title: 10x_9072


title: 10x_9071

status: Public on May 01 2020

type: SRA

city: Rehovot

first: Itay

last: Tirosh

address: Herzl 234

country: Israel

institute: WEIZMANN INSTITUTE OF SCIENCE

library_source: transcriptomic

data_processing:
Paired-end, 38-base reads were mapped to the UCSC hg19 human transcriptome using Bowtie with parameters "-q --phred33-quals -n 1 -e 99999999 -l 25 -I 1 -X 2000 -a -m 15 -S -p 6". Expression values were calculated by   RSEM v1.2.3 in paired-end mode using parameters "--estimate-rspd --paired end -sam -p 6", from which TPM values for each gene  were extracted. For the subset of cells processed with 10X, we used CellRanger with the default parameters.
We examined as quality control the number of genes detected in each cell and conservatively excluded cells with fewer than 2,000 detected genes.
Genome_build: hg19
Supplementary_files_format_and_content: Two tab-delimited files containing log2(TPM/10+1) values (TPM=transcript-per-million reads) of 9609 cells profiled by 10x droplet scRNA-seq (10x file) and of 1297 cell profiled by SmartSeq2 (SS2 file). All quantified 23,686 genes are included in the SS2 file and 11,548 genes detected in at least 10 cells are included in the 10x file. Header lines include Cell ID, patient ID, time point of sample acquisition, and the cells assignment into clusters and coordinates in a tSNE analysis (as shown in an associated manuscript).

molecule: polyA RNA

organism: Homo sapiens

source_name: Malignant ascites  single cell

extract_protocol:
RNA from single cells was first purified with Agencourt RNAClean XP beads (Beckman Coulter)
Libraries from isolated single cells were generated based on the Smart-seq2 protocol (Picelli  2014) with the following modifications.oligo-dT were used to prime reverse transcription with Maxima reverse transcriptase and locked TSO oligonucleotide, which was followed by 20 cycle PCR amplification using KAPA HiFi HotStart ReadyMix (KAPA Biosystems) with subsequent Agencourt AMPure XP bead purification as described. Libraries were tagmented using the Nextera XT Library Prep kit (Illumina) with custom barcode adapters (sequences available upon request). Libraries from 384 cells with unique barcodes were combined and sequenced using a NextSeq 500 sequencer (Illumina). For a subset of samples, single cells were processed through the 10X Chromium 3 Single Cell Platform using the Chromium Single Cell 3’ Library, Gel Bead and Chip Kits (10X Genomics, Pleasanton, CA), following the manufacturer’s protocol. Briefly, cells were added to each channel of a chip to be partitioned into Gel Beads in Emulsion (GEMs) in the Chromium instrument, followed by cell lysis and barcoded reverse transcription of RNA in the droplets. Breaking of the emulsion was followed by amplification, fragmentation and addition of adapter and sample index.

treatment_protocol: Ascites fluid was drained by an interventional radiologist and transferred for further processing in closed vacuum bottles. De-identified patient information, including their ovarian cancer histology, stage, treatment history, and BRCA mutation status were collected. Immediately following drainage, malignant ascites was transported on ice, aliquoted into 50 mL conical tubes (BD Falcon) and spun for 5 min at 580 × g at 4°C. The supernatant was aspirated and the remaining pellet was resuspended with 5 mL of hypotonic lysis buffer ACK (Life technologies) and incubated on ice for 5 min. 20 ml of PBS was used to quench the lysis buffer. Cell suspensions were pooled and pipetted into a new 50 mL conical tube through a 100 µm mesh and spun for 5 min at 580 × g at 4°C. Hypotonic lysis was repeated until no visible red blood cell component was present, usually for a total of 2-3 times (for the plate-based approach). Following red blood cell lysis, the cell pellet was resuspended in PBS with 2% (v/v) FBS. These cells were then used for both plate-based and droplet-based scRNA-seq. For plate-based scRNA-seq, cells were labeled with the following fluorophore-conjugated flow-cytometry antibodies: live/dead stain with Calcein-AM (LifeTechnologies), 7-AAD (7-Aminoactinomycin D) (LifeTechnologies), CD45-FITC (LifeTechnologies), EpCAM-PE (Miltenyi Biotec) and CD24-PE/Cy7 (BioLegend). Cells were incubated for 30 min on ice in the dark. Cells were washed twice by resuspending with PBS with 2% (v/v) FBS and spun 5 min at 580 × g at 4°C. Flow-cytometry and sorting was performed on a BD Biosciences cell sorter (IIu or UV). Following doublet exclusion, Calceinhigh7AAD-CD45-EPCAM+CD24+ single cells were sorted into 96-well microtiter plates (on a plate chiller) that were prepared with 10uL cell lysis buffer (TCL + 1% β-mercaptoethanol). Following completion of cell sorting, plates were covered with aluminum lids, vortexed for 10 seconds, centrifuged for 2 min at 580 × g at 4°C and immediately placed on dry ice prior to storage at -80°C.

tag: cell type

value: Malignant ascites  single cell

tag: patient id

tag: time point


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title: C4: Intestinal organoid bulk RNA-seq

city: Utrecht

first: Joep

last: Beumer

address: Uppsalaan 8

country: Netherlands

institute: Hubrecht Institute

description: Bulk RNA sequencing of human intestinal organoid, in expansion medium, 72 hours after SARS-CoV infection. Biological replicate experiment.

data_processing:
Paired end reads were aligned to the transcriptome using bwa. Paired end reads obtained by CEL-seq were aligned to the transcriptome using bwa (version 0.6.2-r126) with default parameters. The transcriptome contained all RefSeq gene models based on the human genome release hg38. The right mate of each read pair was mapped to the ensemble of all gene loci and to the set of 92 ERCC spike-ins in sense direction. Reads mapping to multiple loci were discarded. The left read contains the barcode information: the first eight bases correspond to the cell specific barcode followed by 4 bases representing the unique molecular identifier. The remainder of the left read contains a polyT stretch followed by few (<15 transcript derived bases). The left read was not used for quantification. For each cell barcode we counted the number of unique molecular identifiers for every transcript and aggregated this number across all transcripts derived from the same gene locus.
Genome_build: hg38
Supplementary_files_format_and_content: The data are in csv format. The table contains UMI deduplicated counts normalized between samples.

molecule: total RNA

source_name: Intestinal organoids

growth_protocol: Organoids were grown in either expansion or differentiation medium as described previously

extract_protocol:
RNA from whole organoids was extracted using Trizol isolation
RNA was processed using the previously described SORT-seq technique (for bulk samples), which is an implemented version of the CEL-seq2 technique. Libraries were sequenced on an Illumina NextSeq500 using 60bp and 26bp paired end sequencing.

treatment_protocol: Organoids were kept as untreated control or infected with either SARS-CoV or SARS-CoV2

tag: genotype

value: Wildtype

tag: tissue

value: Intestinal organoids


title: 6a60_2: Intestinal organoid bulk RNA-seq

description: Bulk RNA sequencing of human intestinal organoid, in expansion medium, 60 hours after SARS-CoV infection.


title: C5: Intestinal organoid bulk RNA-seq

description: Bulk RNA sequencing of human intestinal organoid, in expansion medium, 72 hours after SARS-CoV2 infection. Biological replicate experiment.


title: 6b60_2: Intestinal organoid bulk RNA-seq

description: Bulk RNA sequencing of human intestinal organoid, in expansion medium, 60 hours after SARS-CoV2 infection.


title: 6b24_2: Intestinal organoid bulk RNA-seq

description: Bulk RNA sequencing of human intestinal organoid, in expansion medium, 24 hours after SARS-CoV2 infection.


title: C3: Intestinal organoid bulk RNA-seq


title: C6: Intestinal organoid bulk RNA-seq


title: 6b24_1: Intestinal organoid bulk RNA-seq


title: C2: Intestinal organoid bulk RNA-seq

description: Bulk RNA sequencing of human intestinal organoid, in expansion medium. Biological replicate experiment.


title: C1: Intestinal organoid bulk RNA-seq


title: 6b60_1: Intestinal organoid bulk RNA-seq


title: 6_1: Intestinal organoid bulk RNA-seq

description: Bulk RNA sequencing of human intestinal organoid, in expansion medium.


title: 1b24_2: Intestinal organoid bulk RNA-seq

description: Bulk RNA sequencing of human intestinal organoid, in differentiation medium, 24 hours after SARS-CoV2 infection.


title: 6_2: Intestinal organoid bulk RNA-seq


title: 1b60_2: Intestinal organoid bulk RNA-seq

description: Bulk RNA sequencing of human intestinal organoid, in differentiation medium, 60 hours after SARS-CoV2 infection.


title: 6a60_1: Intestinal organoid bulk RNA-seq


title: 6a24_2: Intestinal organoid bulk RNA-seq

description: Bulk RNA sequencing of human intestinal organoid, in expansion medium, 24 hours after SARS-CoV infection.


title: 1b60_1: Intestinal organoid bulk RNA-seq


title: 1b24_1: Intestinal organoid bulk RNA-seq


title: SS2_1297


title: 1_2: Intestinal organoid bulk RNA-seq

description: Bulk RNA sequencing of human intestinal organoid, in differentiation medium.


title: 6a24_1: Intestinal organoid bulk RNA-seq


title: 1_1: Intestinal organoid bulk RNA-seq


title: SS2_1295


title: SS2_1294


title: SS2_1292


title: SS2_1293


title: SS2_1290


title: SS2_1287


title: SS2_1296


title: SS2_1286


title: SS2_1289


title: SS2_1291


title: SS2_1288


title: SS2_1284


title: SS2_1282


title: SS2_1283


title: SS2_1281


title: SS2_1278


title: SS2_1279


title: SS2_1280


title: SS2_1274


title: SS2_1275


title: SS2_1269


title: SS2_1273


title: SS2_1277


title: SS2_1276


title: SS2_1270


title: SS2_1272


title: SS2_1271


title: SS2_1285


title: SS2_1268


title: SS2_1266


title: SS2_1267


title: SS2_1264


title: SS2_1262


title: SS2_1260


title: SS2_1261


title: SS2_1258


title: SS2_1255


title: SS2_1256


title: SS2_1254


title: SS2_1257


title: SS2_1251


title: SS2_1250


title: SS2_1252


title: SS2_1253


title: SS2_1248


title: SS2_1247


title: SS2_1246


title: SS2_1249


title: SS2_1265


title: SS2_1244


title: SS2_1245


title: SS2_1240


title: SS2_1259


title: SS2_1241


title: SS2_1243


title: SS2_1263


title: SS2_1238


title: SS2_1239


title: SS2_1236


title: SS2_1237


title: SS2_1242


title: SS2_1235


title: SS2_1234


title: SS2_1233


title: SS2_1232


title: SS2_1231


title: SS2_1228


title: SS2_1227


title: SS2_1229


title: SS2_1223


title: SS2_1225


title: SS2_1224


title: SS2_1226


title: SS2_1222


title: SS2_1220


title: SS2_1221


title: SS2_1219


title: SS2_1216


title: SS2_1217


title: SS2_1210


title: SS2_1214


title: SS2_1211


title: SS2_1212


title: SS2_1209


title: SS2_1207


title: SS2_1218


title: SS2_1206


title: SS2_1213


title: SS2_1205


title: SS2_1208


title: SS2_1204


title: SS2_1230


title: SS2_1215


title: SS2_1202


title: SS2_1203


title: SS2_1197


title: SS2_1198


title: SS2_1201


title: SS2_1193


title: SS2_1199


title: SS2_1200


title: SS2_1196


title: SS2_1191


title: SS2_1195


title: SS2_1190


title: SS2_1192


title: SS2_1186


title: SS2_1185


title: SS2_1184


title: SS2_1187


title: SS2_1188


title: SS2_1183


title: SS2_1178


title: SS2_1181


title: SS2_1177


title: SS2_1180


title: SS2_1176


title: SS2_1179


title: SS2_1194


title: SS2_1175


title: SS2_1174


title: SS2_1189


title: SS2_1173


title: SS2_1168


title: SS2_1169


title: SS2_1172


title: SS2_1170


title: SS2_1182


title: SS2_1171


title: SS2_1167


title: SS2_1164


title: SS2_1163


title: SS2_1155


title: SS2_1154


title: SS2_1159


title: SS2_1160


title: SS2_1165


title: SS2_1166


title: SS2_1161


title: SS2_1158


title: SS2_1162


title: ESC(Comp)2 biological replicate 3

city: CAMBRIDGE

first: William

middle: Henry

last: Colledge

address: Dowing Street

country: United Kingdom

institute: University of Cambridge

data_processing:
Datasets for each sample were concatenated into a single file
Reads were trimmed using Fastx Trimmer by 8 and 4 bases at the start and end of each read respectively to improve quality
TopHat2 Galaxy Version 0.9 with default settings was used to align reads to the mouse genome (bam files)
Reads that mapped uniquely were used for downstream analysis. htseq-count Version 0.6.1galaxy1 was applied to count the number of reads mapping to each gene. Intersection-strict mode was chosen to exclude reads that overlap more than one gene or reads that do not intersect a given gene with each read position. The Gencode release M7 was used to annotate the genome.
Normalization of read counts and differential expression analysis was subsequently performed with DESeq2 Galaxy Version 2.1.8.3 (default parameters).
Genome_build: mm10
Supplementary_files_format_and_content: DESeq2 output

organism: Mus musculus

source_name: Embryonic stem cells

growth_protocol: ESCs were cultured on mitotically inactivated mouse embryonic fibroblasts (MEFs) in standard ESC medium (DMEM (Invitrogen) with 15% FCS (PAN Biotech), 4mM GlutaMax (Gibco), 1X non essential amino acids (Gibco), 20 mM Hepes buffer (Gibco), 0.1 mM b-mercaptoethanol (Gibco), 1.5x103 U/ml LIF (Millipore) in a 37°C humidified incubator with 5% CO2. When 70-80% confluent, the cells were passaged.

extract_protocol:
RNA was extracted using the Qiagen RNeasy Mini Kit
Library preparation was performed using the Illumina TruSeqHT kit according to the manufacturer’s protocol.

tag: passage

tag: strain

tag: developmental potential

value: compromised


title: ESC(Comp)3 biological replicate 3


title: ESC(Comp)3 biological replicate 1


title: ESC(Comp)4 biological replicate 1


title: SS2_1157


title: ESC(Comp)2 biological replicate 2


title: ESC(Comp)4 biological replicate 3


title: ESC(Comp)1 biological replicate 1


title: ESC(Comp)1 biological replicate 2


title: ESC(Ctrl)3 biological replicate 1

value: normal


title: ESC(Comp)3 biological replicate 2


title: ESC(Ctrl)3 biological replicate 2


title: ESC(Ctrl)3 biological replicate 3


title: ESC(Comp)1 biological replicate 3


title: ESC(Comp)2 biological replicate 1


title: ESC(Ctrl)2 biological replicate 2


title: ESC(Ctrl)2 biological replicate 1


title: SS2_1156


title: ESC(Comp)4 biological replicate 2


title: ESC(Ctrl)1 biological replicate 3


title: ESC(Ctrl)1 biological replicate 1


title: ESC(Ctrl)1 biological replicate 2


title: T10_Regen_Day28_1

city: Jerusalem

first: Matan

last: Hofree

address: The Edmond J. Safra, Givat Ram Campus

department: School of Computer Science and Engineering | The Lautenberg Center for Immunology and Cancer Research

institute: The Hebrew University of Jerusalem

description: Single cell RNA-Seq (10x)

data_processing:
3' RNAseq (10x kit V2 or V3 chemistry)
Demultiplexing is run using Cell Ranger mkfastq.
Cell-ranger count is run using cell-ranger v3.1 on firecoud.
R package dropletUtils is used to exclude chimeric reads and identify and exclude empty droplets
Genome_build: mm10
Supplementary_files_format_and_content: Raw count matriece are in the HDF5 Feature Barcode Matrix Format used by 10x, and metadata files are comma-delimited text.
mmProstate10x_full_sample_final.tsv: BatchID, cell-type, csv file
mmProstate10x_timecourse_rawCount.h5: hdf5 10x feature barcode matrix format, raw post-QC filtering cells
mmProstate10x_timecourse_log2TP10k.h5: hdf5 10x feature barcode matrix format, post-QC filtering cells, log2 transcripts per 10,000.

source_name: Mouse prostate regeneration day 28

growth_protocol: FVB/NJ mice were purchased from Taconic. Prostates used for scRNA-seq, histology and cell seeding experiments were derived from FVB/NJ mice.

extract_protocol:
Prostates were harvested and subsequently digested with Collagenase Type II (Gibco) for two hours at 37oC, followed by TryplE (Gibco) digestion at 37oC until a single cell suspension was obtained. Digestions were supplemented with Y-27632 (10 μM) to inhibit anoikis. Cells were filtered and checked for viability using trypan blue staining. All experiments were done with a minimum of 80% viable cells.
scRNA-Seq for dissociated mouse tissues was performed using 10X genomics Chromium Single Cell 3’ Library & Gel bead Kit V2 according to the manufacturer’s protocol (CG00052 Rev E). Briefly, samples containing approximately 6,000 FACS-sorted cells (mean viability 78%) were encapsulated in microfluidic droplets resulting in ~3,200 recovered single-transcriptomes per sample with a multiplet rate of ~3.7%. After the RT step, emulsion droplets were broken and barcoded-cDNA was purified with DynaBeads, followed by 12-cycles of PCR-amplification (98 °C for 180 s; [98 °C for 15 s, 67 °C for 20 s, 72 °C for 60 s] x 12-cycles; 72 °C for 60 s). The 50 ng of PCR-amplified barcoded-cDNA was fragmented with the reagents provided in the kit and purified with SPRI beads to obtain an average fragment size of 600 bp. Next, DNA library was ligated to the sequencing adapter followed by indexing PCR (98 °C for 45 s; [98 °C for 20 s, 54 °C for 30 s, 72 °C for 20 s] x 10 cycles; 72 °C for 60 s). The resulting DNA library was double-size purified (0.6-0.8X) with SPRI beads and sequenced on an Illumina NextSeq using HO-SE75 kit or on HiSeq2500 platform using PE50 kit
3' RNAseq (10x kit V2 or V3 chemistry)

treatment_protocol: Mice were castrated at 8-12 weeks of age. For castration time points, tissue was harvested 1 day, 7 days, 14 days, and 28 days post castration. Dihydrotestosterone (DHT) pellets were implanted subcutaneously 4 weeks post castration. For regeneration, tissue was harvested at 1 day, 2 days, 3 days, 7 days, 14 days and 28 days post DHT Pellet implantation.

tag: background strain

value: FVB/NJ

value: Prostate

tag: androgen status

value: DHTpellet

tag: day


title: T09_Regen_Day14_2

description: Single cell RNA-Seq (10x)

source_name: Mouse prostate regeneration day 14


title: T05_Regen_Day1_2

description: Single cell RNA-Seq (10x)

source_name: Mouse prostate regeneration day 1


title: T05_Regen_Day1_1

description: Single cell RNA-Seq (10x)


title: T04_Cast_Day28_1

description: Single cell RNA-Seq (10x)

source_name: Mouse prostate castrate day 28

value: Castrate


title: T04_Cast_Day28_2

description: Single cell RNA-Seq (10x)


title: T08_Regen_Day7_1

description: Single cell RNA-Seq (10x)

source_name: Mouse prostate regeneration day 7


title: T01_Cast_Day1_2

description: Single cell RNA-Seq (10x)

source_name: Mouse prostate castrate day 1


title: T00_Unsorted_1

description: Single cell RNA-Seq (10x)

source_name: Mouse prostate intact (control)

value: Intact


title: T01_Cast_Day1_1

description: Single cell RNA-Seq (10x)


title: T10_Regen_Day28_2

description: Single cell RNA-Seq (10x)


title: Lung_Smooth_Muscle_Cells_WT_1

city: Bad Nauheim

first: Mario

last: Looso

address: Ludwigstrasse 43

country: Germany

institute: Max Planck Institute for Heart and Lung Research

data_processing:
The resulting raw reads were assessed for quality, adapter content and duplication rates with FastQC (Andrews S. 2010, FastQC: a quality control tool for high throughput sequence data. Available online at: http://www.bioinformatics.babraham.ac.uk/projects/fastqc).
Trimmomatic version 0.38 was employed to trim reads after a quality drop below a mean of Q15 in a window of 5 nucleotides (Bolger et al., Trimmomatic: a flexible trimmer for Illumina sequence data). Only reads longer than 15 nucleotides were cleared for further analyses.
Trimmed and filtered reads were aligned versus the Ensembl human genome version hg38 (GRCh38.27) using STAR 2.6.1d with the parameters "--outFilterMismatchNoverLmax 0.1 --outFilterScoreMinOverLread 0.9 --outFilterMatchNminOverLread 0.9 --outFilterMatchNmin 20 --alignIntronMax 200000" (Dobin et al., STAR: ultrafast universal RNA-seq aligner).
The number of reads aligning to genes was counted with featureCounts 1.6.3 tool from the Subread package (Liao et al., featureCounts: an efficient general purpose program for assigning sequence reads to genomic features). Only reads mapping at least partially inside exons were admitted and aggregated per gene. Reads overlapping multiple genes or aligning to multiple regions were excluded.
Differentially expressed genes were identified using DESeq2 version 1.18.1 (Love et al., Moderated estimation of fold change and dispersion for RNA-Seq data with DESeq2).
The Ensemble annotation was enriched with UniProt data (release 08.03.2018) based on Ensembl gene identifiers (Activities at the Universal Protein Resource (UniProt)).
Genome_build: hg38 / GRCh38
Supplementary_files_format_and_content: The tab-delimited matrix shows DESeq normalized counts.

source_name: Transgenic mouse with smooth muscle actin creERT2 and tdTomato

extract_protocol:
RNA was isolated using the miRNeasy micro Kit (Qiagen) combined with on-column DNase digestion (DNase-Free DNase Set; Qiagen) to avoid contamination by genomic DNA according to manufacturer's instructions.
Whole transcriptome libraries were constructed with SMARTer® Stranded Total RNA Sample Prep Kit - HI Mammalian.

value: Lung smooth muscle cells


title: ESC(Ctrl)2 biological replicate 3


title: T00_NonEpi_2

description: Single cell RNA-Seq (10x)

source_name: Mouse prostate intact (control, EPCAM- sorted)


title: T00_Epi_1

description: Single cell RNA-Seq (10x)

source_name: Mouse prostate intact (control, EPCAM+ sorted)


title: T00_Epi_2

description: Single cell RNA-Seq (10x)


title: Lung_Smooth_Muscle_Cells_WT_3


title: T00_NonEpi_1

description: Single cell RNA-Seq (10x)


title: Lung_Smooth_Muscle_Cells_WT_2


title: APP_IL33_4_PU1

city: Hong Kong

first: Nancy

last: Ip

address: Room 6313, Academic Building The Hong Kong University of Science and Technology Clear Water Bay, Kowloon

country: China

library_source: genomic

data_processing:
For ChIP-seq, Base-calling is done by bcl2-fastq
For sequencing alignment and duplicate removal, sequencing data were mapped to the mm10 mice genome assembly by using the Burrows–Wheeler Aligner’s bwa-mem function (Heng Li and Richard Durbin, 2009). Duplicates were marked and removed using the Picard tools MarkDuplicates function with the parameter, REMOVE_DUPLICATES=TRUE.
For peak identification, the HOMER (Heinz et al., 2010) maketagdirectory function was used to combine sequencing data from the biological replicates, and the findPeaks function was used to identify binding/accessible regions with the following parameters: -style factor (for PU.1 ChIP-seq), -style histone (for H3K4me3 ChIP-seq), and -style histone -minDist 200 (for ATAC-seq). Regions were annotated by the annotatePeaks.pl function.  deepTools  bamCoverage function and visualized in igv browser (Robinson et al., 2011).
Read count in the binding/accessible regions was quantified by the bedtools (Quinlan and Hall, 2010) multicov function. Differential binding/accessible regions (p < 0.05) were calculated using  R.
Genome_build: mm10
Supplementary_files_format_and_content: bigWig files were generated using Bamcoverage --normalizeUsing CPM --binSize 10
For scRNA-seq,Base-calling is done by bcl2-fastq
The sequencing data were aligned, quantified, and clustered using Cell Ranger (version 3.0) as previously described (Zheng et al., 2017).
Genome_build: mm10
Supplementary_files_format_and_content: Matrix of read count, barcode were generated using cell ranger v3

molecule: genomic DNA

source_name: Microglia

extract_protocol: Microglia were fixed by 1% PFA immediately after staining and then subjected to sorting. Sorted microglia were then snap-frozen in liquid nitrogen and stored at −80°C until use. ChIP-seq libraries were constructed using ChIPmentation (Schmidl et al., 2015). In brief, approximately 200,000–300,000 sorted microglia were lysed and sonicated. Lysate was incubated with antibodies targeting PU.1 (3 µL) or H3K4me3 (2 μg) overnight at 4°C. After overnight incubation, 10 µL pre-blocked beads was added to each sample and incubated at 4°C for 2 h. Protein-bound beads were then washed and tagmented on beads with Tn5 at 37°C for 5 min. Then, samples were reverse-crosslinked with proteinase K (NEB) overnight. DNA was purified using a Qiagen MinElute Kit (28004). Purified DNA was subsequently amplified by PCR for 17–20 cycles, and the final libraries were size-selected (100–600 bp) by Ampure XP beads (Beckman Coulter). Pooled libraries were single-end sequenced on a NextSeq 500.


title: APP_IL33_3_PU1

institute: Hong Kong University of Science and Technology


title: APP_Con_1_H3K4me3


title: APP_IL33_1_PU1


title: APP_IL33_3_H3K4me3


title: APP_Con_2_H3K4me3


title: APP_IL33_2_PU1


title: APP_IL33_2_H3K4me3


title: APP_IL33_1_H3K4me3


title: APP_Con_2_PU1


title: APP_Con_1_PU1


title: APP_IL33_1_ATAC

extract_protocol: ATAC-seq libraries were generated as previously described with minor modifications (Buenrostro et al., 2013). In brief, approximately 50,000 sorted cells were washed and lysed. Then, nuclei were tagmented by incubation with Tn5 for 30 min at 37°C. Tagmented genomic DNA was then amplified by PCR for 15 cycles. The libraries were size-selected (100–600 bp) by Ampure XP beads (Beckman Coulter). The concentrations of the final libraries were quantified by Qubit (Thermo Fisher), and fragment lengths were quantified by Fragment Analyzer (Advanced Analytical). The pooled libraries were paired-end sequenced on a NextSeq 500.


title: APP_Con_1_ATAC


title: APP_Con_3_ATAC


title: IL33_MHCII+_2_ATAC

value: WT


title: APP_Con_2_ATAC


title: APP_IL33_2_ATAC


title: APP_IL33_2_scRNA

description:
APP_IL33_2/barcodes.tsv.gz
APP_IL33_2/features.tsv.gz
APP_IL33_2/matrix.mtx.gz

extract_protocol: scRNA-seq libraries were generated using the Chromium Single Cell 3′ Library Kit v2 (120237; 10x Genomics) according to the manufacturer’s instructions. The concentrations of the final libraries were quantified by Qubit (Thermo Fisher), and fragment lengths were quantified by Fragment Analyzer (Advanced Analytical). Libraries were paired-end sequenced on a NextSeq 500 according to the manufacturer’s instructions.


title: IL33_MHCII+_1_ATAC


title: DB2313_IL33_scRNA

description:
DB2313_IL33/barcodes.tsv.gz
DB2313_IL33/features.tsv.gz
DB2313_IL33/matrix.mtx.gz


title: IL33_MHCII-_2_ATAC


title: APP_Con_2__scRNA

description:
APP_Con_2/barcodes.tsv.gz
APP_Con_2/features.tsv.gz
APP_Con_2/matrix.mtx.gz


title: WT_Con_2_scRNA

description:
WT_Con_2/barcodes.tsv.gz
WT_Con_2/features.tsv.gz
WT_Con_2/matrix.mtx.gz


title: IL33_MHCII+_3_ATAC


title: IL33_MHCII-_1_ATAC


title: APP_Con_1_scRNA

description:
APP_Con_1/barcodes.tsv.gz
APP_Con_1/features.tsv.gz
APP_Con_1/matrix.mtx.gz


title: Veh_IL33_scRNA

description:
Veh_IL33/barcodes.tsv.gz
Veh_IL33/features.tsv.gz
Veh_IL33/matrix.mtx.gz


title: WT_Con_1_scRNA

description:
WT_Con_1/barcodes.tsv.gz
WT_Con_1/features.tsv.gz
WT_Con_1/matrix.mtx.gz


title: IL33_MHCII-_3_ATAC


title: APP_IL33_1__scRNA

description:
APP_IL33_1/barcodes.tsv.gz
APP_IL33_1/features.tsv.gz
APP_IL33_1/matrix.mtx.gz


title: naiveNR1.LN#3

city: Boston

first: CBDM

last: Lab

state: MA

address: 77 Avenue Louis Pasteur

department: Microbiology and Immunobiology

country: USA

institute: Harvard Medical School

data_processing:
Reads were mapped to the mouse reference genome (mm10) with STAR 2.5.4
Non-uniquely mapped reads were discarded.
The uniquely mapped reads were assigned to genes using featureCounts with GENCODE annotation (vM16)
Genome_build: mm10
Supplementary_files_format_and_content: raw read counts

source_name: iliac lymph node CD4+ T cells

extract_protocol:
1,000 Cells were double-sorted by Moflo into 5ul Buffer TCL (Qiagen) with 1% 2-Mercaptoethanol (Sigma).Total RNA was captured and purified on RNAClean XP beads (Beckman Coulter)
Polyadenylated mRNA was selected using an anchored oligo(dT) primer and converted to cDNA via reverse transcription. First-strand cDNA was subjected to limited PCR amplification followed by transposon-based fragmentation using the Nextera XT DNA Library Preparation Kit (Illumina). Samples were then PCR-amplified using barcoded primers such that each sample carried a specific combination of illumine P5 and P7 barcodes, and were pooled prior to sequencing. Sequencing was performed on an illumina NextSeq500 using 2X38bp reads.

value: iliac lymph node

value: CD4+ T cells

tag: cell population

value: naive

tag: congenic marker


title: naiveNR1.LN#1


title: memNR1.LN#3

value: memory


title: naiveNR1.LN#2


title: memNR1.LN#1


title: PG24-P20

city: Charlestown

first: Erik

last: Abels

state: Massachusetts

address: 149 13th Street

department: Neurology

institute: Massachusetts General Hospital

data_processing:
Total RNA was isolated and sequencing libraries were made using SMARTer Ultra Low Input RNA Kit. Sequencing was done using an Illumina NextSeq and bioinformatic analysis was performed using DESeq2 in R
Duplicate reads were marked using the MarkDuplicates tool in picard-tools-1.8.4 and removed.
The uniquely aligned reads were then counted against Gencode’s GRCm38.p3 GTF annotations using htseq-count in the intersection-strict mode
Data analysis of mapped counts was performed in R 3.2.3 using the DESeq2 package
Samples with less than 6000 genes with at least 5 mapped reads were excluded from analysis
Genome_build: GRCm38.p3
Supplementary_files_format_and_content: tab-delimited text file with read counts per sample

source_name: Ly6CHigh Blood Monocytes

extract_protocol:
Monocytes are isolated from blood. Macrophages and monocytes are isolated from mouse brain following protocol described in Hickman et al. 2013. Total RNA was isolated using RNeasy Plus Micro kit (Qiagen) using the total RNA isolation protocol.
Total RNA was isolated and sequencing libraries were made using SMARTer Ultra Low Input RNA Kit. Sequencing was done using an Illumina NextSeq

tag: age

value: 12 -18 weeks

value: brain

value: Ly6CHigh Blood Monocytes


title: PG24-P21

source_name: Ly6CLow Blood Monocytes

value: Ly6CLow Blood Monocytes


title: PG26-P10

source_name: CCR2High Brain Macrophages GFPneg

value: CCR2High Brain Macrophages GFPneg


title: 2PG23-P21


title: PG26-P11

source_name: CCR2High Brain Macrophages GFPpos

value: CCR2High Brain Macrophages GFPpos


title: PG24-P13

source_name: Ly6CHigh Brain Monocytes GFPneg

value: Ly6CHigh Brain Monocytes GFPneg


title: PG26-P12

source_name: CCR2Low Brain Macrophages GFPneg

value: CCR2Low Brain Macrophages GFPneg


title: PG26-P13


title: PG24-P10


title: PG26-P14

source_name: Ly6CHigh Brain Monocytes GFPpos

value: Ly6CHigh Brain Monocytes GFPpos


title: PG24-P14


title: PG24-P16

source_name: CCR2Low Brain Macrophages GFPpos

value: CCR2Low Brain Macrophages GFPpos


title: PG23-P21


title: memNR1.LN#2


title: PG23-P11


title: PG23-P16


title: PG26-P16


title: PG23-P20


title: PG24-P11


title: PG24-P12


title: 2PG22-P14


title: PG23-P12


title: PG23-P10


title: PG22-P21


title: PG22-P20


title: PG22-P14


title: PG22-P12


title: PG22-P16


title: PG22-P11


title: PG22-P13


title: PG22-P10


title: mmATACldP16R2

city: Baltimore

first: Jie

last: Wang

state: Maryland

address: 400 N Broadway

department: Ophthalmology

institute: Johns Hopkins University

data_processing:
Raw data from mouse and zebrafish were separately mapped to the GRCm38/mm10 and GRCz10/danRer10 genome assembly using STAR
Raw counts of genes were further used to calculate FPKM (Fragments Per Kilobase Of Exon Per Million) and identify differentially expressed genes through EdgeR
After removing adaptors using cutadapt (58), 50bp paired-end ATAC-Seq reads from zebrafish and mouse were separately aligned to GRCz10/danRer10 and GRCm38/mm10 reference genome using Bowtie2 with default parameters
We filtered reads from chromosome M and Y, and included high mapping-quality reads (MAPQ score > 10) through SAMTools for further analysis. Duplicate reads was removed using Picard tools MarkDuplicates program.
ATAC-Seq peak regions were called using MACS2 with parameters --nomodel --shift -100 --extsize 200. The blacklisted regions in mouse were excluded from peak regions (https://www.encodeproject.org/annotations/ENCSR636HFF/).
We counted the raw fragments for each peak region using HTSeq.
Genome_build: GRCm38/mm10 and GRCz10/danRer10
Supplementary_files_format_and_content: FPKM files for gene expression. Peak files in narrowPeak format with following columns: chromosome, start, stop, name, length of peak region, strand, integer score for display, fold-change, -log10(pvalue), -log10(qvalue), relative summit position to peak start.

source_name: Retina

growth_protocol: To induce Cre recombination, GLASTCreERT2; Sun1-sGFP mice at ~2 weeks of age were intraperitoneally injected with Tamoxifen in corn oil for 2 consecutive days at 1mg/dose. Nfialox/lox; Nfiblox/lox, and Nfixlox/lox mice were crossed to GLASTCreERT2; Sun1-sGFP mice. To generate MG-specific loss of function mutants of NFIa/b/x genes, 3 week-old GLASTCreERT2; NFIa/bxlox/lox;Sun1-sGFP mice were fed with tamoxifen diet for 3 weeks following by 2 weeks with normal diet. All mice were housed in a climate-controlled pathogen free facility on a 14 h-10 h light/dark cycle (07:00 lights on – 19:00 lights off). The adult zebrafish used in these studies were 6 to 12 months old (3-5cm in length). Fish were maintained under a light and dark cycle of 14 hours light and 10 hours of dark at 28.5°C.

extract_protocol:
RNA was extracted from both GFP-positive and GFP-negative cell fractions using miRNAeasy Mini Kit (#217004, Qiagen). Ribosomal RNA was depleted, and total RNA was captured from the RNA samples using Illumina TruSeq Stranded RNA LT kit Ribo-ZeroTM Gold (# 15032619, Illumina). For tagmentation, cell nuclei were incubated with 2.5 UL enzyme in 50UL total volume at 37°C in a thermocycler (Illumnia Nextera DNA library prep kit, #FC1211030). DNA was cleaned up using MinElute PCR purification kit (#28006, Qiagen) and eluted in 10UL of EB buffer.
Flow-sorted RNA samples were sent to the Deep Sequencing and Microarray Core (Johns Hopkins University) for library preparation and sequencing. Around 8-10 libraries were pooled and sequenced for paired-end 75 cycles using the NextSeq 500 system with ~400-500 million reads per run, resulting in ~45-55 million reads per library. Sorted cells (~50k-75k) from GFP-positive samples were used for ATAC library preparation. Completed ATAC-Seq libraries were then analyzed by Fragment Bioanalyzer and sequenced for paired-end 75 cycles using the NextSeq 500 system with ~400-500 million reads per run.

treatment_protocol: For NMDA damage, adult mice, either CD1 or GLASTCreERT2; Sun1-sGFP mice at ~2 months of age, were anesthetized with isoflurane inhalation. A puncture was made just behind the limbus with a 30G needle. Two microliters of 100mM NMDA in PBS was intravitreally injected using a syringe with a 33G blunt-ended needle. Mice were sacrificed, and retinas were collected at indicated timepoints. For light damage, the mice were reared in cyclic 12-hour low light/12-hour dark conditions at the University of Florida animal housing facility. Prior to light damage, mice were placed in a modified cage equipped with dimmable white light LED strips. Light intensity was measured using a light meter (Thermo Fisher Scientific Inc., Waltham, MA) and set to 2000 lux. To induce death of rods and cones, adult albino; Tg[gfap:EGFP]nt11 fish were dark adapted for 14 days, then transferred to clear polycarbonate tanks placed between four fluorescent bulbs (20,000 lux) and water temperature maintained at 32°C for up to 72 hours. Fish were euthanized by anesthetic overdose of 0.2% 2-phenoxyethanol in system water. To induce amacrine and ganglion cell death, we injected N-methyl-D-aspartic acid (NMDA) (Sigma-Aldrich; St. Louis, MO) intravitreally. Adult Tg[gfap:GFP]mi2001 zebrafish were anesthetized in 0.1% 2-phenoxyethanol. A sapphire blade was used to make an incision in the posterior cornea and 0.5 μl of 100 mM NMDA was injected into the intravitreal space of the eye using a 33 gauge Hamilton syringe into the intravitreal space of the eye. The fish were revived and placed in a 32°C dark incubator for up to 36 hours. Fish were euthanized by anesthetic overdose of 0.2% 2-phenoxyethanol in system water.

value: Retina

value: GlastCreERT2/Sun1-sGFP CD1

tag: condition

value: Light damage

tag: cell population of facs sorting

value: GFP+

tag: time

tag: replicate

value: Replicate 2


title: mmATACldP16R1

value: Replicate 1


title: mmATACldP00R2

value: Adult


title: mmATACldP24R3


title: mmATACldP36R2


title: mmATACldP24R2


title: mmATACnmdaP48R2

value: NMDA treatment


title: mmATACnmdaP06R1


title: mmATACnmdaP03R1


title: mmATACldP10R2


title: mmATACldP10R1


title: mmATACnmdaP12R2


title: mmATACldP00R1


title: mmATACldP36R1


title: mmATACnmdaP12R1


title: mmATACnmdaP03R2


title: mmATACnmdaP06R2


title: mmATACdevP60R2

value: Control


title: mmATACdevP60R1


title: mmRNAnmdaN48R1

value: GlastCreERT2/Sun1-sGFP, CD1

value: GFP-


title: mmATACnmdaP48R3


title: mmRNAnmdaN36R1


title: mmRNAnmdaN36R2


title: mmRNAnmdaN12R1


title: mmRNAnmdaN06R2


title: mmRNAnmdaN48R3


title: mmRNAnmdaP48R3


title: mmRNAnmdaP12R2


title: mmRNAnmdaP12R1


title: mmRNAnmdaN03R1


title: mmRNAnmdaN03R2


title: mmRNAnmdaP36R1


title: mmRNAnmdaP03R2


title: mmRNAnmdaP06R3


title: mmRNAnmdaP06R2


title: mmRNAnmdaP03R1


title: mmRNAldN24R2


title: mmRNAldN36R2


title: mmRNAldN36R1


title: mmRNAldN24R1


title: mmRNAldN16R2


title: mmRNAldN16R1


title: mmRNAldN04R2


title: mmRNAldN00R2


title: mmRNAldN04R1


title: mmRNAnmdaN12R2


title: mmRNAldN00R1


title: mmRNAldP36R2


title: mmRNAnmdaP36R2


title: mmRNAnmdaN06R3


title: mmRNAnmdaP48R4


title: mmRNAldP36R1


title: mmRNAldP24R2


title: mmRNAldP16R1


title: mmRNAldP16R2


title: mmRNAldP04R2


title: mmRNAdevN60R1

value: Control for light damage


title: mmRNAldP00R2


title: mmRNAdevhN60R1

value: Control for NMDA treatment


title: mmRNAldP04R1


title: mmRNAdevN60R2


title: mmRNAdevhP60R2


title: mmRNAldP00R1


title: mmRNAdevhN60R2


title: mmRNAdevhP60R1


title: T10

city: Santa Barbara

first: Veronique

last: Lisi

state: California

address: Neuroscience Research Institute, Bldg 571, room6131

department: Neuroscience Research Institute

institute: University of California Santa Barbara

description:
read 1 contains both a cell barcode at position 1-12 and a UMI at position 13-20 (technical read)
read 2 is aligned to the reference genome (biological read)
allData.csv

data_processing:
Base calls performed with bcl2fastq v2.18.0.12
Read 2 was aligned with Star v2.2
Each aligned read was tagged with its mate-pair UMI and cell barcode
Each aligned exonic read was tagged with a gene name
A digital expression matrix was built by counting the number of unique UMIs per gene within each cell; columns are cells, and rows are genes
Number of cells was estimated at 100 per PCR reaction
Genome_build: mm10
Supplementary_files_format_and_content: allData.csv  with raw counts. The file sampleIDtoBarcode.txt includes the cell ID and its associated cell barcode.

source_name: hippocampus

extract_protocol:
Single-cell suspensions were processed through Drop-Seq to generate single-cell cDNA libraries attached to microbeads.
Microbeads were counted, and 2000 beads were amplified per tube by PCR, and the 3' end of the cDNA prepared for sequencing using a modified Nextera XT protocol

value: hippocampus

tag: age (weeks)

value: rTta


title: T9


title: T11


title: mmRNAdevP60R1


title: 457T


title: 458T


title: mmRNAdevP60R2


title: 998

value: WT


title: 810


title: 442T


title: 999


title: mmRNAldP24R1


title: 1007


title: 1006


title: 809


title: 794


title: 781


title: 929


title: 918


title: 914


title: 598


title: 567


title: 573


title: 600


title: 576


title: INPUT ChIP-seq

city: Madison

first: Kevin

middle: S

last: Myers

state: WI

address: 5127 WEI, 1552 University Ave

department: Great Lakes Bioenergy Research Center

institute: University of Wisconsin - Madison

data_processing:
For ChIP-seq analysis, the initial 50bp sequence tags were mapped to the R. sphaeroides 2.4.1 genome using SOAP version 2.21, allowing a maximum of 2 mismatches and no gaps. Peaks were identified using MOSAiCS at a FDR of 0.05. The MOSAiCS analysis was conducted as a two-sample analysis, with ChIP-seq data from either input DNA or ChIP conducted with anti-Myc antibody in R. sphaeroides 2.4.1 without a Myc-tagged protein used as a control. Only peaks that were called as significant using both controls (i.e., the intersect of the 2 analysis) were considered as true peaks. The analysis was conducted using cells grown with 3 and 50 μM IPTG
Genome_build: GCA_000012905.2
Supplementary_files_format_and_content: Normalized RPKM read counts for RNA-seq. WIG files for ChIP-seq

organism: Cereibacter sphaeroides 2.4.1

source_name: Bacterial culture

growth_protocol: R. sphaeroides 2.4.1 cultures were grown in Sistrom’s minimal medium (SMM), with 4 g/L succinate.  500 ml cultures were grown in Roux bottles bubbled with 30% O2, 1% CO2, and 69% N2.

extract_protocol:
R. sphaeroides cultures were grown aerobically in 500 ml cultures. At OD600 = 0.3-0.4, formaldehyde and sodium phosphate were added to a final concentration of 1% and 10 mM, respectively. This mixture was incubated at 30 °C for 4 min before glycine was added to 100 mM, and the solution was placed on ice for 30 min with gentle agitation to quench excess formaldehyde. Cells were centrifuged at 3000g, washed twice with chilled phosphate-buffered saline, centrifuged, and flash-frozen at − 80 °C. About 2 × 1010 cells were suspended in 0.5 ml of 100 mM Tris (pH 8.0), 300 mM NaCl, 2% Triton X-100, and 1 mM phenylmethylsulfonyl fluoride, and sonicated eight times for 20 s with a Branson Sonifier (Branson Ultrasonics Corp., Danbury, CT) set to level 6 and 50% output using a 3-mm microtip. A mixture of micrococcal nuclease (50 U) and RNase A (0.5 μg) in 200 μM CaCl2, 1.2 mM KCl, 6 mM sucrose, and 10 μM DTT was added; the mixture was incubated for 1 h at 4 °C; and then nuclease activity was inhibited by addition of 10 mM ethylenediaminetetraacetic acid (EDTA). Cell debris was removed by centrifugation for 10 min at 12,000g, and an aliquot was removed to analyze DNA fragmentation by agarose gel eletrophoresis (desired size of ∼ 200–1000 bp with enrichment for ∼ 500-bp molecules). The resulting supernatant was incubated with gentle mixing with 20 μl of Staphylococcus aureus protein A Sepharose beads (Sigma-Aldrich, St. Louis, MO) for 3 h at 4 °C as pretreatment to remove potential nonspecific binding to the beads. After the beads had been removed by centrifugation (5 min at 3000g), one-tenth of the sample was removed and used as non-antibody-treated control. This supernatant was treated with polyclonal antibodies against the Myc epitope tag (ab9132, Abcam), and the mixture was incubated overnight at 4 °C with gentle mixing before being incubated with protein A Sepharose beads (30 μl) for 2 h at 4 °C. The beads were recovered by centrifugation; washed once (4 °C) with 250 mM LiCl, 100 mM Tris (pH 8.0), and 2% Triton X-100; washed twice with 600 mM NaCl, 100 mM Tris (pH 8.0), and 2% Triton X-100; washed twice with 300 mM NaCl, 100 mM Tris (pH 8.0), and 2% Triton X-100; and washed twice with TE buffer (10 mM Tris pH 8.0 and 1 mM EDTA). Protein–DNA complexes were eluted from the beads by incubating at 65 °C for 30 min in 50 mM Tris (pH 8.0), 10 nM EDTA, and 1% sodium dodecyl sulfate. The beads were removed by centrifugation, and protein–DNA cross-linking was reversed by incubating the samples for 12 h at 65 °C. DNA was purified using the QIAquick PCR Purification Kit (QIAGEN, Inc., Valencia, CA).
ChIP-seq library preparation and sequencing was performed at the University of Wisconsin-Madison Biotechnology Center. Libraries for sequencing were created using the Illumina TruSeq ChIP library preparation kit (Illumina) following the standard protocol. ChIP-seq libraries were sequenced on an Illumina HiSeq 2500 2x150bp reads using the standard protocol.

tag: media

value: SIS medum

tag: oxygen

value: 30% Oxygen

value: Bacterial culture


title: NtrX 3 mM ChIP-seq

growth_protocol: R. sphaeroides 2.4.1 cultures were grown in Sistrom’s minimal medium (SMM), with 4 g/L succinate.  500 ml cultures were grown in Roux bottles bubbled with 30% O2, 1% CO2, and 69% N2. 3 µM IPTG was added at inncoulation.

tag: tissue


title: Myc Control ChIP-seq


title: NtrX 50 mM ChIP-seq

growth_protocol: R. sphaeroides 2.4.1 cultures were grown in Sistrom’s minimal medium (SMM), with 4 g/L succinate.  500 ml cultures were grown in Roux bottles bubbled with 30% O2, 1% CO2, and 69% N2. 50 µM IPTG was added at inncoulation.


title: 10x_1886

source_name: Malignant ascites  single cell

tag: cell type

value: Malignant ascites  single cell

tag: patient id

tag: time point


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