title: Xmoo1 line, ctrl, replicate 2, for bulk RNA-seq

description:
merged_raw_read_counts.txt.gz
HSV1GFPtrunc_corr.fa.gz
HSV1GFPtrunc_corr.gtf.gz
xmoo1_ctrl_rep2
TruSeq Stranded Total LT Sample Prep Kit (Illumina)

data_processing:
For bulk RNA-sequencing, Illumina base calling, demultiplexing and FASTQ conversion with bcl2fastq v2.20.0 (Illumina)
alignment to GRCh38 genome using STAR v2.7.1a (https://github.com/alexdobin/STAR)
reads counted on GENCODE 27 gene models with htseq-count 0.9.1 (https://htseq.readthedocs.io/)
The HSV1 genome was extended from strain 17 (genbank entry NC_001806) with the GFP and loxP sequences, error-corrected based on the total RNA-sequencing data, and terminal repeats removed to avoid multi-mapping reads
Provided here are the resulting HSV-1 fasta and gtf file used in the data analysis
For FLAM-seq, the CCS reads were then used as input to the FLAManalysis pipeline (https://github.com/rajewsky-lab/FLAMAnalysis), that outputs gene assignment and poly(A) tail length and sequence for each read.
For single-cell RNA-sequencing, data was processed using the pigx pipeline version 1.1.4 (http://bioinformatics.mdc-berlin.de/pigx/, Wurmus et al. 2018 doi: 10.1093/gigascience/giy123) using a combined human/HSV1 genome
Genome_build: Homo sapiens hg38
Genome_build: HSV-1 GFP truncated corrected
Supplementary_files_format_and_content: fasta file
Supplementary_files_format_and_content: gtf file
Supplementary_files_format_and_content: tab-separated values

source_name: Brain organoid

extract_protocol:
For isolation of bulk RNA, organoids were dissolved in Trizol. Ribosomal RNA was depleted using Rnase H (Epicentre)
Total bulk RNA-seq libraries were generated using the TruSeq Stranded Total LT Sample Prep Kit (Illumina). FLAMseq libraries were constructed as previously described (Legnini et al. 2019, doi: 10.1038/s41592-019-0503-y)

value: Brain organoid

tag: hsv-1 infection status

value: no

tag: sampling timepoint

tag: rna population

value: rRNA-depleted RNA


title: Female2_VI2c

status: Public on Jan 22 2021

type: SRA

city: Cambridge

first: Evan

last: Macosko

state: MA

address: 75 Ames St, Broad Institute

country: USA

institute: Broad Institute

description:
single-nuclei gene expression data
cb_adult_mouse.mtx.gz
cb_adult_mouse_barcodes.txt
cb_adult_mouse_genes.txt
golgi_joint.mtx.gz
golgi_joint_barcodes.txt
golgi_joint_genes.txt
granule_joint.mtx.gz
granule_joint_barcodes.txt
granule_joint_genes.txt
interneuron_joint.mtx.gz
interneuron_joint_barcodes.txt
interneuron_joint_genes.txt
ubc_joint.mtx.gz
ubc_joint_barcodes.txt
ubc_joint_genes.txt

library_source: transcriptomic

data_processing:
Sequencing performed on Illumina NovaSeq6000
Mouse sequencing reads were demultiplexed and aligned using 10x Cell Ranger software (Ver. 3.0.2) to the mouse reference genome (ENSEMBL Release 78/GRCm38.p3) for each sample individually. Genome_build: mm10
Mouse Digital gene expression matrices (with gene expression counts) were generated by Cell Ranger software (v3.0.2)
Human sequencing reads were demultiplexed and aligned using drop-seq tools to the human reference genome (ENSEMBL Release 78/GRCh37) for each sample individually. The drop-seq pipeline was run using exonic and intronic data as UMIs. The human gene expression matrices were also generated using drop-seq tools (2020-06-17)
Digital gene expression matrices were aggregated and analyzed with Seurat v2.3.4 and liger v0.4.2.
Genome_build: mouse samples: mm10_premrna
Genome_build: human samples: hg19
Supplementary_files_format_and_content: digital gene expression matrix (sparse format): matrix market format, rows = genes/transcripts, columns = barcodes/cells. All files for each set of libraries were included in a tar archive available on the series record.
Supplementary_files_format_and_content: barcodes.txt: names of barcodes/cells for corresponding DGE matrix file
Supplementary_files_format_and_content: genes.txt: names of transcripts/genes for corresponding DGE matrix file
In processed data, human data dropseq tools pipeline used exonic and intronic as UMIS
Developmental mouse cerebellum libraries were aggregated into cb_dev_ints.mtx.gz
Adult mouse cerebellum libraries were aggregated into cb_adult_mouse.mtx.gz.
The file cb_processed_initial.mtx.gz includes all adult mouse cerebellum libraries. Purkinje cell enriched libraries Purk_F004, Purk_F0S1 were removed from cb_processed_initial.mtx.gz (due to batch effects) to create cb_adult_mouse.mtx.gz which was used in subsequent analysis.
Human cerebellum libraries were aggregated into human_combined.mtx.gz
The mouse (adult and developmental) libraries were combined with the human libraries and separated into golgi_joint.mtx.gz (Golgi cells), granule_joint.mtx.gz (Granule Cells), interneuron_joint.mtx.gz (Interneuron cells), and ubc_joint.mtx.gz (Unipolar Brush cells) matrices

molecule: polyA RNA

organism: Mus musculus

source_name: P60 Cerebellum

extract_protocol:
Please see https://www.protocols.io/view/frozen-tissue-nuclei-extraction-for-10xv3-snseq-bi62khge
10X Chromium Single Cell 3' (V3) (manufacturer's protocol)

tag: strain

tag: age

tag: Sex

value: Female

tag: 10x version

tag: genome build


title: Xmoo1 line, ctrl, replicate 1, for bulk RNA-seq

city: Berlin

first: Emanuel

last: Wyler

address: Robert Roessle Str 10

department: Berlin Institute for Medical Systems Biology

country: Germany

institute: Max Delbrück Center for Molecular Medicine

description:
merged_raw_read_counts.txt.gz
HSV1GFPtrunc_corr.fa.gz
HSV1GFPtrunc_corr.gtf.gz
xmoo1_ctrl_rep1
TruSeq Stranded Total LT Sample Prep Kit (Illumina)

molecule: total RNA

organism: Homo sapiens

growth_protocol: Cerebral organoids were generated according to modified Lancaster protocol (Lancaster et al., 2013, doi: 10.1038/nature12517),

treatment_protocol: Organoids were infected using Herpes simplex virus 1, strain 17 containing a GFP gene controlled by an MCMV promoter (Snijder et al. 2012, doi: 10.1038/msb.2012.9)

tag: tissue


title: Male6_VI2b

value: Male


title: iPSC-2 line (Thermo Fisher A18945), ctrl, replicate 1, for bulk RNA-seq

description:
merged_raw_read_counts.txt.gz
HSV1GFPtrunc_corr.fa.gz
HSV1GFPtrunc_corr.gtf.gz
gline_ctrl_rep1
TruSeq Stranded Total LT Sample Prep Kit (Illumina)


title: iPSC-2 line (Thermo Fisher A18945), ctrl, replicate 2, for bulk RNA-seq

description:
merged_raw_read_counts.txt.gz
HSV1GFPtrunc_corr.fa.gz
HSV1GFPtrunc_corr.gtf.gz
gline_ctrl_rep2
TruSeq Stranded Total LT Sample Prep Kit (Illumina)


title: Female2_VI2b


title: Kidney organoid - control (single cell RNA-seq)

city: Rotterdam

first: Hector

last: Tejeda Mora

address: Doctor Molewaterplein 40

department: Developmental Biology

country: Netherlands

institute: Erasmus MC

data_processing:
The raw data was processed into FASTQ files. Raw sequences were inspected for their quality using FastQC (version v0.11.5).
Reads containing sequence information were mapped to the GRCh38 human reference genome.
Generation of BAM files and filtered gene-barcode matrices was accomplished using the Cell Ranger Software (version 4.0.0) (10X Genomics).
Using Seurat (version 3.2.0) standard pre-processing was done. Selection and filtration of cells was done (genes that were expressed in fewer than three cells, and cells with fewer than 200 distinct transcripts were removed). Data was normalized and scaled, followed by the detection of highly variable genes.
From the generated Seurat-Object, unnormalized data (raw counts) were exported as a comma separated table in Sample1.csv. The normalized data matrix was exported similarly in Sample1_2.csv
Genome_build: GRCh38 human reference genome  (hg19)
Supplementary_files_format_and_content: Sample1.csv (raw counts), Sample1_2.csv (normalized data)

source_name: Kidney organoid

growth_protocol: A human iPSC line was pre-treated with CHIR99201 for four days and fibroblast growth factor 9 (FGF9) for three days after which cell pellets were formed, which were placed on a Transwell membrane at the air – medium interphase. The organoids were harvested on day 18.

extract_protocol:
Single cell suspension of organoids were generated using TrypLE Select for 15 minutes at 37°C and stored on ice in APEL medium.
Single cell libraries were prepared using the Chromium Single Cell 3’ Reagent Kit v3 (10x Genomics, Pleasanton, CA, USA). Next generation sequencing (28-8-0-91 cycles) was carried out on an Illumina NovaSeq6000 platform (Illumina, San Diego, USA).

value: human induced pluripotent stem cell-derived kidney organoid

tag: treatment


title: Male1_VIIIa


title: ProteinE_1_i1

city: Shenzhen

first: Ruilin

last: Tian

address: 1088 Xueyuan Avenue

country: China

institute: SUSTech

description:
ProteinE_1_S5
Quant-seq

data_processing:
Raw sequencing reads from QuantSeq were trimmed using Trimmomatic (v0.39)
Salmon v1.3.0 was used to obtain transcript abundance counts
Gene-level count estimates were obtained using tximport  (v1.18.0) with default settings
differential gene-expression analyses were performed using the glmQLFTest method implemented in the edgeR package(v3.28.1)
Genome_build: GRCh38
Supplementary_files_format_and_content: Processed data files are in "CSV(Comma-separated values)" format. Each row is a gene and each column is a sample. Values are normalzied counts

source_name: Calu-3_ProteinE overexpression

extract_protocol:
RNA was extracted from cells using the Quick-RNA Miniprep Kit (Zymo; Cat. No. R1054)
Libraries were generated according to the Quantseq protocol

tag: cell line

tag: genotype/variation

value: ProteinE overexpression

tag: sequencing run


title: Male6_VIII


title: Male6_SIMc


title: Female2_VI2a


title: Male2_SIMd


title: Male2_SIMc


title: Male2_SIMb


title: Male2_SIMa


title: Bone marrow mesenchymal cell clone 006

type: RNA

city: Singapore

first: DARIO

last: CAMPANA

address: 14 Medical Drive

department: Pediatrics

country: Singapore

institute: National University of Singapore

description: Gene expression data from mesenchymal clone 006

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip HG-U133A Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G2500A.

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 500.

label: Biotin

source_name: Supportive Mesechymal cell clone

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 10 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: hTERT-immortalized mesenchymal cell clones were grown to confluence in RPMI-1640, 10% fetal bovine serum

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions

treatment_protocol: Cells were trypsinized and washed twice in RPMI before RNA extraction

tag: Supportive


title: Bone marrow mesenchymal cell clone 005

description: Gene expression data from mesenchymal clone 005


title: Male6_SIMa


title: Bone marrow mesenchymal cell clone 004

description: Gene expression data from mesenchymal clone 004

source_name: Nonsupportive Mesechymal cell clone

tag: Nonsupportive


title: Bone marrow mesenchymal cell clone 002

description: Gene expression data from mesenchymal clone 002


title: Bone marrow mesenchymal cell clone 001

description: Gene expression data from mesenchymal clone 001

source_name: Mesechymal cell clone


title: Bone marrow mesenchymal cell clone 007

description: Gene expression data from mesenchymal clone 007


title: Bone marrow mesenchymal cell clone 003

description: Gene expression data from mesenchymal clone 003


title: Spinal Cord Injury patient 38

city: San Francisco

first: Nikolaos

last: Kyritsis

state: CALIFORNIA

address: 1001 Potrero Ave

department: Neurological Surgery

institute: University of California San Francisco (UCSF)

description:
RNA was processed to deplete rRNA and globin mRNA
normalized_expression_matrix_ComBat_de-ID.csv

data_processing:
alignment with TopHat2
raw gene counts with featureCounts
normalized expression matrix with edgeR
batch-corrected normalized expression matrix with ComBat
Genome_build: hg38
Supplementary_files_format_and_content: the raw gene counts were generated using the featureCounts software
Supplementary_files_format_and_content: the normalized expression matrix file was generated in R with the edgeR package and was corrected for library batch effect with the R package ComBat

source_name: blood

extract_protocol:
total RNA was extracted using the TRIZOL method
libraries were created using Illumina's TruSeq Stranded Total RNA with Ribo-Zero Globin kit

tag: cell type

value: white blood cells

tag: disease state

value: spinal cord injury


title: Female1_SIM


title: Male6_VI2a


title: Spinal Cord Injury patient 36


title: Spinal Cord Injury patient 35


title: Spinal Cord Injury patient 34


title: Spinal Cord Injury patient 33


title: Female4_Purk

description:
single-nuclei gene expression data
cb_processed_initial.mtx.gz
cb_processed_initial_barcodes.txt
cb_processed_initial_genes.txt


title: Spinal Cord Injury patient 32


title: Male6_SIMb


title: Male6_PRMf


title: Spinal Cord Injury patient 30


title: Male6_PRMe


title: Spinal Cord Injury patient 29


title: 86T_ Cryo

city: OMAHA

first: Meng

last: Niu

state: NE

address: 42nd and Emile

department: Department of Neurological sciences

institute: University of Nebraska Medical Center

description: SIVmac251, latent, cART cryo

data_processing:
Cellranger pipeline (version 3.1.0) was used here. Cellranger mkfastq was used for demultiplexing and generate fastq files and cellranger count was used to align the reads to Mmul10 and D01065.1 reference genomes.
Genome_build: Mmul10
Genome_build: D01065.1
Supplementary_files_format_and_content: H5 files were created from cellranger count to store the matrix of UMI per gene per cell for each sample

organism: Macaca mulatta

source_name: Rhesus macaque CD11b enriched brain microgla and macrophages

extract_protocol:
Brain isolates were either cryopreserved or used that day for GEM chip capture. Fresh isolates were immunomagnetically enriched for CD11b microglia and macrophages, and then sorted using flow cytometry for CD11b+, live events. Fresh sorted cells were captured on 10X Genomics Chromium GEM Chip and subsequently processed for scRNA. Cryopreserved were thawed, adapted to room temperature in media containing DNase1 and then immunomagnetically enriched, sorted using flow cytometry, and captured on 10X Genomics Chromium GEM Chip and subsequently processed for scRNA.
Next Generation Sequencing performed on the Illumina NextSeq550
scRNA10x Genomics Chromium GEM Chip and placed into Chromium Controller for library preparation. The prepared libraries  were sequenced using Illumina Nextseq550 sequencer.

value: Enriched brain microglia and macrophages, capture from cryopreserved isolates

tag: tissue preparation

value: cryo

tag: condition

value: SIVmac251 infection, cART d35 post SIV infection, 6 months latent virus (<50 copies SIV/ml plasma). Treated with four drug cART, 4 mg/ml DTG, 1mg/ml tenofovir alafenamide fumerate (TAF), 40 mg/ml FTC, and 12 mg/ml maraviroc (MVC).


title: Spinal Cord Injury patient 28


title: 18499_Total RNA

city: Chicago

first: Yoav

last: GiladLi

state: IL

address: 920 e 58th St

department: Section of Genetic Medicine

institute: University of Chicago

description:
Total RNA
Yoruban Individuals

data_processing:
Map 3' seq libraries to respective genome with STAR 3.30.1. Remove reads mapping to genomic regions with 6 A's in a row or 7 A's in the 10 bases upstream of read.
Merge all libraries and call PAS with in house scripts (available on github https://brimittleman.github.io/Comparative_APA/)
Use ucsc-liftover 377 to reciprocally lift PAS then assigned orthologous PAS to Refseq hg38 gene annotations.
Remove PAS used on average <5% in both human and chimpanzee nuclear libraries. Also remove PAS in genes with expession  < 2 log2CPM in 8 individuals
bed files with hg39 and Pantro 6 genomic locations scores column is the mean usage of the PAS in the respective species Nuclear data, txt file with meta data for each PAS including column for PAS name (as used in bed file), gene, and genic location
Genome_build: human hg38, chimp Pantro6
Supplementary_files_format_and_content: PAS_doublefilter_either_ChimpCoordChimpUsage.sort.bed, bed file with Pantro6 coordinates and average chimpanzee usage
Supplementary_files_format_and_content: PAS_doublefilter_either_HumanCoordHummanUsage.sort.bed, bed file with hg38 coordinates and average human usage
Supplementary_files_format_and_content: PAS_GeneLocation.txt, text file with PAS name, gene, and genic location
Supplementary_files_format_and_content: Supplemental_table1 - meta data for 3' sequencing libraries, column name explanations in second sheet
Supplementary_files_format_and_content: Supplemental_table2 - meta data for RNA sequencing libraries, column name explanations in second sheet

source_name: Imortalized Lymphoblastoid cell line

growth_protocol: LCLs were grown in 20% FBS containing RPMI at 37 and 5% CO2. They were passagd 3 times, maintained at 8 X 10^5, and collected at concentration of 1 X 10^6.

extract_protocol:
The nuclear RNA was extracted using the first part of the nuclear isolation protocl from Mayer and Churchman. Once the sampes were pelleted in the nuclear wash buffer we resuspended in 700 ul of quizol lysis reagent and RNA isolation was complted using an miRNAEasy kit (Quiagen).
For each cell line we sampled both the total RNA in the cell, and the nucear RNA fraction through the ioslated nucleus.
3' RNA seq using Lexogen Rev. QuantSeq & RNA seq using Illumina TruSeq

treatment_protocol: Cells were collected and pelleted at 200 g for 5 min at 4C, washed with cold PBS, then spun again the same way.

value: Imortalized Lymphocyte

value: F


title: Male2_PRMe


title: Spinal Cord Injury patient 31


title: Spinal Cord Injury patient 37


title: Male6_PRMd


title: 86T_ Fresh

description: Fresh isolates from Rhesus SIV  enriched microglia-SIV controlled by cART with no detectable plasma viral load for over 6 months

value: Enriched brain microglia and macrophages, capture from fresh isolates

value: fresh


title: Male2_PRMd


title: Spinal Cord Injury patient 26


title: 85T_Fresh

value: SIVmac251 infection, cART d35 post SIV infection, 6 months latent virus (<50 copies SIV/ml plasma). Treated with two drug cART consisting of 8mg/ml dolutegravier (DTG) and 80 mg/ml emtricitabine (FTC)


title: Spinal Cord Injury patient 27


title: FemaleS1_Purk

description:
single-nuclei gene expression data
cb_processed_initial.mtx.gz
cb_processed_initial_barcodes.txt
cb_processed_initial.mtx.gz


title: Male6_PRMc


title: 85T_ Cryo

description: SIVmac251, latent, cART, cryo


title: Male2_PRMc


title: unperturbed_time_course

city: Vienna

first: Marco

middle: Yannic

last: Hein

address: Dr.-Bohr-Gasse 9

department: Max Perutz Labs

country: Austria

institute: Medical University of Vienna

description:
Human cytomegalovirus (strain Merlin)
Droplet-base single-cell RNA-seq with ~5% spike-in of a guide barcode (GBC) amplicon
RNA (poly-A mRNA and GBC)

data_processing:
Cellranger v.2.0.1 (10x Genomics) and GBC calling as described in Adamson et al., Cell 2016.
Genome_build: Custom, based on GRCh37 (hg19) and the HCMV Merlin genome (NCBI NC_006273.2), see HCMV_merlin_annotation_gtf.tar.gz
Supplementary_files_format_and_content: Tar archive of the cellranger output files (1) cell barcodes. (2) genes. (3) sparse cell x gene matrix of expression values. (4) cell identities, i.e. non-targeting sgRNA expressed in each cell, determined from the guide barcode amplicons, indicating the experimental time point of the sample.

organism:
Homo sapiens
Human herpesvirus 5 strain Merlin

source_name: Primary foreskin fibroblasts

growth_protocol:
Human foreskin fibroblasts (HFFs; CRL-1634) and HCMV (strain Merlin; VR-1590) were purchased from the American Tissue Culture Collection.
HFFs were cultured in DMEM, supplemented with 10 % FBS and penicillin-streptomycin.
HCMV stocks were expanded by two rounds of propagation on HFFs and titered by serial dilution.

extract_protocol:
WT HFFs were lentivirally transduced with barcoded Perturb-seq vectors to encode the experimental condition (see paper), followed by puromycin selection. Cells were seeded at a density of 250,000 per well of a 12-well plate and infected with an MOI of 0.5 or 5.0 with no additional media change before harvest. Infection times were staggered so that all time points for a given MOI were harvested in parallel, and pooled, aiming for roughly equal cell numbers for each time point.
For each MOI, pools of ~10,000 cells were prepared for single-cell transcriptomics using one lane each of the Chromium Single Cell 3′ Gene Expression Solution v2 according to manufacturer’s instructions (10x Genomics). Barcodes encoding the experimental condition were PCR-amplified from the final library and sequenced as a 5 % spike-in as described (as described in Adamson et al., 2016).

treatment_protocol:
HFFs were engineered with lentiviral vectors to express Cas9-BFP or dCas9-BFP-KRAB, followed by enrichment by FACS.
sgRNA libraries were also delivered on lentiviral vectors, followed by Puromycin selection.
Cells were infected with HCMV at MOIs indicated for each sample and harvested at defined time points for extraction of genomic DNA for extraction of the sgRNA cassette, or for droplet-based single-cell RNA-seq.

value: HFF

tag: experiment type

value: single-cell RNA-seq time-course of infection

tag: sgrna target organism


title: CRISPRn_perturb_virus_host

data_processing:
Cellranger v.2.0.1 (10x Genomics) and GBC calling as described in Adamson et al., Cell 2016.
Genome_build: Custom, based on GRCh37 (hg19) and the HCMV Merlin genome (NCBI NC_006273.2), see HCMV_merlin_annotation_gtf.tar.gz
Supplementary_files_format_and_content: Tar archive of the cellranger output files (1) cell barcodes. (2) genes. (3) sparse cell x gene matrix of expression values. (4) cell identities, i.e. sgRNA expressed in each cell, determined from the guide barcode amplicons, indicating the sgRNA target.

extract_protocol:
HFFs expressing Cas9-BFP were lentivirally transduced with a virus+host-targeting Perturb-seq library (see paper), followed by puromycin selection. Cells were seeded at a density of 250,000 per well of a 12-well plate and infected with an MOI of 5.0 with no additional media change before harvest. Infection times were staggered so that all time points were harvested in parallel, and pooled, aiming for roughly equal cell numbers for each time point.
For each MOI, pools of ~10,000 cells were prepared for single-cell transcriptomics using one lane each of the Chromium Single Cell 3′ Gene Expression Solution v2 according to manufacturer’s instructions (10x Genomics). Barcodes encoding the experimental condition were PCR-amplified from the final library and sequenced as a 5 % spike-in as described (as described in Adamson et al., 2016).

value: pooled CRISPR nuclease screen with droplet-based single-cell RNA-seq readout (Perturb-seq)

value: Homo sapiens, HCMV


title: Spinal Cord Injury patient 25


title: Female2_PRMc

tag: strain

tag: age

value: Female


title: CRISPRi_perturb_host

extract_protocol:
HFFs expressing dCas9-BFP-KRAB were lentivirally transduced with a host-targeting Perturb-seq library (see paper), followed by puromycin selection. Cells were seeded at a density of 250,000 per well of a 12-well plate and infected with an MOI of 0.5 for 1h, followed by a media change. Infection times were staggered so that all time points were harvested in parallel, and pooled, aiming for roughly equal cell numbers for each time point.
For each MOI, pools of ~10,000 cells were prepared for single-cell transcriptomics using one lane each of the Chromium Single Cell 3′ Gene Expression Solution v2 according to manufacturer’s instructions (10x Genomics). Barcodes encoding the experimental condition were PCR-amplified from the final library and sequenced as a 5 % spike-in as described (as described in Adamson et al., 2016).

value: pooled CRISPR interference screen with droplet-based single-cell RNA-seq readout (Perturb-seq)

value: Homo sapiens


title: Male6_PRMb

tag: Sex

value: Male

tag: 10x version


title: Spinal Cord Injury patient 22

value: white blood cells

value: spinal cord injury


title: Male2_PRMb

tag: genome build


title: CRISPRn_screen_host

description:
Human cytomegalovirus (strain Merlin)
Genomic DNA fragment amplicon sequencing
DNA (sgRNA cassette amplicon)

library_source: genomic

data_processing:
sgRNA counts were calculated as described (Horlbeck et al., 2016).
Raw count data were normalized for read depth and a small constant added to account for missing values. Phenotypes of individual sgRNAs were expressed as log2-transformed ratios of adjusted read counts between samples. We calculated the mean of all sgRNAs specific to each gene.
Genome_build: Human knockout CRISPR v1 library (Tzelepis et al., 2016)
Supplementary_files_format_and_content: Tar archive of: (1) raw counts for each library element. (2) gene-level phenotypes.

molecule: genomic DNA

extract_protocol:
The pooled screen was carried out at 500-1,000x coverage. A t0 sample was harvested and the remaining cells either passaged normally, or infected with HCMV at an MOI of 0.1. Infected flasks were washed with PBS and given fresh media at days 3, 5, 7 post infection to remove dead cells, and harvested at day 9. Genomic DNA was extracted and digested with HindIII to release a fragment containing the sgRNA cassette, followed by gel-based extraction.
The gel-purified DNA fragment was PCR-amplified and analyzed by deep sequencing as described (Horlbeck et al., 2016).

value: pooled CRISPR nuclease screen


title: CRISPRi_screen_host

data_processing:
sgRNA counts were calculated as described (Horlbeck et al., 2016).
Raw count data were normalized for read depth and a small constant added to account for missing values. Phenotypes of individual sgRNAs were expressed as log2-transformed ratios of adjusted read counts between samples. We calculated the mean of all sgRNAs specific to each gene.
Genome_build: CRISPRi v2 (Horlbeck et al., 2016)
Supplementary_files_format_and_content: Tar archive of: (1) raw counts for each library element. (2) gene-level phenotypes.

extract_protocol:
The pooled screen was carried out at 500-1,000x coverage. A t0 sample was harvested and the remaining cells either passaged normally, or infected with HCMV at an MOI of 0.1. Infected flasks were washed with PBS and given fresh media at days 3 and 5 post infection to remove dead cells, and harvested at day 7. Genomic DNA was extracted and digested with MfeI to release a fragment containing the sgRNA cassette, followed by gel-based extraction.
The gel-purified DNA fragment was PCR-amplified and analyzed by deep sequencing as described (Horlbeck et al., 2016).

value: pooled CRISPR interference screen


title: Spinal Cord Injury patient 21


title: Spinal Cord Injury patient 20


title: Xmoo1 line, 3dpi, replicate 3, for FLAM-seq

description:
NR_AR_ORG_HSV1_6_gene_polyA_length.csv.gz
HSV1GFPtrunc_corr.fa.gz
HSV1GFPtrunc_corr.gtf.gz
NR_AR_ORG_HSV1_6
FLAMseq (Legnini et al. 2019)

data_processing:
For bulk RNA-sequencing, Illumina base calling, demultiplexing and FASTQ conversion with bcl2fastq v2.20.0 (Illumina)
alignment to GRCh38 genome using STAR v2.7.1a (https://github.com/alexdobin/STAR)
reads counted on GENCODE 27 gene models with htseq-count 0.9.1 (https://htseq.readthedocs.io/)
The HSV1 genome was extended from strain 17 (genbank entry NC_001806) with the GFP and loxP sequences, error-corrected based on the total RNA-sequencing data, and terminal repeats removed to avoid multi-mapping reads
Provided here are the resulting HSV-1 fasta and gtf file used in the data analysis
For FLAM-seq, the CCS reads were then used as input to the FLAManalysis pipeline (https://github.com/rajewsky-lab/FLAMAnalysis), that outputs gene assignment and poly(A) tail length and sequence for each read.
For single-cell RNA-sequencing, data was processed using the pigx pipeline version 1.1.4 (http://bioinformatics.mdc-berlin.de/pigx/, Wurmus et al. 2018 doi: 10.1093/gigascience/giy123) using a combined human/HSV1 genome
Genome_build: Homo sapiens hg38
Genome_build: HSV-1 GFP truncated corrected
Supplementary_files_format_and_content: fasta file
Supplementary_files_format_and_content: gtf file
Supplementary_files_format_and_content: comma-separated values

tag: tissue

value: Brain organoid

tag: hsv-1 infection status

value: no

tag: sampling timepoint

tag: rna population

value: polyA+ RNA


title: Spinal Cord Injury patient 19


title: Male6_PRMa

description:
single-nuclei gene expression data
cb_adult_mouse.mtx.gz
cb_adult_mouse_barcodes.txt
cb_adult_mouse_genes.txt
golgi_joint.mtx.gz
golgi_joint_barcodes.txt
golgi_joint_genes.txt
granule_joint.mtx.gz
granule_joint_barcodes.txt
granule_joint_genes.txt
interneuron_joint.mtx.gz
interneuron_joint_barcodes.txt
interneuron_joint_genes.txt
ubc_joint.mtx.gz
ubc_joint_barcodes.txt
ubc_joint_genes.txt


title: CRISPRn_screen_virus

data_processing:
sgRNA counts were calculated as described (Horlbeck et al., 2016).
Raw count data were normalized for read depth and a small constant added to account for missing values. Phenotypes of individual sgRNAs were expressed as log2-transformed ratios of adjusted read counts between samples. We calculated a rolling average in a 250 bp window, with the average of all non-targeting sgRNAs defining the baseline.
Genome_build: Custom, based on the HCMV Merlin genome (NCBI NC_006273.2), see CRISPRn_screen_virus_processed.tar.gz
Supplementary_files_format_and_content: Tar archive of: (1) raw counts for each library element. (2) gene-level phenotypes for consensus genes. (3) gene-level phenotypes for all viral ORFs.

extract_protocol:
The pooled screen was carried out at 500-1,000x coverage. A t0 sample was harvested and the remaining cells either passaged normally, or infected with HCMV at an MOI of 0.5-1.0. Infected flasks were washed with PBS and given fresh media at days 3, 5, 7 post infection to remove dead cells, and harvested at day 9-10. Genomic DNA was extracted and digested with MfeI to release a fragment containing the sgRNA cassette, followed by gel-based extraction.
The gel-purified DNA fragment was PCR-amplified and analyzed by deep sequencing as described (Horlbeck et al., 2016).

tag: cell line

value: HCMV


title: Female2_PRMb


title: Spinal Cord Injury patient 18


title: Xmoo1 line, 3dpi, replicate 2, for FLAM-seq

description:
NR_AR_ORG_HSV1_5_gene_polyA_length.csv.gz
HSV1GFPtrunc_corr.fa.gz
HSV1GFPtrunc_corr.gtf.gz
NR_AR_ORG_HSV1_5
FLAMseq (Legnini et al. 2019)


title: Female2_PRMa


title: Male1_PFd


title: Spinal Cord Injury patient 17


title: Spinal Cord Injury patient 24


title: Male1_PFc


title: Female2_PFc


title: Spinal Cord Injury patient 16


title: Spinal Cord Injury patient 23


title: Spinal Cord Injury patient 15


title: w_Ime4_null_het_Fem_Head_3W_rep1

city: New York

first: Brian

last: Joseph

state: New York

address: 430 E 67th St

department: Department of Developmental Biology

institute: Sloan-Kettering Institute

description: w;mettl3[null]/+, 3week,female head, n=1

data_processing:
miCLIP-seq: Adapters and low quality reads were trimmed using flexbar v2.5. FASTQ files were de-multiplexed using the pyBarcodeFilter.py script from the pyCRAC suite. Random barcodes were removed from sequencing reads and appended to sequence IDs using an awk script and PCR duplicates were removed using the pyCRAC pyDuplicateRemover.py script. Paired end reads were merged and mapped to the Drosophila reference genome sequence (BDGP Release 6/dm6) using Novoalign (Novocraft) with parameters –t 85 and -l 16. Mutations were called using the CIMS software package (Zhang and Darnell, 2011). To identify putative m6A sites, C-to-T transitions with preceding A nucleotides were extracted and filtered such that the number of mutations that support the mismatch (m) > 1 and 0.01 < m/k < 0.5, where k is the number of unique tags that span the mismatch position. Peaks were called by adapting the Model-based Analysis for ChIP-Seq (MACS) algorithm (Zhang et al., 2008). Mettl3-dependent peaks for head libraries were determined using miCLIP versus input, comparing wild type and mettl3 libraries and the MACS2 differential binding events program (bdgdiff) with parameters -g 20 and -l 120. Lastly, peaks were split using PeakSplitter (version 1.0, http://www.ebi.ac.uk/research/bertone/software).
RNA-seq: RNA sequencing libraries were mapped to the Drosophila reference genome sequence (BDGP Release 6/dm6) using HISAT2 (Kim et al., 2015) under the default settings. Gene counts were obtained by assigning and counting reads to the Ensembl transcript models for BDGP6.94 using Rsubread (Liao et al., 2013). Differential gene expression analysis was performed with comparisons as listed in Supplementary Table 5 using the R package DESeq2 (Love et al., 2014) and applying a strict adjusted p-value cutoff of 0.05.
Genome_build: BDGP Release 6/dm6
Supplementary_files_format_and_content: bigwig files

organism: Drosophila melanogaster

source_name: female head

extract_protocol:
Briefly, total RNA was collected from <1 week old w1118 (wild type) and mettl3[null] (mutant) female heads using TRIzol RNA extraction.
miCLIP: Poly(A)+ RNA was enriched using two rounds of selection.RNAs were fragmented, incubated with the α-m6A (202 003 Synaptic Systems) and crosslinked twice in a Stratalinker 2400 (Stratagene) using 150 mJ per cm2. Crosslinked RNAs were immunoprecipitated using Protein A/G magnetic beads (Thermo) and washed under high salt conditions to reduce non-specific binding. Samples were radiolabeled with T4 PNK (NEB), ligated to a 3' adaptor using T4 RNA Ligase I (NEB), and purified using SDS-polyacrylamide gel electrophoresis (SDS-PAGE) and nitrocellulose membrane transfer. RNA fragments containing crosslinked antibody peptides were recovered from the membrane using proteinase K (Invitrogen) digestion. Recovered fragments were subjected to library preparation. First-strand cDNA synthesis was performed using SuperScript III (Life Technologies) and iCLIP-barcoded primers, which contain complementarity to the 3' adaptor on the RNA. cDNAs were purified using denaturing PAGE purification, circularized using CircLigase II (EpiCentre), annealed to the iCLIP Cut Oligo, and digested using BamHI (Thermo). To generate libraries for sequencing, the resulting linear cDNAs were amplified using Accuprime SuperMix I (Invitrogen) and P5 and P3 Solexa primers, and purified using Agencourt AMPure XP beads (Beckman Coulter). For input libraries, poly(A)+ RNAs were fragmented and directly subjected to radiolabelling and 3' adaptor ligation. All subsequent steps are as listed above. Libraries were paired-end sequenced on an Illumina HiSeq2500 instrument at the New York Genome Center (NYGC). RNA-seq: Sequencing libraries were prepared using the TruSeq Stranded Total RNA Sequencing Kit (Illumina) following the manufacturer’s protocol
miCLIP-seq and RNA-seq

value: head

tag: developmental stage

value: 3 week


title: Male6_PFb


title: Male1_PFb


title: Spinal Cord Injury patient 12

tag: cell type


title: Male2_PRMa


title: Spinal Cord Injury patient 13

tag: disease state


title: Male6_PFa


title: Spinal Cord Injury patient 11


title: Female2_PFb


title: Male1_PFa


title: HepG2, sißCat-mut, Rep2

city: Bordeaux

first: Violaine

last: Moreau

address: 146 Leo Saignat

country: France

institute: INSERM

hyb_protocol: 3 μg of cDNAs were hybridized for 16 hours at 45°C on GeneChip® Human Gene 2.0 ST arrays. The chips were washed and stained in the GeneChip® Fluidics Station 450 (Affymetrix)

scan_protocol: The chips were scanned with the GeneChip® Scanner 3000 7G (Affymetrix) at a resolution of 0.7 µm

data_processing: Raw data (.CEL Intensity files) were extracted from the scanned images using the Affymetrix GeneChip® Command Console (AGCC) version 3.2. CEL files were further processed with Affymetrix Expression Console software version 1.1 to calculate probe set signal intensities using Robust Multi-array Average (RMA) algorithms with default settings. Differentially expressed (DE) genes were identified using the fold-change rank ordering statistics (FCROS) method (Dembele and Kastner, 2014), which associates an f-value with genes. Small f-values (near zero) are associated with down-regulated genes, while higher values (near 1) are associated with up-regulated genes.

label: biotin

source_name: HepG2 cells, siRNA mutated ß-catenin, 120 h

label_protocol: Biotinylated single strand cDNA targets were prepared, starting from 150 ng of total RNA, using the Ambion WT Expression Kit (Cat # 4411974) and the Affymetrix GeneChip® WT Terminal Labeling Kit (Cat # 900671) according to Affymetrix recommendations

extract_protocol: RNA was collected from cultured cells using the Trizol reagent


title: Spinal Cord Injury patient 9


title: Female2_PFa


title: HepG2, sißCat-mut, Rep1


title: HepG2, sißCat-both, Rep3

source_name: HepG2 cells, siRNA ß-catenin, 120 h


title: HepG2, sißCat-mut, Rep3


title: HepG2, sißCat-both, Rep2


title: Spinal Cord Injury patient 8


title: Spinal Cord Injury patient 14


title: Male6_PF


title: HepG2, sißCat-WT, Rep3

source_name: HepG2 cells, siRNA WT ß-catenin, 120 h


title: Spinal Cord Injury patient 7


title: Male1_Ib


title: 10X GEX library for Donor 33

first: Arjun

middle: Arkal

last: Rao

state: CA

address: 505 Parnassus Ave, S-447

department: CoLabs

institute: University of California, San Francisco

data_processing:
sequencer-generated bcl files were converted to fastqs using the cellranger mkfastq (cellranger version 3.0.2) command with default parameters.
fastq files were aligned to the human reference genome (with ENSEMBL v85 annotation) using cellranger count (cellranger version 3.0.2). This step also generated the submitted raw feature-barcode matrices
pooled libraries were processed using popscle (github commit hash: 038044660337b50ec89b0b355493ceb707f18ecd) freemuxlet using default parameters.
Freemuxlet derived clusters were assigned to samples using bcftools gtcheck (bcftools version 1.10.2) against gentotypes identified using external rna sequencing libraries.
Genome_build: GRCh38
Supplementary_files_format_and_content: *matrix.mtx.gz: raw count matrix in a sparse matrix format; *barcodes.tsv.gz: barcode ids for each cell in the library; *features.tsv.gz: ENSEMBL and HUGO gene ids; *clust1.samples.gz: Freemuxlet derived barcode-to-cluster assignments along with all relevant statistics; *cluster_assignments.tsv: Assignments of freemuxlet clusters to sample IDs; More information on 10X filetypes at https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/output/matrices

source_name: Whole blood

extract_protocol:
Briefly, peripheral blood was collected into EDTA tubes (BD, catalog no. 366643). Whole blood was prepared by treatment of 500µL of peripheral blood with RBC lysis buffer (Roche, 11-814-389-001) according to manufacturer’s procedures. Cells were then counted and 15.000 cells per individual were directly loaded in the ChromiumTM Controller for partitioning single cells into nanoliter-scale Gel Bead-In-Emulsions (GEMs) following manufacturer’s procedures (10x genomics). Some samples were pooled together (at 15,000 cells/ sample) prior to GEM partitioning.
Single Cell 5’ reagent kit v5.1 was used for reverse transcription, cDNA amplification and library construction of the gene expression libraries (10x Genomics) following the detailed protocol provided by 10x Genomics.

tag: pooled

value: FALSE

value: whole blood

value: CONTROL

tag: phenotype


title: Spinal Cord Injury patient 10


title: 10X GEX library for Donor 31


title: Spinal Cord Injury patient 6


title: Male1_Ia


title: Male6_I


title: Spinal Cord Injury patient 5


title: 10X GEX library for Donor 32


title: HepG2, siCtrl, Rep3

source_name: HepG2 cells, Control siRNA, 120 h


title: 10X GEX library for Donor 30


title: HepG2, sißCat-WT, Rep1


title: HepG2, sißCat-WT, Rep2


title: HepG2, sißCat-both, Rep1


title: HepG2, siCtrl, Rep1


title: 10X GEX library for Donor 29


title: Spinal Cord Injury patient 4


title: HFD End 4

first: Sarah

last: Ackerman

address: 1230 York Ave

institute: Rockefeller University

data_processing:
Reads were mapped to the mm10 genome using TopHat and analyzed using DESeq.
Genome_build: mm10

source_name: Cancer cells from tumor

extract_protocol:
Tumors were dissected and dissociated according to the manufacturer’s instructions using the mouse tumor dissociation kit (Miltenyi). Cells were sorted via FACS. Mcherry positive cells were collcted and resuspended in triazol. RNA was extracted accoring to the Rneasy kit. RNA integrity awas measured with a bioanalyzer.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: 50,000 mcherry positive E0771 cells were impanted into the mammary fat pad of lean or obese animals and harvested at midpoint (14 days) or endpoint (21 days)

tag: lean/obese

value: Obese

tag: timepoint

value: Endpoint


title: HFD End 5

tag: strain


title: Male6_IXd

data_processing:
Sequencing performed on Illumina NovaSeq6000
Mouse sequencing reads were demultiplexed and aligned using 10x Cell Ranger software (Ver. 3.0.2) to the mouse reference genome (ENSEMBL Release 78/GRCm38.p3) for each sample individually. Genome_build: mm10
Mouse Digital gene expression matrices (with gene expression counts) were generated by Cell Ranger software (v3.0.2)
Human sequencing reads were demultiplexed and aligned using drop-seq tools to the human reference genome (ENSEMBL Release 78/GRCh37) for each sample individually. The drop-seq pipeline was run using exonic and intronic data as UMIs. The human gene expression matrices were also generated using drop-seq tools (2020-06-17)
Digital gene expression matrices were aggregated and analyzed with Seurat v2.3.4 and liger v0.4.2.
Genome_build: mouse samples: mm10_premrna
Genome_build: human samples: hg19
Supplementary_files_format_and_content: digital gene expression matrix (sparse format): matrix market format, rows = genes/transcripts, columns = barcodes/cells. All files for each set of libraries were included in a tar archive available on the series record.
Supplementary_files_format_and_content: barcodes.txt: names of barcodes/cells for corresponding DGE matrix file
Supplementary_files_format_and_content: genes.txt: names of transcripts/genes for corresponding DGE matrix file
In processed data, human data dropseq tools pipeline used exonic and intronic as UMIS
Developmental mouse cerebellum libraries were aggregated into cb_dev_ints.mtx.gz
Adult mouse cerebellum libraries were aggregated into cb_adult_mouse.mtx.gz.
The file cb_processed_initial.mtx.gz includes all adult mouse cerebellum libraries. Purkinje cell enriched libraries Purk_F004, Purk_F0S1 were removed from cb_processed_initial.mtx.gz (due to batch effects) to create cb_adult_mouse.mtx.gz which was used in subsequent analysis.
Human cerebellum libraries were aggregated into human_combined.mtx.gz
The mouse (adult and developmental) libraries were combined with the human libraries and separated into golgi_joint.mtx.gz (Golgi cells), granule_joint.mtx.gz (Granule Cells), interneuron_joint.mtx.gz (Interneuron cells), and ubc_joint.mtx.gz (Unipolar Brush cells) matrices

source_name: P60 Cerebellum

extract_protocol:
Please see https://www.protocols.io/view/frozen-tissue-nuclei-extraction-for-10xv3-snseq-bi62khge
10X Chromium Single Cell 3' (V3) (manufacturer's protocol)

tag: age


title: Female1_I

tag: Sex

value: Female


title: Spinal Cord Injury patient 3


title: Male6_IXc

value: Male

tag: 10x version


title: 10X GEX library for Donor 20


title: HFD End 2


title: 10X GEX library for Donor 14


title: Chow End 5

value: Lean


title: Male3_IXc

tag: genome build


title: Spinal Cord Injury patient 1

value: white blood cells

value: spinal cord injury


title: HepG2, siCtrl, Rep2


title: non-CNS Trauma Control 10

value: trauma control


title: Chow End 4


title: Female2_IXc


title: HFD End 3


title: Male6_IXb


title: 10X GEX library for Donor 23

tag: tissue


title: non-CNS Trauma Control 8


title: 10X GEX library for Donor 7


title: Chow End 3


title: 10X GEX library for Donor 6


title: Male3_IXb


title: 10X GEX library for Donor 5


title: non-CNS Trauma Control 7


title: non-CNS Trauma Control 6


title: Chow End 2


title: Chow End 1


title: Male6_IXa


title: HFD Mid 5

value: Midpoint


title: Female2_IXb


title: HFD End 1


title: 10X GEX library for Donor 19


title: 10X GEX library for Donor 3


title: Male3_IXa


title: HFD Mid 4


title: 10X GEX library for Patient 62

value: NEGATIVE

value: M/M


title: HFD Mid 3


title: non-CNS Trauma Control 9


title: non-CNS Trauma Control 5


title: Female2_IXa


title: 10X GEX library for Patient 60

value: POSITIVE

value: SEVERE


title: Male1_IIb


title: non-CNS Trauma Control 3


title: HFD Mid 2


title: non-CNS Trauma Control 2


title: HFD Mid 1


title: 10X GEX library for Patient 55


title: Female1_IIb


title: 10X GEX library for Patient 54


title: Chow Mid 4


title: 10X GEX library for Patient 52


title: Healthy Control 10

value: healthy control


title: non-CNS Trauma Control 4


title: Healthy Control 9


title: Male1_IIa


title: Healthy Control 8


title: 10X GEX library for Patient 47

value: FALSE


title: Male1_IIIb


title: Female1_IIa


title: Chow Mid 3


title: Male6_II


title: Chow Mid 2


title: Healthy Control 6


title: 10X GEX library for Patient 49

value: whole blood


title: Male1_IIIa


title: Female1_III


title: HFD_NT_R_3

description: counts.matrix

data_processing: RNA was isolated as above. For adipose samples, RNA was pooled from two animals per sample. RNA integrity number (RIN) was measured with a bioanalyzer (Aglient) and sequenced using the Illumina HiSeq 2500. Reads were mapped to the mm10 genome using TopHat and analyzed using DESeq. KEGG metabolic pathway analysis was performed using the GAGE method

source_name: 4th mammary subcutaneous adipose

extract_protocol:
flash frozen adipose, total RNA was exracted, DNAse protocol was used
RNA libraries were prepared for sequencing using standard Illumina protocols, rRNA depletion

tag: diet

value: HFD

tag: sample type

value: no tumor


title: Chow Mid 1


title: Healthy Control 7


title: Healthy Control 5


title: 10X GEX library for Patient 46


title: 10X GEX library for Patient 38


title: Healthy Control 4


title: 10X GEX library for Patient 44


title: HFD_NT_R_4

description: counts.matrix


title: Female1_IIIb


title: HFD_NT_R_2

description: counts.matrix


title: Male6_Fc


title: non-CNS Trauma Control 1


title: Healthy Control 3


title: 10X GEX library for Patient 31


title: HFD_NT_R_1

description: counts.matrix


title: Male6_Fa


title: Chow_NT_R_4

description: counts.matrix

value: Chow


title: Healthy Control 2


title: 10X GEX library for Patient 45


title: Male6_F


title: 10X GEX library for Patient 29


title: Chow_NT_R_3

description: counts.matrix


title: Healthy Control 1


title: Male1_F


title: 10X GEX library for Patient 26


title: 10X GEX library for Donor 4

value: CONTROL


title: 10X GEX library for Patient 25


title: Chow_NT_R_1

description: counts.matrix


title: Female1_F

value: Female


title: Male2_CULd

value: Male


title: 10X GEX library for Patient 16


title: Chow_NT_R_2

description: counts.matrix


title: HFD_L_2

description: counts.matrix

value: peritumoral


title: Male2_CULc


title: 10X GEX library for Patient 14


title: HFD_L_4

description: counts.matrix


title: Pooled 10X GEX libraries for Patients 50 and 51

description: Patient 50: POSITIVE, SEVERE; Patient 51: POSITIVE, SEVERE

value: TRUE

value: mixed (pooled sample)


title: HFD_L_3

description: counts.matrix


title: 10X GEX library for Patient 12


title: Male2_CULb


title: HFD_R_4

description: counts.matrix

value: contralateral


title: Male6_CULb


title: HFD_L_1

description: counts.matrix


title: Pooled 10X GEX libraries for Patient 10

description: Patient 10: NEGATIVE, SEVERE. The second patient in this pool retroactively revoked consent to participate in our study and has been effectively redacted from all processed outputs and raw data files.


title: Male2_COPd


title: Spinal Cord Injury patient 2

value: white blood cells

value: spinal cord injury


title: HFD_R_3

description: counts.matrix


title: Male2_CULa


title: HFD_R_2

description: counts.matrix


title: Pooled 10X GEX libraries for Patients 7, 8, and 9

description: Patient 7: POSITIVE, M/M; Patient 8: NEGATIVE, M/M; Patient 9: NEGATIVE, SEVERE


title: Male2_COPc


title: Pooled 10X GEX libraries for Patients 5 and 6

description: Patient 5: POSITIVE, M/M; Patient 6: POSITIVE, M/M


title: Pooled 10X GEX libraries for Patients 17, 20, and 21

description: Patient 17: NEGATIVE, M/M; Patient 20: NEGATIVE, SEVERE; Patient 21: NEGATIVE, SEVERE


title: HFD_R_1

description: counts.matrix


title: Male6_CUL


title: Pooled 10X GEX libraries for Patients 1, 2, and 3

description: Patient 1: POSITIVE, SEVERE; Patient 2: POSITIVE, SEVERE; Patient 3: POSITIVE, SEVERE


title: Xmoo1 line, 6dpi, replicate 2, for bulk RNA-seq

description:
merged_raw_read_counts.txt.gz
HSV1GFPtrunc_corr.fa.gz
HSV1GFPtrunc_corr.gtf.gz
xmoo1_6dpi_rep2
TruSeq Stranded Total LT Sample Prep Kit (Illumina)

data_processing:
For bulk RNA-sequencing, Illumina base calling, demultiplexing and FASTQ conversion with bcl2fastq v2.20.0 (Illumina)
alignment to GRCh38 genome using STAR v2.7.1a (https://github.com/alexdobin/STAR)
reads counted on GENCODE 27 gene models with htseq-count 0.9.1 (https://htseq.readthedocs.io/)
The HSV1 genome was extended from strain 17 (genbank entry NC_001806) with the GFP and loxP sequences, error-corrected based on the total RNA-sequencing data, and terminal repeats removed to avoid multi-mapping reads
Provided here are the resulting HSV-1 fasta and gtf file used in the data analysis
For FLAM-seq, the CCS reads were then used as input to the FLAManalysis pipeline (https://github.com/rajewsky-lab/FLAMAnalysis), that outputs gene assignment and poly(A) tail length and sequence for each read.
For single-cell RNA-sequencing, data was processed using the pigx pipeline version 1.1.4 (http://bioinformatics.mdc-berlin.de/pigx/, Wurmus et al. 2018 doi: 10.1093/gigascience/giy123) using a combined human/HSV1 genome
Genome_build: Homo sapiens hg38
Genome_build: HSV-1 GFP truncated corrected
Supplementary_files_format_and_content: fasta file
Supplementary_files_format_and_content: gtf file
Supplementary_files_format_and_content: tab-separated values

organism:
Homo sapiens
Human alphaherpesvirus 1

source_name: Brain organoid

extract_protocol:
For isolation of bulk RNA, organoids were dissolved in Trizol. Ribosomal RNA was depleted using Rnase H (Epicentre)
Total bulk RNA-seq libraries were generated using the TruSeq Stranded Total LT Sample Prep Kit (Illumina). FLAMseq libraries were constructed as previously described (Legnini et al. 2019, doi: 10.1038/s41592-019-0503-y)

value: Brain organoid

tag: hsv-1 infection status

value: yes

tag: sampling timepoint

tag: rna population

value: rRNA-depleted RNA


title: Male2_COPb


title: Xmoo1 line, 6dpi, replicate 1, for bulk RNA-seq

description:
merged_raw_read_counts.txt.gz
HSV1GFPtrunc_corr.fa.gz
HSV1GFPtrunc_corr.gtf.gz
xmoo1_6dpi_rep1
TruSeq Stranded Total LT Sample Prep Kit (Illumina)


title: Female2_COPb


title: Chow_L_4

description: counts.matrix


title: Tcongolense_ExVivo_rep_4

city: Midlothian

first: Pieter

middle: C

last: Steketee

address: Easter Bush Campus

department: Division of Infection and Immunity

country: United Kingdom

institute: Roslin Institute, University of Edinburgh

data_processing:
Reads were aligned to the respective genomes (T. brucei TREU927 v34 and T. congolense IL3000 2019) using HiSat2 with parameters: --no-spliced-alignment
Sam output was converted to bam and sorted using Samtools. Parameters: 'samtools view -bS -q 1 - | samtools sort -$file; samtools index $file' (where $file is individual alignment file)
Bam files were further filtered using Samtools. Parameters: 'samtools view -b -q 1 -F 0x100' and 'samtools index'
Read counts were calculated from bam files using HTSeq-count (HTSeq python tool). Parameters - T. brucei: -s reverse -f bam -t CDS -i ID -m union -a 0 --nonunique all; T congolense: -s reverse -f bam -t polypeptide -i ID -m union -a 0 --nonunique all
TPM values were calculated for each gene in individual samples as follows: 1) Reads per kilobase (RPK) were calculated by dividing the read counts by the length of gene in kilobases; 2) All RPK values in a sample were summed and divided by 1 million as a scaling factor; 3) Each RPK value was divided by the scaling factor to yield TPM values
OrthoTPM values were calculated using the Orthofinder output (Orthofinder parameters were default). For multi-gene groups, TPM values for all genes in the group were summed. All data was then consolidated into the final dataset
Genome_build: T. brucei: TriTrypDB-34.0_TREU927; T. congolense: TcongolenseIL3000 2019
Supplementary_files_format_and_content: read count files were generated using HTSeq-count
Supplementary_files_format_and_content: Excel spreadsheet: to calculate TPM values: 1) Reads per kilobase (RPK) were calculated by dividing the read counts by the length of gene in kilobases; 2) All RPK values in a sample were summed and divided by 1 million as a scaling factor; 3) Each RPK value was divided by the scaling factor to yield TPM values
Supplementary_files_format_and_content: Excel spreadsheet, OrthoFinder: Orthofinder output required to generate OrthoTPM values for inter-species comparison. Orthofinder was run with default parameters using the translated CDS sequences (amino acids) in fasta format as input
Supplementary_files_format_and_content: orthoTPM count: files containing the output of orthoTPM values for T. brucei and T. congolense, calculated using the Orthofinder output
Supplementary_files_format_and_content: OrthoTPM counts: Final dataset
Supplementary_files_format_and_content: URL for verifying identifiers: https://tritrypdb.org/tritrypdb/app

organism: Trypanosoma congolense

source_name: Parasites from ex vivo murine infection

growth_protocol: T. brucei in vitro were grown in modified HMI-9; T. congolense in vitro were grown in HMI-93

extract_protocol:
10^8 cells per sample group; RNA extracted using QIAgen RNeasy kits with on-column DNase treatment
Libraries were prepared using the Illumina TruSeq Stranded mRNA kit, according to Ilumina's instructions

treatment_protocol: No treatment for in vitro samples, ex vivo samples were purified through DEAE cellulose columns prior to extraction

tag: mouse strain

tag: genotype

value: Wild-type

tag: group

value: Parasites from ex vivo murine infection


title: Xmoo1 line, 3dpi, replicate 2, for bulk RNA-seq

description:
merged_raw_read_counts.txt.gz
HSV1GFPtrunc_corr.fa.gz
HSV1GFPtrunc_corr.gtf.gz
xmoo1_3dpi_rep2
TruSeq Stranded Total LT Sample Prep Kit (Illumina)


title: Male2_COPa


title: Chow_L_3

description: counts.matrix


title: Tcongolense_ExVivo_rep_3


title: Xmoo1 line, 3dpi, replicate 1, for bulk RNA-seq

description:
merged_raw_read_counts.txt.gz
HSV1GFPtrunc_corr.fa.gz
HSV1GFPtrunc_corr.gtf.gz
xmoo1_3dpi_rep1
TruSeq Stranded Total LT Sample Prep Kit (Illumina)


title: Female2_COPa


title: Chow_L_2

description: counts.matrix


title: Chow_L_1

description: counts.matrix


title: iPSC-2 line (Thermo Fisher A18945), 6dpi, replicate 2, for bulk RNA-seq

description:
merged_raw_read_counts.txt.gz
HSV1GFPtrunc_corr.fa.gz
HSV1GFPtrunc_corr.gtf.gz
gline_6dpi_rep2
TruSeq Stranded Total LT Sample Prep Kit (Illumina)


title: Tcongolense_ExVivo_rep_2


title: Male6_COP


title: Tcongolense_ExVivo_rep_1


title: Chow_R_4

description: counts.matrix


title: Male6_AN2e


title: Chow_R_3

description: counts.matrix


title: Tcongolense_InVitro_rep_4

source_name: Parasites from in vitro culture

value: Parasites from in vitro culture


title: iPSC-2 line (Thermo Fisher A18945), 6dpi, replicate 1, for bulk RNA-seq

description:
merged_raw_read_counts.txt.gz
HSV1GFPtrunc_corr.fa.gz
HSV1GFPtrunc_corr.gtf.gz
gline_6dpi_rep1
TruSeq Stranded Total LT Sample Prep Kit (Illumina)


title: Male6_AN2d


title: iPSC-2 line (Thermo Fisher A18945), 3dpi, replicate 2, for bulk RNA-seq

description:
merged_raw_read_counts.txt.gz
HSV1GFPtrunc_corr.fa.gz
HSV1GFPtrunc_corr.gtf.gz
gline_3dpi_rep2
TruSeq Stranded Total LT Sample Prep Kit (Illumina)


title: Tcongolense_InVitro_rep_3


title: Tcongolense_InVitro_rep_2


title: Chow_R_2

description: counts.matrix


title: iPSC-2 line (Thermo Fisher A18945), 3dpi, replicate 1, for bulk RNA-seq

description:
merged_raw_read_counts.txt.gz
HSV1GFPtrunc_corr.fa.gz
HSV1GFPtrunc_corr.gtf.gz
gline_3dpi_rep1
TruSeq Stranded Total LT Sample Prep Kit (Illumina)


title: Tcongolense_InVitro_rep_1


title: Male6_AN2c

description:
single-nuclei gene expression data
cb_adult_mouse.mtx.gz
cb_adult_mouse_barcodes.txt
cb_adult_mouse_genes.txt
golgi_joint.mtx.gz
golgi_joint_barcodes.txt
golgi_joint_genes.txt
granule_joint.mtx.gz
granule_joint_barcodes.txt
granule_joint_genes.txt
interneuron_joint.mtx.gz
interneuron_joint_barcodes.txt
interneuron_joint_genes.txt
ubc_joint.mtx.gz
ubc_joint_barcodes.txt
ubc_joint_genes.txt


title: Male2_AN2c


title: Female2_AN2c


title: PANX1 rep 1 [treatment_0]

city: Ottawa

first: Xiao

last: Xiang

state: ON

address: 451 Smyth Road

country: Canada

institute: University of Ottawa

data_processing:
bcl2fastq-1.8.4 software used for basecalling.
The raw sequence data, in the form of FASTQ files, was aligned to the human  genome (hg19, iGenome GTF definition file) using the BOWTIE/TOPHAT pipeline (BOWTIE v2.2.3, TOPHAT 2.0.13). Accessory programs for the alignment stage include SAMTOOLS (v1.0) and CUTADAPT (v1.7.1).
Transcript assembly, abundance  estimation, and tests for differential regulation were done using CUFFLINKS (v2.2.1).
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited matrix text files include RPKM values for all samples

growth_protocol: Stable Rh30 cells were cultured in RPMI-1640 supplemented with 10% FBS, 1% penicillin/streptomycin, 100 µg/mL geneticin, and 2 µg/mL puromycin.

extract_protocol:
Total RNA was extracted using RNeasy Mini Kit (Qiagen, Germantown, MD, USA). Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 500 ng of total RNA for the construction of sequencing libraries.
RNA was purified first for Poly A tail containing mRNA molecules using poly-T oligo attached magnetic beads.The purified RNA was fragmented on thermocycler at 94 C for 8 min in fragmentation buffer. The cleaved RNA fragments were copied into first strand cDNA using reverse transcriptase and random primers. This was followed by second strand cDNA synthesis using RNase H and DNA Polymerase I. A single “A” base was added and adapter ligated. The cDNA was purified and then enriched by PCR to create cDNA libraries.

treatment_protocol: Expression of PANX1 or GFP under control of a cumate-inducibe switch in stable Rh30 cells was induced by 30 µg/mL of cumate for 48 hours.

tag: cell line

tag: cell type

value: alveolar rhabdomyosarcoma (RMS) cell line

tag: genotype/variation


title: PANX1 rep 3 [treatment_2]


title: HEC1

city: shanghai

first: henan

last: zhang

state: shanghai

address: No. 1000 Jinqi Road

institute: Shanghai Academy of Agricultural Sciences

description:
HEC1
fpkm.txt

data_processing:
Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts. In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing poly-N and low quality reads from raw data. At the same time, Q20, Q30 and GC content the clean data were calculated.
Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using Hisat2 (v2.0.5) and paired-end clean reads were aligned to the reference genome using Hisat2 (v2.0.5). We selected Hisat2 as the mapping tool for that Hisat2 can generate a database of splice junctions based on the gene model annotation file and thus a better mapping result than other non-splice mapping tools.
The mapped reads of each sample were assembled by StringTie (v1.3.3b) (Mihaela Pertea et al. 2015) in a reference-based approach. StringTie uses a novel network flow algorithm as well as an optional de novo assembly step to assemble and quantitate full-length transcripts representing multiple splice variants for each gene locus.
FeatureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene. Then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene. FPKM, expected number of Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced, considers the effect of sequencing depth and gene length for the reads count at the same time, and is currently the most commonly used method for estimating gene expression levels.
[For DESeq2 with biological replicates] Differential expression analysis of two conditions/groups (two biological replicates per condition) was performed using the DESeq2 R package (1.16.1). DESeq2 provide statistical routines for determining differential expression in digital gene expression data using a model based on the negative binomial distribution. The resulting P-values were adjusted using the Benjamini and Hochberg’s approach for controlling the false discovery rate. Genes with an adjusted P-value.
[For edgeR without biological replicates] Prior to differential gene expression analysis, for each sequenced library, the read counts were adjusted by edgeR program package through one scaling normalized factor. Differential expression analysis of two conditions was performed using the edgeR R package (3.18.1). The P values were adjusted using the Benjamini & Hochberg method. Corrected P-value of 0.05 and absolute foldchange of 2 were set as the threshold for significantly differential expression.
Gene Ontology (GO) enrichment analysis of differentially expressed genes was implemented by the clusterProfiler R package, in which gene length bias was corrected. GO terms with corrected Pvalue less than 0.05 were considered significantly enriched by differential expressed genes. KEGG is a database resource for understanding high-level functions and utilities of the biological system, such as the cell, the organism and the ecosystem, from molecular level information, especially large-scale molecular datasets generated by genome sequencing and other high-throughput experimental technologies (http://www.genome.jp/kegg/). We used clusterProfiler R package to test the statistical enrichment of differential expression genes in KEGG pathways.
Genome_build: Hericium erinaceus accession number: JABWEG000000000
Supplementary_files_format_and_content: fpkm.txt: Tab-delimited text files include FPKM values for each Sample.

organism: Hericium erinaceus

source_name: Hericium erinaceus mutated strain

growth_protocol: The mycelia seed culture was carried out in a 250-mL flask containing 100 mL potato dextrose broth (PDB, BD, USA) medium at 26°C on a rotary shaker incubator (150 rev min-1) for 7 d. The fermentation culture was performed in a 500-mL flask containing 200 mL medium by inoculating 10% (v/v) seed culture medium homogenized by homogenizer, and carried out on a rotary shaker incubator (150 rev/min) at 26°C for 6 d. Fermentation medium consisted of 24 g/L PDB, 1 g/L KH2PO4, 1 g/L MgSO4·7H2O, respectively. The mycelia were obtained by centrifuging at 12,000g, 4°C for 10 min, washing the mycelia twice with distilled water, and then transferred to EP tube and frozen by dry ice, - 70°C storage for RNA extraction.

extract_protocol:
The total RNA was extracted from the liquid fermentation mycelia of H. erinaceus (HEA, HEB, and HEC), using RNAprep Pure Plant Kit (Polysaccharides & Polyphenolics-rich) according to the manufacturer's speciﬁcations (TIANGEN, Beijing, China). A total amount of 1 µg RNA per sample was used as input material for the RNA sample preparations.
Sequencing libraries were generated using NEBNext® Ultra™ RNA Library Prep Kit for Illumina® (NEB, USA) following the manufacturer's recommendations, and index codes were added to attribute sequences to each sample.

value: fermentation mycelium

tag: strain

value: HEC


title: PANX1 rep 2 [treatment_1]


title: Male6_AN2b

tag: age


title: Female2_AN2b

tag: Sex

value: Female


title: Male6_AN2a

value: Male

tag: 10x version


title: HEB1

description:
HEB1
fpkm.txt

value: HEB


title: HEB2

description:
HEB2
fpkm.txt


title: Vector rep 3 [control_2]

value: GFP


title: Vector rep 2 [control_1]


title: Chow_R_1

description: counts.matrix

value: Chow


title: Xmoo1 line, ctrl, replicate 2, for single-cell RNA-seq

description:
hg38HSV1GFPtc.Seurat.500.RDS.gz
HSV1GFPtrunc_corr.fa.gz
HSV1GFPtrunc_corr.gtf.gz
NP2-60d-Ctrl-Rep2
Dropseq including second strand synthesis

data_processing:
For bulk RNA-sequencing, Illumina base calling, demultiplexing and FASTQ conversion with bcl2fastq v2.20.0 (Illumina)
alignment to GRCh38 genome using STAR v2.7.1a (https://github.com/alexdobin/STAR)
reads counted on GENCODE 27 gene models with htseq-count 0.9.1 (https://htseq.readthedocs.io/)
The HSV1 genome was extended from strain 17 (genbank entry NC_001806) with the GFP and loxP sequences, error-corrected based on the total RNA-sequencing data, and terminal repeats removed to avoid multi-mapping reads
Provided here are the resulting HSV-1 fasta and gtf file used in the data analysis
For FLAM-seq, the CCS reads were then used as input to the FLAManalysis pipeline (https://github.com/rajewsky-lab/FLAMAnalysis), that outputs gene assignment and poly(A) tail length and sequence for each read.
For single-cell RNA-sequencing, data was processed using the pigx pipeline version 1.1.4 (http://bioinformatics.mdc-berlin.de/pigx/, Wurmus et al. 2018 doi: 10.1093/gigascience/giy123) using a combined human/HSV1 genome
Genome_build: Homo sapiens hg38
Genome_build: HSV-1 GFP truncated corrected
Supplementary_files_format_and_content: fasta file
Supplementary_files_format_and_content: gtf file
Supplementary_files_format_and_content: Seurat R object

extract_protocol:
For single-cell RNA-sequencing, single cell suspensions were generated by enzymatic digestion of organoids, and then fixed using methanol (Alles et al. 2017, doi: 10.1186/s12915-017-0383-5)
Single-cell RNA-seq libraries were generated using an extended Dropseq protocol containing a second-strand synthesis step (Wyler et al. 2020, doi: 10.1101/2020.05.05.079194)

value: no

value: polyA+ RNA


title: HEA3

description:
HEA3
fpkm.txt

source_name: Hericium erinaceus original strain

value: HEA


title: Male2_AN2a

tag: genome build


title: HEC2

description:
HEC2
fpkm.txt

tag: tissue


title: Female2_AN2a


title: Treatment group 2 , biological rep3

city: 成都

first: 旭

middle: 晓

last: 富

state: 四川

address: 十二桥路37号

institute: 成都中医药大学

hyb_protocol: Affymetrix protocol

scan_protocol: Affymetrix protocol

data_processing: sst-rma-combined-dabg

organism: Rattus norvegicus

source_name: Treatment 2 diabetic rats

label_protocol: Affymetrix protocol

extract_protocol: Affymetrix protocol

value: pancreas

tag: agent

value: SQC


title: Xmoo1 line, ctrl, replicate 1, for single-cell RNA-seq

description:
hg38HSV1GFPtc.Seurat.500.RDS.gz
HSV1GFPtrunc_corr.fa.gz
HSV1GFPtrunc_corr.gtf.gz
NP2-60d-Ctrl-Rep1
Dropseq including second strand synthesis

value: Brain organoid


title: HEA1

description:
HEA1
fpkm.txt


title: Male6_AN2

first: Evan

last: Macosko

address: 75 Ames St, Broad Institute

institute: Broad Institute


title: Treatment group 2 , biological rep1


title: Vector rep 1 [control_0]


title: HEB3

description:
HEB3
fpkm.txt


title: Male2_AN2b


title: Male2_AN1c


title: 18523_Nuclear RNA

description:
Nuclear RNA
Yoruban Individuals

data_processing:
Map 3' seq libraries to respective genome with STAR 3.30.1. Remove reads mapping to genomic regions with 6 A's in a row or 7 A's in the 10 bases upstream of read.
Merge all libraries and call PAS with in house scripts (available on github https://brimittleman.github.io/Comparative_APA/)
Use ucsc-liftover 377 to reciprocally lift PAS then assigned orthologous PAS to Refseq hg38 gene annotations.
Remove PAS used on average <5% in both human and chimpanzee nuclear libraries. Also remove PAS in genes with expession  < 2 log2CPM in 8 individuals
bed files with hg39 and Pantro 6 genomic locations scores column is the mean usage of the PAS in the respective species Nuclear data, txt file with meta data for each PAS including column for PAS name (as used in bed file), gene, and genic location
Genome_build: human hg38, chimp Pantro6
Supplementary_files_format_and_content: PAS_doublefilter_either_ChimpCoordChimpUsage.sort.bed, bed file with Pantro6 coordinates and average chimpanzee usage
Supplementary_files_format_and_content: PAS_doublefilter_either_HumanCoordHummanUsage.sort.bed, bed file with hg38 coordinates and average human usage
Supplementary_files_format_and_content: PAS_GeneLocation.txt, text file with PAS name, gene, and genic location
Supplementary_files_format_and_content: Supplemental_table1 - meta data for 3' sequencing libraries, column name explanations in second sheet
Supplementary_files_format_and_content: Supplemental_table2 - meta data for RNA sequencing libraries, column name explanations in second sheet

source_name: Imortalized Lymphoblastoid cell line

extract_protocol:
The nuclear RNA was extracted using the first part of the nuclear isolation protocl from Mayer and Churchman. Once the sampes were pelleted in the nuclear wash buffer we resuspended in 700 ul of quizol lysis reagent and RNA isolation was complted using an miRNAEasy kit (Quiagen).
For each cell line we sampled both the total RNA in the cell, and the nucear RNA fraction through the ioslated nucleus.
3' RNA seq using Lexogen Rev. QuantSeq & RNA seq using Illumina TruSeq

value: Imortalized Lymphocyte

value: F


title: Female2_AN1c


title: plasmaRNA_health H8

city: Beijing

first: Hongcheng

last: Jia

state: Beijing

address: No.8 East Jing Shun Rd, Chaoyang District

department: Stomatology Department

institute: Beijing Ditan Hospital, Capital Medical University

description:
H8
lncRNA expression data from healthy human plasma.

hyb_protocol: The labeled samples were hybridized onto Arraystar Human LncRNA Microarray in Agilent Microarray Hybridization Chambers (Agilent p/n G2530-60029) according to the manufacturer's standard protocols (Agilent Technologies).

scan_protocol: The arrays were scanned by the Agilent Microarray Scanner (Agilent p/n G2565BA).

data_processing: Agilent Feature Extraction software (version 11.0.1.1) was used to analyze acquired array images. Quantile normalization and subsequent data processing were performed with using the GeneSpring GX v12.1 software package (Agilent Technologies).

source_name: plasma RNA, healthy

label_protocol:
Kit and instrument:
RNeasy Mini Kit (Qiagen p/n 74104)
NanoDrop ND-1000

extract_protocol: Trizol extraction of plasma RNA was performed according to the manufacturer's instructions.

treatment_protocol: Blood (4ml) was drawn by standard antecubital vein phlebotomy with EDTA tubes and centrifuged at 10,000 rpm for 10 min at 4℃. The plasma superment was separated from blood cells and frozen at -80℃.

tag: disease status

value: healthy

value: plasma

tag: gender

value: female

tag: age (yr)


title: plasmaRNA_OSCC X574

description:
X574
lncRNA expression data from OSCC plasma.

source_name: plasma RNA, OSCC

value: oral squamous cell carcinoma (OSCC)


title: 18510_Total RNA

description:
Total RNA
Yoruban Individuals

value: M


title: Model group , biological rep3

source_name: diabetic rats

value: model


title: plasmaRNA_health H13

description:
H13
lncRNA expression data from healthy human plasma.


title: plasmaRNA_OSCC X602

description:
X602
lncRNA expression data from OSCC plasma.


title: plasmaRNA_OSCC X474

description:
X474
lncRNA expression data from OSCC plasma.


title: plasmaRNA_health H5

description:
H5
lncRNA expression data from healthy human plasma.


title: Broccoli_GYG1

city: Dalian

first: Yuge

last: Guan

address: Linggong Road 2, Dalian

institute: Dalian University of Technology

data_processing:
Firstly, Cutadapt and perl scripts in house were used to remove the reads that contained adaptor contamination, low quality bases and undetermined bases.
Then sequence quality was verified using FastQC (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/). including the Q20, Q30 and GC-content of the clean data.
All downstream analyses were based on clean data of high quality. De novo assembly of the transcriptome was performed with Trinity 2.4.0. Trinity groups transcripts into clusters based on shared sequence content. Such a transcript cluster is very loosely referred to as a 'gene'. The longest transcript in the cluster was chosen as the 'gene' sequence (aka Unigene).
All assembled Unigenes were aligned against the non-redundant (Nr) protein database (http://www.ncbi.nlm.nih.gov/),Gene ontology (GO)(http://www.geneontology.org), SwissProt(http://www.expasy.ch/sprot/), Kyoto Encyclopedia of Genes and Genomes (KEGG)(http://www.genome.jp/kegg/) and eggNOG(http://eggnogdb.embl.de/) databases using DIAMOND with a threshold of Evalue<0.00001.
Supplementary_files_format_and_content: abundance measurements

organism: Brassica oleracea var. italica

source_name: harvested broccoli_untreated

extract_protocol:
Total RNA was extracted using Trizol reagent (Invitrogen, CA, USA) following the manufacturer's procedure. The total RNA quantity and purity were analysis of Bioanalyzer 2100 and RNA 1000 Nano LabChip Kit (Agilent, CA, USA) with RIN number >7.0. Poly(A) RNA is purified from total RNA(5ug) using poly-T oligo-attached magnetic beads using two rounds of purification.
Following purification, the mRNA is fragmented into smallpieces using divalent cations under elevated temperature. Then the cleaved RNA fragments werereverse-transcribed to create the final cDNA library in accordance with the protocol for the mRNASeq sample preparation kit (Illumina, San Diego, USA), the average insert size for the paired-endlibraries was 300 bp (±50 bp). And then we performed the paired-end sequencing on an IlluminaHiseq4000 at the (LC Sceiences,USA) following the vendor’s recommended protocol.

value: whole broccoli

tag: developmental stage

value: harvested broccoli

tag: treatment

value: untreated


title: Male6_AN1b

city: Cambridge

value: Male


title: 18510_Nuclear RNA

description:
Nuclear RNA
Yoruban Individuals


title: Model group , biological rep1


title: Treatment group 2 , biological rep2


title: 18523_Total RNA

description:
Total RNA
Yoruban Individuals


title: Male2_AN1b


title: 18504_Total RNA

description:
Total RNA
Yoruban Individuals


title: Tbrucei_ExVivo_rep_1

organism: Trypanosoma brucei

tag: mouse strain

tag: genotype

value: Wild-type

value: Parasites from ex vivo murine infection


title: Female2_AN1b

value: Female


title: Tbrucei_ExVivo_rep_4

tag: group


title: 18504_Nuclear RNA

description:
Nuclear RNA
Yoruban Individuals


title: Treatment group 1 , biological rep2

source_name: Treatment 1 diabetic rats

value: pancreas

value: metformin


title: Model group , biological rep2


title: Tbrucei_ExVivo_rep_3


title: Tbrucei_InVitro_rep_4

value: Parasites from in vitro culture


title: Male6_AN1a


title: 18502_Total RNA

description:
Total RNA
Yoruban Individuals

value: Imortalized Lymphocyte

value: F


title: control group , biological rep3

source_name: normal rats

value: control


title: 18502_Nuclear RNA

description:
Nuclear RNA
Yoruban Individuals


title: Treatment group 1 , biological rep1


title: Male2_AN1a


title: Tbrucei_InVitro_rep_3


title: Female2_AN1a


title: Tbrucei_ExVivo_rep_2


title: Tbrucei_InVitro_rep_2


title: 18498_Total RNA

description:
Total RNA
Yoruban Individuals


title: Tbrucei_InVitro_rep_rep_1


title: 18498_Nuclear RNA

description:
Nuclear RNA
Yoruban Individuals


title: Treatment group 1 , biological rep3


title: Male6_AN1


title: control group , biological rep2


title: control group , biological rep1


title: HEC3

description:
HEC3
fpkm.txt

value: fermentation mycelium

value: HEC


title: RZK02689_01

status: Public on Jan 21 2021

city: Madrid

first: Osvaldo

last: Graña

state: Comunidad de Madrid

address: C/ Melchor Fernández Almagro, 3

department: Structural Biology

country: Spain

institute: CNIO

data_processing:
RNA-seq processing:
Read adapters and polyA tails were removed with bbduk.sh, following the Lexogen recommendations. Processed reads were analysed with the nextpresso pipeline, as follows: Sequencing quality was checked with FastQC v0.11.7 (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/). Reads were aligned to the mouse reference genome (GRCm38) with TopHat-2.0.10 using Bowtie 1.0.0 and Samtools 0.1.19 (--library-type fr-secondstrand in TopHat), allowing three mismatches and twenty multihits. Read counts were obtained with HTSeq-count v0.6.1 (--stranded=yes), using the mouse gene annotation from GENCODE (gencode.vM20.GRCm38.Ensembl95). Differential expression was performed with DESeq2, using a 0.05 FDR.  GSEAPreranked was used to perform gene set enrichment analysis for several gene signatures on a pre-ranked gene list, setting 1000 gene set permutations. Only those gene sets with significant enrichment levels (FDR q-value < 0.25) were considered.
Genome_build: GRCm38
Supplementary_files_format_and_content: Normalized counts obtained with DESeq2

source_name: Kidney

growth_protocol: All mice were generated and maintained at the Animal Facility of the Spanish National Cancer Research Centre (CNIO) under specific pathogen-free conditions in accordance with the recommendation of the Federation of European Laboratory Animal Science Associations (FELASA)

extract_protocol:
Total RNA was isolated from the kidney tissues and PTCs using Trizol reagent (Takara, Shiga, Japan)
Total RNA samples (300ng) were used as provided by the user. RNA Quality scores were 6.3 on average (range 4.7-8.0) when assayed on a PerkinElmer LabChip analyzer. Sequencing libraries were prepared with the "QuantSeq 3‘ mRNA-Seq Library Prep Kit (FWD) for Illumina" (Lexogen, Cat.No. 015) by following manufacturer instructions. Library generation is initiated by reverse transcription with oligodT priming, and a second strand synthesis is performed from random primers by a DNA polymerase. Primers from both steps contain Illumina-compatible sequences. Libraries are completed by PCR {This kit generates directional libraries stranded in the sense orientation (the read1 (the only read in single read format) has the sense orientation (--library-type fr-secondstrand in TopHat, --stranded=yes in HTSeq).}  cDNA libraries are purified, applied to an Illumina flow cell for cluster generation and sequenced on an Illumina instrument (see below) by following manufacturer's protocols.

treatment_protocol: -8 weeks of Tert+/+ and generation 3 (G3) Tert-/- male an female mice were  administered a single intraperitoneal injection of FA with low dose of 125 mg/kg body weight or 0.3 M NaHCO3 (200ul).  Mice were sacrificed at day 14 and the kidneys were ice cold PBS perfused and harvested.

tag: cell type

value: kidney cells

value: Tert+/+  Folic acid treated

value: Tert+/+


title: RZK2694_01

description: a single intraperitoneal injection of FA with low dose of 125 mg/kg body weight or 0.3 M NaHCO3 (200ul).


title: RZK02693_01


title: RZK2746_01

value: G3 Tert-/- Folic acid treated

value: G3 Tert-/-


title: RZK02609_01

value: Tert+/+ vehicle treated


title: RZK02562_01

value: Male

value: G3 Tert-/- vehicle treated


title: RZK02563_01

value: Female


title: RZK02610_01


title: RZK2743_01


title: RZK2749_01


title: RZK2740_01


title: RZK2752_01


title: RZK02606_01


title: RZK2747_01


title: RZK2827_01

description: 7 weeks old

extract_protocol:
Total RNA was isolated from the kidney tissues and PTCs using Trizol reagent (Takara, Shiga, Japan)
Total RNA samples (300ng) were processed with the "QuantSeq 3‘ mRNA-Seq Library Prep Kit (FWD) for Illumina" (Lexogen, Cat.No. 015) by following manufacturer instructions. RNA Quality scores were 6.6 on average (range 5.0-7.5) when assayed on a PerkinElmer LabChip analyzer. Library generation is initiated by reverse transcription with oligodT priming, and a second strand synthesis is performed from random primers. Primers from both steps contain Illumina-compatible sequences. Libraries are completed by PCR {This kit generates directional libraries stranded in the sense orientation (the read1 (the only read in single read format) has the sense orientation (--library-type fr-secondstrand in TopHat, --stranded=yes in HTSeq).}  cDNA libraries are purified, applied to an Illumina flow cell for cluster generation and sequenced on an Illumina instrument (see below) by following manufacturer's protocols.

value: G3 Tert-/- young

value: 7 weeks old


title: RZK2819_01

description: 7 weeks old


title: RZK2821_01

description: 7 weeks old


title: RZK2828_01

description: 7 weeks old


title: RZK2820_01

description: 7 weeks old


title: RZK2797_01

description: 7 weeks old

value: Tert+/+ young


title: RZK2798_01

description: 7 weeks old


title: RZK2799_01

description: 7 weeks old


title: RZK2803_01

description: 7 weeks old


title: RZK2510_01

description: 47 weeks old

value: Tert+/+ old

value: 47 weeks old


title: RZK2509_01

description: 47 weeks old


title: RZK02561_01


title: RZK2508_01

description: 47 weeks old


title: RZK2507_01

description: 47 weeks old


title: RZK2802_01

description: 7 weeks old


title: RZK2477_01

description: 47 weeks old

value: G3 Tert-/- old


title: RZK2506_01

description: 47 weeks old


title: SCAF729_B3

city: Bethesda

first: Nataliya

middle: Prokopenko

last: Buxbaum

state: Maryland

address: 10 Center Drive, CRC, 3-3288

department: ETIB

institute: NCI, NIH

data_processing:
The standard 10X Genomics cellranger (version 3.0.2) pipeline was used to extract Fastq’s and 10X Genomics cellranger (version 3.0.2) pipeline was used to perform data processing. Sequenced reads were aligned to the 10X Genomics provided Mouse mm10 reference sequence (refdata-cellranger-mm10-3.0.0).
Featured output files (features, barcode and matrix) were read into R using the scRNAseq analysis package Seurat.
Syngeneic and allogeneic replicates were first merged and filtered for cells containing at least 200 and less than 4500 features as well as a mitochondrial gene content of less than 5%. Samples were normalized and variable genes identified using the FindVariableFeatures function with nfeatures limited to 2000.
Both samples were integrated, scaled and principal components were calculated. Clustering was performed using Uniform Manifold Approximation and Projection (UMAP) with the first 20 dimensions and a resolution of 0.5.
Conserved markers between each cluster for both samples were identified using the FindConservedMarker function. Differentially expressed genes between syngeneic and allogeneic cells were calculated using the FindMarker function.
Genome_build: refdata-cellranger-mm10-3.0.0
Supplementary_files_format_and_content: 2 excel csv files containing either the conserved markers between syngeneic and allogeneic animals for each cluster or the differentially expressed genes within one cluster comparing syngeneic to allogeneic animals.

source_name: liver, sorted CD45+ CD4+ cells

extract_protocol:
Animals were transcardially perfused with PBS and the liver was excised. Single-cell suspensions of liver cells were obtained by mechanically disrupting harvested livers and filtering through 70-μm mesh filters (Thermo Fisher Scientific). Ammonium-chloride potassium (ACK) lysis was performed to remove erythrocytes prior to cell counting. For fluorescence-activated cell sorting (FACS), samples were stained for CD45 and CD4 underwent FACS using BD Influx achieving 95% purity. FACS-purified samples were collected into PBS buffer containing 2% (v/v) BSA. Samples were tested for viability (all samples >82%) and 6000 cells were loade according to the 10X 5' user guide.
3 NextSeq steps were performed (NextSeq High Output 150-cycle v2.5)
Droplet-based single cell RNA sequencing

treatment_protocol: Recipient female mice at 12-13 weeks of age were conditioned with 850 cGy total body irradiation (TBI) delivered in two doses 3 hours apart on day -1. Age-matched female B10.D2 mice were used for as donors for allogeneic transplants. Recipients were reconstituted with 15 million unfractionated splenocytes and 8 million bone marrow cells injected via tail vein on day 0. The injection buffer contained gentamicin (100 μg/ml), however no additional antibiotics were administered post-transplant. Animals were weighed and cGvHD scoring was performed twice weekly using a previously described clinical scoring system (Anderson, 2003)

tag: day post transplant

tag: graft donor strain

tag: graft recipient strain

value: Balb/c

value: liver


title: SCAF728_B2


title: RZK2483_01

description: 47 weeks old

tag: Sex

value: kidney cells

tag: age


title: SCAF726_A3


title: SCAF727_B1


title: S_012-F_AKIN-L____KO-_Tu-ups1-REP_3

city: Cologne

first: Franziska

last: Metge

address: Joseph-Stelzmann-Str 9b

department: Bioinformatics Corefacility

institute: Max Planck Institute for Biology of Ageing

data_processing:
raw reads were aligned to the transcriptome using kallisto quant
raw counts were collected and summarized by gene using R-package tximport
differential gene expression was executed using R-package DESeq2
DESeq2 war run for each pairwise comparison separately
Genome_build: Saccharomyces cerevisiae build 83 (GCA_000146045.2)
Supplementary_files_format_and_content: tab-delimited text files kallisto/DESeq2 tximport raw counts
Supplementary_files_format_and_content: Tab-delimited text files DESeq2 results

organism: Saccharomyces cerevisiae

source_name: S.cerevisiae ups1-null

growth_protocol: Cells were grown to log phase in synthetic complete (SCD) medium at 30°C.

extract_protocol:
Total RNA was isolated with the NucleoSpin® RNA kit (MACHEREY-NAGEL) from 3 OD600 units of cells, according to the manufacturer’s protocol.
Libraries were prepared using the Illumina® TruSeq® mRNA stranded sample preparation Kit. Library preparation started with 1 µg total RNA. After poly-A selection (using poly-T oligo-attached magnetic beads), mRNA was purified and fragmented using divalent cations under elevated temperature. The RNA fragments underwent reverse transcription using random primers. This is followed by second strand cDNA synthesis with DNA Polymerase I and RNase H. After end repair and A-tailing, indexing adapters were ligated. The products were then purified and amplified (14 PCR cycles) to create the final cDNA libraries. After library validation and quantification (Agilent tape station), equimolar amounts of library were pooled. The pool was quantified by using the Peqlab KAPA Library Quantification Kit and the Applied Biosystems 7900HT Sequence Detection System.

treatment_protocol: Cells grown to log phase in SCD medium were treated with 1 μg/ml tunicamycin for 3 h

tag: strain

value: 1 ug/ml tunicamycin


title: RZK2478_01

description: 47 weeks old


title: SCAF725_A2

tag: tissue


title: RZK2484_01

description: 47 weeks old


title: S_008-F_AKIN-L____WT-_Tu-____-REP_2

source_name: S.cerevisiae WT

value: WT


title: RZK2482_01

description: 47 weeks old


title: SCAF724_A1


title: S_009-F_AKIN-L____WT-_Tu-____-REP_3


title: S_007-F_AKIN-L____WT-_Tu-____-REP_1


title: S_010-F_AKIN-L____KO-_Tu-ups1-REP_1


title: S_005-F_AKIN-L____KO-___-ups1-REP_2

value: NO


title: S_006-F_AKIN-L____KO-___-ups1-REP_3


title: S_002-F_AKIN-L____WT-___-____-REP_2


title: S_004-F_AKIN-L____KO-___-ups1-REP_1


title: S_001-F_AKIN-L____WT-___-____-REP_1


title: S_003-F_AKIN-L____WT-___-____-REP_3


title: S_011-F_AKIN-L____KO-_Tu-ups1-REP_2


title: 3xCUP1 no origin

first: Felix

last: Krueger

address: Granta Park

department: Bioinformatics

institute: Altos Labs

data_processing:
Library strategy: TrAEL-seq
Sequencing data was processed with a custom script (location available from the manuscript) to transfer the first 8bp of a each sequence to the readID of the FastQ file (UMI, unique molecular identifier). In addition, up to and including 3 T bases were removed from the 5'-end following the UMI transfer. The resulting FastQ files were trimmed with Trim Galore (v0.6.5) to remove read-through contamination with the Illumina standard adapter as well as poor base call qualities (cutoff: Phred 20). Trimmed reads were then aligned to the relevant genomes using Bowtie2 (v2.4.1) in --local mode. Following the alignments, reads were de-duplicated taking UMIs as well as mapping position into account, using UmiBam (v0.2.0; https://github.com/FelixKrueger/Umi-Grinder).
Samples were imported into Seqmonk v1.47, truncated to a single base and quantified %reverse reads in 1kb windows
Genome_build: S. cerevisiae R64-1-1
Supplementary_files_format_and_content: A tab delimted Seqmonk annotated probe report. The quantification show % reverse reads in 1% windows.
Supplementary_files_format_and_content: TrAEL-seq report

source_name: yeast

extract_protocol:
Cells in ethanol (1-3x107 per plug) were pelleted in round bottom 2 ml tubes by centrifuging 30 s 20,000 g, washed once in 1 ml PFGE wash buffer (10 mM Tris HCl pH 7.5, 50 mM EDTA) and resuspended in 60 µl same with 1 µl lyticase (17 U/ µl in 10 mM KPO4 pH7, 50% glycerol, Merck >2000 U/mg L2524). Samples were heated to 50°C for 1-10 min before addition of 40 µl molten CleanCut agarose (Bio-Rad 1703594), vortexing vigorously for 5 s before pipetting in plug mould (Bio-Rad 1703713) and solidifying 15-30 min at 4°C. Each plug was transferred to a 2 ml tube containing 500 µl PFGE was buffer containing 10 µl 17 U/µl lyticase and incubated 1 hour at 37°. Solution was replaced with 500 µl PK buffer (100 mM EDTA pH 8, 0.2% sodium deoxycholate, 1% sodium N-lauroyl sarcosine, 1 mg/ml Proteinase K) and incubated overnight at 50°. Plugs were rinsed with 1 ml TE, then washed three times with 1 ml TE for 1-2 hours at room temperature with rocking, 10 mM PMSF was added to the second and third washes from 100 mM stock (Merck 93482). Plugs were then digested 1 h at 37°C with 1 µl 1000 U/ml RNase T1 (Thermo EN0541) in 200 µl TE Plugs were stored in 1xTE.
½ an agarose plug of cells was equilibrated once in 100 µl 1x TdT buffer (NEB) for 30 min at room temperature, then incubated for 2 h at 37°C in 100 µl 1x TdT buffer containing 4 µl 10 mM ATP and 2 µl Terminal Transferase (NEB M0315L). Plugs were rinsed with 1 ml tris buffer (10 mM Tris HCl pH 8.0), equilibrated in 100 µl 1x T4 RNA ligase buffer (NEB) containing 40 µl 50% PEG 8000 for 1 hour at room temperature then incubated overnight at 25°C in 100 µl 1x T4 RNA ligase buffer (NEB) containing 40 µl 50% PEG 8000, 1 µl 10 pM/µl TrAEL-seq adaptor 1 ([App]NNNNNNNNAGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTUGCGCAGGCCATTGGCC[BtndT]GCGCUACACTCTTTCCCTACACGACGCT) and 1 µl T4 RNA ligase 2 truncated KQ (NEB M0373L). Plugs were then rinsed with 1 ml tris buffer, transferred to 15 ml tubes and washed three times in 10 ml tris buffer with rocking at room temperature for 1-2 hours each, then washed again overnight under the same conditions. Plugs were equilibrated for 15 min with 1 ml agarase buffer (10 mM Bis-Tris-HCl, 1 mM EDTA pH 6.5), then the supernatant removed and 50 µl agarase buffer added. Plugs were melted for 20 min at 65°C, transferred for 5 min to a heating block pre-heated to 42°C, 1 µl β-agarase (NEB M0392S) was added and mixed by flicking without allowing sample to cool, and incubation continued at 42°C for 1 h. DNA was ethanol precipitated with 25 µl 10 M NH4OAc, 1 µl GlycoBlue, 330 µl of ethanol and resuspended in 10 µl 0.1xTE. 40 µl reaction mix containing 5µl Isothermal amplification buffer (NEB), 3 µl 100 mM MgSO4, 2µl 10 mM dNTPs and 1µl Bst 2 WarmStart DNA polymerase (NEB M0538S) was added and sample incubated 30 min at 65°C before precipitation with 12.5 µl 10 M NH4OAc, 1 µl GlycoBlue, 160 µl ethanol and re-dissolving pellet in 130 µl 1xTE.
The DNA was transferred to an AFA microTUBE (Covaris 520045) and fragmented in a Covaris E220 using duty factor 10, PIP 175, Cycles 200, Temp 11, then transferred to a 1.5 ml tube containing 8 µl pre-washed Dynabeads MyOne streptavidin C1 beads (Thermo, 65001) re-suspended in 300 µl 2xTN (10 mM Tris pH 8, 2 M NaCl) along with 170 µl water (total volume 600 µl) and incubated 30 min at room temperature on a rotating wheel. Beads were washed once with 500 µl 5 mM Tris pH 8, 0.5 mM EDTA, 1 M NaCl, 5 min on wheel and once with 500 µl 0.1x TE, 5 min on wheel before re-suspension in 25 µl 0.1x TE. 3.5 μl NEBNext Ultra II End Prep buffer, 1 µl 1 ng/µl sonicated salmon sperm DNA (this is added as a carrier) and 1.5 μl NEBNext Ultra II End Prep enzyme were added and reaction incubated 30 min at room temperature and 30 min at 65°C. After cooling, 1.25 µl 10 pM/µl TrAEL-seq adaptor 2 ([Phos]GATCGGAAGAGCACACGTCTGAACTCCAGTCUUUUGACTGGAGTTCAGACGTGTGCTCTTCCGATC*T ), 0.5 µl NEBNext ligation enhancer and 15 µl NEBNext Ultra II ligation mix were added and incubated 30 min at room temperature. The reaction mix was removed and discarded and beads were rinsed with 500 µl wash buffer (5 mM Tris pH 8, 0.5 mM EDTA, 1 M NaCl) then washed twice with 1 ml wash buffer for 10 min on wheel at room temperature and once for 10 min with 1 ml 0.1x TE. Libraries were eluted from beads with 11 µl 1x TE and 1.5 µl USER enzyme (NEB) for 15 min at 37°C, then again with 10.5 µl 1x TE and 1.5 µl USER enzyme (NEB) for 15 min at 37°, and the two eluates combined. An initial test amplification was used to determine the optimal cycle number for each library. For this, 1.25 μl library was amplified in 10 µl total volume with 0.4 µl each of the NEBNext Universal and any NEBNext Index primers with 5 µl NEBNext Ultra II Q5 PCR master mix. Cycling program: 98°C 30s then 18 cycles of [98°C 10 s, 65°C 75 s], 65°C 5 min. Test PCR was cleaned with 8 µl AMPure XP beads (Beckman A63881) and eluted with 2.5 µl 0.1x TE, of which 1 µl was examines on a Bioanalyser high sensitivity DNA chip (Agilent 5067-4626). Ideal cycle number should bring final library to final concentration of 1-3 nM, noting that the final library will be 3 cycles more concentrated than the test anyway. 21 µl of library was then amplified with 2 µl each of NEBNext Universal and chosen Index primer and 25 µl NEBNext Ultra II Q5 PCR master mix using same conditions as above for calculated cycle number. Amplified library was cleaned with 40 µl AMPure XP beads (Beckman A63881) and eluted with 26 µl 0.1x TE, then 25 µl of this was again purified with 20µl AMPure XP beads and eluted with 11µl 0.1x TE.

value: yeast

tag: growth media

value: SC 2percent glucose

tag: fixed/unfixed

value: Fixed - 70percent ethanol


title: Pgal-3HA rad52D 2pct glu

value: YP 2percent raffinose + 2percent glucose


title: Pgal-3HA rad52D 2pct gal

value: YP 2percent raffinose + 2percent galactose


title: Pgal-3HA 2pct gal


title: 3xCUP1 RSC30 origin


title: Pgal-3HA sac3D 0pct gal 2

value: YP 2percent raffinose


title: Pgal-3HA sac3D 2pct gal 1


title: Pgal-3HA sac3D 2pct gal 2


title: Pgal-3HA sac3D 0_02pct gal 1

value: YP 2percent raffinose + 0.02percent galactose


title: Pgal-3HA 2pct gal 2


title: Pgal-3HA sac3D 0pct gal 1


title: Pgal-3HA sac3D 0_02pct gal 2


title: Pgal-3HA 0pct gal 2


title: Pgal-3HA 0pct gal 1


title: Pgal-3HA 0_02pct gal 2


title: Pgal-3HA 0_02pct gal 1


title: HEA2

description:
HEA2
fpkm.txt

value: fermentation mycelium

value: HEA


title: 67-7_P6 Blood

city: Davis

first: Smita

last: Iyer

address: county rd 98 & hutchison, ccm room 2075

department: Center for Immunology and Infectious Disease

institute: University of California-Davis

data_processing:
The raw read data was filtered using HTStream (version 1.3.1) which included screening for contaminants (such as PhiX and rRNA), quality-based trimming, and adapter trimming. (https://github.com/s4hts/HTStream)
STAR (version 2.7.3a) was used to align the processed data to the rhesus genome (Mmul_10). Dobin, Alexander, et al. "STAR: ultrafast universal RNA-seq aligner." Bioinformatics 29.1 (2013): 15-21.
MultiQC (custom version) was then used for read and alignment quality assessment. https://github.com/s4hts/MultiQC
Differential expression analyses were conducted using the limma-voom Bioconductor pipeline, using edgeR version 3.30.3 and limma version 3.44.3 in R 4.0.1  The model used in limma included effects for brain region, infection status, and their interaction, and standard errors of log fold changes were adjusted for within-animal correlations.
Supplementary_files_format_and_content: Tables of normalized counts per gene. Comparison between tissue types and characteristics.

source_name: Blood

extract_protocol:
2000 sorted cells were flash frozen in 300 ul of RLT buffer and extracted using the Qiagen mini lipid RNA isolation kit according to manufacturers instructions.
The libraries were constructed following the 3' TagSeq protocol using Lexogen kit (QuantSeq 3’ mRNA-Seq Library Prep Kit FWD for Illumina). 500ng of total RNA was used as input.

tag: cell type code

value: B7+ CD4


title: 69-7_P8 Blood

value: B7+ CD8


title: 70-7_P9 Blood

value: B7- CD8


title: 62-7_P1 GUT

source_name: GUT


title: 64-7_P3 GUT


title: 66-7_P5 Blood

value: Naive CD4


title: 61-7_P0 Blood

value: Naive CD8


title: 60-6_P9 Blood


title: Pgal-3HA 2pct glu


title: 59-6_P8 Blood


title: Pgal-3HA 2pct gal 1


title: 57-6_P6 Blood


title: 65-7_P4 GUT


title: 55-6_P4 GUT


title: 56-6_P5 Blood


title: 54-6_P3 GUT


title: 58-6_P7 Blood

value: B7- CD4


title: 52-6_P1 GUT


title: 68-7_P7 Blood


title: 50-5_P9 Blood


title: 51-6_P0 Blood


title: 49-5_P8 Blood


title: 44-5_P3 GUT


title: 43-5_P2 GUT


title: 63-7_P2 GUT


title: 42-5_P1 GUT


title: 48-5_P7 Blood


title: 45-5_P4 GUT


title: 47-5_P6 Blood


title: 46-5_P5 Blood


title: 41-5_P0 Blood