title: d4c7+CsA

source_name: Mouse ESC

tag: transgene

value: Blimp1-mVenus reporter; Stella-ECFP reporter (BVSC)

value: mVenus sort


title: P14 Ileum WT rep 1

status: Public on Feb 16 2021

type: SRA

city: Gothenburg

first: Thaher

last: Pelaseyed

address: Box 440

department: Medical Biochemistry and Cell Biology

country: Sweden

institute: University of Gothenburg

description:
TPM.txt
DEG_P24vsP14.txt

library_source: transcriptomic

data_processing:
Quality of raw data was assessed using FastQC (version 0.11.2) looking at per base sequence quality and adapter contamination.
If required, Fastq files were quality filtered using prinseq (version 0.20.3) (Schmieder and Edwards, 2011).
The number of mapped reads was calculated using HTseq (version 0.6.1p1) (Anders et al., 2015) with the stranded reverse protocol.
Normalization for transcripts per million (TPM) was performed using “biomaRt” library in R (Durinck et al., 2005).
Normalization for differential gene expression was performed using DESeq2 (version 1.14) in R (Love et al., 2014).
Genome_build: The reads were mapped against the mouse reference genome mm10 from Ensembl using STAR (version 2.4.0f for the DC and 2.5.2b for the Si8).
Supplementary_files_format_and_content: tab-delimited text files include gene name, log2FoldChange and padj for each gene
Supplementary_files_format_and_content: tab-delimited text files include Transcripts Per Million (TPM) for each gene in every sample

molecule: total RNA

organism: Mus musculus

source_name: Mouse whole ileum

extract_protocol:
Ileum samples for mRNA analysis were collected in RNAlater (#76104, Qiagen) and kept at -80°C until RNA extraction. Total RNA was isolated using RNeasy Plus Mini Kit (#74134, Qiagen) and DNase Max Kit (#15200-50, Qiagen), followed by storage at -80°C.
The quality of isolated RNA was determined using a Bioanalyzer (Agilent) with RIN values greater than 8. cDNA libraries were prepared using the TruSeq Stranded Total RNA Sample Preparation kit with Ribo Zero Gold (Rev. E; Illumina) according to manufacturer´s protocol.

treatment_protocol: C57BL/6N mice were injected with 0.1 μg/g bodyweight of rmIl22 in 100 µL PBS or PBS alone at P14 and P15 and sacrificed at P16.

tag: strain

tag: tissue

value: Ileum

tag: age

value: Postnatal day 14


title: Mouse ESC +AlkB rep 3

city: Riverside

first: Junchao

last: Shi

state: CA

address: 900 University Ave

department: Division of Biomedical Sciences, School of Medicine

country: USA

institute: University of California, Riverside

data_processing:
For each RNA library, around 10 million reads (raw data) were generated by Illumina Hi-Seq 2000. Sequence reads that fit any of the following parameters were removed with following standard quality control criteria: 1) The reads with N; more than 4 bases whose quality score is lower than 10 or more than 6 bases whose quality score is lower than 13. 2) The reads with 5’ primer contaminants or without 3’ primer. 3) The reads without the insert tag. 4) The reads with ploy A. 5) The reads shorter than 15nt. The clean reads were obtained after data filtration.
Genome_build: mm10 (for mouse), hg19 (for human)
Supplementary_files_format_and_content: tab-delimited text files include sequences, length of sequences and sequence counts.

source_name: Embryonic stem cells

extract_protocol:
Total RNAs were extracted by Trizol (Invitrogen). Then small RNAs sized at 15-50nt were excised from 15% (w/v) urea polyacrylamide gel.
Small RNA libraries were constructed according to NEBNext® Multiplex Small RNA Library Prep Set for Illumina (New England Biolabs).

value: Embryonic stem cells

tag: treatment

value: RNAs were treated with AlkB before cDNA library construction.

tag: molecule type

value: 15-50 nt RNA


title: Mouse ESC +AlkB rep 2


title: Lymphocytes_Cont_9

city: Chicago

first: Eleonora

last: Gatta

state: IL

address: 1601 W Taylor St

department: Psychiatry

institute: University of Illinois at Chicago

description: C87.2 (column name in supplementary files)

data_processing:
Fastq files were processed and demultiplexed with bcltofastq 1.8.4 for pools 1 and 2 and bcltofastq 2.17.1.14 for pool 3.
Raw reads were then checked for quality using FASTQC (v 0.11.2), trimmed and filtered using Trimmomatic (v 0.33) to remove residual adapter content and low-quality bases (Phred quality score < 28). Trimmed/filtered reads were aligned to UCSC‐hg38 genome and gene models using STAR (v 3.5.0a) using --quantMode GeneCounts to generate gene-level counts; reverse-stranded counts were used.
12,290 genes without logCPM > log2 (1) in at least 3 samples were filtered out, leaving 14,154 genes to be analyzed for differential expression. TMM-values were re-calculated and expression values were normalized using the limma-voom + TMM method,42 then analyzed using a statistical model that accounted for processing batch, sex and age.
Multiple hypothesis testing adjustments for the schizophrenic vs. control comparison were done using the False Discovery Rate method.43
Genome_build: UCSC‐hg38
Supplementary_files_format_and_content: Guidotti_RawCounts_3combined.xlsx contains raw gene-level counts, some gene annotation information and a column indicating which genes passed the filtering thresholds. Guidotti_VoomNormalizedValues_3combined.xlsx contains voom-normalized log2 count per million expression values for genes that passed filtering thresholds. Guidotti_VoomWeights_3combined.xlsx contains voom's weights per-gene and per-sample to adjust for the relationship between mean and variance in expression values.

organism: Homo sapiens

source_name: Lymphocytes

extract_protocol:
Subject’s blood was collected in 4-8 lavender top collection tubes (EDTA) (~8 ml blood per tube), and processed using Balance Salt Solution (BSS, see Ficoll-Paque Plus instructions for reagent preparation). Blood samples were then layered over cold Ficoll-Paque Plus, and centrifuged using a swinging bucket rotor at 400 g for 45 min at 4°C. The lymphocyte layer was removed into sterile collection tubes, centrifuged at 100 g for 10 min at 4°C and loose lymphocyte pellet washed with BSS.
RNA-seq libraries were constructed using the Illumina TruSeq Stranded RNA sample Prep kit (Illumina, CA) following manufacturer’s instructions. A single library was prepared from each sample. All libraries were then quantitated by qPCR, combined in equimolar concentration into three pools of 11-16 individual (half C and half S), and each pool was sequenced on two lanes of a HiSeq2500.

tag: diagnosis

value: Control

tag: batch

tag: Sex

value: F

tag: race

value: African American

tag: cigarette smoked per week

tag: cigarettes pack per day

tag: number of years smoking

tag: mood medications

tag: benzodiazepines

tag: matrics


title: Mouse ESC +AlkB rep 1


title: Mouse ESC traditional rep 3

value: RNAs were sequenced with standard protocols.


title: Lymphocytes_Cont_8

description: C86.2 (column name in supplementary files)

value: M

value: caucaisian


title: Retinal_microglia_control_S6_part2

city: Freiburg

first: Clemens

last: Lange

address: Kilianstraße 5

department: Klinik für Augenheilkunde

country: Germany

institute: Uniklinik Freiburg

data_processing:
Quality control FastQC Galaxy Version 0.72
Reads were mapped to the mouse reference genome (Gencode, version M25) with RNA STAR Galaxy Version 2.7.2b (default parameters) using the Gencode main annotation file (Gencode, version M25). Two BAM files for each sample (one for each flow cell) were combined in one BAM file per sample using Merge BAM files Galaxy Version 1.2.0.
Reads mapped to the mouse reference genome were counted using featureCounts Galaxy Version 1.6.4 (default parameters) using the aforementioned annotation file.
The output of featureCounts was imported to RStudio (Version 1.2.1335, R Version 3.5.3). Gene symbols were determined based on ENSEMBL release 100 (Mouse genes, download at 08/01/2020). Genes with 0 reads in all samples were removed from the analysis. After principal component analysis, differential gene expression was analyzed using the R package DESeq2 Version 1.22.2 (default parameters). Transcripts with log2fold change (log2FC) > 1.5 or < -1.5 and Benjamini-Hochberg adjusted p-value < 0.05 were considered as differentially expressed genes (DEG).
Genome_build: GRCm38.p6

source_name: Retinal microglia

extract_protocol:
C57BL/6J mice were purchased from Charles River and analyzed at the age of 8 weeks. Total bulk RNA was extracted from directly into RNAprotect buffer (QIAGEN, Hilden, Germany) from FACS sorted CD45+CD11b+CX3CR1+Ly6C-Ly6G- retinal microglia according to the “Purification of total RNA from animal and human cells” protocol of the RNeasy Plus Micro Kit (QIAGEN). In brief, cells were stored and shipped in RNAprotect buffer at 2-8 °C. After pelleting, the RNAprotect buffer was replaced by RLT Plus buffer (QIAGEN) and the samples were homogenized by vortexing for 30 sec. Genomic DNA contamination was removed using gDNA Eliminator spin columns. Next ethanol was added and the samples were applied to RNeasy MinElute spin columns followed by several wash steps. Finally, total RNA was eluted in 12 μl of nuclease free water. Purity and integrity of the RNA was assessed on the Agilent 2100 Bioanalyzer with the RNA 6000 Pico LabChip reagent set (Agilent, Palo Alto, CA, USA).   The SMARTer Ultra Low Input RNA Kit for Sequencing v4 (Clontech Laboratories, Inc., Mountain View, CA, USA) was used to generate first strand cDNA from 150 to 600 pg total-RNA. Double stranded cDNA was amplified by LD PCR (12 to 14 cycles) and purified via magnetic bead clean-up. Library preparation was carried out as described in the Illumina Nextera XT Sample Preparation Guide (Illumina, Inc., San Diego, CA, USA). 150 pg of input cDNA were tagmented (tagged and fragmented) by the Nextera XT transposome. The products were purified and amplified via a limited-cycle PCR program to generate multiplexed sequencing libraries. For the PCR step 1:5 dilutions of index 1 (i7) and index 2 (i5) primers were used. The libraries were quantified using the KAPA SYBR FAST ABI Prism Library Quantification Kit (Kapa Biosystems, Inc., Woburn, MA, USA). Equimolar amounts of each library were pooled, and the pools were used for cluster generation on the cBot with the Illumina TruSeq SR Cluster Kit v3.
The sequencing run was performed on an HiSeq 1000 instrument using the indexed, 50 cycles single-read (SR) protocol and the TruSeq SBS v3 Reagents according to the Illumina HiSeq 1000 System User Guide. Image analysis and base calling resulted in .bcl files, which were converted into .fastq files with the bcl2fastq v2.18 software. RNA extraction, library preparation and RNAseq were performed at the Genomics Core Facility “KFB - Center of Excellence for Fluorescent Bioanalytics” (University of Regensburg, Regensburg, Germany).

value: Retinal microglia

value: control


title: Retinal_microglia_control_S6_part1


title: Mouse ESC traditional rep 1


title: Mouse ESC traditional rep 2


title: Mouse iPSC PANDORA-seq rep 3

source_name: iPS cells

value: iPS cells

value: RNAs were treated with T4PNK, then AlkB before cDNA library construction.


title: Retinal_microglia_control_S5_part2


title: Retinal_microglia_control_S5_part1


title: Lymphocytes_Cont_5

description: C65.1 (column name in supplementary files)


title: Lymphocytes_Cont_7

description: C85.2 (column name in supplementary files)

value: White


title: Lymphocytes_Cont_6

description: C71.2 (column name in supplementary files)


title: Mouse iPSC +T4PNK rep 1

value: RNAs were treated with T4PNK before cDNA library construction.


title: Mouse iPSC +T4PNK rep 3


title: Mouse iPSC PANDORA-seq rep 2


title: Mouse iPSC PANDORA-seq rep 1


title: Retinal_microglia_control_S4_part2


title: Mouse iPSC +T4PNK rep 2


title: Lymphocytes_Cont_4

description: C60.1 (column name in supplementary files)


title: Mouse iPSC +AlkB rep 3


title: Lymphocytes_Cont_3

description: C58.1 (column name in supplementary files)


title: Mouse iPSC +AlkB rep 2


title: Lymphocytes_Cont_2

description: C55.1 (column name in supplementary files)


title: Retinal_microglia_control_S3_part2


title: Mouse iPSC +AlkB rep 1


title: Mouse iPSC traditional rep 3


title: Retinal_microglia_control_S3_part1


title: Mouse iPSC traditional rep 2


title: Mouse iPSC traditional rep 1


title: Mouse intermediate PANDORA-seq rep 3

source_name: Reprogramming intermediate cells (day 3)


title: Lymphocytes_Cont_1

description: C40.1 (column name in supplementary files)


title: Retinal_microglia_control_S2_part2


title: Mouse intermediate PANDORA-seq rep 2

value: Reprogramming intermediate cells (day 3)


title: Retinal_microglia_control_S2_part1


title: Retinal_microglia_control_S4_part1


title: Mouse intermediate +T4PNK rep 3


title: Retinal_microglia_control_S1_part1


title: Retinal_microglia_control_S1_part2


title: Mouse intermediate +AlkB rep 2


title: B584_RNA-seq

city: Daejeon

first: Seon-Kyu

last: Kim

address: 125 Gwahak-ro, Yuseong-gu, Daejeon 305-806, Korea

department: Personalized Genomic Medicine Research Center

country: South Korea

institute: Korea Research Institutue of Bioscience & Biotechnology

data_processing:
Reference genome sequence data from Homo sapiens were obtained from the NCBI Genome database (assembly ID: GRCh38). The reference genome indexing and read mapping of tissue samples were performed using STAR software (ver. 2.5.4b).
Then, the read counts per million fragments mapped (CPM) of each sample were estimated.
Genome_build: GRCh38
Supplementary_files_format_and_content: tab-delimited text format with CPM values of mRNA

extract_protocol:
Total RNA was isolated using the RNeasy Mini Kit (Qiagen, CA, USA) according to the manufacturer’s protocol. The quality and integrity of the RNA were confirmed by agarose gel electrophoresis and ethidium bromide staining, followed by visual examination under ultraviolet light.
The sequencing library was prepared using the TruSeq RNA Sample Preparation kit v2 (Illumina, CA, USA) according to the manufacturer’s instructions. In brief, mRNA was purified from total RNA using poly-T oligo-attached magnetic beads, fragmented, and converted into cDNA. Adapters were then ligated to the cDNA, and the fragments were amplified by PCR.

tag: pathological type

value: non-muscle-invasive bladder cancer (NMIBC)

tag: disease event after surgery

value: progression

value: primary bladder tumor


title: T295_RNA-seq


title: T143_RNA-seq


title: Mouse intermediate traditional rep 3

value: 15-50 nt RNA


title: Mouse intermediate +T4PNK rep 1


title: T265_RNA-seq


title: Mouse intermediate +T4PNK rep 2


title: Retinal_microglia_laser_S6

tag: strain

value: laser


title: Mouse intermediate +AlkB rep 3

tag: tissue

value: RNAs were treated with AlkB before cDNA library construction.


title: Mouse intermediate +AlkB rep 1


title: T191_RNA-seq


title: Mouse intermediate traditional rep 1


title: T277_RNA-seq


title: Mouse MEF PANDORA-seq rep 3

source_name: Embryonic fibroblast cells (day 0)

value: Embryonic fibroblast cells (day 0)


title: Retinal_microglia_laser_S5


title: Retinal_microglia_laser_S4_part2


title: Mouse MEF PANDORA-seq rep 2


title: Retinal_microglia_laser_S4_part1


title: Mouse intermediate PANDORA-seq rep 1


title: Mouse MEF PANDORA-seq rep 1


title: Mouse MEF +T4PNK rep 3


title: T298_RNA-seq


title: Retinal_microglia_laser_S3


title: Mouse MEF +T4PNK rep 2


title: Mouse MEF +AlkB rep 3


title: Retinal_microglia_laser_S2


title: B513_RNA-seq

value: recurrence


title: Mouse MEF +T4PNK rep 1


title: B597_RNA-seq


title: Retinal_microglia_laser_S1


title: Mouse intermediate traditional rep 2

value: RNAs were sequenced with standard protocols.


title: B661_RNA-seq


title: Mouse mature sperm PANDORA-seq rep 2

source_name: Mature sperm

value: Mature sperm


title: Mouse MEF traditional rep 1


title: Mouse MEF traditional rep 3


title: T178_RNA-seq


title: T213_RNA-seq


title: KOcDC1 rep 3

city: Vienna

first: Philipp

last: Novoszel

address: Borschkegasse 8A

country: Austria

institute: Institute of Cancer Research

data_processing:
fastq generation, bcl2fastq v2.19.1.403
alignment and extraction of counts/gene, STAR aligner v2.6.1a_08-27, command: STAR --runThreadN 16 --genomeDir GRCm38_RSEM_index --readFilesCommand zcat --readFilesIn $FASTQ --outSAMattributes NH HI NM MD AS nM jM jI XS --outSAMtype BAM SortedByCoordinate --outSAMattrRGline ID:"$sample" SM:"$sample" CN:MUW_CF PG:STAR --quantMode TranscriptomeSAM GeneCounts --twopassMode Basic
count normalization and transformation, DESeq2 v1.20.0
Genome_build: GRCm38
Supplementary_files_format_and_content: plain text, raw counts per gene, one file per sample

growth_protocol: Murine bone marrow (3x10^6 cells/mL) was supplemented with recombinant mFLT3L (80 ng/mL) for 8 days to generate cDC1 in vitro.

extract_protocol:
cDC1 from in vitro cultures were purified by Fluorescence-activated cell sorting. RNA was extracted with Trizol.
NEBNext Poly(A) mRNA Magnetic Isolation Module and the NEBNext Ultra™ II Directional RNA Library Prep Kit for Illumina was used according to manufacturer's protocols (New England Biolabs) for library construction.

tag: cell type

value: FLT3L-derived cDC1

tag: genotype

value: c-Jun/JunB fl/fl Itgax-Cre


title: Mouse mature sperm PANDORA-seq rep 3

tag: treatment

tag: molecule type


title: Mouse MEF traditional rep 2


title: Mouse mature sperm PANDORA-seq rep 1


title: WT cDC1 rep 3

value: c-Jun/JunBfl/fl


title: Mouse MEF +AlkB rep 1


title: KO cDC1 rep 2


title: Mouse mature sperm +T4PNK rep 1


title: KO cDC1 rep 1


title: Mouse mature sperm +T4PNK rep 3


title: Mouse mature sperm +AlkB rep 3


title: WT cDC1 rep 2


title: Mouse mature sperm +AlkB rep 2


title: WT cDC1 rep 1


title: T249_RNA-seq


title: Mouse mature sperm traditional rep 2


title: Mouse mature sperm +T4PNK rep 2


title: T262_RNA-seq


title: Mouse MEF +AlkB rep 2


title: B430_RNA-seq

value: Non-replase


title: T284_RNA-seq


title: Mouse spleen +AlkB rep 2

source_name: Spleen

value: Spleen


title: colon_transverse_SM-CSSDA

city: San Diego

first: Bing

last: Ren

state: California

address: 9500 Gilman Dr

institute: University of California San Diego

library_source: genomic

data_processing:
For each sequenced single nucleus ATAC-Seq library, we obtained four FASTQ files, two for paired end DNA reads and two for the combinatorial indexes for i5 and T7 (768 and 364 indices, respectively). We selected all reads with up to 2 mismatches per i5 and T7 index (Hamming distance between each pair of indices is 4) and integrated the concatenated barcode at the beginning of the read name in the demultiplexed FASTQ files.
snATAC-seq reads were aligned to the GRCh38 genome assembly using BWA version 0.7.17-r1188 with the following parameters: "mem -M -k 32 -t 8".
Aligned reads were name sorted and filtered using Samtools version 1.9 with the following parameters: "-f 2 -F 0x70c -q 30".
Duplicated paired-end fragments were removed for each nucleic and nucleic were filtered based on stringent quality control criteria including an enrichment of reads at transcription start sites (TSS enrichment; TSSe) greater than 7-fold, and a minimum of > 1,000 mapped paired-end fragments per nucleus.
Nuclei were further filtered for potential doublets using a version of Scrublet modified for single cell ATAC-seq.
For each sample, we generated a cell by bin (5kb) count matrix and used it for the initial clustering analysis.
Nuclei from all samples were pooled and subjected to clustering analysis using the Taiji pipeline (https://taiji-pipeline.github.io/).
Genome_build: GRCh38
Supplementary_files_format_and_content: *.mtx.gz: Bin (row) by cell (column) count matrix in Matrix Market format; *.barcodes.txt.gz: column names for the matrix representing cell barcodes; *.features.txt.gz: row names for the matrix representing genomic regions (features); clustering_results.txt: tab-delimited text files containing final clustering result of nucleic from all samples

molecule: genomic DNA

source_name: transverse colon

extract_protocol:
Nuclei were extracted from flash frozen tissue either by manual pulverization via mortar and pestle while submerged in liquid nitrogen, or homogenization in a gentleMACS M-tube (Miltenyi) on a gentleMACS Octo Dissociator (Miltenyi) using the “Protein_01_01” protocol in MACS buffer (5 mM CaCl2, 2 mM EDTA, 1X protease inhibitor (Roche, 05-892-970-001), 300 mM MgAc, 10 mM Tris-HCL pH 8, 0.6 mM DTT) and pelleted with a swinging bucket centrifuge (500 x g, 5 min, 4°C; 5920R, Eppendorf).
Extracted nuclei were permeabilized either in 1 mL Nuclear Permeabilization Buffer (1X PBS, 5% Bovine Serum Albumin, 0.2% IGEPAL CA-630 (Sigma), 1 mM DTT, 1X Protease inhibitor), or 1 mL OMNI Buffer (10mM Tris-HCL (pH 7.5), 10mM NaCl, 3mM MgCl2, 0.1% Tween-20 (Sigma), 0.1% IGEPAL-CA630 (Sigma) and 0.01% Digitonin (Promega) in water). After resuspension in permeabilization buffer, nuclei were rotated at 4 ˚C for 5 minutes before being pelleted with a swinging bucket centrifuge (500 x g, 5 min, 4°C; 5920R, Eppendorf). After centrifugation, permeabilized nuclei were resuspended in 500 μL high salt tagmentation buffer (36.3 mM Tris-acetate (pH = 7.8), 72.6 mM potassium-acetate, 11 mM Mg-acetate, 17.6% DMF) and counted using a hemocytometer. Concentration was adjusted to 2,000 nuclei/9 μl, and 2,000 nuclei were dispensed into each well of a 96-well plate per sample (96 tagmentation wells/sample, samples were processed in batches of 2-4 samples). For tagmentation, 1 μL barcoded Tn5 transposomes were added using a BenchSmart™ 96 (Mettler Toledo), mixed five times, and incubated for 60 min at 37 °C with shaking (500 rpm). To inhibit the Tn5 reaction, 10 µL of 40 mM EDTA (final 20mM) were added to each well with a BenchSmart™ 96 (Mettler Toledo) and the plate was incubated at 37 °C for 15 min with shaking (500 rpm). Next, 20 µL of 2x sort buffer (2 % BSA, 2 mM EDTA in PBS) were added using a BenchSmart™ 96 (Mettler Toledo). All wells were combined into a separate FACS tube for each sample, and stained with Draq7 at 1:150 dilution (Cell Signaling). Using a SH800 (Sony), 20 nuclei per sample were sorted per well into eight 96-well plates (total of 768 wells) containing 10.5 µL EB (25 pmol primer i7, 25 pmol primer i5, 200 ng BSA (Sigma)). Preparation of sort plates and all downstream pipetting steps were performed on a Biomek i7 Automated Workstation (Beckman Coulter). After addition of 1 µL 0.2% SDS, samples were incubated at 55 °C for 7 min with shaking (500 rpm). 1 µL 12.5% Triton-X was added to each well to quench the SDS. Next, 12.5 µL NEBNext High-Fidelity 2× PCR Master Mix (NEB) were added and samples were PCR-amplified (72 °C 5 min, 98 °C 30 s, (98 °C 10 s, 63 °C 30 s, 72°C 60 s) × 12 cycles, held at 12 °C). After PCR, all wells were combined. Libraries were purified according to the MinElute PCR Purification Kit manual (Qiagen) using a vacuum manifold (QIAvac 24 plus, Qiagen) and size selection was performed with SPRISelect reagent (Beckmann Coulter, 0.55x and 1.5x). Libraries were purified one more time with SPRISelect reagent (Beckman Coulter, 1.5x). Libraries were quantified using a Qubit fluorimeter (Life technologies) and a nucleosomal pattern of fragment size distribution was verified using a Tapestation (High Sensitivity D1000, Agilent). Libraries were sequenced on a NextSeq500 or HiSeq4000 sequencer (Illumina) using custom sequencing primers with following read lengths: 50 + 10 + 12 + 50 (Read1 + Index1 + Index2 + Read2).

tag: sample type

value: normal

tag: sample preparation

value: flash-frozen tissue

tag: donor age (years)

tag: donor sex

value: male

value: white

tag: Cause of death

value: anoxia


title: Mouse spleen traditional rep 2

value: 15-50 nt RNA


title: B491_RNA-seq

value: non-muscle-invasive bladder cancer (NMIBC)

value: primary bladder tumor


title: Mouse mature sperm +AlkB rep 1

value: RNAs were treated with AlkB before cDNA library construction.


title: Mouse mature sperm traditional rep 3


title: S9_patient sample

city: Dhaka

first: Rasel

last: Ahmed

state: Dhaka

address: Manik Mia Avenue

country: Bangladesh

institute: Bangladesh Jute Research Institute

data_processing:
Illumina bcl2fastq2 software used for basecalling.
RNAseq data analysis: Quality analysis of RAW reads was done using the tool FASTQC
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to Human genome GRCh38 (Ensembl database) using TopHat v2.1.1; Bowtie 2 v2.4.1
Counting was done using SubRead package, featureCount tool. Absolute count was normalized to library size using DEseq2 (v 1.26), and differential expression was calculated
Genome_build: GRCh38
Supplementary_files_format_and_content: Tab-delimited text file. Gene expression (as count) of each gene for each extracted cell

source_name: Nasopharyngeal swab

extract_protocol:
Total RNA from swab sample was extracted using Trizol reagent following manufacturer's instructions.
Total RNA libraries were prepared using TruSeq Stranded Total RNA Library Prep kit (Illumina) according to the manufacturer’s instructions.

tag: diagnosis

value: COVID-19 patient

value: Nasopharyngeal swab


title: BPD miRNA-seq

city: Guangzhou

first: Xinqi

last: Zhong

state: Guangdong

address: 35 Liwan Rd, Zhong Shan Qi Ba Lu, Liwan District, Guangzhou, Guangdong Province, China

department: Department of Neonatology

country: China

institute: The Third Affiliated Hospital of Guangzhou Medical University

description: miRNA-seq

data_processing:
Small RNA reads were frst trimmed from the 5' adapter sequence searching for a perfect match with at least the frst 8 bp of the adapter.
All the reads without the adapter sequence (or with a mutated adapter sequences) were removed from the libraries. Then, a second trimming round removed the reads shorter than 16 bp and longer than 35bp.
All remaining reads were used in a bowtie analysis, which consisted of aligning the reads to the human genome to predict new putative miRNA precursors. Putative pre-miRNAs was added to the list of 1600 known human pre-miRs from miRBase.
All trimmed reads were then mapped using Patman against this complete human precursor catalogue allowing no mismatches or gap (to avoid mixing the very close miRNA species coming from the same family).
Genome_build: hg19
Supplementary_files_format_and_content: miRNA profile in excell

source_name: Umbilical cord blood from infants with bronchopulmonary dysplasia

extract_protocol: Starting from the total RNA samples, small RNAs were size selected and ligated for sequencing following the TruSeq Small Prep Kit Preparation (Illumina). Samples were sequenced on the NextSeq500 (Illumina) in single-end 75bp.

value: exosome


title: T308_RNA-seq

value: recurrence


title: B403_RNA-seq


title: NBPD miRNA-seq

description: miRNA-seq

source_name: Umbilical cord blood from infants without bronchopulmonary dysplasia


title: Mouse mature sperm traditional rep 1

value: Mature sperm

value: RNAs were sequenced with standard protocols.


title: Mouse spleen PANDORA-seq rep 2

value: RNAs were treated with T4PNK, then AlkB before cDNA library construction.


title: Mouse spleen PANDORA-seq rep 1

value: Spleen


title: S2_patient sample


title: Mouse liver +AlkB rep 3

source_name: Liver

value: Liver


title: T247_RNA-seq

value: Non-replase


title: Mouse liver +AlkB rep 1


title: KD_5_LPS

city: Groningen

first: Adriaan

last: van der Graaf

state: Groningen

address: Antonius Deusinglaan 1

department: Department of Genetics

country: Netherlands

institute: University Medical Center Groningen, University of Groningen

data_processing:
Each sample was run on 4 lanes of the Nextseq 500, with a unique barcode. The fastq sequence files were merged.
Low quality reads, adaptors and poly-A tail reads were removed from FASTQ files. The QC-ed FASTQ files were then aligned to the human_g1k_v37 Ensembl Release 75 reference genome using HISAT default settings
Gene expression quantification was performed using the featurecounts funtion from the Rsubread R package.
Genome_build: GRCh37.75
Supplementary_files_format_and_content: trafd1_KD_count_matrix.txt

source_name: THP-1 (Sigma Aldrich, ECACC 88081201)

growth_protocol: The cell line THP-1 (Sigma Aldrich, ECACC 88081201) was cultured in RPMI 1640 with L-glutamine and 25mM HEPES (Gibco, catalogue 52400-025), and supplemented with 10% fetal bovine serum (Gibco, catalogue 10270) and 1% penicillin/ streptomycin (Lonza, catalog DE17602E). The cells were passed twice per week at a density lower than 0.5 x 106 cells/ml in a humidified incubator at 5% CO2, 37°C.

extract_protocol:
Cell pellets were processed for RNA isolation using the miRVANA kit and stored.
1microgram of total RNA was used as input for library preparation using the quant seq 3’ kit (Lexogen, catalog 015.96), according to the manufacturer’s protocol.

treatment_protocol: THP-1 cells were plated at 0.6 x 106 cells/ml and transfected with 25 nM siRNA using Lipofectamine RNAimax transfection reagent (Invitrogen, catalogue 13788), according to the manufacturer’s protocol. Cells were treated with an siRNA to target TRAFD1 (Qiagen catalogue 1027416, sequence CCCAGCCGACCCATTAACAAT) (Knockdown (KD)), and cells treated with transfection mix without siRNA (Wild type (WT)) or non-targeting control siRNA (scrambled (SCR)) (Qiagen catalog SI03650318, sequence undisclosed by company) were included as controls. All the treatments were performed in triplicate. 72 hours after transfection, a small aliquot of cells was stained for Trypan Blue exclusion to determine cell viability and proliferation. The cells were stimulated with either LPS (10 ng/ml) from E. coli (Sigma catalogue 026:B6) or media alone (unstimulated) for 4h. Subsequently, the cells were centrifuged, and the cell pellets suspended in lysis buffer and stored at -80C until used for RNA and protein isolation.

tag: cell line

tag: genotype/variation

value: treated with siRNA to target TRAFD1 (TRAFD1 KD. 2)


title: muscle_SM-C1MKW

source_name: gastrocnemius muscle

value: normal

value: flash-frozen tissue

value: male

tag: race

value: white


title: T285_RNA-seq

tag: pathological type

value: non-muscle-invasive bladder cancer (NMIBC)

value: primary bladder tumor


title: Mouse spleen +T4PNK rep 1

value: RNAs were treated with T4PNK before cDNA library construction.

value: 15-50 nt RNA


title: Mouse spleen +AlkB rep 1

value: RNAs were treated with AlkB before cDNA library construction.


title: T172_RNA-seq

tag: disease event after surgery


title: Mouse liver PANDORA-seq rep 3

tag: strain


title: Mouse spleen traditional rep 1

tag: tissue


title: S4_patient sample

value: COVID-19 patient

value: Nasopharyngeal swab


title: Mouse liver PANDORA-seq rep 2


title: Mouse liver PANDORA-seq rep 1


title: B321_RNA-seq


title: Mouse spleen +T4PNK rep 2


title: S3_patient sample


title: Mouse liver +T4PNK rep 3


title: B363_RNA-seq


title: KD_3_Unstimulated


title: Mouse liver +T4PNK rep 1


title: KD_6_LPS


title: T263_RNA-seq


title: Mouse liver +AlkB rep 2


title: B472_RNA-seq


title: KD_4_LPS


title: Mouse liver traditional rep 3

value: RNAs were sequenced with standard protocols.


title: T181_RNA-seq


title: KD_1_Unstimulated


title: Mouse brain +T4PNK rep 2

source_name: Brain

value: Brain


title: Mouse liver traditional rep 2


title: Mouse liver traditional rep 1


title: Mouse liver +T4PNK rep 2


title: Mouse brain PANDORA-seq rep 3

value: RNAs were treated with T4PNK, then AlkB before cDNA library construction.


title: T144_RNA-seq


title: B370_RNA-seq


title: Mouse brain +AlkB rep 2


title: Mouse brain +AlkB rep 3


title: T224_RNA-seq


title: Mouse brain +AlkB rep 1


title: KD_2_Unstimulated


title: Mouse brain PANDORA-seq rep 1


title: Mouse brain PANDORA-seq rep 2


title: SCR_5_LPS

value: treated with non-targeting siRNA (SCR)


title: SCR_4_LPS


title: Mouse brain traditional rep 1


title: wt_unsti_1

data_processing:
Trimmed fastq files were aligned to build 37 of the human reference genome using hiSAT (V0.5.1) and sorted using SAM tools V1.2
Gene quantification was performed by HTSeq/0.6.1p1 using mode=union, stranded=no. The ensembl V75 database was used for gene annotation.
Genome_build: Hum_g1k_v7
Supplementary_files_format_and_content: Tab separated count table of all the samples on the columns and all the ensembl id genes on the rows

source_name: Caco-2 cell lines

growth_protocol: 500 ml of Caco-2 cell suspensions at 150.000/ml were seed in transwells in MEM media (GIBCO) , the medium was refreshed every 2-3 days, after 15 days the basal compartment was treated with IFNg (60ng/ml).

extract_protocol:
mirVana RNA isolation kit (Ambion).
Truseq RNA preparation kit (Illumina) using 1 ug of RNA.

treatment_protocol: IFNg 60ng/ml (stimulated cells) or media (control cells)

tag: interferon gamma stimulation

value: no

tag: timepoint

tag: sequencing barcode

value: CAGATC


title: SCR_6_LPS


title: Mouse brain +T4PNK rep 1

tag: treatment

tag: molecule type


title: T257_RNA-seq

value: Non-replase


title: T108_RNA-seq


title: SCR_2_Unstimulated


title: wt_unsti_2

value: GGCTAC


title: Mouse brain traditional rep 3

extract_protocol:
Total RNAs were extracted by Trizol (Invitrogen). Then small RNAs sized at 15-50nt were excised from 15% (w/v) urea polyacrylamide gel.
Small RNA libraries were constructed according to NEBNext® Single Cell/Low Input RNA Library Prep Kit (New England Biolabs)


title: Mouse brain +T4PNK rep 3


title: SCR_3_Unstimulated


title: WT_3h_2

value: yes

value: ATCACG


title: Mouse brain traditional rep 2


title: WT_5_LPS

value: untreated  (WT)


title: WT_3h_1

value: ACAGTG


title: SCR_1_Unstimulated


title: WT_4_LPS


title: batch_5_TCC-04-3_t0

description: paired end technology, only one end analyzed

data_processing:
Samples have been divided over 5 batches. Each batch is divided into the sample and stimulation time. Samples were sequenced single end using Ribozero for batch 2-4. Batch 1 intended to be used for testing this was sequenced paired end. Batch5 was sequenced paired-end accidentally, but only the first file was analyzed.
Sequencing reads were mapped to the human genome using STAR (version 2.3.0) (Dobin et al., 2013). The aligner was provided with a file containing junctions from Ensembl GRCh37.71.
Htseq-count of the Python package HTSeq (version 0.5.4p3) was used to quantify the read counts per gene based on annotation version GRCh37.71, using the default union-counting mode (The HTSeq package, http://www-huber.embl.de/users/anders/HTSeq/doc/overview.html).
Genome_build: GRCh37.71
Supplementary_files_format_and_content: Tab separated table of read counts for all the samples per gene defined by ensembl ID on the rows.

source_name: small intestine derived cell lines

growth_protocol: Polyclonal gluten-specific T-cell lines were isolated from the small intestine of patients with CD as described in Vader, W. et al. (Gastroenterology 122, 1729–1737 2002). Biopsies were cultured with a mixture of gluten and TG2-treated gluten for 5 d. Subsequently, IL-2 (20 Cetus units/ml; Novartis, Arnhem, The Netherlands) and IL-15 (10 ng/ml; R&D systems, Abingdon, UK) were added to expand the T cells. Re-stimulation was performed with mixed irradiated allogeneic PBMCs in the presence of phytohemagglutinin (1 μg/ml; Remel Inc. Lenexa, USA), IL-2 (20 Cetus units/ml) and IL-15 (10 ng/ml). The resulting T-cell lines were stored in liquid nitrogen and later tested for reactivity against a pepsin and trypsin digest of gluten and a pepsin and trypsin digest of gluten treated with TG2 in a T-cell proliferation assay. Gluten-reactive lines were cloned by limiting dilution and were again expanded by re-stimulation at 1- to 3-week intervals. Clones were stored in liquid nitrogen.

extract_protocol:
RNA was extracted with mirVana RNA isolation kit (Ambion, Life Technologies, Carlsbad, CA, USA) according to the manufacturer’s instructions. The quantity and quality of RNA was determined by Bioanalyzer (Agilent technologies, Santa Clara, CA, USA).
The sequencing libraries were prepared from 0.4-1 μg of total RNA using the TruSeq Stranded Total RNA with Ribo-Zero Globin kit (Illumina, San Diego, CA, USA) according to the manufacturer’s instructions.

treatment_protocol: Cells were stimulated for 3 hours with 2.5 microgram/ml of anti-CD3 (Biolegend, catalog317315) and anti-CD28 (Biolegend, catalog302923) antibodies, Untreated cells were included as control. N=22 samples per condition. Measurements were done at t=0 (untreated) and t=180minutes (stimulated)

value: Polyclonal gluten-specific T-cell line

tag: timepoint (minutes)


title: RNase III (rnc) mutant, rep1

city: Gießen

first: Gabriele

last: Klug

address: Heinrich-Buff-Ring 26-32

department: Molecular- and Microbiology

institute: Justus-Liebig University Gießen

description:
L1802000_Nr22_rnc_exp_1
3prime_ends_rnc_vs_wt.bed

data_processing:
XPEAP was used as a wrapper pipeline for the whole workflow. Parameters: cutoff_counts="10"; cutoff_padj="0.05"; cutoff_log2FC="1", cutoff_ratio="0.05"; coverage_style="last_base_only"
All reads were trimmed for adaptor sequences using trim-galore (version 0.6.3), low-quality reads have been rejected in the same data processing step. Options were set to -q 10 --length 15 -j 8
Reads were mapped to the Rhodobacter sphaeroides 2.4.1 whole genome (NC_007493.2, NC_007494.2, NC_009007.1, NC_007488.2, NC_007489.1, NC_007490.2, and NC_009008.1) using the READemption pipeline (version 0.4.3) subcommand align with the integrated mapper segemehl (version 0.2.0)
READemption (version 0.4.3) was used for gene quantification with parameters gene_quanti --features CDS,tRNA,rRNA,tmRNA,ncRNA,sRNA
READemption (version 0.4.3) with DESeq2 (version 1.22.1) was used to perform the differential gene expression analysis, subcommand deseq
differential gene expression was validated with baySeq (version 2.20.0)
Genome_build: GCF_000012905.2 ASM1290v2
Supplementary_files_format_and_content: csv contains raw counts and DESeq2 analysis / baySeq analysis
Supplementary_files_format_and_content: BED files inlcude all true differential 3‘-ends computed with XPEAP

organism: Cereibacter sphaeroides

source_name: RNase III (rnc) mutant

growth_protocol: All cultures were grown in malate minimal medium under microaerobic conditions (25 μM dissolved oxygen) at 32°C and 140 rpm in the dark.

extract_protocol:
Total RNA was isolated using the hot phenol method and remaining DNA was removed by a DNaseI treatment (Invitrogen).
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Cells were harvested during exponential growth phase.

tag: genotype

value: RNase III (rnc) mutant

tag: growth stage

value: exponentially growing


title: batch_5_TCC-04-3_t180


title: WT_6_LPS


title: batch_4_TCC-19-1_t180


title: RNase III (rnc) mutant, rep3

description:
L1802002_Nr24_rnc_exp_3
3prime_ends_rnc_vs_wt.bed


title: RNase III (rnc) mutant, rep2

description:
L1802001_Nr23_rnc_exp_2
3prime_ends_rnc_vs_wt.bed


title: batch_4_TCC-19-1_t0


title: MNase_IAA_10m_5U

city: Seattle

first: Christine

last: Cucinotta

state: Washington

address: 1100 Fairview Ave N

department: Basic Sciences

institute: Fred Hutchinson Cancer Research Center

description: 10 minutes released into YPD

data_processing:
Reads were aligned using Bowtie2
Coverage files were generated using DeepTools
Genome_build: SacCer3
Supplementary_files_format_and_content: BigWig generated using DeepTools. Format documened at https://genome.ucsc.edu/goldenpath/help/bigWig.html

organism: Saccharomyces cerevisiae

source_name: Sth1-HSV-AID; Sfh1-HSV-AID tagged strain

growth_protocol: Yeast were grown for 7 days in YPD medium and purified over a percoll gradient to harvest quiescent cells. Quiescent yeast were released into YPD for exit time points.

extract_protocol:
For ChIP-seq, lysates were sonicated, for Mnase-seq, digested chromatin was extracted using phenol/chloroform, and for RNA-seq experiments RNA was extracted using phenol/chloroform
Libraries for DNA-based experiments (ChIP-seq, Mnase-seq) were created according to manufacturer's protocols using the Nugen Ultralow v2 kit (NuGEN/Tecan, 0344); RNA-seq libraries were generated using the Nugen Ovation SoLo kit (NuGEN/Tecan, using custom anydeplete primers. Contact NuGEN for ordering)
All libraries were sequenced on an Illumina HiSeq 2500 at the Fred Hutchinson Cancer Center genomics core; ChIP-seq experiments were single-end 50bp read lengths and other experiments were paired-end 50bp read length

treatment_protocol: Yeast lacking RSC were treated with auxin

tag: sample type

value: 5U Mnase; Worthington, LS004798

value: iaa or phenanthroline:IAA

tag: strains


title: WT_3_Unstimulated

tag: cell line


title: batch_4_TCC-17-1_t180


title: WT_2_Unstimulated

tag: genotype/variation


title: polynucleotide phosphorylase (pnp) mutant, rep3

description:
L1802005_Nr27_pnp_exp_3
baySeq_pnp_vs_wt.csv
deseq_comp_pnp_vs_wt_with_annotation_and_countings.csv
pnp_merged_div_by_29648232.0_multi_by_27421951.0_forward.wig
pnp_merged_div_by_29648232.0_multi_by_27421951.0_reverse.wig
3prime_ends_pnp_vs_wt.bed


title: polynucleotide phosphorylase (pnp) mutant, rep2

description:
L1802004_Nr26_pnp_exp_2
baySeq_pnp_vs_wt.csv
deseq_comp_pnp_vs_wt_with_annotation_and_countings.csv
pnp_merged_div_by_29648232.0_multi_by_27421951.0_forward.wig
pnp_merged_div_by_29648232.0_multi_by_27421951.0_reverse.wig
3prime_ends_pnp_vs_wt.bed


title: batch_4_TCC-18-2_t0


title: batch_4_TCC-18-2_t180


title: polynucleotide phosphorylase (pnp) mutant, rep1

description:
L1802003_Nr25_pnp_exp_1
baySeq_pnp_vs_wt.csv
deseq_comp_pnp_vs_wt_with_annotation_and_countings.csv
pnp_merged_div_by_29648232.0_multi_by_27421951.0_forward.wig
pnp_merged_div_by_29648232.0_multi_by_27421951.0_reverse.wig
3prime_ends_pnp_vs_wt.bed


title: batch_4_TCC-17-1_t0


title: MNase_IAA_Q_50U

description: Quiescent time point

value: 50U Mnase; Worthington, LS004798


title: MNase_IAA_10m_50U

description: 10 minutes released into YPD


title: MNase_IAA_Q_5U

description: Quiescent time point


title: batch_4_TCC-16-1_t180


title: wildtype, rep3

description:
L1802023_Nr45_WT_neu_3
baySeq_pnp_vs_wt.csv
deseq_comp_pnp_vs_wt_with_annotation_and_countings.csv
wt_merged_div_by_27421951.0_multi_by_27421951.0_forward.wig
wt_merged_div_by_27421951.0_multi_by_27421951.0_reverse.wig

source_name: wildtype

value: wildtype


title: HH-OX-62_5

city: Hamburg

first: Manuel

middle: A

last: Friese

address: Falkenried 94

department: Institut für Neuroimmunologie und Multiple Sklerose

institute: Universitätsklinikum Hamburg-Eppendorf

description:
RNA_counts.tar.gz
RNA_normalised.tar.gz
RNA_SCTnormalised.tar.gz
RNA_integrated.tar.gz
ADT_counts.tar.gz
ADT_integrated.tar.gz
saverx.tar.gz
saverx_integrated.tar.gz
metadata_per_cell.csv
metadata_per_sample.csv

data_processing:
library deconvolution with bcl2fastq (Illumina, v2.20.0.422)
single cell deconvolution and mapping using zUMIs (v2.5.6b) with STAR (v2.6.0c) for RNA and CITE-seq-Count (v. 1.4.2) for protein surface markers
cell hashing demultiplexing with Seurat (v3.1.1)
doublet removal with DoubletFinder (2.0.2)
Standard log normalisation of RNA using Seurat (v3.1.1)
Non-standard normalisation of RNA using sctransform (v0.2.0) as described in Hafemeister and Satija 2019 (Genome Biology)
Sample integration for RNA with Seurat (v3.1.1)
Marker imputation from RNA with SAVER-X (v1.0.0)
Integration of imputed RNA markers with Seurat (v3.1.1)
Normalisation (centered log transformation) and sample integration for surface protein markers with Seurat (v3.1.1)
Genome_build: GRCh38 without alternative contigs
Supplementary_files_format_and_content: All processed data files are provided as tar.gz archives, which contain a sparse matrix in the market matrix format (.mtx) specifying expression values and the cell barcodes and features as tab seperated value files (barcodes.tsv and genes.tsv), the matrices contain cells as columns and features (genes or antibody-derived tags = ADT) as rows; all metadata files are provided as comma separated text files (.csv)

molecule: polyA RNA

source_name: blood

extract_protocol:
10X chromium v2/v3 (see V_10X for each sample)
CITE-seq/Cell hashing as described in Stoeckius et al 2018 (Genome Biology)

tag: donor

tag: hash

tag: match

tag: group

tag: cohort

tag: Sex

value: male

tag: edss

tag: molecule

value: polyA RNA + protein surface markers


title: HH-OX-62_1

value: no


title: HH-OX-62_6


title: WT_1_Unstimulated


title: MNase_crl_10m_5U

description: 10 minutes released into YPD

tag: treatment

value: iaa or phenanthroline:Untreated


title: HH-OX-62_2


title: wildtype, rep2

description:
L1802022_Nr44_WT_neu_2
baySeq_pnp_vs_wt.csv
deseq_comp_pnp_vs_wt_with_annotation_and_countings.csv
wt_merged_div_by_27421951.0_multi_by_27421951.0_forward.wig
wt_merged_div_by_27421951.0_multi_by_27421951.0_reverse.wig

tag: strain


title: MNase_crl_Q_5U

description: Quiescent time point


title: batch_4_TCC-15-1_t180

tag: tissue

tag: timepoint (minutes)


title: HH-OX-62_3


title: HH-OX-62_4


title: HH-OX-61_5

value: PPMS


title: batch_4_TCC-15-1_t0


title: wildtype, rep1

description:
L1802021_Nr43_WT_neu_1
baySeq_pnp_vs_wt.csv
deseq_comp_pnp_vs_wt_with_annotation_and_countings.csv
wt_merged_div_by_27421951.0_multi_by_27421951.0_forward.wig
wt_merged_div_by_27421951.0_multi_by_27421951.0_reverse.wig

tag: genotype

tag: growth stage


title: batch_4_TCC-16-1_t0


title: MNase_crl_10m_50U

description: 10 minutes released into YPD

tag: sample type

tag: strains


title: ZIKV_miRNA_H41R

city: Los Angeles

first: Zhifei

last: Luo

address: 1450 Biggy Street, NRT 6514

institute: University of Southern California

data_processing:
Primary sequences data were checked by FastQC version 0.11.7 for quality control purpose. Reads were trimmed by cutadapt version 1.16 (Martin, 2011) to remove adapter sequences with at least 5bp overlap (-a AACTGTAGGCAC -O 5 -m 15 --max-n 0). To increase accuracy, reads have N base or are shorter than 15bp, the minimal length of miRNA in miRbase, were removed.
Trimmed reads were first mapped to human genome GRCh38 and the reads do not match human genome were mapped against Zika virus genome (KU321639.1) using Bowtie version 1.2.2 (Langmead et al., 2009) with option -n 0 -l 18 -a --best --strata to find the best aligned reads. Seed length for alignment was set as 18 and no mismatch was allowed in seed region.
Peak calling to define the viRNA loci was carried out by HOMER package (Heinz et al., 2010) as previous researches (Luna et al., 2017). Explicitly with the following setting: findPeaks -style factor -size 27 -fragLength 22 -tagThreshold 5 -minDist 20 -o auto -LP 0.05 -L 2.
Reads on positive strand and negative strand were used to define positive strand or negative strand viRNA separately. viRNAs loci with overlapped coordinates were manually split by visualizing read distribution in integrative genomics viewer.
Genome_build: GRCh38 and Zika virus genome KU321639.1
Supplementary_files_format_and_content: xlsx. It has the finalized list of viRNA peaks from AGO-CLIP assay.

source_name: neural stem cells

growth_protocol: NSCs were derived from the H9 human embryonic stem cells via embryoid body and rosette formation, followed by rosette selection using Neural Induction Medium from Stemcell Technology (Catalog #05835). The NSCs were subsequently maintained as monolayer culture before infection. For assays requiring adherent culture, NSCs were plated on poly-L-Orthithine (10 µg/ml) coated plates or cover glasses.

extract_protocol: For In Vivo miRNA-seq, 1x106 NSCs were infected with ZIKV-WT or ZIKV-H41R at MOI of 1 and total RNA was extracted with at 2 dpi. miRNA was isolated for construction of miRNA sequencing library with QIAseq miRNA Library Kit (Qiagen, #331505) by UCLA Technology Center for Genomics & Bioinformatics (TCGB), followed by deep sequenced using Illumina HiSeq3000. Briefly, the workflow consists of 3’ ligation, primer hybridization, 5’ ligation, first strand synthesis and PCR amplification. Different adapters were used for multiplexing samples in one lane. AMPure XP Beads were used for dual size selection. Library quality was checked with Bioanalyzer (Agilent) and Qubit (Life Technologies).

value: neural stem cells


title: MNase_crl_Q_50U

description: Quiescent time point


title: ZIKV_AGO_CLIP_Rep2

data_processing:
Library strategy: HITS-CLIP
Primary sequences data were checked by FastQC version 0.11.7 for quality control purpose. Reads were trimmed by cutadapt version 1.16 (Martin, 2011) to remove adapter sequences with at least 5bp overlap (-a AACTGTAGGCAC -O 5 -m 15 --max-n 0). To increase accuracy, reads have N base or are shorter than 15bp, the minimal length of miRNA in miRbase, were removed.
Trimmed reads were first mapped to human genome GRCh38 and the reads do not match human genome were mapped against Zika virus genome (KU321639.1) using Bowtie version 1.2.2 (Langmead et al., 2009) with option -n 0 -l 18 -a --best --strata to find the best aligned reads. Seed length for alignment was set as 18 and no mismatch was allowed in seed region.
Peak calling to define the viRNA loci was carried out by HOMER package (Heinz et al., 2010) as previous researches (Luna et al., 2017). Explicitly with the following setting: findPeaks -style factor -size 27 -fragLength 22 -tagThreshold 5 -minDist 20 -o auto -LP 0.05 -L 2.
Reads on positive strand and negative strand were used to define positive strand or negative strand viRNA separately. viRNAs loci with overlapped coordinates were manually split by visualizing read distribution in integrative genomics viewer.
Genome_build: GRCh38 and Zika virus genome KU321639.1
Supplementary_files_format_and_content: xlsx. It has the finalized list of viRNA peaks from AGO-CLIP assay.

extract_protocol: For AGO-CLIP, AGO HITS-CLIP was previously utilized to map AGO-bound miRNA (Chi et al., 2009; Clark et al., 2014). To discriminate functional ZIKV-derived viRNAs from ZIKV genome, we conducted the crosslinking and immunoprecipitation (CLIP) with minor modifications. Briefly, NSCs were grown to 90% confluency and infected ZIKV at a MOI of 1 for 48 h. At 24 hpi, Proten A Dynabeads (Invitrogen) were washed 3 times with PBS and resuspended in antibody binding (AB) buffer (1×PBS, 0.02% Tween-20). Per cell sample, 150 μl of the beads was used. Beads were rotated with 10 μl of bridging antibody (rabbit anti-mouse IgG, Jackson Immunoresearch) for 30 min at room temperature. Beads were then washed 3 times in AB buffer before adding 8 μl of pan-Ago antibody (2A8, EMD Millipore). Beads were then rotated for overnight at 4ºC. After 48 h post ZIKV infection, NSCs were washed twice with PBS and UV irradiated at 254 nm for a total energy dispersion of 600 mJ/cm2 in a Stratlinker XL-500 (Stratagene). Cells were lysed with 1×PXL (1×PBS, 0.1% SDS, 0.5% deoxycholate, 0.5% NP-40, protease inhibitors). Cell lysates were treated sequentially with RNAsin (Promega) and RQ1 DNase (Promega) prior to co-immunoprecipitation of RNA-protein complexes on the protein A Dynabeads for 4 h at 4ºC. Beads were then washed twice each with 1×PXL, 5×PXL (5×PBS, 0.1% SDS, 0.5% deoxycholate, 0.5% NP-40, protease inhibitors), and 1×PNK buffer (50mM Tris-Cl, 10mM MgCl2, 0.5% NP-40, protease inhibitors). CLIP-RNAs were liberated with their on-bead protein complexes by treatment with 4 mg/ml protease K (Sigma) and subsequent phenol/chloroform extraction as described previously (Chi et al., 2009). miRNA libraries of CLIP-RNA were constructed and sequenced on HiSeq3000.

treatment_protocol: NSCs were infected with ZIKV-WT or ZIKV-H41R at MOI of 1


title: ZIKV_miRNA_WT


title: HH-OX-61_6


title: 10m_IAA_4tu

description: 10 minutes released into YPD

value: 5 mM 4-thiouracil; Sigma, 440736-1G


title: Q_IAA_4tu

description: Quiescent time point


title: batch_4_TCC-14-1_t0


title: batch_4_TCC-03-2_t180


title: 10m_CRL_4tu

description: 10 minutes released into YPD


title: HH-OX-61_2


title: HH-OX-61_1


title: Q_CRL_4tu

description: Quiescent time point


title: Mouse tsRNA-pool day6 rep3

data_processing:
For each RNA library, 6G base pairs (raw data) were generated by Illumina NovaSeq 6000.
The filtering process is as follows: (1) Remove reads containing adapters. (2) Remove reads containing N > 10% (N represents the base cannot be determined). (3) Remove reads containing low quality (Qscore<= 5) base which is over 50% of the total base.
RNA sequences were annotated using kallisto with Ensembl mouse cDNA annotation information. Expression level of each gene was normalized to TPM (Transcripts Per Kilobase Million).
Genome_build: GRCm38
Supplementary_files_format_and_content: tab-delimited text files include ensembl transcript ID, transcript length, effective length, estimated counts and TPM.

source_name: Embryoid body

extract_protocol:
Total RNAs are extracted by Trizol (Invitrogen).
Transcriptome libraries were constructed according to NEBNext Ultra RNA Library Prep Kit for Illumina (New England Biolabs) following manufacturer’s instruction.

tag: developmental stage

tag: transfection

value: tsRNA-pool (tsRNA-Ala, tsRNA-Arg, tsRNA-Glu, tsRNA-His, and tsRNA-Lys)


title: Mouse tsRNA-pool day6 rep2


title: 10m_IAA_PolII

description: 10 minutes released into YPD

tag: antibody

value: Rpb3; Biolegend # 665004


title: ZIKV_AGO_CLIP_Rep1


title: batch_4_TCC-14-1_t180


title: batch_4_TCC-02-1_t180


title: Mouse tsRNA-pool day6 rep1


title: HH-OX-61_4

tag: donor

tag: hash

tag: match


title: HH-OX-61_3

tag: group

tag: cohort

tag: Sex


title: Mouse tsRNA-pool day3 rep3


title: batch_4_TCC-02-1_t0


title: 5m_IAA_PolII

description: 5 minutes released into YPD

tag: treatment


title: H1299_DAC

type: genomic

city: Taipei

first: Rueyhung

middle: Roc

last: Weng

address: No. 1, Roosevelt Rd., Sec. 4

department: Internal Medicine

country: Taiwan

institute: National Taiwan University Hospital

description: H1299 after drug treatment (DAC)

hyb_protocol: The procedures are performed according to standard Illumina Infinium Methylation protocol.

data_processing:
Raw intensity data were obtained as IDAT files and processed using R package minfi.
Normalized beta values are calculated using the preprocessQuantile function of minfi v1.30.0.

label: Cy5 and Cy3

source_name: H1299 after drug treatment (DAC)

growth_protocol: Lung cancer cell lines were cultured in RPMI-1640 medium with 10% FBS and 1% antibiotics.

extract_protocol: Genomic DNA of cancer cells was extracted with the QIAamp DNA Mini Kit (QIAGEN) according to the manufacturer's instructions. Bisulfite conversion of 1 µg genomic DNA was performed using EZ DNA Methylation Kit.

treatment_protocol: Lung cancer cell lines were treated with 100 nM decitabine (DAC) for 72 hours followed by growing in drug-free medium for three days.

tag: cell line

value: lung cancer cell line H1299

value: DAC


title: Q_IAA_PolII

description: Quiescent time point


title: batch_3_TCC-13-1_t180

tag: tissue

value: Polyclonal gluten-specific T-cell line


title: HH-OX-60_3

tag: edss

tag: molecule


title: batch_3_TCC-13-1_t0

tag: timepoint (minutes)


title: Mouse tsRNA-pool day3 rep2


title: HH-OX-60_4


title: 10m_crl_PolII

description: 10 minutes released into YPD


title: batch_3_TCC-12-1_t180


title: 5m_crl_PollII

description: 5 minutes released into YPD


title: batch_3_TCC-12-1_t0


title: CL1-0_DAC

description: CL1-0 after drug treatment (DAC)

scan_protocol: The procedures are performed according to standard Illumina Infinium Methylation protocol.

source_name: CL1-0 after drug treatment (DAC)

value: lung cancer cell line CL1-0


title: Mouse tsRNA-pool day1 rep3


title: Mouse tsRNA-pool day3 rep1


title: HH-OX-60_5


title: HH-OX-60_6


title: H1299_Mock

description: H1299 before drug treatment (Mock)

source_name: H1299 before drug treatment (Mock)

label_protocol: The procedures are performed according to standard Illumina Infinium Methylation protocol.

value: Mock


title: batch_4_TCC-03-2_t0


title: H1792_DAC

description: H1792 after drug treatment (DAC)

source_name: H1792 after drug treatment (DAC)

value: lung cancer cell line H1792


title: 10m_IAA_H3

description: 10 minutes released into YPD

value: iaa or phenanthroline:IAA


title: batch_3_TCC-11-1_t0


title: PC9_Mock

description: PC9 before drug treatment (Mock)

source_name: PC9 before drug treatment (Mock)

value: lung cancer cell line PC9


title: A549_Mock

description: A549 before drug treatment (Mock)

source_name: A549 before drug treatment (Mock)

value: lung cancer cell line A549


title: PC9_DAC

description: PC9 after drug treatment (DAC)

source_name: PC9 after drug treatment (DAC)


title: Q_crl_PolII

description: Quiescent time point


title: CL1-0_Mock

description: CL1-0 before drug treatment (Mock)

source_name: CL1-0 before drug treatment (Mock)


title: Mouse tsRNA-pool day1 rep1


title: HH-OX-59_3

value: male

value: polyA RNA + protein surface markers


title: batch_3_TCC-11-1_t180


title: 10m_crl_H3

description: 10 minutes released into YPD

value: iaa or phenanthroline:Untreated


title: batch_3_TCC-07-1_t180


title: HH-OX-60_1

value: no


title: Mouse tsRNA-pool day1 rep2


title: batch_3_TCC-10-1_t180


title: HH-OX-60_2


title: CL1-5_DAC

description: CL1-5 after drug treatment (DAC)

source_name: CL1-5 after drug treatment (DAC)

value: lung cancer cell line CL1-5


title: A549_DAC

description: A549 after drug treatment (DAC)

source_name: A549 after drug treatment (DAC)


title: HH-OX-59_5

value: PPMS


title: Q_IAA_H3

description: Quiescent time point


title: 5m_IAA_H3

description: 5 minutes released into YPD


title: batch_3_TCC-10-1_t0

source_name: small intestine derived cell lines


title: Mouse tsRNA-Lys day6 rep2

value: tsRNA-Lys


title: HH-OX-59_6


title: Q_crl_H3

description: Quiescent time point


title: batch_3_TCC-07-1_t0


title: H1792_Mock

description: H1792 before drug treatment (Mock)

source_name: H1792 before drug treatment (Mock)


title: HH-OX-59_4


title: Input for 10m_phen_Sth1 and 10m_phen_PolII

source_name: wild-type yeast cells

value: input


title: Mouse tsRNA-Lys day6 rep3


title: batch_3_TCC-06-1_t180


title: 5m_crl_H3

description: 5 minutes released into YPD

source_name: Sth1-HSV-AID; Sfh1-HSV-AID tagged strain


title: Mouse tsRNA-Lys day6 rep1


title: CL1-5_Mock

description: CL1-5 before drug treatment (Mock)

source_name: CL1-5 before drug treatment (Mock)


title: Mouse tsRNA-Lys day3 rep3


title: batch_3_TCC-06-1_t0


title: Mouse tsRNA-Lys day3 rep2


title: HH-OX-59_1

source_name: blood


title: HH-OX-59_2


title: batch_3_TCC-05-1_t180


title: Mouse tsRNA-Lys day3 rep1

source_name: Embryoid body


title: 10m_phen_PolII

description: 10 minutes released into YPD

value: Rpb3; Biolegend # 665004

value: iaa or phenanthroline:Phenanthroline


title: Mouse tsRNA-Lys day1 rep3


title: Mouse tsRNA-Lys day1 rep2


title: 10m_phen_Sth1

description: 10 minutes released into YPD

value: Flag; Sigma # F1804


title: HH-OX-58_1

value: female


title: batch_3_TCC-05-1_t0

value: Polyclonal gluten-specific T-cell line


title: HH-OX-58_2


title: HH-OX-58_3


title: batch_3_TCC-04-2_t180


title: Input for 10m_none_Sth1 and 10m_none_PolII


title: Mouse tsRNA-Lys day1 rep1


title: 10m_none_PolII

description: 10 minutes released into YPD


title: HH-OX-58_4


title: batch_3_TCC-04-2_t0


title: batch_3_TCC-01-3_t180


title: 10m_none_Sth1

description: 10 minutes released into YPD


title: Mouse tsRNA-His day6 rep3

value: tsRNA-His


title: HH-OX-58_5


title: Mouse tsRNA-His day6 rep2


title: 10m_Sth1

description: 10 minutes released into YPD


title: batch_3_TCC-01-3_t0


title: HH-OX-58_6


title: Log_Sth1

description: Log cells


title: Mouse tsRNA-His day6 rep1


title: batch_3_TCC-01-2_t180


title: batch_3_TCC-01-2_t0


title: 5m_Sth1

description: 5 minutes released into YPD


title: 0m_Sth1

description: Quiescent time point


title: HH-OX-57_2

value: intrathecal steroids


title: Mouse tsRNA-His day3 rep2


title: batch_3_TCC-01-1_t180


title: batch_3_TCC-01-1_t0


title: Mouse tsRNA-His day3 rep1


title: 10m_H4ac

description: 10 minutes released into YPD

value: H4ac "Penta", Millipore, cat# 06-946


title: HH-OX-57_3


title: HH-OX-57_4


title: Mouse tsRNA-His day1 rep3


title: 0m_H4ac

description: Quiescent time point


title: batch_2_TCC-04-1_t0


title: Mouse tsRNA-His day1 rep2


title: Mouse tsRNA-His day1 rep1


title: HH-OX-57_6


title: batch_2_TCC-03-1_t180


title: HH-OX-57_1


title: Mouse tsRNA-His day3 rep3


title: Mouse tsRNA-Glu day6 rep3

value: tsRNA-Glu


title: HH-OX-56_1

value: male


title: Mouse tsRNA-Glu day6 rep2


title: batch_2_TCC-03-1_t0


title: HH-OX-56_2

value: polyA RNA + protein surface markers


title: 5m_H3

description: 5 minutes released into YPD

value: iaa or phenanthroline:Untreated


title: BPA rep2

city: Seoul

first: Jung-Woong

address: 84 Heuksuk-ro Dongjak-ku

department: Life Science

institute: Chung-Ang University

data_processing:
Illumina Casava software used for basecalling
Sequenced read were trimmed for adaptor sequence, and masked for low-quality sequence using TrimGalore
Alignment to GRCh38.98 whole genome with STAR 2.7 and read feature counting with Rsubread 1.34.6
Normalized by voom function from limma and edgeR 3.28.0
FPKM were calculated using a fpkm function from DESeq2 1.26.0 and differential gene expression by edgeR 3.28.0
Genome_build: GRCh38.98
Supplementary_files_format_and_content: txt files include raw counts, normalized counts(FPKM)

extract_protocol:
Total RNA was extracted using Trizol reagent and mRNA was extracted by mRNA pull-down using poly-A tagged bead.
RNA libraries were prepared for sequencing using standard Truseq RNA Illumina protocols.

treatment_protocol: 40 mM of bisphenol A (BPA) was treated in Y79 cells for 48 hours.

tag: agent

value: BPA treatment


title: Mouse tsRNA-Glu day6 rep1


title: HH-OX-56_3

value: no


title: 0m_H3

description: Quiescent time point

tag: strains


title: HH-OX-56_4


title: BPA rep1


title: DMSO rep2

value: DMSO


title: HH-OX-56_5


title: 5min_Sua7

description: 5 minutes released into YPD


title: 5m_H4ac

description: 5 minutes released into YPD


title: 240m_H3

description: 240 minutes released into YPD


title: Mouse tsRNA-Glu day3 rep2

tag: developmental stage


title: DMSO rep1


title: HH-OX-56_6


title: 0min_Sua7

description: Quiescent time point


title: 10m_H3

description: 10 minutes released into YPD


title: HH-OX-55_1

value: PPMS


title: Mouse tsRNA-Glu day1 rep3

tag: transfection


title: HH-OX-55_2


title: Log_PolII

description: Log cells

tag: antibody


title: PED_17

data_processing:
Aligment was done using hisat against he human_1k_v37 ensemble Release 75 reference with default settings and sorted using SAMtool.
Gene level quantification was done using HTSeq-count, using default mode=unión.
After filtering out all genes with 0 reads in all samples, differential expression analysis was performed using DESeq2 (Differentially expressed genes (DEGs) between contols and patients were defined as genes presenting a |log2 FC|>1 and an FDR ≤ 0.05))
Genome_build: Hum_g1k_v7
Supplementary_files_format_and_content: tab delimited count able containing ensembl ids on the rows, and samples in the columns.

source_name: PED_duodenal biopsy

extract_protocol:
After biopsy remotion,  the samples were flash frozen on dry ice,  RNA was harvested using Trizol reagent (Invitrogen).
TruSeq strand total RNA library kit using 1 ug of RNA , includind a ribozero rRNA depetion step

tag: subject status

value: histology proven celiac disease (PED)

value: duodenal biopsy


title: Mouse tsRNA-Glu day1 rep2


title: 240min_PolII

description: 240 minutes released into YPD

value: Rpb3; Biolegend # 665004


title: CTR_20

source_name: CTR_duodenal biopsy

value: healthy controls (CTR)


title: Mouse tsRNA-Glu day1 rep1


title: HH-OX-55_3

tag: donor

tag: hash


title: Mouse tsRNA-Glu day3 rep3


title: 10min_Sua7

description: 10 minutes released into YPD

value: Flag; Sigma # F1804


title: PED_37


title: 10min_PolII

description: 10 minutes released into YPD


title: Mouse tsRNA-Arg day6 rep3

value: tsRNA-Arg


title: PED_16


title: 5min_PolII

description: 5 minutes released into YPD


title: HH-OX-55_4

tag: match

tag: group


title: Mouse tsRNA-Glu day3 rep1


title: 0min_PolII

description: Quiescent time point


title: Mouse tsRNA-Arg day6 rep2


title: PED_61


title: Mouse tsRNA-Arg day6 rep1


title: HH-OX-55_6

tag: cohort

tag: Sex


title: PED_48


title: HH-OX-54_3


title: Mouse tsRNA-Arg day3 rep3


title: Exp-2

city: xian

first: zhao

last: le

address: Yanta Western Road NO.227

institute: The First Affiliated Hospital of Xi'an Jiao Tong University

data_processing:
Reads filtering under criteria removing reads with 20% of the base quality lower than 13
MapSplice mapping to reference genome
count counting
Genome_build: GRCh37
Supplementary_files_format_and_content: TXT file contain counts for each sample

source_name: Exp, SKOV3

growth_protocol: Cells were cultured in RPMI 1640 with 10% fetal bovine serum at 37℃, 5%CO2

extract_protocol:
Total RNA was extracted from cells using TRIzol reagent (Invitrogen)
cDNA Library Construction:   The cDNA libraries were constructed for each pooled RNA sample using the VAHTSTM Total RNA-seq (H/M/R) according to the manufacturer’s instructions. Generally, the protocol consists of the following steps: depletion of rRNA and fragmented into 150-200 bp using divalent cations at 94 ℃ for 8 min. The cleaved RNA fragments were reverse-transcribed into first-strand cDNA, second-strand cDNA synthesis, fragments were end repaired, A-tailed and ligated with indexed adapters. Target bands were harvested through VAHTSTM DNA Clean Beads .The products were purified and enriched by PCR to create the final cDNA libraries and quantified by Agilent2200. The tagged cDNA libraries were pooled in equal ratio and used for 150 bp paired-end sequencing in a single lane of the Illumina Xten with 51 plus 7 cycles by NovelBio Corp. Laboratory, Shanghai.

treatment_protocol: 80 μg/mL of 20(S)-Rg3 for 24 h

tag: cell line

value: ovarian cancer cell line SKOV3

tag: cell type

value: ovarian cancer

tag: treatment

value: Ginsenoside 20(S)-Rg3


title: PED_10

tag: tissue


title: Exp-1


title: HH-OX-54_4

tag: edss

tag: molecule


title: CTR_12


title: HH-OX-54_5


title: Mouse tsRNA-Arg day3 rep1


title: NC-1

source_name: NC, SKOV3

value: control


title: CTR_60


title: HH-OX-54_6

value: male


title: CTR_07


title: HH-OX-54_1

value: polyA RNA + protein surface markers


title: CTR_18


title: Mouse tsRNA-Arg day1 rep1


title: RV6_C: HIF2_AAA_donor_C

city: Cambridge

first: David

last: Bargiela

address: 4, 7 Downing Pl

country: United Kingdom

institute: University of Cambridge

data_processing:
RNA-sequencing: 75-nt sequence reads using Illumina NextSeq 550.
Basecalling and demultiplexing was performed using Illumina bcl2fastq.
Reads were aligned to the mm10 reference genome using STAR.
Read summarization to gene counts was performed using featureCounts.
Normalization of raw counts and differential gene expression were performed using EdgeR.
Genome_build: mm10.
Supplementary_files_format_and_content: Tab-delimited text file includes raw counts for each sample.

source_name: OT-I CD8+ T cells

growth_protocol: Splenocytes from OT-I transgenic animals were activated for in complete RPMI for 24 hours with 100 ng/ml OVA peptide before retroviral transduction. After transduction cells were expanded in the presence of 10 U/ml recombinant human IL-2 for further 5 days at cell density lower than 2e6/ml.

extract_protocol:
On day 5 post-tranduction OT-I cells were stained with Near-IR Dead Cell Stain Kit (Thermo Fisher) followed by surface staining of CD8a and Thy-1.1 and sorted on Thy-1.1 surface expression on a BD FACSAria Fusion cell sorter (BD Biosciences) directly into RLT Plus lysis buffer (Qiagen)
To construct libraries suitable for Illumina sequencing the Illumina TruSeq Stranded mRNA Sample preparation protocol which includes cDNA synthesis, ligation of adapters and amplification of indexed libraries was used. The yield and quality of the amplified libraries were analysed using Qubit by Thermo Fisher and the Agilent Tapestation. The indexed cDNA libraries were normalised and combined and the pools were sequenced on the Nextseq 550 for a 50-cycle v2.5 sequencing run generating 75 bp single-end reads. Basecalling and demultiplexing was performed using CASAVA software with default settings generating Fastq files for further downstream mapping and analysis.

treatment_protocol: 24 hours after activation with OVA, cells were transduced in retronectin-coated plates with supernatants containing viral particles encoding Thy-1.1 alone or in combination with mouse HIF. Transduction efficiency was measured on day 3 and 5 post-transduction by flow cytometry by analysing surface expression levels of Thy-1.1

value: OT-I CD8 T cells

tag: transduced with

tag: mouse donor

value: C


title: HH-OX-55_5

value: no


title: RV6_B: HIF2_AAA_donor_B

value: B


title: HH-OX-53_3

value: PPMS


title: batch_2_TCC-04-1_t180

value: Polyclonal gluten-specific T-cell line

tag: timepoint (minutes)


title: Mouse tsRNA-Ala day6 rep3

city: Riverside

first: Junchao

address: 900 University Ave

institute: University of California, Riverside

tag: developmental stage

tag: transfection

value: tsRNA-Ala


title: Mouse tsRNA-Ala day6 rep2


title: RV6_A: HIF2_AAA_donor_A

value: A


title: HH-OX-54_2

tag: donor


title: RV11_C: HIF2_AAN_donor_C


title: Mouse tsRNA-Arg day3 rep2


title: HH-OX-53_5

tag: hash


title: NC-2


title: HH-OX-53_4

tag: match


title: Mouse tsRNA-Ala day6 rep1


title: Mouse tsRNA-Ala day3 rep3


title: RV11_B: HIF2_AAN_donor_B


title: CMV_CD4_pd1_pos_neg_96_well_TCR

city: Birmingham

first: Paul

last: Moss

state: West Midlands

address: Vincent Drive

department: Immunology and Immunotherapy

institute: University of Birmingham

data_processing:
Paired-end TCR sequencing reads were grouped by experiment into forward and reverse pairs, demultiplexed according to their single cell specific barcodes and assigned to the Plate-Well-single cell source. These reads were aligned to germline segments of human TCR sequences and clonotypes assembled with MiXCR
hg19
txt file containing the identified TCRclonotypes

source_name: Peripheral Blood

extract_protocol:
Class-II tetramer+ cells were sorted on a BD FACSMelody cell sorter into 96 well PCR plates containing 10ul/well of a 10mM Tris and 500U/ml RNasin Inhibitor solution.
TCR sequencing was performed as previously described (Han et al., 2014). Briefly, nested PCR of the TCR alpha and beta CDR3 region was performed by firstly using a Onestep RT-PCR kit (Qiagen) for cDNA synthesis and first round PCR, followed by second amplification with HotStar Taq (Qiagen). Finally a barcoding reaction was carried out using HotStar Taq. PCR products were then pooled and gel purified (Qiagen)
paired end sequencing reaction using a MiSeq v2 500 sequencing kit (Illumina)

value: CMV-specific CD4 T cell

tag: pd1 expression

value: PD1 pos and neg cells in even numbers from each donor sorted into a 96-well plate

tag: tcr sequencing protocol

value: TCR sequencing protocol


title: RV11_A: HIF2_AAN_donor_A


title: HH-OX-53_6

tag: group

tag: cohort

tag: Sex


title: Mouse tsRNA-Arg day1 rep3

last: Shi

value: tsRNA-Arg


title: HH-OX-53_1


title: Mouse tsRNA-Arg day1 rep2


title: RV13_C: HIF2_PPA_donor_C

tag: cell type


title: Mouse tsRNA-Ala day3 rep2


title: Mouse tsRNA-Ala day3 rep1


title: RV13_B: HIF2_PPA_donor_B


title: Mouse tsRNA-Ala day1 rep3


title: HH-OX-52_3


title: HH-OX-52_4


title: Mouse tsRNA-Ala day1 rep2


title: RV13_A: HIF2_PPA_donor_A


title: Mouse tsRNA-Ala day1 rep1


title: RV15_C: HIF2_PPN_donor_C


title: RV15_B: HIF2_PPN_donor_B


title: Mouse rsRNA-28S-1 day6 rep3


title: RV15_A: HIF2_PPN_donor_A


title: HH-OX-52_1


title: HH-OX-52_6


title: RV3_C: VC_donor_C


title: HH-OX-52_2


title: HH-OX-51_3

value: Endoxan, Betaferon, MTX, Mitoxantron


title: RV3_B: VC_donor_B


title: RV3_A: VC_donor_A


title: Mouse rsRNA-28S-1 day3 rep2


title: HH-OX-53_2


title: Mouse rsRNA-28S-1 day3 rep3


title: HH-OX-51_4


title: RV14_N3: HIF1_PPN_donor_C


title: Mouse rsRNA-28S-1 day3 rep1


title: RV12_N3: HIF1_PPA_donor_C


title: HH-OX-51_5


title: Mouse rsRNA-28S-1 day1 rep3


title: HH-OX-51_6


title: HH-OX-51_2


title: Mouse rsRNA-28S-1 day6 rep2


title: RV05_N3: HIF1_AAA_donor_C


title: Mouse rsRNA-28S-1 day6 rep1


title: Mouse rsRNA-28S-1 day1 rep2


title: RV03_N3: VC_donor_C


title: RV14_N2: HIF1_PPN_donor_B


title: HH-OX-50_5

value: female


title: Mouse rsRNA-28S-1 day1 rep1


title: Mouse Control day6 rep3

value: vehicle


title: RV12_N2: HIF1_PPA_donor_B


title: HH-OX-50_6


title: Mouse Control day6 rep2


title: Mouse Control day6 rep1


title: HH-OX-52_5

value: male


title: RV10_N2: HIF1_AAN_donor_B


title: RV05_N2: HIF1_AAA_donor_B


title: Mouse Control day3 rep3


title: HH-OX-50_1

value: polyA RNA + protein surface markers


title: Mouse Control day3 rep2


title: HH-OX-50_3


title: 18B [6_22_F3_Group_16]

city: Columbus

first: Amy

last: Hite

state: OH - Ohio

address: 1800 Cannon Drive 250 Lincoln Tower

department: Biomedical Informatics

institute: The Ohio State University

data_processing:
RNAseq sequences were aligned to the International Human Genome Sequencing Consortium human reference sequence (hg19 refGene annotation from the University of California at Santa Cruz genome browser) using SOLiDLifescope v2.5.1 (Life Technologies)
Gene expression was measured in reads per kilobase per million (RPKM), as reported by the wtcounts module of Lifescope calculated based on reads that aligned to coding regions of genes annotated by RefSeq
Genome_build: hg19
Supplementary_files_format_and_content: square table with RPKM per gene per sample

extract_protocol:
Each blood sample consisted of:  a) 8 ml of peripheral blood drawn into a CPT® tube with sodium citrate anticoagulant (Becton & Dickenson, Franklin Lakes, NJ), and b) 2.5 ml of peripheral blood drawn into a PaxGene® tube (PreAnalytiX GmbH, Switzerland).  Samples in CPT tubes were processed immediately to isolate peripheral blood leukocytes and plasma, or, depending on the participating center, were shipped overnight at ambient temperature before processing.  Leukocytes were isolated from blood by standard protocols and stored at -80oC.  Frozen PaxGene tubes were processed to isolate total peripheral blood RNA according to the manufacturer's instructions (PreAnalytiX).
Total leukocyte RNA was extracted using Trizol reagent (Life Technologies, Grand Island, NY) according to the manufacturer's instructions.  RNA quality was verified on a 2100 Bioanalyzer (Agilent, Santa Clara, CA), with all samples showing an RNA integrity number >6.5.  NuGen Ovation RNASEQ System (San Carlos, CA) was used to generate cDNA libraries from 10 ng of total RNA per sample (NuGen Technologies, San Carlos, CA).  This kit employs poly-dT and random hexamer primers for cDNA synthesis, the latter designed to reduce cDNAs from rRNA by at least 90%.  This NuGen library preparation is able to capture RNA lacking polyA tails, including ncRNA RNAs, although in this study we focused sequence analysis on annotated coding genes1.  A linear amplification step enables RNAseq analysis of small amounts of RNA (we used 10-20 ng total RNA).  Samples were processed to produce 8-barcoded, paired-end libraries or 16-barcoded, single-end libraries. Samples were sequenced using the SOLiD 5500 Next-Generation Sequencing instrument (Life Technologies).

tag: subject status

value: children with nephrotic syndrome

tag: treatment

value: Post-treatment

tag: response

value: Steroid Sensitive

tag: tissue/cell type

value: peripheral blood leukocytes


title: RV10_N3: HIF1_AAN_donor_C

value: OT-I CD8 T cells

tag: transduced with

tag: mouse donor

value: C


title: Mouse Control day3 rep1

tag: developmental stage


title: HH-OX-50_4

tag: edss

value: no

tag: molecule


title: RV03_N2: VC_donor_B

value: B


title: HH-OX-51_1

tag: donor

tag: hash

value: PPMS


title: 18A [6_22_F3_Group_15]

value: Pre-treatment


title: HH-OX-50_2

tag: match


title: 17B [6_22_F3_Group_14]

value: Steroid Resistant


title: RV14_N1: HIF1_PPN_donor_A

value: A


title: HH-OX-49_6


title: RV10_N1: HIF1_AAN_donor_A


title: HH-OX-49_5


title: Mouse Control day1 rep3

tag: transfection


title: RV05_N1: HIF1_AAA_donor_A


title: Mouse Control day1 rep1


title: 17A [6_22_F3_Group_13]


title: 16B [6_22_F3_Group_12]


title: RV03_N1: VC_donor_A


title: HH-OX-49_2

tag: group


title: 7B [6_22_F3_Group_10]


title: artFG-KDM5A_III

first: Thomas

last: Eder

address: Veterinaerplatz 1

department: Department for Biological Sciences and Pathobiology

institute: University of Veterinary Medicine, Vienna

data_processing:
Quality control with FastQC
Quality trimming, quality filtering and length filtering by PRINSEQ-lite
Alignment against the  mouse reference genome (GRCm38/mm10) with STAR
Processed with SAMtools
Counts per gene were obtained by featureCounts
Normalization and differential gene expression analysis where then done with DESeq2
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include normalized values for each sample

source_name: artFG-KDM5A-modified fetal liver cells of C57BL/6N mice from embryos between day E13.5 and E14.5

growth_protocol: We isolated cells from fetal livers from C57BL/6N mice between day E13.5 and E14.5. Cells were cultured in DMEM/IMDM (50:50% vol/vol), supplemented with 10% FBS, 100 U/ml Penicillin-Streptomycin, 4 mM L-Glutamine and 50 uM beta-mercaptoethanol in the presence of murine stem cell factor (mSCF, 150 ng/ml), murine interleukin 3 (mIL-3, 10 ng/ml) and murine interleukin 6 (mIL-6, 10 ng/ml) (all PreproTech).

extract_protocol:
RNA was isolated using RNeasy Mini Kit (QIAGEN)
QuantSeq 3‘ mRNA-Seq Library Prep Kit (Lexogen)

treatment_protocol: Cells were retrovirally transduced with corresponding constructs and cell sorted to obtain a pure population

tag: strain

tag: tissue

value: liver

tag: genotype


title: Visium-C1

city: Montreal

first: Alain

last: Pacis

state: QC

address: 740 Dr Penfield Ave

country: Canada

institute: Canadian Centre for Computational Genomics (C3G)

data_processing:
Raw sequencing data for each sample was converted to matrices of expression counts using the Space Ranger software provided by 10X Genomics (version 1.0).
Using Space Ranger’s count, reads were aligned to the mm10 mouse reference genome, and transcript counts quantified for each annotated gene within every spot. The resulting UMI count matrices (genes × spots) were then provided as input to Seurat suite (version 3.2.0).
Genome_build: mm10
Supplementary_files_format_and_content: Genes by barcode counts matrices in HDF5 binary data format, PNG of all replicate images, JSON file containing scaling factors that converts pixel positions and, text file containing spot barcode position information per replicate.

source_name: 3 Pax2GFP E9.5 mouse embryosCapture area C1

growth_protocol: Fresh frozen dissected mouse embryos

extract_protocol:
Tissue preparation was performed according to the Visium Tissue Preparation Guide (CG000240 Rev A, 10X Genomics). Briefly, the trunk of 3 stage-matched E9.5 Pax2-GFP mouse embryos was dissected  in cold DMEM containing 10% fetal bovine serum (FBS) and 1% penicillin/streptomycin, embedded in Optimal Cutting Temperature (OCT) VWR clear frozen section compound and cryosectioned at 10 μm. Some sections were placed in pre-chilled DNA LoBind microcentrifuge tubes 1.5 ml (Eppendorf) for total RNA extraction and assessment of  average RNA integrity (RIN) quality score. RNA quality of the samples was good, RIN score=9.5, as defined using 2200 TapeStation (Agilent) with High Sensitivity RNA ScreenTape Assay (Agilent). Other sections were placed in pre-chilled Visium Tissue Optimization Slides (10X Genomics) or Visium Spatial Gene Expression Slide (10X Genomics) for tissue optimization and gene expression experiments, respectively, and stored  at -80 °C for less than a week. Tissue slides were processed following Visium guidelines (Visium Spatial Tissue Optimization User Guide (CG000238 Rev A, 10X Genomics) or Visium Spatial Gene Expression User Guide (CG000239 Rev A, 10X Genomics). Tissue sections on the gene expression slide were permeabilized for 12 minutes, which was pre-determined as the optimal time established after the Tissue Optimization experiments. Brightfield histology images for Tissue Optimization were taken using a 10x objective on an EVOS FL Auto imaging system (ThermoFisher Scientific). Fluorescent images were taken with a TRITC filter using a 10X objective and 300 ms exposure time. For Tissue Expression, brightfield images were taken using a 20X objective on a Nikon Eclipse Ti2 microscope. Raw images were stitched together using NIS-Elements AR 5.11.00 (Nikon) and exported as .tiff files with low- and high-resolution settings.
Library preparation was performed according to the Visium Spatial Gene Expression User Guide (CG000239 Rev A, 10X Genomics). Libraries were loaded and sequenced on a NovaSeq 6000 System (Illumina) as paired-end-dual-indexed with NovaSeq SP PE150 Reagent Kit (Illumina), at  a sequencing depth of approximately 25M read-pairs per capture area.

value: C57BL6 xC3H background

value: trunk of Pax2GFP mouse embryo

value: E9.5 (21 somite stage)


title: HH-OX-49_4

tag: cohort

tag: Sex

value: female

value: polyA RNA + protein surface markers


title: HH-OX-48_3

value: male


title: artFG-KDM5A_I

city: Vienna


title: Visium-A1

source_name: 3 Pax2GFP E9.5 mouse embryosCapture area A1


title: 6B [6_22_F3_Group_8]

tag: subject status

value: children with nephrotic syndrome

tag: treatment

value: Post-treatment

tag: response

value: Steroid Sensitive


title: 7A [6_22_F3_Group_9]

tag: tissue/cell type

value: peripheral blood leukocytes


title: artFG-KDM5A_II

tag: developmental stage


title: RV12_N1: HIF1_PPA_donor_A

tag: cell type

value: OT-I CD8 T cells

tag: transduced with

tag: mouse donor


title: Mouse Control day1 rep2

value: vehicle


title: 50perc_Epcam_SC-6_repC

description: 50perc_Epcam_SC-6_repABC_filtered_feature_bc_matrix.h5

data_processing:
Raw BCL files from the Illumina HiSeq were demultiplexed into paired-end, gzip-compressed FASTQ files for each channel using Cell Ranger’s mkfastq.
Using Cell Ranger’s count, reads were aligned to the mouse reference transcriptome (mm10), and transcript counts quantified for each annotated gene within every cell.
Genome_build: mm10
Supplementary_files_format_and_content: HDF5 binary data format

source_name: Wild type caudal Urogenital system E11.5 Replica C

growth_protocol: dissected embryos

extract_protocol:
Dissociated cells and FACS
10X Chromium Single Cell 3'

value: Dissected caudal urogenital system

tag: genotype/group

value: Wild type. Mixture of 50% Epcam +ve (epithelial cells including cauda nephric duct, ureteric bud and the cloaca epithelium), and 50% Epcam –ve (mesenchymal cells including the metanephric and surrounding caudal mesenchyme)


title: HH-OX-49_1

tag: donor

tag: hash

tag: match

value: PPMS

tag: edss

value: no

tag: molecule


title: HH-OX-48_4

tag: group


title: 50perc_Epcam_SC-6_repB

source_name: Wild type caudal Urogenital system E11.5 Replica B

tag: strain

tag: tissue


title: HH-OX-49_3

tag: cohort

tag: Sex


title: HH-OX-48_5


title: 6A [6_22_F3_Group_7]

tag: subject status

tag: treatment

value: Pre-treatment

tag: response


title: 5B [6_22_F3_Group_6]

value: Steroid Resistant

tag: tissue/cell type


title: 50perc_Epcam_SC-6_repA

source_name: Wild type caudal Urogenital system E11.5 Replica A

value: C57BL6 xC3H background

tag: developmental stage


title: Visium-D1

source_name: 3 Pax2GFP E9.5 mouse embryosCapture area D1

value: trunk of Pax2GFP mouse embryo

value: E9.5 (21 somite stage)


title: artAA-KDM5A_III

source_name: artAA-KDM5A-modified fetal liver cells of C57BL/6N mice from embryos between day E13.5 and E14.5

value: liver

tag: genotype


title: Visium-B1

source_name: 3 Pax2GFP E9.5 mouse embryosCapture area B1


title: 16A [6_22_F3_Group_11]


title: artAA-KDM5A_II


title: Pax2-GFP_SC-5

description: Pax2-GFP_SC-5_filtered_feature_bc_matrix.h5

source_name: Pax2GFP embryo E9.0 (14 somite stage)

value: trunk of mouse embryo

value: E9.0 (14 somite stage)

tag: genotype/group

value: Pax2-GFP Single-cell


title: artAA-KDM5A_I


title: HH-OX-48_6

source_name: blood

tag: donor

value: male

value: polyA RNA + protein surface markers


title: HH-OX-48_1

tag: hash


title: 5A [6_22_F3_Group_5]

value: children with nephrotic syndrome

value: peripheral blood leukocytes


title: NUP98-KDM5A_III

source_name: NUP98-KDM5A-modified fetal liver cells of C57BL/6N mice from embryos between day E13.5 and E14.5


title: 4B [6_22_F3_Group_4]

value: Post-treatment

value: Steroid Sensitive


title: 4A [6_22_F3_Group_3]


title: Pax2-GFP_SC-4

description: Pax2-GFP_SC-4_filtered_feature_bc_matrix.h5

source_name: Pax2GFP embryo E8.75 (11 somite stage)

value: E8.75 (11 somite stage)


title: NUP98-KDM5A_II


title: HH-OX-48_2

tag: match

value: no


title: HH-OX-47_3

value: PPMS

tag: edss


title: HH-OX-57_5

value: female

value: intrathecal steroids

tag: molecule


title: Spermatogonia Vehicle

city: Kansas City

first: Sumedha

middle: S

last: Gunewardena

state: Kansas

address: 2146 West 39th Avenue

department: Dept. of Molecular and Integrative Physiology

institute: University of kansas medical center

data_processing:
The data was analyzed using the 10x Genomics Chromium Single Cell software suite (cellranger-3.0.2).
The demultiplexing and conversion of Illumina base call files (BCL) to raw FASTQ files was done using "cellranger mkfastq" with default parameters.
The sequencing reads were aligned to the human reference (GRCh38: refdata-cellranger-GRCh38-3.0.0) and analyzed using "cellranger count".
Read 1: 26bp; Index Read 1: 8bp; Read 2: 96bp
Genome_build: mm10
Supplementary_files_format_and_content: Hierarchical Data Format (H5); cellranger generated unfiltered feature-barcode matrix file.

source_name: Single cells obtained from cultured spermatogonia with induced meiosis treatment

growth_protocol: spermatogonia normal culture protocol

extract_protocol:
Single cells were obtained from enzymatic digestion of cultured spermatogonia. Cell viability and concentration were measured by Countess II FL Automated Cell Counter (Life Technologies) targeting ≥75% cell viability. The cell emulsification is performed with the 10X Chromium Controller using the Chromium Single Cell 3’ GEM Library & Gel Bead Kit v3 (10X Genomics 1000092) and Chromium Chip B Single Cell Kit (10X Genomics 1000074).
The RT reaction to generate 10X barcoded single stranded cDNA, in the single cell containing GEMs, is performed using an Eppendorf MasterCycler Pro thermal cycler. Post GEM-RT Cleanup is conducted by breaking the GEMS with 10X Recovery Agent to separate the aqueous phase from the Recovery Agent and Partitioning oil. A cleanup of the sscDNA containing aqueous phase is completed using Dynabeads MyOne Silane beads (Life Technologies 37002D). The second strand cDNA amplification is performed using the cDNA Amplification Mix on the Eppendorf MasterCycler Pro. The 3’ gene expression library construction is initiated with fragmentation, end repair and A-tailing of the dscDNA followed by adapter ligation and a sample index PCR using the Illumina compatible indexed adapters in the Chromium i7 Multiplex kit (10X Genomics 120262). Validation of the single cell library is conducted using the Agilent Tapestation 4200 ScreenTape assay (Agilent 5067-5576).
scRNA-seq 10x Genomics; 10x Genomics Chromium Single Cell Gene Expression data

treatment_protocol: Induced meiosis treatment

value: spermatogonia


title: 3B [6_22_F3_Group_2]

value: Steroid Resistant


title: NUP98-KDM5A_I

value: liver


title: Spermatogonia induced meiosis 3 days


title: HH-OX-47_4

tag: group


title: 3A [6_22_F3_Group_1]

value: Pre-treatment


title: fl_wt_III

description: unmodified fetal liver cells of C57BL/6N mice from embryos between day E13.5 and E14.5

tag: strain

value: wildtype


title: Spermatogonia induced meiosis 4 days

tag: tissue


title: HH-OX-47_5

tag: cohort


title: 15A [3_7_F3_Group_15]


title: fl_wt_I

source_name: unmodified fetal liver cells of C57BL/6N mice from embryos between day E13.5 and E14.5


title: HH-OX-47_6

tag: Sex


title: 15B [3_7_F3_Group_16]

tag: subject status


title: CD1 spermatogonia Veh replicate 2

data_processing:
Illumina bcl2fastq2 conversion software used for basecalling.
reads were aligned using the STAR (2.6.1c) software.
raw read counts were obtained using featureCounts (1.6.4)
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files of raw count values for each Sample (not normalized)

source_name: CD1 spermatogonia Veh

growth_protocol: Spermatogonia culture supplemented with  N2 and 10 ng/ml of both bFGF and GDNF.

extract_protocol:
RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA-seq (NuGENUPRNA); RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: NRRA

tag: treatment

value: Veh


title: Spermatogonia induced meiosis 2 days


title: HH-OX-47_2

value: male


title: CD1 spermatogonia Veh replicate 1


title: E9.5c5+CsA, rep2

city: Kyoto

first: Yukihiro

last: Yabuta

state: Kyoto

address: Yoshida-Konoe-cho, Sakyo-ku

department: Anatomy and Cell Biology

country: Japan

institute: Kyoto University, Graduate school of medicine

description: 3'-RNAseq amplified from 1ng RNA

data_processing:
All the reads were surveyed and the adaptor or the poly-A sequences were trimmed by cutadapt-1.3 with options "-e 0.1 -q 20 -n 2 -O 1 -m 30 -a CTCGAGGGCGCGCCGGATCC -g CTCGAGGGCGCGCCGGATCC -a AAAAAAAAAAAAAAAAAAAA -a TTTTTTTTTTTTTTTTTTTT". The trimmed reads with less than 30 bp were discarded.
Untrimmed and trimmed reads of 30 bp or longer were mapped onto the mouse genome mm10 and the ERCC spike-in RNA sequences with tophat-1.4.1/bowtie1.0.1 with the “—no-coverage-search” option.
Mapped reads on the genome and the ERCC were separated, and the reads on the genome were converted into the expression levels by cufflinks-2.2.0 using the “—compatible-hits-norm”,  “—max-mle-iterations 50000", “—no-length-correction” and “—library-type fr-secondstrand” options and macfas5.0 reference gene annotations with extended TTSs. For the reference gene annotations used in cufflinks, we extended the TTSs of the reference genes up to 10 kb downstream to correctly estimate the expression levels of genes whose transcripts are longer than the reference toward the 3 prime.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include RPM values for each Sample

source_name: Mouse E9.5 PGC

growth_protocol:
ESCs were cultured and maintained in N2B27 medium with 2i (PD0325901,0.4 mM: Stemgent; CHIR99021, 3 mM: Stemgent) and LIF (1,000 U/ml; Merck Millipore) on a dish coated with poly-L-ornithine (0.01%; Sigma) and laminin (10 ng/ml; BD Biosciences)
Induction of EpiLCs and PGCLCs was performed as reported previously.  Briefly, the EpiLCs were induced by plating 1 × 105 ESCs on a well of a 12-well plate coated with human plasma fibronectin (16.7 mg/ml: Merck Millipore) in N2B27 medium containing activin A (20 ng/ml: Peprotech), FGF2 (12 ng/ml: Thermo Fisher Scientific), and KSR (1%: Thermo Fisher Scientific). The PGCLCs were induced from d2 EpiLCs under a floating condition in a well of a low-cell-binding U-bottom 96-well plate (Thermo Scientific) in serum-free medium [GK15; GMEM (Thermo Fisher Scientific) with 15% KSR, 0.1 mM NEAA, 1 mM sodium pyruvate, 0.1 mM 2-mercaptoethanol, 100 U/ml penicillin, 0.1 mg/ml streptomycin, and 2 mM L-glutamine] in the presence of the cytokines BMP4 (500 ng/ml; R&D Systems), LIF (1,000 U/ml; Merck Millipore), SCF (100 ng/ml; R&D Systems), and EGF (50 ng/ml; R&D Systems).
Fluorescence-activated cell sorting (FACS) was performed with a FACSAriaIII (BD) cell sorter for purifying BV-positive-d4 PGCLCs or EGFP-positive-E9.5 PGCs (B6D2F1×Stella–EGFP).  m220-5 cells were used as the feeder cells for PGCLCs or E9.5 PGCs as described previously.  Briefly, m220-5 cells were cultured for three passages with 10 µM of both forskolin and rolipram (FR10) to permit adaptation to these compounds prior to mitomycin C (MMC) treatment (1–2 µg/ml, 2 h).  Purified d4 PGCLCs or E9.5 PGCs were plated on m220-5 cells in GMEM containing 10% KSR, 0.1 mM NEAA, 1 mM sodium pyruvate, 0.1 mM 2-mercaptoethanol, 100 U/ml penicillin, 0.1 mg/ml streptomycin, 2 mM L-glutamine, 2.5% FCS, 100 ng/ml SCF, 10 µM forskolin, and 10 mM rolipram.  Half of the culture medium was changed every 2 days.  Following chemicals and cytokine were used in this study: cyclosporin A (Sigma), FK506 (Sigma), FGF2 (Thermo Fisher Scientific), FGF7 (R&D Systems), FGF10 (R&D Systems), and WNT5A (R&D Systems).

extract_protocol:
Total RNAs were purified from d4c7 PGCLCs and E9.5c5 PGCs cultured with each condition (two biological replicates for each) using an RNAeasy Micro Kit (Qiagen).
For SC3-seq analysis, cDNA synthesis / amplification from single cells and library construction from the cDNAs were performed as described previously [Nakamura et al. 2015, NAR, 43, e60].

value: B6D2F1 x C57BL/6

tag: transgene

value: Stella-EGFP reporter

tag: cell sorting

value: EGFP sort


title: 14B [3_7_F3_Group_14]

value: children with nephrotic syndrome

value: Post-treatment

tag: response

tag: tissue/cell type

value: peripheral blood leukocytes


title: 14A [3_7_F3_Group_13]

value: Steroid Sensitive


title: E9.5c5+CsA, rep1

description: 3'-RNAseq amplified from 1ng RNA


title: HH-OX-47_1

data_processing:
library deconvolution with bcl2fastq (Illumina, v2.20.0.422)
single cell deconvolution and mapping using zUMIs (v2.5.6b) with STAR (v2.6.0c) for RNA and CITE-seq-Count (v. 1.4.2) for protein surface markers
cell hashing demultiplexing with Seurat (v3.1.1)
doublet removal with DoubletFinder (2.0.2)
Standard log normalisation of RNA using Seurat (v3.1.1)
Non-standard normalisation of RNA using sctransform (v0.2.0) as described in Hafemeister and Satija 2019 (Genome Biology)
Sample integration for RNA with Seurat (v3.1.1)
Marker imputation from RNA with SAVER-X (v1.0.0)
Integration of imputed RNA markers with Seurat (v3.1.1)
Normalisation (centered log transformation) and sample integration for surface protein markers with Seurat (v3.1.1)
Genome_build: GRCh38 without alternative contigs
Supplementary_files_format_and_content: All processed data files are provided as tar.gz archives, which contain a sparse matrix in the market matrix format (.mtx) specifying expression values and the cell barcodes and features as tab seperated value files (barcodes.tsv and genes.tsv), the matrices contain cells as columns and features (genes or antibody-derived tags = ADT) as rows; all metadata files are provided as comma separated text files (.csv)

extract_protocol:
10X chromium v2/v3 (see V_10X for each sample)
CITE-seq/Cell hashing as described in Stoeckius et al 2018 (Genome Biology)

value: PPMS

value: no

value: polyA RNA + protein surface markers


title: CD1 spermatogonia NRRA treatment replicate 2

source_name: CD1 spermatogonia NRRA treatment

value: spermatogonia

value: NRRA treatment


title: 13B [3_7_F3_Group_12]

value: Steroid Resistant


title: CD1 spermatogonia NRRA treatment replicate 1


title: E9.5c5 FR10, rep2

description: 3'-RNAseq amplified from 1ng RNA


title: HH-OX-46_6


title: 13A [3_7_F3_Group_11]

value: Pre-treatment


title: stra8-ko_V (replicate 2)

source_name: STRA8KO spermatogonia Veh

tag: strain background

tag: genotype/variation


title: E9.5c5 FR10, rep1

description: 3'-RNAseq amplified from 1ng RNA


title: HH-OX-46_1

tag: donor

tag: hash


title: 12B [3_7_F3_Group_10]


title: 12A [3_7_F3_Group_9]


title: d4c7+FGF2, rep2

description: 3'-RNAseq amplified from 1ng RNA

source_name: Mouse PGCLC

value: Blimp1-mVenus reporter; Stella-ECFP reporter (BVSC)

value: mVenus sort


title: stra8-ko_T (replicate 2)

source_name: STRA8KO spermatogonia NRRA treatment


title: d4c7+FGF2, rep1

description: 3'-RNAseq amplified from 1ng RNA


title: 11B [3_7_F3_Group_8]


title: fl_wt_II

value: liver

tag: developmental stage

tag: genotype

value: wildtype


title: HH-OX-46_3

tag: match

tag: group

value: male

tag: edss

tag: molecule


title: stra8-ko_T (replicate 1)

tag: tissue


title: HH-OX-46_5

tag: cohort

tag: Sex


title: HH-OX-46_2


title: spo11-ko_V (replicate 2)

source_name: SPO11KO spermatogonia Veh

tag: treatment

value: Veh


title: HH-OX-45_5


title: HH-OX-46_4


title: d4c7+FGF10, rep1

description: 3'-RNAseq amplified from 1ng RNA

tag: strain

tag: transgene

tag: cell sorting


title: d4c7+FGF10, rep2

description: 3'-RNAseq amplified from 1ng RNA


title: spo11-ko_V (replicate 1)

tag: strain background


title: 10B [3_7_F3_Group_6]

tag: subject status

value: children with nephrotic syndrome

tag: response

tag: tissue/cell type


title: 11A [3_7_F3_Group_7]


title: HH-OX-45_6

tag: donor

tag: hash


title: 10A [3_7_F3_Group_5]


title: d4c7+CsA, rep1

description: 3'-RNAseq amplified from 1ng RNA


title: d4c7+CsA, rep2

description: 3'-RNAseq amplified from 1ng RNA


title: HH-OX-45_1

tag: match


title: 9B [3_7_F3_Group_4]

value: Post-treatment


title: stra8-ko_V (replicate 1)

tag: genotype/variation


title: spo11-ko_T (replicate 1)

source_name: SPO11KO spermatogonia NRRA treatment


title: spo11-ko_T (replicate 2)


title: 9A [3_7_F3_Group_3]

value: peripheral blood leukocytes


title: d4c7+FR10, rep2

description: 3'-RNAseq amplified from 1ng RNA


title: d4c7+FR10, rep1

description: 3'-RNAseq amplified from 1ng RNA


title: HH-OX-45_3

tag: group

tag: edss


title: HH-OX-45_2

tag: molecule


title: 8B [3_7_F3_Group_2]

value: Steroid Sensitive


title: Veh (replicate 1)

source_name: spermatogonia Veh

treatment_protocol: RA, NR and NRRA

tag: tissue


title: HH-OX-45_4

value: PPMS

tag: cohort

tag: Sex


title: d4 mPGCLC, rep2

description: 3'-RNAseq amplified from 1ng RNA

tag: strain


title: Veh (replicate 2)

tag: treatment


title: 8A [3_7_F3_Group_1]


title: d4 mPGCLC, rep1

description: 3'-RNAseq amplified from 1ng RNA

tag: transgene

tag: cell sorting


title: RA_EBSS (replicate 2)

source_name: spermatogonia NRRA treatment


title: HH-OX-44_5

value: female

value: no


title: RA_EBSS (replicate 1)

value: spermatogonia