title: BU-HY-13

value: amyloid


title: BU-HY-12

status: Public on Sep 08 2022

type: SRA

city: Jacksonville

first: Tadafumi

middle: Clark

last: Ikezu

address: 4500 San Pablo Rd

country: USA

institute: Mayo Clinic

library_source: transcriptomic

data_processing:
Raw gene read counts, along with sequencing quality control, were generated using the Mayo Clinic RNA-Seq analytic pipeline: MAP-RSeq Version 3.0 (Kalari et al., 2014).
Reads were mapped to the mouse reference genome mm10 using STAR v.2.5.2b using default settings (Dobin et al., 2013). The gene counts were generated using FeatureCounts v.1.5.1 (Liao et al., 2014) with the gene definitions files from Ensembl v78. Quality checks after alignment was done using RSeqQC v.3.0.0 (Wang et al., 2012).
Genes were filtered out from further analyses if there were not at least four samples with 10 counts of the gene. Trimmed Mean of M-values (TMM) normalization was performed with calcNormFactors from the edgeR R package (Lun ATL et al, 2016). Using this selection threshold, 20,337 genes were included in the downstream analysis.
Sample BU-HY-19 had outlying gene count percentage (39%) and strand-ness check (0.5009), and was removed from subsequent analyses.
Assembly: mm10
Supplementary files format and content: .tsv file of raw gene counts

molecule: total RNA

organism: Mus musculus

source_name: cortex

extract_protocol:
Total RNA was extracted from the cortex using Trizol reagent and cleaned using RNeasy spin columns with DNase treatment to remove contaminating genomic DNA.
RNA libraries were prepared from 200 ng of total RNA using the TruSeq RNA Sample Prep Kit (Illumina, San Diego, CA) according to the manufacturer’s instructions, employing poly-A mRNA enrichment using oligo-dT magnetic beads. The final adaptor-modified cDNA fragments were enriched by 15 cycles of PCR using Illumina TruSeq PCR primers. The concentration and size distribution of the completed libraries were determined using an Agilent Tape Station, (Agilent, Santa Clara, CA) and Qubit fluorometer (Invitrogen, Carlsbad, CA).
Libraries from all the 40 samples were sequenced on Illumina’s NovaSeq 6000 at 75 million fragment reads/sample following Illumina’s standard protocol on a S2 flow cell.

treatment_protocol: No specific trearment was applied to each group of mice.

tag: cohort

tag: genotype

value: WT

tag: Sex

value: female


title: CNTO1275CRD3002-20009 rectum biopsy week 0

type: RNA

city: London

first: Nick

last: Powell

address: Du Cane Road

department: Department of Metabolism, Digestion and Reproduction

country: United Kingdom

institute: Imperial College London

hyb_protocol: Following fragmentation, 1.875ug of cDNA was hybridized for 16 hr at 45oC on GeneChip HT HG-U133+ PM 96 array plates. GeneChips were washed and stained in the Affymetrix GeneChip Array Station.

scan_protocol: GeneChips were scanned using the GeneChipHT Scanner.

data_processing: The data was normalized by RMA using ArrayStudio version 10.

label: biotin

organism: Homo sapiens

source_name: rectum biopsy

label_protocol: Target was prepared from 100ng total RNA using the NuGEN Ovation V2 kit, followed by NuGEN Encore biotin labeling module, using the manufacturer’s protocol.

extract_protocol: Total RNA was isolated with Qiagen's RNeasy mini kit according to the manufacturer’s instructions.

tag: tissue

value: rectum

tag: donor id

tag: visit

tag: diagnosis

value: Crohn's disease

tag: treatment

value: Placebo IV

tag: inflamed area at week 0

value: Ileum and colon

tag: mucosal healing at week 8

value: N


title: BU-HY-10

value: Hom

value: male


title: BU-HY-11

value: non-amyloid


title: BU-HY-9


title: BU-HY-7


title: BU-HY-8


title: BU-HY-6


title: BU-HY-4


title: BU-HY-3


title: CNTO1275CRD3002-20894 rectum biopsy week 0

value: Ustekinumab 130 mg IV


title: BU-HY-1


title: BU-HY-2


title: WT_D10

city: Chicago

first: Timothy

middle: Jon

last: Koh

state: IL

address: 1919 W Taylor Room 650

institute: University of Illinois at Chicago

library_source: transcriptomic single cell

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v3.0.2 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

molecule: polyA RNA

source_name: Skin wound

extract_protocol: Monocytes and macrophages isolated from skin wounds on male C57BL6/J on day 3, 6, and 10 post-injury, subjected to enzymatic digestion to obtain single cells and pooled from two mice per time point. Fresh cells with viability over 70% processed using the 10x Chromium platform. Libraries sequenced on HiSeq with paired-end reads. Fastq files were generated and demultiplexed into single cells using Cell Ranger software

value: Skin wound

tag: timepoint

value: day 10 post-injury


title: CNTO1275CRD3002-20986 rectum biopsy week 0


title: CNTO1275CRD3002-20047 rectum biopsy week 0

value: Colon only


title: WT_D6

value: day 6 post-injury


title: CNTO1275CRD3002-20116 rectum biopsy week 0


title: CNTO1275CRD3002-20814 rectum biopsy week 0

value: Ustekinumab 6 mg/kg (390 mg)


title: CNTO1275CRD3002-20021 rectum biopsy week 0


title: CNTO1275CRD3002-20058 rectum biopsy week 0


title: CNTO1275CRD3002-20484 rectum biopsy week 0


title: CNTO1275CRD3002-20429 rectum biopsy week 0


title: BU-HY-5

value: amyloid


title: CNTO1275CRD3002-20863 rectum biopsy week 0


title: CNTO1275CRD3002-20155 rectum biopsy week 0


title: CNTO1275CRD3002-20004 rectum biopsy week 0


title: CNTO1275CRD3002-20542 rectum biopsy week 0


title: CNTO1275CRD3002-20133 rectum biopsy week 0

value: Y


title: WT_D3

value: day 3 post-injury


title: CNTO1275CRD3002-20286 rectum biopsy week 0

value: rectum

value: Ustekinumab 6 mg/kg (520 mg)


title: CNTO1275CRD3002-20978 rectum biopsy week 0

value: Crohn's disease

value: Placebo IV


title: CNTO1275CRD3002-20673 rectum biopsy week 0

value: Ileum and colon

value: N


title: CNTO1275CRD3002-20548 rectum biopsy week 0


title: BU-HY-16

value: Hom

value: female


title: CNTO1275CRD3002-20963 rectum biopsy week 0


title: BU-HY-35

value: non-amyloid

value: male


title: CNTO1275CRD3002-20843 rectum biopsy week 0

value: Ustekinumab 130 mg IV


title: CNTO1275CRD3002-20616 rectum biopsy week 0


title: HS_siRPRD1B_B3 [RNA-seq]

first: Richard

middle: James

last: Mitter

state: LONDON

address: 1 Midland Road

department: Bioinformatics & Biostatistics

institute: The Francis Crick Institute

description:
CUG4409A12
mRNA-Seq
poly(A)+ mRNA

data_processing:
Data were processed using nf-core rnaseq pipeline revision: 3.3 using RSEM/STAR for abundance estimation against Homo sapiens GRCh38 genome and Ensembl release 104 transcript annotations for human.
bigWig files were subsequently scaled to total library size using size factors derived from a standard DESeq2 analysis of the human gene-level counts.
Genome_build: GRCh38
Supplementary_files_format_and_content: Normalised read depth coverage (unstranded) in bigWig format.

source_name: MRC5-VA cell line

growth_protocol: DMEM (Thermo Fisher Scientific, 11965118) supplemented with 10% v/v FBS (Clontech, 631106), 100 U/ml penicillin, 100 μg/ml streptomycin.

extract_protocol:
RNA was extracted using the RNeasy kit (Qiagen, 74104) according to the manufacturer’s instruction including the on-column DNase treatment. 200ng total RNA was used for oligo(dT) purification.
Libraries were prepared using the KAPA mRNA HyperPrep kit (Roche).

treatment_protocol: Cells were treated with RPRD1B siRNA or a control siRNA for 72h. Cells were then either exposed to 120min heat shock (43C) or not and total RNA was extracted.

tag: cell line

tag: sirna

value: RPRD1B siRNA

tag: condition

value: 120min heat shock


title: CNTO1275CRD3002-20682 rectum biopsy week 0

value: Ustekinumab 6 mg/kg (260 mg)


title: NGP_ATRX KO_C-4_rep04

city: Kitaadachi-gun

first: Hisanori

last: Takenobu

state: Saitama

address: 818, Komuro, Ina-machi

department: Research Institute for Clinical Oncology

country: Japan

institute: Saitama Cancer Center

description: human neuroblastoma cell line NGP, electroporated with Cas9  (pHL-EF1a-SphcCas9-iP-A, Addgene ID: 60599) and custom ATRX gRNA expression vectors  (pHL-H1-ccdB-mEF1a-RiH, Addgene ID: 60601), Puromycin (0.5 μg/mL, 3 days) selection, Single clone formation, C-4

hyb_protocol: 600 ng of Cy3-labelled cRNA was fragmented at 60°C for 30 minutes in a reaction volume of 25 uL containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 25 uL of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Human Genome Oligo Microarrays (G4851C) for 17 hours at 65 °C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37 °C GE Wash buffer 2 (Agilent).

scan_protocol: Slides were scanned immediately after washing on the SureScan Agilent DNA Microarray Scanner (G4900DA) using one color scan setting for 8x60k array slides.

data_processing: The scanned images were analyzed with Feature Extraction Software 9.1 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities.

source_name: human neuroblastoma cell line NGP, electroporated with Cas9  (pHL-EF1a-SphcCas9-iP-A, Addgene ID: 60599) and custom ATRX gRNA  vectors  (pHL-H1-ccdB-mEF1a-RiH, Addgene ID: 60601), Puromycin (0.5 μg/mL, 3 days) selection, Single clone formation, C-4

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 200 ng RNA using the One-Color Low Input Quick Amp Labeling kit (Agilent) according to the manufacturer's instructions (Protocol version 6.9), followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: The  Ctrl and two ATRX KO NGP clones were cultured in RPMI1640 (Wako, Osaka, Japan) supplemented with 10% heat-inactivated fetal bovine serum (FBS, Invitrogen, Carlsbad, CA, USA) and 100 μg/mL penicillin/streptomycin (Sigma-Aldrich, St. Louis, MO, USA). Cultures were maintained at 37ºC under 5% CO2 in air.

extract_protocol: RNA was prepared using the RNeasy Mini kit (Qiagen) following the manufacturer's recommendations. RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was guaranteed by an RNA Integrity Number (RIN) > 6.8.

treatment_protocol: Cas9 expression vector (pHL-EF1a-SphcCas9-iP-A) and gRNA expression vector (pHL-H1-ccdB-mEF1a-RiH), were purchased from Addgene.  Custom ATRX gRNA expression vectors were constructed in the pHL-H1-ccdB-mEF1a-RiH vector. NGP cells were then electroporated with Cas9 or Cas9 and ATRX gRNA expression vectors using the NEPA21 electroporation system (Nepa Gene) under optimum conditions. Puromycin (0.5 μg/mL, 3 days)-selected cells were trypsinized and diluted in medium for single colony formation. Single colonies were selected and the ATRX KO status was examined.

tag: cell type

value: neuroblastoma

value: ATRX -/-


title: NGP_ATRX KO_C-4_rep01


title: CNTO1275CRD3002-20679 rectum biopsy week 0


title: NHS_siRPRD1B_B3 [RNA-seq]

description:
CUG4409A11
mRNA-Seq
poly(A)+ mRNA

value: No heat shock


title: CNTO1275CRD3002-20851 rectum biopsy week 0

value: rectum

value: Ustekinumab 6 mg/kg (390 mg)


title: CNTO1275CRD3002-20458 rectum biopsy week 0

value: Crohn's disease


title: CNTO1275CRD3002-20291 rectum biopsy week 0

value: Placebo IV


title: CNTO1275CRD3002-20106 rectum biopsy week 0

value: Colon only


title: NGP_Ctrl_rep03

source_name: human neuroblastoma cell line NGP, electroporated with Cas9 expression vector (pHL-EF1a-SphcCas9-iP-A, Addgene ID: 60599), Puromycin (0.5 μg/mL, 4 days)-selected bulk cells.

value: ATRX wild-type


title: NGP_ATRX KO_C-1_rep04

description: human neuroblastoma cell line NGP, electroporated with Cas9  (pHL-EF1a-SphcCas9-iP-A, Addgene ID: 60599) and custom ATRX gRNA expression vectors  (pHL-H1-ccdB-mEF1a-RiH, Addgene ID: 60601), Puromycin (0.5 μg/mL, 3 days) selection, Single clone formation, C-1

source_name: human neuroblastoma cell line NGP, electroporated with Cas9  (pHL-EF1a-SphcCas9-iP-A, Addgene ID: 60599) and custom ATRX gRNA  vectors  (pHL-H1-ccdB-mEF1a-RiH, Addgene ID: 60601), Puromycin (0.5 μg/mL, 3 days) selection, Single clone formation, C-1


title: CNTO1275CRD3002-20196 rectum biopsy week 0

value: Ileum and colon


title: CNTO1275CRD3002-20149 rectum biopsy week 0

value: N


title: CNTO1275CRD3002-20171 rectum biopsy week 0


title: CNTO1275CRD3002-20441 rectum biopsy week 0


title: NGP_Ctrl_rep04

source_name: human neuroblastoma cell line NGP, electroporated with Cas9 expression vector (pHL-EF1a-SphcCas9-iP-A, Addgene ID: 60599), Puromycin (0.5 μg/mL, 5 days)-selected bulk cells.


title: CNTO1275CRD3002-20685 rectum biopsy week 0


title: CNTO1275CRD3002-20209 rectum biopsy week 0


title: NGP_ATRX KO_C-4_rep02


title: NGP_ATRX KO_C-1_rep03


title: NGP_ATRX KO_C-1_rep01


title: CNTO1275CRD3002-20908 rectum biopsy week 0

value: Ustekinumab 6 mg/kg (520 mg)

value: Y


title: CNTO1275CRD3002-20393 rectum biopsy week 0

value: Ustekinumab 130 mg IV


title: NGP_Ctrl_rep01

source_name: human neuroblastoma cell line NGP, electroporated with Cas9 expression vector (pHL-EF1a-SphcCas9-iP-A, Addgene ID: 60599), Puromycin (0.5 μg/mL, 3 days)-selected bulk cells.


title: HS_siNT_B3 [RNA-seq]

description:
CUG4409A10
mRNA-Seq
poly(A)+ mRNA

value: non-targeting siRNA


title: NHS_siNT_B3 [RNA-seq]

description:
CUG4409A9
mRNA-Seq
poly(A)+ mRNA


title: NGP_ATRX KO_C-4_rep03


title: CNTO1275CRD3002-20930 rectum biopsy week 0


title: NGP_Ctrl_rep02


title: NGP_ATRX KO_C-1_rep02


title: HS_siRPRD1B_B2 [RNA-seq]

description:
CUG4409A8
mRNA-Seq
poly(A)+ mRNA

value: RPRD1B siRNA

value: 120min heat shock


title: NHS_siRPRD1B_B2 [RNA-seq]

description:
CUG4409A7
mRNA-Seq
poly(A)+ mRNA


title: HS_siRPRD1B_B2 [TTchem-seq]

description:
CUG4410A8
Nascent RNA

data_processing:
Library strategy: TTchem-seq
Data were processed using nf-core rnaseq pipeline revision: 3.3 using RSEM/STAR for abundance estimation against Homo sapiens GRCh38 genome and Ensembl release 104 transcript annotations for human supplemented with Saccharomyces cerevisiae R64-1-1 cDNA sequences used as a spike-in.
bigWig files were subsequently scaled to total library size using size factors derived from a DESeq2 analysis of the yeast gene-level counts.
Genome_build: GRCh38
Supplementary_files_format_and_content: Normalised read depth coverage (unstranded) in bigWig format.

extract_protocol:
RNA was extracted by TRIzol (Thermo Fisher Scientific, 15596026) according to the manufacturer’s instructions. As a control for equal sample preparation, we spiked-in S. cerevisiae (strain BY4741, MATa, his3D1, leu2D0, met15D0, ura3D0) 4-thiouracil (4TU)-labelled RNA. S. cerevisiae were grown in YPD medium overnight, diluted to an OD600 of 0.1, and grown to mid-log phase (OD600 of 0.8) and labelled with 5 mM 4TU (Sigma-Aldrich, 440736) for 6 min. Total RNA was extracted using the PureLink RNA Mini kit (Thermo Fisher Scientific, 12183020) following the enzymatic protocol. For purification of 4SU labelled RNA, 100 μg mammalian 4SU labelled RNA was spiked-in 1/100 of 4TU-labelled S. cerevisiae RNA. The 101 μg RNA was fragmented by addition of 20 μL 1 M NaOH to fragment RNA and left on ice for 20 min. Fragmentation was stopped by addition of 80 μL 1 M Tris pH 6.8 and cleaned up twice with Micro Bio-Spin™ P-30 Gel Columns (BioRad, 7326223) according to the manufacturer’s instructions. Biotinylation of 4SU-residues were carried out in a total volume of 250 μl, containing 10 mM Tris-HCl [pH 7.4], 1 mM EDTA and 5mg MTSEA biotin-XX linker (Biotium, BT90066) for 30 min at room temperature in the dark. RNA was then purified by phenol:chloroform extraction, denatured by 10 min incubation at 65°C and added to 200 μL μMACS Streptavidin MicroBeads (Miltenyi, 130-074-101). RNA was incubated with beads for 15 min at room temperature and beads applied to a μColumn in the magnetic field of a μMACS magnetic separator. Beads were washed twice with pull-out wash buffer (100 mM Tris-HCl, pH 7.4, 10 mM EDTA, 1 M NaCl and 0.1% Tween20). 4SU-RNA was eluted twice by addition of 100 mM DTT and RNA cleaned up using the RNeasy MinElute kit (Qiagen, 74204).
Libraries were prepared using the KAPA RNA HyperPrep kit (Roche) using 5 min 65°C fragmentation incubation to anneal primers but to prevent further fragmentation of the samples.

treatment_protocol: Cells were treated with RPRD1B siRNA or a control siRNA for 72h. Cells were then either exposed to 120min heat shock (43C) or not. Nascent RNA labelling was carried out by addition of 1 mM 4-thiourdine to cell media for 10 min prior to harvest.

value: 10 min 4-thiouridine pulse


title: NHS_siRPRD1B_B2 [TTchem-seq]

description:
CUG4410A7
Nascent RNA


title: NHS_siNT_B1 [RNA-seq]

description:
CUG4409A1
mRNA-Seq
poly(A)+ mRNA


title: HS_siRPRD1B_B1 [RNA-seq]

description:
CUG4409A4
mRNA-Seq
poly(A)+ mRNA


title: HS_siNT_B2 [TTchem-seq]

description:
CUG4410A6
Nascent RNA


title: NHS_siRPRD1B_B1 [RNA-seq]

description:
CUG4409A3
mRNA-Seq
poly(A)+ mRNA


title: NHS_siNT_B2 [TTchem-seq]

description:
CUG4410A5
Nascent RNA


title: HS_siRPRD1B_B1 [TTchem-seq]

description:
CUG4410A4
Nascent RNA


title: NHS_siRPRD1B_B1 [TTchem-seq]

description:
CUG4410A3
Nascent RNA


title: HS_siNT_B1 [TTchem-seq]

description:
CUG4410A2
Nascent RNA


title: HS_siNT_B2 [RNA-seq]

description:
CUG4409A6
mRNA-Seq
poly(A)+ mRNA


title: NHS_siNT_B2 [RNA-seq]

description:
CUG4409A5
mRNA-Seq
poly(A)+ mRNA


title: HC-23 rectum biopsy week 0

value: healthy control


title: HS_siNT_B1 [RNA-seq]

description:
CUG4409A2
mRNA-Seq
poly(A)+ mRNA


title: single- nuclei RNA sequencing data from AKI post mortem specimen 8

city: Hannover

first: Christian

last: Hinze

address: Carl-Neuberg-Str. 1

department: Department of Nephrology and Hypertension

country: Germany

institute: Hannover Medical School

description:
AKI8
single nuclei RNA-seq
10x v3.1 chemistry

data_processing:
Initial filtering was performed by excluding nuclei with more than 5% mitochondrial reads and less than 500 detected genes. Nuclei passing this filter of all samples were then analyzed using Seurat’s best practice work flow for data integration using the reciprocal PCA approach (https://satijalab.org/seurat/articles/integration_rpca.html) with default parameters.
Emerging clusters were then analyzed for marker gene expression using Seurat’s FindAllMarkers function and subsequently assigned to the major renal cell types. Each major cell type was then subclustered using Seurat’s best practice standard work flow for data integration:(https://satijalab.org/seurat/articles/integration_introduction.html). Followed by RunUMAP(seu, dims = 1:30), FindNeighbors(seu, dims = 1:30) and FindClusters(seu, resolution = 0.5) using the integrated assay. Marker genes for all emerging clusters were calculated.
During the next steps, the aim was to identify destroyed nuclei and doublets. For the destroyed nuclei, in the initial clustering, they clearly clustered away from major kidney cell types and showed a significantly reduced complexity of gene expression (nUMI, nGene) when compared to major cell types. Removal of destroyed nuclei led to a reduction of initially 121933 nuclei to 113137 nuclei in our dataset. Doublets could be detected by clusters in the subclusterings of the major cell types showing canonical marker genes from another major cell type (e.g. TAL marker gene expression in a PT subcluster). Also, these subclusters clearly clustered away from the subclusters of the respective major cell type. Canonical marker genes used for doublet removal were NPHS2 (Podo), LRP2 (PT),  AQP1, CLCNKA (tL), SLC12A1 (TAL), SLC12A3 (DCT), CALB1 (CNT), AQP2 (CD-PC), FOXI1 (CD-IC), PECAM1 (EC), PTPRC (Leuk), ACTA2 (IntC).
Destroyed and doublet cells were removed and the whole clustering process was repeated to avoid any influence of the excluded cells on the clusterings.

source_name: kidney post mortem biopsy

extract_protocol:
After consent of next of kin, post mortem biopsies were collected using 18G biopsy needles within 2 hours from death from individuals who had died in a clinical setting of critical illness on intensive care units of Charité-Universitätsmedizin Berlin (ethics approval EA2/045/18) (see Additional file 2: Table S1 for detailed patient characteristics). Control tissue from tumor-adjacent normal tissue of tumor nephrectomies was collected during tumor nephrectomies (ethics approval EA4/026/18). Kidney specimen were either stored in pre-cooled RNAlater at 4°C for 24 hours and then stored at -80°C (for snRNA-seq) or in 4% formaldehyde (for histopathological studies and in situ hybridizations). Kidney specimen subjected to snRNA-seq were kept at 4°C at all times. All specimens were treated as described in detail in Leiz, Hinze et al. 2021.   Main steps included: Specimens were thoroughly minced in nuclear lysis buffer 1 (nuclear lysis buffer (Sigma) + Ribolock (1U/µl) + VRC (10mM)) and homogenated using a dounce homogenizer with pastel A (Sigma D8938-1SET), filtered (100 µm), homogenized again (douncer with pastel B), filtered through a 35 µm strainer and centrifuged (5 min, 500g). The pellet was then resuspended in nuclear lysis buffer 2 (nuclear lysis buffer + Ribolock (1U/µl)). To remove debris from the suspension, we underlayed the suspension with lysis buffer containing 10% sucrose and 1U/µl of Ribolock. After centrifugation (5 min, 500g), the supernatant and debris were carefully removed. Pelleted nuclei were resuspended in PBS/0.04%BSA + Ribolock (1U/µl), filtered through a 20 µm strainer and stained with DAPI.   All samples were subjected to single-nuclei sequencing following the 10x genomics protocol for Chromium Next GEM Single Cell 3’ v3.1 chemistry targeting 10000 nuclei. Obtained libraries were sequenced on Illumina HiSeq 4000 sequencers (paired-end). Digital expression matrices were generated using the Cellranger software version 3.0.2 with –force-cells 10000 against a genome composed of the human HG38 genome (GRCh38 3.0.0) and the genome of Sars-CoV-2.
library preparation were performed according to the 10x Genomics single cell protocol (10X Genomics toolkit version v3.1, Pleasanton, CA)
single nucleus RNA-sequencing

tag: disease state

value: AKI


title: single- nuclei RNA sequencing data from AKI post mortem specimen 7

description:
AKI7
single nuclei RNA-seq
10x v3.1 chemistry


title: single- nuclei RNA sequencing data from AKI post mortem specimen 6

description:
AKI6
single nuclei RNA-seq
10x v3.1 chemistry


title: PBMCs - Patient 5 in D19

city: Hangzhou

first: He

last: Huang

address: 79 Qingchun Rd., Shangcheng District, Hangzhou

country: China

institute: the First Affiliated Hospital, Zhejiang University School of Medicine

data_processing:
Basecalls performed using CASAVA version 1.8
Cellranger was utilized to calculate the raw counts and cell whitelist by default parameter
We applied the Seurat [https://satijalab.org/seurat/] package for cell normalization and cell filtering considering the MT percentage, minimum and maximum gene numbers under following criteria:   MT% < 40%;    Cell Gene Number < Median Gene Number * 2;   Cell Gene Number > 200.  PCA and tSNE analysis was used for the single cell to cell relation description. Graphcluster and K-mean was utilized for cell clustering and based on the marker gene achieved some cluster was combined. Wilcox rank sum test was then used for marker gene analysis.
Genome_build: GRCh38
Supplementary_files_format_and_content: MTX file and TSV file contain counts for each barcodes and genes

source_name: Peripheral blood mononuclear cells

growth_protocol: RD13-01 contains a CAR comprising a CD7-binding scFv, a 4-1BB costimulatory domain, a CD3ζ signaling domain, and a γc intracellular domain, in addition to a EC1-EC2 extracellular domain of E-cadherin fused to a CD28 costimulatory domain. The CAR and the NKi ligand are linked by a F2A self-cleaving peptide.  The retrovirus was produced in 293GP cells, cryopreserved at -80 °C, and thawed immediately before transduction. CD3+ T cells were isolated and activated using anti-CD3/CD28 Dynabeads (Gibco, Cat no: 40203D) following the manufacturer’s protocols. The cells were cultured in X-VIVO 15 medium (Lonza, Cat no: 04-418Q) supplemented with 5% fetal bovine serum (FBS) and 300 IU/mL IL-2. Two days after T cell stimulation, the Dynabeads were removed, and CD7, TRAC, and RFX5 genes were knocked out using CRISPR/Cas9 before transduction. In brief, the T cells were washed twice with OPTI-MEM (Gibco, Cat no: 11058021) and resuspended in OPTI-MEM at a final concentration of 1~3 × 108 cells/mL. Subsequently, 0.4 mL of these cells were mixed with 120 µg of Cas9 mRNA and electroporated into the cells using a BTX Agile Pulse apparatus (500v, 1ms). Following electroporation, the cells were immediately cultured at 37 °C and 5% CO2. After 16-18 h, 40 μg of total single guide (sg)RNA targeting TRAC, CD7, and RFX5 at an equal molecular ratiowas electroporated as described below. Lastly, the T cells were centrifuged at 2,000g for 2 h at 32℃ twice with the retrovirus on days 4 and 5 in retronectin-coated plates. The CAR-T cells were expanded for an extra 6 days.  Cas9 plasmid was linearized and purified via FastPure® Gel DNA Extraction Mini Kit (Vazyme). Cas9 mRNA was synthesized by in vitro transcription with linearized Cas9 plasmid using MEGAscript™ T7 Transcription Kit (Invitrogen)，and then purified via Monarch RNA Cleanup Kit (New England Biolabs).  All sgRNAs were synthesized on Dr. Oligo 192 synthesizer using standard solid phase method. The crude product was further purified by RP-HPLC. Both termini were modified with 2′-O-methyl 3′phosphorothioate modification. Both Mass-spectrum and Next-generation sequencing were used to confirm the sequence correctness. The sgRNA was dissolved in RNase-free water and the concentration was measured using UV microplate reader.  The genomic sgRNA target sequences (with the protospacer adjacent motif in bold) were as follows: TRAC: 5'-AGAGTCTCTCAGCTGGTACACGG-3';  CD7: 5'-GTAGACATTGACCTCCGTGATGG-3';  RFX5: 5'-GGGGTTGCGGATCCACCTATAGG-3'.

extract_protocol:
Sample washing with PBS containing 0.04% BSA, the cell pellets were re-suspended in PBS containing 0.04% BSA. Dissociated single cells were then stained with AO/PI for viability assessment using Countstar Fluorescence Cell Analyzer.
RNA libraries were generated by 10xGenomics Single Cell 3’ Library Gel Bead Kit V3 and prepared for sequencing using standard Illumina protocols

treatment_protocol: The patients received lymphodepletion chemotherapy (Fludarabine 30 mg/m2 on day -7 to -3, cyclophosphamide 300 mg/m2 on day -7 to -3, and etoposide 100 mg/day on day -7 to -3) followed by RD13-01 infusion (day 0)

tag: time point

value: D19 post CAR-T infusion

value: PBMC from patient


title: HC-21 rectum biopsy week 0

value: rectum


title: HC-18 rectum biopsy week 0


title: HC-19 rectum biopsy week 0


title: CNTO1275CRD3002-20660 rectum biopsy week 0

value: Crohn's disease


title: HC-16 rectum biopsy week 0


title: PBMCs - Patient 5 in D14

value: D14 post CAR-T infusion


title: HC-22 rectum biopsy week 0


title: HC-20 rectum biopsy week 0


title: RD13-01 product - CAR-T cells

source_name: Lymphocytes

value: Baseline CAR-T

value: CAR-T cell product


title: NHS_siNT_B1 [TTchem-seq]

description:
CUG4410A1
Nascent RNA

value: No heat shock


title: single- nuclei RNA sequencing data from AKI post mortem specimen 5

description:
AKI5
single nuclei RNA-seq
10x v3.1 chemistry


title: s005_SCVI-273 ISS 1G

city: Atlanta

first: Gregory

middle: K

last: Tharp

state: GA

address: 954 Gatewood Dr

department: Developmental and Cognitive Neuroscience

institute: Yerkes National Primate Research Center

data_processing:
Illumina bcl2fastq v2.17.1.14 was used for demultiplexing.
Reads were aligned using STAR v2.7.3a.(Dobin et al.)
Transcript abundance was estimated in STAR during alignment using the algorithm or htseq-count
Genome_build: GRCh38 Ensemble release 86: Homo_sapiens.GRCh38.dna.primary_assembly.fa, Homo_sapiens.GRCh38.86.gtf
Supplementary_files_format_and_content: comma delimited text file containing ensembl ID, gene symbol, gene description and raw read counts for each sample (in columns) for each annotated transcript (in rows).

source_name: cardiomyocytes

growth_protocol: thawed the cardiac progenitor spheres into the CO2-independent medium with freshly added Rock inhibitor and cultured the cells at 37°C

extract_protocol:
RNA was isolated using RNeasy Mini Kit (Qiagen) as per the manufacturer's instructions. RNA concentration was measured using a NanoDrop ND-1000 spectrophotometer (Thermo Fisher Scientific)
Two nanograms of total RNA was used as input for cDNA synthesis, using the Clontech SMART-Seq v4 Ultra Low Input RNA kit (Takara Bio) according to the manufacturer’s instructions. Amplified cDNA was fragmented and appended with dual-indexed bar codes using the NexteraXT DNA Library Preparation kit (Illumina). Libraries were validated by capillary electrophoresis on an Agilent 4200 TapeStation, pooled at equimolar concentrations, and sequenced on an Illumina NovaSeq 6000 at 100SR.

value: cardiomyocytes

tag: gravity

value: space 1g


title: s003_SCVI-273 ISS µG

value: space ug


title: s006_SCVI-273 ISS 1G


title: HC-15 rectum biopsy week 0


title: single- nuclei RNA sequencing data from AKI post mortem specimen 3

description:
AKI3
single nuclei RNA-seq
10x v3.1 chemistry


title: s002_SCVI-273 ISS µG


title: s001_SCVI-273 ISS µG


title: single- nuclei RNA sequencing data from AKI post mortem specimen 2

description:
AKI2
single nuclei RNA-seq
10x v3.1 chemistry


title: MPH01_OUH746-DMSO

city: Oxford

first: Adam

last: Cribbs

state: Oxfordshire

address: Botnar Research Centre

department: NDORMS

institute: University of Oxford

data_processing:
Fastqc report
Kallisto index built
Kallisto bus ran k-mer size of 31
output.bus sorted. Bustools sorts
Counts quantified with bustools count, gene count matrix generated.
Genome_build: hg38
Supplementary_files_format_and_content: genes.barcodes.txt give cell barcodes, genes.genes.txt give genes, genes.mtx give matrix of genes by cells and their counts. Output from kallisto bustools count

source_name: Bone marrow

extract_protocol:
Approximately 300,000 cells were harvested for each sample for RNA extraction. Cells were centrifuged for 5 minutes at 1500rpm, the supernatant was removed, and the cell pellets were resuspended in 300ul of Trizol. 6-hour samples were stored at -80C overnight and 24 hour samples were kept on ice, prior to RNA extraction. RNA was extracted using Direct-zol RNA Miniprep kits (Zymo Research, USA), following the manufacturer’s instructions. RNA was quantified using a NanoDropTM 2000 spectrophotometer and standardised to 100ng of RNA in 50ul of nuclease free water.
Library prep was performed using Nebnext Ultra II directional RNA library prep kit for Illumina with Poly(A) mRNA Magnetic Isolation Module (New England Biolabs, USA), following the manufacturer’s instructions

treatment_protocol: AMO-1 cells and CFZr L363 cells at a confluence of 1x10^6/ml were treated with 1microM of NCP22, NCP26, MAZ1392 (halofuginone) and MAZ1805 (halofuginol), or DMSO-treated controls, for 6 and 24 hours. All conditions were performed in triplicate.

tag: experiment

tag: patient

value: Relapsed

value: DMSO

tag: drug concentration

tag: time


title: single- nuclei RNA sequencing data from AKI post mortem specimen 1

description:
AKI1
single nuclei RNA-seq
10x v3.1 chemistry


title: single- nuclei RNA sequencing data from AKI post mortem specimen 4

description:
AKI4
single nuclei RNA-seq
10x v3.1 chemistry


title: MPH01_OUH746-5-NCP26


title: s004_SCVI-273 ISS 1G


title: single- nuclei RNA sequencing data from control post mortem biopsy 120min post mortem

description:
Control-120min
single nuclei RNA-seq
10x v3.1 chemistry

value: control


title: MPH01_OUH746-1-NCP26


title: HC-17 rectum biopsy week 0

tag: tissue

tag: donor id

tag: visit


title: HC-13 rectum biopsy week 0

tag: diagnosis

tag: treatment

tag: inflamed area at week 0


title: HC-11 rectum biopsy week 0

tag: mucosal healing at week 8


title: HC-14 rectum biopsy week 0


title: HC-10 rectum biopsy week 0


title: MPH01_OUH717-1-NCP26


title: HC-12 rectum biopsy week 0


title: MPH01_OUH717-DMSO


title: Pool samples 13T, 14T, 18T

city: Bauru

first: Bruna

last: Ribeiro de Andrade Ramos

state: São Paulo

address: R. Prof Gérson Rodrigues

department: Pathology

country: Brazil

institute: São Paulo State University

hyb_protocol: This assay was performed at São Paulo State University (UNESP),according to the manufacturer’s protocol (available at https://www.nanostring.com/application/files/9614/8964/8051/MAN-C0009-05_nCounter_miRNA_Expression_Assay.pdf).

data_processing: The nSolver™ Analysis Software (www.nanostring.com/nsolver) was used to normalize miRNA expression data against positive and negative controls, exogenous and endogenous controls (miR-6721), and to calculate fold change (FC) and associated p-values for deregulated miRNAs in patient plasma compared to reference, healthy controls.

label: Color codes

source_name: Plasma samples from patient at term out of labor

label_protocol: This assay was performed at the São Paulo State University (UNESP),according to the manufacturer’s protocol (available at https://www.nanostring.com/application/files/9614/8964/8051/MAN-C0009-05_nCounter_miRNA_Expression_Assay.pdf).

extract_protocol: sEV were isolated from 1 ml of plasma using Total Exosome Isolation Reagent (from plasma – Invitrogen) following proteinase K protocol. The RNA/DNA/Protein Purification Plus Kit (Norgen) was used to extract total RNA from sEV samples.

treatment_protocol: After the lysis step of the recommended protocol, 5ul of spike-in Ath-miR-159a at 200pM was added, according to the Nanostring protocol.

tag: gender

value: F

tag: median age

value: Plasma

value: at term out of labor


title: single- nuclei RNA sequencing data from control tumor nephrectomy specimen 3

description:
Control-TN3
single nuclei RNA-seq
10x v3.1 chemistry

source_name: tumor adjacent normal kidney tissue


title: single- nuclei RNA sequencing data from control post mortem biopsy 15min post mortem

description:
Control-15min
single nuclei RNA-seq
10x v3.1 chemistry


title: MPH01_OUH717-1-Halo

value: Halofuginone


title: Pool samples 6T, 8T, 10T

scan_protocol: This assay was performed at São Paulo State University (UNESP),according to the manufacturer’s protocol (available at https://www.nanostring.com/application/files/9614/8964/8051/MAN-C0009-05_nCounter_miRNA_Expression_Assay.pdf).

tag: condition


title: HC-8 rectum biopsy week 0

value: healthy control


title: HC-7 rectum biopsy week 0

value: rectum


title: Pool samples 7T, 9T, 12T


title: single- nuclei RNA sequencing data from control tumor nephrectomy specimen 2

description:
Control-TN2
single nuclei RNA-seq
10x v3.1 chemistry

tag: disease state


title: NCP26-48H

value: Newly diagnosed


title: HC-9 rectum biopsy week 0


title: single- nuclei RNA sequencing data from control post mortem biopsy 60min post mortem

description:
Control-60min
single nuclei RNA-seq
10x v3.1 chemistry


title: MPH01_OUH746-1-Halo


title: NCP26-24H


title: single- nuclei RNA sequencing data from control tumor nephrectomy specimen 1

description:
Control-TN1
single nuclei RNA-seq
10x v3.1 chemistry


title: Pool samples 15RPM, 16RPM, 19RPM

source_name: Plasma samples from patient with preterm premature rupture of membranes

value: preterm premature rupture of membranes


title: Halo-48H


title: Pool samples 7RPM and 9RPM


title: P5_NOTCH_IGM

city: Cambridge

first: Irina

last: Mohorianu

address: Puddicombe Way

department: Wellcome-MRC Cambridge Stem Cell Institute

institute: University of Cambridge

data_processing:
the quality checking of the sequencing output was performed with FastQC, and summarised using MultiQC; additional checks include PCAs, Jaccard Similarity Indices and MA plots
the trimming was done using Trim Galore (option –paired)
the alignment of reads against the reference genome (hg38, version GRCh38.p13) was performed using tophat (option –no-coverage-search)
The count matrix was obtained using featureCounts version v1.5.0
DE analysis performed on quantile and TMM normalised expression levels with edgeR version 3.28.0; a noise filtering of 50 was applied, briefly is the maximum expression of a gene, across all samples was <50, then the gene was excluded from subsequent analyses
the enrichment analysis was performed using g:profiler (Reimand et al., Nucleic Acids Research, 2016)
Genome_build: hg38 (version GRCh38.p13)
Supplementary_files_format_and_content: raw.csv, raw count matrix.

source_name: primary CLL cells

extract_protocol:
RNA was extracted using the RNeasy Plus Micro Kit (Qiagen)
Libraries were prepared using the NEBNext Ultra™ II DNA Library Prep Kit for Illumina

value: notch

tag: igm

value: IGM

tag: disease


title: Halo-24H

tag: experiment


title: Pool samples 1RPM and 12RPM


title: HC-6 rectum biopsy week 0

source_name: rectum biopsy


title: Pool samples 10T+TP, 12T+TP, 15T+TP

source_name: Plasma samples from patient with term labor

value: term labor


title: GAK-48H

tag: patient

value: GAK


title: 10x genomics scRNA-Seq

city: NEW YORK

first: WENHUO

last: HU

email: huwenhuo@gmail.com, huw@mskcc.org

state: NEW YORK

address: 1275 YORK AVENUE

department: HOPP

institute: MEMORIAL SLOAN KETTERING CANCER CENTER

data_processing:
fastq files were aligned to  genome by cellranger v3.1 with default parameters
results from filtered_feature_bc_matrix were analyzed by Seurat 4.0 package for live cell filtering, data normalization, dimention redution analysis, differential expressed gene analysis,  and cluster identification
Trajectory analysis was performed by Slingshot package with default parameters
Genome_build: GRCh38
Supplementary_files_format_and_content: barcode, reads per cells

source_name: bladder carcinoma

extract_protocol:
Single cell RNA-Seq was performed using Chromium controller using 3' reagent kits.
according to 3' library kit (10x genomics)

tag: cell type

value: bladder carcinoma with extensive squamous cell differentiation


title: P5_NOTCH


title: GAK-24H

tag: drug concentration

tag: time


title: HC-3 rectum biopsy week 0

tag: tissue

tag: donor id


title: Pool samples 8T+TP, 11T+TP, 16T+TP


title: HC-4 rectum biopsy week 0

tag: visit

tag: diagnosis


title: HC-2 rectum biopsy week 0

tag: treatment

tag: inflamed area at week 0


title: HC-1 rectum biopsy week 0

tag: mucosal healing at week 8


title: HC-5 rectum biopsy week 0


title: P5_CTR

value: ctr


title: P4_NOTCH_IGM


title: Pool sample 1T+TP

tag: gender

tag: median age


title: P5_CTR_IGM


title: Pool samples 18TPP, 19TPP, 21TPP

source_name: Plasma samples from patient with preterm labor

tag: condition

value: preterm labor


title: CNTO1275CRD3002-20346 rectum biopsy week 0

value: Crohn's disease

value: Placebo IV

value: Ileum and colon

value: N


title: P4_NOTCH

tag: igm


title: CSNK2-24H

tag: disease state


title: DMSO-24H

tag: experiment

value: DMSO


title: Pool samples 11TPP, 13TPP, 17TPP

value: F

value: Plasma


title: CNTO1275CRD3002-20109 rectum biopsy week 0

value: rectum

value: Ustekinumab 6 mg/kg (520 mg)


title: CNTO1275CRD3002-20072 rectum biopsy week 0

value: Colon only


title: CLK-24H

tag: patient

value: Newly diagnosed

value: CLK


title: CNTO1275CRD3002-20270 rectum biopsy week 0

value: Ustekinumab 130 mg IV


title: P4_CTR_IGM

value: IGM

tag: disease


title: Cold_PBZ_3

city: Montreal

first: Lawrence

last: Kazak

state: Quebec

address: 3655 Prom Sir-William-Osler

country: Canada

institute: McGill University

library_source: genomic

data_processing:
ATAC-seq reads were first trimmed for adapter sequences and low quality score bases using Trimmomatic. The resulting reads were mapped to the mouse reference genome (mm10) using BWA-ME in paired-end mode at default parameters. Only reads that had a unique alignment (mapping quality > 20) were retained and PCR duplicates were marked using Picard tools (https://broadinstitute.github.io/picard/).
Peaks were called and annotated using MACS2. Peak annotation and transcription factor (TF) motif enrichment analysis were performed using the annotatePeaks and findMotifsGenome commands, respectively, from HOMER software suite. Peaks were associated to a gene if located within 20 kb of the TSS.
To assess differences in chromatin accessibility, a “reference peak set” was generated by merging ATAC-seq peaks across samples, using bedtools merge with parameters: -sorted -d -125 (https://bedtools.readthedocs.io/). Read counts were obtained within these genomic regions using HOMER. Raw counts were normalized using edgeR’s TMM algorithm and were then transformed to log2-counts per million (logCPM) using the voom function implemented in the limma R package.
To test for differential occupancy, we fitted a linear model that takes into account the batch effects in the experiment. Nominal p-values were corrected for multiple testing using the Benjamini-Hochberg method. Read density metagene plots and heatmaps were obtained using ngs.plot with the following parameters: -G mm10 -BOX 0 -SE 0 -VLN 0 -LWD 2 -WD 9 -L 1500.
Genome browser tracks were created with the HOMER makeUCSCfile command and bedGraphToBigWig utility from UCSC. Tracks were normalized so that each value represents the read count per base pair per 10 million reads. UCSC Genome Browser (http://genome.ucsc.edu/) was implemented for track visualization.
Assembly: mm10 mouse
Supplementary files format and content: bigWig files contain alignment data to the genome, peaks infromations

molecule: genomic DNA

source_name: Brown adipose tissue

extract_protocol:
Briefly, for nuclei preparation, BAT pads were homogenized (with pestle A) in a pre-chilled 2 ml Dounce homogenizer containing 2 ml cold 1x Homogenization Buffer (60 mM Tris pH 7.8, 30 mM CaCl2, 18 mM MgAc2, 320 mM sucrose, 0.1 mM EDTA, 0.1% NP40, 0.1mM PMSF, 1mM b-mercaptoethanol). The resulting solution was pre-cleared using a 100 μm filter and grounded 20 times (with pestle B). To generate the iodixanol gradient, 1 volume (800 μl) of 50% Iodixanol solution was added to 800 μl of grounded BAT solution to give a final concentration of 25% Iodixanol in a 5 ml Low-Bind Eppendorf tube. Then, 1.2 ml of 29% Iodixanol solution was added under the 25% mixture, and another 1.2 ml of 35% Iodixanol solution wad added under the 29% mixture. The gradient was centrifuged 3,000 g for 20 minutes at 4°C with the brake off. The nuclei band was collected into a new tube and nuclei were counted using trypan blue staining and Countess® II FL automated cell counter. 50,000 nuclei were transferred into a tube containing 1 ml of ATAC-RSB+0.1% Tween-20 and centrifuged 500 g for 10 minutes at 4°C. For optimized transposition, Omni-ATAC ATAC-seq reaction mix (25 μl 2x TD buffer, 100 nM transposase, 16.5 μl PBS, 0.01% digitonin, 0.1% Tween-20)58 was added to the nuclei pellet. Nuclei were resuspended by pipetting up and down 6 times. The resulting solution was incubated at 37°C for 30 minutes in a thermomixer (1,000 RPM). For the pre-amplification of transposed fragments, solution was cleaned with a Zymo DNA Clean and Concentrator-5 kit  (Cat. No. D4014) according to the manufacturer’s instructions. DNA was eluted in a 21 μl elution buffer and amplified for 5 cycles using NEBNext 2x MasterMix (NEB, M0541L) as previously described (PMID: 28846090), using published primers (PMID: 24097267).
10% of the pre-amplified mixture, was used to run a qPCR to determine the number of additional cycles needed as previously described58. Next, the amplification profiles were manually assessed and the required number of additional cycles were determined as previously described59. The final PCR reaction was purified using a Qiagen MinElute PCR Purification Kit and eluted in 20 μl elution buffer. A subsample of each library was diluted to 1:1,000 to fall within range of the standards to perform concentration quantification using the KAPA Library Quantification Kit (Cat No. KK4854) according to the manufacturer’s instructions.

treatment_protocol: For each condition, nuclei were isolated from 4 individual frozen BAT pads from 2 male wild-type (C57Bl6/N) mice. Animals were housed at 30°C for 5 days then exposed to cold (6°C) or kept at 30°C for 24 hours. Mice were injected with vehicle (0.9% saline) or phenoxybenzamine (5 mg kg-1) 1 hour prior to cold exposure.

value: Brown adipose tissue

tag: strain

tag: cell type

value: Adipocyte

tag: genotype

value: WT

value: 6°C + PBZ injection


title: P4_CTR

value: ctr


title: P3_NOTCH_IGM

value: notch


title: Pool samples 14TPP and 16TPP

tag: tissue

value: preterm labor


title: ORB8266-Verteporfin

value: Verteporfin

tag: drug concentration

tag: time


title: Cold_PBZ_2

tag: treatment


title: DMSO-48H

value: DMSO


title: P3_NOTCH


title: ORB8266-SGCGAK

value: SGC-GAK


title: CAMKK2-24H


title: Cold_PBZ_1


title: ORB8266-NCP26


title: CNTO1275CRD3002-20667 rectum biopsy week 0

value: rectum

tag: donor id

tag: visit

tag: diagnosis

value: Crohn's disease

tag: inflamed area at week 0

value: Ileum and colon

value: N


title: ORB8266-Halofuginono

value: Newly diagnosed

value: Halofuginone


title: Cold_veh_2

value: 6°C + saline solution injection


title: ATR_CTL

city: Kiel

first: Elmar

last: Wolf

state: Schleswig-Holstein

address: Rudolf-Höber-Str. 1

department: Biochemical Institute

institute: Christian-Albrechts-University Kiel

data_processing:
Base calling perfomed using Illumina's FASTQ Generation software v1.0.0
ChIPseq reads or CUT&RUN rerads were aligned with Bowtie2 to hg19 and to mm10 or e.coli for the spike-in
human reads were normalized to the number of spike-in reads
For 4sU Seq, only intron spanning reads were considered and read normalized before analysis.
Genome_build: hg19, mm10
Supplementary_files_format_and_content: begraph files were generated with bedtools genomecov

source_name: osteosarcoma cell line

growth_protocol: U2OS Myc TetON in DMEM with 5% FCS

extract_protocol:
crosslink (5 min), harvest, spike-in with 10 % NIH-3T3, lysis of cells, fragment with covaris
libraries were prepared for sequencing using standard NEB protocols

treatment_protocol: treat with DMSO, MG-132, Aphidicolin or hydroxyurea

tag: cell line

value: U2OS Myc TetON

tag: chip antibody

value: ATR (rabbit, A300-138A, Bethyl laboratories)

tag: label


title: P3_CTR_IGM

tag: igm

value: IGM


title: P3_CTR

tag: patient


title: CNTO1275CRD3002-20927 rectum biopsy week 0

value: Ustekinumab 6 mg/kg (390 mg)

tag: mucosal healing at week 8


title: ORB8266-GSKJ4

tag: experiment

tag: disease state


title: FANCD2_APH

value: Aphidicolin

value: FANCD2 (rabbit, abcam, ab108928)


title: FANCD2_CTL


title: TN_PBZ_3

value: Brown adipose tissue

tag: strain

tag: cell type

value: Adipocyte

tag: genotype

value: WT

value: 30°C + PBZ injection


title: P2_NOTCH_IGM

value: notch

tag: disease


title: ORB8266-DMSO

tag: treatment

value: DMSO

tag: drug concentration

tag: time


title: P2_NOTCH


title: Cold_veh_1

tag: tissue


title: Cold_veh_3


title: TN_PBZ_1


title: IgG_merged_1

value: IgG (rabbit, mouse, I5381-10MG,I5006-10MG)


title: TN_PBZ_2


title: ATR_HU

value: Hydroxyurea


title: MYC_MG132_R2

value: MG132 20 microM, 5H

value: MYC (rabbit, abcam, Y69 clone)


title: CNTO1275CRD3002-20554 rectum biopsy week 0

value: rectum

tag: donor id

tag: visit

tag: diagnosis

value: Crohn's disease

value: Ustekinumab 130 mg IV

tag: inflamed area at week 0

value: Ileum and colon

value: N


title: P2_CTR

value: ctr

tag: igm


title: Embryo.48h.n.2226

description: BRC 2226 -

data_processing:
Quality checks were performed using FastQC (v0.11.2), summarised with MultiQC (v1.8). Fastq files were randomly subsampled to 50M reads and read trimming of the first 3 nucleotides (due to poor quality) was performed using TrimGalore (v0.6.4_dev). Alignment to the human reference genome (build GRCh38.p13) was performed using STAR (STAR_2.5.2a) with default parameters. Density plots, violin plots, MA plots, Jaccard similarity index, dendrograms and PCA were performed as further quality checks
The data was normalised using quantile normalisation and noise was removed using noisyR (v1.0.0) (https://doi.org/10.1093/nar/gkab433). Differential expression analysiss was performed using edgeR (v3.28.1) and DESeq2 (1.30.0).
Enrichment analysis on the set of differentially expressed genes against a background of all genes expressed in the dataset was performed using the g:profiler (https://biit.cs.ut.ee/gprofiler/gost) R package (v0.1.8).
Genome_build: GRCh38.p13
Supplementary_files_format_and_content: Csv of raw and normalised abundances. Rows represent features and columns represent samples. Values are raw in the first instance, and normalised with noise removed in the second.

source_name: Human Developing Brain

growth_protocol: Primary patient GBM and human developing brain cultures were generated by dissociation of primary tissue samples and plated in standard adherent serum-free culture conditions supplemented with laminin, EGF and FGF (10ng/ml ea) according to published protocols (Pollard et al., Cell Stem Cell 2009), but with precoating of plastics with 1:20 laminin to improve attachment. Representative wells were dissociated for counting the day after plating, then infections performed using Zika-mCherry reporter virus at MOI 10 for 1 hour. Infected cultures were dissociated for FACS sorting and analydsasis at 48 hours or 72 hours as indicated.

extract_protocol:
Zika mCherry positive and negative fractions were sorted by FACS directly into Buffer RLT Plus, followed by extraction using Rneasy micro Plus kit according to manufacturer's instructions.
Takara Clontech Smartseq pico V2

treatment_protocol: mCherry MOI 1 48 hours (embryo); MOI 3 72 hours (GBM)

tag: infection time

tag: zika mcherry reporter status

tag: sample id


title: CNTO1275CRD3002-20449 rectum biopsy week 0

value: Placebo IV

tag: mucosal healing at week 8


title: MYC_DMSO_R2

tag: cell line

value: U2OS Myc TetON

tag: chip antibody

tag: label


title: Embryo.48h.p.2226

description: BRC 2226 +


title: TN_veh_3

value: Brown adipose tissue

tag: strain

tag: cell type

value: Adipocyte

tag: genotype

value: 30°C + saline solution injection


title: P1_NOTCH_IGM

tag: patient

tag: treatment

value: notch

value: IGM

tag: disease


title: GBM_MR.72h.n.57

description: 057 -

source_name: Glioblastoma

tag: tissue


title: MYC_MG132_R1


title: P1_NOTCH


title: TN_veh_2

value: WT


title: GBM_MR.72h.p.57

description: 057 +


title: MYC_DMSO_R1


title: ORB8266-Casin

tag: experiment

tag: disease state

value: Newly diagnosed

value: Casin

tag: drug concentration

tag: time


title: P2_CTR_IGM

tag: igm


title: P1_CTR_IGM


title: SG_DGDdgd

city: Zhengzhou

first: yanyong

last: cao

state: henan

address: No. 116, Huayuan Road

institute: Henan Academy of Agricultural Sciences

data_processing:
The program ACGT101-miR (LC Sciences, Houston, Texas, USA) used for raw data analysis of miRNAs sequencing was independently developed.
The main steps are below:  removal of 3′ adaptor and junk sequences to obtain clean sequences;
screening of miRNA length of 18-25nt; compared the sequencing data to other database, including Rfam and Repbase; Rfam is a family database of non-coding Rnas (Ncrnas), including rRNA, tRNA, snoRNA, snRNA, miRNA and other non-coding Rnas. We selected Rfam database to annotate the small RNA sequences obtained by sequencing. rRNA, snoRNA, snRNA, tRNA and other non-mirNA sequences were found and removed as far as possible.  identification of miRNAs by compare the precursors to the genome;  differential expression analysis of miRNAs;  target prediction of miRNAs.
The degradome main steps are below: a) mRNA 3' and 5' adaptor were captured by magnetic beads; b) Mixed reverse transcription of Biotinylated random primers and mRNA; c) PCR amplification. Completed degradome library was sequenced with Illumina Hiseq2000/2500.
Independently developed program ACGT101-DEG was used for degradome sequencing analysis and target genes prediction analysis was performed with CleaveLand program.
Supplementary_files_format_and_content: xls include all miRNA expressed for each Sample;xls include the degradome Identified target genes

organism: Zea mays

source_name: seed

growth_protocol: Two maize inbred lines, Yu82 and Yu537A were selected and used in this study. These two inbred lines were derived from Yuzong5, which is an improved population cultivar and is cultivated widely in China.

extract_protocol:
The embryos of five individual seeds were dissected with a sterile knife in each sample and then the samples were immediately frozen in liquid nitrogen and stored at −80 °C.Total RNA was extracted using RNAprep Pure Plant Kit (Tiangen) following the procedure of the manufacturer. The concentration was measured by Nanodrop 2000 and integrity of total RNA was tested on 1.0% agarose gel.
Small RNA library construction was conducted with TruSeq Small RNA Sample Prep Kits (Illumina, San Diego, USA). Small RNA libraries were sequenced with Illumina Hiseq2000/2500 and the sequencing read length is single-ended 1×50bp.

treatment_protocol: The seeds were harvested at the same developmental stage (mature stage, black layer formed). Then these seeds with consistent physiological state were selected and surface-sterilized with 75% ethanol. The seeds of Yu537A were pretreated with 400mg/L gibberellin (GA3) for its lower seed vigor. Two inbred lines were germinated on the two layers of filter paper with the moisture in sterile petri dishes (the diameter was about 12 cm). The seeds were incubated at a constant temperature of 25℃ under a 14/10 h (light/dark) photoperiod with photosynthetically active radiation of 25 μmol photons m−2 s−1.

value: seeds

tag: treat

value: different treatments of seeds


title: Input_merged_1


title: P1_CTR


title: SGA_53h3


title: GBM.72h.p.54

description: 054 +

tag: infection time

tag: zika mcherry reporter status

tag: sample id


title: HG2_M48

city: Dalian

first: Wang

last: Yang

address: 9 Lvshun South Rd West Section, Lüshunkou District, Dalian, Liaoning, China

department: Institute of Cancer Stem Cell

institute: Dalian Medical University

description: sample :HepG2_treat_with_Melatonin_48h

data_processing:
Raw data(raw reads) of fastq format were firstly processed through in-house perl scripts. In this step, clean data(clean reads) were obtained by removing reads containing adapter, reads on containing ploy-N and low quality reads from raw data. At the same time, Q20, Q30 and GC content of the clean data were calculated. All the down stream analyses were based on the clean data with high quality.
Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using Bowtie v2.0.6 and paired-end clean reads were aligned to the reference genome using TopHat v2.0.9.
The mapped reads of each sample were assembled by both Scripture (beta2) (Guttman et al. 2010) and Cufflinks (v2.1.1) (Trapnell et al. 2010) in a reference-based approach. Both methods use spliced reads to determine exons connectivity, but with two different approaches. Scripture uses a statistical segmentation model to distinguish expressed loci from experimental noise and uses spliced reads to assemble expressed segments. It reports all statistically expressed isoforms in a given locus. Cufflinks uses a probabilistic model to simultaneously assemble and quantify the expression level of a minimal set of isoforms that provides a maximum likelihood explanation of the expression data in a given locus (Cabili et al. 2011). Scripture was run with default parameters, Cufflinks was run with ‘min-frags-per-transfrag=0’ and ‘--library-type’, other parameters were set as default.
Cuffdiff (v2.1.1) was used to calculate FPKMs of both lncRNAs and coding genes in each sample (Trapnell, C. et al. 2010). Gene FPKMs were computed by summing the FPKMs of transcripts in each gene group. FPKM means fragments per kilo-base of exon per million fragments mapped, calculated based on the length of the fragments and reads count mapped to this fragment.
Cuffdiff provides statistical routines for determining differential expression in digital transcript or gene expression data using a model based on the negative binomial distribution (Trapnell, C. et al. 2010). Transcripts with an P-adjust <0.05 were assigned as differentially expressed.
Assembly: human NCBI genome build 38
Supplementary files format and content: The gene expression matrix from RNA-seq

growth_protocol: HepG2 cells were maintained at standard culture conditions (37°C, 5% CO2) in MEM medium with 10% FBS, Sodium Pyruvate , Nonessential Amino Acids Solution .

extract_protocol:
RNA was harvested using TRIzol and cleaned using RNAeasy Kit (Qiagen). 2 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: HepG2 cells were treated with melatonin 1 mM or DMSO for 24 h and 48 h.

tag: cell line

value: Hepatocelluar Carcinoma

value: Melatonin


title: GBM.72h.n.54

description: 054 -


title: SGA_53h2


title: SGA_53h1


title: GBM_MR.72h.n.51

description: 051 -


title: HG2_D48

description: sample :HepG2_treat_with_DMSO_48h

value: DMSO


title: GBM_MR.72h.p.51

description: 051 +


title: HG2_D24

description: sample :HepG2_treat_with_DMSO_24h


title: GBM_HR.72h.n.50

description: 050 -


title: P9_CNT.replicate1

extract_protocol:
RNA was extracted post cell sorting using the RNeasy Plus Micro Kit (Qiagen)
HiSeq4000

tag: condition

tag: replicate


title: S_78h3


title: S_78h2


title: P9_CNT.replicate2


title: GBM_HR.72h.p.50

description: 050 +


title: TN_veh_1

tag: strain

tag: cell type

tag: genotype


title: S_78h1


title: P8_Notch.replicate2

tag: patient

tag: disease


title: P8_Notch.replicate1


title: Embryo.48h.p.2215

description: 8- BRC2215 48hr positive

tag: tissue


title: BATF_cKO_DN ILC3_Rep1

first: Weiguo

last: Cui

address: 303 E Chicago Ave

institute: Northwestern University

description: BATF_cKO_DN ILC3_Rep1

data_processing:
Reads were aligned to mouse reference genome mm10 using Bowtie2.
Reads were then filtered using SAMtools (-F1796).
Peaks were called using MACS2 (--no model --shift -100 --ext size 200 -q 0.01) (version 2.1.1).
Assembly: mm10
Supplementary files format and content: bigwig files were generated using the bamCoverage function of deepTools.

source_name: small intestine

extract_protocol: ATAC-seq was performed according to a published protocol (Buenrostro et al., 2015) with minor modification.

treatment_protocol: WT or BATF_cKO mice were used for ATAC-seq experiments. 50,000-80,000 DN ILC3 cells were sorted from the intestine.

value: Batf fl/fl PLZF-cre

tag: age

value: small intestine


title: P8_CNT.replicate2

value: ctr


title: P9_Notch.replicate2


title: WT_DN ILC3_Rep2

description: WT_DN ILC3_Rep2


title: P9_Notch.replicate1


title: S_53h3


title: S_53h2


title: BATF_cKO_DN ILC3_Rep2

description: BATF_cKO_DN ILC3_Rep2


title: WT_DN ILC3_Rep1

description: WT_DN ILC3_Rep1


title: GBM_MR.72h.p.46

description: 6- 046 72hr positive


title: Colon stromal cells CD31+RSPO3+ rep 3

first: Charles

middle: Arthur

last: Whittaker

state: MA

institute: Koch Institute

description:
ngoto_200909Yil_intCt.txt.gz
ngoto_200909Yil_l2tpm.txt.gz

data_processing:
Illumina NextSeq 500 using v3 chemistry. Software: Control v2.2.0.4, RTA 2.4.11. BCL files were converted to fastq using bcl2qseq. Indexes were split using custom scripts allowing 1 mismatch.
Transcripts were quantified using Salmon version 1.3.0 (Patro et al. 2017) and the mm10 mouse assembly with the Ensembl version 101 transcriptome.  Gene level summaries were prepared using tximport version 1.16.1 (Soneson, Love, and Robinson 2015) running under R version 4.0.1 (R Core Team 2021).
Genome_build: mm10 with ensembl version 101 annotation
Supplementary_files_format_and_content: ngoto_200909Yil_intCt.txt.gz tab is a delimited text file of integer count data
Supplementary_files_format_and_content: ngoto_200909Yil_l2tpm.txt.gz is a tab delimited text file of l2tpm data

source_name: colonic stromal cells

growth_protocol: 8-12 week C57Bl6 background

extract_protocol:
Qiagen RNAeasy Kit
SMARTseq - clontech v4 chemistry from Takara

tag: cd31 expression

value: positive

tag: rspo3 gfp transgene expression


title: HG2_M24

description: sample :HepG2_treat_with_Melatonin_24h

tag: treatment

tag: time


title: S_53h1

tag: treat


title: P8_CNT.replicate1


title: GBM_MR.72h.n.46

description: 5- 046 72 hr negative

tag: infection time

tag: zika mcherry reporter status


title: MPH01_OUH717-5-NCP26

tag: experiment

tag: disease state

value: Relapsed

tag: drug concentration


title: P7_Notch.replicate2

tag: condition

tag: replicate


title: S_6h3


title: Colon stromal cells CD31-RSPO3+ rep 3

value: negative

tag: strain


title: S_6h2


title: P7_Notch.replicate1

tag: patient


title: GBM_MR.72h.p.45

description: 4- 045 72hr positive

tag: sample id


title: GBM_MR.72h.n.45

description: 3- 045 72hr negative

tag: tissue


title: Colon stromal cells CD31-RSPO3- rep 3


title: Embryo.48h.n.2215

description: 7- BRC2215 48hr negative


title: P7_CNT.replicate2

tag: disease


title: P7_CNT.replicate1


title: GBM.72h.p.43

description: 2- 043 72hr positive


title: E_53h3


title: GBM.72h.n.43

description: 1 - 043 72 hr negative


title: Colon stromal cells CD31+RSPO3+ rep 2

tag: cd31 expression


title: S_6h1


title: E_53h2


title: GBM.72h.p.39

description: 039 mCh 72hr Positive


title: P6_Notch.replicate1


title: P6_Notch.replicate2


title: E_53h1


title: GBM.72h.n.39

description: 039 mCh 72hr Negative


title: Colon stromal cells CD31-RSPO3- rep 2

tag: rspo3 gfp transgene expression


title: GBM.48h.p.39

description: 039 mCh 48hr Positive


title: P6_CNT.replicate2


title: Colon stromal cells CD31+RSPO3- rep 3


title: E_6h2


title: Colon stromal cells CD31+RSPO3+ rep 1


title: P5_Notch.replicate2


title: Colon stromal cells CD31-RSPO3+ rep 1


title: GBM_HR.72h.p.42

description: 042 mCh 72hr Positive


title: GBM.48h.n.39

description: 039 mCh 48hr Negative


title: P6_CNT.replicate1


title: P5_Notch.replicate1


title: Colon stromal cells CD31+RSPO3- rep 1


title: Rcrin knockout, scRNAseq

city: Beijing

first: Yanying

last: Wang

address: 15 Datun Road, Chaoyang District,Beijing 100101, China

institute: Institute of Biophysics, Chinese Academy of Sciences

description: 10x Genomics

data_processing:
For 10X Genomics single cells, the 10X Genomics Cell ranger software (version 2.1.1), “mkfastq,” was used to create the fastq files from the sequencer. After fastq file generation, Cell ranger “count” was used to align the raw sequence reads to the reference genome using STAR (Mus musculus (mm10 1.2.0)). The “count” software created three data files (barcodes.tsv, genes.tsv, matrix.mtx) from the “filtered_gene_bc_matrices” folder that were loaded into the R package Seurat version 2.3.4, which allows for selection and filtration of cells on the basis of quality control metrics, data normalization and scaling, and detection of highly variable genes. In brief, we kept all genes expressed in more than three cells and cells with at least 200 detected genes. Cells with mitochondrial gene percentages ＞20% and unique gene counts＞2500 or ＜200 were discarded. The data were normalized using Seurat’s “Normalize Data” function, which uses a global scaling normalization method, Log Normalize, to normalize the gene expression measurements for each cell to the total gene expression. The result is multiplied by a scale factor of 1e4 and the result is log-transformed. Highly variable genes were then identified using the function “Find Variable Genes” in Seurat. We also regressed out the variation arising from library size and percentage of mitochondrial genes using the function “Scale Data” in Seurat. We performed PCA of the variable genes as input and determined significant principal components on the basis of the “Jack Straw” function in Seurat. The first 15 principal components were selected as input for tSNE using the functions “Find Clusters” and “Run TSNE” in Seurat.
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: liver

extract_protocol:
Briefly, liver tissues were digested with Collagenase IV. Sorted single-cell suspension, 103 barcoded gel beads, and oil were loaded into Chromium Single Cell A Chip to capture single cells in nanoliter-scale oil droplets by Chromium Controller and to generate GEMs. Full-length cDNA libraries were prepared by incubation of GEMs in a thermo cycler machine. GEMs containing cDNAs were broken and all single-cell cDNA libraries were pooled together, cleaned using Dyna Beads My One Silane beads, and pre-amplified by PCR to generate sufficient mass for sequencing library construction.
Sequencing libraries were constructed by following the steps cDNA fragmentation, end repair and A-tailing, size selection by SPRI select beads, adaptor ligation, sample index PCR amplification, and repeat SPRI select beads size selection. The final constructed single-cell libraries were sequenced by Illumina Nova seq machine with total reads per cell targeted, for a minimum of 50,000.

tag: cell type

value: immune cells

value: liver

tag: age

value: 8 weeks old

tag: genotype

value: Rcrin KO


title: GBM_HR.72h.n.42

description: 042 mCh 72hr Negative

tag: infection time


title: Colon stromal cells CD31-RSPO3+ rep 2


title: WT, scRNAseq

description: 10x Genomics

value: WT


title: Colon stromal cells CD31+RSPO3- rep 2


title: P5_CNT.replicate1


title: GBM_HR.48h.n.42

description: 042 mCh 48hr Negative

tag: zika mcherry reporter status


title: Colon stromal cells CD31-RSPO3- rep 1


title: E_6h3

tag: treat


title: P4_Notch.replicate2

value: notch


title: Rcrin knockout

data_processing:
CLC Genomics Workbench v 11.0.1
Sequence reads were trimmed for adaptor sequence/low-quality sequence using CLC genomic benchwork (parameter- Quality limit: 0.05)
Trimmed sequence reads were mapped to GrCM38/mm10 using CLC genomic benchwork (parameters- mismath cost: 2 insertion cost: 3 deletion cost: 3 length fraction: 0.8 similarity fraction: 0.8)
Read count extraction and normalization were performed using CLC genomic benchwork
Assembly: mm10
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

extract_protocol:
RNA was harvested using Trizol (Invitrogen) protocol. 1.0 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacturer's protocols.

value: liver cells

value: Rcrin knockout

tag: time

value: 8 weeks


title: Small intestine stromal cells CD31+RSPO3+ rep 3

source_name: small intestinal stromal cells


title: GBM_HR.48h.p.42

description: 042 mCh 48hr Positive


title: WT


title: Small intestine stromal cells CD31-RSPO3+ rep 3


title: Embryo.72h.p.2208

description: 2208 mCh 72hr Positive


title: P4_Notch.replicate1


title: Small intestine stromal cells CD31+RSPO3- rep 3


title: E_6h1

value: seeds

value: different treatments of seeds


title: Embryo.72h.n.2208

description: 2208 mCh 72hr Negative


title: P4_CNT.replicate2


title: Small intestine stromal cells CD31-RSPO3- rep 3


title: P5_CNT.replicate2


title: IgG_C_HTO

city: New York

first: Yu-Jui

last: Ho

state: New York

address: 417 E 68th St

department: Cancer Biology & Genetics Program

institute: Memorial Sloan Kettering Cancer Center

description: polyA HTO

data_processing:
The data was processed using the tool SEQC wich was created by the Pe'er lab. It can be accessed on github: https://github.com/dpeerlab/seqc
The genome these samples were aligned against is a custom build that can be found (and is publicly available) here:s3://seqc-public/genomes/mm38_long_polya/
Supplementary files format and content: The output (the dense.csv files) is a filtered count matrix where: Rows are cells and columns are genes. Note that the first column may be called CLUSTER , which indicates clustering assignment of each cell and must not be treated as a gene.
Supplementary files format and content: For the HTO data: The data was processed using the tool SHARP, github link here: https://github.com/hisplan/sharp. The "final_classification" file is a gzipped tsv file that contains the cell barcode with its hashtag assignment on every row.

source_name: CD45+ cells from pancreas tumor

growth_protocol: Mice undergo a survival surgery where the pancreas is exposed and 100.000 cells of the different genotypes are injected. Mice are then monitored and when they have overt disease assessed by palpation (~4 weeks after injection), the tumors are collected and a piece is flash frozen for total RNA extraction.

extract_protocol:
The single-cell RNA-Seq of FACS-sorted cell suspensions was performed on Chromium instrument (10X genomics) following the user guide manual for 3′ v3.1
Cells were captured in droplets. Following reverse transcription and cell barcoding in droplets, emulsions were broken and cDNA purified using Dynabeads MyOne SILANE followed by PCR amplification per manual instruction. Between 15,000 to 25,000 cells were targeted for each sample. Samples were multiplexed together on one lane of 10X Chromium following cell hashing protocol.
Final libraries were sequenced on Illumina NovaSeq S4 platform (R1 – 28 cycles, i7 – 8 cycles, R2 – 90 cycles). The cell-gene count matrix was constructed using the Sequence Quality Control (SEQC) package.

treatment_protocol: Mice were pre-treated with either IgG or anti-IFNAR1 antibodies (200 ug i.p. 3 times a week) starting one week before injection of cells and kept until the end of the experiment.

value: Sorted cells

tag: treatment

value: IgG antibody


title: IFNAR_A_HTO

description: polyA HTO

value: IFNAR1 antiody


title: Small intestine stromal cells CD31+RSPO3+ rep 2

value: positive


title: P4_CNT.replicate1

tag: condition

value: ctr


title: IgG_A_HTO

description: polyA HTO


title: control_2251EMB_BRC2251_2

data_processing:
Quality checks were performed using FastQC (v0.11.2), summarised with MultiQC (v1.8). Fastq files were randomly subsampled to 25M reads. Alignment to the human reference genome (build GRCh38.p13) was performed using STAR (STAR_2.5.2a) with default parameters. Density plots, violin plots, MA plots, Jaccard similarity index, dendrograms and PCA were performed as further quality checks
The data was normalised using quantile normalisation and noise was removed using noisyR (v1.0.0) (https://doi.org/10.1093/nar/gkab433). Differential expression analysiss was performed using edgeR (v3.28.1) and DESeq2 (1.30.0).
Enrichment analysis on the set of differentially expressed genes against a background of all genes expressed in the dataset was performed using the g:profiler (https://biit.cs.ut.ee/gprofiler/gost) R package (v0.1.8).
Genome_build: GRCh38.p13
Supplementary_files_format_and_content: Csv of raw and normalised abundances. Rows represent features and columns represent samples. Values are raw in the first instance, and normalised with noise removed in the second.

source_name: Human Developing brain

growth_protocol: GSCs, primary microglia and human developing brian cultures were plated in standard adherent serum-free culture conditions supplemented with laminin, EGF and FGF (10ng/ml ea) according to published protocols (Pollard et al., Cell Stem Cell 2009), at a plating density 35,000 cells per cm2 and media volume 250ul per cm2. Conditioned media was harvested from these cultures after 48 hours, mixed 50:50 with fresh media and applied to cultures for 48 hours prior to harvesting cells for RNA extraction.

extract_protocol:
Extraction using Rneasy micro Plus kit according to manufacturer's instructions.
NEB Ultra II

treatment_protocol: MG vs GSC CM 48 hours

tag: conditioned media type

tag: conditioned media origin

tag: treated stem cells

tag: sequencing lane


title: control_2251EMB_BRC2251_1


title: P3_Notch.replicate2

tag: patient

tag: replicate


title: Small intestine stromal cells CD31-RSPO3+ rep 2

tag: cd31 expression

value: negative

tag: strain


title: IFNAR_A

description: polyA RNA


title: control_G334_BRC2251_2


title: IgG_C

description: polyA RNA


title: P3_Notch.replicate1

tag: disease


title: control_G334_BRC2251_1


title: IgG_A

description: polyA RNA


title: P3_CNT.replicate2


title: P3_CNT.replicate1


title: Small intestine stromal cells CD31+RSPO3+ rep 1

tag: rspo3 gfp transgene expression


title: Small intestine stromal cells CD31-RSPO3- rep 2


title: Myeloid, scRNAseq

city: shang hai

first: Qian

last: Zhang

address: xiangyin road 800

institute: Second military medical university

description: 10x Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v2.1.1 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: mm10
Supplementary files format and content: hdf5 file

source_name: B16-F10 allografts

growth_protocol: Briefly, B16-F10, were inoculated subcutaneously in the right flank of C57BL/6 mice

extract_protocol:
Tumors were mechanically dissociated and digested with collagenase type IV  and DNase I for acquiring single cells. CD45+CD19-CD3-NK1.1- cells were sorted.
Library was performed according to the manufacter’s instructions (single cell 3’ v2 protocol, 10x Genomics). Briefly, cells were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead-in-emulsion (GEM). The poly-A RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA, which contains an Ilumina R1 primer sequence, Unique Molecular Identifier (UMI) and the 10x Barcode. The pooled barcoded cDNA was then cleaned up with Silane DynaBeads, amplified by PCR and the apropiated sized fragments were selected with SPRIselect reagent for subsequent library construction. During the library construction Ilumina R2 primer sequence, paired-end constructs with P5 and P7 sequences and a sample index were added.

tag: cell type

value: Myeloid cells

tag: tissue

value: B16-F10 allografts

tag: age

value: 6-8 weeks old


title: control_G322_BRC2251_2


title: control_G322_BRC2251_1


title: Small intestine stromal cells CD31+RSPO3- rep 2


title: Cold_PBZ_3 [JF48-12]

data_processing:
Base calling was performed with RTA v3.4.4 .
Program bcl2fastq2 v2.20 was then used to demultiplex samples and generate fastq reads.
Adaptor sequences and low quality score bases (Phred score < 30) were first trimmed using Trimmomatic v.0.36.
The resulting reads were aligned to the GRCm38 mouse reference genome assembly, using STAR v.2.0.2.
Read counts were obtained using HTSeq v.0.6.0 with parameters -m intersection-nonempty -stranded=reverse.
For all downstream analyses, we excluded lowly-expressed genes with an average read count lower than 10 across all samples, resulting in 17,952 genes in total. Raw counts were normalized using edgeR’s TMM algorithm v3.26.8 and were then transformed to log2-counts per million (logCPM) using the voom function implemented in the limma R package. To assess differences in gene expression levels between the different conditions, we fitted a linear model using limma’s lmfit function. Nominal p-values were corrected for multiple testing using the Benjamini-Hochberg method.
Assembly: GRCm38 mouse
Supplementary files format and content: tab-delimited text files include CPM or TPM values for each Sample

extract_protocol:
Total RNA was extracted from frozen tissue using QIAzol (Qiagen) and purified with RNeasy Mini spin columns (Qiagen) according to the manufacturer’s instructions. Libraries were generated from 250 ng of total RNA.
mRNA enrichment was performed using the NEBNext Poly(A) Magnetic Isolation Module (New England BioLabs). cDNA synthesis was achieved with the NEBNext RNA First Strand Synthesis and NEBNext Ultra Directional RNA Second Strand Synthesis Modules (New England BioLabs). The remaining steps of library preparation were done using and the NEBNext Ultra II DNA Library Prep Kit for Illumina (New England BioLabs). Adapters and PCR primers were purchased from New England BioLabs. Libraries were quantified using the Kapa Illumina GA with Revised Primers-SYBR Fast Universal kit (Kapa Biosystems). Average size fragment was determined using a LabChip GX (PerkinElmer) instrument. The libraries were normalized and pooled and then denatured in 0.05N NaOH and neutralized using HT1 buffer.

treatment_protocol: RNA-seq transcriptomes from BAT of mice pre-treated with either a single intraperitoneal injection of the a-AR antagonist, phenoxybenzamine (PBZ) or saline control and then housed at 30°C or 6°C

value: Brown adipose tissue

value: Adipocyte

tag: genotype

value: 6°C + PBZ injection


title: P2_Notch.replicate2

source_name: primary CLL cells

value: notch


title: microglia_070MG_BRC2251_2


title: Small intestine stromal cells CD31-RSPO3+ rep 1


title: P2_Notch.replicate1


title: P2_CNT.replicate1


title: P2_CNT.replicate2


title: Cold_PBZ_1 [JF48-10]

value: WT


title: microglia_069MG_BRC2251_2


title: Small intestine stromal cells CD31+RSPO3- rep 1


title: Cold_veh_3 [JF48-9]

value: 6°C + saline solution injection


title: Small intestine stromal cells CD31-RSPO3- rep 1


title: P13_Notch.replicate2


title: microglia_070MG_BRC2251_1


title: microglia_069MG_BRC2251_1


title: Cold_veh_2 [JF48-8]


title: microglia_067MG_BRC2251_2


title: P13_Notch.replicate1


title: t24h_wt4

city: Basel

first: DBM Bioinformatics

last: Core Facility

state: BS

address: Hebelstrasse 20

department: Departement of Biomedicine

country: Switzerland

institute: University of Basel

data_processing:
Read quality was assessed with the FastQC tool (version 0.11.5). Reads were mapped to the mouse genome (UCSC version mm10) with STAR (version 2.5.2a) with default parameters, except filtering out reads mapping to more than 10 genomic locations (outFilterMultimapNmax=10), reporting only one hit in the final alignment for multimappers (outSAMmultNmax=1) and filtering reads without evidence in the spliced junction table (outFilterType="BySJout").
Gene expression data analysis was performed using the R software (version 3.5). Read alignment quality was evaluated using the qQCReport function of the R Bioconductor package QuasR (version 1.18). Gene expression was quantified using the qCount function of QuasR as the number of reads (5'ends) overlapping with the exons of each gene assuming an exon union model (using the UCSC knownGenes annotation downloaded on 2015-12-18).
The R Bioconductor package edgeR (version 3.24.3) was used for differential gene expression analysis. Between samples normalization was done using the TMM method. Only genes with CPM (counts per million reads mapped) values more than 1 in at least 4 samples (the number of biological replicates) were retained. An generalized linear model including a genotype effect, an activation effect, and a replicate effect (nested within genotype) was fitted to the raw counts (function glmFit), and differential expression was tested using likelihood ratio tests (function glmLRT). P-values were adjusted by controlling the false-discovery rate (Benjamini-Hochberg method) and genes with a FDR lower than 1% were considered differentially expressed.
Gene set enrichment analysis was performed with the function camera from the edgeR package (using the default parameter value of 0.01 for the correlations of genes within gene sets) using gene sets from the curated gene set collection of the Molecular Signature Database (MSigDB v6.0). We considered only sets containing more than 10 genes and gene sets with a false discovery rate lower than 1% were considered significant.
Genome_build: mm10
Supplementary_files_format_and_content: gzipped text file with tab-separated counts for each gene; each row contains the annotation and raw counts per gene; columns correspond to: 1. Entrez Gene ID, 2. gene length (exon union model), 3.-40. read counts per gene and sample.

source_name: CD4+ T cells

growth_protocol: Naïve CD4+ T cells were isolated from cell suspensions of pooled lymph nodes and spleen from single mice (male or female). Isolation was performed with StemCell mouse naïve CD4+ T cell isolation kit according to manufacturer’s instructions.

extract_protocol:
2.5*10^5 cells were washed with PBS and resuspend in 200µl TRI Reagent. RNA was extracted from Trizol-samples with a Zymo Direct-zol kit which includes DNAse treatment.
RNA quality was assessed with a Fragment Analyzer (Advanced Analytical) and RNA-seq library preparation was performed using Illumina Truseq stranded kit. Sequencing was performed on an Illumina NexSeq 500 machine to produce single-end 76-mers reads. All steps were performed at the Genomics Facility Basel (ETH Zurich).

treatment_protocol: Cells were cultured for 24 hours on plates coated with a combination of anti-CD3 (0.5µg per ml PBS) and anti-CD28 (0.2µg per ml PBS) mAb to mimic activation and co-activation signals. Plates were washed with PBS before plating the cells in complete T cell medium supplied with 50U IL2/ml.

value: wt

tag: activation

value: CD4+ T cells


title: t24h_wt3


title: t24h_wt2


title: microglia_067MG_BRC2251_1


title: control_2251EMB_G334_2

source_name: Cell Line


title: Cold_veh_1 [JF48-7]

tag: treatment


title: TN_PBZ_3 [JF48-6]

value: 30°C + PBZ injection


title: P13_CNT.replicate1

tag: condition


title: control_2251EMB_G334_1

tag: conditioned media type


title: TN_PBZ_2 [JF48-5]


title: t24h_tg4


title: P12_Notch.replicate2


title: Cold_PBZ_2 [JF48-11]


title: t24h_tg3


title: t24h_wt1


title: control_G334_G334_1

tag: conditioned media origin


title: P12_CNT.replicate2


title: P12_Notch.replicate1


title: t24h_tg1


title: TN_PBZ_1 [JF48-4]


title: TN_veh_2 [JF48-2]

value: 30°C + saline solution injection


title: P12_CNT.replicate1


title: t24h_tg2


title: TN_veh_1 [JF48-1]


title: P13_CNT.replicate2


title: t24h_res3

value: rescue


title: control_G322_G334_1

tag: treated stem cells


title: P11_Notch.replicate2


title: microglia_070MG_G334_2

tag: sequencing lane


title: t24h_res2


title: P11_Notch.replicate1

tag: patient


title: t24h_res1


title: MmES_Cbx2.VD-2x_Eed-KO_run2

city: Toronto

first: Gianluca

last: Veggiani

address: 160 College Street

department: Banting and Best Department of Medical Research, University of Toronto

institute: Donnelly Centre for Cellular and Biomolecular Research

description: enriched DNA

data_processing:
Adaptor sequences were removed using Trim Galore (https://github.com/FelixKrueger/TrimGalore). Trimmed reads were mapped to the mm9 mouse genome reference using Bowtie2 version 2.3.5.1 using the --no-unal and --very-sensitive options. Alignments were stored as BAM files, low-quality reads (excluding reads with mapping quality < 40) were filtered out using SAMtools 1.11, and identical reads from PCR duplicates removed with Picard Toolkit (version:2.23.9).
BAM files were checked for GC-bias and corrected using the correctGCBias module of deepTools (3.5.0). GC-corrected BAM files were converted to bigWig files for visual inspection in genome browsers at 100 base-pair resolution, normalized by Reads Per Kilobase per Million mapped reads (RPKM), and excluding mm9-blacklisted regions using the bamCoverage module of deepTools.
Genome_build: mm9
Supplementary_files_format_and_content: bigWig track format: read coverage per consecutive 100bp windows, RPKM-normalized.

source_name: embryonic stem cell

growth_protocol: Wild type embryonic stem cells derived from mixed 129-C57Bl/6 background blastocysts, were cultivated on feeder cells or 0.2% gelatine coated dishes. ES cell growth medium consisted of DMEM (Invitrogen) supplemented with 15% foetal calf serum (Invitrogen), 1x non-essential amino acids (Invitrogen), 1mM L-glutamine, LIF and 0.001% beta-mercaptoethanol.

extract_protocol:
ChIP samples were collected from two biological replicates (independent mESC cell lines). For chromatin extraction, 30-50 x 106 cells were trypsinized, washed once in PBS and fixed with 1% formaldehyde for 8 minutes at 25 ºC, followed by reaction quenching with addition of glycine to a final concentration 0.12 M and incubation on ice for 10 minutes. Cells were washed twice in 10 ml ice-cold PBS, followed by centrifugation at 680 × g for 5 min. Cells were resuspended and incubated for 10 min in 10 ml Paro Rinse 1 buffer (10 mM EDTA, 10 mM TRIS, 0.5 mM EGTA) on ice, followed by centrifugation at 680 × g for 5 min. Cells were resuspended in 10 ml Paro Rinse 2 buffer containing 0.25% Triton X-100, 1 mM EDTA, 10 mM TRIS, 0.5 mM EGTA, and 200 mM NaCl, pass three times through a prechilled G26 syringe, and incubated for 10 min on ice followed by centrifugation at 680 × g for 5 min. Final cell lysis was performed with Mnase Digest Buffer (20 mM TRIS, 5 mM MgCl2, 1 mM CaCl2, 10 mM NaCl, 0.25 M Sucrose, 1% Triton X-100, supplemented with protease inhibitor cocktail mix (Roche, 11836170001)) in a concentration-dependent volume (16500 cells per microliter) for 0.5 to 1 hour on ice. Cross-linked chromatin was subjected to MNase digestion (50 Units MNase per 1 ml buffer) in a waterbath at 37°C for 20 minutes with repeated stirring. The digest was stopped by adding 10x Stop Buffer to a final concentration of 150 mM NaCl, 100 mM EDTA, 200 mM EGTA on ice and SDS to 0.1 % final concentration. MNase-digested chromatin was subjected to sonication (four cycles of 32’’ON/50’’OFF) in a Bioruptor Pico instrument (Diagenode) according to the manufacturer's instructions. Sonicated chromatin was centrifuged at 12,000 × g for 10 min at 4°C and supernatant was used for further steps. For biotin ChIP-seq, 100 µg chromatin, extracted from mESCs expressing biotinylated Cbx.VDs were applied to 30 µl of streptavidin M280 magnetic beads previously blocked for 1 hour at 4ºC with 1% cold fish skin gelatin (Sigma-Aldrich, G7041) and 100 ng yeast tRNA (Thermo Fischer, 15401011) supplemented with protease inhibitor cocktail mix (Roche, 11836170001). Chromatin was incubated with beads at 4ºC, overnight with end-over-end rotation. Following overnight incubations, beads were washed with two rounds of 2% SDS, 1x high salt buffer, 1x LiCl Buffer and two rounds of TE. Beads were treated with RNaseA for 30 min at 37°C, Proteinase K for 3 hours at 50°C then de-crosslinked over night at 55°C. DNA was purified with Phenol-Chloroform extraction and EtOH precipitation.
ChIP-seq, libraries were prepared using the NEBNext Ultra II DNA library prep Kit for Illumina (New England Biolabs, E7645L) according to the manufacturer’s instructions. Samples tagged with unique index barcodes were combined at equal molar ratios and sequenced as pools on a NovaSeq 6000 sequencing system (Illumina) according to Illumina standards with 100 base-pair single-end sequencing. Library demultiplexing was performed following Illumina standards.

value: embryonic stem cells

value: Eed-KO

tag: ChIP

value: streptavidin


title: MmES_Cbx7.VD-2x_Eed-KO_run2

description: enriched DNA


title: P11_CNT.replicate2

data_processing:
the quality checking of the sequencing output was performed with FastQC, and summarised using MultiQC; additional checks include PCAs, Jaccard Similarity Indices and MA plots
the trimming was done using Trim Galore (option –paired)
the alignment of reads against the reference genome (hg38, version GRCh38.p13) was performed using tophat (option –no-coverage-search)
The count matrix was obtained using featureCounts version v1.5.0
DE analysis performed on quantile and TMM normalised expression levels with edgeR version 3.28.0; a noise filtering of 50 was applied, briefly is the maximum expression of a gene, across all samples was <50, then the gene was excluded from subsequent analyses
the enrichment analysis was performed using g:profiler (Reimand et al., Nucleic Acids Research, 2016)
Genome_build: hg38 (version GRCh38.p13)
Supplementary_files_format_and_content: raw.csv, raw count matrix.

value: ctr

tag: replicate


title: microglia_070MG_G334_1


title: TN_veh_3 [JF48-3]

tag: strain


title: t24h_lox4


title: microglia_069MG_G334_2


title: P11_CNT.replicate1

tag: disease


title: control_G334_G334_2


title: MmES_Cbx2.VD-2x_Eed-KO_run1

description: enriched DNA


title: control_G322_G334_2


title: t24h_lox3


title: P10_Notch.replicate2


title: MmES_Cbx7.VD-2x_run2

description: enriched DNA

value: wild type


title: t24h_lox2


title: microglia_069MG_G334_1


title: t24h_lox1


title: control_2251EMB_G322_2


title: MmES_Cbx7.VD-2x_run1

description: enriched DNA


title: control_2251EMB_G322_1


title: MmES_Cbx7.VD_run2

description: enriched DNA


title: P10_CNT.replicate2


title: MmES_Cbx7.VD-2x_Eed-KO_run1

description: enriched DNA


title: t24h_ko4


title: control_G334_G322_2


title: MmES_Cbx7.VD_run1

description: enriched DNA


title: control_G334_G322_1


title: t24h_ko3


title: P1_Notch.replicate1


title: MmES_Cbx2.VD-2x_run2

description: enriched DNA


title: P1_Notch.replicate2


title: control_G322_G322_1


title: t24h_ko2


title: t24h_ko1


title: P1_CNT.replicate2


title: microglia_070MG_G322_2


title: naive_wt4

value: naive


title: MmES_Cbx2.VD-2x_run1

description: enriched DNA


title: P1_CNT.replicate1


title: MmES_Cbx7.wt-2x_run2

description: enriched DNA


title: microglia_070MG_G322_1


title: MmES_Cbx2.VD_run1

description: enriched DNA


title: microglia_069MG_G322_2


title: P10_Notch.replicate1


title: MmES_Cbx7.wt-2x_run1

description: enriched DNA


title: FSE_RAS_day4_2

city: Jerusalem

first: Dan

last: Sarni

address: Givart Ram

country: Israel

institute: The Hebrew University of Jerusalem

description: Gene.counts.matrix.txt

data_processing:
Reads were aligned to the hg19 genome (UCSC, downloaded from iGenomes) using TopHat (v2.0.10)
HTSeq-count (version 0.6.1p1) was used to count reads on gene exons (UCSC Annotation from March 9, 2012).
The number of fragments obtained for each gene in each sample was normalized to the total number of fragments obtained from this sample
Genome_build: hg19
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: FSE

growth_protocol: Human foreskin fibroblasts FSE-hTERT cells were grown in DMEM supplemented with 10% fetal bovine serum, 1000,000 U l-1 penicillin and 100 mg l-1 streptomycin. The cells were tested and found negative for mycoplasma.

extract_protocol:
Total RNA was extracted using the RNeasy Mini Kit extraction kit (QIAGEN)
Sequencing libraries were prepared using the Illumina TruSeq mRNA kit

treatment_protocol: Cells were treated with 0.2mM 4-OHT in growth media for the indicated time periods

tag: 4-oht treatment length (days)


title: naive_wt2

tag: cell type


title: naive_wt3


title: microglia_069MG_G322_1


title: P10_CNT.replicate1


title: control_G322_G322_2


title: naive_wt1


title: MmES_Cbx2.wt-2x_run2

description: enriched DNA


title: FSE_RAS_day4_1

description: Gene.counts.matrix.txt


title: naive_tg4


title: MmES_Cbx2.VD_run2

description: enriched DNA


title: microglia_067MG_G322_2


title: FSE_RAS_day4_3

description: Gene.counts.matrix.txt


title: microglia_067MG_G322_1


title: CLL_ NOTCH1ΔPEST vector H3K27ac  [P5]

data_processing:
Raw fastq files alignment using bwa 0.7.7, picard & samtools.
Wiggle plots generation using PhantomPeakQualTools.
Narrow peak calling using MACS2 callpeak function with q-value < 0.01 and without input control.
Genome_build: GRCh38.p3
Supplementary_files_format_and_content: *.bed: Bed files describing the location of the peaks.

source_name: Primary CLL cells

extract_protocol:
ChIP-seq were generated as described: http://www.blueprint-epigenome.eu/index.cfm?p=7BF8A4B6-F4FE-861A-2AD57A08D63D0B58
Libraries were constructed using the Kapa Hyper Prep Kit as previously described (https://www.blueprint-epigenome.eu/UserFiles/File/Protocols/Blueprint_Kapa_hyper_prep_kit.pdf).
SE, 50bp

treatment_protocol: Cells were crosslinked with 1% formaldehyde, 15 minutes at 4º. Reaction was stopped with 1.25 M glycine for 5 minutes.

tag: diagnosis

value: Chronic lymphocytic leukemia

value: Primary CLL cells from peripheral blood

tag: genotype/variation

tag: chip antibody


title: MmES_EGFP

description: enriched DNA

tag: genotype


title: naive_tg2

tag: activation


title: FSE_RAS_day2_1

description: Gene.counts.matrix.txt


title: B6_GAL_rep3

city: Ann Arbor

first: Brian

last: Magnuson

state: MI

address: 1500 East Medical Center Drive

institute: University of Michigan

data_processing:
Libraries were sequenced on a NovaSeq 6000 (Illumina) with 101 cycles (per read) of paired-end sequencing. Bcl2fastq2 (Illumina) was used to generate demultiplexed Fastq files.
Reads were trimmed using Trimmomatic v0.39 (Bolger et al. Bioinformatics. 2014) with parameters ILLUMINACLIP: TruSeq3-PE.fa:2:30:10:2:true LEADING:3 TRAILING:3 MINLEN:35 SLIDINGWINDOW:4:15.
Paired-end alignments and gene level counts were obtained using RSEM v1.3.1 (Li and Dewey. BMC Bioinformatics. 2011). STAR v2.5.2a was the aligner called by RSEM and the default parameters were used (Dobin et al. Bioinformatics. 2013.)
The mouse reference sequence mm10 and annotations, including gene IDs, were obtained from GENCODE version M21 (Frankish et al. Nucleic Acids Res. 2018).
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: B6_*.txt: Sample genes and isoforms files are standard RSEM output (tab-delimited text files with headers). See the RSEM documentation for column descriptions.
Supplementary_files_format_and_content: genes.*.txt, isoforms.*.txt: Sample matrices (tab-delimited text with headers) for counts, FPKM, and TPM are provided for both genes and transcript isoforms. The first 4 columns contain gene and transcript IDs.

source_name: TH17 Cells

growth_protocol: Naïve CD4 T cells were isolated from mice spleens and lymph nodes by magnetic bead separation (Miltenyi Biotec) following the manufacturers’ protocols. Cells were cultured in glucose-free RPMI (Gibco) supplemented with 10% heat-inactivated FBS (Corning), 1% penicillin/streptomycin (Gibco), 50μM 2-Mercaptoethanol (Gibco), and either 10mM glucose (Sigma) or 10mM galactose (Sigma). Naïve CD4 T cells were activated with plate-bound anti-CD3e (5μg/ml; clone 145-2C11; eBioscience) and soluble anti-CD28 (2μg/ml; clone 37.51; eBioscience) in the presence of mIL-1β (10 ng/ml; R&D Systems), mIL-23 (10ng/ml; R&D Systems), mIL-6 (50ng/ml; R&D Systems), and hTGF-β (5ng/ml; Peprotech) for TH17 cell polarization. All cells were cultured at 37°C and 5% CO2. TH17 differentiation was verified on day 3 or 4, and cytokine expression on day 5, at which point cells were used for subsequent assays.

extract_protocol:
Total RNA was extracted using RNeasy Plus Micro Kit (Qiagen).
Strand-specific, polyA-selected libraries were prepared using the NEBNext Poly(A) mRNA Magnetic Isolation Module (NEB, E7490) and the NEBNext Ultra II Directional RNA Library Prep Kit (NEB, E7760).

value: T helper 17

tag: culture condition

value: galactose (10mM)


title: CLL_empty vector_H3K27ac  [P5]

value: Control


title: naive_tg1


title: FSE_RAS_day2_3

description: Gene.counts.matrix.txt


title: CLL_ NOTCH1ΔPEST vector H3K27ac  [P4]


title: B6_GAL_rep2


title: FSE_control _3

description: Gene.counts.matrix.txt


title: naive_res3


title: FSE_RAS_day2_2

description: Gene.counts.matrix.txt


title: naive_res2


title: B6_GAL_rep1


title: FSE_control_2

description: Gene.counts.matrix.txt


title: FSE_control_1

description: Gene.counts.matrix.txt


title: CLL_empty vector_H3K27ac  [P4]


title: CLL_ NOTCH1ΔPEST vector H3K27ac  [P1]


title: naive_res1


title: CLL_ NOTCH1ΔPEST vector H3K27ac  [P3]


title: B6_GLC_rep2

value: glucose (10mM)


title: MmES_Cbx2.wt-2x_run1

description: enriched DNA


title: B6_GLC_rep3


title: naive_tg3


title: CLL_empty vector_H3K27ac  [P3]


title: naive_lox4


title: B6_GLC_rep1


title: naive_lox3


title: CLL_ NOTCH1ΔPEST vector H3K27ac  [P2]


title: PBS_rep3

city: Suita

first: Masayuki

last: Nakamori

state: Osaka

address: 2-2, D-4, Yamadaoka

department: Neurology

institute: Osaka University Graduate School of Medicine

data_processing:
The libraries were sequenced on an Illumina Nova Seq 6000 (Illumina),
FastQC evaluated FASTQ files after the trimming process using PRINSEQ v0.19.2 (Schmieder and Edwards, 2011).
The FASTQ files were aligned to the genomic reference sequence using TopHat v.2.0.13 (Kim et al., 2013).
The estimated transcript abundance was calculated, and the count values were normalized to the upper quartile of the fragments per kilobase of transcript per million mapped reads using Cufflinks v2.2.1 (Trapnell et al., 2010).
Genome_build: GRCm38
Supplementary_files_format_and_content: Tab-delimited text files include FPKM values for each Sample.

extract_protocol:
At 22 weeks of age, mice were sacrificed, and RNA were isolated from the murine brain tissue. RNA was harvested using Trizol reagent. Illumina TruSeq stranded mRNA library prep was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols.

tag: tissue

value: striatum

tag: treatment

value: PBS

value: Q113 DRPLA transgenic mice