title: mESC Input rep1

description: mESC Input rep1

value: mouse embryonic stem cells

value: WT


title: Donor 12 Peripheral blood CD14+CD16+ SLAMF7 Low

status: Public on Feb 11 2022

type: SRA

city: Boston

first: Daimon

last: Simmons

state: MA

address: 75 Francis Street

country: USA

institute: Brigham and Women's Hospital

description: Sample 75

library_source: transcriptomic

data_processing:
Reads were aligned using STAR version 2.4.2a
Transcripts were quantified using RSEM version 1.2.2.1
Genome_build: GRCh38.83
Supplementary_files_format_and_content: tab delimited text files with gene level TPM, FPKM, counts

molecule: total RNA

organism: Homo sapiens

source_name: Peripheral blood

extract_protocol:
Cells were lysed in TCL buffer and stored at -80C.
Libraries were processed at the Broad Institute using the Smart-seq2 protocol.

tag: tissue

value: Peripheral blood

tag: cell type

value: Monocyte

tag: disease state

value: Control

tag: donor

value: Donor 12

tag: monocyte population

tag: slamf7  expression

value: Low


title: THDS_91m_KLV_p1_F3_CC

city: Kensington

first: Jerome

last: Samir

state: NSW

address: Level 5, Wallace Wurth Building, High Street

department: IVPP

country: Australia

institute: Kirby Institute

data_processing:
Illumina NextSeq was used
Sequenced paired-end reads were trimmed using Trimmomatic (v0.39) (using parameters:  LEADING = 3, TRAILING = 3, SLIDINGWINDOW = 4:10, MINLEN = 50), then aligned to the human reference genome (GRCh38) using STAR (v2.7.3a). Gene expression was then quantified at the counts and TPM level with RSEM (v1.3.1)
Genome_build: GRCh38
Supplementary_files_format_and_content: .mtx.gz files contain matrices including raw counts, TPM and scaled TPM values for each sample and each gene.
Supplementary_files_format_and_content: .txt and and .tsv files contain tab delimited information on sample names and gene names (as per ordering in matrices), and gene annotation information.

source_name: CD8+ T cell

extract_protocol:
Single HCV-specific CD8+ T cells were sorted using flow cytometry, with RNA isolation and sequencing library construction performed according to the Smart-seq2 protocol.
Single cell RNA libraries were prepared for sequencing using standard Illumina protocols

tag: subject

value: CH-THDS

tag: epitope

value: KLV

tag: dpi

value: CD8+ T cell


title: THDS_91m_KLV_p1_F2_CC


title: mESC H3K79me3 rep2

city: GuangZhou

first: Hanwen

last: Yu

state: GuangDong

address: North Campus, Sun Yat-Sen University, No. 74, 2nd Yat-*Sen Road, Yuexiu District, Guangzhou City, Guangdong Province, 510080, PRC

country: China

institute: SUN YAT-SEN UNIVERSITY

description: mESC H3K79me3 rep2

library_source: genomic

data_processing:
The bioinformatics analysis of ChIP-seq datasets generated in this study or downloaded from publicly available repositories and data portals were performed by custom shell scripts in which raw data were first trimmed and filtered by TrimGalore with default parameter. Qualified read pairs were then aligned to mouse genome (mm10) by Bowtie2 (release 2.4.1). Biological and optical duplicates were removed with Sambamba (release 0.7.1). Last we used MACS2 (release 2.2.7.1; parameters for narrow peaks such as H3K27ac and H3K4me3: -p 0.05 -g mm -f BAMPE; broad peaks such as H3K27me3, H3K4me1, H3K79me2, H3K79me3 and H3K4me3: --broad --broad-cutoff 0.05 -g mm -f BAMPE; ATAC-seq: --broad --broad-cutoff 0.05 -g mm -f BAMPE) to call peaks. The highly reproducible peaks were identified by package IDR, which is a uni?ed approach to measure the reproducibility of ?ndings identi?ed from replicate experiments and provide highly stable thresholds based on reproducibility.
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content:
Peak bed files.
wig files were generated using deeptools; Scores represent RPKM values.

molecule: genomic DNA

organism: Mus musculus

source_name: mouse embryonic stem cells

growth_protocol: Mouse ESCs were cultured in N2B27 medium comprising 10ng/ml of LIF, 1 μM PD03, 3 μM CHIR9901 (Nichols and Ying, 2006) or in KnockOut medium comprising 20% KnockOut serum replacement, 1X non-essential amino acids solution, 2 mM L-glutamine, 55 µM 2-mercaptoethanol and 10 ng/ml LIF. The medium was changed every other day. When passaging, cells were dissociated by 0.05% Trypsin-EDTA into single cells and re-plated every 3 days at a ratio of 1:8-1:10.

extract_protocol:
For each ChIP, 5×10^6 cells were used. Cells were fixed in 1% formalin/mESC medium (v/v) for 10 min with gentle agitation on a rotator at room temperature. Fixation was stopped by the addition of glycine (125 mM) and agitation for 5 minutes at room temperature. Fixed cells were washed twice in ice-cold PBS, re-suspended in LB1 (50 mM HEPES-KOH, pH 7.5, 140 mM NaCl, 1 mM EDTA, 10% glycerol, 0.5%NP-40, 0.25% Triton X-100 and protease inhibitors). After 10 min of incubation, cells were pelleted by centrifugation and resuspended in LB2 (10 mM Tris-HCl, pH 8.0, 200 mM NaCl, 1 mM EDTA, 0.5 mM EGTA and protease inhibitors). After 10 min of incubation, cells were pelleted and resuspended in 0.25ml of freshly prepared LB3 (10 mM Tris-HCl, pH 8.0,100 mM NaCl, 1 mM EDTA, 0.5 mM EGTA, 0.1% Na-deoxycholate, 0.5%N-lauroylsarcosine and protease inhibitors) and sonicated to about 100 - 500 bp fragments using a Bioruptor (Diagenode). Anti-H3K79me2 and anti-H3K79me3 antibodies were diluted into 5 mg/ml BSA (PBS/BSA) and incubated with preblocked protein G magnetic beads (Invitrogen) at 4°C with gentle agitation on a rotator for 4 hours. Antibody-bead complexes were rotated overnight with sonicated chromatin solution at 4°C. Immune chromatin-bead precipitates were collected by the magnetic device (Invitrogen). Precipitates were washed sequentially with high-salt wash buffer (20 mMTris·HCl, pH 8.0, 500 mM NaCl, 2 mM EDTA, 0.1% SDS, and 1% Triton X-100), then with LiCl wash buffer (10 mM Tris·HCl, pH 8.0, 250 mM LiCl, 1 mM EDTA, and 1% Nonidet P-40), and then with Tris-EDTA (TE)-NaCl buffer (1 mM EDTA, 10 mM Tris·HCl, pH 8.0, and 50 mM NaCl). Immunoprecipitated DNA was eluted by incubating the beads with 100 µl elution buffer (50 mM Tris·HCl, pH 8.0, 10 mM EDTA, and 1% SDS), shaking at room temperature at a setting of 1300 rpm for one hour. To reverse crosslinking, sample was treated with proteinase K and incubated at 65°C for 4 hours. Add 100 µl TE buffer to each sample. The DNA was purified using phenol-chloroform extraction, and suspended in 40 µl TE buffer.
ChIP-seq library was constructed with the Accel-NGS 2S Plus DNA Library kit (Swift Biosciences, catalog. no. 21096) according to the manufacturer’s instructions. The libraries were sequenced on an Illumina Hiseq platform and 150 bp paired-end reads were generated.

treatment_protocol: 2C::GFP+/SGC cells were cultured in KnockOut medium comprising 20% KnockOut serum replacement, 1X non-essential amino acids solution, 2 mM L-glutamine, 55 µM 2-mercaptoethanol and 10 ng/ml LIF, under treatment with SGC0946 (2 µM). 2C::GFP+/SA cells were cultured in KnockOut medium comprising 20% KnockOut serum replacement, 1X non-essential amino acids solution, 2 mM L-glutamine, 55 µM 2-mercaptoethanol and 10 ng/ml IL6/sIL-6R, under treatment with SGC0946 (2 µM) and AS8351 (2 μM).

tag: genotype/variation

tag: treatment

value: untreated

tag: chip antibody

value: H3K79me3 (Abcam, ab2621)


title: mESC H3K79me3 rep1

description: mESC H3K79me3 rep1


title: THDS_91m_KLV_p1_F1_CC


title: JS_HsSc_0927_JFS543

city: Seattle

first: Hannele

last: Ruohola-Baker

state: WA

address: 850 Republican Street

institute: Institute for Stem Cell and Regenerative Medicine

description: AutoCUT&RUN

data_processing:
Library strategy: AutoCUT&RUN
Genome_build: Masked UCSC dm6
1. We used Bowtie2 2.2.5 with options "--end-to-end --very-sensitive --no-mixed --no-discordant --phred33 -I 10 -X 700" to map the 25bp paired-end Illumina reads to UCSC hg19. 2. We used bowtie 2.2.5 with options "--local --very-sensitive-local --no-overlap --no-dovetail --no-mixed --no-discordant --phred33 -I 10 -X 700" to map the same 25bp paired-end Illumina reads to masked UCSC dm6. 3. We extracted properly paired reads from the marked alignments to both genomes. 4. We used the bedtools 2.17.0 genomecov command with a scaling factor of 10000/(number of fragments mapped to D.melanogaster) to create a normalized yeast track file (Supplementary file .bedgraph.gz).
Genome_build: Genome_build: UCSC hg19

source_name: hiPSC WTC #11

value: hiPSC WTC #11

tag: antibody

value: anti-CTCF Millipore 07-729


title: JS_HsSc_1121_JFS114

description: AutoCUT&RUN


title: Donor 12 Peripheral blood CD14++CD16+ SLAMF7 High

description: Sample 74

value: High


title: Donor 12 Peripheral blood CD14++CD16+ SLAMF7 Low

description: Sample 73


title: JS_HsSc_0927_JFS542

description: AutoCUT&RUN


title: mESC H3K79me2 rep2

description: mESC H3K79me2 rep2

value: H3K79me2 (Abcam, ab3594)


title: JS_HsSc_0927_JFS540

description: AutoCUT&RUN


title: THDS_91m_KLV_p1_E2_CC


title: Donor 12 Peripheral blood CD14++CD16- SLAMF7 High

description: Sample 72


title: THDS_91m_KLV_p1_E3_CC


title: SL_HsSc_g1K4me3

description: AutoCUT&RUN


title: mESC H3K79me2 rep1

description: mESC H3K79me2 rep1


title: THDS_91m_KLV_p1_D2_CC


title: SL_HsSc_mgK4me3

description: AutoCUT&RUN


title: Donor 12 Peripheral blood CD14++CD16- SLAMF7 Low

description: Sample 71


title: THDS_91m_KLV_p1_E1_CC


title: 2C::GFP+/SA Input rep2

description: 2C::GFP+/SA Input rep2

value: SGCAS treated


title: THDS_91m_KLV_p1_D1_CC


title: Donor 11 Peripheral blood CD14+CD16+ SLAMF7 Low

description: Sample 69

value: Donor 11


title: 2C::GFP+/SA Input rep1

description: 2C::GFP+/SA Input rep1

value: mouse embryonic stem cells


title: Donor 11 Peripheral blood CD14++CD16+ SLAMF7 High

description: Sample 68

value: Peripheral blood


title: 2C::GFP+/SA H3K79me3 rep2

description: 2C::GFP+/SA H3K79me3 rep2


title: THDS_91m_KLV_p1_C2_CC


title: THDS_91m_KLV_p1_C3_CC


title: Donor 11 Peripheral blood CD14++CD16- SLAMF7 High

description: Sample 66

value: Monocyte


title: L425_25_premrna

city: Cambridge

last: Sun

address: 455 Main St

department: EECS

institute: Whitehead Institute

description: brain.BBB.human.counts.rds

data_processing:
Raw sequencing reads were aligned to the pre-mRNA annotated  Homo sapiens reference genome version GRCh38.
Counts were estimated using Cellranger 3.0.1 (10x Genomics, Pleasanton CA)
The generated cell-by-gene unique molecular identifier (UMI) count matrix was analyzed using the Seurat R package v.3.2.021.
Genome_build: GRCh38
Supplementary_files_format_and_content: counts.rds, meta.rds

molecule: nuclear RNA

source_name: ex vivo resection

growth_protocol: Not applicable

extract_protocol:
Tissue was homogenized in media followed by either enrichment (BVE)/nuclei extraction or only nuclei extraction. Nuclei were processed through the 10X Single Cell Gene Expression platform per manufacturer's protocol
Libraries were constructed using the 10X Genomics Chromium Single Cell 3′ Reagent Kit v3

treatment_protocol: Not applicable

value: brain

value: intractable epilepsy

tag: protocol

value: Blood Vessel Enrichment


title: L425_33_premrna

description: brain.BBB.human.counts.rds


title: 2C::GFP+/SA H3K79me2 rep1

description: 2C::GFP+/SA H3K79me2 rep1


title: Donor 11 Peripheral blood CD14++CD16- SLAMF7 Low

description: Sample 65

value: Control

value: Low


title: 2C::GFP+/SA H3K79me2 rep2

description: 2C::GFP+/SA H3K79me2 rep2


title: THDS_91m_KLV_p1_B3_CC

value: CH-THDS

value: KLV

value: CD8+ T cell


title: frozen liver biopsy from IPH75 sample

city: Barcelona

first: Juanjo

last: Lozano

address: C/ Rosselló 153

department: Plataforma de Bioinformatica

country: Spain

institute: CIBEREHD

description: frozen liver biopsy from IPH75 sample

data_processing:
Mapping of the reads were obtained using the STAR program against human genome (hg38) and the quantification of genes and transcripts were done with the RSEM program using GENCODE v26.
We use TMM method and limma-voom transformation from rounded expected counts to normalize the non biological variability
Genome_build: Human genome (hg38)
Supplementary_files_format_and_content: RSEM expected counts

molecule: polyA RNA

source_name: frozen liver biopsy

extract_protocol:
RNA was extracted from frozen liver biopsy remnants with Trizol (Promega) according to manufacturer’s extraction.
Libraries were synthetized with the TruSeq stranded mRNA Library Prep (Illumina) and sequenced 2 * 125 bp on Illumina's HiSeq2500, obtaining a minimum of 35 million reads per sample.

tag: group

value: PSVD


title: THDS_91m_KLV_p1_C1_CC


title: Donor 11 Peripheral blood CD14+CD16+ SLAMF7 High

description: Sample 70


title: frozen liver biopsy from IPH94 sample

description: frozen liver biopsy from IPH94 sample


title: frozen liver biopsy from IPH68 sample

description: frozen liver biopsy from IPH68 sample


title: 2C::GFP+/SGC Input rep2

description: 2C::GFP+/SGC Input rep2

value: SGC treated


title: 2C::GFP+/SA H3K79me3 rep1

description: 2C::GFP+/SA H3K79me3 rep1

value: H3K79me3 (Abcam, ab2621)


title: Donor 10 Peripheral blood CD14+CD16+ SLAMF7 High

description: Sample 64

value: Donor 10

value: High


title: frozen liver biopsy from IPH60 sample

description: frozen liver biopsy from IPH60 sample


title: Donor 11 Peripheral blood CD14++CD16+ SLAMF7 Low

description: Sample 67

value: Donor 11


title: THDS_91m_KLV_p1_B2_CC


title: L425_23_premrna

description: brain.BBB.human.counts.rds


title: 2C::GFP+/SGC H3K79me3 rep2

description: 2C::GFP+/SGC H3K79me3 rep2

value: mouse embryonic stem cells


title: 2C::GFP+/SGC Input rep1

description: 2C::GFP+/SGC Input rep1


title: Donor 10 Peripheral blood CD14+CD16+ SLAMF7 Low

description: Sample 63

value: Peripheral blood


title: Donor 10 Peripheral blood CD14++CD16+ SLAMF7 Low

description: Sample 61

value: Monocyte


title: Donor 10 Peripheral blood CD14++CD16+ SLAMF7 High

description: Sample 62


title: 2C::GFP+/SGC H3K79me3 rep1

description: 2C::GFP+/SGC H3K79me3 rep1


title: THDS_91m_KLV_p1_B1_CC


title: THDS_91m_KLV_p1_A3_CC


title: 2C::GFP+/SGC H3K79me2 rep2

description: 2C::GFP+/SGC H3K79me2 rep2

value: H3K79me2 (Abcam, ab3594)


title: frozen liver biopsy from IPH12 sample

description: frozen liver biopsy from IPH12 sample


title: frozen liver biopsy from IPH114 sample

description: frozen liver biopsy from IPH114 sample


title: Donor 10 Peripheral blood CD14++CD16- SLAMF7 High

description: Sample 60


title: 2C::GFP+/SGC H3K79me2 rep1

description: 2C::GFP+/SGC H3K79me2 rep1


title: THDS_91m_KLV_p1_A1_CC


title: frozen liver biopsy from IPH101 sample

description: frozen liver biopsy from IPH101 sample


title: 2C::GFP+ Input rep2

description: 2C::GFP+ Input rep2

value: untreated


title: THDS_91m_KLV_p1_A2_CC


title: Donor 9 Peripheral blood CD14+CD16+ SLAMF7 Low

description: Sample 57

value: Rheumatoid arthritis

value: Donor 9


title: 3089_30m_GPR_p3_D7_CC

value: GPR


title: Donor 10 Peripheral blood CD14++CD16- SLAMF7 Low

description: Sample 59

value: Control

value: Low


title: frozen liver biopsy from CH68 sample

description: frozen liver biopsy from CH68 sample

value: LC


title: frozen liver biopsy from IPH29 sample

description: frozen liver biopsy from IPH29 sample

value: PSVD


title: Donor 9 Peripheral blood CD14+CD16+ SLAMF7 High

description: Sample 58


title: 2C::GFP+ H3K79me3 rep2

description: 2C::GFP+ H3K79me3 rep2


title: 3089_30m_GPR_p3_D6_CC

value: CD8+ T cell


title: 3089_30m_GPR_p3_D8_CC


title: 3089_30m_GPR_p3_D5_CC


title: 2C::GFP+ H3K79me3 rep1

description: 2C::GFP+ H3K79me3 rep1

value: H3K79me3 (Abcam, ab2621)


title: Donor 9 Peripheral blood CD14++CD16+ SLAMF7 High

description: Sample 56


title: Donor 9 Peripheral blood CD14++CD16+ SLAMF7 Low

description: Sample 55


title: frozen liver biopsy from CH50 sample

description: frozen liver biopsy from CH50 sample


title: frozen liver biopsy from CH66 sample

description: frozen liver biopsy from CH66 sample


title: 2C::GFP+ H3K79me2 rep2

description: 2C::GFP+ H3K79me2 rep2


title: Donor 9 Peripheral blood CD14++CD16- SLAMF7 High

description: Sample 54


title: frozen liver biopsy from CH60 sample

description: frozen liver biopsy from CH60 sample


title: 2C::GFP+ Input rep1

description: 2C::GFP+ Input rep1


title: frozen liver biopsy from CH43 sample

description: frozen liver biopsy from CH43 sample


title: 3089_30m_GPR_p3_C2_CC


title: 3089_30m_GPR_p3_C5_CC


title: Donor 9 Peripheral blood CD14++CD16- SLAMF7 Low

description: Sample 53


title: 2C::GFP+ H3K79me2 rep1

description: 2C::GFP+ H3K79me2 rep1


title: frozen liver biopsy from CH3 sample

description: frozen liver biopsy from CH3 sample


title: 2C::GFP+/SA Rep2

description: 2C::GFP+/SA Rep2 RNA-seq

data_processing:
The scRNA-seq data generated by SMART-seq2 and bulk RNA-seq data were pre-processed according to the following pipeline. Sequencing quality of all high-throughput sequencing data were first comprehensively examined by FastQC (release 0.11.9). Next, adapter sequences and bases with sequencing quality < 20 were trimmed from raw data by TrimGalore (release 0.6.5; default parameter). Trimmed read pairs were aligned to mouse genome (mm10) with STAR (release 2.7.4a). For quantification of gene and repeat locus expression, the following command-line arguments were used: --outSAMmapqUnique 255 ?outFilterMultimapNmax 10. We computed the number of uniquely mapped reads of each gene and repeat element using the featureCounts package (release 2.0.0; default parameter). The 10X Genomics scRNA-seq reads were demultiplexed, aligned to the mm10 reference genome and quantified using the toolkit Cell Ranger (release v6.0.2).!Sample_data_processing = Genome_build: mm10 (GRCm38)
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content:
TPM values for each sample.
Matrix table with raw gene counts for every gene and every sample.

extract_protocol:
Total RNA was extracted from mESC, 2C::GFP+, 2C::GFP+/SGC and 2C::GFP+/SA cells using the Trizol kit (Thermo Fisher Scientific, catalog. no. 15596018) following the manufacturer’s instructions. PolyA(+) RNA was isolated for library construction.
RNA libraries were prepared for sequencing using standard Illumina protocols.

value: SGCAS treated


title: Donor 8 Peripheral blood CD14+CD16+ SLAMF7 High

description: Sample 52

value: Donor 8

value: High


title: frozen liver biopsy from CH15 sample

description: frozen liver biopsy from CH15 sample


title: 3089_30m_GPR_p3_B8_CC


title: 3089_30m_GPR_p3_C1_CC


title: Donor 8 Peripheral blood CD14+CD16+ SLAMF7 Low

description: Sample 51


title: 2C::GFP+/SA Rep1

description: 2C::GFP+/SA Rep1 RNA-seq

value: mouse embryonic stem cells


title: 2C::GFP+/SGC Rep2

description: 2C::GFP+/SGC Rep2 RNA-seq

value: SGC treated


title: frozen liver biopsy from CT6 sample

description: frozen liver biopsy from CT6 sample


title: 2C::GFP+/SGC Rep1

description: 2C::GFP+/SGC Rep1 RNA-seq


title: Donor 8 Peripheral blood CD14++CD16+ SLAMF7 High

description: Sample 50

value: Peripheral blood

value: Monocyte


title: frozen liver biopsy from CT47 sample

description: frozen liver biopsy from CT47 sample

value: HNL


title: 2C::GFP+ Rep1

description: 2C::GFP+ Rep1 RNA-seq

value: untreated


title: Donor 8 Peripheral blood CD14++CD16+ SLAMF7 Low

description: Sample 49

value: Rheumatoid arthritis


title: 2C::GFP+ Rep2

description: 2C::GFP+ Rep2 RNA-seq


title: frozen liver biopsy from CT62 sample

description: frozen liver biopsy from CT62 sample


title: 3089_30m_GPR_p3_B3_CC

value: GPR


title: frozen liver biopsy from CT2 sample

description: frozen liver biopsy from CT2 sample


title: 3089_30m_GPR_p3_B6_CC


title: mESC Rep2

description: mESC Rep2 RNA-seq

value: WT


title: 3089_30m_GPR_p3_B4_CC


title: Donor 8 Peripheral blood CD14++CD16- SLAMF7 High

description: Sample 48


title: Donor 7 Peripheral blood CD14+CD16+ SLAMF7 High

description: Sample 46

value: Donor 7


title: Donor 8 Peripheral blood CD14++CD16- SLAMF7 Low

description: Sample 47

value: Low


title: frozen liver biopsy from CH30 sample

description: frozen liver biopsy from CH30 sample

value: LC


title: 3089_30m_GPR_p3_B2_CC

value: CD8+ T cell


title: frozen liver biopsy from CT18 sample

description: frozen liver biopsy from CT18 sample


title: frozen liver biopsy from CT23 sample

description: frozen liver biopsy from CT23 sample


title: mESC_Rep1

description: mESC Rep1 RNA-seq


title: 3089_30m_GPR_p3_A8_CC


title: frozen liver biopsy from CT16 sample

description: frozen liver biopsy from CT16 sample


title: 3089_30m_GPR_p3_A7_CC


title: 3089_30m_GPR_p3_B7_CC


title: Donor 7 Peripheral blood CD14++CD16+ SLAMF7 High

description: Sample 44


title: 3089_30m_GPR_p3_A6_CC


title: Donor 7 Peripheral blood CD14++CD16+ SLAMF7 Low

description: Sample 43


title: mESC-C15-R/plus-5/2

city: Bonn

first: Joachim

last: Schultze

state: NRW

address: Carl-Troll-Strasse 31

department: Genomics and Immunoregulation

country: Germany

institute: LIMES (Life and Medical Sciences Center Genomics and Immunoregulation)

data_processing:
base calling and de-multipexing using CASAVA version 1.8
Alignment and quatification with STAR version v2.7.3a using the default parameters
reads mapped to each transcript against the RefSeq mm38 annotation download on March 2018
Normalization using DeSeq2
Genome_build: mm38
Supplementary_files_format_and_content: comma separated files include DeSeq2 rlog counts for each Sample.

source_name: mESC

extract_protocol:
mES cells were cultivated in complete mES medium (FCS+LIF+2i).
Cells lysed in TRIZOL (Invitrogen), and total RNA was extracted according to the manufactures’ protocol
Illumina TruSeq RNA Sample Preparation Kit v2
200 bp paired-end run was performed on a HiSeq1500

tag: strain

tag: Sex

value: male

tag: day

tag: clone

tag: genotype


title: mESC-C16-WT-5/2


title: 3089_30m_GPR_p3_A5_CC

tag: cell type


title: mESC-C23-R/plus-5/2


title: Donor 7 Peripheral blood CD14++CD16- SLAMF7 Low

description: Sample 41

tag: tissue

tag: disease state

tag: donor

tag: monocyte population


title: mESC-C24-R/R-5/2


title: 3089_30m_GPR_p3_A4_CC

tag: subject

tag: epitope

tag: dpi


title: Donor 6 Peripheral blood CD14+CD16+ SLAMF7 High

description: Sample 40

value: Donor 6

tag: slamf7  expression


title: Donor 7 Peripheral blood CD14++CD16- SLAMF7 High

description: Sample 42


title: TX+g5-g5

data_processing:
RNA-seq reads in fastq files were aligned to hg19 using Hisat (version 2.0.5).
Gene-level read counts were quantified using htseq-count 62 using Ensembl GRCh37 gene annotations.
FeatureCounts was used to do gene-level quantification.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited file of gene-level read counts for each sample.

source_name: hiPSC WTC_TX+g5-g5

growth_protocol: The hiPSC line WTC #11, previously derived in the Conklin laboratory, were cultured on Matrigel (1:30) growth factor-reduced basement membrane matrix (Corning) in mTeSR media (StemCell Technologies). Cells were passaged using versene once reaching 70% confluency and plated at 1:6 density. For EPS conditions, cells were grown as previously described. Briefly, WTC cells were reprogrammed in base medium containing 100 mL DMEM/F12, 100 mL Neurobasal, 1 mL N2 supplement, 2 mL B27 supplement, 1% GlutaMAX , 1% NEAA, 0.1 mM β-mercaptoethanol, penicillin-streptomycin and 5% KSR, and freshly supplemented with 10 ng/ml hLIF, GSK3i (1 μM), ROCKi (2 μM ), (S)-(+)-Dimethindene maleate (2 μM; Tocris), Minocycline hydrochloride (2 μM; Santa Cruz Biotechnology) and IWR-endo-1 (0.5-1 μM; Selleckchem). Cells were adapted to EPS conditions for at least 3 passages before analysis. EPS cells were pushed toward differentiation using TX media: TX medium formulation was DMEM/F12 without HEPES and L-glutamine (Life Technologies), 64 mg/l l-ascorbic acid-2-phosphate magnesium, 14 mg/l sodium selenite, 19.4 mg/l insulin, 543 mg/l NaHCO3, 10.7 mg/l holo-transferrin (all Sigma-Aldrich), 25 ng/ml human recombinant FGF4 (Reliatech), 2 ng/ml human recombinant TGF-ß1 (PeproTech), 1 mg/ml heparin (Sigma-Aldrich), 2 mM L-glutamine, 1% penicillin, and streptomycin (all PAN-biotech). Medium was prepared without growth factors (TX-growth factors) and stored at 40 C. To prepare complete TX, the growth factors: FGF4, heparin, and TGF-b1 were added prior to use. Medium was changed every other day. All cells were cultured at 370 C in 5% CO2. For Elf1 iCas9 conditions, cells were treated as described before but toggled to ‘primed’ cell state for efficient gRNA transfection. Briefly, Elf1 iCas9 were cultured on Matrigel (1:30) growth factor-reduced basement membrane matrix (Corning) in mTeSR media (StemCell Technologies). Cells were passaged using versene once reaching 70% confluency and plated at 1:6 density.

extract_protocol:
RNA was extracted using Trizol (Life Technologies) according to manufacturer’s instructions. RNA samples were treated with Turbo DNase (Thermo Fisher Scientific) and quantified using Nanodrop ND-1000. Reverse transcription was performed using iScript cDNA Synthesis Kit (Bio-Rad). 10 ng of cDNA was used to perform qRT-PCR using SYBR Green (Applied Biosystems) or TaqMan (Applied Biosystems) on a 7300 real time PCR system (Applied Biosystems). The PCR conditions were set up as the following: stage 1 50°C for 2mins, stage 2 as 95°C for 10mis, 95°C for 15sec, 60°C for 1min (40 Cycles). ß-actin was used as an endogenous control. The primer sequences used in this work are shown in Supplementary Table S5.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: EPS programming: WTC colonies reached 60%–70% of confluence. 12 hr after seeding, the conventional WTC medium (TeSR) was replaced with the LCDM medium as described in derivation of pluripotent stem cells with in vivo embryonic and extraembryonic potency 52: 240 mL DMEM/F12 (Thermo Fisher Scientific, 11330-032),240 mL Neurobasal (Thermo Fisher Scientific, 21103-049), 2.5 mL N2 supplement (Thermo Fisher Scientific, 17502-048), 5 mL B27 supplement (Thermo Fisher Scientific, 12587-010), 1% GlutaMAX (Thermo Fisher Scientific, 35050-061), 1% nonessential amino acids (Thermo Fisher Sci- entific, 11140-050), 0.1 mM b-mercaptoethanol (Thermo Fisher Scientific, 21985-023), penicillin-streptomycin (Thermo Fisher Scientific, 15140-122), and 5% knockout serum replacement (KSR, Thermo Fisher Scientific, A3181502, optional) and the following factors : 10 ng/ml hLIF, 1 mM CHIR 9902, 2 mM (S)-(+)-Dimethindene maleate (DiM), 2 mM Minocycline hydrochloride (MiH), 0.5-1 mM IWR-1-endo, and 2mM Y-27632.  The N2B27-LCDM medium was changed daily. Dome-shaped colonies gradually emerged during this period. Then, 3-6 days later, 0.05% Trypsin-EDTA was used to trypsinize the cells for 3 min at 370 C in the incubator. LCDM base medium (without factors) was used to stop the trypsinization. The cells were washed off the surface of dish by pipetting the medium slowly up and down: they were collected in an appropriately sized tube and centrifuged at 1, 200 at room temperature for 3 min. The cells were re-suspended in an appropriate volume of N2B27-LCDM medium (according to the cell lines and growth ratio) and seeded into the plate with MEF feeders. For one six-well plate, approximately 50,000-100,000 cells per well were seeded. The split ratio was usually from 1:3 to 1:10. Then, the cells were incubated under 20% O2 and 5% CO2 at 370C. . Trophoblast differentiation: EPS Cells were incubated with 0.05% Trypsin-EDTA for 3 min at 370 C. TX base medium (DMEM/F12 w/o HEPES or L-Glu (21331-020), 64mg/ml ascorbic acid phosphate Mg, 14ug/l sodium selenite, 19.4mg/l insulin, 10.7 mg/l holo-transferrin, 543mg/l NaHCO3, 1% Pen Strep and, 2mM Glutamax) (without factors) was applied to stop the trypsinization. 50k-100k cells were plated on 35mm matrigel (1:30) coated plate. TX Medium was prepared without growth factors and stored at 40C. TX factors (25ng/ml FGF4, 2ng/ml TGF-beta1and 1 mg /mL Heparin) were added to TX media prior to use. TX media was changed every other day. Cells were passaged when sub-confluent.

tag: cell line background

value: WTC #11

tag: source cell type

value: human pluripotent stem cell (hiPSC) line


title: TX+g1-g1

source_name: hiPSC WTC_TX+g1-g1


title: Donor 7 Peripheral blood CD14+CD16+ SLAMF7 Low

description: Sample 45


title: mESC-C21-R/plus-5/2


title: TX-g

source_name: hiPSC WTC_TX-g


title: 3089_30m_GPR_p2_E7_CC


title: 3089_30m_GPR_p3_A3_CC


title: WTC-g

source_name: hiPSC WTC_WTC-g


title: 3089_30m_GPR_p2_E6_CC


title: mESC-C20-R/R-5/2


title: Donor 6 Peripheral blood CD14++CD16+ SLAMF7 High

description: Sample 38

value: High


title: mESC-C5-WT-5/2


title: mESC-C14-R/R-5/2


title: Donor 6 Peripheral blood CD14+CD16+ SLAMF7 Low

description: Sample 39


title: frozen liver biopsy from CT15 sample

description: frozen liver biopsy from CT15 sample

tag: group


title: Guide 5 rep2

source_name: hiPSC WTC_Guide 5


title: Donor 6 Peripheral blood CD14++CD16+ SLAMF7 Low

description: Sample 37


title: 3089_30m_GPR_p2_E5_CC


title: mESC-C7-WT-5/2

tag: strain


title: Guide 5 rep1


title: 3089_30m_GPR_p2_E4_CC


title: Donor 6 Peripheral blood CD14++CD16- SLAMF7 Low

description: Sample 35


title: Donor 6 Peripheral blood CD14++CD16- SLAMF7 High

description: Sample 36


title: 3089_30m_GPR_p2_E3_CC


title: 3089_30m_GPR_p2_E2_CC


title: mESC-C16-WT-20/1

tag: Sex


title: Donor 3 Peripheral blood CD14+CD16+ SLAMF7 High

description: Sample 34

value: Donor 3


title: Guide 1 rep2

source_name: hiPSC WTC_Guide 1


title: mESC-C14-R/R-20/1

tag: day


title: Donor 3 Peripheral blood CD14+CD16+ SLAMF7 Low

description: Sample 33

value: Peripheral blood


title: Guide 1 rep1


title: mESC-C15-R/plus-20/1

tag: clone


title: No guide rep1

source_name: hiPSC WTC_No guide


title: mESC Trim71-KO 3B

value: x

tag: genotype


title: Donor 3 Peripheral blood CD14++CD16+ SLAMF7 High

description: Sample 32

tag: cell type

value: Monocyte


title: Donor 3 Peripheral blood CD14++CD16+ SLAMF7 Low

description: Sample 31

tag: tissue


title: 3089_30m_GPR_p2_D9_CC


title: mESC Trim71-cond 3B

value: Trimfl/fl


title: 3089_30m_GPR_p2_E1_CC


title: mESC Trim71-KO 2B


title: 6D EB-flag -Dox

description: ACCG9HANXX_US-1680455_CGATCGAT-CGATCGAT_L002

source_name: hiPSC WTC_6D EB-flag -Dox


title: mESC Trim71-cond 2B


title: EVT EB-flag

description: ACCG9HANXX_US-1680437_ATTAGCCG-ATTAGCCG_L002

source_name: hiPSC WTC_EVT EB-flag


title: Donor 3 Peripheral blood CD14++CD16- SLAMF7 Low

description: Sample 29

tag: disease state

value: Rheumatoid arthritis


title: 6D EB-flag +Dox

description: ACCG9HANXX_US-1680416_ATCATGCG-ATCATGCG_L002

source_name: hiPSC WTC_6D EB-flag +Dox


title: 3089_30m_GPR_p2_D8_CC

value: GPR


title: 3089_30m_GPR_p2_E10_CC


title: 3089_30m_GPR_p2_E11_CC


title: 4D EB-flag +Dox

description: ACCG9HANXX_US-1680433_TGTTCCGT-TGTTCCGT_L002

source_name: hiPSC WTC_4D EB-flag +Dox


title: No guide rep2


title: mESC Trim71-cond 3A


title: 4D EB-flag -Dox

description: ACCG9HANXX_US-1680466_GATCTTGC-GATCTTGC_L002

source_name: hiPSC WTC_4D EB-flag -Dox


title: 3089_30m_GPR_p2_D7_CC

source_name: CD8+ T cell


title: Donor 2 Peripheral blood CD14+CD16+ SLAMF7 High

description: Sample 28

source_name: Peripheral blood

tag: donor

value: Donor 2


title: Donor 3 Peripheral blood CD14++CD16- SLAMF7 High

description: Sample 30

tag: monocyte population


title: 3089_30m_GPR_p2_D6_CC

tag: subject


title: Donor 2 Peripheral blood CD14+CD16+ SLAMF7 Low

description: Sample 27


title: 3089_30m_GPR_p2_D5_CC

tag: epitope


title: Donor 2 Peripheral blood CD14++CD16+ SLAMF7 High

description: Sample 26


title: Astrocytes with anti-amyloid beta antibody - rep3

city: New York

first: Kelly

last: Ruggles

state: NY

address: 227 East 30th Street

institute: NYU Grossman School of Medicine

data_processing:
FastQC v0.11.7 (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/) was used to check fastq files for poor sequencing quality; all samples had high quality
Illumina adapter sequences and poor-quality bases were  trimmed using trimmomatic v0.36
Trimmed sequences were mapped to rn6 using STAR v2.6.0a, indexed using samtools v1.9, then quantified for UCSC genes using HTSeq-count v0.11.1.
Comparative analysis between conditions was performed using DESeq2 v1.24.0 with default parameters.
Genome_build: rn6
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

organism: Rattus norvegicus

source_name: Sprague Dawley rat pup astrocytes

growth_protocol: Astrocytes were plated at 5x10^4 astrocytes/well in 6-well plates. Astrocyte-conditioned media (ACM) was obtained by culture of astrocytes in astrocyte media for 1 week. 1.5 mL of ACM were then transferred and incubated with 12-273 BM cells in 6-well plates for 24 hours

extract_protocol:
RNeasy Mini Kit (Qiagen 74104)
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: 24-hour incubation in melanoma-conditioned media

value: Sprague Dawley

value: astrocytes

tag: treatment

value: anti-amyloid beta antibody

tag: culture

value: melanoma co-culture


title: mESC Trim71-KO 1A

value: male


title: Astrocytes with anti-amyloid beta antibody - rep2


title: mESC Trim71-cond 1A


title: 3089_30m_GPR_p2_D4_CC

tag: dpi

value: CD8+ T cell


title: Donor 2 Peripheral blood CD14++CD16+ SLAMF7 Low

description: Sample 25

tag: slamf7  expression

value: Low


title: 845 [striatum]

first: Camron

middle: D

last: Bryant

state: Massachusetts

address: 72 E Concord St

department: Pharmacology

institute: Boston University School of Medicine

data_processing:
We used the R/Bioconductor package “scruff” to conduct demultiplexing, read alignment, read counting, quality checking and data visualization (Wang et al., 2019).
Reads were trimmed for quality using Trimmomatic (Bolger et al., 2014).
Trimmed reads were then aligned to the mm10 mouse reference genome (Ensembl) to generate BAM files for alignment using STAR (Dobin et al., 2013)
For differential gene analysis in the spinal cord, the featureCounts read summarization program was used to count reads mapping to the “exon” feature in a GTF file obtained from Ensembl (GRCm38).
Genome_build: GRCm38
Supplementary_files_format_and_content: Raw counts from featureCounts.

source_name: Striatum

extract_protocol:
RNA was extracted in RNAlater-preserved tissue using Trizol (Qiagen), ethanol precipitation, filtering columns (Qiagen), DNAse digestion (Qiagen), and elution with RNAse and nucleotide free water (Yazdani et al., 2015) and diluted to 100 ng/ul.
RNA library preparation (poly-A selection) and RNA-seq was conducted at the University of Chicago Genomics Facility on an Illumina NovaSeq 6000 using a NovaSEQ SP-100 bp flowcell/reagent cassette. ~30M clusters/sample, 60M PE reads/sample.

value: BALBcJ x BALBcByJ F2

tag: cpp treatment

value: OXYCODONE

value: M

value: Striatum

tag: rna extraction cohort


title: Donor 2 Peripheral blood CD14++CD16- SLAMF7 High

description: Sample 24

value: Peripheral blood

value: High


title: mESC Trim71-KO 3A

source_name: mESC

tag: strain

tag: Sex

value: x


title: Astrocytes with sh-APP - rep3

value: sh-APP


title: RB29 (3.5K BAC-CGH)

type: genomic

city: paris

first: Elodie

last: chapeaublanc

address: 26 rue d'ulm

department: UMR 144

country: France

institute: Institut Curie

description:
3.5K BAC CGH array data for retinoblastoma samples
Sample name: SAMPLE 52

hyb_protocol: see platform's Manufacture protocol

scan_protocol: ScanArray 4000 (Packard Bioscience)

data_processing:
HG19 version of the genome used, data processed with GLAD algorithm (Hupé et al, Bioinformatics, 2004)
Raw data matrix : raw log ratio values, Processed data matrix: Gap-smoothed log ratio values

source_name: retinoblastoma sample RB29

extract_protocol: For DNA extraction, samples were first incubated in a lysis buffer with proteinase K, recombinant. They were next incubated with RNAse A. DNA was then extracted using a standard phenol-chloroform protocol

value: SAMPLE 21

value: retinoblastoma


title: Donor 2 Peripheral blood CD14++CD16- SLAMF7 Low

description: Sample 23

value: Monocyte

value: Rheumatoid arthritis

value: Donor 2


title: 844 [striatum]


title: 3089_30m_GPR_p2_D11_CC

value: GPR


title: Donor 1 Peripheral blood CD14+CD16+ SLAMF7 High

description: Sample 22

value: Donor 1


title: Astrocytes with sh-APP - rep2

value: Sprague Dawley

value: astrocytes

value: melanoma co-culture


title: 841 [striatum]

value: BALBcJ x BALBcByJ F2

value: OXYCODONE

value: F


title: Astrocytes with sh-APP - rep1


title: 3089_30m_GPR_p2_D10_CC

value: CD8+ T cell


title: Donor 1 Peripheral blood CD14+CD16+ SLAMF7 Low

description: Sample 21

value: Peripheral blood

value: Low


title: 838 [striatum]

value: Striatum


title: Astrocyte control - rep2

value: control


title: Donor 1 Peripheral blood CD14++CD16+ SLAMF7 High

description: Sample 20

value: High


title: 3089_30m_GPR_p2_D1_CC


title: Astrocytes with anti-amyloid beta antibody - rep1

value: anti-amyloid beta antibody


title: 836 [striatum]

value: SALINE

value: M


title: Astrocyte control - rep1


title: 3089_30m_GPR_p2_C8_CC

value: GPR


title: Donor 1 Peripheral blood CD14++CD16- SLAMF7 High

description: Sample 18

value: Monocyte

value: Rheumatoid arthritis

value: Donor 1


title: 3089_30m_GPR_p2_D2_CC


title: 3089_30m_GPR_p2_C9_CC


title: 3089_30m_GPR_p2_D3_CC


title: 835 [striatum]


title: 3089_30m_GPR_p2_C7_CC


title: 842 [striatum]


title: Donor 1 Peripheral blood CD14++CD16- SLAMF7 Low

description: Sample 17


title: 833 [striatum]


title: 834 [striatum]


title: Donor 4 Synovial fluid CD14++CD16+ SLAMF7 High

description: Sample 16

source_name: Synovial fluid

value: Synovial fluid

value: Donor 4


title: 3089_30m_GPR_p2_C6_CC


title: 832 [striatum]

value: BALBcJ x BALBcByJ F2

value: OXYCODONE


title: Pkd1F_RC_Pkd2_UTR_DD_28

city: Dallas

first: Ronak

last: Lakhia

state: Texas

address: 5323 Harry Hines Blvd

department: Internal Medicine

institute: UTSW

data_processing:
QC was performed by FastQCv0.11.8 RNA-seq reads were trimmed and low-quality reads were removed using Trimgalore v0.6.3_dev
trimmed fastq sequences were aligned to the mouse reference genome GRCm38 using STAR aligner v2.5.3a
raw counts were normalized to total number of reads by calculateing log2CPM and lowly expressed genes (average log2CPM<-3) were eliminated before differential gene expression analysis
Genome_build: GRCm38
Supplementary_files_format_and_content: raw counts txt matrix for all samples and genes

source_name: whole kidney

growth_protocol: mice were sacrificed using IACUC approved protocols and whole kidneys were flash frozen at 18 days of age

extract_protocol:
Total RNA was extracted using Qiagen miRNEASY kit
Library preparation was performed by Genewiz

value: whole kidney

tag: control or cystic

value: cystic


title: Pkd1F_RC_Pkd2_UTR_DD_29


title: Pkd1F_RC_Pkd2_UTR_DD_30


title: Pkd1F_RC_27


title: 3089_30m_GPR_p2_C5_CC

value: CD8+ T cell


title: 831 [striatum]

value: Striatum


title: 3089_30m_GPR_p2_C4_CC


title: Donor 1 Peripheral blood CD14++CD16+ SLAMF7 Low

description: Sample 19

value: Peripheral blood

value: Low


title: Donor 4 Synovial fluid CD14++CD16- SLAMF7 High

description: Sample 14

value: High


title: Donor 4 Synovial fluid CD14++CD16+ SLAMF7 Low

description: Sample 15


title: 829 [striatum]


title: 830 [striatum]


title: Donor 3 Synovial fluid CD14++CD16+ SLAMF7 High

description: Sample 12

value: Donor 3


title: 3089_30m_GPR_p2_C3_CC


title: Pkd1_RC_Pkd2_UTR_DD_24

value: control


title: 3089_30m_GPR_p2_C2_CC

value: GPR


title: Donor 3 Synovial fluid CD14++CD16+ SLAMF7 Low

description: Sample 11

value: Monocyte


title: 3089_30m_GPR_p2_C10_CC


title: 826 [striatum]

value: M


title: 827 [striatum]


title: Pkd1_RC_Pkd2_UTR_DD_23


title: Pkd1F_RC_26


title: 825 [striatum]


title: Pkd1_RC_Pkd2_UTR_DD_22


title: Pkd1_RC_21


title: 3089_30m_GPR_p2_B9_CC


title: 822 [striatum]

value: SALINE

value: F


title: Pkd1F_RC_25


title: Pkd1_RC_20


title: Donor 4 Synovial fluid CD14++CD16- SLAMF7 Low

description: Sample 13

value: Synovial fluid

value: Rheumatoid arthritis

value: Donor 4


title: Donor 3 Synovial fluid CD14++CD16- SLAMF7 Low

description: Sample 9


title: 3089_30m_GPR_p2_B8_CC


title: Donor 2 Synovial fluid CD14++CD16+ SLAMF7 High

description: Sample 8

value: Donor 2


title: 3089_30m_GPR_p2_C11_CC


title: 3089_30m_GPR_p2_B7_CC


title: Donor 3 Synovial fluid CD14++CD16- SLAMF7 High

description: Sample 10


title: Donor 2 Synovial fluid CD14++CD16- SLAMF7 High

description: Sample 6


title: 3089_30m_GPR_p2_B6_CC


title: Pkd1_minus_RC_D53_26

tag: cell tissue

value: whole kidney

tag: found id

value: founder 2

value: cystic


title: Donor 2 Synovial fluid CD14++CD16+ SLAMF7 Low

description: Sample 7

tag: tissue

tag: cell type


title: Pkd1_RC_19


title: 819 [striatum]

value: BALBcJ x BALBcByJ F2

value: Striatum


title: Pkd1_minus_RC_D53_27


title: Pkd1_minus_RC_D53_25


title: 821 [striatum]


title: Donor 2 Synovial fluid CD14++CD16- SLAMF7 Low

description: Sample 5

tag: disease state

tag: donor

value: Low


title: 818 [striatum]


title: Donor 1 Synovial fluid CD14++CD16+ SLAMF7 High

description: Sample 4

value: Donor 1

tag: monocyte population

value: High


title: Pkd1_minus_RC_D53_24


title: 3089_30m_GPR_p2_B3_CC

tag: subject

tag: epitope

value: GPR

value: CD8+ T cell


title: 816 [striatum]

value: OXYCODONE


title: 3089_30m_GPR_p2_B4_CC


title: 815 [striatum]


title: Donor 1 Synovial fluid CD14++CD16- SLAMF7 High

description: Sample 2

value: Monocyte


title: Donor 1 Synovial fluid CD14++CD16+ SLAMF7 Low

description: Sample 3


title: Pkd1_minus_RC_D53_23


title: 3089_30m_GPR_p2_B2_CC


title: 3089_30m_GPR_p2_B11_CC


title: 812 [striatum]

value: M


title: 813 [striatum]

value: F


title: Donor 1 Synovial fluid CD14++CD16- SLAMF7 Low

description: Sample 1

value: Synovial fluid

value: Rheumatoid arthritis


title: 3089_30m_GPR_p2_B5_CC


title: 817 [striatum]

value: SALINE


title: 3089_30m_GPR_p2_B10_CC


title: SamplePool_4

city: Tarrytown

first: Sandra

last: Kleiner

address: 777 Old Saw Mill River Rd

institute: Regeneron Pharmaceuticals, Tarrytown, New York, USA

data_processing:
BCLs converted to Fastq performed using Cell Ranger v2.2
Reads were aligned to the GCRh37 genome assembly using Cell Ranger 3.0.2
Genome_build: GRCh37

source_name: differential ES cells

extract_protocol:
SC-derived clusters at d27 were dissociated into single cells using TrypLE Express. The resulting dissociated cells were filtered through a 30 µm cell strainer and collected by centrifugation at 400 x g for 5 min. The cell pellet was resuspended in 5 mL 1X PBS containing 0.04% BSA and filtered through a 30 µm strainer. Cells were collected by centrifugation at 400 x g for 5 min and the pellet was resuspended with 1X PBS+0.04% BSA to a final concentration of 400-500 cells/µL.
RNAseq libraries were prepared using Chromium Signle Cell 3' Library, Gel Breads & Muliplex Kit (10X Genomics)
Total seq-A anti-human hashtag antibodies (BioLegend) were used for cell hashing. Each sample was individually stained with one of the hashtag antibodies and washed three times. Twelve samples (4 control samples, 4 R138X, and 4 SLC30A8 NULL) were pooled at equal concentrations, and the pool was loaded into the 10X Chromium instrument.

value: ES-derived pancertia beta cells


title: Pkd1_minus_RC_D18_21

value: whole kidney

value: founder 3


title: 3089_30m_GPR_p2_A9_CC


title: 810 [striatum]

value: BALBcJ x BALBcByJ F2


title: Pkd1_minus_RC_D18_20

value: cystic


title: 3089_30m_GPR_p2_B1_CC


title: 811 [striatum]

value: Striatum


title: Pkd1_minus_RC_D18_22


title: SamplePool_2


title: Pkd1_minus_RC_D18_19


title: 809 [striatum]


title: SamplePool_1


title: 3089_30m_GPR_p2_A8_CC


title: Pkd1_minus_RC_D18_18


title: 3089_30m_GPR_p2_A7_CC


title: Pkd1_minus_RC_17


title: 808 [striatum]


title: 3089_30m_GPR_p2_A6_CC


title: 805 [striatum]


title: Day_13_Non-T_P7_WT_3

first: Yu-Jui

last: Ho

state: New York

address: 417 E 68th St

department: Cancer Biology & Genetics Program

institute: Memorial Sloan Kettering Cancer Center

data_processing:
Rnaseq reads were aligned to (GRCm38 - mm10) with STAR
Genome wide transcript counting was performed by HTSeq or featureCounts to generate FPKM matrix
Differential expression analysis was performed with DESeq2 package in R
Genome_build: GRCm38 - mm10
Supplementary_files_format_and_content: csv text file includes raw count value for each sample

source_name: CD45+CD8-CD4- sorted from B16-TME in WT mice

growth_protocol: B16 tumors were implanted in super p53 or WT mice. WT mice were treated with vehicle or APR-246  starting day 7 for 6 days and single cell suspensions of the tumors were obtained and antibody stained for CD45, CD8. CD4 and live/dead. CD45+ CD8+, CD45+CD8+ and CD45+CD4-CD8- sorted

extract_protocol:
RNA was extracted with the PAXgene RNA kit and purified in accordance with the manufacturer’s protocols
RNA sequencing libraries were generated using Illumina mRNA TruSeq kit with dual index barcoding.

tag: cell line

tag: mouse

value: Mouse #1.5


title: Pkd1_minus_RC_15


title: 807 [striatum]


title: Pkd1_minus_RC_14


title: Pkd1_minus_RC_16


title: Day_13_Non-T_P7_WT_1

treatment_protocol: WT mice were treated with vehicle or APR-246  starting day 7 for 6 day

value: Mouse #1.3


title: 806 [striatum]


title: 3089_30m_GPR_p2_A5_CC

value: GPR

tag: dpi


title: SamplePool_3


title: Day_13_Non-T_P7_WT_2

value: Mouse #1.4


title: 803 [striatum]

tag: cpp treatment


title: 3089_30m_GPR_p2_A4_CC

value: CD8+ T cell


title: Day_13_Non-T_P7_Apr246_4

source_name: CD45+CD8-CD4- sorted from B16-TME in APR246 treated WT mice

value: Mouse #2.5


title: Pkd1_minus_RC_13


title: Pkd1_plus_RC_D53_12

value: founder 2

value: control


title: 3089_30m_GPR_p2_A3_CC


title: Day_13_Non-T_P7_Apr246_5

value: Mouse #2.1


title: 801 [striatum]

value: M

tag: rna extraction cohort


title: Day_13_Non-T_P7_Apr246_3

value: Mouse #2.4


title: 3089_30m_GPR_p2_A11_CC


title: 748 [striatum]

tag: strain

value: OXYCODONE

value: F


title: Pkd1_plus_RC_D53_11

value: whole kidney


title: 3089_30m_GPR_p2_A10_CC


title: Day_13_Non-T_P7_Apr246_2

value: Mouse #2.3


title: Pkd1_plus_RC_D53_10


title: 3089_30m_GPR_p2_A2_CC


title: Day_13_Non-T_P7_SuperP53_4

source_name: CD45+CD8-CD4- sorted from B16-TME in SuperP53 mice

value: Mouse #3.2


title: Pkd1_plus_RC_D18_9

value: founder 3


title: 3089_30m_GPR_p2_A1_CC


title: Day_13_Non-T_P7_Apr246_1

value: Mouse #2.2


title: 3089_24m_GPR_p1_H9_CC


title: 746 [striatum]

value: BALBcJ x BALBcByJ F2

tag: Sex

value: Striatum


title: Pkd1_plus_RC_D18_8

tag: control or cystic


title: 745 [striatum]


title: Day_13_Non-T_P7_SuperP53_2

value: Mouse #3.4


title: 3089_24m_GPR_p1_H8_CC

value: GPR

value: CD8+ T cell


title: Day_13_Non-T_P7_SuperP53_3

value: Mouse #3.5


title: 744 [striatum]


title: 739 [striatum]

value: SALINE


title: Pkd1_plus_RC_D18_7

tag: cell tissue

value: control


title: 3089_24m_GPR_p1_H7_CC


title: Day_13_Non-T_P7_SuperP53_1

value: Mouse #3.3


title: Pkd1_plus_RC_6


title: 3089_24m_GPR_p1_H6_CC


title: 737 [striatum]


title: 3089_24m_GPR_p1_H5_CC


title: Day_13_CD8_WT_3

source_name: CD8 sorted from B16-TME in WT mice

value: Mouse #1.3


title: 747 [striatum]

value: OXYCODONE


title: 733 [striatum]

value: F


title: Day_13_CD8_WT_4

value: Mouse #1.5


title: Day_13_CD8_WT_2

value: Mouse #1.2


title: Pkd1_plus_RC_4

value: whole kidney


title: 729 [striatum]


title: Decr2 shRNA2 infected B16.SIY1

city: Chicago

first: shuyin

last: Li

address: 5801 S Ellis Ave

institute: University of Chicago

data_processing:
Alignment was performed using the Kallisto software.
All submitted samples passed quality control using the R package FastQC.
Raw read counts were processed by TMM normalization followed by log2 transformation.
Limma voom was used to identify differentially expressed genes between DECR2 knockdown and control cells.
Supplementary_files_format_and_content: Matrix table with  log2-normalized expression values for every gene and every sample

source_name: melanoma cell line

growth_protocol: B16.SIY cells were cultured in DMEM medium supplemented with 10% fetal calf serum under standard conditions.

extract_protocol:
RNA was isolated using the Qiagen micro mRNA kit
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Control shRNA (SHC002) and Decr2 shRNAs (TRCN0000042100 shRNA2 and TRCN0000042099 shRNA1) were purchased from Sigma. 293T cells were transfected with lipofectamine 3000 according to manufacturer’s instruction (Invitrogen). B16.SIY were infected by shRNA lentivrius and stable lines can be generated by puromycine seletion.

value: melanoma cell line

tag: tag

value: model antigen SIYRYYGL (SIY) fused with dsRED

tag: treatment

value: Decr2 shRNA2 infected stable line


title: Decr2 shRNA2 infected B16.SIY2

tag: cell type


title: 727 [striatum]

value: BALBcJ x BALBcByJ F2

tag: tissue

value: Striatum


title: Decr2 shRNA2 infected B16.SIY0


title: Day_13_CD8_WT_1

value: Mouse #1.1


title: 3089_24m_GPR_p1_H2_CC

value: GPR

value: CD8+ T cell


title: Day_13_CD8_Apr246_5

source_name: CD8 sorted from B16-TME in APR246 treated WT mice

value: Mouse #2.3


title: 726 [striatum]


title: Decr2 shRNA1 infected B16.SIY2

value: Decr2 shRNA1 infected stable line


title: 3089_24m_GPR_p1_H10_CC


title: 738 [striatum]

value: SALINE

value: M


title: Day_13_CD8_Apr246_4

value: Mouse #2.5


title: 725 [striatum]

value: OXYCODONE

value: F


title: 3089_24m_GPR_p1_G9_CC


title: Decr2 shRNA1 infected B16.SIY1


title: 3089_24m_GPR_p1_H4_CC


title: 3089_24m_GPR_p1_G8_CC


title: Pkd1_plus_RC_5

value: control


title: Day_13_CD8_Apr246_2

value: Mouse #2.2


title: 723 [striatum]


title: 3089_24m_GPR_p1_H1_CC


title: Day_13_CD8_Apr246_3

value: Mouse #2.4


title: 3089_24m_GPR_p1_H3_CC


title: Control shRNA infected B16.SIY2

value: melanoma cell line

value: model antigen SIYRYYGL (SIY) fused with dsRED

value: Control shRNA infected stable line


title: 722 [striatum]

value: BALBcJ x BALBcByJ F2

value: Striatum


title: 719 [striatum]


title: Decr2 shRNA1 infected B16.SIY0


title: Control shRNA infected B16.SIY1


title: Day_13_CD8_SuperP53_4

source_name: CD8 sorted from B16-TME in SuperP53 mice

value: Mouse #3.5


title: Day_13_CD8_Apr246_1

value: Mouse #2.1


title: 721 [striatum]


title: 3089_24m_GPR_p1_G7_CC

value: GPR

value: CD8+ T cell


title: Day_13_CD8_SuperP53_3

value: Mouse #3.4


title: 3089_24m_GPR_p1_G6_CC


title: 3089_24m_GPR_p1_G5_CC


title: Day_13_CD8_SuperP53_2

value: Mouse #3.3


title: Control shRNA infected B16.SIY0


title: 716 [striatum]

value: M


title: 718 [striatum]

value: SALINE


title: Kidney WT - furosemide_rep3

city: Stanford

first: Purvesh

last: Khatri

state: California

address: 279 Campus Dr. Beckman Center B235A

department: BMIR

institute: Stanford University

description: PassGenes_doubletsmixed2removed_equalnumcells_DataTable.csv

data_processing:
Processing of reads was carried out with the BD Rhapsody Analysis Pipeline (v1.02; https://www.bd.com/documents/guides/user-guides/GMX_BD-Rhapsody-genomics-informatics_UG_EN.pdf). The summary of the pipeline steps are provided below. All processing was carried out within the Seven Bridges (sbgenomics.com) platform. Samples were sequenced across 5 total lanes (4 lanes in run 1 and 1 lane in run 2). FASTQ files for each sample were combined in the first step of the Rhapsody analysis pipeline.
1. Read pairs were filtered out based on quality (read 1 length <66 or read 2 length <64, mean base quality <20, highest single nucleotide frequency >= 0.55 for read 1 or >= 0.80 for read 2)
2. Cell labels, UMIs were extracted from read 1s and reads were dropped if <6 Ts were found in the PolyT tail or if cell label, UMI, polyT tail regions could not be annotated/extracted.
3. Read 2s were aligned using Bowtie2 v2.2.9  with the reference panel sequences. Reads were dropped which do not uniquely map to a transcript in the reference file, aligned after the first 5 nucleotides in the read, aligned to phiX174, or had an alignment length of <= 60 bases.
4. Remaining read 1 and read 2 pair information was combined. Reads without an accompanying valid pair were dropped.
5. Reads arising from the same original molecule were combined by matching cell label, UMI, and gene. PCR artifacts were adjusted using the BD recursive substation error correction (RSEC) and and distribution-based error correction (DBEC) algorithms (see Rhapsody pipeline documentation for details).
6. Putative cells were labeled by plotting log cumulative reads vs. cell index (sorted in descending order based on number of reads). Cells labels were retained if they are before the inflection point in the graph (using the second derivative to determine the inflection point). False positive cells are removed as described in the Rhapsody pipeline document.
7. Expression matrices were generated for each cell using the RSEC and DBEC-adjusted molecule counts.
8. BD Data View v1.2 was used to identify and filter out doublets (using the “Identify doublet clusters” function - this function, developed by BD, generates synthetic doublets, uses tSNE to embed the synthetic doublets with the original data, and removes data points which have a high proportion of synthetic doublets within a given radius in the 2D tSNE embedding) and do identify nephron cell types.
Genome_build: A4galt|ENSMUST00000164614.1  Ace|ENSMUST00000001963.13  Acsm2|ENSMUST00000167935.9  Acsm3|ENSMUST00000063770.9  Acta2|ENSMUST00000039631.8  Acy3|ENSMUST00000054030.7  Adamts1|ENSMUST00000023610.14  Adh1|ENSMUST00000004232.9  Adora1|ENSMUST00000086465.5  Adora2b|ENSMUST00000018644.2  Ager|ENSMUST00000015596.9  Agt|ENSMUST00000063278.6  Ahsa1|ENSMUST00000021425.6  Akr1b3|ENSMUST00000102980.10  Akt1|ENSMUST00000001780.9  Aldob|ENSMUST00000029987.9  Apln|ENSMUST00000039026.7  Apoe|ENSMUST00000174064.8  Aqp1|ENSMUST00000004774.3  Aqp2|ENSMUST00000023752.4  Aqp6|ENSMUST00000023754.5  Aqp7|ENSMUST00000030136.12  Arg1|ENSMUST00000020161.8  Atf3|ENSMUST00000027941.13  Atp12a|ENSMUST00000007340.2  Atp1a1|ENSMUST00000036493.7  Atp1b1|ENSMUST00000027863.12  Atp2a2|ENSMUST00000031423.9  Atp4a|ENSMUST00000005692.13  Atp6ap2|ENSMUST00000033313.2  Atp6v1c2|ENSMUST00000095820.11  Atp6v1g3|ENSMUST00000027643.5  Axl|ENSMUST00000002677.10  Bcat1|ENSMUST00000032402.11  Becn1|ENSMUST00000130916.7  Bhmt|ENSMUST00000099309.4  Birc5|ENSMUST00000081387.10  Bmp7|ENSMUST00000009143.7  Bsnd|ENSMUST00000054472.3  C1galt1|ENSMUST00000040159.5  C1galt1c1|ENSMUST00000058265.7  C1qa|ENSMUST00000046285.5  C3|ENSMUST00000024988.14  Cacna1a|ENSMUST00000121390.7  Cacna1c|ENSMUST00000186889.6  Cacna1g|ENSMUST00000100561.9  Cacna1h|ENSMUST00000159610.7  Calb1|ENSMUST00000029876.1  Calm1|ENSMUST00000110082.9  Casp1|ENSMUST00000027015.5  Casp3|ENSMUST00000093517.5  Casr|ENSMUST00000063597.13  Ccl17|ENSMUST00000034232.1  Ccl2|ENSMUST00000000193.5  Ccl22|ENSMUST00000034231.3  Ccl24|ENSMUST00000201401.1  Ccl3|ENSMUST00000001008.5  Ccl4|ENSMUST00000019074.3  Ccl5|ENSMUST00000035938.2  Ccnd1|ENSMUST00000093962.4  Ccr2|ENSMUST00000168841.1  Cd3e|ENSMUST00000102832.1  Cd4|ENSMUST00000024044.6  Cd68|ENSMUST00000018918.11  Cd74|ENSMUST00000167610.1  Cd80|ENSMUST00000099816.2  Cd8a|ENSMUST00000066747.13  Cdh1|ENSMUST00000000312.11  Cdh5|ENSMUST00000034339.8  Cdk9|ENSMUST00000009699.15  Cdkn1a|ENSMUST00000023829.6  Cdkn1b|ENSMUST00000067327.10  Cebpb|ENSMUST00000070642.3  Cela1|ENSMUST00000023775.7  Cftr|ENSMUST00000045706.11  Chil3|ENSMUST00000063062.8  Chrna1|ENSMUST00000028515.3  Ckb|ENSMUST00000001304.7  Clcn5|ENSMUST00000004428.13  Clcnka|ENSMUST00000105790.7  Clcnkb|ENSMUST00000105788.1  Cldn10|ENSMUST00000100314.3  Cldn16|ENSMUST00000161053.7  Cldn23|ENSMUST00000060128.5  Cldn4|ENSMUST00000051401.3  Cldn5|ENSMUST00000043577.1  Clu|ENSMUST00000022616.12  Col1a1|ENSMUST00000001547.7  Col1a2|ENSMUST00000031668.9  Col2a1|ENSMUST00000023123.14  Col3a1|ENSMUST00000087883.12  Col4a1|ENSMUST00000033898.9  Col4a3|ENSMUST00000113457.8  Col4a4|ENSMUST00000087050.6  Crem|ENSMUST00000082141.11  Crtc1|ENSMUST00000076615.5  Cryab|ENSMUST00000034562.7  Ctgf|ENSMUST00000020171.11  Ctnnb1|ENSMUST00000007130.14  Ctxn3|ENSMUST00000091892.2  Cux1|ENSMUST00000176745.7  Cxcl1|ENSMUST00000031327.8  Cxcl10|ENSMUST00000038816.12  Cxcl15|ENSMUST00000031322.6  Cxcl2|ENSMUST00000200681.3  Cxcr4|ENSMUST00000052172.6  Cyp1a1|ENSMUST00000034865.4  Cyp1b1|ENSMUST00000024894.1  Cyp2a4|ENSMUST00000098657.4  Cyp2d9|ENSMUST00000089129.5  Cyp2e1|ENSMUST00000026552.7  Cyp4b1|ENSMUST00000102707.9  Cyr61|ENSMUST00000029846.4  Des|ENSMUST00000027409.9  Dkk3|ENSMUST00000033036.5  Dnajb1|ENSMUST00000005620.8  Dpp4|ENSMUST00000047812.7  Dyrk1a|ENSMUST00000023614.4  Edn1|ENSMUST00000021796.7  Egf|ENSMUST00000029653.6  Egfr|ENSMUST00000020329.12  Egln2|ENSMUST00000080058.10  Egr1|ENSMUST00000064795.5  Eif2b4|ENSMUST00000114603.7  Elk1|ENSMUST00000009550.13  Eln|ENSMUST00000015138.12  Emp1|ENSMUST00000111907.1  Ephb1|ENSMUST00000035129.13  Ephb2|ENSMUST00000105845.8  Epo|ENSMUST00000111038.7  Esm1|ENSMUST00000038144.8  Fabp1|ENSMUST00000067492.7  Fas|ENSMUST00000025691.11  Fasl|ENSMUST00000000834.3  Fbxo32|ENSMUST00000022986.6  Fgf2|ENSMUST00000200585.4  Fkbp4|ENSMUST00000032508.10  Fn1|ENSMUST00000055226.12  Fos|ENSMUST00000021674.6  Foxo3|ENSMUST00000105502.7  Fst|ENSMUST00000022287.5  Fxyd2|ENSMUST00000041005.5  Fxyd4|ENSMUST00000203082.2  G6pc|ENSMUST00000019469.2  Gata4|ENSMUST00000118022.7  Gatm|ENSMUST00000028624.8  Gdf15|ENSMUST00000110103.1  Glyat|ENSMUST00000119960.1  Gpam|ENSMUST00000061856.5  Gpd1|ENSMUST00000023760.12  Gprc5a|ENSMUST00000050104.7  Gpx1|ENSMUST00000082429.6  Gpx3|ENSMUST00000082430.9  Gpx6|ENSMUST00000004453.7  Grap2|ENSMUST00000043149.7  Gsk3b|ENSMUST00000023507.12  Gsta1|ENSMUST00000098537.3  Gsta2|ENSMUST00000034902.11  Guca2a|ENSMUST00000024015.2  Gypc|ENSMUST00000174459.1  H2-Aa|ENSMUST00000040655.12  Havcr1|ENSMUST00000109223.7  Hbegf|ENSMUST00000025363.5  Hdac2|ENSMUST00000019911.13  Hdac4|ENSMUST00000097644.8  Hdac8|ENSMUST00000087916.10  Hgf|ENSMUST00000199581.4  Hif1a|ENSMUST00000021530.7  Hist1h1c|ENSMUST00000040914.2  Hmox1|ENSMUST00000005548.6  Hnf1a|ENSMUST00000031535.11  Hnf1b|ENSMUST00000021016.9  Hsd11b2|ENSMUST00000034363.5  Hspa1a|ENSMUST00000087328.3  Icam1|ENSMUST00000086399.4  Id3|ENSMUST00000008016.2  Ifit1|ENSMUST00000102824.3  Ifrd1|ENSMUST00000001672.11  Igf1|ENSMUST00000095360.10  Igf1r|ENSMUST00000005671.9  Igfbp1|ENSMUST00000020704.7  Igfbp2|ENSMUST00000047328.10  Igfbp3|ENSMUST00000020702.10  Igfbp4|ENSMUST00000017637.12  Igfbp5|ENSMUST00000027377.8  Igfbp6|ENSMUST00000023807.6  Igfbp7|ENSMUST00000163898.5  Igkc|ENSMUST00000103410.2  Iglc1|ENSMUST00000200568.1  Il10|ENSMUST00000016673.5  Il11|ENSMUST00000094892.11  Il12b|ENSMUST00000170513.2  Il13|ENSMUST00000020650.1  Il18|ENSMUST00000180021.1  Il1a|ENSMUST00000028882.1  Il1b|ENSMUST00000028881.13  Il1r1|ENSMUST00000027241.10  Il1rn|ENSMUST00000114487.8  Il23a|ENSMUST00000026449.1  Il4|ENSMUST00000000889.6  Il4ra|ENSMUST00000033004.7  Il5|ENSMUST00000048605.2  Il6|ENSMUST00000199183.4  Il6st|ENSMUST00000183663.7  Ilk|ENSMUST00000163389.7  Inmt|ENSMUST00000003569.5  Insr|ENSMUST00000091291.4  Insrr|ENSMUST00000029711.8  Isg15|ENSMUST00000085425.4  Itga5|ENSMUST00000023128.6  Itgax|ENSMUST00000033053.7  Jak2|ENSMUST00000065796.9  Jun|ENSMUST00000107094.1  Kap|ENSMUST00000048032.4  Kcna1|ENSMUST00000203094.1  Kcne1|ENSMUST00000051705.5  Kcnj1|ENSMUST00000047334.8  Kcnj10|ENSMUST00000056136.3  Kcnj16|ENSMUST00000180023.7  Kcnma1|ENSMUST00000179097.7  Kcnmb1|ENSMUST00000020362.2  Kcnmb4|ENSMUST00000068233.10  Kcnn3|ENSMUST00000000811.7  Kl|ENSMUST00000078856.7  Klf4|ENSMUST00000107619.2  Krt18|ENSMUST00000023803.6  Lamc2|ENSMUST00000185356.6  Lcn2|ENSMUST00000050785.13  Lgals3|ENSMUST00000142734.7  Lpar1|ENSMUST00000107575.8  Lpl|ENSMUST00000015712.14  Ly6e|ENSMUST00000051698.13  Ly6g|ENSMUST00000190262.1  Lypd2|ENSMUST00000023260.4  Lyz2|ENSMUST00000092163.7  Map2k1|ENSMUST00000005066.8  Map2k2|ENSMUST00000143517.7  Map2k4|ENSMUST00000046963.9  Map3k11|ENSMUST00000004156.8  Map3k7|ENSMUST00000080933.12  Mapk11|ENSMUST00000088823.3  Mapk14|ENSMUST00000062694.14  Mapk8|ENSMUST00000111945.8  Mapk9|ENSMUST00000020634.13  Med13|ENSMUST00000043624.8  Mef2a|ENSMUST00000156690.7  Mep1a|ENSMUST00000117137.7  Mgp|ENSMUST00000032342.2  Mki67|ENSMUST00000033310.7  Mmp2|ENSMUST00000034187.7  Mmp7|ENSMUST00000018767.7  Mmp9|ENSMUST00000017881.2  Mrc1|ENSMUST00000028045.3  Mstn|ENSMUST00000027269.6  Mt2|ENSMUST00000034214.6  Myc|ENSMUST00000188482.6  Myod1|ENSMUST00000072514.1  Myog|ENSMUST00000027730.5  Napsa|ENSMUST00000002274.9  Nbl1|ENSMUST00000042844.6  Nccrp1|ENSMUST00000057974.3  Ncf2|ENSMUST00000186568.6  Nedd4l|ENSMUST00000080418.4  Nfat5|ENSMUST00000169453.7  Nfatc1|ENSMUST00000035800.7  Nfatc2|ENSMUST00000074618.9  Nfkb2|ENSMUST00000111881.2  Nlrp3|ENSMUST00000101148.8  Nos2|ENSMUST00000018610.6  Nov|ENSMUST00000050027.8  Nphs1|ENSMUST00000006825.8  Nphs2|ENSMUST00000027896.9  Npnt|ENSMUST00000042744.15  Nr0b2|ENSMUST00000042706.2  Nr1h4|ENSMUST00000058126.14  Nr3c1|ENSMUST00000115571.7  Nr3c2|ENSMUST00000109913.8  Nupr1|ENSMUST00000032961.3  Osgin1|ENSMUST00000152420.7  Oxsr1|ENSMUST00000040853.10  Pappa2|ENSMUST00000159861.8  Pcbd1|ENSMUST00000020298.6  Pck1|ENSMUST00000029017.5  Pdgfa|ENSMUST00000076095.13  Pdgfb|ENSMUST00000000500.6  Pdk1|ENSMUST00000006669.5  Pdzk1ip1|ENSMUST00000030488.2  Pfkm|ENSMUST00000163507.7  Phlda1|ENSMUST00000164773.1  Pigr|ENSMUST00000027675.13  Pik3ca|ENSMUST00000029201.13  Pik3cb|ENSMUST00000035037.13  Pik3cg|ENSMUST00000053215.13  Pim3|ENSMUST00000042818.9  Pkd1|ENSMUST00000035565.3  Pkd2|ENSMUST00000086831.3  Plac8|ENSMUST00000112910.1  Plat|ENSMUST00000033941.5  Plau|ENSMUST00000022368.2  Plaur|ENSMUST00000002284.10  Podxl|ENSMUST00000026698.7  Postn|ENSMUST00000073012.12  Pparg|ENSMUST00000000450.4  Ppp1r1a|ENSMUST00000023133.6  Ppp3ca|ENSMUST00000070198.13  Prkar2b|ENSMUST00000036497.15  Prkci|ENSMUST00000108249.8  Psca|ENSMUST00000023265.4  Pten|ENSMUST00000013807.7  Ptgds|ENSMUST00000114259.2  Ptger3|ENSMUST00000041175.12  Ptgs2|ENSMUST00000035065.8  Pvalb|ENSMUST00000120592.1  Rab30|ENSMUST00000032879.14  Raf1|ENSMUST00000112949.7  Rasa1|ENSMUST00000109552.2  Ren1|ENSMUST00000094556.2  Retnla|ENSMUST00000023329.4  Rhbg|ENSMUST00000171887.3  Rhcg|ENSMUST00000032766.4  Rheb|ENSMUST00000030787.8  Rock1|ENSMUST00000067947.5  Rock2|ENSMUST00000020904.6  Rps6kb1|ENSMUST00000154617.7  S100a4|ENSMUST00000001046.6  S100a6|ENSMUST00000001051.8  S100g|ENSMUST00000038769.2  Sav1|ENSMUST00000021467.7  Scnn1a|ENSMUST00000081440.13  Scnn1b|ENSMUST00000033161.6  Scnn1g|ENSMUST00000000221.5  Sele|ENSMUST00000027874.5  Selp|ENSMUST00000162746.1  Serpina3n|ENSMUST00000021506.5  Serpine1|ENSMUST00000077523.3  Sfrp1|ENSMUST00000033952.7  Sgk1|ENSMUST00000092673.10  Shh|ENSMUST00000002708.4  Siglec1|ENSMUST00000028794.9  Sirt1|ENSMUST00000120239.7  Slc12a1|ENSMUST00000110495.2  Slc12a2|ENSMUST00000115366.2  Slc12a3|ENSMUST00000034218.3  Slc14a2|ENSMUST00000025434.13  Slc16a10|ENSMUST00000092566.6  Slc22a18|ENSMUST00000105917.2  Slc22a6|ENSMUST00000010250.2  Slc22a7|ENSMUST00000087012.5  Slc26a11|ENSMUST00000050880.7  Slc26a4|ENSMUST00000001253.7  Slc27a2|ENSMUST00000061491.13  Slc2a1|ENSMUST00000030398.9  Slc2a2|ENSMUST00000029240.13  Slc2a4|ENSMUST00000018710.12  Slc34a2|ENSMUST00000094787.7  Slc34a3|ENSMUST00000006638.7  Slc38a3|ENSMUST00000167868.7  Slc38a7|ENSMUST00000040481.3  Slc4a1|ENSMUST00000006749.9  Slc4a3|ENSMUST00000124341.7  Slc4a4|ENSMUST00000148750.7  Slc4a8|ENSMUST00000023776.12  Slc4a9|ENSMUST00000074298.12  Slc5a1|ENSMUST00000011178.4  Slc5a10|ENSMUST00000148584.1  Slc5a2|ENSMUST00000118169.7  Slc6a19|ENSMUST00000022048.5  Slc7a12|ENSMUST00000037321.7  Slc7a13|ENSMUST00000035890.7  Slc7a5|ENSMUST00000045557.9  Slc8a1|ENSMUST00000086538.9  Slc9a3|ENSMUST00000036208.6  Slc9a4|ENSMUST00000027233.8  Smad2|ENSMUST00000168423.7  Smad3|ENSMUST00000034973.9  Smad4|ENSMUST00000025393.13  Smad7|ENSMUST00000026999.9  Snai1|ENSMUST00000052631.7  Snai2|ENSMUST00000023356.6  Socs3|ENSMUST00000054002.3  Sod3|ENSMUST00000101208.5  Sparc|ENSMUST00000018737.12  Sphk1|ENSMUST00000106387.8  Spink1|ENSMUST00000025381.2  Spink8|ENSMUST00000198988.4  Spp1|ENSMUST00000112748.7  Spp2|ENSMUST00000027518.11  Sprr1a|ENSMUST00000054599.7  Sprr2f|ENSMUST00000050397.1  Spry1|ENSMUST00000108109.7  St6galnac2|ENSMUST00000079545.5  St6galnac3|ENSMUST00000200397.4  Stat3|ENSMUST00000103114.7  Stk39|ENSMUST00000102715.3  Synpo|ENSMUST00000130044.1  Taz|ENSMUST00000069722.12  Tek|ENSMUST00000102798.7  Tff3|ENSMUST00000024827.4  Tfrc|ENSMUST00000023486.14  Tgfb1|ENSMUST00000002678.9  Tgfb2|ENSMUST00000045288.13  Thbs1|ENSMUST00000039559.8  Timp1|ENSMUST00000115342.9  Timp2|ENSMUST00000017610.9  Timp3|ENSMUST00000020234.13  Tjp2|ENSMUST00000099558.4  Tkfc|ENSMUST00000037678.6  Tmem213|ENSMUST00000031851.4  Tmem252|ENSMUST00000057243.4  Tmigd1|ENSMUST00000102495.7  Tmsb10|ENSMUST00000114049.1  Tmsb4x|ENSMUST00000112172.3  Tnc|ENSMUST00000107372.7  Tnf|ENSMUST00000025263.14  Tnfsf12|ENSMUST00000181810.7  Tnfsf13|ENSMUST00000018896.13  Trf|ENSMUST00000035158.15  Trim63|ENSMUST00000105875.7  Trp53|ENSMUST00000108658.9  Trp53inp1|ENSMUST00000029865.3  Trpc1|ENSMUST00000189137.6  Trpc3|ENSMUST00000029271.4  Trpc5|ENSMUST00000040184.3  Trpc6|ENSMUST00000050433.6  Trpm2|ENSMUST00000105401.8  Trpm6|ENSMUST00000040489.7  Trpv4|ENSMUST00000112225.7  Trpv5|ENSMUST00000031901.10  Tsc2|ENSMUST00000097373.1  Ttr|ENSMUST00000075312.3  Twist1|ENSMUST00000049089.5  Ugt3a2|ENSMUST00000072403.6  Umod|ENSMUST00000033263.5  Vcam1|ENSMUST00000029574.12  Vegfa|ENSMUST00000071648.11  Vim|ENSMUST00000028062.7  Wfdc2|ENSMUST00000017867.9  Wnk1|ENSMUST00000060043.12  Wnk4|ENSMUST00000103108.7  Wnt1|ENSMUST00000023734.7  Wnt10a|ENSMUST00000006718.14  Wnt10b|ENSMUST00000166022.1  Wnt11|ENSMUST00000067495.8  Wnt2|ENSMUST00000010941.5  Wnt2b|ENSMUST00000029429.5  Wnt3|ENSMUST00000000127.5  Wnt4|ENSMUST00000045747.4  Wnt5a|ENSMUST00000063465.10  Wnt5b|ENSMUST00000118120.7  Wnt6|ENSMUST00000006716.7  Wnt7a|ENSMUST00000032180.6  Wnt7b|ENSMUST00000023015.13  Wnt8a|ENSMUST00000012426.2  Wnt8b|ENSMUST00000041163.4  Wnt9a|ENSMUST00000108783.3  Wnt9b|ENSMUST00000018630.2  Yap1|ENSMUST00000086580.11  Agr2|ENSMUST00000020898.11  Agtr1a|ENSMUST00000066412.7  Agtr2|ENSMUST00000089188.8  Atf4|ENSMUST00000109605.3  Atf6|ENSMUST00000027974.6  Atg5|ENSMUST00000039286.4  Bak1|ENSMUST00000078691.11  Bax|ENSMUST00000033093.8  Bfar|ENSMUST00000023365.12  Bgn|ENSMUST00000033741.14  Bok|ENSMUST00000027499.12  Casp12|ENSMUST00000027009.10  Ccne1|ENSMUST00000108023.9  Ccne2|ENSMUST00000029866.15  Cdk2|ENSMUST00000026415.7  Col6a1|ENSMUST00000001147.4  Cops5|ENSMUST00000027050.9  Creb3|ENSMUST00000102944.10  Cul3|ENSMUST00000163119.7  Edem2|ENSMUST00000040833.4  Edem3|ENSMUST00000059498.11  Eif2ak3|ENSMUST00000034093.14  Ern1|ENSMUST00000001059.8  Fkbp1a|ENSMUST00000044011.11  Hspa5|ENSMUST00000028222.12  Itgb4|ENSMUST00000106460.8  Itgb5|ENSMUST00000115028.9  Mir17hg|ENSMUST00000134140.2  Nck1|ENSMUST00000116522.7  Nck2|ENSMUST00000086421.8  Nfe2l2|ENSMUST00000102672.4  Odc1|ENSMUST00000171737.1  Ptpn1|ENSMUST00000029053.7  Ptpn2|ENSMUST00000025420.13  Slc13a3|ENSMUST00000029208.14  Slc22a2|ENSMUST00000046959.7  Slc22a8|ENSMUST00000170817.1  Socs2|ENSMUST00000172070.7  Tlr4|ENSMUST00000048096.11  Tmbim6|ENSMUST00000023749.14  Tmem33|ENSMUST00000161369.2  Wfs1|ENSMUST00000043964.12  Xbp1|ENSMUST00000063084.15
Supplementary_files_format_and_content: Filtered cell-level expression matrix - cell level expression data file produced by BD Data View software post-doublet filtering; Cluster and animal annotation data table - output of BD Data View software containing manual nephron cell-type annotation and animal annotation

source_name: Kidney

extract_protocol:
Kidneys were removed, nephron cells were isolated by mechanical force, collagenase incubation, and multiple washes and filtering. Single cells were individually isolated and lysed in cartridges and mRNA molecules captured on BD Rhapsody mRNA capture beads for reverse transcription.
cDNA libraries were prepared with BD Rhapsody WTA and Targeted assays, followed by sequencing using standard Illumina protocols.

treatment_protocol: Two groups C57BL/6J mice fed monitored gel food diet of steady sodium content (104 µmols per kcal) daily with either furosemide (70 mg/kg body weight) or vehicle control for 1 week.

value: kidney

tag: age

value: 16 weeks

value: furosemide


title: Day_13_CD8_SuperP53_1

value: Mouse #3.2


title: 3089_24m_GPR_p1_G3_CC

source_name: CD8+ T cell


title: 715 [striatum]

value: OXYCODONE


title: Kidney WT - vehicle_rep3

value: vehicle


title: Day_13_CD4_WT_4

source_name: CD4 sorted from B16-TME in WT mice

value: Mouse #1.3


title: 3089_24m_GPR_p1_G4_CC


title: Day_13_CD4_WT_3

value: Mouse #1.2


title: 714 [striatum]

value: BALBcJ x BALBcByJ F2

value: F

value: Striatum


title: Kidney WT - furosemide_rep2


title: 712 [striatum]


title: 3089_24m_GPR_p1_G2_CC

value: GPR


title: Kidney WT - furosemide_rep1


title: Day_13_CD4_WT_2

value: Mouse #1.5


title: 3089_24m_GPR_p1_G10_CC

value: CD8+ T cell


title: Day_13_CD4_WT_1

value: Mouse #1.4


title: 3089_24m_GPR_p1_G1_CC


title: 708 [striatum]


title: 707 [striatum]


title: Kidney WT - vehicle_rep2


title: Kidney WT - vehicle_rep1


title: 3089_24m_GPR_p1_F9_CC


title: ATAC-seq_9h_Recovery_rep2

city: Göttingen

first: Le

last: Xiong

address: Fassberg 11

department: Molecular Biology

institute: MPI for biophysical chemistry

description: Oct4 recovery experiments, 9h doxycycline washout

data_processing:
For TT-seq data: Paired-end 42 bp reads were mapped to the mouse genome assembly mm10 using STAR 2.5.3 (Dobin et al., 2013) with the following parameters: outFilterMismatchNmax 2, outFilterMultimapScoreRange 0 and alignIntronMax 500,000. SAMtools (Li et al., 2009) were then used to remove alignments with MAPQ smaller than 7 (-q 7) and only proper pairs (-f 2) were selected. HTSeq-count (Anders et al., 2015) was used to calculate fragment counts for different features. R/Bioconductor package DESeq2 (Love et al., 2014) was used to call differentially expressed mRNAs and eRNAs applying DESeq2’s default size factor normalization. For both cases DESeq2 size factors were calcualted using counts for protein-coding genes. An adjusted P-value of 0.01 was used to identify significantly changed mRNAs or eRNAs by comparing each time point to the 0 hours measurement.  Further data processing was carried out using the R/Bioconductor environment.
For ATAC-seq data: Paired-end 76 bp reads were obtained for each of the samples and Nextera Transposase adapter sequence was removed using (Martin, 2011). Bowtie2 (Langmead and Salzberg, 2012) was used to align paired-end reads to the mouse genome assembly mm10 with the “--local” and “--no-discordant” options. SAMtools (Li et al., 2009) was then used to remove alignments with MAPQ smaller than 7 (-q 7) and only proper pairs (-f 2) were selected. Reads mapped to custom blacklist regions and mitochondria were removed. Two replicates were pooled and MACS2 (Zhang et al., 2008) was used to call chromatin opening peaks with options: -f BAMPE -g mm --broad --broad-cutoff 0.05. Peaks for all time point were then merged to create non-overlapping unified peaks. For quantitative comparison, HTSeq-count (Anders et al., 2015) was used to calculate fragment counts for the non-overlapping unified peaks and DESeq2 was used to call regions with significantly changed chromatin accessibility. For normalization, ATAC-seq peaks overlapping with promoters of protein-coding genes with unchanged mRNA expression were used to calculate DESeq2 size factors. An adjusted P-value of 0.01 was used to identify significantly changed regions by comparing each time point to the 0 hour measurement. Further data processing was carried out using the R/Bioconductor environment.
Genome_build: mm10
Supplementary_files_format_and_content: Normalized coverage files for TT-seq and ATAC-seq at each time point are provided in bigwig format.

source_name: ZHBTc4 mouse embryonic stem cell

growth_protocol: Mouse embryonic stem cells (mESCs) harbouring a doxycycline repressible Pou5f1 transgene (ZHBTc4, Niwa et al.,  2000) were propagated on gelatin-coated plates in equal parts DMEM-F12 (Life Technology, 21331-020) and Neuralbasal (Life Technology, 21103-049) Medium supplemented with 2% Fetal Bovin Serum (Sigma Aldrich, G1393-100 ml), 2% Knockout Serum Replacement Medium (Gibco, 10828-028), 0.04 µg/ml Leukemia Inhibitory Factor (prepared in-house), Pennicilin/Streptomycin (Sigma Aldrich, P4333-100ml), 0.1 mM ß-Mercaptoethanol (Gibco, 31350-010), 0.5x B27 supplement (Life Technology, 12587-010), 0.5x N2 supplement (Gibco, AM9759, 3 µM CHIR99021 (Cayman Chemicals, 13122), 1 µM PD0325901 (Biomol, 103034-25). Cells were passaged using Accutase (Sigma Aldrich, 6964-100ml).

extract_protocol:
ATAC-seq (Buenrostro et al. 2015)
Nextera Tn5 enzyme-NEBNext High fidelity master mix

treatment_protocol: Pou5f1 expression was abolished by treatment with 1/600µg/ml doxycycline (Sigma Aldrich D9891-1G) for 15 hours and partially recovered after 4.5 hours and 9 hours doxycycline washout.

value: ZHBTc4 mouse embryonic stem cell

tag: treatment condition

value: 1:600 diluted doxycycline (1/600 ug/ml) treatment 15h + 9h doxycycline washout


title: Day_13_CD4_Apr246_5

source_name: CD4 sorted from B16-TME in APR246 treated WT mice

value: Mouse #2.4


title: 706 [striatum]

source_name: Striatum

value: SALINE


title: 3089_24m_GPR_p1_F8_CC

data_processing:
Illumina NextSeq was used
Sequenced paired-end reads were trimmed using Trimmomatic (v0.39) (using parameters:  LEADING = 3, TRAILING = 3, SLIDINGWINDOW = 4:10, MINLEN = 50), then aligned to the human reference genome (GRCh38) using STAR (v2.7.3a). Gene expression was then quantified at the counts and TPM level with RSEM (v1.3.1)
Genome_build: GRCh38
Supplementary_files_format_and_content: .mtx.gz files contain matrices including raw counts, TPM and scaled TPM values for each sample and each gene.
Supplementary_files_format_and_content: .txt and and .tsv files contain tab delimited information on sample names and gene names (as per ordering in matrices), and gene annotation information.

tag: subject


title: ATAC-seq_9h_Recovery_rep1


title: 705 [striatum]


title: 704 [striatum]


title: Day_13_CD4_Apr246_3

value: Mouse #2.2


title: ATAC-seq_4.5h_Recovery_rep2

description: Oct4 recovery experiments, 4.5h doxycycline washout

value: 1:600 diluted doxycycline (1/600 ug/ml) treatment 15h + 4.5h doxycycline washout


title: 3089_24m_GPR_p1_F6_CC

tag: epitope


title: 703 [striatum]

value: M


title: Day_13_CD4_Apr246_2

tag: cell line

value: Mouse #2.1


title: ATAC-seq_15h_1:600_rep1

description: Oct4 recovery experiments, 15h doxycycline (1/600ug/ml) treatment

value: 1:600 diluted doxycycline (1/600ug/ml) treatment 15h


title: Day_13_CD4_Apr246_1

tag: mouse

value: Mouse #2.5


title: 3089_24m_GPR_p1_F5_CC

tag: dpi


title: 3089_24m_GPR_p1_F4_CC


title: 702 [striatum]

value: BALBcJ x BALBcByJ F2

tag: cpp treatment


title: Day_13_CD4_SuperP53_3

source_name: CD4 sorted from B16-TME in SuperP53 mice

value: Mouse #3,4


title: ATAC-seq_4.5h_Recovery_rep1


title: 3089_24m_GPR_p1_F3_CC


title: Day_13_CD4_SuperP53_2

value: Mouse #3,3


title: Day_13_CD4_Apr246_4

value: Mouse #2.3


title: 3089_24m_GPR_p1_F2_CC

value: GPR


title: 701 [striatum]

value: Striatum

tag: rna extraction cohort


title: 845

source_name: Hippocampus

extract_protocol:
RNA was extracted in RNAlater-preserved tissue using Trizol (Qiagen), ethanol precipitation, filtering columns (Qiagen), DNAse digestion (Qiagen), and elution with RNAse and nucleotide free water (Yazdani et al., 2015) and diluted to 100 ng/ul.
RNA library preparation (poly-A selection) and RNA-seq was conducted at the University of Chicago Genomics Facility on an Illumina NovaSEQ6000 using a NovaSEQ SP-100 bp flowcell/reagent cassette. ~30M clusters/sample, 60M PE reads/sample.

tag: strain

value: OXYCODONE

value: Hippocampus


title: 844

tag: Sex


title: Day_13_CD4_SuperP53_1

value: Mouse #3,2


title: ATAC-seq_15h_1:600_rep2

value: ZHBTc4 mouse embryonic stem cell


title: 3089_24m_GPR_p1_F7_CC

extract_protocol:
Single HCV-specific CD8+ T cells were sorted using flow cytometry, with RNA isolation and sequencing library construction performed according to the Smart-seq2 protocol.
Single cell RNA libraries were prepared for sequencing using standard Illumina protocols

value: CD8+ T cell


title: 842


title: 3089_24m_GPR_p1_E9_CC


title: TT-seq_9h_Recovery_rep2

description:
Oct4 recovery experiments, 9h doxycycline washout
4sU-labeled RNA

extract_protocol:
TT-seq (Schwalb et al, 2016)
Ovation Universal RNA-seq System (Nugen, 0343)

value: 1:600 diluted doxycycline (1/600 ug/ml) treatment 15h + 9h doxycycline washout + 5 min 4sU labeling


title: TT-seq_4.5h_Recovery_rep2

description:
Oct4 recovery experiments, 4.5h doxycycline washout
4sU-labeled RNA

value: 1:600 diluted doxycycline (1/600 ug/ml) treatment 15h + 4.5h doxycycline washout + 5 min 4sU labeling


title: 3089_24m_GPR_p1_E6_CC


title: 841

value: F


title: 3089_24m_GPR_p1_E8_CC


title: TT-seq_4.5h_Recovery_rep1


title: Sample_5129: Ly6Ch_50_ctrl

first: Branko

last: Cirovic

address: Carl-Troll Str 31

institute: LIMES

data_processing:
raw data was converted and multiplexed using bcl2fastq2 (v2.20).
reads were aligned to mouse reference transcriptome mm10 from UCSC and transcript abundance quantified using kallisto (v0.440) with default parameters.
abundance measurements were imported into R using tximport (v1.8.0).
for further filtering transcripts were removed not matching HGNC gene symbols, read sum lower than 10 across all samples or corresponding antisense, LINC or pseudogenes.
filtered data was imported into the DESeq2 package (v1.20.0) in R to generated a normalized expression table.
Genome_build: mm10
Supplementary_files_format_and_content: normalised expression table derived from DESeq2 analysis containing all samples

source_name: bone marrow

extract_protocol:
total RNA from FACS-enriched cell populations was isolated using Qiazol (QIAGEN GmbH, Germany) and the miRNeasy Micro Kit (QIAGEN GmbH, Germany).
libraries were constructed following the SMART-seq2 protocol.

tag: condition

value: control fathers

tag: sample group


title: Sample_5126: Ly6Ch_47_ctrl


title: Sample_5128: Ly6Ch_49_ctrl


title: TT-seq_15h_1:600_rep2

description:
Oct4 recovery experiments, 15h doxycycline (1/600ug/ml) treatment
4sU-labeled RNA

value: 1:600 diluted doxycycline (1/600 ug/ml) treatment 15h + 5 min 4sU labeling


title: 3089_24m_GPR_p1_E5_CC


title: Sample_5127: Ly6Ch_48_ctrl


title: ATAC-seq_0h_ctl_rep2

description: Oct4 recovery experiments, 0h control

value: untreated control 0h


title: 838


title: TT-seq_15h_1:600_rep1


title: 836

value: SALINE

value: M


title: ATAC-seq_0h_ctl_rep1

description: Oct4 recovery experiments, 0h control


title: 835


title: TT-seq_9h_Recovery_rep1


title: 3089_24m_GPR_p1_F1_CC


title: Sample_5124: Ly6Ch_45_inf

value: infected fathers


title: TT-seq_0h_ctl_rep2

description:
Oct4 recovery experiments, 0h control
4sU-labeled RNA

value: untreated control 0h + 5 min 4sU labeling


title: 3089_24m_GPR_p1_E3_CC

value: GPR


title: Sample_5123: Ly6Ch_44_inf


title: 833


title: 3089_24m_GPR_p1_E2_CC


title: 832


title: igg_adultGV_ctr_3

city: Ashburn

first: Di

last: Wu

state: Virginia

address: 19700 Helix Drive

institute: HHMI Janelia

data_processing:
Library strategy: CUT&Tag
For RNA-seq: Raw sequence reads were trimmed with Cutadapt 2.5 to remove adapters while performing light quality trimming with parameters "-m 10 -q 20, 20". For CUT&Tag seq: data analysis were performed according to CUT&Tag Data Processing and Analysis Tutorial
For RNA-seq, the sequencing library quality was assessed with FastQC v0.11.8 with default parameters. Trimmed reads were mapped to the Mus musculus mm10 reference genome plus ERCC.fasta using STAR v2.7.2a.
Multi-mapping reads were filtered using samtools 1.9. Uniquely aligned reads were then mapped to gene features using HTseq v0.9.1 as an unstranded library with default parameters (for polyA RNA-seq) and using stranded=yes for ribominus analysis.
A gene/ERCC count was considered valid when present in at least 5 reads in at least 2 libraries. Differential expression between groups of samples was tested using R version 3.5.1 (2018-07-02) with DESeq2 v1.24.0. The oocyte libraries were normalized by ERCC counts by defining the ERCC genes as the controlGenes when estimating the sizeFactors in DESeq2.
Genome_build: mm10, ERCC
Supplementary_files_format_and_content: RNA-seq: provide tab deliminated original counts of each gene obtained form Htseq-count. For CUT&Tag: provide tab diliminated bed files of all peaks from each library obtained by SEACR using igg as negative control. The protocol follows CUT&Tag Data Processing and Analysis Tutorial.

source_name: bulk mouse oocytes

growth_protocol: All GV oocytes and 3 hr oocytes were dissected from ovaries and cultured ex vivo in M2 medium. MII eggs are dissected from oviducts from superovulated mice.

extract_protocol:
polyA RNAs: Each oocyte was lysed in RLT-plus buffer. The oligo-dT beads were used to isolate the polyA RNA. RiboMinus RNAs and ribosomal RNA: with Ovation Solo kit. CUT&Tag: oocytes were collected according to Bench top CUT&Tag V.3 protocol
For polyA RNA seq: Single oocyte RNA-seq libraries were prepared according to a published single-cell RNA seq pipeline with subtle modifications (Macaulay et al., 2016). Briefly, the oocytes at desired stages were collected individually into 2.5 ml RLT plus and stocked at -80 °C until all samples were collected. In the beginning of RNA purification, ERCC RNA spike-in mix (ThermoFisher 4456740) was diluted 10^5 fold, and 1 ml of the diluted ERCC mix was added to each lysis. Poly(A) RNA were isolated by oligo (dT) beads, reverse transcribed, amplified and purified. The purified cDNAs were analyzed by Bioanalyzer 2100 to confirm successful amplification range and quality. cDNAs passing a quality test were further constructed into sequencing libraries by Nextera DNA Sample Preparation Kit. For RiboMinus Total RNA-seq: single oocyte libraries were prepared according to the Ovation Solo system, but random hexamer primer is used for reverse transcription. For CUT&Tag sequencing: libraries were constructed according to the protocol Bench top CUT&Tag V.3, with fresh GV oocytes without light fixation.

treatment_protocol: Mutant oocytes were dissected from the mutant mice (constructed by CRISPR/Cas9)

value: bulk mouse oocytes

tag: Stage

value: GV

tag: genotype

value: control


title: 3089_24m_GPR_p1_E10_CC

last: Samir

address: Level 5, Wallace Wurth Building, High Street

institute: Kirby Institute

tag: cell type


title: Sample_5125: Ly6Ch_46_ctrl


title: 831

value: OXYCODONE

tag: tissue

value: Hippocampus


title: TT-seq_0h_ctl_rep1

value: ZHBTc4 mouse embryonic stem cell

value: untreated control 0h  + 5 min 4sU labeling


title: 3089_24m_GPR_p1_D9_CC

value: CD8+ T cell


title: igg_adultGV_ctr_1


title: 3089_24m_GPR_p1_D8_CC


title: Sample_5120: Ly6Ch_41_inf


title: igg_adultGV_ctr_2


title: pols2s5_adultGV_dis3cKO_3


title: 829


title: Sample_5119: cMOP_50_ctrl

value: cMOP


title: 3089_24m_GPR_p1_D5_CC


title: 834


title: 827


title: 3089_24m_GPR_p1_D3_CC


title: Sample_5118: cMOP_49_ctrl

value: control fathers


title: Sample_5117: cMOP_48_ctrl


title: 3089_24m_GPR_p1_D2_CC


title: 826


title: Sample_5122: Ly6Ch_43_inf


title: pols2s5_adultGV_dis3cKO_1


title: Sample_5116: cMOP_47_ctrl


title: Sample_5121: Ly6Ch_42_inf


title: 825


title: 830


title: pols2s5_p20_ctr_3


title: 3089_24m_GPR_p1_D11_CC


title: Sample_5115: cMOP_46_ctrl


title: pols2s5_p20_ctr_2


title: 822

value: F


title: 3089_24m_GPR_p1_D10_CC


title: Sample_5114: cMOP_45_inf


title: 821


title: pols2s5_adultGV_dis3cKO_2


title: pols2s5_p20_ctr_1


title: 3089_24m_GPR_p1_C8_CC


title: 3089_24m_GPR_p1_C9_CC


title: 3089_24m_GPR_p1_C6_CC


title: 818


title: 819


title: Sample_5113: cMOP_44_inf


title: pols2s5_adultGV_ctr_3


title: 3089_24m_GPR_p1_C4_CC


title: 817


title: Sample_5111: cMOP_42_inf


title: k27me3_p20_dcKO_2

value: dcKO


title: pols2s5_adultGV_ctr_1


title: Sample_5110: cMOP_41_inf


title: Sample_4492: GMP_46_ctrl

value: GMP


title: 815


title: 3089_24m_GPR_p1_C5_CC


title: Sample_5112: cMOP_43_inf


title: pols2s5_adultGV_ctr_2


title: 816


title: Sample_4496: GMP_50_ctrl


title: k27me3_p20_dcKO_3


title: 3089_24m_GPR_p1_C3_CC


title: Sample_4491: GMP_45_inf


title: 813


title: Sample_4495: GMP_49_ctrl


title: k27me3_p20_dcKO_1


title: 3089_24m_GPR_p1_B9_CC


title: k27me3_adultGV_dis3cKO_2


title: 3089_24m_GPR_p1_C2_CC


title: k27me3_adultGV_dis3cKO_1


title: 812

value: M


title: 809


title: k27me3_adultGV_dis3cKO_3


title: Sample_4488: GMP_42_inf

value: infected fathers


title: 808

value: SALINE


title: 807


title: k27me3_p20_ctr_2


title: 810


title: e_LFD

first: Nabil

last: Rabhi

address: Silvio Conte Building, 72 E. Concord St

department: Biochemistry

institute: Boston University

data_processing:
The Cell Ranger Single-Cell Software Suite (v.3.1.0) was used to perform sample demultiplexing, barcode processing, single-cell 3′ counting, and counts alignment to mm10 mouse reference genome
Cellranger mkfastq was used to demultiplexes raw base call files
Cellranger count was used to takes FASTQ files from cellranger mkfastq and performs alignment, filtering, barcode counting, and UMI counting.
Genome_build: mm10
Supplementary_files_format_and_content: matrix file, barcodes file and features file for each sample

source_name: epididymal adipose tissue stromal vascular fraction

extract_protocol:
epididymal white adipose tissues (WAT) from low fat diet and high fat diet feed mice were processed for SVC isolation using mouse adipose tissue dissociation kit (Miltenyi biotec) according to manufactures.
10x Chromium 3'v3 libraries; 10 X genomics Single cell  RNA seq

treatment_protocol: One replicate was feed a low fat diet  for 24 weeks started at 6 week old and the second replicate was feed a low fat diet  for 24 weeks started at 6 week old

tag: treatment

value: Low fat diet feeding for 24 weeks started at 6 week old


title: 3089_24m_GPR_p1_C11_CC

first: Jerome

value: GPR


title: 811


title: 3089_24m_GPR_p1_B8_CC


title: 806


title: k27me3_p20_ctr_3

value: bulk mouse oocytes


title: 3089_24m_GPR_p1_B7_CC


title: k27me3_adultGV_ctr_3

value: GV

value: control


title: e_HFD

value: High fat diet feeding for 24 weeks started at 6 week old

value: epididymal adipose tissue stromal vascular fraction


title: k27me3_adultGV_ctr_2


title: 3089_24m_GPR_p1_B6_CC


title: normal adrenal cortex 10

city: Utrecht

first: Frank

last: van Steenbeek

state: Select State/Province

address: Yalelaan 104

country: Netherlands

institute: Utrecht University

data_processing:
reads were demultiplexed and aligned to canine cDNA reference using the BWA
Genome_build: CanFam3.1
Supplementary_files_format_and_content: raw counts

organism: Canis lupus familiaris

source_name: normal adrenal cortex

extract_protocol:
cells were trypsinized and stored in RLT. Total RNA was isolated using a RNeasy Mini Kit (Qiagen).
Sequencing libraries were prepared using CEL-Seq2

tag: disease

value: healthy


title: Sample_4487: GMP_41_inf


title: normal adrenal cortex 9


title: 805

value: Hippocampus


title: 3089_24m_GPR_p1_B3_CC

tag: subject

value: CD8+ T cell


title: 3089_24m_GPR_p1_B5_CC

tag: epitope


title: 3089_24m_GPR_p1_B2_CC


title: k27me3_p20_ctr_1


title: normal adrenal cortex 7


title: 801


title: 748

value: OXYCODONE


title: normal adrenal cortex 6


title: 3089_24m_GPR_p1_B4_CC


title: 3089_24m_GPR_p1_B11_CC


title: 3089_24m_GPR_p1_A9_CC


title: M4.1.3_S28

city: Merelbeke

first: Anne-Sofie

last: Vermeersch

address: Salisburylaan 133

department: Internal medicine, reproduction and population medicine

country: Belgium

institute: Ghent University

data_processing:
Quality and length of raw sequencing reads inspection with FastQc (v0.11.7). Fastq_screen was utilized for putative contamination check.
Adaptor and quality trimming with cutadapt (v2.8).
The reads were mapped on the Bos_taurus_ARS-UCD1.2 cow reference genome using splice-aware Spliced Transcripts Alignment to a Reference (STAR) (v2.5.3a) mapper.
Features were counted at the gene and transcript isoform level using rsem_calc_expression (RSEM v1.3.1).
An analysis was done by pairwise comparisons between M0 and each of the different disease stages, using the edgeR package in R.
Genome_build: Bos_taurus_ARS-UCD1.2
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

organism: Bos taurus

source_name: Skin lesion site

extract_protocol:
Samples were taken with a biopsy punch tool and flash frozen in liquid nitrogen. RNA isolation was performed using the Qiagen RNeasy Minikit (Qiagen Benelux, Venlo, the NL).
Sequencing libraries were constructed using the ‘QuantSeq 3’ mRNA-Seq Library Prep Kit FWD for Illumina’ from Lexogen (Lexogen Inc, Greenland, NH, USA).

value: skin

value: Disease stage M4.1


title: 3089_24m_GPR_p1_A8_CC


title: normal adrenal cortex 8


title: 803

city: Boston

value: F


title: normal adrenal cortex 4


title: M4.1.4_S29


title: M4.1.2_S27


title: normal adrenal cortex 5


title: 747


title: 745


title: 3089_24m_GPR_p1_A7_CC

city: Kensington


title: k27me3_adultGV_ctr_1


title: 744


title: M4.5_S25

value: Disease stage M4


title: M4.1.1_S26


title: normal adrenal cortex 3


title: M4.4_S24


title: 3089_24m_GPR_p1_A5_CC


title: 739

value: M


title: normal adrenal cortex 2


title: normal adrenal cortex 1


title: canine cortisol-secreting adrenocortical tumor 49

source_name: cortisol-secreting adrenocortical tumor


title: 746


title: M4.2_S22


title: 3089_24m_GPR_p1_A3_CC


title: M4.3_S23


title: 3089_24m_GPR_p1_A4_CC


title: 737

value: SALINE


title: 738


title: M4.1_S21


title: canine cortisol-secreting adrenocortical tumor 47


title: 733


title: 3089_24m_GPR_p1_A11_CC


title: 3089_24m_GPR_p1_A2_CC


title: canine cortisol-secreting adrenocortical tumor 46


title: M3.5_S20

value: Disease stage M3


title: 729


title: canine cortisol-secreting adrenocortical tumor 48


title: RA 221 Synovium

city: Rochester

first: Andrew

last: McDavid

address: 265 Crittenden Boulevard, CU 420630

institute: University of Rochester

data_processing:
Raw reads generated from the Illumina basecalls were demultiplexed using Cell Ranger mkfastq version 2.1.1 utilizing bcl2fastq version 2.19.1.403. Cells were aligned and counted against the Cell Ranger reference refdata-cellranger-GRCh38-1.2.0 using Cell Ranger count version 2.1.1, utilizing only the library index, project, and sample ID for a given sample.
Genome_build: GRCh38-1.2.0
Supplementary_files_format_and_content: Unfiltered feature-barcode matrices containing all barcodes in HDF5 format

source_name: synovium biopsy

extract_protocol:
Cryopreserved synovial fragments were thawed. Synovial tissue fragments were then disaggregated by combination of an enzymatic digestion and mechanical disruption. PBMCs were thawed by rapidly warming the cryovial in a 37 °C water bath. To stain cells for sorting, cells were first incubated with Fc-Block (Biolegend) for 5 minutes at room temperature. Cells were then incubated with a mixture of fluorochrome-conjugated antibodies for 30 minutes on ice, washed with PBS and then resuspended in PBS solution containing DAPI (Biolegend). Cells were sorted on a FACSAria II (BD biosciences) into 5%FBS/RPMI media using a 100-μm nozzle. B cells were gated as CD45+CD3-CD14-CD19+.
Cellular suspensions were loaded on a Chromium Single-Cell Instrument (10x Genomics, Pleasanton, CA, USA). Single-cell RNA-Seq libraries were prepared using Chromium Single-Cell 5′ Library & Gel Bead Kit (PN-1000006, PN-1000014, 10x Genomics).  Enzymatic fragmentation and size selection was used to optimize the cDNA amplicon size and indexed sequencing libraries were constructed by End Repair, A-tailing, Adaptor Ligation, and PCR. Final libraries contain the P5 and P7 priming sites used in Illumina bridge amplification. Paired end reads of 150nt were generated for each B-cell enriched library using the MiSeq sequencer (Illumina). The 5’ gene expression libraries were sequenced following 10X Genomics read length guidelines on the NovaSeq6000 sequencer (Illumina).

tag: disease state

value: rheumatoid arthritis


title: 3089_24m_GPR_p1_E4_CC

value: GPR


title: canine cortisol-secreting adrenocortical tumor 45


title: M3.3_S18


title: 727


title: M3.2_S17


title: 726


title: RA172 Synovium


title: canine cortisol-secreting adrenocortical tumor 44


title: canine cortisol-secreting adrenocortical tumor 43


title: 725


title: M3.1_S16


title: 3089_24m_GPR_p1_A6_CC


title: RA134 Synovium


title: 723


title: canine cortisol-secreting adrenocortical tumor 42


title: canine cortisol-secreting adrenocortical tumor 41


title: 722


title: RA134 Peripheral Blood

source_name: peripheral blood


title: M2.4_S14

value: Disease stage M2


title: 719


title: M2.3_S13


title: canine cortisol-secreting adrenocortical tumor 40


title: D20-169008

last: Sun

address: 455 Main St

institute: Whitehead Institute

description: brain.BBB.humanHD.counts.rds

data_processing:
Raw sequencing reads were aligned to the pre-mRNA annotated  Homo sapiens reference genome version GRCh38.
Counts were estimated using Cellranger 3.0.1 (10x Genomics, Pleasanton CA)
The generated cell-by-gene unique molecular identifier (UMI) count matrix was analyzed using the Seurat R package v.3.2.021.
Genome_build: GRCh38
Supplementary_files_format_and_content: counts.rds, meta.rds

source_name: post mortem tissue

extract_protocol:
Tissue was homogenized in media followed by either enrichment (BVE)/nuclei extraction or only nuclei extraction. Nuclei were processed through the 10X Single Cell Gene Expression platform per manufacturer's protocol
Libraries were constructed using the 10X Genomics Chromium Single Cell 3′ Reagent Kit v3

value: brain

value: Huntington's

tag: protocol

value: Blood Vessel Enrichment


title: D20-169009

description: brain.BBB.humanHD.counts.rds


title: canine cortisol-secreting adrenocortical tumor 39


title: RA195 Synovium


title: M2.2_S12


title: 718


title: D20-169007

description: brain.BBB.humanHD.counts.rds


title: M2.1_S11


title: canine cortisol-secreting adrenocortical tumor 37


title: D20-169006

description: brain.BBB.humanHD.counts.rds


title: canine cortisol-secreting adrenocortical tumor 38


title: 716


title: M1.5_S10

value: Disease stage M1


title: M2.5_S15


title: M3.4_S19


title: canine cortisol-secreting adrenocortical tumor 36


title: 191108_BBB_8_snRNA-G5

description: brain.BBB.humanHD.counts.rds

value: Pathologically Normal


title: 715

value: Hippocampus


title: canine cortisol-secreting adrenocortical tumor 35


title: 191108_BBB_7_snRNA-G4

description: brain.BBB.humanHD.counts.rds


title: 714

value: OXYCODONE


title: M1.3_S8

value: skin


title: M1.4_S9


title: 191108_BBB_6_snRNA-G3

description: brain.BBB.humanHD.counts.rds


title: 721


title: 712


title: M1.2_S7


title: 191108_BBB_5_snRNA-G2

description: brain.BBB.humanHD.counts.rds


title: canine cortisol-secreting adrenocortical tumor 32


title: M0.5_S5

source_name: Skin above interdigital cleft

value: control group


title: 707

value: F


title: canine cortisol-secreting adrenocortical tumor 33


title: M0.4_S4


title: 706


title: canine cortisol-secreting adrenocortical tumor 30


title: canine cortisol-secreting adrenocortical tumor 31


title: 191108_BBB_4_snRNA-G1

description: brain.BBB.humanHD.counts.rds


title: M0.3_S3


title: 191108_BBB_2_snRNA-F11

description: brain.BBB.humanHD.counts.rds


title: M0.2_S2


title: 704


title: 191108_BBB_1_snRNA-F10

description: brain.BBB.humanHD.counts.rds


title: canine cortisol-secreting adrenocortical tumor 29


title: 190726_BBB_snRNA-H3

description: brain.BBB.humanHD.counts.rds


title: 703


title: canine cortisol-secreting adrenocortical tumor 34


title: canine cortisol-secreting adrenocortical tumor 28


title: 702


title: 708


title: canine cortisol-secreting adrenocortical tumor 27


title: M0.1_S1


title: 190726_BBB_snRNA-H2

description: brain.BBB.humanHD.counts.rds


title: Female brain

city: Columbia

first: Susanta

middle: K.

last: Behura

state: Missouri

address: 920 East Campus Drive

department: Division of Animal Sciences

institute: Univeristy of Missouri

data_processing:
The base call (BCL) files generated from the Illumina sequencing were processed by Cell Ranger (v. 3.0.1) and converted to FASTQ files by the ‘mkfastq’ function.
The reads were mapped to the Ae. aegypti reference genome Aaegl5 using STAR aligner
The Cell Ranger pipeline was used to perform background filtration based on UMI (unique molecular identities) versus barcode counts, and to generate feature-barcode matrices from the libraries
The read count data of genes of single cells, generated by the Cell Ranger pipeline, was analyzed using the R package ‘Seurat’.
Genome_build: Aaegl5
Supplementary_files_format_and_content: Three processed data files (tsv.gz) were generated per library that included information of barcodes, features and read counts.

organism: Aedes aegypti

source_name: Adult brain

growth_protocol: 7-day old Ae. aegypti (LVP strain) males and females were used in the study.

extract_protocol:
Brain was dissected from 30 males and females, resuspended in Schneider’s Drosophila Medium on ice, and subjected to single nucleus isolation using the Pure Prep Nuclei Isolation kit (Sigma, St. Louis, MO, USA). Complete brain tissue was resuspended in Schneider’s Drosophila Medium on ice.
Chromium Next GEM Single Cell 3ʹ GEM, Library & Gel Bead Kit v3.1 protocol

value: Female

tag: developmental stage

value: 7 day old adult


title: canine cortisol-secreting adrenocortical tumor 26


title: M1.1_S6


title: 191108_BBB_3_snRNA-F12

city: Cambridge

description: brain.BBB.humanHD.counts.rds


title: 190726_BBB_snRNA-G9

description: brain.BBB.humanHD.counts.rds