title: Input_1_lncSMAD7-KO_Rep2

city: Turin

first: Andrea

last: Lauria

address: Via Accademia Albertina, 13

department: Life Sciences and Systems Biology

country: Italy

institute: University of Turin

data_processing:
Following adaptor/base-quality trimming, reads shorter than 60bp were discarded. Processing of even and odd ChIRP-seq samples was performed with the ENCODE pipeline 2 (v1.6.1,https://github.com/ENCODE-DCC/chip-seq-pipeline2)) as described for ChIP-seq data, using the default software and parameters settings for ‘Transcription Factors’ mode (i.e. narrow peak signals) and the UCSC mm10 reference genome. To determine a consensus set of lncSmad7 genomic binding sites conserved in both the ‘even’ and ‘odd’ libraries, the following strategy was adopted: first, peak calling was performed in all the replicated lncSMAD7 WT and KO samples using MACSv2 (Zhang, Y., Liu, T., Meyer, C.A. et al. Model-based Analysis of ChIP-Seq (MACS). Genome Biol 9, R137 (2008). https://doi.org/10.1186/gb-2008-9-9-r137 ) with parameters: --nomodel --shift 0 --extsize 200 -q 0.001, using deduplicated, quality-filtered alignments and the respective input RNA as control. Next, a consensus set of binding regions was determined by taking overlapping peak calls across replicates and excluding peaks called in at least one KO sample (bedtools v2.29.2 intersect utility). Finally, a peak quality filter was applied, retaining peaks that were covered by more than 20 reads in all WT samples as the final set of lncSMAD7 binding sites.
Genome_build: mm10/GRCm38
Supplementary_files_format_and_content: BigWig files containing ChIRP-seq signal as fold enrichment over control.

source_name: mouse embryo

growth_protocol: Mouse embryonic stem cells (E14) were cultured on gelatin-coated plates (0,1% gelatin, Sigma-Aldrich) in high-glucose DMEM (Invitrogen) supplemented with 15% heat-inactivated FBS (Millipore), 0.1 mM NEAA (Invitrogen), 1 mM Sodium pyruvate (Invitrogen), 0.1 mM 2-Mercaptoethanol, 1500 U ml−1 LIF (GeneSpin), 25 U ml−1 penicillin, and 25 μg ml−1 streptomycin.

extract_protocol:
ChIRP experiments were performed using the described protocol (Chu et al., 2011) in two replicates. A total of 48 antisense oligonucleotide biotinylated probes against lncSmad7 were designed with Stellaris Probe Designer and were split for the ChIRP experiments in two subsets (Odd and Even). Briefly, 5×107 lncSmad7-overexpressing ESCs and lncSmad7 KO cells were cross-linked with 1% formaldehyde for 10 min at RT and processed to obtain nuclear extracts. The isolated nuclei pellets were lysed with 1% SDS Lysis buffer (50 mM Tris pH 7.0, 10 mM EDTA, 1% SDS, 1 mM DTT, protease inhibitors). The lysate was sonicated using the Bioruptor Twin (Diagenode) (20 cycles, 30s on/off) and incubated with biotinylated probes in hybridization buffer (500 mM NaCl, 1% SDS, 50 mM Tris-HCl, pH 7.0, 1 mM EDTA, 15% formamide, protease inhibitors cocktail, PMSF, and RNase inhibitor) for 4 hours at 37°C with shaking. After hybridization and washes with ChIRP wash buffer (2xSSC, 0.5% SDS, 1 mM DTT, protease inhibitors), the complexes were recovered by incubation with MyOne Streptavidin C1 Dynabeads (Invitrogen) in a total volume of 1 ml and associated DNA fragments from 900 ul of bead samples were eluted with a cocktail of RNase A (Sigma-Aldrich) and RNase H (Invitrogen) at 37°C in DNA elution buffer (50 mM NaHCO3, 1% SDS, 200 mM NaCl) followed by reverse crosslinked at 65°C overnight, acidic phenol/chloroform (ThermoFisher) extraction and ethanol precipitated. Eluted DNA was subject to qPCR and high-throughput sequencing. In parallel, RNA was isolated in a buffer with 95% formamide and 10 mM EDTA pH 8.0 for 10 min at 90°C followed by TRIzol extraction (Invitrogen), from 100 ul of bead samples. Eluted RNA was subject to RT-qPCR analysis as reported for the detection of enriched transcript (Table 4).
ChIRP libraries were prepared using NEBNext® Ultra™ II DNA Library Prep Kit for Illumina (NEB), according to manufacturer's instructions and were checked by Bioanalyzer (Agilent) for quality.
ChIRP-seq

tag: cell type

value: mouse embryonic stem cell

value: lncSmad7 knock-out E14

value: untreated


title: ECA703_GZ_B8_G4_GZpool_05_2019

status: Public on Feb 10 2022

type: SRA

city: Evanston

first: Gaotian

last: Zhang

address: 2205 Tech Drive

department: Department of Molecular Biosciences

country: USA

institute: Northwestern University

library_source: transcriptomic

data_processing:
fastp (v0.20.0) was used to trim raw FASTQ files
Kallisto (v0.44.0) was used for alignment and expression quantification
Genome_build: Caenorhabditis elegans N2 reference genome (WS276)
Supplementary_files_format_and_content: Matrix tables with raw  counts and raw TPM for every transcript and every sample

molecule: total RNA

organism: Caenorhabditis elegans

source_name: whole animals

growth_protocol: Animals were cultured at 20°C on modified nematode growth medium (NGMA) containing 1% agar and 0.7% agarose to prevent burrowing and fed Escherichia coli (E. coli) strain OP50.

extract_protocol:
Total RNA was extracted using Trizol (Invitrogen)
For each sample, mRNA was purified and enriched from 1 µg of total RNA using the NEBNext Poly(A) mRNA Magnetic Isolation Module (New England Biolabs, catalog no. E7490L). RNA libraries were constructed with the NEBNext Ultra II RNA Library Prep with Sample Purification Beads (New England Biolabs, catalog no. E7775L). The cDNA libraries were adapter-ligated using adapters and unique dual indexes in the NEBNext Multiplex Oligos for Illumina (New England Biolabs, catalog no. E6440, E6442) and amplified using 12 PCR cycles. All procedures were performed according to the manufacturer’s protocols.

tag: strain

tag: developmental stage

value: young adult

tag: Sex

value: hermaphrodite


title: Sample_4_mut

city: Canberra

first: Carola

last: Vinuesa

state: ACT

address: 131 Garran Rd, Acton

country: Australia

institute: The John Curtin School of Medical Research

description:
batch: 1
bam2_2021/Sample_4_S4_sorted.bam

data_processing:
RNAseq reads were aligned to the mm10 genome assembly using Hisat2 [version 2.04] with single end read settings.
The mapped reads were assigned based on NCBI Refseq annotation (mm10.refGene.gtf.gz) with FeatureCounts [v2.4] with reverse stranded setting.
Counts per million (CPM) and log2-counts per million (log-CPM) were calculated and processed following Law, C. W., et al., (2016). https://doi.org/10.12688/f1000research.9005.3, with R version 4.1.0; Rstudio Version 1.4.1106; ‘limma’ version 3.48.1 and ‘edgeR’ version 3.34.0.
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: counts_genes.txt: Tab-delimited text file includes raw counts; edgeR.
Supplementary_files_format_and_content: Differentially_expressed_genes.xlsx: Excel file includes differentially expressed genes.

organism: Mus musculus

source_name: Spleen Kika mice

extract_protocol:
Total B cells were purified from the spleens of wild type and kika mice using Magnetic-Activated Cell Sorting (MACS).
RNA was extracted following the Qiagen RNeasy mini kit (Cat. No. / ID: 74104) protocol.
RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: Purified B cells were treated with anti-IgM for 20h.

value: B cells

tag: genotype

tag: treatment

value: anti-IgM for 20h


title: Sample_2_wt

description:
batch: 2
bam2_2021/Sample_2_S2_sorted.bam

source_name: Spleen wild type mice

value: WT


title: Sample_1_wt

description:
batch: 1
bam2_2021/Sample_1_S1_sorted.bam


title: Sample_6_mut

description:
batch: 2
bam2_2021/Sample_6_S6_sorted.bam


title: Sample_3_wt

description:
batch: 2
bam2_2021/Sample_3_S3_sorted.bam


title: Sample_5_mut

description:
batch: 2
bam2_2021/Sample_5_S5_sorted.bam


title: Input_1_lncSMAD7-KO_Rep1

library_source: genomic

molecule: genomic DNA


title: ChIRP_lncSMAD7-KO_ODD_Rep2


title: ChIRP_lncSMAD7-KO_ODD_Rep1


title: ECA703_GZ_B8_B7_GZpool_03_2019


title: ECA594_GZ_B8_E2_GZpool_04_2019


title: ChIRP_lncSMAD7-KO_EVEN_Rep2


title: ECA594_GZ_B8_G3_GZpool_07_2020


title: ChIRP_lncSMAD7-KO_EVEN_Rep1


title: ECA594_GZ_B8_B6_GZpool_03_2019


title: C42 cells Metformin 5mM replicate 2

city: Nashville

first: LaMonica

middle: V

last: Stewart

state: TN

address: 1005 DB Todd JR BLVD

department: School of Graduate Studies and Research (SOGSR)

institute: Meharry Medical College

description:
Gene expression data from 5 mM Metformin tissue culture T media
C42_Met_5mM_rep2

data_processing:
Qiagen CLC Genomics Workbench (version 7.0) for mapping, alignment and normalized FPKM abundance measurements
Genome_build: GRCh37.p13
Supplementary_files_format_and_content: Microsoft Excel (.xlsx) matrix table with RPKM processed counts for every gene and every sample

organism: Homo sapiens

source_name: C4-2 prostate cancer tissue culture

growth_protocol: Cells were cultured for two days in T medium containing 5% heat inactivated FBS and 1% penicillin/streptomycin in a humidified incubator humidified incubator at 37 °C, 5% CO2

extract_protocol:
Total RNA was extracted from treated cells using the Trizol reagent and further purified using the Qiagen RNeasy Mini kit.
A standardized TruSeq mRNA protocol was used for library preparation.
Sequence runs were performed on an Illumina HiSeq 2500 utilizing a 50-bp RNA-Seq protocol.

treatment_protocol: The cells were treated for 24 hours with either PBS vehicle or 5 mM metformin

tag: experimental condition

value: 5mM Metformin 24 hour

tag: cell line


title: C42 cells Control PBS replicate 2

description:
Gene expression data from PBS control tissue culture T media
C42_CONTROL_PBS_rep2

value: PBS Control 24 hour


title: C42 cells Metformin 5mM replicate 3

description:
Gene expression data from 5 mM Metformin tissue culture T media
C42_Met_5mM_rep3


title: C42 cells Control PBS replicate 3

description:
Gene expression data from PBS control tissue culture T media
C42_CONTROL_PBS_rep3


title: C42 cells Metformin 5mM replicate 1

description:
Gene expression data from 5 mM Metformin tissue culture T media
C42_Met_5mM_rep1


title: C42 cells Phenformin 1mM replicate 1

description:
Gene expression data from 1 mM Phenformin tissue culture T media
C42_Phen_1mM_rep1

value: 1mM Phenformin 24 hour


title: C42 cells Phenformin 1mM replicate 2

description:
Gene expression data from 1 mM Phenformin tissue culture T media
C42_Phen_1mM_rep2


title: ECA592_GZ_B8_G2_GZpool_07_2020


title: Input_1_lncSMAD7-WT_Rep2

value: lncSmad7 wild type E14


title: C42 cells Control PBS replicate 1

description:
Gene expression data from PBS control tissue culture T media
C42_CONTROL_PBS_rep1


title: ChIRP_lncSMAD7-WT_ODD_Rep2


title: Input_2_lncSMAD7-WT_Rep1


title: RhoPlus__Stat__2

city: Jouy-en-Josas

first: Cyprien

last: Guérin

address: INRAE - Domaine de Vilvert

country: France

institute: INRAE

data_processing:
Cutadapt to remove adapters (version 1.15).
Low quality trimming with sickle (version 1.33, options: -t sanger -x -n -q 20 -l 20).
Read mapping using bowtie2 (version 2.3.5.1, options: -N 1 -L 16 -R 4).
Mapped read manipulation using samtools (version 1.9).
Read counts were obtained using HTSeq-count (version 0.11.0, options: -m union –nonunique=all).
Sequencing depth normalisation with R library "DESeq2" (version 1.32.0) based on sense-strand signal of 728 AL009126.3-annotated genes well-expressed in all 4 WT samples (i.e. in both mid exponential and early stationary phase).
Differential expression analysis with R library "DESeq2".
DESeq2 p-values were converted into q-values using R library "fdrtool" (version 1.2.17).
FPKM values computed using library size factor obtained with "DESeq2". Log2(FPKM+5) reported in attached table.
Genome_build: Bacillus subtilis (AL009126.3)
Supplementary_files_format_and_content: rho_mutant_gene_expression.csv: Comma-separated text file containing for each gene/sample raw data counts, log2rpkm with differential expression analysis results.

organism: Bacillus subtilis

source_name: Cell culture

growth_protocol: B. subtilis cells were grown in Luria-Bertani liquid medium at 37°C under vigorous agitation.

extract_protocol:
RNA preparation and DNase treatment were done as described (Nicolas et al., 2012). Quality and quantity of RNA samples were analyzed on Bioanalyzer (Agilent, CA).
RNAseq libraries were prepared with ScriptSeq protocol using RiboZero for rRNA-depletion (Illumina, San Diego, California).

treatment_protocol: RNA was extracted from independent cultures of B. subtilis BsB1 WT, Δrho and Rho+ strains grown up to mid exponential or early stationary phase of growth (OD600 ~0.5 and ~2.0, respectively).

value: RhoPlus

tag: growth phase

value: Stationary

tag: biological replicate


title: RhoPlus__Stat__3


title: Input_1_lncSMAD7-WT_Rep1


title: RhoPlus__Stat__1


title: ECA592_GZ_B8_E1_GZpool_04_2019


title: ECA592_GZ_B8_B5_GZpool_03_2019


title: ChIRP_lncSMAD7-WT_ODD_Rep1


title: ChIRP_lncSMAD7-WT_EVEN_Rep2


title: ECA372_GZ_B8_G1_GZpool_06_2019


title: ECA372_GZr_B8_D9_GZpool_07_2020


title: C3-76

type: genomic

city: Stockholm

first: Ewoud

last: Ewing

address: CMM L8:05, Karolinska University Hospital

department: Clinical Neuroscience

country: Sweden

institute: Karolinska Institutet

hyb_protocol: Genomic DNA was isolated using QIAmp DNA micro kit (QIAGEN), resuspended in water and stored at -80oC until further use.

scan_protocol: We used Illumina Infinium Human MethylationEPIC BeadChip (Illumina, Inc., San Diego, CA, U.S.A, EPIC) for quantitative and genome-wide DNA methylation profiling. Genomic DNA were processed at GenomeScan (GenomeScan B.V., Leiden, The Netherlands), according to manufacturer’s instructions and the BeadChip images were scanned on the iScan system

data_processing: All samples passed quality control and were subsequently processed using the Chip Analysis Methylation Pipeline (ChAMP) version 2.9.1.0 and minfi version 1.24.0 R-Bioconductor  packages

label: Cy5 and Cy3

label_protocol:
Nuclei were further labelled with Alexa Fluor 488 (Invitrogen #A11029)-conjugated anti-NeuN antibodies (1:700, Millipore #MAB377) and separated into neuronal and non-neuronal nuclei by flow cytometry (MoFloTM high speed cell sorter). Non-neuronal nuclei were pelleted and stored at -80oC until DNA isolation.
Standard Illumina Protocol.

extract_protocol: Fluorescence activated cell sorting (FACS)-based neuronal nuclei isolation from dissected brain tissue was performed as previously described (PMID:31146783). Briefly, following resuspension of the homogenized brain tissue in hypotonic lysis buffer (0.32M sucrose, 5mM CaCl2, 3mM MgAc2, 0.1 mM EDTA, 10mM Tris pH.8, 1mM DTT, 0.1 % Triton), nuclei were extracted by ultracentrifugation in sucrose gradient (1.8M sucrose, 3mM MgAc2, 1mM DTT, 10mM Tris pH.8) for 2.5 hours at 4oC.

tag: disease state

value: NNC

tag: gender

value: M

tag: age

tag: tissue

value: Brain, Anterior


title: ECA372_GZ_B8_B4_GZpool_03_2019


title: C3-73

value: MS

value: Brain, Posterior


title: DeltaRho__Stat__3

value: DeltaRho


title: C3-18

value: Brain, Middle


title: C3-1

value: F


title: C3-71


title: RhoPlus__Expo__2

value: Exponential


title: C3-80


title: C3-63


title: RhoPlus__Expo__1


title: C3-15


title: C3-65


title: C3-40


title: C3-30


title: AGM pre-HSCs/endothelial cells

city: Boston

first: Sachin

last: Patel

state: MA

address: 1 Blackfan Circle

institute: Children's Hospital, Boston

data_processing:
Sequencing data from above were pre-processed using 10x Genomics CellRanger 3.0.4 using the standardized workflow, using the mm10 reference genome for alignment.
The generated count matrices were analyzed using Seurat v4.0.0 and merged into a single Seurat object. Cells with a UMI count < 1000 and/or mitochondrial gene percentage > 10% were filtered out. A total of 225 pre-HSCs/endothelial cells, 520 AGM progenitors, and 545 fetal liver progenitors passed filter and were used for downstream analysis.
Dimensionality reduction and clustering were then performed (resolution of 0.4), and cells were visualized using UMAP plots.
Genome_build: mm10
Supplementary_files_format_and_content: h5 files: filtered counts matrices and barcodes

molecule: polyA RNA

source_name: AGM

extract_protocol:
The AGM and fetal liver were isolated from E11.5 embyros as delineated in the Methods section. Each tissue was dissociated in 0.125% collagenase type I at 37°C for 30 minutes, after which cells were further dissociated by gentle pipetting and then passed through a 40 µm strainer. Single cells were washed with PBS and then incubated with anti-mouse CD16/32 at 4°C for 10 minutes for Fc blocking prior to antibody staining.
Single-cell encapsulation was performed using 10X Chromium single cell 3’ technology. Whole-transcriptome libraries were prepared using the 10X v3 protocol and sequenced on Illumina NextSeq500 paired-end 150 cycles (Read 1: 28 cycles; Index Read 1 (i7): 8 cycles; Read 2: 91 cycles).

tag: cell population

value: Lin- cKit+ CD45lo/mid CD31+ VE-Cad

value: AGM pre-HSCs/endothelial cells


title: BT12

city: Chicago

first: Yukitomo

last: Ishi

state: IL

address: 303 East Superior Street, Simpson Querrey

description:
AT/RT cell without treatment
SAMPLE 1

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to Infinium Methylation EPIC BeadChip Kit using standard Illumina protocol

scan_protocol: Arrays were imaged using BeadArray Reader using standard recommended Illumina scanner setting

data_processing: Unprocessed

source_name: AT/RT cell

label_protocol: Standard Illumina Protocol

growth_protocol: AT/RT cells were cultured with DMEM containing 10% FBS

extract_protocol: genomic DNA was extracted and purified from AT/RT samples using Qiagen DNeasy Kit according to standard instructions

treatment_protocol: No treatment

value: AT/RT

value: Female


title: C3-75


title: C3-79


title: DeltaRho__Stat__1


title: C3-8


title: C3-33


title: ECA363_GZ_B8_F9_GZpool_06_2019

value: young adult

value: hermaphrodite


title: C3-55


title: DeltaRho__Expo__1


title: C3-48


title: ECA363_GZ_B8_D8_GZpool_04_2019


title: ECA349_GZ_B4_H4_GZpool_07_2020


title: WildType__Stat__2

value: WildType


title: RNA-seq ESC KO+lncSmad7 rep2

data_processing:
Sequencing was performed on the Illumina NextSeq 500 platform. Sequencing reads were aligned to mouse reference genome (UCSC mm10/GRCm38) using STAR v2.7.7a0 (with parameters --outFilterMismatchNmax 999 --outFilterMismatchNoverLmax 0.04) and providing a list of known splice sites extracted from GENCODE M25 comprehensive annotation. Gene expression levels were quantified with featureCounts v1.6.3 [PMID:24227677] (options: -t exon -g gene_name) using GENCODE M25 basic gene annotation. Multi-mapped reads were excluded from quantification.
Genome_build: mm10/GRCm38
Supplementary_files_format_and_content: Tab-delimited text file of normalized read counts per gene/samples.

extract_protocol:
Total RNA was extracted using TRIzol reagent (Invitrogen), according to the manufacturer’s protocol.
Approximately 2 μg of total RNA were subjected to poly(A) selection, and libraries were prepared using the TruSeq RNA Sample Prep Kit (Illumina) following manufacturer’s instructions. Sequencing was performed on the Illumina NextSeq 500 platform.

value: mouse embryonic stem cell

value: lncSmad7-/- E14

value: lncSmad7 transfected


title: WildType__Stat__1

value: Stationary


title: C3-60

value: MS


title: AGM progenitors

value: Lin- cKit+ CD45+

value: AGM progenitors


title: C3-39

value: Brain, Anterior


title: ECA363_GZ_B8_B3_GZpool_03_2019


title: WildType__Expo__2


title: DeltaRho__Expo__2

value: DeltaRho


title: ECA348_GZ_B8_A3_GZpool_06_2019


title: ECA349_GZr_B2_D1_GZpool_08_2020


title: BT16

description:
AT/RT cell without treatment
SAMPLE 2

value: Male


title: ECA348_GZ_B6_D1_GZpool_04_2019


title: RNA-seq ESC KO+Smad7 rep1

value: Smad7 transfected


title: RNA-seq ESC KO+Smad7 rep2


title: ECA349_GZ_B2_A4_GZpool_01_2019


title: C3-35

value: NNC

value: M

value: Brain, Middle


title: ECA348_GZr_B6_A3_GZpool_08_2020

value: young adult


title: RNA-seq ESC KO+lncSmad7 rep1


title: C3-6

value: F

value: Brain, Posterior


title: RNA-seq ESC KO rep2

value: mouse embryonic stem cell

value: untreated


title: WildType__Expo__1

value: WildType

value: Exponential


title: C3-66

value: MS


title: RNA-seq ESC KO rep1

value: lncSmad7-/- E14


title: C3-23


title: treat3

city: Shanghai

first: Kailin

last: Li

address: Tian Ping

department: Shanghai Institute of Nutrtion and Health

country: China

institute: Chinese Academy of Sciences

data_processing:
Illumina HiSeq X Ten (2×150bp) sequencer with two paired-end was used for sequencing
Sequenced reads were trimmed for adaptor sequence, mapped with reference genome Lactobacillus plantarum ATCC 14917 ENA| Accession:   ACGZ02000000 by Bowtie
Software RSEM was used to quantitatively analyze gene expression levels respectively
Genome_build: ACGZ02000000
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for every gene and every sample

organism: Lactiplantibacillus plantarum

source_name: L. plantarum_treated

growth_protocol: A single colony of Lactobacillus plantarum NMM.1 from MRS agar plate was inoculated in a falcon tube containing MRS broth and grown 24 h at 37°C under dynamic incubation.

extract_protocol:
Total RNA was extracted using RNAiso Plus Kits (Takara, China) according to the manufacturer’s recommendation. To eliminate genomic DNA contamination, the DNase I (TaKara, China) was used.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Lactobacillus plantarum NMM.1 cells were recovered by centrifugation (5000 g, 10 min, 4 ℃), washed twice with saline magnesium buffer (100 mM NaCl, 8 mM MgSO4, 50 mM Tris–HCl, pH 8.0), and adjusted to an OD=2.0 with buffer containing 5μg/mL deoxynivalenol-3-glucoside

value: Exponential phase cells

value: 5 μg/mL D3G-treated


title: ECA259_GZr_B3_A5_GZpool_07_2020

value: hermaphrodite


title: C3-42

value: Brain, Anterior


title: RNA-seq ESC WT rep1

value: wild type E14


title: ChIRP_lncSMAD7-WT_EVEN_Rep1

value: lncSmad7 wild type E14


title: ECA259_GZ_B3_D2_GZpool_03_2019


title: treat2


title: RNA-seq ESC WT rep2


title: C3-16


title: ECA259_GZ_B7_G4_GZpool_06_2019


title: treat1


title: Input DNA ESC lncSmad7 KO

data_processing:
Following quality controls (performed with FastQC v0.11.2), sequencing reads were processed with Trim Galore! v0.5.0 (https://www.bioinformatics.babraham.ac.uk/projects/trim_galore) to perform quality and adapter trimming (parameters: --stringency 3 –q 20). Trimmed reads were next analysed with the ENCODE Transcription Factors and Histone Modifications ChIP-seq pipeline 2 (v1.6.1, available from https://github.com/ENCODE-DCC/chip-seq-pipeline2), using default software and parameter settings for the ‘Histone Modifications’ processing mode. Briefly, reads were aligned to the mouse reference genome (UCSC mm10) using Bowtie2. Duplicated, multi-mapping and poor-quality alignments were discarded, and peak calling was performed using MACS2, using the input DNA as control library. Signal tracks were generated as fold enrichment over control for both individual and pooled replicates using MACS2. Both WT and lncSmad7 KO (KO) sample groups were processed identically.
Genome_build: mm10/GRCm38
Supplementary_files_format_and_content: BigWig files containing ChIP-seq signal as fold enrichment over control.

extract_protocol:
For ChIP-seq, approximately 20x106 ESCs were cross-linked by addition of formaldehyde to 1% for 10 min at RT, quenched with 0.125 M glycine for 5 min at RT. Nuclear extracts were prepared as described in Native RIP protocol and were sonicated using the Bioruptor Twin (Diagenode) (20 cycles, 30s on/off) at high-power setting in SDS ChIP Buffer (20 mM Tris-HCl pH 8.0, 10 mM EDTA, 0.5% SDS and protease inhibitors). Cell lysate was diluted with ChIP dilution buffer (20 mM Tris-HCl pH 8.0, 150 mM NaCl, 2 mM EDTA, 1% Triton) before the immunoprecipitation with 2 ug of Histone H3, acetyl-K27 antibody (Abcam) or 2 ug of p300 antibody (Millipore) overnight at 4°C on a rotator.   Protein-DNA complexes were immobilized on protein G-Dynabeads (Life technologies) and washed 6 times with RIPA buffer (500 mM LiCl, 50 mM HEPES-KOH pH 7.6, 1 mM EDTA, 1% NP-40, 0.7% Na-Deoxycholate). The de-crosslinking was performed at 65°C overnight. De-crosslinked DNA was purified using QiaQuick PCR Purification Kit (Qiagen), according to the manufacturer's instruction.
To prepare ChIP-seq libraries, approximately 10 ng of purified ChIP DNA from two replicates of WT and two replicates of lncSmad7 KO ESCs were end-repaired, dA-tailed, and adaptor-ligated using the NEBNext ChIP-seq Library Prep Master Mix Set (NEB), according to the manufacturer’s instructions. The data are expressed as a percentage of the DNA Input.


title: ECA251_GZ_B4_E7_GZpool_05_2019


title: Input DNA ESC WT


title: control3

source_name: L. plantarum_control

value: none (control)


title: ECA251_GZ_B3_I5_GZpool_03_2019


title: control2


title: C3-44

value: Brain, Middle


title: control1


title: ChIP-seq H3K27ac ESC lncSmad7 KO rep2

tag: chip antibody

value: H3K27ac (Abcam, ab4729)


title: ChIP-seq H3K27ac ESC lncSmad7 KO rep1


title: ECA250_GZr_B5_D8_GZpool_08_2020

value: young adult


title: ECA251_GZ_B1_C9_GZpool_01_2019


title: ChIP-seq H3K27ac ESC WT rep2


title: ECA250_GZ_B7_E7_GZpool_06_2019


title: DeltaRho__Stat__2

value: DeltaRho

value: Stationary


title: ChIP-seq H3K27ac ESC WT rep1

value: mouse embryonic stem cell

value: untreated


title: Lung Carcinoma Epithelial Cell (A549) - RSV-B Buenos Aires - 72hr

city: Houston

first: Pedro

last: Piedra

state: TX

address: One Baylor Plaza

department: Virol & Micro

institute: Baylor College of Medicine

data_processing:
bcl2fastq (version 2.20.0.422) was used to generate demultiplexed fastq files at sample level
Fastq files were trimmed to remove adapters and base-pairs that did not meet standards using Trim Galore (Version 0.4.1)
Cell lines: Sequences were aligned against the human genome hg38 (GRCh38) using Hisat2 (version 2.1.0), sorted through samtools (version 1.5) and count matrix was generated by mapping reads using featureCounts (version 1.6.0). Non-overlapping uniquely mapped features were counted for further analysis.
Virus only: Sequences were aligned against the 4 RSV strain reference genomes to determine the average read depth across the 10 gene coding sequences and 8 intergenic regions. Average read depths across each coding sequence and intergenic region were divided by the total number of reads mapping to all coding sequences and intergenic regions for each sample and before averaging across time-points for each of the 4 RSV strains.
Genome_build: Genome Reference Consortium Human Build 38 patch release 87 (GRCh38.p87). Novel viral genomes have been created and submitted to GenBank. Accession ID pending.
Supplementary_files_format_and_content: .xlsx files containing data used to generate figures 1, 2, 6-13. Figures 3 and 4 contain images from immunofluorescence microscopy.
Supplementary_files_format_and_content: The HWYC5DSXX-1*csv tables contain the processed viral data on which the viral analysis was conducted.

organism:
Homo sapiens
Respiratory syncytial virus type B

source_name: Lung Carcinoma Epithelial Cell (A549)

growth_protocol: HEp-2 and A549 cell lines were cultured in Minimum Essential Medium (MEM, Corning) supplemented with 10% Fetal Bovine Serum (Hyclone), 1% of 10000 U/ml penicillin/streptomycin/ 25µg/mL Fungizone™ (Gibco), 1 % of L-Glutamine (200 mM) (Gibco) and maintained in 5% CO2 at 36 °C.

extract_protocol:
Cells were lysed using Trizol and RNA was extracted using Mini Viral RNA Kit (Qiagen Sciences, Germantown, Maryland) and automated platform QIAcube (Qiagen, Hilden, Germany) according to the manufacturer’s instructions.
Illumina TruSeq Stranded Total RNA with Ribo-Zero Globin kits (20020612, Illumina Inc.) was used for the Total RNA Seq. The kit enables rRNA Removal: Depletes human, mouse, and rat rRNA (cytoplasmic and mitochondrial) and globin mRNA. For the mRNA sequencing, briefly, poly-A+ mRNA was extracted from 1 μg total RNA using Oligo(dT)25 Dynabeads (Life Technologies, Cat. No. 61002). Paired-end libraries both sequecing sets were prepared on Beckman BioMek FXp liquid handlers using TruSeq kit reagents. For this, cDNA was A-tailed followed by ligation of the TruSeq UD Indexes and amplified for 15 PCR cycles following manufacturer’s recommendation.  AMPure XP beads (Beckman Coulter) were used for cDNA and library purification. Libraries were quantified using fragment analyzer and pooled in equimolar ratios. This pool was quantified using qPCR to determine loading concentration for sequencing. Sequencing was performed on the NovaSeq 6000 instrument using the S4 reagent kit (300 cycles) to generate 2x150bp paired-end reads, each lane was spiked in with 1% PhiX control library for run quality control.

treatment_protocol: Cells were infected with one of four RSV strains (RSV/A/GA1/Tracy, RSV/A/ON/Ontario, RSV/B/GB1/18537, RSV/B/BA/Buenos Aires) at MOI = 0.01 or mock-infected and samples (media or cell lysates) collected at 24, 48, 72, 96 hrs post-inoculation for sequencing and other measurements (e.g., cytokine levels) or fixed for immunostaining and microscopy.

value: Lung adenocarcinoma (A549)

value: immortalized cell line

value: Cells collected 72 hrs after  virus inoculation.


title: Lung Carcinoma Epithelial Cell (A549) - RSV-B Buenos Aires - 48hr

value: Cells collected 48 hrs after virus inoculation.


title: PAR-CLIP IgG ESC rep2

description: nuclear RNA

data_processing:
After de-multiplexing, sequencing reads were processed using UMI-tools v1.0.0 in order to remove adaptor sequences, keep the small-RNA insert and extract the UMI, which was removed from the read sequence and appended to the read name. Reads not containing the UMI sequence were excluded. These processed reads were aligned to mouse reference genome (mm10/GRCm38) using Bowtie v1.2.3 7 (options: -S -v 2 -m 10 --best --strata -q). Aligned reads were next de-duplicated using the UMI-tools dedup utility (default parameters), exploiting the UMI sequence present in read name. The resulting unique alignments were used to find protein-RNA interaction sites with PARalyzer v1.5. Genome-wide PAR-CLIP signals were computed as read per millions (RPM) using the deepTools bamCoverage utility (options: --binSize 1 --normalizeUsing CPM) after filtering out reads with no T > C conversion mismatches.
Genome_build: mm10/GRCm38
Supplementary_files_format_and_content: BigWig files containing PAR-CLIP signal densities for p300-IP and IgG control (RPM unit).

extract_protocol:
For PAR-CLIP, approximately 200x106 ES cells, were acutely treated for 16 h with 100 μM 4-thioridine (4-SU) (Sigma) and were cross-linked using 150 mJ/cm2 of 365 nm UV light in a UVP crosslinker (Analytic Jena). The isolated nuclei pellets were lysed on ice with NP40 Lysis buffer (150 mM KCl, 50 mM HEPES pH 7.5, 2 mM EDTA, 1 mM NaF, 0,5% NP40, 0.5 mM DTT, protease inhibitors). The cleared lysates were subjected to SUPERase-In digestion using RNAase A/T1 cocktail enzyme mix (Ambion) for 3 min at 37°C to improve IP efficiency. The cross-linked p300-RNA complexes are immunoprecipitated with p300 antibody (Millipore) bound to BSA blocked protein G-Dynabeads (Life technologies). Beads were washed 3 times with IP wash buffer (300 mM KCl, 50 mM HEPES, pH 7.5, 0,05% NP40, 0.5 mM DTT, SUPERase-In, protease inhibitors) and  resuspended in dephosphorylation buffer by adding Recombinant Shrimp Alkaline Phosphatase (rSAP, NEB) for 15 min at 37°C to dephosphorylate the RNA. The beads were washed with Phosphatase wash buffer (50 mM Tris-HCl, pH 7.5, 20 mM EGTA, 0.5% NP40, SUPERase-In, protease inhibitors) and T4-PNK buffer (50 mM NaCl, 50 mM Tris HCl pH 7.5, 10 mM MgCl2, 5 mM DTT, SUPERase-In, protease inhibitors) and were incubated with non-radioactive ATP. The protein-RNA complexes were separated by Novex Bis-Tris 4–12% polyacrylamide gel (Invitrogen) for 55 min at 220 V. p300-RNA bands that correspond to the expected size of p300 revealed in Input were excised from the nitrocellulose membrane, eluted by incubating with RNA elution buffer (50 mM NaCl, 50 mM HEPES pH7.0, 1 mM EDTA, 2 mM CaCl2, 1% SDS, SUPERase-In) and digested with Proteinase K (4mg/ml, NEB) and 3.5M Urea for 30 min at 55°C. RNA was purified using acidic phenol/chloroform (ThermoFisher) followed by ethanol precipitation.
PAR-CLIP libraries were prepared using NEB next small RNA library set for Illumina sequencing (NEB), according to manufacturers instructions and were checked by Bioanalyzer (Agilent) for quality. pproximately 2 μg of total RNA were subjected to poly(A) selection, and libraries were prepared using the TruSeq RNA Sample Prep Kit (Illumina) following manufacturer’s instructions. Sequencing was performed on the Illumina NextSeq 500 platform.

value: wild type

tag: par-clip antibody

value: normal Mouse IgG (Millipore, 12-371)


title: ECA250_GZ_B7_C1_GZpool_04_2019

value: hermaphrodite


title: Lung Carcinoma Epithelial Cell (A549) - RSV-B Buenos Aires - 24hr

tag: cell type

value: Cells collected 24 hrs after virus inoculation.


title: ECA248_GZr_B3_A4_GZpool_07_2020

tag: strain


title: PAR-CLIP IgG ESC rep1

description: nuclear RNA

tag: developmental stage


title: C3-34

value: MS

value: F

value: Brain, Posterior


title: Lung Carcinoma Epithelial Cell (A549) - RSV-B Buenos Aires - 96hr

value: Cells collected 96 hrs after  virus inoculation.


title: Lung Carcinoma Epithelial Cell (A549) - RSV-B 18537 - 96hr


title: ECA248_GZ_B5_A9_GZpool_05_2019

value: young adult

tag: Sex


title: ECA248_GZ_B3_D1_GZpool_03_2019


title: Lung Carcinoma Epithelial Cell (A549) - RSV-B 18537 - 72hr


title: C3-46


title: C3-32

value: Brain, Middle


title: C3-51


title: C3-25


title: Lung Carcinoma Epithelial Cell (A549) - RSV-B 18537 - 48hr


title: ECA189_GZr_B7_I7_GZpool_08_2020


title: Lung Carcinoma Epithelial Cell (A549) - RSV-B 18537 - 24hr


title: cva1Δ24h_2

city: beijing

first: lei

last: chen

address: NO.1 Beichen West  Road, Chaoyang District, Beijing 100101, China

institute: the institute of microbiology chinese academy of sciences

data_processing:
Strand-specific sequencing for WT and cva1Δ at one time point with two repeats. Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, and then ~2 GB of clean data of each sample (representing over 100 × coverage) was mapped to the genome sequence of XL280 using STATR_2.6.0c.  All unigenes were subsequently aligned against the well-annotated genome of XL280.
The gene expression level was measured in TPM to determine unigenes by StringTie v1.3.3.
The differentially expressed genes (DEGs) were assessed using the DEseq2 v1.16.1 Bioconductor package and defined based on the fold change criterion.
Genome_build: XL280
Supplementary_files_format_and_content: tab-delimited text files include TPM values for each Sample ...

organism: Cryptococcus deneoformans XL280

source_name: Mating type α

growth_protocol: Strains were cultured in YPD liquid medium at 30°C for 16 hours. Then, the cells were washed with cold water and spotted onto V8 juice medium (pH 7.0) for 24 hours for the isolation of total RNA.

extract_protocol:
Total RNA was extracted using Ultrapure RNA Kit (Kangweishiji, CW0581S) according to the manufacturer’s instructions.
The VAHTS mRNA-seq v2 Library Prep Kit (Vazyme Biotech Co., Ltd, Nanjing, China) was used to generate transcriptome libraries following the manufacturer’s protocols.

tag: growth

value: V8 medium at 25C, 24h

tag: genotype

value: cva1 deletion


title: E12.5 neural tube Lbx1Δ/Δ_rep2

city: Dunedin

first: Lyvianne

last: Decourtye

address: 270 Great King Street

department: Anatomy

country: New Zealand

institute: University of Otago

data_processing:
Sequence reads were filtered and trimmed by the sequencing platform.
Sequence reads were aligned to the mouse reference genome (mm9) using TopHat (v.2.1.1) on Galaxy using paired-end (as individual datasets) with default settings and supply own junction data using a gene annotation model UCSC Main on Mouse: knownGene (genome).
FeatureCount (v.4.6.0.1) on Galaxy to measure gene expression against UCSC mm9 refGenes and defaults settings.
Combine FeatureCount into a matrix using Generate Count Matrix (v. 1.0) on Galaxy with default settings.
EdgeR (v. 3.4.3) on Rstudio, the batch effect was removed during the Count Per Million (CPM) analysis. Differential gene expressions were considered significant when the False Discovery Rate (FDR) adjusted p-value was <0.05.
Genome_build: UCSC Mus musculus mm9 (MGSCv37)
Supplementary_files_format_and_content: *.tabular.txt: Tab-delimited text files, reads per gene, gene ID is RefSeq accession number.

source_name: neural tube

extract_protocol:
Control or Lbx1Δ/Δ neural tubes from a same litter were pooled together and be considered as one replicate. Total RNA of E12.5 neural tubes was extracted using the Ambion Purelink RNA mini kit (ThermoFisher, #12183018A). A total of 10ug of RNA was sent to perform the construction of sequencing libraries.
The library preparation and RNA-sequencing were performed on an Illumina HiSeq platform (NEBNext Ultra RNA Library prep kit for Illumina).

tag: strain/background

tag: genotype/variation

value: Neural tube


title: Fetal liver progenitors

description: The two fetal liver populations were independently sorted and then mixed before encapsulation.

source_name: Fetal liver

value: cKit+/high CD45+ CD41- and cKit+/high CD45+ CD41high

value: Fetal liver progenitors


title: ECA189_GZ_B8_A1_GZpool_06_2019


title: C3-4

value: M


title: PAR-CLIP p300 ESC rep1

description: nuclear RNA

value: mouse embryonic stem cell


title: C3-62


title: E12.5 neural tube Lbx1Δ/Δ_rep1


title: E12.5 neural tube WT_rep2

value: WT


title: C3-17

value: Brain, Anterior


title: DL238_GZ_B6_C8_GZpool_06_2019

value: hermaphrodite


title: cva1Δ24h_1


title: Epithelial Cell (HEp2) - RSV-B Buenos Aires - 96hr

source_name: Epithelial Cells (HEp2)

tag: cell line

value: Epithelial cells (HEp2)

value: immortalized cell line

tag: treatment


title: Epithelial Cell (HEp2) - RSV-B Buenos Aires - 72hr

value: Cells collected 72 hrs after  virus inoculation.


title: WT24h_1

value: wild type


title: WT24h_2


title: Epithelial Cell (HEp2) - RSV-B Buenos Aires - 48hr

value: Cells collected 48 hrs after virus inoculation.


title: DL238_GZ_B6_A2_GZpool_04_2019

value: young adult


title: E12.5 neural tube WT_rep1


title: ECA189_GZ_B7_I8_GZpool_04_2019


title: C3-52

tag: disease state

value: MS

value: F

value: Brain, Middle


title: Lung Carcinoma Epithelial Cell (A549) - RSV-A Tracy - 72hr

organism:
Homo sapiens
Respiratory syncytial virus type A

value: Lung adenocarcinoma (A549)


title: Activated_P1KO_ONT_2

city: Cambridge

first: Louise

last: Matheson

address: Babraham Research Campus

department: Laboratory of Lymphocyte Signalling and Development

country: United Kingdom

institute: The Babraham Institute

data_processing:
Raw reads were basecalled using Guppy (4.0.11), in fast mode.
Sequence reads with a mean sequence quality of 7 were classified as passed reads; these were first demultiplexed with the Guppy debarcoder option and then processed with pychopper (2.5.0) in order to identify, orient and trim the full-length cDNA reads.
Pychopped reads were aligned with minimap2 (2.17) with splice aware setting (-ax splice), which is compatible with pipelines for further isoform identification analysis. The sequences were aligned to mouse genome reference GRCm38.
Aligned read counts over each gene were quantified using SeqMonk (https://www.bioinformatics.babraham.ac.uk/projects/seqmonk/). Reads were imported with the parameters Single End; Dedup=No; MAPQ>=20, and without treating as RNA-seq data in order to prevent splitting of spliced reads. Feature probes over genes from the GRCm38.96 annotation were then generated and reads quantified, only including those mapping to the same strand as the gene.
Genome_build: GRCm38
Supplementary_files_format_and_content: ONT_cDNAPCR_raw_counts.tsv: tab-delimited text file containing gene names and IDs together with raw counts over each gene for each long-read ONT RNA sequencing library, generated with Seqmonk.

source_name: Activated CD8 T cells

growth_protocol: Single cell suspensions were prepared from spleen and lymph nodes by passing the organs through 70 and 40 mm cell strainers consecutively. Negative naïve CD8 T cell isolation was achieved by depletion of cells bound by biotinylated antibodies: CD4 (GK1.5), CD11b (M1/70), CD11c (N418), CD19 (1D3), B220 (A3-6B3), CD105 (MJ7/18), TER-119, gamma/delta TCR (GL3), Gr1 (RB6-8C5), NK1.1 (PK136), F4/80 (BM8), CD44 (1M7) and magnetic Dynabeads™ M-280 Streptavidin (Thermofisher cat#:11206D), except for iCLIP experiments where the anti-CD44 antibody was omitted.

extract_protocol:
RNA was extracted from naïve and activated CD8 T cells using the RNeasy Micro Kit (cat# 74004, Qiagen).
ONT cDNA-PCR libraries were generated essentially according to the CELLO-seq protocol (Berrens et al, 2021, Nat. Biotech.; doi:10.1038/s41587-021-01093-1) with the following modifications: The addition of UMIs by splint ligation was omitted. Reverse transcription was performed using 1 ng total RNA isolated from a pool of cells. PCR reactions were performed using standard Oxford Nanopore Technologies barcoded primers under the following conditions: 90 °C for 45 s, 20 cycles (90 °C for 15 s, 64 °C for 30 s, 72 °C for 10 min), 72 °C for 5 min. PCR products were purified using 0.6X AMPure XP beads (Beckman). Equal quantities of each cDNA sequencing library were pooled using a total of 200 fmol, before sequencing on a MinION R9.4.1 flow cell using the SQK-LSK109 kit (1D sequencing). The standard MinKNOW procedure was used for a 72 hour run, according to manufacturers’ instructions.

treatment_protocol: Naïve cells were either used unstimulated, or were activated ex vivo for 24h by culturing in RPMI 1640 Medium (Dutch modification) with 20 mM HEPES (ThermoFisher cat#:22409-015), 50 μM b-Mercaptoethanol, 100 units/ml penicillin and streptomycin, GlutaMAX and 10% FCS on 96 flat-bottom well plates precoated with 5μg/ml anti-CD3 (2C11) and 1μg/ml anti-CD28 (37.51) antibodies, in the presence of 20ng/ml murine IL2.

value: Spleen + LN

value: 24h activation, anti-CD3 + anti-CD28 + IL2

value: CD4-CreTg Ptbp1-fl/fl

value: Female

value: 13 weeks


title: Epithelial Cell (HEp2) - RSV-B Buenos Aires - 24hr

value: Cells collected 24 hrs after virus inoculation.


title: Activated_P1KO_ONT_3

value: 9 weeks


title: DL238_GZ_B1_H5_GZpool_01_2019

value: hermaphrodite


title: Epithelial Cell (HEp2) - RSV-B 18537 - 96hr

value: Epithelial cells (HEp2)

value: immortalized cell line

value: Cells collected 96 hrs after  virus inoculation.


title: Activated_P1KO_ONT_1

value: 10 weeks


title: Lung Carcinoma Epithelial Cell (A549) - RSV-A Tracy - 48hr

value: Cells collected 48 hrs after virus inoculation.


title: DL226_GZr_B3_F8_GZpool_07_2020

value: young adult


title: DL226_GZ_B4_H3_GZpool_07_2020


title: Epithelial Cell (HEp2) - RSV-B 18537 - 72hr

value: Cells collected 72 hrs after  virus inoculation.


title: C3-22

value: NNC

tag: gender

value: M

value: Brain, Anterior


title: Epithelial Cell (HEp2) - RSV-B 18537 - 48hr


title: Activated_Ctrl_ONT_3

value: Spleen + LN

value: 24h activation, anti-CD3 + anti-CD28 + IL2

tag: age


title: DL226_GZ_B4_C3_GZpool_04_2019


title: Epithelial Cell (HEp2) - RSV-B 18537 - 24hr


title: Activated_Ctrl_ONT_2

tag: tissue

value: Female


title: Lung Carcinoma Epithelial Cell (A549) - RSV-A Ontario - 72hr

value: Lung adenocarcinoma (A549)


title: PAR-CLIP p300 ESC rep2

description: nuclear RNA

value: mouse embryonic stem cell

value: wild type


title: Lung Carcinoma Epithelial Cell (A549) - RSV-A Tracy - 96hr


title: Naive_P1KO_ONT_4

source_name: Naïve CD8 T cells

value: Unstimulated

value: CD4-CreTg Ptbp1-fl/fl

value: 9 weeks


title: Lung Carcinoma Epithelial Cell (A549) - RSV-A Ontario - 48hr

value: immortalized cell line


title: C3-64


title: C3-19

value: MS

value: F

value: Brain, Middle


title: C3-67

value: Brain, Posterior


title: DL200_GZ_B4_C2_GZpool_05_2019

value: young adult

value: hermaphrodite


title: CX11315_GZ_B8_F8_GZpool_06_2019


title: Lung Carcinoma Epithelial Cell (A549) - RSV-A Tracy - 24hr

value: Cells collected 24 hrs after virus inoculation.


title: DL200_GZ_B3_F7_GZpool_03_2019


title: C3-14

value: NNC


title: Activated_Ctrl_ONT_1

value: Spleen + LN

value: 24h activation, anti-CD3 + anti-CD28 + IL2

value: 11 weeks


title: C3-11

value: M


title: Lung Carcinoma Epithelial Cell (A549) - RSV-A Ontario - 24hr

value: Lung adenocarcinoma (A549)


title: RSV-B Buenos Aires - 24hr

description: This sample was used for viral genome sequencing.

organism: Respiratory syncytial virus type B

extract_protocol: The RNA was extracted using the Ambion viral extraction kit called MagMAX   -96 Viral RNA Isolation Kit.


title: Naive_P1KO_ONT_3

value: Unstimulated

value: Female


title: RSV-B 18537 - 48hr

value: Cells collected 48 hrs after virus inoculation.


title: RSV-B 18537 - 24hr


title: Naive_P1KO_ONT_2

value: CD4-CreTg Ptbp1-fl/fl

value: 13 weeks


title: Naive_Ctrl_ONT_4

value: 9 weeks


title: Epithelial Cell (HEp2) - RSV-A Tracy - 96hr

value: Epithelial cells (HEp2)

value: immortalized cell line

value: Cells collected 96 hrs after  virus inoculation.


title: CX11315_GZ_B8_B2_GZpool_03_2019

value: young adult

value: hermaphrodite


title: C3-28

value: NNC

value: F

value: Brain, Anterior


title: RSV-B Buenos Aires - 48hr


title: CX11315_GZ_B8_D7_GZpool_04_2019


title: CX11314_GZ_B6_A1_GZpool_04_2019


title: Naive_Ctrl_ONT_3

value: Spleen + LN


title: C3-50

value: M


title: monthly_12_16H

city: Beijing

first: Jiesi

last: Lei

state: Beijing

address: School of Environment, Tsinghua

institute: Tsinghua University

description: collected in Dec, warming, replicate 4

hyb_protocol: The mixed solution was kept at 90 °C for 3 min for denaturation, and incubated at 37°C for 30 min before GeoChip hybridization was carried out at 67 °C for 24 hrs with a rotation at 20rpm in Agilent hybridization oven.

scan_protocol: After hybridization, Agilent Wash Buffers were applied to wash away unbounded DNA at ordinary temperature, and the arrays were scanned with a NimbleGen MS200 Microarray Scanner (Roche NimbleGen, Madison, WI, USA) at 633 nm. Eventually the images data were extracted by Agilent Feature Extraction program.

data_processing:
Raw signals were uploaded to Microarray Data Manager (http://ieg.ou.edu/microarray) for data quality control and normalization. Samples from January to June and from July to December were hybridized in separate batches. The signal-to-noise ratio (SNR) was set to 7 for Jan to Jun samples or 3.5 for Jul to Dec samples to minimize the batch effect. Spots with minimum intensity < 100 or detected in < 50% replicate samples were removed before statistical analyses. Both the universal standard and functional gene spot intensities are used to normalize the signals among arrays. Data were logarithmically transformed after quality control and normalization.
Probe names and detailed info for PROBE_ID in raw data and proteinGI in the data matrix are provided seperately. One shall be able to easily process the raw data, get normalized data, and complete annotations using http://ieg.ou.edu/microarray/.
Processed data file includes: Normalized signal intensity

organism: uncultured soil bacterium

source_name: soil DNA, Dec, warming, replicate 4

label_protocol: Purified DNA was first labeled with the fluorescent dye Cy-3 (GE Healthcare, CA, USA) using random priming as described previously (Cong et al., 2015), then purified by a QIAquick Purification kit (Qiagen, Valencia, CA, USA), and dried in a SpeedVac (Thermo Savant, NY, USA) at 45 °C for 45 min. The dried DNA was then resuspended into ??? μl of DNase/RNase-free distilled water and evenly mixed with ??? μl of hybridization solution, which contains 1 × Acgh blocking, 1 × HI-RPM hybridization buffer, 10 pM universal standard DNA, 0.05 μg/μl Cot-1 DNA, and 10% formamide (final concentrations).

extract_protocol: DNA was extracted by MoBio PowerSoil DNA isolation kit (MoBio Laboratories, Carlsbad, CA, USA). DNA concentrations were quantified with PicoGreen using a FLUOstar OPTIMA fluorescence plate reader (BMG LabTech, Jena, Germany), and DNA purity was determined by the ratios of O.D. 260/280 nm and O.D. 260/230 nm using a NanoDrop ND-1000 Spectrophotometer (NanoDrop Technologies Inc., Wilmington, DE, USA).

tag: collection time

value: collected in Dec

tag: condition

value: warming

tag: replicate

value: replicate 4


title: monthly_12_10H

description: collected in Dec, warming, replicate 2

source_name: soil DNA, Dec, warming, replicate 2

value: replicate 2


title: Naive_Ctrl_ONT_2

value: Unstimulated

value: Female


title: Epithelial Cell (HEp2) - RSV-A Tracy - 72hr

tag: cell type

value: Cells collected 72 hrs after  virus inoculation.


title: Epithelial Cell (HEp2) - RSV-A Tracy - 48hr

value: Epithelial cells (HEp2)

value: Cells collected 48 hrs after virus inoculation.


title: Epithelial Cell (HEp2) - RSV-A Tracy - 24hr

value: immortalized cell line

value: Cells collected 24 hrs after virus inoculation.


title: Epithelial Cell (HEp2) - RSV-A Ontario - 96hr

value: Cells collected 96 hrs after  virus inoculation.


title: monthly_12_1H

description: collected in Dec, warming, replicate 1

source_name: soil DNA, Dec, warming, replicate 1

value: replicate 1


title: Epithelial Cell (HEp2) - RSV-A Ontario - 72hr


title: CX11314_GZ_B1_H4_GZpool_01_2019

source_name: whole animals

extract_protocol:
Total RNA was extracted using Trizol (Invitrogen)
For each sample, mRNA was purified and enriched from 1 µg of total RNA using the NEBNext Poly(A) mRNA Magnetic Isolation Module (New England Biolabs, catalog no. E7490L). RNA libraries were constructed with the NEBNext Ultra II RNA Library Prep with Sample Purification Beads (New England Biolabs, catalog no. E7775L). The cDNA libraries were adapter-ligated using adapters and unique dual indexes in the NEBNext Multiplex Oligos for Illumina (New England Biolabs, catalog no. E6440, E6442) and amplified using 12 PCR cycles. All procedures were performed according to the manufacturer’s protocols.

tag: strain

value: young adult

value: hermaphrodite


title: Naive_Ctrl_ONT_1

value: Spleen + LN

value: 11 weeks


title: monthly_12_20H

description: collected in Dec, warming, replicate 3

source_name: soil DNA, Dec, warming, replicate 3

value: collected in Dec

value: replicate 3


title: CX11314_GZ_B6_F4_GZpool_06_2019

tag: developmental stage


title: Epithelial Cell (HEp2) - RSV-A Ontario - 48hr


title: CX11307_GZr_B5_D7_GZpool_08_2020

tag: Sex


title: monthly_12_19C

description: collected in Dec, control, replicate 3

source_name: soil DNA, Dec, control, replicate 3

value: control


title: DL200_GZ_B1_B4_GZpool_01_2019


title: Naive_P1KO_ONT_1

value: CD4-CreTg Ptbp1-fl/fl

value: 10 weeks


title: monthly_12_6C

description: collected in Dec, control, replicate 2

source_name: soil DNA, Dec, control, replicate 2

value: replicate 2


title: monthly_12_23C

description: collected in Dec, control, replicate 4

source_name: soil DNA, Dec, control, replicate 4

value: replicate 4


title: 13dT_K3+K3-cr8 3

first: Yunfei

state: China

address: 38 Xueyuan Road, Haidian District, Beijing

department: Institute of Systems Biomedicine, Department of Immunology, School of Basic Medical Sciences, Beijing Key Laboratory of Tumor Systems Biology, Peking University Health Science Center, Beijing, China

institute: Peking University

description:
13dT-K3G8-3-LDJ7778_L1
3-fpkm.xlsx

data_processing:
The raw fastq files were trimmed to clean data by trim-galore software.
The clean data were aligned to human hg38 genome using subread, which produced the BAM type file directly.
The featureCounts command line tool was used to calculate the gene count matrix.
Then the count matrix was normalized with FPKM formula.
The GFOLD software was used to identify the differentially expressed genes.
Genome_build: UCSC hg38 genome was used as reference genome.
Supplementary_files_format_and_content: 3-fpkm.xlsx: Excel spreadsheet includes the FPKM values for each sample.

source_name: HEK293T cells

growth_protocol: HEK293T cells were cultured in DMEM medium supplemented with 10% FBS (Gibco) and 100U/ml Penicillin-Streptomycin in a humidified incubator at 37 °C with 5% CO2.

extract_protocol:
Total RNA was extracted using Trizol reagent.
The transcriptome library for sequencing was generated using VAHTSTM mRNA-seq v2 Library Prep Kit for Illumina® (Vazyme Biotech Co., Ltd, Nanjing, China) following the manufacturer’s recommendations.

treatment_protocol: Transfecting plasmids encoding Sik3 and Sik3 crRNA 8 into HEK293T cells stably expressing RfxCas13d. Cells were collected for total RNA extraction 24 hour after transfection.

value: Stably expressing RfxCas13d

tag: transfection

value: Sik3 and Sik3 crRNA 8


title: 13dT_K3+K3-cr8 2

description:
13dT-K3G8-2-LDJ7777_L1
3-fpkm.xlsx

tag: genotype


title: CX11307_GZ_B7_B9_GZpool_04_2019

data_processing:
fastp (v0.20.0) was used to trim raw FASTQ files
Kallisto (v0.44.0) was used for alignment and expression quantification
Genome_build: Caenorhabditis elegans N2 reference genome (WS276)
Supplementary_files_format_and_content: Matrix tables with raw  counts and raw TPM for every transcript and every sample


title: Epithelial Cell (HEp2) - RSV-A Ontario - 24hr

value: Epithelial cells (HEp2)

value: immortalized cell line


title: monthly_12_3C

description: collected in Dec, control, replicate 1

source_name: soil DNA, Dec, control, replicate 1


title: C3-54

value: NNC

value: M

value: Brain, Anterior


title: CX11292_GZr_B5_G6_GZpool_08_2020

value: young adult

value: hermaphrodite


title: monthly_11_16H

description: collected in Nov, warming, replicate 4

source_name: soil DNA, Nov, warming, replicate 4

value: collected in Nov

value: warming


title: RSV-A Tracy - 24hr

organism: Respiratory syncytial virus type A

value: Cells collected 24 hrs after virus inoculation.


title: CX11307_GZ_B7_E6_GZpool_06_2019


title: 13dT_K3+K3-cr1 2

description:
13dT-K3G1-2-LDJ7774_L1
3-fpkm.xlsx

treatment_protocol: Transfecting plasmids encoding Sik3 and Sik3 crRNA 1 into HEK293T cells stably expressing RfxCas13d. Cells were collected for total RNA extraction 24 hour after transfection.

value: Sik3 and Sik3 crRNA 1


title: RSV-A Tracy - 48hr

value: Cells collected 48 hrs after virus inoculation.


title: 13dT_K3+K3-cr8 1

description:
13dT-K3G8-1-LDJ7776_L1
3-fpkm.xlsx


title: 13dT_K3+K3-cr1 3

description:
13dT-K3G1-3-LDJ7775_L1
3-fpkm.xlsx


title: CX11292_GZ_B7_B8_GZpool_04_2019


title: 13dT_K3+K3-cr1 1

description:
13dT-K3G1-1-LDJ7773_L1
3-fpkm.xlsx


title: CX11285_GZm_B1_B3_GZpool_0108_2020


title: monthly_11_20H

description: collected in Nov, warming, replicate 3

source_name: soil DNA, Nov, warming, replicate 3

value: replicate 3


title: RSV-A Ontario - 24hr


title: Lung Carcinoma Epithelial Cell (A549) - Mock 96hr

source_name: Lung Carcinoma Epithelial Cell (A549)

value: Lung adenocarcinoma (A549)

value: Cells collected 96 hrs after mock-infection.


title: monthly_11_10H

description: collected in Nov, warming, replicate 2

source_name: soil DNA, Nov, warming, replicate 2

value: replicate 2


title: RSV-A Ontario - 48hr

source_name: Epithelial Cells (HEp2)


title: CX11285_GZr_B4_C1_GZpool_07_2020


title: CX11285_GZ_B3_I4_GZpool_03_2019


title: 13dT_K3+NT 2

description:
13dT-K3NT-2-LDJ7771_L1
3-fpkm.xlsx

treatment_protocol: Transfecting plasmids encoding Sik3 and NT crRNA into HEK293T cells stably expressing RfxCas13d. Cells were collected for total RNA extraction 24 hour after transfection.

value: Stably expressing RfxCas13d

value: Sik3 and NT crRNA


title: CX11276_GZr_B3_F6_GZpool_07_2020


title: CX11292_GZ_B7_E5_GZpool_06_2019


title: CX11276_GZ_B6_F3_GZpool_06_2019


title: monthly_11_6C

description: collected in Nov, control, replicate 2

source_name: soil DNA, Nov, control, replicate 2

value: control


title: monthly_11_23C

description: collected in Nov, control, replicate 4

source_name: soil DNA, Nov, control, replicate 4

value: replicate 4


title: 13dT_K3+NT 3

description:
13dT-K3NT-3-LDJ7772_L1
3-fpkm.xlsx


title: Lung Carcinoma Epithelial Cell (A549) - Mock 48hr

value: immortalized cell line

value: Cells collected 48 hrs after mock-infection.


title: 13dT_K3+NT 1

description:
13dT-K3NT-1-LDJ7770_L1
3-fpkm.xlsx


title: 13dT_td+td-cr7 2

description:
13dT-TdG7-2-LDJ7768_L1
3-fpkm.xlsx

treatment_protocol: Transfecting plasmids encoding tdTomato and tdTomato crRNA 7 into HEK293T cells stably expressing RfxCas13d. Cells were collected for total RNA extraction 24 hour after transfection.

value: tdTomato and tdTomato crRNA 7


title: 13dT_td+td-cr7 1

description:
13dT-TdG7-1-LDJ7767_L1
3-fpkm.xlsx


title: Epithelial Cell (HEp2) - Mock 96hr

value: Epithelial cells (HEp2)


title: monthly_11_19C

description: collected in Nov, control, replicate 3

source_name: soil DNA, Nov, control, replicate 3

value: collected in Nov


title: CX11271_GZm_B3_I3_GZpool_0307_2020

value: young adult

value: hermaphrodite


title: Lung Carcinoma Epithelial Cell (A549) - Mock 24hr

value: Cells collected 24 hrs after mock-infection.


title: monthly_11_3C

description: collected in Nov, control, replicate 1

source_name: soil DNA, Nov, control, replicate 1

value: replicate 1


title: CX11276_GZ_B6_C7_GZpool_04_2019


title: monthly_10_20H

description: collected in Oct, warming, replicate 3

source_name: soil DNA, Oct, warming, replicate 3

value: collected in Oct

value: warming

value: replicate 3


title: monthly_11_1H

description: collected in Nov, warming, replicate 1

source_name: soil DNA, Nov, warming, replicate 1


title: CX11271_GZ_B4_E6_GZpool_05_2019

source_name: whole animals


title: 13dT_td+td-cr4 3

description:
13dT-TdG4-1-LDJ7764_L1
3-fpkm.xlsx

treatment_protocol: Transfecting plasmids encoding tdTomato and tdTomato crRNA 4 into HEK293T cells stably expressing RfxCas13d. Cells were collected for total RNA extraction 24 hour after transfection.

value: tdTomato and tdTomato crRNA 4


title: Lung Carcinoma Epithelial Cell (A549) - Mock 72hr

value: Lung adenocarcinoma (A549)

value: Cells collected 72 hrs after mock-infection.


title: monthly_10_1H

description: collected in Oct, warming, replicate 1

source_name: soil DNA, Oct, warming, replicate 1


title: monthly_10_16H

description: collected in Oct, warming, replicate 4

source_name: soil DNA, Oct, warming, replicate 4


title: 13dT_td+td-cr4 1

description:
13dT-TdG4-2-LDJ7765_L1
3-fpkm.xlsx

value: Stably expressing RfxCas13d


title: 13dT_td+NT 2

description:
13dT-TdNT-2-LDJ7762_L1
3-fpkm.xlsx

treatment_protocol: Transfecting plasmids encoding tdTomato and NT crRNA into HEK293T cells stably expressing RfxCas13d. Cells were collected for total RNA extraction 24 hour after transfection.

value: tdTomato and NT crRNA


title: monthly_10_10H

description: collected in Oct, warming, replicate 2

source_name: soil DNA, Oct, warming, replicate 2

value: replicate 2


title: Epithelial Cell (HEp2) - Mock 24hr

value: immortalized cell line


title: 13dT_td+NT 3

description:
13dT-TdNT-3-LDJ7763_L1
3-fpkm.xlsx

source_name: HEK293T cells


title: 13dT_td+td-cr4 2

description:
13dT-TdG4-3-LDJ7766_L1
3-fpkm.xlsx


title: Epithelial Cell (HEp2) - Mock 48hr

value: Cells collected 48 hrs after mock-infection.


title: CX11271_GZ_B1_B2_GZpool_01_2019


title: monthly_10_19C

description: collected in Oct, control, replicate 3

source_name: soil DNA, Oct, control, replicate 3

value: control


title: monthly_10_23C

description: collected in Oct, control, replicate 4

source_name: soil DNA, Oct, control, replicate 4

value: replicate 4


title: 13dT_td+td-cr7 3

description:
13dT-TdG7-3-LDJ7769_L1
3-fpkm.xlsx

value: tdTomato and tdTomato crRNA 7


title: iBET151 treated

city: Chapel Hill

first: Edward

middle: Patrick

last: Browne

state: NC

address: 120 Mason Farm Road

institute: UNC-Chapel Hill

data_processing:
cellranger count for genome-mapping and single-cell data processing, cellranger version: 6.1.1
seurat for QC and secondary analysis, Seurat version 4.0.2
seurat doublet discrimination based on RNA feature counts and removal of cells with greater than 15% mitochondrial gene counts
seurat merge to combine all 4 datasets retaining sample metadata
seurat sctransform to generate normalized count matrix
Genome_build: Base human genome: GRCh38-3.0.0. Generated custom reference genome with N6 cell-line proviral genome added as chromosome 24. Custom reference genome was generated using cellranger (v6.1.1) mkref function.
Supplementary_files_format_and_content: Counts matrix contains gene expression matrix for each cell-barcode after SCTransform normalization. Metadata contains descriptors for each cell-barcode. Both files contain all 4 samples aggregated into a single file using Seurat merge command.

source_name: Jurkat N6

growth_protocol: Cells grown in RPMI supplemented with 10% FCS, L-Glutamine, HEPES, PenStrep, and Sodium Pyruvate. Cultured in the presence of 500nM Reverse Transcriptase inhibitor Efavirenz. Culture density maintained between 300,000 and 1,000,000 cells per mL.

extract_protocol:
10x genomics 3' scRNA seq v3. Single-cell suspension generated and cells loaded onto chromium device for droplet encapsulation
10x genomics 3' scRNA seq v3. cDNA synthesis in GEM, emulsion breaking and clean up, cDNA bulking amplification for 11 cycles, fragmentation and end repair, adapter ligation, sample indexing with i7 barcoding primer for 13 cycles.

treatment_protocol: 24 hour treatment with DMSO vehicle (1:1000), 500nM iBET151, 100nM AZD5582, or both 500nM iBET151 and 100nM AZD5582

value: Latently infected N6 clone of Jurkat cell line

value: 500nM iBET151

tag: cell-line tissue source

value: T cell leukemia cell line


title: AZD5582_iBET151 treated

value: 500nM iBET151 and 100nM AZD5582


title: Epithelial Cell (HEp2) - Mock 72hr

value: Epithelial cells (HEp2)


title: DMSO treated

value: DMSO vehicle (1:1000)


title: CX11264_GZr_B5_G5_GZpool_08_2020

value: young adult

value: hermaphrodite


title: monthly_10_6C

description: collected in Oct, control, replicate 2

source_name: soil DNA, Oct, control, replicate 2

value: collected in Oct


title: CX11262_GZr_B5_G4_GZpool_08_2020


title: AZD5582 treated


title: non-SDR_after_treatment_N-P221-3

city: Hsinchu

first: Jinn-Moon

last: Yang

address: 75 Po-Ai Street

country: Taiwan

institute: National Chiao Tung University

description: non-SDR samples after 3HP treatment from peripheral blood mononuclear cells

data_processing:
The reads were aligned to the human reference genome (GRCh38) using the HISAT2 package (v.2.1.0).
The mapped reads were assembled into transcripts and the gene abundances were estimated using StringTie package (v.1.3.4).
The expression levels of all transcripts were estimated using StringTie package and calculated based on fragments per kilobase of transcript per million fragments mapped (FPKM) using the Ballgown package (v.2.22.0) in R (v. 3.5.3).
Genome_build: GRCh38
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample using ballgown package

source_name: non-SDR_samples _after_treatment

growth_protocol: This prospective, multicentre observational study recruited subjects with LTBI and received at least one dose of 3HP. The candidate transcripts highly associated with the occurrence of SDR were identified from the peripheral blood transcriptomic profiling of samples from randomly selected 8 participants with SDR and 12 without SDR between January 2017 and December 2019

extract_protocol:
Total RNA of each sample was extracted using TRIzol Reagent (Invitrogen)/RNeasy Mini Kit (Qiagen)/other kits. Total RNA of each sample was quantified and qualified by Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA, USA), NanoDrop (Thermo Fisher Scientific Inc.) and 1% agrose gel. 1 μg total RNA with RIN value above 6.5 was used for following library preparation.
Next generation sequencing library preparations were constructed according to the manufacturer’s protocol. The poly(A) mRNA isolation was performed using Poly(A) mRNA Magnetic Isolation Module or rRNA removal Kit. The mRNA fragmentation and priming was performed using First Strand Synthesis Reaction Buffer and Random Primers. First strand cDNA was synthesized using ProtoScript II Reverse Transcriptase and the second-strand cDNA was synthesized using Second Strand Synthesis Enzyme Mix. The purified double-stranded cDNA by beads was then treated with End Prep Enzyme Mix to repair both ends and add a dA-tailing in one reaction, followed by a T-A ligation to add adaptors to both ends. Size selection of Adaptor-ligated DNA was then performed using beads, and fragments of ~420 bp (with the approximate insert size of 300 bp) were recovered. Each sample was then amplified by PCR for 13 cycles using P5 and P7 primers, with both primers carrying sequences which can anneal with flow cell to perform bridge PCR and P7 primer carrying a six-base index allowing for multiplexing. The PCR products were cleaned up using beads, validated using an Qsep100 (Bioptic，Taiwan， China), and quantified by Qubit3.0 Fluorometer (Invitrogen, Carlsbad, CA, USA).

treatment_protocol: Each eligible diagnosed as LTBI received weight-adjusted weekly 3HP regimen, including rifapentine (900 mg for participants with body weight >50.0 kg; 750 mg for 32.1–50.0 kg; 600 mg for 25.1–32.0 kg; and 450 mg for 14.1–25.0 kg) plus isoniazid (15 mg/kg, rounded up to nearest 150 mg; maximum 900 mg) for a total of 12 doses. Treatment was supervised by government-paid directly observed therapy (DOT) supporters.

value: peripheral blood mononuclear cells

tag: sample type

value: non-SDR

value: after treatment


title: CX11264_GZ_B7_E4_GZpool_06_2019


title: HC B cells rep6 (BCR-seq)

city: Harbin

first: Pingping

last: Wang

address: 92 West Dazhi Street,Nan Gang

institute: HIT

description: Single cell 5' and V(D)J sequencing

data_processing:
Single cell 5’ gene expression and V(D)J data was processed by Cell Ranger pipeline (version 3.1.0) for each sample. Reference data files refdata-cellranger-GRCh38-3.0.0 and refdata-cellranger-vdj-GRCh38-alts-ensembl-3.1.0 downloaded from 10x Genomics official website were used in Cell Ranger analysis pipelines for single-cell transcriptome and V(D)J data processing, separately.
Genome_build: GRCh38
Supplementary_files_format_and_content: Matrix table with UMI counts for every gene and every cell

source_name: Peripheral blood B cells

extract_protocol:
Fresh blood samples were collected from 8 PD patients and 6 age-matched healthy controls. Then, peripheral blood mononuclear cells (PBMCs) were isolated by Percoll density gradient centrifugation. Next, CD19+ B cells were sorted using fluorescence-activated cell sorting (FACS).
Single-cell 5’ gene expression libraries and V(D)J enriched libraries were prepared according to the standard protocols provided by the 10x Genomics Chromium Single Cell Immune Profiling Solution. Finally, single-cell 5’ gene expression and V(D)J libraries were sequenced on Illumina Noveseq 6000, providing 150 bp paired-end reads.
scRNA-seq

value: Male

value: Healthy control


title: 13dT_td+NT 1

description:
13dT-TdNT-1-LDJ7761_L1
3-fpkm.xlsx

tag: cell line

value: Stably expressing RfxCas13d

value: tdTomato and NT crRNA


title: HC B cells rep5 (BCR-seq)

description: Single cell 5' and V(D)J sequencing


title: CX11262_GZ_B7_E3_GZpool_06_2019

first: Gaotian

address: 2205 Tech Drive


title: monthly_10_3C

description: collected in Oct, control, replicate 1

source_name: soil DNA, Oct, control, replicate 1

value: control

value: replicate 1


title: non-SDR_after_treatment_N-T201-3

tag: treatment


title: CX11262_GZ_B6_I1_GZpool_04_2019


title: CX11264_GZ_B7_B7_GZpool_04_2019


title: monthly_9_16H

description: collected in Sep, warming, replicate 4

source_name: soil DNA, Sep, warming, replicate 4

value: collected in Sep

value: warming

value: replicate 4


title: non-SDR_after_treatment_N-N223-3


title: non-SDR_after_treatment_N-F226-3


title: CX11254_GZ_B8_F7_GZpool_06_2019


title: monthly_9_10H

description: collected in Sep, warming, replicate 2

source_name: soil DNA, Sep, warming, replicate 2

value: replicate 2


title: Lung Carcinoma Epithelial Cell (A549) - RSV-A Ontario - 96hr

source_name: Lung Carcinoma Epithelial Cell (A549)

value: Lung adenocarcinoma (A549)

value: immortalized cell line

value: Cells collected 96 hrs after  virus inoculation.


title: HC B cells rep3 (BCR-seq)

description: Single cell 5' and V(D)J sequencing

tag: disease state


title: non-SDR_after_treatment_N-F220-3


title: HC B cells rep4 (BCR-seq)

description: Single cell 5' and V(D)J sequencing


title: monthly_9_23C

description: collected in Sep, control, replicate 4

source_name: soil DNA, Sep, control, replicate 4


title: monthly_9_1H

description: collected in Sep, warming, replicate 1

source_name: soil DNA, Sep, warming, replicate 1


title: non-SDR_after_treatment_N-F129-3


title: CX11254_GZ_B8_D6_GZpool_04_2019

source_name: whole animals

value: young adult

value: hermaphrodite


title: CX11254_GZ_B8_B1_GZpool_03_2019


title: CB4856_GZ_B1_H3_GZpool_07_2020


title: non-SDR_after_treatment_N-B222-3

value: peripheral blood mononuclear cells

value: non-SDR


title: HC B cells rep2 (BCR-seq)

description: Single cell 5' and V(D)J sequencing

value: Female


title: monthly_9_19C

description: collected in Sep, control, replicate 3

source_name: soil DNA, Sep, control, replicate 3

value: replicate 3


title: CB4856_GZ_B6_C6_GZpool_06_2019


title: PD B cells rep8 (BCR-seq)

description: Single cell 5' and V(D)J sequencing

value: Male

value: Parkinson's disease


title: monthly_9_20H

description: collected in Sep, warming, replicate 3

source_name: soil DNA, Sep, warming, replicate 3


title: non-SDR_after_treatment_N-A120-3

value: after treatment


title: PD B cells rep7 (BCR-seq)

description: Single cell 5' and V(D)J sequencing


title: non-SDR_after_treatment_KMUH-0119


title: CB4856_GZ_B5_I9_GZpool_04_2019


title: monthly_9_6C

description: collected in Sep, control, replicate 2

source_name: soil DNA, Sep, control, replicate 2

value: control


title: PD B cells rep6 (BCR-seq)

description: Single cell 5' and V(D)J sequencing


title: CB4852_GZr_B5_G3_GZpool_08_2020


title: PD B cells rep5 (BCR-seq)

description: Single cell 5' and V(D)J sequencing


title: monthly_9_3C

description: collected in Sep, control, replicate 1

source_name: soil DNA, Sep, control, replicate 1

value: collected in Sep

value: replicate 1


title: non-SDR_after_treatment_KMTH-0211


title: HC B cells rep1 (BCR-seq)

description: Single cell 5' and V(D)J sequencing

value: Healthy control


title: CB4852_GZ_B7_B6_GZpool_06_2019


title: PD B cells rep4 (BCR-seq)

description: Single cell 5' and V(D)J sequencing


title: monthly_8_10H

description: collected in Aug, warming, replicate 2

source_name: soil DNA, Aug, warming, replicate 2

value: collected in Aug

value: warming

value: replicate 2


title: PD B cells rep3 (BCR-seq)

description: Single cell 5' and V(D)J sequencing


title: CB4852_GZ_B6_H9_GZpool_04_2019


title: monthly_8_20H

description: collected in Aug, warming, replicate 3

source_name: soil DNA, Aug, warming, replicate 3


title: BRC20263_GZr_B7_I5_GZpool_08_2020


title: monthly_8_1H

description: collected in Aug, warming, replicate 1

source_name: soil DNA, Aug, warming, replicate 1


title: non-SDR_after_treatment_KMTH-0060


title: non-SDR_after_treatment_KMTH-0205


title: non-SDR_before_treatment_TDM-0198

description: non-SDR samples before 3HP treatment from peripheral blood mononuclear cells

source_name: non-SDR_samples _before_treatment

value: before treatment


title: PD B cells rep1 (BCR-seq)

description: Single cell 5' and V(D)J sequencing


title: monthly_8_23C

description: collected in Aug, control, replicate 4

source_name: soil DNA, Aug, control, replicate 4

value: replicate 4


title: monthly_8_19C

description: collected in Aug, control, replicate 3

source_name: soil DNA, Aug, control, replicate 3


title: non-SDR_before_treatment_TDM-0150


title: BRC20263_GZ_B7_I6_GZpool_04_2019

value: young adult

value: hermaphrodite


title: HC B cells rep6 (GEX)

description: Single cell 5' and V(D)J sequencing

source_name: Peripheral blood B cells


title: monthly_8_6C

description: collected in Aug, control, replicate 2

source_name: soil DNA, Aug, control, replicate 2


title: non-SDR_before_treatment_TDM-0096

value: peripheral blood mononuclear cells

value: non-SDR


title: HC B cells rep5 (GEX)

description: Single cell 5' and V(D)J sequencing


title: BRC20067_GZr_B1_H2_GZpool_08_2020


title: monthly_8_16H

description: collected in Aug, warming, replicate 4

source_name: soil DNA, Aug, warming, replicate 4


title: BRC20067_GZr_B4_B9_GZpool_07_2020


title: non-SDR_before_treatment_KMUH-0099


title: BRC20067_GZ_B1_A3_GZpool_01_2019


title: non-SDR_before_treatment_KMTH-0207


title: non-SDR_before_treatment_TDM-0204


title: HC B cells rep4 (GEX)

description: Single cell 5' and V(D)J sequencing


title: PD B cells rep2 (BCR-seq)

description: Single cell 5' and V(D)J sequencing

value: Female


title: monthly_7_20H

description: collected in Jul, warming, replicate 3

source_name: soil DNA, Jul, warming, replicate 3

value: collected in Jul

value: replicate 3


title: monthly_8_3C

description: collected in Aug, control, replicate 1

source_name: soil DNA, Aug, control, replicate 1


title: monthly_7_16H

description: collected in Jul, warming, replicate 4

source_name: soil DNA, Jul, warming, replicate 4


title: AB1_GZr_B3_C9_GZpool_07_2020

source_name: whole animals


title: non-SDR_before_treatment_KMTH-0204


title: AB1_GZr_B3_A3_GZpool_07_2020


title: HC B cells rep2 (GEX)

description: Single cell 5' and V(D)J sequencing


title: HC B cells rep3 (GEX)

description: Single cell 5' and V(D)J sequencing

value: Male


title: monthly_7_10H

description: collected in Jul, warming, replicate 2

source_name: soil DNA, Jul, warming, replicate 2


title: BRC20263_GZ_B7_I9_GZpool_02_2019


title: HC B cells rep1 (GEX)

description: Single cell 5' and V(D)J sequencing


title: AB1_GZ_B5_D6_GZpool_02_2019


title: SDR_after_treatment_N-F228-1

description: SDR samples after 3HP treatment from peripheral blood mononuclear cells

source_name: SDR_samples _after_treatment

value: SDR

value: after treatment


title: PD B cells rep8 (GEX)

description: Single cell 5' and V(D)J sequencing

value: Parkinson's disease


title: monthly_7_1H

description: collected in Jul, warming, replicate 1

source_name: soil DNA, Jul, warming, replicate 1

value: replicate 1


title: SDR_after_treatment_N-A201-1


title: 3F-N2A-td-cr7 3

description:
2-fpkm.xlsx
3F-N2A-Td-G7-2-LDK0859_L1

data_processing:
The raw fastq files were trimmed to clean data by trim-galore software.
The clean data were aligned to mm10 genome using subread, which produced the BAM type file directly.
The featureCounts command line tool was used to calculate the gene count matrix.
Then the count matrix was normalized with FPKM formula.
The GFOLD software was used to identify the differentially expressed genes.
Genome_build: UCSC mm10 genome was used as reference genome.
Supplementary_files_format_and_content: *-fpkm.xlsx: Excel spreadsheets include the FPKM values for each sample.

source_name: N2a cells

growth_protocol: N2a cells were cultured in DMEM medium supplemented with 10% FBS (Gibco) and 100U/ml Penicillin-Streptomycin in a humidified incubator at 37 °C with 5% CO2.

treatment_protocol: Transfecting plasmids encoding RfxCas13d and tdTomato crRNA 7 into N2a cells stably expressing tdTomato. Cells were collected for total RNA extraction 48 hour after transfection.

value: Stably expressing tdTomato

value: RfxCas13d and td-cr7 cRNA


title: PD B cells rep6 (GEX)

description: Single cell 5' and V(D)J sequencing


title: 3F-N2A-td-cr7 2

description:
2-fpkm.xlsx
3F-N2A-Td-G7-1-LDK0858_L1


title: monthly_7_19C

description: collected in Jul, control, replicate 3

source_name: soil DNA, Jul, control, replicate 3

value: control


title: SDR_after_treatment_K-R221-1


title: SDR_after_treatment_K-T260-1


title: 3F-N2A-td-cr7 1

description:
2-fpkm.xlsx
3F-N2A-Td-G7-LDM1725_L0


title: monthly_7_6C

description: collected in Jul, control, replicate 2

source_name: soil DNA, Jul, control, replicate 2

value: replicate 2


title: monthly_7_3C

description: collected in Jul, control, replicate 1

source_name: soil DNA, Jul, control, replicate 1


title: 3F-N2A-td-cr4 3

description:
2-fpkm.xlsx
3F-N2A-Td-G4-2-LDK0857_L1

treatment_protocol: Transfecting plasmids encoding RfxCas13d and tdTomato crRNA 4 into N2a cells stably expressing tdTomato. Cells were collected for total RNA extraction 48 hour after transfection.

value: RfxCas13d and td-cr4 cRNA


title: monthly_6_16H

description: collected in Jun, warming, replicate 4

source_name: soil DNA, Jun, warming, replicate 4

value: collected in Jun

value: warming

value: replicate 4


title: non-SDR_before_treatment_KMTH-0056

source_name: non-SDR_samples _before_treatment

value: peripheral blood mononuclear cells

value: non-SDR

value: before treatment


title: SDR_after_treatment_K-E223-1


title: PD B cells rep3 (GEX)

description: Single cell 5' and V(D)J sequencing

value: Female


title: 3F-N2A-td-cr4 1

description:
2-fpkm.xlsx
3F-N2A-Td-G4-LDM1724_L0


title: PD B cells rep2 (GEX)

description: Single cell 5' and V(D)J sequencing


title: PD B cells rep1 (GEX)

description: Single cell 5' and V(D)J sequencing


title: monthly_6_10H

description: collected in Jun, warming, replicate 2

source_name: soil DNA, Jun, warming, replicate 2


title: SDR_after_treatment_K-G120-1


title: monthly_7_23C

description: collected in Jul, control, replicate 4

source_name: soil DNA, Jul, control, replicate 4

value: collected in Jul


title: PD B cells rep7 (GEX)

description: Single cell 5' and V(D)J sequencing

source_name: Peripheral blood B cells

value: Male


title: 3F-N2A-td-cr4 2

description:
2-fpkm.xlsx
3F-N2A-Td-G4-1-LDK0856_L1


title: 3F-N2A-NT 2

description:
2-fpkm.xlsx
3F-N2A-NT-1-LDK0854_L1

treatment_protocol: Transfecting plasmids encoding RfxCas13d and NT crRNA into N2a cells stably expressing tdTomato. Cells were collected for total RNA extraction 48 hour after transfection.

value: RfxCas13d and NT cRNA


title: SDR_before_treatment_N-F228-0

description: SDR samples before 3HP treatment from peripheral blood mononuclear cells

source_name: SDR_samples _before_treatment

value: SDR


title: PD B cells rep4 (GEX)

description: Single cell 5' and V(D)J sequencing

value: Parkinson's disease


title: monthly_6_23C

description: collected in Jun, control, replicate 4

source_name: soil DNA, Jun, control, replicate 4


title: 3F-N2A-NT 1

description:
2-fpkm.xlsx
3F-N2A-NT-LDM1726_L0

value: Stably expressing tdTomato


title: PD B cells rep5 (GEX)

description: Single cell 5' and V(D)J sequencing


title: SDR_before_treatment_N-A201-0


title: WT-N2A-Rbfox3-cr5 3

description:
1-fpkm.xlsx
N-NEUN-G5-3-LDL3806_L3

treatment_protocol: Transfecting plasmids encoding RfxCas13d and Rbfox3 crRNA 5 into WT N2a cells. Cells were collected for total RNA extraction 48 hour after transfection.

value: WT

value: RfxCas13d and Rbfox3-cr5 cRNA


title: SDR_before_treatment_K-T260-0


title: monthly_6_6C

description: collected in Jun, control, replicate 2

source_name: soil DNA, Jun, control, replicate 2

value: control

value: replicate 2


title: monthly_6_19C

description: collected in Jun, control, replicate 3

source_name: soil DNA, Jun, control, replicate 3

value: collected in Jun

value: replicate 3


title: WT-N2A-Rbfox3-cr5 2

description:
1-fpkm.xlsx
N-NEUN-G5-2-LDL3818_L3


title: SDR_after_treatment_K-E220-1

value: after treatment


title: WT-N2A-Rbfox3-cr5 1

description:
1-fpkm.xlsx
N-NEUN-G5-1-LDL3814_L3


title: SDR_before_treatment_K-R221-0

value: peripheral blood mononuclear cells


title: SDR_before_treatment_K-G120-0


title: WT-N2A-Rbfox3-cr3 3

description:
1-fpkm.xlsx
WT-NEUN-G3-LDL3816_L3

treatment_protocol: Transfecting plasmids encoding RfxCas13d and Rbfox3 crRNA 3 into WT N2a cells. Cells were collected for total RNA extraction 48 hour after transfection.

value: RfxCas13d and Rbfox3-cr3 cRNA


title: SDR_after_treatment_K-E120-1


title: monthly_6_20H

description: collected in Jun, warming, replicate 3

source_name: soil DNA, Jun, warming, replicate 3

value: warming


title: SDR_before_treatment_K-E223-0

value: before treatment


title: monthly_5_16H

description: collected in May, warming, replicate 4

source_name: soil DNA, May, warming, replicate 4

value: collected in May

value: replicate 4


title: 3F-N2A-NT 3

description:
2-fpkm.xlsx
3F-N2A-NT-2-LDK0855_L1

value: RfxCas13d and NT cRNA


title: SDR_before_treatment_K-E220-0

value: SDR


title: SDR_before_treatment_K-E120-0


title: WT-N2A-Mapt-cr6 3

description:
1-fpkm.xlsx
WT-TAU-G6-LDL3808_L3

treatment_protocol: Transfecting plasmids encoding RfxCas13d and Mapt crRNA 6 into WT N2a cells. Cells were collected for total RNA extraction 48 hour after transfection.

value: RfxCas13d and Mapt-cr6 cRNA


title: monthly_5_20H

description: collected in May, warming, replicate 3

source_name: soil DNA, May, warming, replicate 3


title: WT-N2A-Rbfox3-cr3 1

description:
1-fpkm.xlsx
WT-N2A-NeuN-G3-1-LDK0838_L1


title: monthly_6_1H

description: collected in Jun, warming, replicate 1

source_name: soil DNA, Jun, warming, replicate 1

value: replicate 1


title: monthly_5_10H

description: collected in May, warming, replicate 2

source_name: soil DNA, May, warming, replicate 2


title: chronic ethanol alone, rep2

city: duarte

first: LU

last: YANG

address: 1500 duarte rd

institute: city of hope

description:
24955_4_S29
mRNA-seq

data_processing:
Illumina RTA was used to create .bcl files, and bcl2fastq v2.20.0.422 software was used for base calling (for samples split between flowcells and later merged per run).
RNA-seq reads aligned to the GRCm38 genome assembly using STAR_2.6.0a. Aligned reads was normalized by edgeR bioconductor package and outputed as rpkm.txt file.
Genome_build: Genome Reference Consortium GRCm38
Supplementary_files_format_and_content: HTseq_counts_4s.txt: Raw count table in txt format of every sample in RNAseq project.

source_name: Liver

extract_protocol:
Livers were removed, flash frozen on dry ice, and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit was used with 1 ug of total RNA for the construction of sequencing libraries.
mRNA sequencing libraries were constructed with KAPA mRNA HyperPrep Kits (KAPA Biosystems; Cat # KK8580) followed by manufacturer's protocol.

treatment_protocol: Wild type (8-10 week old) mice were subjected to chronic ethanol feeding using the Lieber-DeCarli liquid diet containing 5% ethanol for 10 days followed by ethanol binge (5g/kg body weight). 9 hours later, the animals were sacrificed.

value: Wild type

value: liver

value: adult (8-10 weeks)

value: chronic ethanol alone


title: WT-N2A-Mapt-cr6 2

description:
1-fpkm.xlsx
WT-N2A-TAU-G6-2-LDK0845_L1

source_name: N2a cells

value: WT


title: chronic ethanol + gavage 9 hour, rep2

description:
24954_3_S28
mRNA-seq

value: chronic ethanol + gavage 9 hour


title: monthly_5_23C

description: collected in May, control, replicate 4

source_name: soil DNA, May, control, replicate 4

value: control


title: monthly_5_1H

description: collected in May, warming, replicate 1

source_name: soil DNA, May, warming, replicate 1


title: chronic ethanol alone, rep1

description:
24953_2_S27
mRNA-seq


title: WT-N2A-Mapt-cr4 3

description:
1-fpkm.xlsx
WT-TAU-G4-LDL3810_L3

treatment_protocol: Transfecting plasmids encoding RfxCas13d and Mapt crRNA 4 into WT N2a cells. Cells were collected for total RNA extraction 48 hour after transfection.

value: RfxCas13d and Mapt-cr4 cRNA


title: WT-N2A-Mapt-cr6 1

description:
1-fpkm.xlsx
WT-N2A-TAU-G6-1-LDK0844_L1


title: monthly_6_3C

description: collected in Jun, control, replicate 1

source_name: soil DNA, Jun, control, replicate 1

value: collected in Jun


title: monthly_5_19C

description: collected in May, control, replicate 3

source_name: soil DNA, May, control, replicate 3

value: replicate 3


title: monthly_5_6C

description: collected in May, control, replicate 2

source_name: soil DNA, May, control, replicate 2

value: replicate 2


title: 1°OGC_Zfp276cko, biological replicate 2

city: Erlangen

first: Melanie

last: Küspert

address: Fahrstraße 17

department: Institute of Biochemistry

country: Germany

description:
OGC_Zfp276cko_2
RNA-Seq data from 1° mouse OGCs (Zfp276cko).

data_processing:
Sequencing data were pooled using the Illumina HiSeq 2500 platform and converted into fastq files.
Reads from rRNA, tRNA, mt-rRNA and mt-tRNA were purged from demultiplexed reads.
Reads were aligned to mm10 reference genome (GRCm38, Ensembl Annotation Release 91) using STAR aligner (version 2.5.4a).
Read counts per gene were obtained using featureCounts program version 1.5.1 (Liao et al., 2014) and the Ensembl gtf annotation file (Release 91).
Statistical analysis of raw data was done with DESeq2 by R version 1.22.2.
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: *_counts.tabular.txt: Tab-delimited text files
Supplementary_files_format_and_content: OGC_Zfp276cko_vs_Ctrl.xlsx: Excel file

source_name: primary oligodendrocyte culture of Zfp276cko mice

growth_protocol: 1°OGCs were kept in differentiating conditions for 3 days after shake off and microglia depletion.

extract_protocol:
Total RNA was extracted from 1° OGCs using the RNeasy Mini Kit according to the manufacturer's (QIAGEN) protocol and underwent DNaseI treatment.
RNA libraries were prepared for sequencing using TruSeq Stranded mRNA Kit (Illumina).
Single end sequencing (101 bp) on HiSeq-2500 platform (Illumina, San Diego, CA).

value: primary mouse oligodendroglial cultures from P2-P4 forebrain tissue

value: Sox10::Cre tg; Zfp276 flox/flox


title: chronic ethanol + gavage 9 hour, rep1

description:
24952_1_S26
mRNA-seq


title: monthly_4_16H

description: collected in Apr, warming, replicate 4

source_name: soil DNA, Apr, warming, replicate 4

value: collected in Apr

value: warming

value: replicate 4


title: WT-N2A-Rbfox3-cr3 2

description:
1-fpkm.xlsx
WT-N2A-NeuN-G3-2-LDK0839_L1

value: RfxCas13d and Rbfox3-cr3 cRNA


title: WT-N2A-Mapt-cr4 1

description:
1-fpkm.xlsx
WT-N2A-TAU-G4-1-LDK0842_L1


title: monthly_4_20H

description: collected in Apr, warming, replicate 3

source_name: soil DNA, Apr, warming, replicate 3


title: WT-N2A-Mapt-cr4 2

description:
1-fpkm.xlsx
WT-N2A-TAU-G4-2-LDK0843_L1


title: WT-N2A-Map2-cr3 3

description:
1-fpkm.xlsx
WT-MAP2-G3-LDL3807_L3

treatment_protocol: Transfecting plasmids encoding RfxCas13d and Map2 crRNA 3 into WT N2a cells. Cells were collected for total RNA extraction 48 hour after transfection.

value: RfxCas13d and Map2-cr3 cRNA


title: WT-N2A-Map2-cr3 2

description:
1-fpkm.xlsx
WT-N2A-Map2-G3-2-LDK0837_L1


title: monthly_4_10H

description: collected in Apr, warming, replicate 2

source_name: soil DNA, Apr, warming, replicate 2


title: WT-N2A-Map2-cr3 1

description:
1-fpkm.xlsx
WT-N2A-Map2-G3-1-LDK0836_L1


title: 1°OGC_Ctrl, biological replicate 1

description:
OGC_Ctrl_1
RNA-Seq data from 1° mouse OGCs (Ctrl).

source_name: primary oligodendrocyte culture of Ctrl mice

value: Zfp276 flox/flox


title: monthly_4_1H

description: collected in Apr, warming, replicate 1

source_name: soil DNA, Apr, warming, replicate 1

value: replicate 1


title: anti-PDL1-54

city: Seattle

first: Mark

last: Maurer

state: WA

address: 188 E Blaine St. Suite 200

department: Translation Science

institute: Alpine Immune Sciences

data_processing:
Dual-index, single-read sequencing of pooled libraries was carried out on a HiSeq2500 sequencer (Illumina) with 58-base reads, using HiSeq v4 Cluster and SBS kits (Illumina) with a target depth of 5 million reads per sample.
Base calls were processed to FASTQs on BaseSpace (Illumina), and a base call quality-trimming step was applied to remove low-confidence base calls from the ends of reads using Galaxy FASTQ Trimmer tool v1.0.0.
The FASTQs were aligned to the mouse reference genome, using TopHat aligner (v1.4.1) with the NCBIM37 reference genome and gene annotations from ensembl release 67.
Gene counts were generated using HTSeq-count (v0.4.1).
Quality metrics were compiled from PICARD (v1.134), FASTQC (v0.11.3), Samtools (v1.2), and HTSeq-count (v0.4.1).
Genome_build: NCBIM37
Supplementary_files_format_and_content: Processed_RNAseq_data_Maurer_etal.xlsx

source_name: MC38/hPD-L1 tumor - anti-PDL1 mAb Rep 4

extract_protocol:
Tumors were snap frozen and then RNA isolated by sonication and standard mRNA isolation kit from Qiagen.
Total RNA (0.5 ng) was added to lysis buffer from the SMART-Seq v4 Ultra Low Input RNA Kit for Sequencing (Takara), and reverse transcription was performed followed by PCR amplification to generate full length amplified cDNA. Sequencing libraries were constructed using the NexteraXT DNA sample preparation kit (Illumina) to generate Illumina-compatible barcoded libraries.  Libraries were pooled and quantified using a Qubit® Fluorometer (Life Technologies).

treatment_protocol: Animals were dosed intraperitoneally with a single dose of test article and then tumors were collected and mRNA isolated 72 hours later

value: MC38/hPD-L1 tumor

value: Anti-PDL1 mAb (durvalumab)

tag: mouse strain


title: WT-N2A-Map2-cr1 3

description:
1-fpkm.xlsx
WT-MAP2-G1-LDL3813_L3

treatment_protocol: Transfecting plasmids encoding RfxCas13d and Map2 crRNA 1 into WT N2a cells. Cells were collected for total RNA extraction 48 hour after transfection.

value: WT

value: RfxCas13d and Map2-cr1 cRNA


title: monthly_4_23C

description: collected in Apr, control, replicate 4

source_name: soil DNA, Apr, control, replicate 4

value: control


title: monthly_5_3C

description: collected in May, control, replicate 1

source_name: soil DNA, May, control, replicate 1

value: collected in May


title: anti-PDL1-52

source_name: MC38/hPD-L1 tumor - anti-PDL1 mAb Rep 2


title: WT-N2A-Map2-cr1 2

description:
1-fpkm.xlsx
WT-N2A-Map2-G1-2-LDK0835_L1


title: monthly_4_19C

description: collected in Apr, control, replicate 3

source_name: soil DNA, Apr, control, replicate 3

value: replicate 3


title: monthly_4_6C

description: collected in Apr, control, replicate 2

source_name: soil DNA, Apr, control, replicate 2

value: replicate 2


title: monthly_4_3C

description: collected in Apr, control, replicate 1

source_name: soil DNA, Apr, control, replicate 1


title: WT-N2A-Sik3-SI-cr8 2

description:
1-fpkm.xlsx
WT-N2A-K3-SI-G8-2-LDK0849_L1

source_name: N2a cells

treatment_protocol: Transfecting plasmids encoding RfxCas13d and Sik3-SI crRNA 8 into WT N2a cells. Cells were collected for total RNA extraction 48 hour after transfection.

value: RfxCas13d and Sik3-SI-cr8 cRNA


title: 1°OGC_Zfp276cko, biological replicate 1

description:
OGC_Zfp276cko_1
RNA-Seq data from 1° mouse OGCs (Zfp276cko).

value: primary mouse oligodendroglial cultures from P2-P4 forebrain tissue

value: Sox10::Cre tg; Zfp276 flox/flox


title: ALPN202-29

source_name: MC38/hPD-L1 tumor - ALPN-202 Rep 4


title: anti-PDL1-51

source_name: MC38/hPD-L1 tumor - anti-PDL1 mAb Rep 1


title: WT-N2A-Map2-cr1 1

description:
1-fpkm.xlsx
WT-N2A-Map2-G1-1-LDK0834_L1


title: WT-N2A-Sik3-SI-cr8 1

description:
1-fpkm.xlsx
WT-N2A-K3-SI-G8-1-LDK0848_L1


title: monthly_3_10H

description: collected in Mar, warming, replicate 2

source_name: soil DNA, Mar, warming, replicate 2

value: collected in Mar

value: warming


title: monthly_3_20H

description: collected in Mar, warming, replicate 3

source_name: soil DNA, Mar, warming, replicate 3


title: ALPN202-26

source_name: MC38/hPD-L1 tumor - ALPN-202 Rep 1


title: WT-N2A-Sik3-SI-cr1 3

description:
1-fpkm.xlsx
WT-K3-SI-G1-LDL3817_L3

treatment_protocol: Transfecting plasmids encoding RfxCas13d and Sik3-SI crRNA 1 into WT N2a cells. Cells were collected for total RNA extraction 48 hour after transfection.

value: RfxCas13d and Sik3-SI-cr1 cRNA


title: ALPN202-27

source_name: MC38/hPD-L1 tumor - ALPN-202 Rep 2


title: anti-PDL1-53

source_name: MC38/hPD-L1 tumor - anti-PDL1 mAb Rep 3


title: monthly_3_1H

description: collected in Mar, warming, replicate 1

source_name: soil DNA, Mar, warming, replicate 1


title: WT-N2A-Sik3-SI-cr1 1

description:
1-fpkm.xlsx
WT-N2A-K3-SI-G1-1-LDK0846_L1


title: 1°OGC_Ctrl, biological replicate 2

description:
OGC_Ctrl_2
RNA-Seq data from 1° mouse OGCs (Ctrl).

source_name: primary oligodendrocyte culture of Ctrl mice


title: Fc-04

source_name: MC38/hPD-L1 tumor - Fc control Rep 4

value: Fc Control


title: WT-N2A-Sik3-SI-cr1 2

description:
1-fpkm.xlsx
WT-N2A-K3-SI-G1-2-LDK0847_L1


title: Fc-03

source_name: MC38/hPD-L1 tumor - Fc control Rep 3


title: monthly_3_19C

description: collected in Mar, control, replicate 3

source_name: soil DNA, Mar, control, replicate 3


title: Fc-01

source_name: MC38/hPD-L1 tumor - Fc control Rep 1


title: WT-N2A-NT 5

description:
1-fpkm.xlsx
N-NT-3-LDL3804_L3

treatment_protocol: Transfecting plasmids encoding RfxCas13d and NT crRNA into WT N2a cells. Cells were collected for total RNA extraction 48 hour after transfection.

value: RfxCas13d and NT cRNA


title: monthly_3_6C

description: collected in Mar, control, replicate 2

source_name: soil DNA, Mar, control, replicate 2


title: WT-N2A-Sik3-SI-cr8 3

description:
1-fpkm.xlsx
WT-K3-SI-G8-LDL3811_L3


title: monthly_3_23C

description: collected in Mar, control, replicate 4

source_name: soil DNA, Mar, control, replicate 4

value: replicate 4


title: monthly_3_3C

description: collected in Mar, control, replicate 1

source_name: soil DNA, Mar, control, replicate 1

value: replicate 1


title: WT-N2A-NT 6

description:
1-fpkm.xlsx
WT-NT-LDL3812_L3

source_name: N2a cells


title: WT-N2A-NT 3

description:
1-fpkm.xlsx
N-NT-1-LDL3803_L3


title: monthly_2_16H

description: collected in Feb, warming, replicate 4

source_name: soil DNA, Feb, warming, replicate 4

value: collected in Feb


title: monthly_3_16H

description: collected in Mar, warming, replicate 4

source_name: soil DNA, Mar, warming, replicate 4


title: ALPN202-28

source_name: MC38/hPD-L1 tumor - ALPN-202 Rep 3

value: MC38/hPD-L1 tumor


title: 1566 SARS-CoV-2 1 DPI replicate 2

first: Feiya

address: 670 Albany street, 2nd floor

institute: Center for Regenerative Medicine, Boston University

source_name: 1566 SARS-CoV-2 1 DPI replicate 2

growth_protocol: Both BU3 NGPT and 1566 iPSC lines were differentiated into airway epithelium according to the methods described by Hawkins et al., Cell Stem Cell, 2021 (PMID: 33098807). The protocol involves the step-wise directed differentiation of iPSCs to airway as published previously.  In brief, it recapitulates the major stages of embryonic lung development as follows:   Stage 1) Definitive endoderm (D0-3) using STEMdiff™ Definitive Endoderm Kit;  Stage 2) Anterior foregut endoderm (D3-6) through TGFb and BMP inhibition; Stage 3) Lung specification (D6-15) using a combination of CHIR 99021 (to activate WNT signaling), BMP4, and retinoid acid and evidenced by the expression of NKX2-1. We then purify these NKX2-1+ lung epithelial progenitors at D15 through either sorting on GFP (BU3 NGPT) or for non-reporter line, utilizing a CD47hi/CD26neg sorting strategy;  Stage 4) Early airway organoids (D15-30), where  GFP+ (BU3 NGPT) or CD47hi/CD26neg sorted cells (1566) are plated in 3D Matrigel and cultured in media containing FGF2 and FGF10 for patterning toward proximal airway-like organoids composed of immature secretory and basal progenitors.  Stage 5) iBCs (D30-45), during which the iPSC-3D organoids are further expanded in dual-SMAD inhibition media with DMH-1 and A83-01 for ~12 days 74, 75.   iBCs were either serially passaged or cryopreserved, thawed and then serially passaged to generate cells for stage 6. Stage 6) Airway differentiation on ALI culture (>D45) iBCs are identified and purified by sorting on NGFR+ cells, and purified cells are expanded and differentiated on Transwells in dual-SMAD inhibition media then transitioned to ALI media when >80% confluent. Apical chamber media is removed to initiate ALI to recapitulate a physiologically-relevant environment and stimulate differentiation.  After 14 days, iBCs form a pseudostratified airway epithelium that displays morphologic, molecular, and functional similarities to primary human airway epithelial cells and is comprised of the major airway cell types of multi-ciliated, secretory, and basal cells40.

extract_protocol:
RNeasy Mini Kit (Qiagen)
poly(A) selection & reverse transcription

treatment_protocol: Prior to infection, the apical side of iPSC-airway plated in ALI culture was washed with 100 μL of PBS for 5-10 minutes at 37 C to remove the mucus.  Then, purified SARS-CoV-2 stock (100 μL of inoculum prepared in PBS) or PBS without virus (mock infection) was added at the apical chambers of each Transwell at a multiplicity of infection (MOI) of 4 and allowed to adsorb for 1 hour at 37oC and 5% CO2.  After adsorption, the inoculum was removed and cells were incubated at ALI at 37 C for 3 days.

tag: media

value: PneumaCult ALI

tag: culture format

value: Air liquid interface culture on Transwells

value: iPSC-derived airway epithelium


title: 1566 SARS-CoV-2 1 DPI replicate 3

source_name: 1566 SARS-CoV-2 1 DPI replicate 3