title: RNAseq_45 mir-802fl/fl

city: Zurich

first: Algera

last: Goga

state: Schweiz

address: Otto-Sttern-Weg 7

department: Biology

country: Switzerland

institute: ETH Zurich

description: Total RNA was extracted from samples. PolyA-enrichment.

data_processing:
bcl2Fastq v2.19 software used for demultiplexing + basecalling.
Reads trimmed with trimmomatic, options: ILLUMINACLIP:adapters.fa:1:20:7:5:true AVGQUAL:10 MINLEN:20
Reads mapped and quantified with RSEM 1.2.22.
Differential expression analysis: EdgeR, options: normMethod = TMM; backgroundExpression =10; testMethod = glm; deTest =QL
Genome_build: Mus_musculus/Ensembl/GRCm38
Supplementary_files_format_and_content: *.txt: Tab-delimited text file with the following columns: 1. Identifier (Ensembl TranscriptID), 2. gene_id (= Ensembl GeneID) , 3. gc (=transcript gc-content), 4. width (= transcriptLength in [nt]), 5. transcriptCout (= raw counts), 6.-7. TPM/FPKM (= normalized counts), 8.-10. Applying PosteriorEstimates to previous count information.

source_name: Enterocytes isolated from upper jejunum

extract_protocol:
RNA was extracted from jejunum enterocytes isolated from 18-week-old mice using Trizol (Sigma-Aldrich) followed by column purification using the RNeasy column purification kit (Qiagen), with on-column DNase (Qiagen) digestion for all samples. 1ug of total RNA was used for library preparation.
Illumina TruSeq stranded mRNA.

tag: genotype

value: Intestinal miR-802 WT

value: Upper jejunum enterocytes

value: 18 weeks (adult)

tag: Sex

value: Female


title: HC_H007_RNA_control

status: Public on Dec 11 2020

type: SRA

city: Kiel

first: Neha

last: Mishra

address: Rosalind-Franklin-Str. 12

country: Germany

institute: Institute of Clinical Molecular Biology

library_source: transcriptomic

data_processing:
Base Calling perofmed by RTA1(MiSeq) and RTA3 (Novaseq 6000)
Transcriptome Processing: Fastq files were mapped and aligned using nf-core ((https://github.com/nf-core/rnaseq)) rnaseq pipeline. Adapters and low-quality bases from the RNA-seq reads were removed using Trim Galore (version 0.4.4), which is a wrapper tool for Cutadapt and FastQC. Reads that were shorter than 35 bp after trimming were discarded. . The filtered reads were mapped to the human genome (GRCh38, gencode version 25) using STAR aligner (version 2.5.2b) (Dobin et al., 2013). featureCounts (version 1.5.2) was used to estimate the expression counts of the genes.
BCRseq Processing: Sequencing reads were aligned to BCR gene reference and clonotypes were identified and grouped using the software MiXCR (Bolotin et al., 2015). Relative proportions of IGH classes were calculated. Alpha diversity measures were calculated using the R packages vegan and tcR (versions 1.5-6 and 2.3.2).
Genome_build: (GRCh38, gencode version 25)
Supplementary_files_format_and_content: tab-delimited text files include feature counts and BCR Clonotype count tables

molecule: total RNA

organism: Homo sapiens

source_name: Peripheral Whole-Blood

extract_protocol:
RNA sequencing libraries were prepared according to the Illumina TruSeq® messenger (mRNA) sequencing protocol (TruSeq® RNA Seq Library Prep Kit v2). The resulting libraries were sequenced on the NovaSeq 6000 (2× 50 bp, S2 chemistry).
Patient peripheral blood was collected in 2.5mL tubes PAXgene Blood RNA Tubes, RNA was automated isolated in QIAGEN’s QIAcube using the PAXgene Blood miRNA Kit from QIAGEN PreAnalytiX.

tag: remission

value: Healthy

tag: gender

value: f

tag: age

tag: pseudotime

tag: patient number


title: IIH10999: patient with idiopathic intracranial hypertension (IIH), patient#IIH10999

city: Muenster

first: I-Na

last: Lu

state: NRW

address: Domagkstraße 20

department: Department of Pediatric Hematology and Oncology

institute: University Children's Hospital Münster

description: single-cell RNA seq data of a patient with idiopathic intracranial hypertension (IIH), patient#IIH10999

data_processing:
Raw bcl files were de-multiplexed using the cellranger mkfastq pipeline (cellranger v3.1.0)
Subsequent reads alignments and transcript counting was done individually for each sample using the cellranger count pipeline with standard parameters
 The cellranger aggr pipeline was employed to aggregate samples with mapping normalization to leave each sample with similar sequencing depth per cell.
Genome_build: GRCh38
Supplementary_files_format_and_content: Standard cellranger output format

source_name: CSF

extract_protocol:
CSF samples were collected into round bottom polypropylene tubes and then centrifuged for 10 min at 300 x g. The CSF supernatant was removed and CSF cells were resuspended in 5 ml of X-Vivo15 media (Lonza) and stored at 4°C. The samples were then transported to the laboratory of the Department of Neurology with Institute of Translational Neurology at the University Clinic Münster, Germany for scRNA-seq. Transport time of samples collected in Münster was 10-30 minutes. Transport time of samples collected in Essen was < 60 minutes. Cell suspensions were then centrifuged again for 5 min at 400 x g and then resuspended in 40 μl of media. Out of this volume, 6 μl were used for cell counting and the remaining volume was entirely used for scRNA-seq.
Four Neuro-COVID samples were processed with the Chromium Single Cell 5’ Library & Gel Bead Kit and barcoded, full-length VDJ segments from T cells were enriched from first-strand cDNA via PCR amplification with the Chromium Single Cell VDJ Enrichment Kit, Human T Cell (from 10X Genomics) following the manufacturer’s instructions. Further library preparation was performed using the Chromium Single Cell 5' Library Construction Kit (10X Genomics). Three Neuro-COVID samples were processed with the Chromium Single Cell 3’ Library & Gel Bead Kit and we developed a novel method to sequence antigen receptor information  from 3’ scRNA-seq libraries. The method allows removing the constant region of antigen receptors during enrichment, while maintaining their cell barcode and unique molecular identifier (UMI) information attached to the 3' of the cDNA molecules. In summary, the method involves self-circulating the cDNA library, enriching the VDJ region and re-linearizing. Each step maintains the VDJ region together with the cell barcode and UMI in the same molecule. Sample processing and library preparation was performed according to manufacturer instructions using AMPure XP beads (Beckman Coulter). Sequencing was either carried out on a local Illumina Nextseq 500 using the High-Out 75 cycle kit with a 26-8-0-57 read setup or commercially (Microanaly, China) on a NovaSeq 6000 using the 300 cycle kit with paired end 150 read setup. All the samples were sequenced with a sequencing depth >50,000 reads per cell.

tag: tissue

value: CSF-derived leukocytes

tag: diagnosis

value: IIH

tag: type of library

value: RNA expression

tag: subject id


title: RNAseq_43 mir-802fl/fl

organism: Mus musculus

tag: strain

tag: cell type


title: RNAseq_34 Vil-Cre mir-802fl/fl

value: Intestinal miR-802 KO


title: RNAseq_33 Vil-Cre mir-802fl/fl


title: HC_H004_RNA_control

value: m


title: HC_H009_RNA_control


title: RNAseq_28 Vil-Cre mir-802fl/fl


title: HC_H002_RNA_control


title: HC_H003_RNA_control


title: HC_H010_RNA_control


title: PC_7_RNA_rec

value: Remission


title: SCMNK cells_Rep1

city: Tyler

first: Sachin

last: Mulik

state: Texas

department: Pulmonary Immunology

country: USA

institute: The University of Texas Health Science Center at Tyler

data_processing:
Reads were trimmed using Trim galore
Reads were aligned to mouse genome (mm10) using HISAT2
Counting of aligned reads in the BAM files that overlap features in a GFF file using HTseq-counts
Genome_build: mm10
Supplementary_files_format_and_content: Tab delimited txt file; Htseq counts data; deseq2 normalized data;

growth_protocol: NK cells were harvested from mice spleen on day 37 post-infection

extract_protocol:
Total RNA was isolated using nucleospin RNA XS kit (Machery-Nagel, Duren, Germany)
Low-Input RNA-Sequencing Library Prep for Illumina

treatment_protocol: CD27+ and CD27- cells were FACS sorted and frozen at -80oC till RNA isolation.

tag: strain background

value: Spleen

value: SCMNK cells


title: HC_H013_RNA_control


title: HC_H014_RNA_control


title: HC_H011_RNA_control


title: PC_6_RNA_TA


title: PC_6_RNA_TA2


title: DpnII-Seq-K562-5min-R1

city: Worcester

first: Houda

last: Belaghzal

state: MA

address: 55 N Lake Ave

department: Program in Systems Biology

institute: University of Massachusetts Medical School

library_source: genomic

data_processing:
Sequenced reads were mapped to the genome using the Bowtie read aligner (Langmead et al., 2009) and reads mapping to multiple sites of the genome were removed. As expected, a high percentage of reads mapped precisely to their associated restriction cut site. To remove potential artificial biases, we filtered out paired-end reads from fragments whose start or end coordinate was more than three nucleotides from an appropriate restriction cut site. Filtered reads were then binned to 500 kb or 40 kb resolutions. The K562 cell line has a primarily triploid karyotype with regions of the genome in diploid and tetraploid states. Copy number state assignments for each 500 kb or 40 kb bin were assigned using publicly available K562 copy number data from the Catalogue of Somatic Mutations In Cancer (COSMIC) database (https://cancer.sanger.ac.uk/cell_lines/download). Copy number segments in the COSMIC dataset were identified by PICNIC analysis of Affymetrix SNP6.0 array data (PMID:19837654). Read coverage files at 500 kb and 40 kb were corrected to a genome wide diploid state using the copy number state assignments and dividing coverage by appropriate correction value (diploid = 1, triploid =1.5, tetraploid = 2, etc.) per bin. Final copy number corrected coverage files were used for all downstream analysis and are available. DpnII-seq computational workflow is maintained at https://github.com/tborrman/DpnII-seq
Genome_build: hg19
Genome_build: 5C*-samples: Custom built based on the 5C primers as described in https://github.com/dekkerlab/5C-CBFb-SMMHC-Inhib/blob/master/data_processing_steps.md
Supplementary_files_format_and_content: hdf5 files contain iced and scaled Hi-C intearction matrices. LOS bedGraphs represent loss of structure for pre-digested genomic bins relative to control for indicated timepoints. half-life bedGraph represents chromatin interaction stability for genomic bins. half-life_residuals bedGraph represents chromatin interaction stability after accounting for digestion efficiency.
Supplementary_files_format_and_content: bedGraphs represent DpnII-seq copy number corrected read coverage for indicated digestion time.
Supplementary_files_format_and_content: Processed data is a matrix file that represents the pair-wise interactions between loci for 1 Mb around the Beta-Globin locus

molecule: genomic DNA

growth_protocol: RPMI Medium  (Gibco)15% FBS (Gibco) 1% Antibiotic-Antimycotic (Gibco)  1% L-Glutamine (Gibco)

extract_protocol:
DpnII-Seq  was performed as described in DpnII_Seq Method
DpnII-Seq  was performed as described in DpnII_Seq Method

treatment_protocol: Nuclei were purified as described in method, then the nuclei pellet was washed twice with 1XNEB3.1. For this protocol we used 10 million of nuclei, each sample of two million nuclei was resuspended in 500 µL of 1X NEB3.1 on ice. Next, 120 U of DpnII was added to the sample in order to obtain 10 U DpnII/µg DNA, and samples were incubated at 37°C on a thermocycler for 5 min. Afterward, a final volume of 10 mM of EDTA was added to inactivate the endonuclease, a 20 µl aliquot is taken for assessment of fragmentation level, and the remaining sample were immediately processed as described in method section of DpnII-seq protocol

tag: cell line

value: The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises.

tag: protocol

value: DpnII-Seq

tag: enzyme

value: DpnII


title: DpnII-Seq-K562-1h-R1

treatment_protocol: Nuclei were purified as described in method, then the nuclei pellet was washed twice with 1XNEB3.1. For this protocol we used 10 million of nuclei, each sample of two million nuclei was resuspended in 500 µL of 1X NEB3.1 on ice. Next, 120 U of DpnII was added to the sample in order to obtain 10 U DpnII/µg DNA, and samples were incubated at 37°C on a thermocycler for 1 h. Afterward, a final volume of 10 mM of EDTA was added to inactivate the endonuclease, a 20 µl aliquot is taken for assessment of fragmentation level, and the remaining sample were immediately processed as described in method section of DpnII-seq protocol


title: DpnII-Seq-K562-2h-R1

treatment_protocol: Nuclei were purified as described in method, then the nuclei pellet was washed twice with 1XNEB3.1. For this protocol we used 10 million of nuclei, each sample of two million nuclei was resuspended in 500 µL of 1X NEB3.1 on ice. Next, 120 U of DpnII was added to the sample in order to obtain 10 U DpnII/µg DNA, and samples were incubated at 37°C on a thermocycler for 2 h. Afterward, a final volume of 10 mM of EDTA was added to inactivate the endonuclease, a 20 µl aliquot is taken for assessment of fragmentation level, and the remaining sample were immediately processed as described in method section of DpnII-seq protocol


title: DpnII-Seq-K562-3h-R1

treatment_protocol: Nuclei were purified as described in method, then the nuclei pellet was washed twice with 1XNEB3.1. For this protocol we used 10 million of nuclei, each sample of two million nuclei was resuspended in 500 µL of 1X NEB3.1 on ice. Next, 120 U of DpnII was added to the sample in order to obtain 10 U DpnII/µg DNA, and samples were incubated at 37°C on a thermocycler for 3 h. Afterward, a final volume of 10 mM of EDTA was added to inactivate the endonuclease, a 20 µl aliquot is taken for assessment of fragmentation level, and the remaining sample were immediately processed as described in method section of DpnII-seq protocol


title: PC_6_RNA_TB


title: PC_6_RNA_rec


title: RNAseq_31 mir-802fl/fl

tag: genotype

value: Intestinal miR-802 WT


title: PC_5_RNA_TB


title: HiC-K562-Cell-R1

data_processing:
Hi-C read mapping, filtering, binning and matrix normalization were performed using the cMapping pipeline available at https://github.com/dekkerlab/cMapping (Lajoie et al., 2015). In brief, Hi-C reads were mapped to reference human genome assembly hg19 using an iterative mapping strategy and Bowtie 2 (Langmead et al., 2009). Successfully mapped reads were then filtered to remove reads mapping to the same restriction fragment and to remove PCR duplicates. Interaction frequency versus distance plots displayed high variance for interactions below 1 kb for all samples. Hence, after mapping of valid pair, we removed all pairs with a genomic distance less than 1 kb. The remaining valid read pairs were then binned to 500 kb, 40 kb, and 10 kb resolution matrices. Outlier bins of these matrices with low signal were assigned values of NA. Then as a bias correction step, matrices were normalized such that the sum of interactions in each row/column are approximately equivalent via an iterative correction procedure (ICE) (Imakaev et al., 2012). Lastlly, for comparison between samples, matrices were scaled such that the total interactions for a genome-wide matrix equals one billion for each sample. These ICEd scaled matrices were used for subsequent analyses
Genome_build: hg19
Genome_build: 5C*-samples: Custom built based on the 5C primers as described in https://github.com/dekkerlab/5C-CBFb-SMMHC-Inhib/blob/master/data_processing_steps.md
Supplementary_files_format_and_content: hdf5 files contain iced and scaled Hi-C intearction matrices. LOS bedGraphs represent loss of structure for pre-digested genomic bins relative to control for indicated timepoints. half-life bedGraph represents chromatin interaction stability for genomic bins. half-life_residuals bedGraph represents chromatin interaction stability after accounting for digestion efficiency.
Supplementary_files_format_and_content: bedGraphs represent DpnII-seq copy number corrected read coverage for indicated digestion time.
Supplementary_files_format_and_content: Processed data is a matrix file that represents the pair-wise interactions between loci for 1 Mb around the Beta-Globin locus

extract_protocol:
Hi-C was performed as described (Hi-C 2.0 Belaghzal et al., 2017) . For intact cells: 5 million K562 cells or nuclei were washed twice with 15 mL of HBSS and pelleted at 300 g for 10 min, then resuspended in 2.5 mL of HBSS. The sample was transferred to 20.625 mL crosslinking mix [625 μL of 37% formaldehyde + 20 mL of HBSS]. Samples were incubated at RT for 10 min on a rocking platform. Next, to stop cross-linking 1.25 mL of 2.5 M glycine was added to each sample and the mix was incubated at RT for 5 min on a rocking platform. To pellet the crosslinked cells the sample was centrifuged at 1,000 g for 10 min at 4°C. The supernatant was discarded and the pellet was washed twice with HBSS before going to the next step or storing samples at -80°C. Lysis For Hi-C with intact cells: the 5 million cross-linked cells were lysed by adding 1 mL cold lysis buffer [10 mM Tris-HCl (pH=8.0), 10 mM NaCl, 0.2% Igepal CA-630 (NP40)] and 10 µL of 100X Protease inhibitors. The sample was incubated on ice for 15 min to let the cells swell. The cells were lysed on ice using a dounce homogenizer with pestle A by moving the pest
Hi-C 2.0: We prepare the library for sequencing as described in Hi-C 2.17

treatment_protocol: No treatment

value: HindIII


title: siha cell SLUG OE

type: RNA

city: GUANGZHOU

first: Senwei

last: Jiang

state: GUANGDONG

address: 651 dongfengdong road

country: China

institute: Sun Yat-sen University Cancer Center

description: Gene expression of SLUG overexpressing SiHa cells

hyb_protocol: Each slide was hybridized with 600 ng Cy3-labeled cRNA using Gene Expression Hybridization Kit (Cat.# 5188-5242, Agilent technologies, Santa Clara, CA, US) in Hybridization Oven (Cat.# G2545A, Agilent technologies, Santa Clara, CA, US), according to the manufacturer’s instructions. After 17 hours hybridization, slides were washed in staining dishes (Cat.# 121, Thermo Shandon, Waltham, MA, US) with Gene Expression Wash Buffer Kit(Cat.# 5188-5327, Agilent technologies, Santa Clara, CA, US), followed the manufacturer’s instructions。

scan_protocol: Slides were scanned by Agilent Microarray Scanner (Cat#G2565CA, Agilent technologies, Santa Clara, CA, US) with default settings, Dye channel: Green, Scan resolution=3μm, PMT 100%, 20bit.

data_processing:
Data were extracted with Feature Extraction software 10.7 (Agilent technologies, Santa Clara, CA, US).
Raw data were normalized by Quantile algorithm, limma packages in R.

source_name: siha cell SLUG overexpressing

label_protocol: Total RNA was amplified and labeled by Low Input Quick Amp Labeling Kit, One-Color (Cat.# 5190-2305, Agilent technologies, Santa Clara, CA, US), following the manufacturer’s instructions. Labeled cRNA were purified by RNeasy mini kit (Cat.# 74106, QIAGEN, GmBH, Germany).

growth_protocol: Cells were grown in a DMEM  medium (Gibco BRL, San Francisco, CA, USA), supplemented with a 10% fetal bovine serum (Gibco BRL, San Francisco, CA, USA).

extract_protocol: Total RNA was checked for a RIN number to inspect RNA integrity by an Agilent Bioanalyzer 2100 (Agilent technologies, Santa Clara, CA, US). Qualified total RNA was further purified by RNeasy micro kit (Cat#74004, QIAGEN, GmBH, Germany) and RNase-Free DNase Set (Cat#79254, QIAGEN, GmBH, Germany).

treatment_protocol: Using SLUG overexpressing/control plasmids and Lentiviral Transfection System to  construct stable transduced cells.

value: Siha

value: cervical cancer cell line

value: SLUG overexpressing


title: siha cell NC

description: Gene expression of control SiHa cells

source_name: siha cell nagetive control

value: control


title: PC_5_RNA_TA2


title: HC_H001_RNA_control

value: Healthy

value: f


title: DpnII-Seq-K562-4h-R1

treatment_protocol: Nuclei were purified as described in method, then the nuclei pellet was washed twice with 1XNEB3.1. For this protocol we used 10 million of nuclei, each sample of two million nuclei was resuspended in 500 µL of 1X NEB3.1 on ice. Next, 120 U of DpnII was added to the sample in order to obtain 10 U DpnII/µg DNA, and samples were incubated at 37°C on a thermocycler for 4 h. Afterward, a final volume of 10 mM of EDTA was added to inactivate the endonuclease, a 20 µl aliquot is taken for assessment of fragmentation level, and the remaining sample were immediately processed as described in method section of DpnII-seq protocol


title: HiC-K562-Nuclei-R1

extract_protocol:
Hi-C was performed as described (Hi-C 2.0 Belaghzal et al., 2017) with some modifications in the crosslinking and lysis steps as described below. Crosslinking: isolated, undigested, and  pre-digested (with liquified chromatin) nuclei were not pelleted after the pre-digestion step above but were crosslinked immediately as follows: for each sample 1,250 µL volume of nuclei in the digestion buffer was transferred to a 21.875 mL mix [625 μL of 37% formaldehyde + 21.25 mL of HBSS]. Samples were incubated at RT for 10 min on a rocking platform. Next, to stop cross-linking 1.25 mL of 2.5 M glycine was added to each sample and the mix was incubated at RT for 5 min on a rocking platform. To pellet the crosslinked nuclei, the sample was centrifuged at 1,000 g for 10 min at 4°C. The supernatant was discarded and the pellet was washed twice with HBSS before going to the next step or storing samples at -80°C. Cells lysis: This step is not needed for isolated, undigested, and pre-digested (with liquified chromatin) nuclei
Hi-C 2.0: We prepare the library for sequencing as described in Hi-C 2.17

treatment_protocol: Nuclei were purified as described in Methods


title: HC_H012_RNA_control


title: PC_5_RNA_TA


title: PC_4_RNA_TB


title: HiC-K562-HindIII-predigest-4h-R1

extract_protocol:
Hi-C was performed as described (Hi-C 2.0 Belaghzal et al., 2017) with some modifications in the crosslinking and lysis steps as described below. Crosslinking: isolated, undigested, and  pre-digested (with liquified chromatin) nuclei were not pelleted after the pre-digestion step above but were crosslinked immediately as follows: for each sample 1,250 µL volume of nuclei in the digestion buffer was transferred to a 21.875 mL mix [625 μL of 37% formaldehyde + 21.25 mL of HBSS]. Samples were incubated at RT for 10 min on a rocking platform. Next, to stop cross-linking 1.25 mL of 2.5 M glycine was added to each sample and the mix was incubated at RT for 5 min on a rocking platform. To pellet the crosslinked nuclei, the sample was centrifuged at 1,000 g for 10 min at 4°C. The supernatant was discarded and the pellet was washed twice with HBSS before going to the next step or storing samples at -80°C. Cells lysis: This step is not needed for isolated, undigested, and pre-digested (with liquified chromatin) nuclei
Hi-C 2.0: We prepare the library for sequencing as described in Hi-C 2.16

treatment_protocol: Nuclei were purified as described in Methods. Then the nuclei pellet was washed twice with 1XNEB2.1. Each sample of two million nuclei was resuspended in 500 µL of 1X NEB2.1 on ice. Next, 600 U of HindIII was added to the sample in order to obtain 50 U HindIII/µg of DNA, and samples were incubated at 37°C on a thermocycler for 4 h. Afterward, samples were placed on ice for 10 min and then we proceeded to the Hi-C protocol immediately

value: Liquid Chromatin Hi-C


title: HC_H005_RNA_control


title: DpnII-Seq-K562-16h-R1

treatment_protocol: Nuclei were purified as described in method, then the nuclei pellet was washed twice with 1XNEB3.1. For this protocol we used 10 million of nuclei, each sample of two million nuclei was resuspended in 500 µL of 1X NEB3.1 on ice. Next, 120 U of DpnII was added to the sample in order to obtain 10 U DpnII/µg DNA, and samples were incubated at 37°C on a thermocycler for 16 h. Afterward, a final volume of 10 mM of EDTA was added to inactivate the endonuclease, a 20 µl aliquot is taken for assessment of fragmentation level, and the remaining sample were immediately processed as described in method section of DpnII-seq protocol


title: PC_2_RNA_TA2

value: No Remission


title: HiC-K562-DpnII-predigest-5min-R1

description:
HBHiCK562DN10-5mDpR1
processed data file: half-life_R1.bedGraph; half-life_residuals_R1.bedGraph

extract_protocol:
Hi-C was performed as described (Hi-C 2.0 Belaghzal et al., 2017) with some modifications in the crosslinking and lysis steps as described below. Crosslinking: isolated, undigested, and  pre-digested (with liquified chromatin) nuclei were not pelleted after the pre-digestion step above but were crosslinked immediately as follows: for each sample 1,250 µL volume of nuclei in the digestion buffer was transferred to a 21.875 mL mix [625 μL of 37% formaldehyde + 21.25 mL of HBSS]. Samples were incubated at RT for 10 min on a rocking platform. Next, to stop cross-linking 1.25 mL of 2.5 M glycine was added to each sample and the mix was incubated at RT for 5 min on a rocking platform. To pellet the crosslinked nuclei, the sample was centrifuged at 1,000 g for 10 min at 4°C. The supernatant was discarded and the pellet was washed twice with HBSS before going to the next step or storing samples at -80°C. Cells lysis: This step is not needed for isolated, undigested, and pre-digested (with liquified chromatin) nuclei
Hi-C 2.0: We prepare the library for sequencing as described in Hi-C 2.14

treatment_protocol: Nuclei were purified as described in Methods. Then the nuclei pellet was washed twice with 1XNEB3.1. Each sample of two million nuclei was resuspended in 500 µL of 1X NEB3.1 on ice. Next, 120 U of DpnII was added to the sample in order to obtain 10 U DpnII/µg DNA, and samples were incubated at 37°C on a thermocycler for 5 min. Afterward, samples were placed on ice for 10 min and then we proceeded to the Hi-C protocol immediately


title: PC_3_RNA_TA


title: PC_5_RNA_TB2

value: m


title: PC_4_RNA_TA

value: Remission


title: PC_4_RNA_TA2


title: HiC-K562-DpnII-predigest-16h-R1

description:
HBHiCK562DN10-ONDpR1
processed data file: half-life_R1.bedGraph; half-life_residuals_R1.bedGraph

extract_protocol:
Hi-C was performed as described (Hi-C 2.0 Belaghzal et al., 2017) with some modifications in the crosslinking and lysis steps as described below. Crosslinking: isolated, undigested, and  pre-digested (with liquified chromatin) nuclei were not pelleted after the pre-digestion step above but were crosslinked immediately as follows: for each sample 1,250 µL volume of nuclei in the digestion buffer was transferred to a 21.875 mL mix [625 μL of 37% formaldehyde + 21.25 mL of HBSS]. Samples were incubated at RT for 10 min on a rocking platform. Next, to stop cross-linking 1.25 mL of 2.5 M glycine was added to each sample and the mix was incubated at RT for 5 min on a rocking platform. To pellet the crosslinked nuclei, the sample was centrifuged at 1,000 g for 10 min at 4°C. The supernatant was discarded and the pellet was washed twice with HBSS before going to the next step or storing samples at -80°C. Cells lysis: This step is not needed for isolated, undigested, and pre-digested (with liquified chromatin) nuclei
Hi-C 2.0: We prepare the library for sequencing as described in Hi-C 2.9

treatment_protocol: Nuclei were purified as described in Methods. Then the nuclei pellet was washed twice with 1XNEB3.1. Each sample of two million nuclei was resuspended in 500 µL of 1X NEB3.1 on ice. Next, 120 U of DpnII was added to the sample in order to obtain 10 U DpnII/µg DNA, and samples were incubated at 37°C on a thermocycler for 16 h . Afterward, samples were placed on ice for 10 min and then we proceeded to the Hi-C protocol immediately


title: DpnII-Seq-K562-30min-R1

treatment_protocol: Nuclei were purified as described in method, then the nuclei pellet was washed twice with 1XNEB3.1. For this protocol we used 10 million of nuclei, each sample of two million nuclei was resuspended in 500 µL of 1X NEB3.1 on ice. Next, 120 U of DpnII was added to the sample in order to obtain 10 U DpnII/µg DNA, and samples were incubated at 37°C on a thermocycler for 30 min. Afterward, a final volume of 10 mM of EDTA was added to inactivate the endonuclease, a 20 µl aliquot is taken for assessment of fragmentation level, and the remaining sample were immediately processed as described in method section of DpnII-seq protocol


title: PC_2_RNA_TC


title: PC_1_RNA_TC


title: c1954_TCR: patient with neurological manifestations of COVID-19 (Neuro-COVID), patient#COV1954

description: single-cell TCR seq data of a patient with neurological manifestations of COVID-19 (Neuro-COVID), patient#COV1954

data_processing:
Library strategy: TCR-seq
Raw bcl files were de-multiplexed using the cellranger mkfastq pipeline (cellranger v3.1.0)
Subsequent reads alignments and transcript counting was done individually for each sample using the cellranger count pipeline with standard parameters
 The cellranger aggr pipeline was employed to aggregate samples with mapping normalization to leave each sample with similar sequencing depth per cell.
Genome_build: GRCh38
Supplementary_files_format_and_content: Standard cellranger output format

value: CSF-derived leukocytes

value: Neuro-COVID

value: TCR


title: c1950_TCR: patient with neurological manifestations of COVID-19 (Neuro-COVID), patient#COV1950

description: single-cell TCR seq data of a patient with neurological manifestations of COVID-19 (Neuro-COVID), patient#COV1950


title: PC_1_RNA_TB2


title: PC_1_RNA_TB


title: PC_1_RNA_TA2


title: DpnII-Seq-K562-75min-R1

treatment_protocol: Nuclei were purified as described in method, then the nuclei pellet was washed twice with 1XNEB3.1. For this protocol we used 10 million of nuclei, each sample of two million nuclei was resuspended in 500 µL of 1X NEB3.1 on ice. Next, 120 U of DpnII was added to the sample in order to obtain 10 U DpnII/µg DNA, and samples were incubated at 37°C on a thermocycler for 75 min. Afterward, a final volume of 10 mM of EDTA was added to inactivate the endonuclease, a 20 µl aliquot is taken for assessment of fragmentation level, and the remaining sample were immediately processed as described in method section of DpnII-seq protocol

value: The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises.

value: DpnII-Seq


title: PC_1_RNA_TA


title: c1943_TCR: patient with neurological manifestations of COVID-19 (Neuro-COVID), patient#COV1943

description: single-cell TCR seq data of a patient with neurological manifestations of COVID-19 (Neuro-COVID), patient#COV1943


title: c1930_TCR: patient with neurological manifestations of COVID-19 (Neuro-COVID), patient#COV1930

description: single-cell TCR seq data of a patient with neurological manifestations of COVID-19 (Neuro-COVID), patient#COV1930


title: PC_13_RNA_TA


title: DpnII-Seq-K562-90min-R1

treatment_protocol: Nuclei were purified as described in method, then the nuclei pellet was washed twice with 1XNEB3.1. For this protocol we used 10 million of nuclei, each sample of two million nuclei was resuspended in 500 µL of 1X NEB3.1 on ice. Next, 120 U of DpnII was added to the sample in order to obtain 10 U DpnII/µg DNA, and samples were incubated at 37°C on a thermocycler for 90min. Afterward, a final volume of 10 mM of EDTA was added to inactivate the endonuclease, a 20 µl aliquot is taken for assessment of fragmentation level, and the remaining sample were immediately processed as described in method section of DpnII-seq protocol

value: DpnII


title: PC_13_RNA_TB


title: HiC-K562-MockNuclei-4h-R1

description:
HBHiC-K562-MN-Dp-2
processed data file: half-life_R1.bedGraph; half-life_residuals_R1.bedGraph

extract_protocol:
Hi-C was performed as described (Hi-C 2.0 Belaghzal et al., 2017) with some modifications in the crosslinking and lysis steps as described below. Crosslinking: isolated, undigested, and  pre-digested (with liquified chromatin) nuclei were not pelleted after the pre-digestion step above but were crosslinked immediately as follows: for each sample 1,250 µL volume of nuclei in the digestion buffer was transferred to a 21.875 mL mix [625 μL of 37% formaldehyde + 21.25 mL of HBSS]. Samples were incubated at RT for 10 min on a rocking platform. Next, to stop cross-linking 1.25 mL of 2.5 M glycine was added to each sample and the mix was incubated at RT for 5 min on a rocking platform. To pellet the crosslinked nuclei, the sample was centrifuged at 1,000 g for 10 min at 4°C. The supernatant was discarded and the pellet was washed twice with HBSS before going to the next step or storing samples at -80°C. Cells lysis: This step is not needed for isolated, undigested, and pre-digested (with liquified chromatin) nuclei
Hi-C 2.0: We prepare the library for sequencing as described in Hi-C 2.15

treatment_protocol: Nuclei were purified as described in Methods. Then the nuclei pellet was washed twice with 1XNEB3.1. Mock nuclei sample of two million nuclei was resuspended in 500 µL of 1X NEB3.1 on ice, and samples were incubated at 37°C on a thermocycler for 4 h. Afterward, samples were placed on ice for 10 min and proceed to the Hi-C protocol immediately


title: c1924_TCR: patient with neurological manifestations of COVID-19 (Neuro-COVID), patient#COV1924

description: single-cell TCR seq data of a patient with neurological manifestations of COVID-19 (Neuro-COVID), patient#COV1924


title: PC_12_RNA_TC


title: HiC-K562-DpnII-predigest-2h-R1

description:
HBHiCK562DN10-2hDpR1
processed data file: half-life_R1.bedGraph; half-life_residuals_R1.bedGraph

extract_protocol:
Hi-C was performed as described (Hi-C 2.0 Belaghzal et al., 2017) with some modifications in the crosslinking and lysis steps as described below. Crosslinking: isolated, undigested, and  pre-digested (with liquified chromatin) nuclei were not pelleted after the pre-digestion step above but were crosslinked immediately as follows: for each sample 1,250 µL volume of nuclei in the digestion buffer was transferred to a 21.875 mL mix [625 μL of 37% formaldehyde + 21.25 mL of HBSS]. Samples were incubated at RT for 10 min on a rocking platform. Next, to stop cross-linking 1.25 mL of 2.5 M glycine was added to each sample and the mix was incubated at RT for 5 min on a rocking platform. To pellet the crosslinked nuclei, the sample was centrifuged at 1,000 g for 10 min at 4°C. The supernatant was discarded and the pellet was washed twice with HBSS before going to the next step or storing samples at -80°C. Cells lysis: This step is not needed for isolated, undigested, and pre-digested (with liquified chromatin) nuclei
Hi-C 2.0: We prepare the library for sequencing as described in Hi-C 2.12

treatment_protocol: Nuclei were purified as described in Methods. Then the nuclei pellet was washed twice with 1XNEB3.1. Each sample of two million nuclei was resuspended in 500 µL of 1X NEB3.1 on ice. Next, 120 U of DpnII was added to the sample in order to obtain 10 U DpnII/µg DNA, and samples were incubated at 37°C on a thermocycler for 2 h . Afterward, samples were placed on ice for 10 min and then we proceeded to the Hi-C protocol immediately


title: PC_12_RNA_TD


title: c1919_TCR: patient with neurological manifestations of COVID-19 (Neuro-COVID), patient#COV1919

description: single-cell TCR seq data of a patient with neurological manifestations of COVID-19 (Neuro-COVID), patient#COV1919


title: c1923_TCR: patient with neurological manifestations of COVID-19 (Neuro-COVID), patient#COV1923

description: single-cell TCR seq data of a patient with neurological manifestations of COVID-19 (Neuro-COVID), patient#COV1923


title: PC_12_RNA_TB


title: PC_12_RNA_TA


title: VE66730: patient with viral encephalitis (VE), patient#VE66730

description: single-cell RNA seq data of a patient with viral encephalitis (VE), patient#VE66730

value: VE

value: RNA expression


title: PC_12_RNA_TE


title: HiC-K562-DpnII-predigest-3h-R1

description:
HBHiCK562DN10-3hDpR1
processed data file: half-life_R1.bedGraph; half-life_residuals_R1.bedGraph

extract_protocol:
Hi-C was performed as described (Hi-C 2.0 Belaghzal et al., 2017) with some modifications in the crosslinking and lysis steps as described below. Crosslinking: isolated, undigested, and  pre-digested (with liquified chromatin) nuclei were not pelleted after the pre-digestion step above but were crosslinked immediately as follows: for each sample 1,250 µL volume of nuclei in the digestion buffer was transferred to a 21.875 mL mix [625 μL of 37% formaldehyde + 21.25 mL of HBSS]. Samples were incubated at RT for 10 min on a rocking platform. Next, to stop cross-linking 1.25 mL of 2.5 M glycine was added to each sample and the mix was incubated at RT for 5 min on a rocking platform. To pellet the crosslinked nuclei, the sample was centrifuged at 1,000 g for 10 min at 4°C. The supernatant was discarded and the pellet was washed twice with HBSS before going to the next step or storing samples at -80°C. Cells lysis: This step is not needed for isolated, undigested, and pre-digested (with liquified chromatin) nuclei
Hi-C 2.0: We prepare the library for sequencing as described in Hi-C 2.11

treatment_protocol: Nuclei were purified as described in Methods. Then the nuclei pellet was washed twice with 1XNEB3.1. Each sample of two million nuclei was resuspended in 500 µL of 1X NEB3.1 on ice. Next, 120 U of DpnII was added to the sample in order to obtain 10 U DpnII/µg DNA, and samples were incubated at 37°C on a thermocycler for 3 h . Afterward, samples were placed on ice for 10 min and then we proceeded to the Hi-C protocol immediately


title: PC_14_RNA_TA


title: PC_11_RNA_TB


title: HiC-K562-DpnII-predigest-4h-R1

description:
HBHiCK562DN10-4hDpR1
processed data file: half-life_R1.bedGraph; half-life_residuals_R1.bedGraph

extract_protocol:
Hi-C was performed as described (Hi-C 2.0 Belaghzal et al., 2017) with some modifications in the crosslinking and lysis steps as described below. Crosslinking: isolated, undigested, and  pre-digested (with liquified chromatin) nuclei were not pelleted after the pre-digestion step above but were crosslinked immediately as follows: for each sample 1,250 µL volume of nuclei in the digestion buffer was transferred to a 21.875 mL mix [625 μL of 37% formaldehyde + 21.25 mL of HBSS]. Samples were incubated at RT for 10 min on a rocking platform. Next, to stop cross-linking 1.25 mL of 2.5 M glycine was added to each sample and the mix was incubated at RT for 5 min on a rocking platform. To pellet the crosslinked nuclei, the sample was centrifuged at 1,000 g for 10 min at 4°C. The supernatant was discarded and the pellet was washed twice with HBSS before going to the next step or storing samples at -80°C. Cells lysis: This step is not needed for isolated, undigested, and pre-digested (with liquified chromatin) nuclei
Hi-C 2.0: We prepare the library for sequencing as described in Hi-C 2.10

treatment_protocol: Nuclei were purified as described in Methods. Then the nuclei pellet was washed twice with 1XNEB3.1. Each sample of two million nuclei was resuspended in 500 µL of 1X NEB3.1 on ice. Next, 120 U of DpnII was added to the sample in order to obtain 10 U DpnII/µg DNA, and samples were incubated at 37°C on a thermocycler for 4 h . Afterward, samples were placed on ice for 10 min and then we proceeded to the Hi-C protocol immediately


title: PC_14_RNA_TA2


title: DpnII-Seq-K562-45min-R1

treatment_protocol: Nuclei were purified as described in method, then the nuclei pellet was washed twice with 1XNEB3.1. For this protocol we used 10 million of nuclei, each sample of two million nuclei was resuspended in 500 µL of 1X NEB3.1 on ice. Next, 120 U of DpnII was added to the sample in order to obtain 10 U DpnII/µg DNA, and samples were incubated at 37°C on a thermocycler for 45 min. Afterward, a final volume of 10 mM of EDTA was added to inactivate the endonuclease, a 20 µl aliquot is taken for assessment of fragmentation level, and the remaining sample were immediately processed as described in method section of DpnII-seq protocol


title: VE57538: patient with viral encephalitis (VE), patient#VE57538

description: single-cell RNA seq data of a patient with viral encephalitis (VE), patient#VE57538


title: PC_11_RNA_TA


title: VE23642: patient with viral encephalitis (VE), patient#VE23642

description: single-cell RNA seq data of a patient with viral encephalitis (VE), patient#VE23642


title: PC_11_RNA_TA2


title: PC_10_RNA_TC


title: PC_10_RNA_TB2


title: COV1954: patient with neurological manifestations of COVID-19 (Neuro-COVID), patient#COV1954

description: single-cell RNA seq data of a patient with neurological manifestations of COVID-19 (Neuro-COVID), patient#COV1954


title: HiC-K562-DpnII-predigest-5min-R2

description:
HBHiCK562DN10-5mDp2
processed data file: half-life_R2.bedGraph; half-life_residuals_R2.bedGraph

extract_protocol:
Hi-C was performed as described (Hi-C 2.0 Belaghzal et al., 2017) with some modifications in the crosslinking and lysis steps as described below. Crosslinking: isolated, undigested, and  pre-digested (with liquified chromatin) nuclei were not pelleted after the pre-digestion step above but were crosslinked immediately as follows: for each sample 1,250 µL volume of nuclei in the digestion buffer was transferred to a 21.875 mL mix [625 μL of 37% formaldehyde + 21.25 mL of HBSS]. Samples were incubated at RT for 10 min on a rocking platform. Next, to stop cross-linking 1.25 mL of 2.5 M glycine was added to each sample and the mix was incubated at RT for 5 min on a rocking platform. To pellet the crosslinked nuclei, the sample was centrifuged at 1,000 g for 10 min at 4°C. The supernatant was discarded and the pellet was washed twice with HBSS before going to the next step or storing samples at -80°C. Cells lysis: This step is not needed for isolated, undigested, and pre-digested (with liquified chromatin) nuclei
Hi-C 2.0: We prepare the library for sequencing as described in Hi-C 2.7


title: PC_010_RNA_TB


title: HiC-K562-DpnII-predigest-1h-R2

description:
HBHiCK562DN10-1hDp2
processed data file: half-life_R2.bedGraph; half-life_residuals_R2.bedGraph

extract_protocol:
Hi-C was performed as described (Hi-C 2.0 Belaghzal et al., 2017) with some modifications in the crosslinking and lysis steps as described below. Crosslinking: isolated, undigested, and  pre-digested (with liquified chromatin) nuclei were not pelleted after the pre-digestion step above but were crosslinked immediately as follows: for each sample 1,250 µL volume of nuclei in the digestion buffer was transferred to a 21.875 mL mix [625 μL of 37% formaldehyde + 21.25 mL of HBSS]. Samples were incubated at RT for 10 min on a rocking platform. Next, to stop cross-linking 1.25 mL of 2.5 M glycine was added to each sample and the mix was incubated at RT for 5 min on a rocking platform. To pellet the crosslinked nuclei, the sample was centrifuged at 1,000 g for 10 min at 4°C. The supernatant was discarded and the pellet was washed twice with HBSS before going to the next step or storing samples at -80°C. Cells lysis: This step is not needed for isolated, undigested, and pre-digested (with liquified chromatin) nuclei
Hi-C 2.0: We prepare the library for sequencing as described in Hi-C 2.6

treatment_protocol: Nuclei were purified as described in Methods. Then the nuclei pellet was washed twice with 1XNEB3.1. Each sample of two million nuclei was resuspended in 500 µL of 1X NEB3.1 on ice. Next, 120 U of DpnII was added to the sample in order to obtain 10 U DpnII/µg DNA, and samples were incubated at 37°C on a thermocycler for 1 h . Afterward, samples were placed on ice for 10 min and then we proceeded to the Hi-C protocol immediately


title: DpnII-Seq-K562-15min-R1

treatment_protocol: Nuclei were purified as described in method, then the nuclei pellet was washed twice with 1XNEB3.1. For this protocol we used 10 million of nuclei, each sample of two million nuclei was resuspended in 500 µL of 1X NEB3.1 on ice. Next, 120 U of DpnII was added to the sample in order to obtain 10 U DpnII/µg DNA, and samples were incubated at 37°C on a thermocycler for 15 min. Afterward, a final volume of 10 mM of EDTA was added to inactivate the endonuclease, a 20 µl aliquot is taken for assessment of fragmentation level, and the remaining sample were immediately processed as described in method section of DpnII-seq protocol


title: USDA110_GM_WT_3

city: Gif sur Yvette

first: Florian

last: Lamouche

address: 1, Avenue de la Terrasse

department: Institute of Integrative Biology of the Cell (I2BC)

country: France

institute: Centre national de la Recherche Scientifique (CNRS)

data_processing:
CLC Workbench 10 software (CLC bio, Aarhus, Denmark) was used for trimming, sizing, and mapping the reads on the reference genome of Bradyrhizobium diazoefficiens USDA110 strain. Only unique gene reads mapping on 80% of their length and displaying a 90% identity have been conserved.
Genome_build: NC_004463 (see reannotation tar archive on series record)
Supplementary_files_format_and_content: tab-delimited text files including the raw counts of sequencing reads for each sample. Each sheet contains Gene Name/Region/Gene length/Unique gene reads/Total gene reads columns.

organism: Bradyrhizobium diazoefficiens USDA 110

source_name: From G. max nodule tissues at 14 days post inoculation

growth_protocol: Bacterial culture was grown in YM rich medium. Bacteroid were obtained from nodulated plants. Aeschynomene spp. seeds were scarified and surface-sterilized using pure sulfuric acid and calcium hypochlorite, germinated in Khalys agar plates and transferred in transparent, light permissive test tubes filled with BNM medium (Erhardt et al., 1992).

extract_protocol:
Nodules were harvested at 14 days post inoculation (dpi), frozen in liquid N2 and kept at -80°C until RNA extraction. For transcriptomic analysis, total nodule RNA was extracted as previously described in Mergaert et al., 20036, and submitted to plant and bacterial rRNA and eukaryotic mRNA depletion using RiboZero kits for plants and for Gram-negative bacteria (Epicentre, Madison, USA). Total RNA of free-living cells were extracted from bacterial pellets obtained from cultures grown in YM medium at OD600= 0.5 using hot phenol and hot SDS method according to Chapelle et al. (2015).
Oriented libraries of bacterial mRNA were produced using the SOLiD total RNA-seq kit and sequenced on a SOLiD 5500XL (50bp per read).

treatment_protocol: Five days after transfer, plants were inoculated with 2mL of bacterial suspension at OD600=0.1, according to Guefrachi et al., 2015. Mock inoculations were performed when necessary using 2 mL sterile BNM medium. Plants were grown at 28°C, 80% humidity and under a 16/8 hour of light/dark photoperiod.

tag: condition

value: G. max Undifferentiated bacteroids (no phenotype of differentiation)

value: WT strain


title: COV1950: patient with neurological manifestations of COVID-19 (Neuro-COVID), patient#COV1950

description: single-cell RNA seq data of a patient with neurological manifestations of COVID-19 (Neuro-COVID), patient#COV1950


title: USDA110_GM_WT_2


title: USDA110_GM_WT_1


title: PC_10_RNA_TA2

extract_protocol:
RNA sequencing libraries were prepared according to the Illumina TruSeq® messenger (mRNA) sequencing protocol (TruSeq® RNA Seq Library Prep Kit v2). The resulting libraries were sequenced on the NovaSeq 6000 (2× 50 bp, S2 chemistry).
Patient peripheral blood was collected in 2.5mL tubes PAXgene Blood RNA Tubes, RNA was automated isolated in QIAGEN’s QIAcube using the PAXgene Blood miRNA Kit from QIAGEN PreAnalytiX.

tag: remission


title: COV1943: patient with neurological manifestations of COVID-19 (Neuro-COVID), patient#COV1943

description: single-cell RNA seq data of a patient with neurological manifestations of COVID-19 (Neuro-COVID), patient#COV1943

extract_protocol:
CSF samples were collected into round bottom polypropylene tubes and then centrifuged for 10 min at 300 x g. The CSF supernatant was removed and CSF cells were resuspended in 5 ml of X-Vivo15 media (Lonza) and stored at 4°C. The samples were then transported to the laboratory of the Department of Neurology with Institute of Translational Neurology at the University Clinic Münster, Germany for scRNA-seq. Transport time of samples collected in Münster was 10-30 minutes. Transport time of samples collected in Essen was < 60 minutes. Cell suspensions were then centrifuged again for 5 min at 400 x g and then resuspended in 40 μl of media. Out of this volume, 6 μl were used for cell counting and the remaining volume was entirely used for scRNA-seq.
Four Neuro-COVID samples were processed with the Chromium Single Cell 5’ Library & Gel Bead Kit and barcoded, full-length VDJ segments from T cells were enriched from first-strand cDNA via PCR amplification with the Chromium Single Cell VDJ Enrichment Kit, Human T Cell (from 10X Genomics) following the manufacturer’s instructions. Further library preparation was performed using the Chromium Single Cell 5' Library Construction Kit (10X Genomics). Three Neuro-COVID samples were processed with the Chromium Single Cell 3’ Library & Gel Bead Kit and we developed a novel method to sequence antigen receptor information  from 3’ scRNA-seq libraries. The method allows removing the constant region of antigen receptors during enrichment, while maintaining their cell barcode and unique molecular identifier (UMI) information attached to the 3' of the cDNA molecules. In summary, the method involves self-circulating the cDNA library, enriching the VDJ region and re-linearizing. Each step maintains the VDJ region together with the cell barcode and UMI in the same molecule. Sample processing and library preparation was performed according to manufacturer instructions using AMPure XP beads (Beckman Coulter). Sequencing was either carried out on a local Illumina Nextseq 500 using the High-Out 75 cycle kit with a 26-8-0-57 read setup or commercially (Microanaly, China) on a NovaSeq 6000 using the 300 cycle kit with paired end 150 read setup. All the samples were sequenced with a sequencing depth >50,000 reads per cell.


title: HiC-K562-DpnII-predigest-3h-R2

description:
HBHiCK562DN10-3hDp2
processed data file: half-life_R2.bedGraph; half-life_residuals_R2.bedGraph

extract_protocol:
Hi-C was performed as described (Hi-C 2.0 Belaghzal et al., 2017) with some modifications in the crosslinking and lysis steps as described below. Crosslinking: isolated, undigested, and  pre-digested (with liquified chromatin) nuclei were not pelleted after the pre-digestion step above but were crosslinked immediately as follows: for each sample 1,250 µL volume of nuclei in the digestion buffer was transferred to a 21.875 mL mix [625 μL of 37% formaldehyde + 21.25 mL of HBSS]. Samples were incubated at RT for 10 min on a rocking platform. Next, to stop cross-linking 1.25 mL of 2.5 M glycine was added to each sample and the mix was incubated at RT for 5 min on a rocking platform. To pellet the crosslinked nuclei, the sample was centrifuged at 1,000 g for 10 min at 4°C. The supernatant was discarded and the pellet was washed twice with HBSS before going to the next step or storing samples at -80°C. Cells lysis: This step is not needed for isolated, undigested, and pre-digested (with liquified chromatin) nuclei
Hi-C 2.0: We prepare the library for sequencing as described in Hi-C 2.4


title: USDA110_AA_WT_3

source_name: From A. afraspera nodule tissues at 14 days post inoculation

value: A. afraspera Elongated bacteroids  (no phenotype of differentiation)


title: COV1930: patient with neurological manifestations of COVID-19 (Neuro-COVID), patient#COV1930

description: single-cell RNA seq data of a patient with neurological manifestations of COVID-19 (Neuro-COVID), patient#COV1930


title: HiC-K562-DpnII-predigest-4h-R2

description:
HBHiCK562DN10-4hDp2
processed data file: half-life_R2.bedGraph; half-life_residuals_R2.bedGraph

extract_protocol:
Hi-C was performed as described (Hi-C 2.0 Belaghzal et al., 2017) with some modifications in the crosslinking and lysis steps as described below. Crosslinking: isolated, undigested, and  pre-digested (with liquified chromatin) nuclei were not pelleted after the pre-digestion step above but were crosslinked immediately as follows: for each sample 1,250 µL volume of nuclei in the digestion buffer was transferred to a 21.875 mL mix [625 μL of 37% formaldehyde + 21.25 mL of HBSS]. Samples were incubated at RT for 10 min on a rocking platform. Next, to stop cross-linking 1.25 mL of 2.5 M glycine was added to each sample and the mix was incubated at RT for 5 min on a rocking platform. To pellet the crosslinked nuclei, the sample was centrifuged at 1,000 g for 10 min at 4°C. The supernatant was discarded and the pellet was washed twice with HBSS before going to the next step or storing samples at -80°C. Cells lysis: This step is not needed for isolated, undigested, and pre-digested (with liquified chromatin) nuclei
Hi-C 2.0: We prepare the library for sequencing as described in Hi-C 2.3


title: USDA110_AA_WT_2


title: COV1924: patient with neurological manifestations of COVID-19 (Neuro-COVID), patient#COV1924

description: single-cell RNA seq data of a patient with neurological manifestations of COVID-19 (Neuro-COVID), patient#COV1924


title: PC_9_RNA_TB

tag: gender


title: PC_10_RNA_TA

tag: age


title: HiC-K562-MockNuclei-4h-R2

description:
HBHiCK562MN-4hDp3
processed data file: half-life_R2.bedGraph; half-life_residuals_R2.bedGraph

extract_protocol:
Hi-C was performed as described (Hi-C 2.0 Belaghzal et al., 2017) with some modifications in the crosslinking and lysis steps as described below. Crosslinking: isolated, undigested, and  pre-digested (with liquified chromatin) nuclei were not pelleted after the pre-digestion step above but were crosslinked immediately as follows: for each sample 1,250 µL volume of nuclei in the digestion buffer was transferred to a 21.875 mL mix [625 μL of 37% formaldehyde + 21.25 mL of HBSS]. Samples were incubated at RT for 10 min on a rocking platform. Next, to stop cross-linking 1.25 mL of 2.5 M glycine was added to each sample and the mix was incubated at RT for 5 min on a rocking platform. To pellet the crosslinked nuclei, the sample was centrifuged at 1,000 g for 10 min at 4°C. The supernatant was discarded and the pellet was washed twice with HBSS before going to the next step or storing samples at -80°C. Cells lysis: This step is not needed for isolated, undigested, and pre-digested (with liquified chromatin) nuclei
Hi-C 2.0: We prepare the library for sequencing as described in Hi-C 2.8


title: PC_9_RNA_TA2

tag: pseudotime


title: COV1923: patient with neurological manifestations of COVID-19 (Neuro-COVID), patient#COV1923

description: single-cell RNA seq data of a patient with neurological manifestations of COVID-19 (Neuro-COVID), patient#COV1923


title: USDA110_AA_WT_1

value: A. afraspera Elongated bacteroids (no phenotype of differentiation)


title: PC_9_RNA_TA

tag: patient number


title: HiC-K562-HindIII-predigest-4h-R2

extract_protocol:
Hi-C was performed as described (Hi-C 2.0 Belaghzal et al., 2017) with some modifications in the crosslinking and lysis steps as described below. Crosslinking: isolated, undigested, and  pre-digested (with liquified chromatin) nuclei were not pelleted after the pre-digestion step above but were crosslinked immediately as follows: for each sample 1,250 µL volume of nuclei in the digestion buffer was transferred to a 21.875 mL mix [625 μL of 37% formaldehyde + 21.25 mL of HBSS]. Samples were incubated at RT for 10 min on a rocking platform. Next, to stop cross-linking 1.25 mL of 2.5 M glycine was added to each sample and the mix was incubated at RT for 5 min on a rocking platform. To pellet the crosslinked nuclei, the sample was centrifuged at 1,000 g for 10 min at 4°C. The supernatant was discarded and the pellet was washed twice with HBSS before going to the next step or storing samples at -80°C. Cells lysis: This step is not needed for isolated, undigested, and pre-digested (with liquified chromatin) nuclei
Hi-C 2.0: We prepare the library for sequencing as described in Hi-C 2.1


title: USDA110_YM_WT_3

source_name: Culture in rich medium

value: YM culture


title: COV1919: patient with neurological manifestations of COVID-19 (Neuro-COVID), patient#COV1919

description: single-cell RNA seq data of a patient with neurological manifestations of COVID-19 (Neuro-COVID), patient#COV1919

tag: tissue


title: PC_8_RNA_TA

value: f


title: USDA110_YM_WT_2


title: HiC-K562-DpnII-predigest-2h-R2

description:
HBHiCK562DN10-2hDp2
processed data file: half-life_R2.bedGraph; half-life_residuals_R2.bedGraph

extract_protocol:
Hi-C was performed as described (Hi-C 2.0 Belaghzal et al., 2017) with some modifications in the crosslinking and lysis steps as described below. Crosslinking: isolated, undigested, and  pre-digested (with liquified chromatin) nuclei were not pelleted after the pre-digestion step above but were crosslinked immediately as follows: for each sample 1,250 µL volume of nuclei in the digestion buffer was transferred to a 21.875 mL mix [625 μL of 37% formaldehyde + 21.25 mL of HBSS]. Samples were incubated at RT for 10 min on a rocking platform. Next, to stop cross-linking 1.25 mL of 2.5 M glycine was added to each sample and the mix was incubated at RT for 5 min on a rocking platform. To pellet the crosslinked nuclei, the sample was centrifuged at 1,000 g for 10 min at 4°C. The supernatant was discarded and the pellet was washed twice with HBSS before going to the next step or storing samples at -80°C. Cells lysis: This step is not needed for isolated, undigested, and pre-digested (with liquified chromatin) nuclei
Hi-C 2.0: We prepare the library for sequencing as described in Hi-C 2.5

value: Liquid Chromatin Hi-C


title: LGC3

city: Baltimore

first: Michelle Grace

last: Acoba

state: MD

address: 725 N Wolfe St

department: Physiology

institute: Johns Hopkins University

description:
Psd1 autocatalytic site LGS was substituted for three alanines (LGS/AAA), which completely prevented autocatalysis and fail to rescue the ethanolamine auxotrophy of the psd1Δpsd2Δ strain.
LGCvsLGD_DEG.txt

data_processing:
Built indexes using STAR and aligned paired-end clean reads to the reference genome using STAR (v2.5)
HTSeq v0.6.1 was used to count the read numbers mapped of each gene
FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene
Differential expression analysis was performed using the DESeq2 R package (2_1.6.3)
P-values were adjusted using the Benjamini and Hochberg’s approach for controlling the False Discovery Rate (FDR).
Genome_build: release 98 reference genome
Supplementary_files_format_and_content: Original image data file from high-throughput sequencing is transformed into sequenced reads (called Raw Data or Raw Reads) by CASAVA base recognition (Base Calling).
Supplementary_files_format_and_content: Raw data are stored in FASTQ(fq) format files, which contain sequences of reads and corresponding base quality
Supplementary_files_format_and_content: *DEG.txt: read count, fpkm and DESeq2 statistics

organism: Saccharomyces cerevisiae

source_name: Yeast GA74-1A

growth_protocol: Yeast were grown in YPD (1% (w/v) yeast extract, 2% (w/v) tryptone, 2% (w/v) dextrose) shaking (220 rpms) to an OD600 between 0.5-0.7

extract_protocol:
RNA was extracted using the hot phenol extraction protocol.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Strains were treated with YPD (D), YPD containing 2 mM ethanolamine (E), YPD containing 2 mM choline (C), or YPD containing 1% (v/v) tergitol and 0.5 mM lyso-phosphatidylethanolamine (L).

value: mutant LGS/AAA

tag: treatment

value: Choline


title: USDA110_YM_WT_1


title: LGC2


title: Clone Ct-RNAseq Rep3

city: Montpellier

first: Amal

last: Makrini

address: 1919 route de mende

institute: IGMM

data_processing:
All samples were aligned to human genome (Hg38) using Tophat2
Genome_build: Hg38
Supplementary_files_format_and_content: Raw counts from featureCounts using the option ”reversely stranded” (-s 2)

source_name: Control HEK cells

extract_protocol:
Tri-Reagent extraction with 500 ul on a 3,6 cm plates, Ribosomic RNAs were depleted of total RNA after RQ1 digestion,
Kit TruSeq Stranded total RNA Sample Preparation kit d'Illumina,

value: HEK

value: wildtype


title: Clone Ct-RNAseq Rep1


title: Clone Ct-RNAseq Rep2

description: CtA


title: Clone D-RNAseq Rep3

source_name: NOPCHAP1 KO HEK cells

value: NOPCHAP1 KO


title: MS71658: patient with multiple sclerosis (MS), patient#MS71658

description: single-cell RNA seq data of a patient with multiple sclerosis (MS), patient#MS71658 (previously uploaded in GSE138266)

value: CSF-derived leukocytes

tag: diagnosis

value: MS

tag: type of library


title: Clone D-RNAseq Rep2


title: HiC-K562-DpnII-predigest-1h-R1

description:
HBHiCK562DN10-1hDpR1
processed data file: half-life_R1.bedGraph; half-life_residuals_R1.bedGraph

extract_protocol:
Hi-C was performed as described (Hi-C 2.0 Belaghzal et al., 2017) with some modifications in the crosslinking and lysis steps as described below. Crosslinking: isolated, undigested, and  pre-digested (with liquified chromatin) nuclei were not pelleted after the pre-digestion step above but were crosslinked immediately as follows: for each sample 1,250 µL volume of nuclei in the digestion buffer was transferred to a 21.875 mL mix [625 μL of 37% formaldehyde + 21.25 mL of HBSS]. Samples were incubated at RT for 10 min on a rocking platform. Next, to stop cross-linking 1.25 mL of 2.5 M glycine was added to each sample and the mix was incubated at RT for 5 min on a rocking platform. To pellet the crosslinked nuclei, the sample was centrifuged at 1,000 g for 10 min at 4°C. The supernatant was discarded and the pellet was washed twice with HBSS before going to the next step or storing samples at -80°C. Cells lysis: This step is not needed for isolated, undigested, and pre-digested (with liquified chromatin) nuclei
Hi-C 2.0: We prepare the library for sequencing as described in Hi-C 2.13

value: The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises.

value: DpnII


title: HiC-K562-DpnII-predigest-16h-R2

description:
HBHiCK562DN10-16hDp2
processed data file: half-life_R2.bedGraph; half-life_residuals_R2.bedGraph

extract_protocol:
Hi-C was performed as described (Hi-C 2.0 Belaghzal et al., 2017) with some modifications in the crosslinking and lysis steps as described below. Crosslinking: isolated, undigested, and  pre-digested (with liquified chromatin) nuclei were not pelleted after the pre-digestion step above but were crosslinked immediately as follows: for each sample 1,250 µL volume of nuclei in the digestion buffer was transferred to a 21.875 mL mix [625 μL of 37% formaldehyde + 21.25 mL of HBSS]. Samples were incubated at RT for 10 min on a rocking platform. Next, to stop cross-linking 1.25 mL of 2.5 M glycine was added to each sample and the mix was incubated at RT for 5 min on a rocking platform. To pellet the crosslinked nuclei, the sample was centrifuged at 1,000 g for 10 min at 4°C. The supernatant was discarded and the pellet was washed twice with HBSS before going to the next step or storing samples at -80°C. Cells lysis: This step is not needed for isolated, undigested, and pre-digested (with liquified chromatin) nuclei
Hi-C 2.0: We prepare the library for sequencing as described in Hi-C 2.2


title: LGE3

description:
Psd1 autocatalytic site LGS was substituted for three alanines (LGS/AAA), which completely prevented autocatalysis and fail to rescue the ethanolamine auxotrophy of the psd1Δpsd2Δ strain.
LGEvsLGD_DEG.txt

tag: strain

value: Ethanolamine


title: MS58637: patient with multiple sclerosis (MS), patient#MS58637

description: single-cell RNA seq data of a patient with multiple sclerosis (MS), patient#MS58637 (previously uploaded in GSE138266)

value: RNA expression

tag: subject id


title: LGE2


title: Clone D-RNAseq Rep1


title: LGE1


title: HiC-K562-MockNuclei-5min-R2

extract_protocol:
Hi-C was performed as described (Hi-C 2.0 Belaghzal et al., 2017) with some modifications in the crosslinking and lysis steps as described below. Crosslinking: isolated, undigested, and  pre-digested (with liquified chromatin) nuclei were not pelleted after the pre-digestion step above but were crosslinked immediately as follows: for each sample 1,250 µL volume of nuclei in the digestion buffer was transferred to a 21.875 mL mix [625 μL of 37% formaldehyde + 21.25 mL of HBSS]. Samples were incubated at RT for 10 min on a rocking platform. Next, to stop cross-linking 1.25 mL of 2.5 M glycine was added to each sample and the mix was incubated at RT for 5 min on a rocking platform. To pellet the crosslinked nuclei, the sample was centrifuged at 1,000 g for 10 min at 4°C. The supernatant was discarded and the pellet was washed twice with HBSS before going to the next step or storing samples at -80°C. Cells lysis: This step is not needed for isolated, undigested, and pre-digested (with liquified chromatin) nuclei
Hi-C 2.0: We prepare the library for sequencing as described in Hi-C 2.0

treatment_protocol: Nuclei were purified as described in Methods. Then the nuclei pellet was washed twice with 1XNEB3.1. Mock nuclei sample of two million nuclei was resuspended in 500 µL of 1X NEB3.1 on ice, and samples were incubated at 37°C on a thermocycler for 5 min. Afterward, samples were placed on ice for 10 min and proceed to the Hi-C protocol immediately

tag: cell type


title: 49_Endosperm_rep3

city: Beaucouze

first: Julia

last: Buitink

address: 42 rue Georges Morel

department: BAP

institute: INRAE

description:
49_End_3
AllSamples_GeneExpression_Count.txt

data_processing:
Clean reads were mapped to the reference genome tomato SL4.0 using SALMON to calculate gene expression level.
Genome_build: SL4.0
Supplementary_files_format_and_content: AllSamples_GeneExpression_Count.txt: Tab-delimited text file with count values for every gene and every sample.

organism: Solanum lycopersicum

source_name: 49 DAF endosperm

growth_protocol: Plants were grown under controlled greenhouse conditions in 10 L pots containing substrate (Irish peat, perlite, coconut fiber; 50/40/10; v/v/v), watered with a nutrient solution and supplemented with 16 h of 250 µmol m2 s-1 light. The day and night temperatures were maintained at > 23°C/20°C.

extract_protocol:
Total RNAs were extracted from the frozen grinded seed tissues using the NucleoSpin® RNA Plant and Fungi kit (Macherey-Nagel, Düren, Germany), according to the manufacturer instructions (protocol 5.1) without the incubation step at 56°C using the following recommended sample type: alfalfa for embryo, potato tuber for the endosperm and grape vine leaf for seed coat.
Samples were sent to BGI, Hong Kong, for library preparation. Libraries were constructed following a custom protocol from samples that passed quality controls (mass > 2µg, concentration>80ng/microl, OD260/280 ~= 2.00, OD260/230 ~= 2.20, RIN>6.5, 28S/18S<1.0, baseline smooth). After mRNA enrichment, RNA was fragmented and reverse transcribed to double-strand cDNA (dscDNA) by N6 random primer. The synthesized cDNA was subjected to end-repair and then was 3’ adenylated. Adaptors were ligated to the ends of these 3’ adenylated cDNA fragments. The ligation products were purified and many rounds of PCR amplification were performed to enrich the purified cDNA template using PCR primer, splint oligo and DNA ligase, followed by sequencing on BGISEQ-500 platform, generating an average 20M reads of 50bp per sample.

treatment_protocol: Seeds were manually extracted from the equatorial section of the fruit. The embryo, endosperm and seed coat were hand-dissected, immediately frozen in liquid nitrogen and stored at -80°C prior to RNA isolation.

tag: cultivar

value: Moneymaker

value: Endosperm

tag: age (daf)

tag: developmental stage

value: 49 DAF


title: LGL3

description:
Psd1 autocatalytic site LGS was substituted for three alanines (LGS/AAA), which completely prevented autocatalysis and fail to rescue the ethanolamine auxotrophy of the psd1Δpsd2Δ strain.
LGLvsLGD_DEG.txt

tag: genotype

value: LPE


title: MS19270: patient with multiple sclerosis (MS), patient#MS19270

description: single-cell RNA seq data of a patient with multiple sclerosis (MS), patient#MS19270 (previously uploaded in GSE138266)


title: 49_Endosperm_rep2

description:
49_End_2
AllSamples_GeneExpression_Count.txt


title: LGL2


title: LGC1


title: 49_Endosperm_rep1

description:
49_End_1
AllSamples_GeneExpression_Count.txt


title: 13_Do_d2

city: Münster

first: Kornelius

last: Kerl

address: Albert-Schweitzer-Campus 1

data_processing:
After explorative quality control with FastQC (v0.11.8) and MultiQC (v1.7), we used Salmon (v0.14.1) for pseudo-alignment and quantification of the samples to the human and mouse transcriptomes (downloaded from Ensembl, release 94). Default parameters were used.
Further analyses were performed in R. We employed the Bioconductor package tximport (v1.10.1) to summarize transcript-level estimates computed by Salmon for a gene-level analysis.
To find differentially expressed genes, we used the package DESeq2 (v1.22.2) and tested for co-culture effects. In order to control for possible batch effects, we included this variable in the formula definition of DESeq2 (i.e. ~batch + condition).
Genome_build: GRCm38, GRCh38
Supplementary_files_format_and_content: Supplementary file abundances.tar.gz contains three tab-separated text files (one for each different cell line: D341, MB1 and OLI) with transcript-level abundances for each sample, generated as in the preprocessing steps above.

source_name: cell line

growth_protocol: All cells were maintained at 37°C and 5% CO2 in DMEM/F-12 medium containing B-27 and N-2 supplements (Gibco, Thermo Fisher Scientific), 20 ng/mL of recombinant murine EGF and basic fibroblast growth factor (bFGF) (PeproTech Germany), and 1% penicillin/streptomycin (Gibco). For co-culture experiments 30 mm Millicell cell culture inserts with hydrophilic PTFE membranes (0.4 µm pore size) were used (Millipore, Merck).

extract_protocol:
Total RNA was isolated using RNeasy mini Kit (Qiagen) as specified by the manufacturer.
Sequencing libraries were generated with the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (New England Biolabs), following the manufacturer's guidelines.

value: Group 3 medulloblastoma cells

tag: culture

value: Co-culture


title: LGL1

value: mutant LGS/AAA


title: 13_Do_d1

treatment_protocol: For co-culture experiments 30 mm Millicell cell culture inserts with hydrophilic PTFE membranes (0.4 µm pore size) were used (Millipore, Merck).


title: 12_D_d2

value: monoculture


title: 42_Endosperm_rep2

description:
42_End_2
AllSamples_GeneExpression_Count.txt

source_name: 42 DAF endosperm

value: 42 DAF


title: MS49131: patient with multiple sclerosis (MS), patient#MS49131

description: single-cell RNA seq data of a patient with multiple sclerosis (MS), patient#MS49131 (previously uploaded in GSE138266)


title: A498_E. coli 83972_exp3

city: Lund

first: Ines

last: Ambite

address: Klinikgatan 28

department: Laboratory Medicine

country: Sweden

institute: Lund University

description: Gene expression data from 83972 infected A498 cells

hyb_protocol: 6ug of fragmented and labelled aRNA was hybridized onto Human Genome U219 array strips (Affymetrix) for 16 hours at 45 °C, washed, stained (Applied Biosystems, ThermoFisher Scientific).

scan_protocol: Scanning was done using the GeneAtlas system (Affymetrix).

data_processing: Transcriptomic data was normalized using Robust Multi Average implemented in the Transcriptome Analysis Console software (v.4.0.1.36, Applied Biosystems, ThermoFisher Scientific).

label: biotin

source_name: A498 kidney cells infected with E. coli 83972

label_protocol: 100 ng of total RNA was amplified, labeled and fragmented using the GeneChip 3´IVT PLUS Kit (ThermoFisher Scientific). Biotinylated cRNA was prepared according to the standard Affymetrix's protocol.

growth_protocol: E. coli strains were grown on tryptic soy agar (16 h, 37˚C). The human epithelial cell line A498 (ATCC HTB44, human kidney carcinoma) was cultured in RPMI-1640 supplemented with 1 mM sodium pyruvate, 1 mM non-essential amino acids and 10% fetal calf serum. Bacteria activation of the cells was studied on confluent cell layers in 6-well tissue culture plates (Nunc). A498 cells on confluent cell layers in 6-well tissue culture plates were treated. For bacterial supernatant, 10^8 CFU/ml of bacteria was grown in serum-free RPMI for 4 hours.

extract_protocol: Total RNA was extracted using the RNeasy Mini Kit (Qiagen) and on-column DNase digestion, according to the manufacturer's instructions.

treatment_protocol: Cell culture medium was aspirated and replaced with fresh serum-free RPMI. E. coli strains were diluted in PBS and added to the cells at a concentration of 10^8 CFU/ml for 4 hours. Alternatively, cells were treated with bacterial supernatant or treated with recombinant protein (50, 100 or 250 ug/ml) for 4 hours. The control sample was treated with a similar volume of PBS.

tag: cell line

tag: concentration

value: 10^8 CFU/ml


title: A498_NlpD100_3_exp2

description: Gene expression data from NlpD100 treated A498 cells

source_name: A498 kidney cells treated with NlpD 100ug/ml

value: NlpD

value: 100 ug/ml


title: LGD2

description:
Psd1 autocatalytic site LGS was substituted for three alanines (LGS/AAA), which completely prevented autocatalysis and fail to rescue the ethanolamine auxotrophy of the psd1Δpsd2Δ strain.
LGDvsWTD_DEG.txt

value: Untreated


title: A498_E. coli SN25-pRH_exp3

description: Gene expression data from SN25-pRH320 infected A498 cells

source_name: A498 kidney cells infected with E. coli SN25-pRH320

value: E. coli SN25-pRH320


title: A498_NlpD50_3_exp2

description: Gene expression data from NlpD50 treated A498 cells

source_name: A498 kidney cells treated with NlpD 50ug/ml

value: 50 ug/ml


title: LGD1


title: A498_E. coli SN25_exp3

description: Gene expression data from SN25 infected A498 cells

source_name: A498 kidney cells infected with E. coli SN25

value: E. coli SN25


title: A498_NlpD250_3_exp2

description: Gene expression data from NlpD250 treated A498 cells

source_name: A498 kidney cells treated with NlpD 250ug/ml

value: 250 ug/ml


title: A498_PBS_exp3

description: Gene expression data from control A498 cells

source_name: A498 kidney cells uninfected

value: PBS


title: 35_Endosperm_rep3

description:
35_End_3
AllSamples_GeneExpression_Count.txt

source_name: 35 DAF endosperm

value: Moneymaker

value: Endosperm

value: 35 DAF


title: A498_NlpD250_2_exp2


title: 35_Endosperm_rep2

description:
35_End_2
AllSamples_GeneExpression_Count.txt


title: WTC3

description:
Psd1 construct subcloned into pRS305 plasmid and has a3XFLAG tag and is functional
WTCvsWTD_DEG.txt

value: wild type

value: Choline


title: B-ALL tumoral clones, mRNA_library

city: Marseille

first: Delphine

last: Potier

address: 27 boulevard Lei Roure

institute: CRCM

data_processing:
Reads from the mRNA library were mapped to GRch38 transcripts and cells using CellRanger software (v3.0.1), giving mRNA_barcodes.tsv.gz, mRNA_features.tsv.gz and mRNA_matrix.mtx.gz files.
Reads from the HTO library were processed with CITE-seq-count (v1.4.3), giving HTO_barcodes.tsv.gz, HTO_features.tsv.gz and HTO_matrix.mtx.gz files
Data was loaded using R (v3.5.3) in a Seurat (v3.0.1) object for further processing
Filtering : Low-quality cells were excluded in an initial quality-control (QC) step, by removing genes expressed in fewer than three cells, cells with less than 200 genes expressed. Cells with more than 0.1% of mitochondrial-associated genes among their expressed genes were also removed.
Demultiplexing :  We used HTO demux to assign each cell to its sample of origin; doublet cells and negative cells were removed. Information on the sample of origin for each cell can be found in filtered_metadata_matrix.tsv file
Expression data were normalized using the Seurat R package NormalizeData function giving the filtered_normalized_expression_matrix.tsv, raw count for the same cells can be found in the filtered_raw_expression_matrix.tsv file.
Expression data were scaled and centred using the Seurat R package ScaleData function. PCA calculation was done using Seurat R package RunPCA function. Clusters were defined using Seurat R package FindNeighbors (using the 20 first PCA dimensions) and FindClusters (resolution =1). Information on the cluster for each cell can be found in filtered_metadata_matrix.tsv file
Genome_build: GRch38
Supplementary_files_format_and_content: tsv and mtx files

source_name: Bone marrow

extract_protocol:
10x Genomics Chromium Single-Cell 5’ protocol
Single-cell RNAseq

value: bone marrow from B-ALL patient

value: before and after anti-CD19 CAR therapy


title: WTC2


title: B-ALL tumoral clones, HTO_library

description: Anti-CD45 antibody tagged with hashtag oligonucleotide


title: 42_Endosperm_rep3

description:
42_End_3
AllSamples_GeneExpression_Count.txt

value: 42 DAF


title: 42_Endosperm_rep1

description:
42_End_1
AllSamples_GeneExpression_Count.txt


title: LGD3

value: mutant LGS/AAA


title: C42_shWHSC1

city: BUFFALO

first: Eduardo

last: Cortes

state: NY

address: ELM AND CARLTON STREETS

department: Biostatistics and Bioinformatics

institute: ROSWELL PARK CANCER INSTITUTE

data_processing:
Basecalls performed using CASAVA version 1.8.2
Reads aligned using bowtie2 (v2.2.9) using GRCh38 reference
Aligned reads are coordinate sorted using samtools (v1.9) and then duplicates are removed using Picard tools (v1.101)
Broad peaks detection using MACS2 using a q-value cut-off of 0.05
Peaks are annotated using ChIPseeker (v1.22.1)
Genome_build: GRCh38
Supplementary_files_format_and_content: broadPeaks format from MACS2 for each sample

growth_protocol: RPMI 10%FBS, P/S

extract_protocol: qiagen kit

treatment_protocol: shWHSC1, shCTR

value: prostate

tag: condition


title: A498_NlpD250_1_exp2

value: NlpD


title: 35_Endosperm_rep1

description:
35_End_1
AllSamples_GeneExpression_Count.txt


title: 12_D_d1

value: Group 3 medulloblastoma cells

value: monoculture


title: C42_CTR

value: CTR


title: A498_PBS_1_exp2


title: 49_Embryo_rep3

description:
49_Em_3
AllSamples_GeneExpression_Count.txt

source_name: 49 DAF embryo

value: Embryo

value: 49 DAF


title: WTC1


title: WTE3

description:
Psd1 construct subcloned into pRS305 plasmid and has a3XFLAG tag and is functional
WTEvsWTD_DEG.txt

value: Ethanolamine


title: A498_PBS_2_exp2

value: PBS


title: 49_Embryo_rep2

description:
49_Em_2
AllSamples_GeneExpression_Count.txt

value: Moneymaker


title: WTE2


title: A498_E. coli SN25_exp1

description: Gene expression data from SN25 supernatant treated A498 cells

source_name: A498 kidney cells treated with E. coli SN25 supernatant

value: E. coli SN25 supernatant

value: 10^8 CFU/ml


title: A498_PBS_3_exp2


title: C42_shNSD2_3

data_processing:
Basecalls performed using CASAVA version 1.8.2
Sequenced reads were mapped to GRCh38 reference NCBI annotation (p10) using STAR (v2.6.0a)
Raw reads quantified at the gene level obtained from STAR output
Sample raw read counts are summarized into a single matrix using tximport from R
Genome_build: GRCh38
Supplementary_files_format_and_content: Raw read counts in txt format

extract_protocol:
qiagen kit
KAPA mRNA HyperPrep Kit

tag: disease

value: prostate cancer

tag: shRNA


title: C42_shNSD2_2


title: 49_Embryo_rep1

description:
49_Em_1
AllSamples_GeneExpression_Count.txt

tag: tissue


title: C42_shNSD2_1


title: 42_Embryo_rep3

description:
42_Em_3
AllSamples_GeneExpression_Count.txt

source_name: 42 DAF embryo


title: C42_shCTR_4

value: shCTR


title: WTL3

description:
Psd1 construct subcloned into pRS305 plasmid and has a3XFLAG tag and is functional
WTLvsWTD_DEG.txt

source_name: Yeast GA74-1A

value: wild type

tag: treatment

value: LPE


title: 42_Embryo_rep2

description:
42_Em_2
AllSamples_GeneExpression_Count.txt

value: 42 DAF


title: A498_PBS_2_exp1


title: A498_E. coli 83972_exp1

description: Gene expression data from 83972 supernatant treated A498 cells

source_name: A498 kidney cells treated with E. coli 83972 supernatant

value: E. coli 83972 supernatant


title: Nonmemory NK cells_Rep2

description:
CD27-_N_2
Chromatin

data_processing:
Reads were aligned to mouse genome (mm10) using BWA.
Peak calling was performed using Homer.
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: *_ATAC_Normalized_counts.txt: Tab-delimited text files include TMM normalized data.

source_name: Spleen

growth_protocol: NK cells were harvested from mice spleen on day 37 post-infection.

extract_protocol:
Intact nuclei were isolated after cell lysis, and tagmentation was performed using tagment DNA enzyme I (Illumina) and DNA was purified using Qiagen MinElute Reaction Cleanup Kit.
Standard ATACseq protocol from 50000 cells.
Paired-end 150 bp reads, Illumina HiseqX.

treatment_protocol: Naive, CD27+ and CD27- NK cells were FACS sorted and proceeded for tagmentation immediately as per standard protocol.

value: CD27- NK cells

tag: infection

value: Zika virus


title: A498_PBS_1_exp1

description: Gene expression data from control A498 cells


title: WTL2


title: Nonmemory NK cells_Rep3

description:
CD27-_N_3
Chromatin


title: 42_Embryo_rep1

description:
42_Em_1
AllSamples_GeneExpression_Count.txt


title: 35_Embryo_rep3

description:
35_Em_3
AllSamples_GeneExpression_Count.txt

source_name: 35 DAF embryo

value: 35 DAF


title: WTD3

description:
Psd1 construct subcloned into pRS305 plasmid and has a3XFLAG tag and is functional
LGDvsWTD_DEG.txt

value: Untreated


title: WTL1


title: SCMNK cells_Rep3

description:
CD27+_M_3
Chromatin

value: CD27+ NK cells


title: C42_shCTR_1


title: SCMNK cells_Rep1

description:
CD27+_M_1
Chromatin


title: WTE1


title: 35_Embryo_rep2

description:
35_Em_2
AllSamples_GeneExpression_Count.txt

value: Embryo


title: 9_Mo_d2

source_name: cell line

value: SHH-MB tumor cells from tumors of Atoh1-cre:SmoM2 mice at P12

value: Co-culture


title: WTD2


title: SCMNK cells_Rep2

description:
CD27+_M_2
Chromatin


title: 9_Mo_d1


title: 35_Embryo_rep1

description:
35_Em_1
AllSamples_GeneExpression_Count.txt

value: Moneymaker


title: WTD1


title: 8_M_d2

value: monoculture


title: 49_Seedcoat_rep3

description:
49_SC_3
AllSamples_GeneExpression_Count.txt

source_name: 49 DAF seedcoat

value: Seed coat

value: 49 DAF


title: Naïve NK cells_Rep3

description:
Naive_NK_3
Chromatin

value: Naive NK cells


title: C42_shCTR_2

value: prostate cancer

value: shCTR


title: Nonmemory NK cells_Rep1

description:
CD27-_N_1
Chromatin


title: Naïve NK cells_Rep2

description:
Naive_NK_2
Chromatin


title: 8_M_d1


title: Naïve NK cells_Rep1

description:
Naive_NK_1
Chromatin


title: 49_Seedcoat_rep1

description:
49_SC_1
AllSamples_GeneExpression_Count.txt


title: 49_Seedcoat_rep2

description:
49_SC_2
AllSamples_GeneExpression_Count.txt


title: 5_Od_d2

value: OPC oligodendrocytic precursor cells


title: PABP IP Rep1

city: Bloomington

first: Nicholas

middle: S

last: Sokol

state: IN

institute: Indiana University

data_processing:
Quality trimming was performed using Cutadapt version 2.9.
Ribosomal RNA (rRNA) reads were removed using Tagdust2 version 2.2.
Remaining reads were aligned to the BDGP assembly release 6.28 (Ensembl release 99) reference genome using STAR version 2.7.3a.
Alignment output files were coordinate sorted and duplicated reads were removed using SAMtools version 1.10.
Aligned reads were counted to the nearest overlapping feature suing the Subread version 2.0.0 function featureCounts.
Genome_build: BDGP assembly release 6.28 (Ensembl release 99)
Supplementary_files_format_and_content: CSV file containing raw read counts
Supplementary_files_format_and_content: CSV file containing differential gene expression results obtained using DESeq2
Supplementary_files_format_and_content: Bigwig files for genome browser visualization

organism: Drosophila melanogaster

source_name: Whole animals

extract_protocol:
Two hundred flies (100 male and 100 female) of each sample were ground into a fine powder, exposed to UV, lysed in the lysis buffer, immunoprecipitated PABP using magnetic FLAG-beads and isolated RNA using the Trizol reagent. For total input libraries, RNA was isolated from total extracts prior to immunoprecipitation using the Trizol reagent.
RNA libraries were prepared for sequencing using the Ovation SoLo RNA-Seq System (Tecan Genomics, S02240).
CLIP-Seq

value: Intestinal progenitor cells

value: Adult


title: PABP IP Rep2


title: 42_Seedcoat_rep1

description:
42_SC_1
AllSamples_GeneExpression_Count.txt

source_name: 42 DAF seedcoat

value: 42 DAF


title: 42_Seedcoat_rep2

description:
42_SC_2
AllSamples_GeneExpression_Count.txt


title: PABP Input Rep2

value: All cells


title: 2_Om_d1


title: PABP Input Rep1


title: 1_O_d2


title: 35_Seedcoat_rep3

description:
35_SC_3
AllSamples_GeneExpression_Count.txt

source_name: 35 DAF seedcoat

value: 35 DAF


title: FMRP UV Rep2

data_processing:
Quality trimming was performed using Cutadapt version 2.9.
UMI sequences were extracted using UMI-tools.
Ribosomal RNA (rRNA) reads were removed using Tagdust2 version 2.2.
Remaining reads were aligned to the BDGP assembly release 6.28 (Ensembl release 100) reference genome using STAR version 2.7.3a.
Alignment output files were coordinate sorted using SAMtools version 1.10.
Duplicated reads were removed using UMI-tools.
Input normalized peaks were called using PureCLIP.
Genome_build: BDGP assembly release 6.28 (Ensembl release 100)
Supplementary_files_format_and_content: CSV file containing raw read counts
Supplementary_files_format_and_content: CSV file containing differential gene expression results obtained using DESeq2
Supplementary_files_format_and_content: Bigwig files for genome browser visualization

extract_protocol:
Two hundred flies (100 male and 100 female) of each sample were ground into a fine powder, exposed to UV, lysed in the lysis buffer and immunoprecipitated FMRP using magnetic FLAG-beads. Subsequently, RNA from the IP and size-matched input were isolated as described in the method described in Nostrand et al., 2016.
RNA libraries were prepared for sequencing using the method described in Nostrand et al., 2016.
Enhanced CLIP-Seq


title: 35_Seedcoat_rep2

description:
35_SC_2
AllSamples_GeneExpression_Count.txt


title: FMRP UV Rep1


title: SLP-2 sh2-3

city: Sendai

first: Kyohei

last: Ariake

address: 1-1, Seiryo-machi, Aoba-ku

department: Department of Surgery

country: Japan

institute: Tohoku university

description: Cell type: pancreatic cancer cell lines AsPC-1. The shRNA-2 of SLP-2 was inserted into pBAsi-hU6 NEO plasmids and transfected to AsPC-1. Transfected clones were selected using Geneticin over a period of 3 weeks, after which a single colony was chosen and cultured.

hyb_protocol: directions for the GeneChip WT Plus Reagent kit (Thermo Fisher Scientific). Overnight hybridisation to the Clariom S GeneChip took place at 45℃ for 16 hours at 60 rpm using the Hybridization oven 645 (Affymetrix). GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: The GeneChip was svanned on a GeneChip Scanner 3000 7G System (Thermo Fisher Scientific),

data_processing: The data were analyzed with Transcriptome Analysis Console (TAC) software 4.0 using Affymetrix default analysis settings and global scaling as normalization method.

source_name: ASPC-1 SLP2 sh2

label_protocol: Total RNA (100 ng) was used to generate amplified sense strand DNA followed by fragmentation and biotinylation using the WT Plus Reagent kit (Thermo Fisher Scientific).

extract_protocol: Total RNA is isolated from cells with the Nucleospin RNA Kit (Takara. Bio) according to the manufacturer's protocol.

value: shRNA-2 of SLP-2


title: SLP-2 sh2-2


title: SLP-2 sh2-1


title: 42_Seedcoat_rep3

description:
42_SC_3
AllSamples_GeneExpression_Count.txt


title: 35_Seedcoat_rep1

description:
35_SC_1
AllSamples_GeneExpression_Count.txt


title: 2_Om_d2


title: 5_Od_d1


title: FMRP smInput


title: SLP-2 sh1-3

description: Cell type: pancreatic cancer cell lines AsPC-1. The shRNA-1 of SLP-2 was inserted into pBAsi-hU6 NEO plasmids and transfected to AsPC-1. Transfected clones were selected using Geneticin over a period of 3 weeks, after which a single colony was chosen and cultured.

source_name: ASPC-1 SLP2 sh1

value: shRNA-1 of SLP-2


title: 28_Seed_rep3

description:
28_S_3
AllSamples_GeneExpression_Count.txt

source_name: 28 DAF seed

value: Whole seed

value: 28 DAF


title: PC_11_RNA_TB2

data_processing:
Base Calling perofmed by RTA1(MiSeq) and RTA3 (Novaseq 6000)
Transcriptome Processing: Fastq files were mapped and aligned using nf-core ((https://github.com/nf-core/rnaseq)) rnaseq pipeline. Adapters and low-quality bases from the RNA-seq reads were removed using Trim Galore (version 0.4.4), which is a wrapper tool for Cutadapt and FastQC. Reads that were shorter than 35 bp after trimming were discarded. . The filtered reads were mapped to the human genome (GRCh38, gencode version 25) using STAR aligner (version 2.5.2b) (Dobin et al., 2013). featureCounts (version 1.5.2) was used to estimate the expression counts of the genes.
BCRseq Processing: Sequencing reads were aligned to BCR gene reference and clonotypes were identified and grouped using the software MiXCR (Bolotin et al., 2015). Relative proportions of IGH classes were calculated. Alpha diversity measures were calculated using the R packages vegan and tcR (versions 1.5-6 and 2.3.2).
Genome_build: (GRCh38, gencode version 25)
Supplementary_files_format_and_content: tab-delimited text files include feature counts and BCR Clonotype count tables

source_name: Peripheral Whole-Blood

extract_protocol:
RNA sequencing libraries were prepared according to the Illumina TruSeq® messenger (mRNA) sequencing protocol (TruSeq® RNA Seq Library Prep Kit v2). The resulting libraries were sequenced on the NovaSeq 6000 (2× 50 bp, S2 chemistry).
Patient peripheral blood was collected in 2.5mL tubes PAXgene Blood RNA Tubes, RNA was automated isolated in QIAGEN’s QIAcube using the PAXgene Blood miRNA Kit from QIAGEN PreAnalytiX.

tag: remission

value: Remission

tag: gender

value: f

tag: age

tag: pseudotime

tag: patient number


title: SLP-2 sh1-2


title: 28_Seed_rep2

description:
28_S_2
AllSamples_GeneExpression_Count.txt

tag: cultivar

value: Moneymaker

tag: age (daf)


title: SLP-2 sh1-1


title: MB 3 (scRNA-seq)

data_processing:
*R1_001.fastq.gz: contain cell barcode (first 16 nt) and UMI (next 10 nt)
*R2_001.fastq.gz: contains the 57 nt RNA sequence.
*I1_001.fastq.gz: contains the 8 nt sample index.
The 10x Genomics Cell Ranger Suite (version 2.0.2) was used to perform sample demultiplexing, barcode processing, alignment (mm10) and generation of digital gene expression matrix. For sample 1 (MB1) two sequencing runs were merged following Cell Ranger pipeline, i.e. specifying multiple fastq files to be considered together. Default parameters were used.
Processed data files are gene expression matrices with genes by rows, cells by colums. Gene expression is measured in UMI counts.
The four gene expression matrices were loaded in R separately, retaining genes expressed in at least 3 cells, and cells expressing at least 100 genes. Then, we merged them using the Seurat (https://satijalab.org/seurat/) function MergeSeurat and applied quality filtering on the merged dataset.
In particular, we filtered out cells with more than 10% expression of mitochondrial genes (which may be apoptotic cells), cells with number of UMIs greater than 10,000 (to exclude doublets) and cells expressing less than 200 different genes (to remove poor quality cells).
After this step, the merged data consisted of 13,596 genes and 4,790 cells.
Genome_build: mm10
Supplementary_files_format_and_content: Digital gene expression matrix for each sample. Files provided in tab-delimited format.

molecule: polyA RNA

source_name: SHH subgroup-specific medulloblastoma tumor

extract_protocol:
Fresh tumor tissues were isolated macroscopically and minced using scalpels prior to enzymatic dissociation for 20 minutes at 37°C using PBS-diluted Accutase, accompanied by mechanical dissociation and followed by the lysis of red blood cells using ACK lysis buffer. Cells were stained with the dye 7-AAD for cell sorting to exclude dead cells. 10000 vital cells per sample were loaded as input on the 10x Genomics Chromium controller.
Indexed-single cell RNA libraries were prepared for sequencing using the 10X Chromium Single Cell 3' Gel Bead Kit and Chromium i7 Multiplex Kit (10x Genomics, PN-120262). Each sample was sequenced across 4 lanes with Illumina NextSeq 500 System (2 x 75bp). For sample 1, we sequenced the same library at to subsequent time points, to improve saturation.

value: post natal day 20

tag: strain

tag: tumor

tag: tumor localization

value: cerebellum


title: MB 2 (scRNA-seq)

value: SHH subgroup-specific medulloblastoma tumor


title: MB 1 (scRNA-seq)


title: SLP-2 Cont-3

description: Cell type: pancreatic cancer cell lines AsPC-1. The blank pBAsi-hU6 NEO plasmid was transfected as a negative control. Transfected clones were selected using Geneticin over a period of 3 weeks, after which a single colony was chosen and cultured.

source_name: ASPC-1 SLP2 Control

tag: cell line

value: negative control


title: 1_O_d1

tag: cell type

value: OPC oligodendrocytic precursor cells

tag: culture

value: monoculture


title: SCA1-Low-FAPs_3

city: Rome

first: Giulio

last: Giuliani

address: Via della ricerca scientifica 1

country: Italy

institute: Univerisity of Rome Tor Vergata

data_processing:
Illumina novaSeq base call (BCL) files were converted in fastq file through bcl2fastq (version v2.20.0.422).
Sequence reads were trimmed using bbduk software (bbmap suite 37.31) in order to remove adapter sequences, poly-A tails and low-quality end bases (regions with average quality below 6).
Alignment was performed with STAR 2.6.0a27 on mm10 reference assembly obtained from cellRanger website (Ensembl assembly release 93).
The expression levels of genes were determined with htseq-count 0.9.1528 by using mm10 Ensembl assembly (release 93) downloaded from cellRanger website.
The expression data was analyzed by Rosalind, with a HyperScale architecture developed by OnRamp BioInformatics. Individual sample counts were normalized via Relative Log Expression (RLE) using DESeq2 R library29.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files Htseq counts for each Sample

source_name: fibro/adipogenic progenitors (FAPs) isolated from hind limb muscles of mdx mice

growth_protocol: FAP cell states isolate from mdx mice were cultured for 5 days in growth medium composed by Dulbecco’s Modified Eagle Medium, High Glucose, GlutaMAXTM (Gibco 61965-026) supplemented with 20% fetal bovine serum (FBS) (Euroclone, Pero, Milan, Italy, ECS0180L), 100 U/ml penicillin and 100 mg/ml streptomycin (Gibco 15140122), 1 mM sodium pyruvate (Sigma-Aldrich, St. Louis, Missouri, United States, S8636) and 10 mM 4-(2-hydroxyethyl)-1-piperazineethanesulfonic acid (HEPES) (Sigma H0887).

extract_protocol:
Total RNA was isolated from the harvested cells using RNeasy micro kit (Qiagen, Hilden, Germany 74004)
Libraries were prepared from 100 ng of total RNA using the QuantSeq 3' mRNA-Seq Library Prep Kit FWD for Illumina (Lexogen GmbH, Vienna, Austria)

value: Hind limb skeletal muscles

value: fibro/adipogenic progenitors (FAPs)

value: 45 days

tag: condition


title: SLP-2 Cont-1


title: SCA1-Low-FAPs_4

tag: tissue


title: 28_Seed_rep1

description:
28_S_1
AllSamples_GeneExpression_Count.txt

tag: developmental stage


title: SLP-2 Cont-2

tag: treatment


title: SCA1-Low-FAPs_1


title: MB 4 (scRNA-seq)


title: 21_Seed_rep2

description:
21_S_2
AllSamples_GeneExpression_Count.txt

source_name: 21 DAF seed

value: 21 DAF