted from the right SNpc tissues of mice using TRIzol reagent (Thermo Fisher Scientific) and its concentration and quality were measured by Qubit fluorometer (Thermo Fisher Scientific) and 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA), respectively. The quality of data processing of raw reads was checked by FastQC-v0.11.8, and low-quality bases and adaptors contamination were trimmed with Fastp-v0.19.5 if necessary.
RNA library preparation was performed according to the manufacturer’s instructions, using 1 μg of DNase-treated total RNA as input. The libraries were quantified by using an ABI 9700HT Fast Real-Time PCR system (Thermo Fisher Scientific).

value: human alpha-syn (A53T) overexpressing mice

value: Injected intraperitoneally with 10 mg/kg AVE0991 once a day for 30 consecutive days


title: LEO1 KO CSTF64 CUT&Tag rep2


title: LEO1 KO CSTF64 CUT&Tag rep1


title: Group J, O2-01, 2psi, 3 day, D5, S59


title: AVE0991-2


title: Group I, O2-01, 0-3psi, 3 day, D5, S58


title: Paf1 WT RNA-seq rep2


title: control for PAF1 data CSTF64 CUT&Tag rep2


title: AVE0991-1


title: control for PAF1 data CSTF64 CUT&Tag rep1


title: Paf1 WT RNA-seq rep1


title: model-3

value: Injected intraperitoneally with vehicle (0.9% sterile saline) once a day for 30 consecutive days


title: control for PAF1 data TOX4 CUT&Tag rep2


title: control for PAF1 data TOX4 CUT&Tag rep1


title: model-2


title: Group G, O2-12, 2psi, 3 day, D6, S61


title: Group H, O2-05, 0-6psi, 3 day, D5, S57


title: model-1


title: Group G, O2-12, 2psi, 3 day, D5, S56


title: LEO1 KO PPP1CC CUT&Tag rep2

value: LEO1 knockout


title: Paf1 WT ser2p CUT&Tag rep2

value: WT (Paf1 F/F)


title: LEO1 KO PPP1CC CUT&Tag rep1


title: Paf1 cKO ser2p CUT&Tag rep2

value: Paf1 cKO (Paf1F/F;Lck+)


title: Group L, O2-12, 2psi, 7 day, D6, S53

value: 7 day


title: Group F, O2-20, 0psi, 3 day, D5, S55


title: Paf1 cKO Pol II CUT&Tag rep2

value: Pol II


title: Group K, O2-20, 0psi, 7 day, D6, S52

value: blood


title: Group M, O2-05, 0-6psi, 7 day, D6, S54

value: NK cells


title: control for PAF1 data PPP1CC CUT&Tag rep1

value: control


title: Paf1 cKO Pol II CUT&Tag rep1


title: Group L, O2-12, 2psi, 7 day, D3, S51


title: control for PAF1 data PPP1CC CUT&Tag rep2


title: ME/CFS #14

type: RNA

city: Southport

first: Natalie

last: Eaton-Fitch

state: Queensland

address: Parklands Dr

institute: Griffith University

description: Human primary cells

hyb_protocol: Processed according to nCounter manufacturers instructions

data_processing: Ingenuity Pathway Analysis (IPA) (Qiagen Digital Insights, California, USA) was used for the interpretation of RNA in biological pathways and networks. The following filters were applied to all analyses, a fold change (FC) >1.5 or <-1.5 and a P-value <0.05.   Normality of participant data was determined using the Shapiro-Wilk test. Normally distributed continuous data was compared using one-way analysis of variance (ANOVA) corrected using Bonferroni, and non-normally distributed continuous data was compared using the Kruskal-Wallis test with Dunn’s corrections. Continuous data are presented as mean ± standard deviation (SD) unless otherwise stated. Categorical variables were compared using the Chi-Square test and the Fisher’s exact test. Participant demographic data was analysed using SPSS (version 27). Cell profile abundance scores were compared using one-way ANOVA corrected using Bonferroni or the Kruskal-Wallis test with Dunn’s corrections using GraphPad Prism (version 10). Significance is set at p<0.05. Adjusted (Adj.) p-values are provided unless otherwise stated.

source_name: Primary Whole Blood, PBMCs

growth_protocol: 10^7 PBMCs were resuspended in fetal bovine serum (FBS) (Invitrogen Life Technologies, Carlsbad, CA, USA) containing 10% dimethyl sulfoxide (DMSO) for storage at -80oC until ribonucleic acid (RNA) extraction. Frozen PBMCs were thawed and immediately pelleted by centrifugation.

extract_protocol: Total RNA was isolated from PBMC pellets (5-10x106 cells) using either Trizol or an RNeasy Mini kit (Qiagen, Hilden, Germany) according to manufacturer instructions. The concentration and quality of the RNA were checked using Nanodrop.

value: PBMCs

tag: age (years)

tag: Sex

value: Male

tag: disease

value: ME/CFS


title: LEO1 KO PNUTS CUT&Tag rep2

value: PNUTS


title: ME/CFS #13

description: Human primary cells

scan_protocol: Processed according to nCounter manufacturers instructions


title: Paf1 WT Pol II CUT&Tag rep2


title: LEO1 KO PNUTS CUT&Tag rep1


title: ME/CFS #11

description: Human primary cells

value: Female


title: ME/CFS #12

description: Human primary cells


title: Group G, O2-12, 2psi, 3 day, D3, S50

value: 3 day


title: control for PAF1 data PNUTS CUT&Tag rep2

description: Ctrl.PNUTS.CUTTag.bw


title: Group F, O2-20, 0psi, 3 day, D3, S49


title: control for PAF1 data PNUTS CUT&Tag rep1

description: Ctrl.PNUTS.CUTTag.bw


title: Group H, O2-05, 0-6psi, 3 day, D4, S48


title: LEO1 KO NELFE CUT&Tag rep2

value: NELFE


title: ME/CFS #10

description: Human primary cells


title: pnd14pfc, beta, rep5

city: Toronto

first: Stephen

last: Matthews

address: 1 King's College Circle, Rm 3302

institute: University of Toronto

data_processing:
Quality control of data was performed using Trim Galore to trim low-quality reads (Phred <30) and accessory sequences from adaptors. Reads that did not contain an MspI site signature at the 5’ end were removed using a script provided by NuGEN (https://github.com/nugentechnologies/NuMetRRBS/blob/master/ trimRRBSdiversityAdaptCustomers.py). The reads were then aligned using Bismark (version 0.16.0) and Bowtie2 (v2.3.4.3) and sorted by Samtools (v1.9). We then used MethPipe (version 3.4.2) to identify significant differentially methylated CpG sites (DMCs). DMCs were filtered for those with at least 10X reads with FDR < 0.05. CompEpitool was used to annotate the differentially methylated CpG sites to the guinea pig genome (cavPor3).
Assembly: cavPor3
Supplementary files format and content: Tab-delimited text files of DMCs with at least 10X reads (formatted as "chr", "loc", "fdr", "MethDiff")

organism: Cavia porcellus

source_name: Prefrontal Cortex

extract_protocol:
DNA from the prefrontal cortex of each animal was extracted using the AllPrep DNA/RNA/miRNA Universal Kit from Qiagen.
RRBS libraries were generated from 100ng of high-quality dsDNA using the RRBS Methyl_seq System 1-16 (Ovation: Part #0353) and EpiTect Fast DNA Bisulfite kit (Qiagen: Cat. #59824) following the manufacturer’s protocols.

treatment_protocol: Pregnant guinea pigs were administered betamethasone or saline on gestational day 50/51.

value: Prefrontal Cortex

tag: cohort

value: beta


title: pnd14pfc, beta, rep6

tag: tissue


title: Group G, O2-12, 2psi, 3 day, D4, S47


title: ME/CFS #9

description: Human primary cells


title: LEO1 KO NELFE CUT&Tag rep1

tag: genotype

value: LEO1 knockout


title: pnd14pfc, beta, rep4


title: control for PAF1 data NELFE CUT&Tag rep2

description: Ctrl.NELFE.CUTTag.bw


title: ME/CFS #7

description: Human primary cells


title: pnd14pfc, beta, rep3


title: Group F, O2-20, 0psi, 3 day, D4, S46


title: control for PAF1 data NELFE CUT&Tag rep1

description: Ctrl.NELFE.CUTTag.bw


title: Group C, O2-05, 0-6psi, 1 day, D3, S45

value: 1 day


title: ME/CFS #5

description: Human primary cells


title: Group B, O2-12, 2psi, 1 day, D4, S44


title: LEO1 KO SPT5 CUT&Tag rep2


title: pnd14pfc, beta, rep2


title: Paf1 WT Pol II CUT&Tag rep1

value: WT (Paf1 F/F)


title: Group B, O2-12, 2psi, 1 day, D1, S43


title: LEO1 KO SPT5 CUT&Tag rep1


title: ME/CFS #4

description: Human primary cells


title: ME/CFS #8

description: Human primary cells


title: Group O, O2-01, 2psi, 7 day, D4, S42

value: 7 day


title: control for PAF1 data SPT5 CUT&Tag rep2


title: pnd14pfc, saline, rep6

value: saline


title: Group O, O2-01, 2psi, 7 day, D3, S41

value: blood


title: pnd14pfc, saline, rep7


title: Group O, O2-01, 2psi, 7 day, D2, S40

value: NK cells


title: ME/CFS #6

description: Human primary cells


title: PNUTS KO ser2p CUT&Tag rep2

value: PNUTS knockout


title: pnd14pfc, saline, rep5


title: ME/CFS #2

description: Human primary cells

value: PBMCs


title: ME/CFS #3

description: Human primary cells


title: Group O, O2-01, 2psi, 7 day, D1, S39


title: PNUTS KO ser2p CUT&Tag rep1


title: pnd14pfc, saline, rep4


title: Paf1 cKO ser2p CUT&Tag rep1

value: Paf1 cKO (Paf1F/F;Lck+)


title: pnd14pfc, beta, rep1


title: Group N, O2-01, 0-3psi, 7 day, D4, S38


title: pnd14pfc, saline, rep3


title: Group N, O2-01, 0-3psi, 7 day, D3, S37


title: LEO1 KO ser2p CUT&Tag rep2


title: Long COVID #14

description: Human primary cells

value: Long COVID


title: pnd14pfc, saline, rep2


title: pnd14pfc, saline, rep1


title: control for PAF1 data SPT5 CUT&Tag rep1

value: control


title: LEO1 KO ser2p CUT&Tag rep1


title: Long COVID #13

description: Human primary cells

value: Male


title: Group N, O2-01, 0-3psi, 7 day, D2, S36


title: Long COVID #12

description: Human primary cells

value: Female


title: pnd1 pfc, beta, rep7


title: Group N, O2-01, 0-3psi, 7 day, D1, S35


title: ME/CFS #1

description: Human primary cells

value: ME/CFS


title: Long COVID #11

description: Human primary cells


title: control for PAF1 data ser2p CUT&Tag rep2

description:
Ctrl_for_LEO1_KO.ser2p.CUTTag.bw
Ctrl_for_PNUTS_KO.ser2p.CUTTag.bw


title: pnd1 pfc, beta, rep6

value: Prefrontal Cortex


title: control for PAF1 data ser2p CUT&Tag rep1


title: Group M, O2-05, 0-6psi, 7 day, D2, S34


title: Long COVID #15

description: Human primary cells


title: Group M, O2-05, 0-6psi, 7 day, D2, S33


title: PNUTS KO ser5p CUT&Tag rep2


title: Long COVID #10

description: Human primary cells


title: pnd1 pfc, beta, rep4

value: beta


title: control for PAF1 data ser2p CUT&Tag rep3


title: Group M, O2-05, 0-6psi, 7 day, D2, S32


title: pnd1 pfc, beta, rep5


title: PNUTS KO ser5p CUT&Tag rep1


title: pnd1 pfc, beta, rep3


title: Group L, O2-12, 2psi, 7 day, D4, S31


title: LEO1 KO ser5p CUT&Tag rep2

value: LEO1 knockout


title: pnd1 pfc, beta, rep2


title: Group L, O2-12, 2psi, 7 day, D2, S30


title: pnd1 pfc, beta, rep1


title: control for PAF1 data ser5p CUT&Tag rep3


title: Group K, O2-20, 0psi, 7 day, D4, S29


title: Long COVID #9

description: Human primary cells


title: Long COVID #8

description: Human primary cells


title: Long COVID #6

description: Human primary cells


title: pnd1 pfc, saline, rep7


title: Group K, O2-20, 0psi, 7 day, D2, S28


title: control for PAF1 data ser5p CUT&Tag rep2


title: Group K, O2-20, 0psi, 7 day, D1, S27


title: Long COVID #4

description: Human primary cells


title: control for PAF1 data ser5p CUT&Tag rep1

description:
Ctrl_for_LEO1_KO.ser5p.CUTTag.bw
Ctrl_for_PNUTS_KO.ser5p.CUTTag.bw


title: Long COVID #3

description: Human primary cells


title: Group J, O2-01, 2psi, 3 day, D4, S26

value: 3 day


title: pnd1 pfc, saline, rep5


title: Long COVID #2

description: Human primary cells


title: pnd1 pfc, saline, rep4


title: PNUTS KO Pol II CUT&Tag rep2

value: Pol II


title: Group J, O2-01, 2psi, 3 day, D3, S25


title: PNUTS KO Pol II CUT&Tag rep1


title: Long COVID #7

description: Human primary cells


title: LEO1 KO ser5p CUT&Tag rep1


title: pnd1 pfc, saline, rep3


title: pnd1 pfc, saline, rep2


title: Long COVID #5

description: Human primary cells


title: control for PAF1 data Pol II CUT&Tag rep3


title: pnd1 pfc, saline, rep1


title: Group I, O2-01, 0-3psi, 3 day, D4, S22


title: LEO1 KO Pol II CUT&Tag rep2


title: Group J, O2-01, 2psi, 3 day, D2, S24


title: pnd1 pfc, saline, rep6


title: Healthy Control #18

description: Human primary cells

value: Healthy control


title: Healthy Control #17

description: Human primary cells


title: Group I, O2-01, 0-3psi, 3 day, D3, S21


title: Basal-200

city: wuhan

first: ye

last: zi

address: donghu street

institute: wuhan university

data_processing:
The sequencing data was filtered with SOAPnuke by (1) Removing reads containing sequencing adapter; (2) Removing reads whose low-quality base ratio (base quality less than or equal to 15) 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.
Bowtie2 was applied to align the clean reads to the gene set, in which known and novel, coding and noncoding transcripts were included.
Expression level of gene was calculated by RSEM (v1.3.1).
Differential expression analysis was performed using the DESeq2(v1.4.5)with Q value ≤ 0.05 (or FDR ≤ 0.001).
The subsequent analysis and data mining were performed on Dr. Tom Multi-omics Data mining system (https://biosys.bgi.com).
Assembly: mm10
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

source_name: primary mammary basal cells

extract_protocol:
Sorted primary basal cells or cultured basal colonies were lysed in RNAiso plus (Takara). total RNA was extracted following the manufacturer’s instructions.
RNA-seq libraries were prepared according to the mRNA Library Prreparation (DNBSEQ)

value: primary mammary basal cells

value: WT

value: salbutamol+phenylephrine


title: Group I, O2-01, 0-3psi, 3 day, D1, S20

value: blood

value: NK cells


title: control for PAF1 data Pol II CUT&Tag rep2


title: Healthy Control #16

description: Human primary cells

value: PBMCs


title: Group H, O2-05, 0-6psi, 3 day, D3, S19


title: Basal-0


title: control for PAF1 data Pol II CUT&Tag rep1

description:
Ctrl_for_LEO1_KO.PolII.CUTTag.bw
Ctrl_for_PNUTS_KO.PolII.CUTTag.bw


title: Long COVID #1

description: Human primary cells

value: Long COVID


title: Basal-6OHDA


title: PNUTS KO 4sUDRB-seq 10min rep2

data_processing:
Raw reads were trimmed for adaptor sequence and low-complexity or low-quality sequence were filtered using fastp v0.13.1 with default parameters. 4sUDRB-seq reads were aligned using bowtie2 v2.3.4.1.
Normalized aboundency in each 50-bp genomic bin were generated into bigWig file using deepTools bamCoverage command with parameter --normalizeUsing CPM.
Genome_build: hg19
Supplementary_files_format_and_content: BigWig files contains normalized read count (CPM, in 50-bp bins).

extract_protocol:
After RNA biotinylation and free biotin removal, biotinylated RNA was purified by streptavidin-coupled Dynabeads (Thermo, cat. no. 11205D). rRNA was depleted before library construction. Sequencing libraries were constructed by following the Illumina TruSeq RNA Library preparation protocol.
Sequencing libraries were constructed by following the Illumina TruSeq RNA Library preparation protocol.
4sU-DRB-seq

treatment_protocol: 10 million cells were used for each experiment. After DRB (Sigma, cat. no. D1916) treatment and 4sU (Sigma, cat. no. T4509) incorporation, total RNA was extracted.

value: PNUTS KO


title: Group F, O2-20, 0psi, 3 day, D2, S18


title: Healthy Control #14

description: Human primary cells


title: Healthy Control #13

description: Human primary cells

value: Male


title: Healthy Control #12

description: Human primary cells


title: Basal-ctrl


title: Group E, O2-01, 2psi, 1 day, D4, S17

value: 1 day


title: PNUTS KO 4sUDRB-seq 0min rep2


title: LEO1 KO 4sUDRB-seq 10min rep2

value: LEO1 KO


title: Group E, O2-01, 2psi, 1 day, D2, S15


title: LEO1 KO Pol II CUT&Tag rep1


title: Ednrb-/- NT explants containing neural crest cells biol rep 5

city: wenzhou

first: yu

last: chen

address: 270 West Xueyuan Road

institute: Wenzhou Medical University

data_processing:
Data quality control: Raw data (raw reads) of fastq format were firstly processed through fastp software. In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data. At the same time, Q20, Q30 and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality.
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: featureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene. 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: mm10
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

growth_protocol: The NT explant culture medium consisted of 90% DMEM, 1 mM L-glutamine, 50 μg/ml gentamicin, 10% fetal bovine serum (FBS, Gibco) and 20 nM EDN3 (Sigma).

extract_protocol:
RNAs were extracted using TRIzol reagent (Invitrogen)
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Ednrb-/-


title: Ednrb-/- NT explants containing neural crest cells biol rep 4


title: Ednrb-/- NT explants containing neural crest cells biol rep 3


title: Group E, O2-01, 2psi, 1 day, D3, S16


title: Healthy Control #11

description: Human primary cells

value: Female


title: Paf1 WT ser2p CUT&Tag rep1

value: WT (Paf1 F/F)


title: LEO1 KO 4sUDRB-seq 0min rep2


title: Healthy Control #10

description: Human primary cells


title: Ednrb-/- NT explants containing neural crest cells biol rep 2


title: control for PAF1 data 4sUDRB-seq 10min rep2

value: control


title: Group E, O2-01, 2psi, 1 day, D1, S14


title: Group D, O2-01, 0-3psi, 1 day, D4, S13


title: control for PAF1 data 4sUDRB-seq 0min rep2


title: Healthy Control #9

description: Human primary cells


title: Healthy Control #8

description: Human primary cells


title: Ednrb-/- NT explants containing neural crest cells biol rep 1


title: Healthy Control #15

description: Human primary cells


title: Healthy Control #7

description: Human primary cells


title: PNUTS KO 4sUDRB-seq 10min rep1


title: Group D, O2-01, 0-3psi, 1 day, D3, S12


title: WT NT explants containing neural crest cells biol rep 5


title: Group D, O2-01, 0-3psi, 1 day, D2, S11


title: PNUTS KO 4sUDRB-seq 0min rep1


title: WT NT explants containing neural crest cells biol rep 4


title: Group D, O2-01, 0-3psi, 1 day, D1, S10


title: LEO1 KO 4sUDRB-seq 10min rep1


title: Healthy Control #5

description: Human primary cells


title: WT NT explants containing neural crest cells biol rep 3


title: WT NT explants containing neural crest cells biol rep 2


title: LEO1 KO 4sUDRB-seq 0min rep1


title: control for PAF1 data 4sUDRB-seq 10min rep1


title: Healthy Control #4

description: Human primary cells


title: Healthy Control #3

description: Human primary cells


title: control for PAF1 data 4sUDRB-seq 0min rep1


title: WT NT explants containing neural crest cells biol rep 1


title: Group C, O2-05, 0-6psi, 1 day, D1, S07


title: Healthy Control #2

description: Human primary cells


title: Group C, O2-05, 0-6psi, 1 day, D2, S08


title: Group B, O2-12, 2psi, 1 day, D3, S06


title: WT-PD-1

city: Daejeon

first: Keun Bon

last: Ku

address: 291 Daehak-ro

department: Biological Sciences

institute: Korea Advanced Institute of Science and Technology

data_processing:
The Cell Ranger package (10x Genomics) was used to perform single-cell data processing and to read alignments and feature-barcode matrices generation.
Samples were aligned mm10-2020-A and GRCm38-alts-ensembl-5.0.0 as references.
Assembly: mm10-2020-A, GRCm38-alts-ensembl-5.0.0
Supplementary files format and content: feature, barcode, matrix

source_name: Brain

extract_protocol:
Brains were harvested and single cells were obtained using a Tumor Dissociation Kit (Miltenyi Biotec) following the manufacturer’s instructions. Brain cells were separated from debris using Percoll (GE Healthcare Life Sciences) density gradient centrifugation and were treated with ammonium-chloride-potassium lysis buffer to eliminate red blood cells. Cell suspensions were pooled from five brains/group, and blocked with anti-CD16/CD32 (clone 2.4G2). Cells were stained with PE anti-mouse CD45.2 (eBioscience) antibody and 7-AAD (BioLegend) at 4°C for 30 min. After washing with DPBS containing 1% FBS, CD45.2+7-AAD- live lung immune cells were isolated using a BD FACSAria II (BD Biosciences).
Sorted cells were counted and resuspended to perform library preparation using Chromium Next GEM Single Cell 5' v2 (Dual Index) kits (10x Genomics) and Chromium Next GEM Single Cell VDJ library v2 kits (10x Genomics) according to the manufacturer’s protocol. Libraries were sequenced using a HiSeq X ten (Illumina) platform for 10,000 cells.

value: Brain

value: Immune cells

value: Wild type


title: Healthy Control #6

description: Human primary cells

value: Healthy control


title: Healthy Control #1

description: Human primary cells


title: Fcgr2b_KO-PD-1

value: Fcgr2b knockout


title: SAMPLE5-Xp-tdT-RNA

city: San Francisco

first: Dena

last: Dubal

state: California

address: 675 Nelson Rising Lane, Rm 292

department: Department of Neurology

institute: University of California San Francisco

data_processing:
The quality of the reads was obtainedd using FastQC
Trimmed reads were mapped to the Mus musculus GRCm38 reference genome available on ENSEMBL using the STAR aligner v.2.5.2b
Unique gene hit counts from exons were calculated usig featureCounts from the Subread package v.1.5.2.
Downstream differential expression analysis was performed using DESeq2
Assembly: GRCm38
Supplementary files format and content: tab-delimited excel files include normalised mean gene counts for each Sample

extract_protocol:
Cells were stored in TRIzol and extracted using a Qiagen Rneasy micro kit
Library was prepared using the SMART-Seq v4 Ultra Low input RNA kit following the manufacturer's protocol

value: Neurons

value: paternal X (Xp) cells


title: Group B, O2-12, 2psi, 1 day, D2, S05

value: blood

value: NK cells


title: Group A, O2-20, 0psi, 1 day, D4, S04


title: SAMPLE4-Xp-tdT-RNA