title: JMB77 in Plasma rep 3

description: Adhesive isolate  JMB77 grown in adhesion inducing medium: Plasma at 37 degrees C


title: Ro75 in M199 rep 1

status: Public on Feb 01 2021

type: SRA

city: Providence

first: Alper

last: Uzun

state: RI

address: 200 Chestnut St.

department: Pediatrics

country: USA

institute: Women and Infants Hospital of Rhode Island

description: Adhesive isolate  Ro75 grown in adhesion inducing medium: M199 at 37 degrees C

library_source: transcriptomic

data_processing:
Raw sequence quality control and trimming was performed with FastQC v0.11.5 and Skewer v0.2.1
Reads were simultaneously aligned to the CDC317 C. parapsilosis reference genome and quantified using Salmon v1.0.0 in mapping-based mode
Gene-level expression values in quant files were imported into DESeq2 v1.18.1 R package using the tximport v1.6.0 R package
DESeq2 v1.18.1 R package was used to run differential expression analysis
Genome_build: CDC317
Supplementary_files_format_and_content: Salmon quant files containing gene level expression counts which have been corrected for gc content and sequence-specific random hexamer priming biases

molecule: total RNA

organism: Candida parapsilosis

source_name: Liquid Culture

growth_protocol: Isolates were confirmed as C. parapsilosis sensu stricto using PCR probes specific to the ITS1 region. Yeast were grown overnight in YPD medium (1% yeast extract, 2% peptone, 2% dextrose) with vigorous agitation at 37°C. Stationary phase cultures were washed with sterile water, and resuspended in fresh YPD medium, tissue culture medium M199 (BioWhittaker/Lonza #BW12-117Q) or pooled human blood plasma (sodium heparin anticoagulated) at 3 x 106 / ml, and further incubated at 37°C for 3 hours without shaking. Under these growth conditions, filaments (hyphae or pseudohyphae) were not observed. Parallel samples were tested in adhesion assays to confirm the adhesive phenotype, or yeast were centrifuged, and pellets flash frozen in liquid N2, and stored at -80° C for later RNA extraction for RNA seq or qPCR validation.

extract_protocol:
Total RNA was extracted from each and purified using RiboPure Yeast extraction kit (Ambion/Life Technologies). RNA integrity was assessed using agarose gels and Agilent Bioanalyzer.
RNA-seq library preparation and sequencing of extracted total RNA was performed following ribosomal RNA depletion using paired end reads (Illumina HiSeq2000), 2x150 bp, from all samples.

tag: growth medium

tag: strain


title: C7-1001000358-AK111-1

city: Stanford

first: Gerlinde

last: Wernig

state: CA

address: 265 Campus Drive

department: Pathology

institute: Institute for Regenerative Medicine and Stem Cell Research, Stanford University School of Medicine

description: Single cell from HSC

data_processing:
Sequencing reads were trimmed, adapter sequences removed and the reads aligned using STAR with default parameters.
Duplicate reads were removed using picard. Transcript counts were obtained using HT-Seq and hg19 UCSC exon/transcript annotations.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample

organism: Homo sapiens

source_name: CD34+ CD38- CD90+ CD45RA- HSC

growth_protocol: Human bone marrows were obtained from Stanford Medical Center with informed consent, according to Institutional Review Board (IRB)-approved protocols (Stanford IRB 39881). CD34+ progenitors from each sample were isolated by Ficoll separation and CD34+ progenitors were isolated by a positive selection using an immunomagnetic cell sorting system (AutoMacs; Miltenyi Biotec,Bergisch Gladbach, Germany). 56,000 cells were incubated in IMDM media supplemented with 10% BSA, 1% L-glutamine, 450 µM MTG, 1% ITG, liposomes (composition and concentration???), 1% penicillin/streptomycin, in the presence SCF 20 ng/ml and different diabodies at 100 nM for 12 days, with change medium every other day, and addition of new cytokines 3 times per day. After 12 days, cells were pelleted and resuspended in PBS 2% FCS. Fc block was performed for 20 min and the mononuclear cells were stained with directly conjugated anti-mouse CD34, CD38, CD45RA, CD90 and HSC were isolated as DAPI-CD34+CD38-CD45RA-CD90+ cells on a BD FACS ARIA sorter.

extract_protocol:
Single-cells were collected  in lysis buffer in 96-well plates, followed by reverse transcription with template-switch using an LNA-modified template switch oligo to generate cDNA. After 21 cycles of pre-amplification, DNA was purified and analyzed on an automated Fragment Analyzer (Advanced Analytical).
Each cells cDNA fragment profile was individually inspected and only wells with successful amplification products (concentration higher than 0.06 ng/ul) and with no detectable RNA degradation were selected for final library preparation. Tagmentation assays and barcoded sequencing libraries were prepared using Nextera XT kit (FC-131-1024; Illumina) according to the manufacturers instructions. Barcoded libraries were pooled and subjected to 75 bp paired-end sequencing on the Illumina NextSeq instrument.

treatment_protocol: CD34+ Bone Marrow derived cells were culture in IMDM media supplemented with 10% BSA, 1% L-glutamine, 450 µM MTG, 1% ITG, liposomes (composition and concentration???), 1% penicillin/streptomycin for 12 days. In all conditions 20 ng/ml SCF was added. Additional conditions receive 100 nM of TPO or different agonist or antagonist, with or without 14 µg/ml of TPO blocking antibody. Media was changed every other day and cytokines were added 3 times per day.

tag: cell type

value: HSC

tag: treatment

tag: days in culture

tag: date sequencing


title: 004_T4631_HC_T

city: La Jolla

first: Ferhat

last: Ay

address: 9420 Athena Circle

institute: La Jolla Institute for Immunology

description:
Bulk_Human_RawCounts.txt
Bulk_Human_TPM.txt

data_processing:
Bulk RNA-seq data (FASTQ files) were mapped against the hg38 genome (GRCh38.p7) reference using TopHat (Trapnell et al. 2009); v2.0.9 (--max-multihits 1 --microexon-search --bowtie1) with FastQC (v0.11.2), and Samtools v0.1.19.0 (Li et al. 2009).
Trimmomatic (v0.36) was used to remove adapters (Bolger et al. 2014).
HTSeq-count with -m union -s no -t exon -i gene_name parameters (part of the HTSeq framework, version v0.7.1 (Anders et al. 2015)) was used for calculating read counts.
Genome_build: hg38
Supplementary_files_format_and_content: Bulk_Human_RawCounts.txt contains raw counts of sequencing reads obtained with HTSeq-count
Bulk_Human_TPM.txt contains Transcript per Million normalized counts

molecule: polyA RNA

source_name: PBMCs

growth_protocol: Cell types were isolated from blood samples and directly sorted by Flow cytometry into trizol or lysis buffer. No particular cell growth procedure was required.

extract_protocol:
Total RNA was isolated from sorted cell populations using miRNAeasy Micro kit (Qiagen, USA) and quantified. 3ng of total RNA was used to generate cDNA following the Smart-seq2 protocol. cDNA was purified using AMPure XP beads (0.8x, Beckman Coulter).
Whole Transcriptome Amplification (Smart-seq2 - Picelli et al.2014)
1ng of cDNA from each sample was used to generate a sequencing library (Nextera XT DNA sample preparation kit and index kit, Illumina). The libraries were pooled and sequenced on a HiSeq2500 (Illumina) to obtain 50-bp single end reads. Both full-transcriptome amplification and sequencing library preparations were performed in a 96-well format to reduce assay-to-assay variability. Quality control steps were included after each step to eliminate samples with low quality from downstream process. A detailed protocol has been previously published (Rosales et al. 2018).
Libraries were sequenced on a HiSeq2500 Illumina to obtain a minimum of 10 million 50-bp single-end reads (HiSeq SR Cluster Kit v4 cBot, HiSeq SBS Kit v4).

tag: disease state

value: healthy control

tag: cell type surface markers

value: T cells

tag: ifn status

value: HC

tag: patientuid

tag: patientid

tag: visit number

tag: gender

value: Female

tag: age

tag: race

value: Black

tag: ethnicity

value: Non Hispanic


title: C12-1001000361-SCF-1

description: Single cell from HSC

value: SCF


title: C9-1001000359-AK113_AB-1

description: Single cell from HSC


title: JMB77 in Plasma rep 2

value: Plasma


title: B9-1001000359-AK113_AB-1

description: Single cell from HSC


title: C10-1001000360-AK119-1

description: Single cell from HSC


title: H10-1001000359-AK113_AB-1

description: Single cell from HSC


title: JMB77 in Plasma rep 1


title: JMB77 in M199 rep 3

description: Adhesive isolate  JMB77 grown in adhesion inducing medium: M199 at 37 degrees C


title: D9-1001000359-AK113_AB-1

description: Single cell from HSC


title: Ro75 in YPD rep 3

description: Adhesive isolate  Ro75 grown in adhesion supressing medium: YPD at 37 degrees C

value: YPD


title: G9-1001000359-AK113_AB-1

description: Single cell from HSC


title: Ro75 in YPD rep 1


title: JMB77 in M199 rep 1


title: JMB77 in YPD rep 3

description: Adhesive isolate  JMB77 grown in adhesion supressing medium: YPD at 37 degrees C


title: A9-1001000359-AK113_AB-1

description: Single cell from HSC


title: JMB77 in YPD rep 2


title: F1-1001000361-SCF-1

description: Single cell from HSC


title: D1-1001000353-AK111_AB-1

description: Single cell from HSC


title: JMB77 in YPD rep 1


title: JMB81 in Plasma rep 3

description: Adhesive isolate JMB81 grown in adhesion inducing medium: Plasma at 37 degrees C


title: JMB81 in Plasma rep 2


title: JMB81 in Plasma rep 1


title: A1-1001000353-AK111_AB-1

description: Single cell from HSC


title: F1-1001000353-AK111_AB-1

description: Single cell from HSC


title: C1-1001000353-AK111_AB-1

description: Single cell from HSC


title: JMB81 in M199 rep 3

description: Adhesive isolate JMB81 grown in adhesion inducing medium: M199 at 37 degrees C


title: JMB81 in M199 rep 2


title: E9-1001000359-AK113_AB-1

description: Single cell from HSC


title: B1-1001000353-AK111_AB-1

description: Single cell from HSC


title: JMB81 in M199 rep 1


title: JMB77 in M199 rep 2


title: E1-1001000353-AK111_AB-1

description: Single cell from HSC


title: F9-1001000359-AK113_AB-1

description: Single cell from HSC


title: A8-1001000358-AK111-1

description: Single cell from HSC


title: B8-1001000358-AK111-1

description: Single cell from HSC


title: C8-1001000358-AK111-1

description: Single cell from HSC


title: JMB81 in YPD rep 2

description: Adhesive isolate JMB81 grown in adhesion supressing medium: YPD at 37 degrees C


title: JMB81 in YPD rep 3


title: D8-1001000358-AK111-1

description: Single cell from HSC


title: JMB81 in YPD rep 1


title: E8-1001000358-AK111-1

description: Single cell from HSC


title: FLAG-Siwi_smRNA-seq_DDX43_KD_1

city: Tokyo

first: Ryo

last: Murakami

address: 2-11-16, Yayoi, Bunkyo-ku

department: Department of biological sciences

country: Japan

institute: The University of Tokyo

description: Small_RNA_associating with Siwi

data_processing:
Adapters were cut with Cutadapt.
The reads were also mapped to the B. mori reference genome (downloaded from Silkbase; silkbase.ab.a.u-tokyo.ac.jp) using bowtie as above.
The reads were normalized to RPM
Supplementary_files_format_and_content: RPM

organism: Bombyx mori

source_name: BmN4 Cells

growth_protocol: BmN4 cells were cultured at 26°C in EX-CELL 420 medium, supplemented with 10% fetal bovine serum and Penicillin-Streptomycin-Glutamine

extract_protocol:
Lysates were clarified from buffer containing NP-40 and small RNAs were extracted from immunoisolated FLAG-Siwi using anti-DDDDK-tag mAb.
Sequence libraries were generated with NEBNext Small RNA Library Prep Set for Illumina (NEB)

treatment_protocol: To knock down genes of interest, BmN4 cells (0.5–1 × 10^6 cells) were transfected with 500 pmol siRNA duplex by electroporation. To exogenously express  FLAG-Siwi in BmN4 cells, the cells (6 × 105 cells) were transfected with 2 µg of plasmid diluted in 5 µL of FuGENE HD transfection reagent (Promega). After transfection, cells were incubated at 26°C for 24 h.

tag: cell ine

value: The Bombyx ovary-derived cell line


title: D12-1001000361-SCF-1

description: Single cell from HSC


title: FLAG-Siwi_smRNA-seq_DDX43_KD_2

description:
Small_RNA_associating with Siwi
Replication of 1st column.


title: B6-1001000360-AK119-1

description: Single cell from HSC


title: F8-1001000358-AK111-1

description: Single cell from HSC


title: H9-1001000358-AK111-1

description: Single cell from HSC


title: YN14_248_Macaque_NeuN

city: Atlanta

first: Soojin

middle: V

last: Yi

state: GA

address: 950 Atlantic Dr

department: Biological Sciences

institute: Georgia Institute of Technology

library_source: genomic

data_processing:
Quality and adapter trimming was performed using TrimGalore version 0.4.1 (Babraham Institute).
Reads were mapped to the human GRCh37 reference genome using Bismark version: v0.14.4 (Krueger and Andrews 2011) and Bowtie2
Methylation calling was performed after deduplication using Bismark
Bsseq and DSS bioconductor packages were used to process DNA methylation data
Genome_build: Human hg19, Chimpanzee PanTro5, Rhesus Macaque RheMac8
Supplementary_files_format_and_content: Methylated read count and coverage for CpGs (bismark cytosine report format)

molecule: genomic DNA

organism: Macaca mulatta

source_name: brain

extract_protocol:
Genomic DNA was isolated from 1mg to 5mg of tissue sample, using the Qiagen DNeasy Blood and Tissue DNA extraction kit according to manufacturer’s instructions. The extracted DNA was suspended in TE buffer and quantified by Qubit (Thermo Fisher Scientific).
Libraries were made with In-House Illumina sequencer compatible protocol. The extracted DNA was fragmented by S-series focused ultrasonicator (Covaris) using the “200bp-target peak size protocol”. Fragmented DNA was then size selected (200bp-600bp) with Agencourt aMPure XP bead-based (Beckman Coulter Cat. No. A63880) size selection protocol (Mark. A. Urich et al. 2015). The DNA End repair step was performed with End-It DNA end repair kit (Epicentre, Cat. No. ER81050. After End repair step, A-tailing (NEB, cat. No. M0202) and Ligation steps are performed to ligate methylated adaptors. Bisulfite treatment of genomic DNA was performed using the MethylCode Bisulfite Conversion Kit (Life technologies). Purified genomic DNA was treated with CT conversion reagent in a thermocycler for 10 minutes at 980C, followed by 2.5 hours at 640C. Bisulfite-treated DNA fragments remain Single-stranded as they are no longer complementary. Low-cycle (4-8) PCR amplification was performed with Kapa HiFi Uracil Hotstart polymerase enzyme (KAPA Biosystems, cat. No. KK2801) which can tolerate Uracil residues. The final library fragments contain Thymines and Cytosines in place of the original unmethylated cytosine and methylated cytosines, respectively.

tag: tissue

value: brain

tag: nuclei

value: NeuN

tag: tissue preparation

value: Frozen Brain Tissue

tag: region

value: Brodmann Area 46

value: M

tag: pmi

tag: bisulfite conversion rate


title: YN12_654_Macaque_Olig2

value: F


title: YN12_654_Macaque_NeuN


title: G8-1001000358-AK111-1

description: Single cell from HSC

tag: cell type

value: HSC

tag: treatment

tag: days in culture

tag: date sequencing


title: E10-1001000360-AK119-1

description: Single cell from HSC


title: C11-1001000360-AK119-1

description: Single cell from HSC


title: YN12_409_Macaque_NeuN


title: YN12_335_Macaque_Olig2


title: YN12_335_Macaque_NeuN


title: B1-1001000361-SCF-1

description: Single cell from HSC


title: G7-1001000360-AK119-1

description: Single cell from HSC


title: YN11_78_Macaque_NeuN


title: A1-1001000361-SCF-1

description: Single cell from HSC


title: C1-1001000361-SCF-1

description: Single cell from HSC


title: YN11_78_Macaque_Olig2


title: D1-1001000361-SCF-1

description: Single cell from HSC


title: YN11_77_Macaque_NeuN


title: YN14_248_Macaque_Olig2


title: YN11_77_Macaque_Olig2


title: B10-1001000359-AK113_AB-1

description: Single cell from HSC


title: D10-1001000359-AK113_AB-1

description: Single cell from HSC


title: YN11_64_Macaque_NeuN


title: C10-1001000359-AK113_AB-1

description: Single cell from HSC


title: YN09_72_Macaque_Olig2


title: E10-1001000359-AK113_AB-1

description: Single cell from HSC


title: F10-1001000359-AK113_AB-1

description: Single cell from HSC


title: A10-1001000359-AK113_AB-1

description: Single cell from HSC


title: YN11_300_Macaque_Olig2


title: YN09_59_Macaque_NeuN


title: YN09_179_Macaque_Olig2


title: F2-1001000361-SCF-1

description: Single cell from HSC


title: YN09_179_Macaque_NeuN


title: H11-1001000359-AK113_AB-1

description: Single cell from HSC


title: YN09_173_Macaque_Olig2


title: YN09_173_Macaque_NeuN


title: YN11_300_Macaque_NeuN


title: B2-1001000353-AK111_AB-1

description: Single cell from HSC


title: YN09_72_Macaque_NeuN


title: YN11_64_Macaque_Olig2


title: A2-1001000353-AK111_AB-1

description: Single cell from HSC


title: E2-1001000353-AK111_AB-1

description: Single cell from HSC


title: YN09_122_Macaque_Olig2


title: YN09_122_Macaque_NeuN


title: C2-1001000353-AK111_AB-1

description: Single cell from HSC


title: D2-1001000353-AK111_AB-1

description: Single cell from HSC


title: YN08_380_Macaque_NeuN


title: G10-1001000359-AK113_AB-1

description: Single cell from HSC


title: YN04_200-Macaque_Olig2


title: YN04_200_Macaque_NeuN


title: A9-1001000358-AK111-1

description: Single cell from HSC


title: E1-1001000361-SCF-1

description: Single cell from HSC


title: C9-1001000358-AK111-1

description: Single cell from HSC


title: Invasive lobular breast cancer, case 13, IntD-ID_1214

type: genomic

city: Hannover

first: Doris

last: Steinemann

address: Carl-Neuberg-Straße 1

department: Human Genetics

country: Germany

institute: Medizinische Hochschule Hannover

description: hybridized to [OncoScan] Affymetrix OncoScan array

hyb_protocol: DNA was restriction digested, PCR amplified, fragmented, labeled and hybridized to each array according to the manufacturer's instructions.

scan_protocol: The Arrays were then washed using Affymetrix fluidics stations, and scanned using the Gene Chip Scanner 3000 7G.

data_processing:
CEL files were generated after scanning by the Affymetrix GeneChip Command Console (AGCC).
[primary data description]  Data was processed and analyzed using Chromosome Analysis Suite (ChAS) version 4.0.0.385

label: biotin

source_name: primary tumor

label_protocol: as given by the manufacturer

growth_protocol: primary formalin fixed parafffin embedded tissue

extract_protocol: genomic DNA was extracted from macrodissected with DNAeasy blood and tissue kit (Qiagen)

value: breast tumor tissue

tag: tumor type

value: primary tumor

tag: histological subtype

value: ILBC

tag: e-cadherin status

value: negative

tag: er status

value: positive


title: Invasive lobular breast cancer, case 11, IntD-ID_1130


title: Invasive lobular breast cancer, case 12, IntD-ID_1224


title: Invasive lobular breast cancer, case 9, tumor 1, IntD-ID_1216


title: G9-1001000358-AK111-1

description: Single cell from HSC


title: Invasive lobular breast cancer, case 9, tumor 2, IntD-ID_836


title: Invasive lobular breast cancer, case 8, IntD-ID_804


title: H10-1001000358-AK111-1

description: Single cell from HSC


title: Invasive lobular breast cancer, case 6, IntD-ID_1222


title: B7-1001000360-AK119-1

description: Single cell from HSC


title: Invasive lobular breast cancer, case 5, tumor 2, IntD-ID_54


title: F9-1001000358-AK111-1

description: Single cell from HSC


title: E11-1001000360-AK119-1

description: Single cell from HSC


title: C12-1001000360-AK119-1

description: Single cell from HSC


title: YN08_380_Macaque_Olig2

tag: gender

tag: age


title: A2-1001000361-SCF-1

description: Single cell from HSC


title: F2-1001000353-AK111_AB-1

description: Single cell from HSC


title: Invasive lobular breast cancer, case 3, region 1, IntD-ID_46

source_name: ovarian metastasis

value: ovarian metastasis


title: B9-1001000358-AK111-1

description: Single cell from HSC


title: Invasive lobular breast cancer, case 5, IntD-ID_55


title: E9-1001000358-AK111-1

description: Single cell from HSC


title: Invasive lobular breast cancer, case 2, IntD-ID_1221


title: C2-1001000361-SCF-1

description: Single cell from HSC

value: SCF


title: B2-1001000361-SCF-1

description: Single cell from HSC


title: G8-1001000360-AK119-1

description: Single cell from HSC


title: Invasive lobular breast cancer, case 3, region 2, IntD-ID_45


title: Invasive lobular breast cancer, case 1, tumor 2, IntD-ID_47


title: D9-1001000358-AK111-1

description: Single cell from HSC


title: Lobular carcinoma in situ (LCIS), case 1, IntD-ID_50

source_name: LCIS

value: LCIS


title: D2-1001000361-SCF-1

description: Single cell from HSC


title: Invasive lobular breast cancer, case 7, IntD-ID_803


title: B11-1001000359-AK113_AB-1

description: Single cell from HSC


title: A11-1001000359-AK113_AB-1

description: Single cell from HSC


title: C11-1001000359-AK113_AB-1

description: Single cell from HSC


title: E11-1001000359-AK113_AB-1

description: Single cell from HSC


title: F11-1001000359-AK113_AB-1

description: Single cell from HSC


title: D11-1001000359-AK113_AB-1

description: Single cell from HSC


title: A1-1001000360-AK119-1

description: Single cell from HSC


title: ZAP-g3 knockout HFF, CMV infected 72hpi, replicate 1 [ZAP-g3-48hpi-rep1]

city: Berlin

first: Emanuel

last: Wyler

address: Robert Roessle Str 10

department: Berlin Institute for Medical Systems Biology

institute: Max Delbrück Center for Molecular Medicine

description:
RNAseq_ZAP191-KD-untr-rep1
processed data file:
RNAseq_hg19_readcounts.tsv
RNAseq_CMV-MF871618_readcounts.tsv

data_processing:
For bulk RNA-sequencing, alignments were done using hisat2 (Kim et al, 2015)
Sequencing reads were aligned to the hg19 version of the human genome using standard parameter, using the Refseq gtf file downloaded from the UCSC genome browser.
Reads were then quantified using quasR (Gaidatzis et al, 2015) and the above mentioned gtf file, or the HCMV TB40/E annotation (accession number MF871618).
Differential expression and corresponding p-values were calculated using edgeR (McCarthy et al, 2012).
For 4sU sequencing, reads were mapped to a combined index of the human genome (Hg38 / Ensembl v90) and the HCMV genome (accession number KF297339.1) using STAR (v2.5.3a) with parameters --outFilterMismatchNmax 20 --outFilterScoreMinOverLread 0.3 --outFilterMatchNminOverLread 0.3 --alignEndsType Extend5pOfReads12 --outSAMattributes nM MD NH.
We used GRAND-SLAM (v2.0.5d) (Jurges et al., 2018) to estimate the new-to-total RNA ratios.
We only used the parts of the reads that were sequenced by both mates in a read pair (parameter -double) for the estimation.
New RNA was computed by multiplying total RNA with the maximum a posteriori estimate of the new-to-total RNA ratio.
For further analyses, we removed all cellular genes that had less than 10 transcripts per million transcripts (TPM) in more than 6 (cellular genes) or 2 (viral genes) samples.
To remove artefacts due to imprecise quantification, we furthermore removed all viral genes with less than 100 new reads. Log2 fold changes were estimated using PsiLFC (Erhard, 2018) with uninformative prior (corresponding to no pseudocounts).
Normalization factors were computed from total RNA such that the median log2 foldchange was 0 and applied to both total and new RNA.
Genome_build: hg19 and HCMV MF871618 (bulk RNA-seq); hg38 and HCMV KF297339.1 (4sU seq)
Supplementary_files_format_and_content: tab-separated values

source_name: ZAP-g3 knockout HFF, CMV infected 72hpi

growth_protocol:
Primary human foreskin fibroblasts (HFF-1) cells (ATCC SCRC-1041) were maintained in DMEM (high glucose) supplemented with 15% FCS, 1% P/S and 1% non‐essential amino acids (NEAA). Cells were cultured at 37°C and 7.5% CO2.
Knockouts of ZAP (ZC3HAV1) were done using CRISPR/Cas9, with components transduced by lentiviruses

extract_protocol:
NEBNext Ultra II Directional RNA Library Prep Kit for Illumina
adapter sequence: GATCGGAAGAGCACACGT
For  RNA-sequencing, Cells were resuspended in Trizol (Invitrogen) and RNA extracted from Trizol.
RNA-sequencing libraries were constructed using commercial kits (New England Biolabs)

treatment_protocol: Cells were subjected to CMV infection and 4sU treatment as indicated

value: Primary human foreskin fibroblasts (HFF) cells

tag: genotype/variation

value: ZAP-g3 knockout

value: CMV infected 72hpi

tag: grna sequence forward

value: CACCGGCCGGGATCACCCGATCGG

tag: grna sequence reverse

value: AAACCCGATCGGGTGATCCCGGCC

tag: grna name

tag: 4su treatment

tag: cmv infection

value: yes

tag: harvesting timepoint


title: ZAP-g3 knockout HFF, CMV infected 72hpi, replicate 2 [ZAP-g3-48hpi-rep2]

description:
RNAseq_ZAP191-KD-untr-rep2
processed data file:
RNAseq_hg19_readcounts.tsv
RNAseq_CMV-MF871618_readcounts.tsv

tag: cell type


title: G11-1001000359-AK113_AB-1

description: Single cell from HSC

tag: treatment


title: ZAP-g3 knockout HFF, mock 8h, replicate 1 [ZAP-g3-mock-rep1]

description:
RNAseq_ZAP191-KD-48hpi-rep1
processed data file:
RNAseq_hg19_readcounts.tsv

source_name: ZAP-g3 knockout HFF, mock 8h

value: mock 8h

value: no


title: ZAP-g3 knockout HFF, CMV infected 8hpi, replicate 1 [ZAP-g3-8hpi-rep1]

description:
RNAseq_ZAP191-KD-8hpi-rep1
processed data file:
RNAseq_hg19_readcounts.tsv
RNAseq_CMV-MF871618_readcounts.tsv

source_name: ZAP-g3 knockout HFF, CMV infected 8hpi

value: CMV infected 8hpi


title: F3-1001000361-SCF-1

description: Single cell from HSC

value: HSC

tag: days in culture


title: ZAP-g3 knockout HFF, CMV infected 8hpi, replicate 2 [ZAP-g3-8hpi-rep2]

description:
RNAseq_ZAP191-KD-8hpi-rep2
processed data file:
RNAseq_hg19_readcounts.tsv
RNAseq_CMV-MF871618_readcounts.tsv


title: ZAP-g3 knockout HFF, mock 8h, replicate 2 [ZAP-g3-mock-rep2]

description:
RNAseq_ZAP191-KD-48hpi-rep2
processed data file:
RNAseq_hg19_readcounts.tsv


title: Invasive lobular breast cancer, case 1, tumor 1, IntD-ID_48

tag: tissue

value: breast tumor tissue

value: primary tumor


title: ZAP-g1 knockout HFF, CMV infected 72hpi, replicate 2 [ZAP-g1-48hpi-rep2]

description:
RNAseq_ZAP2-KD-untr-rep2
processed data file:
RNAseq_hg19_readcounts.tsv
RNAseq_CMV-MF871618_readcounts.tsv

source_name: ZAP-g1 knockout HFF, CMV infected 72hpi

value: ZAP-g1 knockout

value: CACCGGCCGGGCCCGACCGCTTTG

value: AAACCAAAGCGGTCGGGCCCGGCC


title: ZAP-g3 knockout HFF, untreated, replicate 2 [ZAP-g3-untr-rep2]

description:
RNAseq_ZAP191-KD-24hpi-rep2
processed data file:
RNAseq_hg19_readcounts.tsv

source_name: ZAP-g3 knockout HFF, untreated

value: untreated


title: ZAP-g3 knockout HFF, untreated, replicate 1 [ZAP-g3-untr-rep1]

description:
RNAseq_ZAP191-KD-24hpi-rep1
processed data file:
RNAseq_hg19_readcounts.tsv


title: D3-1001000353-AK111_AB-1

description: Single cell from HSC

tag: date sequencing


title: C3-1001000353-AK111_AB-1

description: Single cell from HSC


title: B3-1001000353-AK111_AB-1

description: Single cell from HSC


title: ZAP-g1 knockout HFF, CMV infected 8hpi, replicate 2 [ZAP-g1-8hpi-rep2]

description:
RNAseq_ZAP2-KD-8hpi-rep2
processed data file:
RNAseq_hg19_readcounts.tsv
RNAseq_CMV-MF871618_readcounts.tsv

source_name: ZAP-g1 knockout HFF, CMV infected 8hpi


title: ZAP-g1 knockout HFF, CMV infected 8hpi, replicate 1 [ZAP-g1-8hpi-rep1]

description:
RNAseq_ZAP2-KD-8hpi-rep1
processed data file:
RNAseq_hg19_readcounts.tsv
RNAseq_CMV-MF871618_readcounts.tsv


title: F3-1001000353-AK111_AB-1

description: Single cell from HSC


title: E3-1001000353-AK111_AB-1

description: Single cell from HSC


title: ZAP-g1 knockout HFF, mock 8h, replicate 2 [ZAP-g1-mock-rep2]

description:
RNAseq_ZAP2-KD-48hpi-rep2
processed data file:
RNAseq_hg19_readcounts.tsv

source_name: ZAP-g1 knockout HFF, mock 8h


title: E2-1001000361-SCF-1

description: Single cell from HSC

value: SCF


title: ZAP-g1 knockout HFF, mock 8h, replicate 1 [ZAP-g1-mock-rep1]

description:
RNAseq_ZAP2-KD-48hpi-rep1
processed data file:
RNAseq_hg19_readcounts.tsv

value: Primary human foreskin fibroblasts (HFF) cells


title: ZAP-g1 knockout HFF, CMV infected 72hpi, replicate 1 [ZAP-g1-48hpi-rep1]

description:
RNAseq_ZAP2-KD-untr-rep1
processed data file:
RNAseq_hg19_readcounts.tsv
RNAseq_CMV-MF871618_readcounts.tsv


title: D10-1001000358-AK111-1

description: Single cell from HSC


title: ZAP-g1 knockout HFF, untreated, replicate 2 [ZAP-g1-untr-rep2]

description:
RNAseq_ZAP2-KD-24hpi-rep2
processed data file:
RNAseq_hg19_readcounts.tsv

source_name: ZAP-g1 knockout HFF, untreated


title: A3-1001000353-AK111_AB-1

description: Single cell from HSC


title: G10-1001000358-AK111-1

description: Single cell from HSC


title: E10-1001000358-AK111-1

description: Single cell from HSC


title: C10-1001000358-AK111-1

description: Single cell from HSC


title: control knockout HFF, CMV infected 72hpi, replicate 2 [Ctrl-KD-48hpi-rep2]

description:
RNAseq_FFLuc-KD-untr-rep2
processed data file:
RNAseq_hg19_readcounts.tsv
RNAseq_CMV-MF871618_readcounts.tsv

value: control knockout

value: CACCGGATTCTAAAACGGATTACC

value: AAACGGTAATCCGTTTTAGAATCC

value: control


title: D2-1001000360-AK119-1

description: Single cell from HSC


title: F10-1001000358-AK111-1

description: Single cell from HSC


title: B8-1001000360-AK119-1

description: Single cell from HSC


title: H11-1001000358-AK111-1

description: Single cell from HSC


title: control knockout HFF, CMV infected 72hpi, replicate 1 [Ctrl-KD-48hpi-rep1]

description:
RNAseq_FFLuc-KD-untr-rep1
processed data file:
RNAseq_hg19_readcounts.tsv
RNAseq_CMV-MF871618_readcounts.tsv

value: CMV infected 72hpi

value: yes


title: ZAP-g1 knockout HFF, untreated, replicate 1 [ZAP-g1-untr-rep1]

description:
RNAseq_ZAP2-KD-24hpi-rep1
processed data file:
RNAseq_hg19_readcounts.tsv

value: no


title: G9-1001000360-AK119-1

description: Single cell from HSC


title: A10-1001000358-AK111-1

description: Single cell from HSC


title: F12-1001000359-AK113_AB-1

description: Single cell from HSC


title: control knockout HFF, mock 8h, replicate 2 [Ctrl-KD-mock-rep2]

description:
RNAseq_FFLuc-KD-48hpi-rep2
processed data file:
RNAseq_hg19_readcounts.tsv

source_name: control knockout HFF, mock 8h

value: mock 8h


title: E12-1001000360-AK119-1

description: Single cell from HSC

value: HSC


title: control knockout HFF, CMV infected 8hpi, replicate 1 [Ctrl-KD-8hpi-rep1]

description:
RNAseq_FFLuc-KD-8hpi-rep1
processed data file:
RNAseq_hg19_readcounts.tsv
RNAseq_CMV-MF871618_readcounts.tsv

source_name: control knockout HFF, CMV infected 8hpi

value: CMV infected 8hpi


title: control knockout HFF, CMV infected 8hpi, replicate 2 [Ctrl-KD-8hpi-rep2]

description:
RNAseq_FFLuc-KD-8hpi-rep2
processed data file:
RNAseq_hg19_readcounts.tsv
RNAseq_CMV-MF871618_readcounts.tsv


title: B10-1001000358-AK111-1

description: Single cell from HSC

source_name: CD34+ CD38- CD90+ CD45RA- HSC


title: F4-1001000353-AK111_AB-1

description: Single cell from HSC


title: C4-1001000353-AK111_AB-1

description: Single cell from HSC


title: B4-1001000353-AK111_AB-1

description: Single cell from HSC


title: parental wild type HFF, CMV infected 72hpi, replicate 2 [WT-48hpi-rep2]

description:
RNAseq_WT-untr-rep2
processed data file:
RNAseq_hg19_readcounts.tsv
RNAseq_CMV-MF871618_readcounts.tsv

value: parental wild type


title: control knockout HFF, mock 8h, replicate 1 [Ctrl-KD-mock-rep1]

description:
RNAseq_FFLuc-KD-48hpi-rep1
processed data file:
RNAseq_hg19_readcounts.tsv


title: D4-1001000353-AK111_AB-1

description: Single cell from HSC


title: control knockout HFF, untreated, replicate 1 [Ctrl-KD-untr-rep1]

description:
RNAseq_FFLuc-KD-24hpi-rep1
processed data file:
RNAseq_hg19_readcounts.tsv

source_name: control knockout HFF, untreated


title: control knockout HFF, untreated, replicate 2 [Ctrl-KD-untr-rep2]

description:
RNAseq_FFLuc-KD-24hpi-rep2
processed data file:
RNAseq_hg19_readcounts.tsv


title: parental wild type HFF, CMV infected 72hpi, replicate 1 [WT-48hpi-rep1]

description:
RNAseq_WT-untr-rep1
processed data file:
RNAseq_hg19_readcounts.tsv
RNAseq_CMV-MF871618_readcounts.tsv


title: E12-1001000359-AK113_AB-1

description: Single cell from HSC


title: E4-1001000353-AK111_AB-1

description: Single cell from HSC


title: B12-1001000359-AK113_AB-1

description: Single cell from HSC


title: D12-1001000359-AK113_AB-1

description: Single cell from HSC


title: parental wild type HFF, mock 8h, replicate 2 [WT-mock-rep2]

description:
RNAseq_WT-48hpi-rep2
processed data file:
RNAseq_hg19_readcounts.tsv

source_name: parental wild type HFF, mock 8h


title: parental wild type HFF, mock 8h, replicate 1 [WT-mock-rep1]

description:
RNAseq_WT-48hpi-rep1
processed data file:
RNAseq_hg19_readcounts.tsv


title: C3-1001000361-SCF-1

description: Single cell from HSC


title: parental wild type HFF, untreated, replicate 1 [WT-untr-rep1]

description:
RNAseq_WT-24hpi-rep1
processed data file:
RNAseq_hg19_readcounts.tsv

source_name: parental wild type HFF, untreated


title: D3-1001000361-SCF-1

description: Single cell from HSC


title: A12-1001000359-AK113_AB-1

description: Single cell from HSC


title: B3-1001000361-SCF-1

description: Single cell from HSC


title: A3-1001000361-SCF-1

description: Single cell from HSC


title: parental wild type HFF, CMV infected 8hpi, replicate 2 [WT-8hpi-rep2]

description:
RNAseq_WT-8hpi-rep2
processed data file:
RNAseq_hg19_readcounts.tsv
RNAseq_CMV-MF871618_readcounts.tsv


title: Human pancreatic islets - SARS-Cov-2 and Remdesivir - experiment 3

city: Ulm

first: Alexander

last: Kleger

address: Albert Einstein Allee 23

institute: Ulm University

description:
S_3_Rem_5dpi_S69995
mRNA
rnaseq_deseq_5dpi_counts_raw.tsv
rnaseq_deseq_5dpi_fpkms.tsv

data_processing:
Illumina HiSeq Control Software (HCS) HD 3.4.0.38 was used for the data acquisition on the sequencing instrument.
On-instrument base-calling performed by the Illumina Real-Time Analysis (RTA) software 2.7.7.
BCL to BAM file conversion and demultiplexing with custom programs (https://github.com/DanieleBarreca/picard/) based on Picard tools 2.19.2 (https://broadinstitute.github.io/picard/).
Spliced genome alignments to GRCh38 (UCSC Genome Browser hg38) and Ensembl reference transcriptome e100 (April 2020) with STAR 2.7.1a and options recommended by the ENCODE project (--alignIntronMax 1000000 --alignIntronMin 20 --alignMatesGapMax 1000000 --alignSJDBoverhangMin 1 --alignSJoverhangMin 8 --outFilterMismatchNmax 999 --outFilterMismatchNoverReadLmax 0.04 --outFilterMultimapNmax 20 --outFilterType BySJout)
Differential expression modelling with Bioconductor 3.11 package DESeq2 1.28.1, running under R 4.0.2.
Genome_build: UCSC hg38 based on GRCh38
Supplementary_files_format_and_content: rnaseq_deseq_5dpi_counts_raw.tsv: Per gene and sample raw (integer) counts in tab-separated value (TSV) format.
Supplementary_files_format_and_content: rnaseq_deseq_5dpi_fpkms.tsv: DESeq2-calculated FPKMs in tab-separated value (TSV) format.

source_name: Human pancreatic islets

growth_protocol: Preparations of human pancreatic islets were obtained from the Alberta Diabetes Institute IsletCore at University of Alberta headed by Patrick E. MacDonald. Islet material is derived from excess donor organs used for clinical transplantation and with the written informed consent for research (approval #Pro00013094).

extract_protocol:
RNA from cells was isolated using the Qiagen RNeasy Plus Mini Kit (Qiagen #74136).
For the generation of full-length cDNA, the Smart-seq2 protocol (Picelli, S. et al., Nat Protoc. 2014 Jan;9(1):171-81. doi:10.1038/nprot.2014.006) was used.
The subsequent library preparation from the amplified cDNA was performed using the Nextera XT DNA library prep kit (Illumina).
For sequencing, libraries were pooled, diluted and sequenced on Illumina HiSeq 3000/4000 using 50 bp single-read chemistry.

treatment_protocol: Pancreatic islets were infected with viral isolate BetaCoV/Netherlands/01/NL/2020 (#010V-03903) and an MOI of approximately 2.5. After 3 h incubation, cells were washed three times and cultured for 5 days before cell harvest.

value: pancreatic islets

tag: Sex

value: male

value: SARS-CoV-2 infection and Remdesivir

tag: timepoint

value: 5 dpi


title: G12-1001000359-AK113_AB-1

description: Single cell from HSC


title: Human pancreatic islets - Control - experiment 3

description:
S_3_mock_5dpi_S69997
mRNA
rnaseq_deseq_5dpi_counts_raw.tsv
rnaseq_deseq_5dpi_fpkms.tsv

value: Uninfected


title: parental wild type HFF, untreated, replicate 2 [WT-untr-rep2]

description:
RNAseq_WT-24hpi-rep2
processed data file:
RNAseq_hg19_readcounts.tsv

value: Primary human foreskin fibroblasts (HFF) cells

value: untreated


title: Human pancreatic islets - SARS-Cov-2 - experiment 3

description:
S_3_SARS_5dpi_S69996
mRNA
rnaseq_deseq_5dpi_counts_raw.tsv
rnaseq_deseq_5dpi_fpkms.tsv

value: SARS-CoV-2 infection


title: E3-1001000361-SCF-1

description: Single cell from HSC

value: SCF


title: A4-1001000353-AK111_AB-1

description: Single cell from HSC


title: Human pancreatic islets - SARS-Cov-2 and Remdesivir - experiment 2

description:
S_2_Rem_5dpi_S70001
mRNA
rnaseq_deseq_5dpi_counts_raw.tsv
rnaseq_deseq_5dpi_fpkms.tsv

value: female


title: Human pancreatic islets - SARS-Cov-2 - experiment 2

description:
S_2_SARS_5dpi_S70003
mRNA
rnaseq_deseq_5dpi_counts_raw.tsv
rnaseq_deseq_5dpi_fpkms.tsv


title: F4-1001000361-SCF-1

description: Single cell from HSC


title: F6-1001000357-TPO_AB-1

description: Single cell from HSC


title: E6-1001000357-TPO_AB-1

description: Single cell from HSC


title: C12-1001000359-AK113_AB-1

description: Single cell from HSC


title: parental wild type HFF, CMV infected 8hpi, replicate 1 [WT-8hpi-rep1]

description:
RNAseq_WT-8hpi-rep1
processed data file:
RNAseq_hg19_readcounts.tsv
RNAseq_CMV-MF871618_readcounts.tsv


title: Input

city: Neuherberg

first: Lara

last: Zorro Shahidian

state: Bavaria

address: Ingolstädter Landstraße 1

department: Institute of Functional Epigenetics

institute: Helmholtz Zentrum Muenchen

data_processing:
Image analysis and base calling were performed using RTA 2.7.3 and bcl2fastq 2.17.1.14.
Sequence reads were mapped to reference genome hg38 using Bowtie 1.0.0 with the following parameters -m 1 --strata --best -y -S -l 40 -p 2.
Genome_build: hg38
Supplementary_files_format_and_content: Wig files were generated using with an in-house script (Variable step, span=25, reads were elongated to 200b).

source_name: breast cancer cell line

growth_protocol: MCF7 were grown on DMEM, supplemented with 10% FBS, 1% penicillin/streptomycin and 1% L-glutamine. The cells were harvested while at 80% confluency.

extract_protocol:
Lysates were fragmented by Mnase digestion and histone-DNA complexes were isolated with antibody.
ChIP samples were purified using Agencourt AMPure XP beads (Beckman Coulter) and quantified with the Qubit (Invitrogen). For the H3K122succ samples and respective input, the ChIP-seq libraries were prepared from 5 to 10 ng of double-stranded purified DNA using the MicroPlex Library Preparation kit v2 (C05010014, Diagenode s.a., Seraing, Belgium), according to manufacturer's instructions. While for H3K4me3, H3K9ac, H3K27ac and respective input, the ChIP-seq libraries were prepared from 5 ng of double-stranded purified DNA using the NEBNextâ Ultra II (E7645S, New England Biolabs). In the first step, the DNA was repaired and yielded molecules with blunt ends. In the next step, stem-loop adaptors with blocked 5 prime ends were ligated to the 5 prime end of the genomic DNA, leaving a nick at the 3 prime end. The adaptors cannot ligate to each other and do not have single-strand tails, avoiding non-specific background. In the final step, the 3 prime ends of the genomic DNA were extended to complete library synthesis and Illumina compatible indexes were added through a PCR amplification (8 cycles). Amplified libraries were purified and size-selected using Agencourt AMPure XP beads (Beckman Coulter) to remove unincorporated primers and other reagents.

tag: chip antibody

tag: cell line


title: Human pancreatic islets - Control - experiment 2

description:
S_2_mock_5dpi_S70002
mRNA
rnaseq_deseq_5dpi_counts_raw.tsv
rnaseq_deseq_5dpi_fpkms.tsv


title: H3K27ac

value: H3K27ac (Abcam, catalogue number ab4729, lot GR243994-1)


title: G6-1001000357-TPO_AB-1

description: Single cell from HSC


title: H3K4me3

value: H3K4me3 (Millipore, catalogue number 17-614, lot 2716111)


title: C5-1001000357-TPO_AB-1

description: Single cell from HSC


title: H3K122succ_AB#3

value: H3K122succ (in-house AB)


title: B9-1001000355-AK113-1

description: Single cell from HSC


title: E9-1001000355-AK113-1

description: Single cell from HSC


title: H3K122succ_AB#1


title: H3K122succ_AB#2


title: E12-1001000356-TPO-1

description: Single cell from HSC

value: TPO


title: Input_for_H3K122succ


title: MDMs_siGAPLINC_1_RNA_Seq

city: Santa Cruz

first: Susan

last: Carpenter

address: 1156 High St

department: MCD Biology

institute: UC Santa Cruz

data_processing:
All samples were sequenced together on an Illumina HiSeq system (single-end, 50bp), and sequencing reads were mapped to hg19 using STAR. For analysis of differential genes, STAR outputs were processed using DESeq2.
Genome_build: hg19
Supplementary_files_format_and_content: DESeq output

source_name: human monocyte-derived macrophages

growth_protocol: Peripheral blood mononuclear cells (PBMCs) were isolated from the buffy coats of healthy blood donors (Stanford Blood Center) by Ficoll-Paque PLUS (GE Healthcare) density gradient centrifugation. The cells were washed 3X in HBSS (Sigma Aldrich), resuspended in complete RPMI-1640 (Life Technologies) supplemented with 5 mL pen/strep (100X), 10% FCS, 12.5 ml HEPES (25 mM), 5 ml NEAAs (100X), 5 ml GlutaMax (100X), 5 ml Na-Pyruvate (1 mM), 500μl ciprofloxacin (10mg/ml) and plated onto 10-cm dishes. Nonadherent cells were aspirated after 2 hours of incubation at 37°C in 5% CO2. The remaining cells were expanded and cultivated in the presence of 50ng/mL recombinant human M-CSF (R&D, 216-MC-025) to generate monocyte-derived macrophages (MDMs)

extract_protocol:
Total RNA was purified from MDMs treated with non-targeting siRNA and GAPLINC pooled-siRNA using Direct-zol RNA MiniPrep Kit (Zymo Research) and TRIzol reagent (Ambion) according to the manufacturer’s instructions.
Total RNA was used to generate libraries using a NEXTflex Rapid Directional RNA-Seq kit (Bioo Scientific, $5138-07) according to the manufacturer’s instructions. Samples were quality assessed using TapeStation (Agilent, Santa Clara, CA) and read on a High-Seq System (Illumina, San Diego, CA.

treatment_protocol: Monocytes isolated from PBMCs were treated with recombinant human M-CSF (R&D, 216-MC-025) to generate monocyte-derived macrophages (MDMs). MDMs were treated with siRNA (25 nm final) on day 2 of differentiation. Transfection was allowed to proceed for 72h before RNA isolation.

value: monocyte-derived macrophages

value: GAPLINC pooled siRNA


title: MDMs_siControl_2_RNA_Seq

value: Non-targeting control siRNA


title: MDMs_siControl_1_RNA_Seq


title: C11-1001000356-TPO-1

description: Single cell from HSC

value: HSC


title: G2-1001000356-TPO-1

description: Single cell from HSC


title: B10-1001000356-TPO-1

description: Single cell from HSC


title: MDMs_siGAPLINC_2_RNA_Seq


title: H3K9ac

value: H3K9ac (Abcam, catalogue number ab4441, lot GR284977-1)


title: A10-1001000356-TPO-1

description: Single cell from HSC


title: D11-1001000356-TPO-1

description: Single cell from HSC


title: THP1_PMA2_RNA_seq

data_processing:
All samples were sequenced together on an Illumina HiSeq system (single-end, 50bp), and sequencing reads were mapped to hg19 using STAR. For analysis of differential genes, STAR outputs were processed using DESeq2.
Genome_build: hg19
Supplementary_files_format_and_content: deseq output text file

source_name: THP1 cells

growth_protocol: THP-1 cells were cultured in complete RPMI 1640 media + 10% FCS + pen/strep cocktail (1%) + 0.05 mM betamercaptoethanol

extract_protocol:
Total RNA was purified from -/+ PMA-treated THP-1 cells using Direct-zol RNA MiniPrep Kit (Zymo Research) and TRIzol reagent (Ambion) according to the manufacturer’s instructions.
Total RNA was used to generate libraries using a NEXTflex Rapid Directional RNA-Seq kit (Bioo Scientific, $5138-07) according to the manufacturer’s instructions. Samples were quality assessed using Bioanalyzer (Agilent, Santa Clara, CA) and read on a High-Seq System (Illumina, San Diego, CA.

treatment_protocol: For differentiation of THP-1 cells, cells were treated with PMA to a final concentration of 100 nM for 24h .

value: human monocytic

value: PMA


title: H10-1001000355-AK113-1

description: Single cell from HSC


title: THP1_PMA1_RNA_seq


title: H6-1001000357-TPO_AB-1

description: Single cell from HSC


title: THP1_control2_RNA_seq


title: D5-1001000357-TPO_AB-1

description: Single cell from HSC


title: THP1_control1_RNA_seq


title: H9-1001000355-AK113-1

description: Single cell from HSC


title: G5-1001000357-TPO_AB-1

description: Single cell from HSC


title: F5-1001000357-TPO_AB-1

description: Single cell from HSC


title: A11-1001000356-TPO-1

description: Single cell from HSC


title: E5-1001000357-TPO_AB-1

description: Single cell from HSC


title: SUIT-2_Reverse_Adapted_RNA_clone4

city: Boston

first: Nada

middle: Y

last: Kalaany

state: MA

address: 3 Blackfan Circle CLS 16067

institute: Boston Children's Hospital

data_processing:
RNA-seq: Data was aligned to the hg19 genome using STAR. Read counts were obtained using Salmon and analyzed using the tximport and DESeq2 packages in R.
ATAC-seq: Data was aligned to the hg19 genome using Bowtie2. Bigwigs were obtained using bamCoverage from the deeptools tool suite, normalized to 1X coverage
Genome_build: hg19
Supplementary_files_format_and_content: ATAC-seq: bigwig files; RNA-seq: raw gene counts file

source_name: SUIT-2 cells

growth_protocol: Grown in RPMI medium with low glucose (0.5 mM) and low glutamine (0.1 mM). Then regrown in RPMI medium with high glucose (11 mM) and high glutamine (2 mM).

extract_protocol:
RNA was isolated and purified using miRNeasy Mini Kit (Qiagen-217004)
mRNA libraries were prepared using the Illumina TruSeq Stranded mRNA kit modified for improved performance and multiplexing

treatment_protocol: Cells were seeded overnight at 700,000 per 10 cm plate. The cells were then washed once with PBS and incubated in L-L medium for 24 h. L-L medium refers to customized RPMI medium with low glucose (0.5 mM) and low glutamine (0.1 mM).


title: SUIT-2_Reverse_Adapted_RNA_clone5


title: SUIT-2_Reverse_Adapted_RNA_clone6


title: SUIT-2_Adapted_RNA_clone6

growth_protocol: Grown in RPMI medium with low glucose (0.5 mM) and low glutamine (0.1 mM).


title: B11-1001000356-TPO-1

description: Single cell from HSC


title: SUIT-2_Adapted_RNA_clone5


title: D4-1001000357-TPO_AB-1

description: Single cell from HSC


title: SUIT-2_Adapted_RNA_clone4


title: C4-1001000357-TPO_AB-1

description: Single cell from HSC


title: B4-1001000357-TPO_AB-1

description: Single cell from HSC


title: SUIT-2_Non-Adapted_RNA_clone2

growth_protocol: Grown in RPMI medium with high glucose (11 mM) and high glutamine (2 mM).


title: C12-1001000356-TPO-1

description: Single cell from HSC


title: SUIT-2_Non-Adapted_RNA_clone3


title: Tumor_89

type: RNA

city: Bellinzona

first: Luciano

last: Cascione

state: Ticino

address: Via Chiesa 5

department: Lymphoma & Genomics Research Program

country: Switzerland

institute: IOR

hyb_protocol: RNA was hybridized to capture probes and detection probes using the NanoString nCounter system according to the manufacturer's protocol. Detection probes were provided by the manufacturer and were labeled with a proprietary fluorescent barcode system.

scan_protocol: Scanning was conducted using the NanoString confocal microscope scanner/Digital Analyzer according to manufacturer's instructions.

data_processing: Data were collected as NanoString RCC files and provided as an Excel spreadsheet. Raw values are the number of copies of a feature-specific molecular barcode that is attached to a detection probe and counted by a confocal system. The data were normalized for lane-to-lane variation with a dilution series of six spike-in positive controls using vsn normalization.

source_name: Breast tissue

label_protocol: RNA was not labeled; instead, RNA (33 ng/ul) was pre-processed following the NanoString manufacturer's protocol by the Ohio State Microarray Core Facility

extract_protocol: RNA was isolated from FFPE tissue using Recover ALL kit (Ambion)

value: Breast

tag: status

value: primary triple negative cancer


title: Tumor_94


title: Tumor_96


title: Tumor_95


title: Tumor_90


title: Tumor_9


title: SUIT-2_Non-Adapted_RNA_clone1


title: Tumor_86


title: Tumor_87


title: F8-1001000355-AK113-1

description: Single cell from HSC


title: Tumor_85


title: Tumor_82


title: Tumor_84


title: Tumor_81


title: A3-1001000357-TPO_AB-1

description: Single cell from HSC


title: Tumor_80


title: H1-TSCM-3-Resub

city: Raleigh

first: Balaji

last: Rao

state: NC

institute: North Carolina State University

description:
hTSCs obtained by transitioning hTESCs in TM4 at passage 10
Cells were cultured in a 6-well plate pre-coated with 3 µg/ml of vitronectin and 1 µg/ml of Laminin 521 in TSCM (DMEM/F12 supplemented with 0.1 mM 2-mercaptoethanol, 0.2% FBS, 0.5% Penicillin-Streptomycin, 0.3% BSA, 1% ITS-X supplement, 1.5 µg/ml L-ascorbic acid, 50 ng/ml EGF, 2 µM CHIR99021, 0.5 µM A83-01, 1 µM SB431542, 0.8 mM VPA and 5 µM Y27632). hTSCs were cultured (TM4 and TSCM) in 2 ml of culture medium at 37C in 5% CO2.  Culture medium was replaced every 2 days. When hTSCs reached 70-90% confluence, they were dissociated with TrypLE at 37°C for 5-10 minutes and passaged to a new 6-well plate pre-coated with 3 µg/ml of vitronectin and 1 µg/ml of Laminin 521 at a 1:4-1:6 split ratio. Cells were routinely passaged approximately every 4-6 days.

data_processing:
The sequencing libraries were clustered on 4 lanes of a flowcell. After clustering, the flowcell was loaded on the Illumina HiSeq 4000 instrument according to manufacturer’s instructions.  The samples were sequenced using a 2x150bp Paired End (PE) configuration. Image analysis and base calling were conducted by the HiSeq Control Software (HCS). Raw sequence data (.bcl files) generated from Illumina HiSeq was converted into fastq files and de-multiplexed using Illumina's bcl2fastq 2.17 software. One mismatch was allowed for index sequence identification.
After investigating the quality of the raw data, sequence reads were trimmed to remove possible adapter sequences and nucleotides with poor quality using Trimmomatic v.0.36. The trimmed reads were mapped to the Homo sapiens reference genome available on ENSEMBL using the STAR aligner v.2.5.2b. The STAR aligner is a splice aligner that detects splice junctions and incorporates them to help align the entire read sequences. BAM files were generated as a result of this step. Unique gene hit counts were calculated by using feature Counts from the Subread package v.1.5.2. Only unique reads that fell within exon regions were counted.
After extraction of gene hit counts, the gene hit counts table was used for downstream differential expression analysis. Genome-wide RNA sequencing count data were processed and statistically assessed using the DESeq2 package (v1.22.2) in R Software (3.6.0) (The R Foundation, 2019). Count data were first filtered to include transcripts expressed above background, requiring the median across samples to be greater than the overall median signal intensity, as implemented in DESeq2. Count data were then normalized by median signal intensity using algorithms enabled within DESeq2, resulting in variance stabilized expression values (Love et al., 2014).
Genome_build: Homo sapiens reference genome available on ENSEMBL
Supplementary_files_format_and_content: Processed data for all samples is provided in CSV files

source_name: H1 hTSCs

extract_protocol:
Total RNA was extracted with TrizolTM reagent using manufacturer’s protocol.  RNA was purified using GeneJET RNA Purification Kit using manufacturer’s protocol. Isolated RNA samples were then used to evaluate genome-wide mRNA expression profiles using next generation RNA-sequencing, conducted at GENEWIZ, LLC. (South Plainfield, NJ, USA). RNA samples received at GENEWIZ were quantified using Qubit 2.0 Fluorometer (Life Technologies, Carlsbad, CA, USA) and RNA integrity was checked using Agilent TapeStation 4200 (Agilent Technologies, Palo Alto, CA, USA).
RNA sequencing libraries were prepared using the NEBNext Ultra RNA Library Prep Kit for Illumina following manufacturer’s instructions (NEB, Ipswich, MA, USA). Briefly, mRNAs were first enriched with Oligo(dT) beads.  Enriched mRNAs were fragmented for 15 minutes at 94 °C. First strand and second strand cDNAs were subsequently synthesized. cDNA fragments were end repaired and adenylated at 3’ends, and universal adapters were ligated to cDNA fragments, followed by index addition and library enrichment by limited-cycle PCR. The sequencing libraries were validated on the Agilent TapeStation (Agilent Technologies, Palo Alto, CA, USA), and quantified by using Qubit 2.0 Fluorometer (Invitrogen, Carlsbad, CA) as well as by quantitative PCR (KAPA Biosystems, Wilmington, MA, USA).

tag: culture medium

value: TSCM

tag: passage

value: passage 14 in TSCM


title: H1-TSCM-4-Resub

description:
hTSCs obtained by passaging day 3 differentiated hESCs in TSCM
Cells were cultured in a 6-well plate pre-coated with 3 µg/ml of vitronectin and 1 µg/ml of Laminin 521 in TSCM (DMEM/F12 supplemented with 0.1 mM 2-mercaptoethanol, 0.2% FBS, 0.5% Penicillin-Streptomycin, 0.3% BSA, 1% ITS-X supplement, 1.5 µg/ml L-ascorbic acid, 50 ng/ml EGF, 2 µM CHIR99021, 0.5 µM A83-01, 1 µM SB431542, 0.8 mM VPA and 5 µM Y27632). hTSCs were cultured (TM4 and TSCM) in 2 ml of culture medium at 37C in 5% CO2.  Culture medium was replaced every 2 days. When hTSCs reached 70-90% confluence, they were dissociated with TrypLE at 37°C for 5-10 minutes and passaged to a new 6-well plate pre-coated with 3 µg/ml of vitronectin and 1 µg/ml of Laminin 521 at a 1:4-1:6 split ratio. Cells were routinely passaged approximately every 4-6 days.

value: passage 6 in TSCM


title: Tumor_78


title: G8-1001000355-AK113-1

description: Single cell from HSC


title: Tumor_77


title: Tumor_76


title: H1-TSCM-2-Resub

value: passage 13 in TSCM


title: Tumor_88


title: D12-1001000356-TPO-1

description: Single cell from HSC


title: Tumor_75


title: D8-1001000355-AK113-1

description: Single cell from HSC


title: H1-TSCM-1

value: passage 7 in TSCM


title: Tumor_74


title: H9-TSCM-4

description:
hTSCs obtained by transitioning hTESCs in TM4 at passage 5
Cells were cultured in a 6-well plate pre-coated with 3 µg/ml of vitronectin and 1 µg/ml of Laminin 521 in TSCM (DMEM/F12 supplemented with 0.1 mM 2-mercaptoethanol, 0.2% FBS, 0.5% Penicillin-Streptomycin, 0.3% BSA, 1% ITS-X supplement, 1.5 µg/ml L-ascorbic acid, 50 ng/ml EGF, 2 µM CHIR99021, 0.5 µM A83-01, 1 µM SB431542, 0.8 mM VPA and 5 µM Y27632). hTSCs were cultured (TM4 and TSCM) in 2 ml of culture medium at 37C in 5% CO2.  Culture medium was replaced every 2 days. When hTSCs reached 70-90% confluence, they were dissociated with TrypLE at 37°C for 5-10 minutes and passaged to a new 6-well plate pre-coated with 3 µg/ml of vitronectin and 1 µg/ml of Laminin 521 at a 1:4-1:6 split ratio. Cells were routinely passaged approximately every 4-6 days.

source_name: H9 hTSCs

value: passage 12 in TSCM


title: H9-TSCM-3

description:
hTSCs obtained by transitioning hTESCs in TM4 at passage 8
Cells were cultured in a 6-well plate pre-coated with 3 µg/ml of vitronectin and 1 µg/ml of Laminin 521 in TSCM (DMEM/F12 supplemented with 0.1 mM 2-mercaptoethanol, 0.2% FBS, 0.5% Penicillin-Streptomycin, 0.3% BSA, 1% ITS-X supplement, 1.5 µg/ml L-ascorbic acid, 50 ng/ml EGF, 2 µM CHIR99021, 0.5 µM A83-01, 1 µM SB431542, 0.8 mM VPA and 5 µM Y27632). hTSCs were cultured (TM4 and TSCM) in 2 ml of culture medium at 37C in 5% CO2.  Culture medium was replaced every 2 days. When hTSCs reached 70-90% confluence, they were dissociated with TrypLE at 37°C for 5-10 minutes and passaged to a new 6-well plate pre-coated with 3 µg/ml of vitronectin and 1 µg/ml of Laminin 521 at a 1:4-1:6 split ratio. Cells were routinely passaged approximately every 4-6 days.

value: passage 10 in TSCM


title: H9-TSCM-2

value: passage 5 in TSCM


title: E8-1001000355-AK113-1

description: Single cell from HSC


title: Tumor_7


title: Tumor_71


title: Tumor_68


title: Tumor_58


title: C8-1001000355-AK113-1

description: Single cell from HSC


title: F1-1001000356-TPO-1

description: Single cell from HSC

value: TPO


title: Tumor_55


title: H9-TSCM-1

description:
hTSCs obtained by transitioning hTESCs in TM4 at passage 16
Cells were cultured in a 6-well plate pre-coated with 3 µg/ml of vitronectin and 1 µg/ml of Laminin 521 in TSCM (DMEM/F12 supplemented with 0.1 mM 2-mercaptoethanol, 0.2% FBS, 0.5% Penicillin-Streptomycin, 0.3% BSA, 1% ITS-X supplement, 1.5 µg/ml L-ascorbic acid, 50 ng/ml EGF, 2 µM CHIR99021, 0.5 µM A83-01, 1 µM SB431542, 0.8 mM VPA and 5 µM Y27632). hTSCs were cultured (TM4 and TSCM) in 2 ml of culture medium at 37C in 5% CO2.  Culture medium was replaced every 2 days. When hTSCs reached 70-90% confluence, they were dissociated with TrypLE at 37°C for 5-10 minutes and passaged to a new 6-well plate pre-coated with 3 µg/ml of vitronectin and 1 µg/ml of Laminin 521 at a 1:4-1:6 split ratio. Cells were routinely passaged approximately every 4-6 days.

value: passage 8 in TSCM


title: Tumor_52


title: H1-C3ACF-4-Resub

description: For propagation of hTESCs, cells were cultured in a 6-well plate pre-coated with 3 µg/ml of vitronectin and 1 µg/ml of Laminin 521 in 2 ml of TM4 medium [TeSR-E6 medium supplemented with CYM5541 (2 µM), A 83-01 (0.5 µM), FGF10 (25ng/ml) and CHIR99021 (2 µM)].  Culture medium was replaced every 2 days. When hTESCs  reached 70-90% confluence, they were dissociated with TrypLE at 37°C for 5-10 minutes and passaged to a new 6-well plate pre-coated with 3 µg/ml of vitronectin and 1 µg/ml of Laminin 521 at a 1:3-1:4 split ratio.  hTESCs grown in TM4 medium were supplemented with Y-27632 upon passage to aid in single cell attachment.  Cells were routinely passaged approximately every 4-6 days.

source_name: H1 hTESCs

value: passage 5 in TM4


title: G4-1001000356-TPO-1

description: Single cell from HSC

value: HSC


title: A8-1001000355-AK113-1

description: Single cell from HSC


title: Tumor_50


title: Tumor_51


title: Tumor_5


title: B8-1001000355-AK113-1

description: Single cell from HSC


title: Tumor_46


title: Tumor_48


title: H2-1001000356-TPO-1

description: Single cell from HSC


title: Tumor_45


title: Tumor_53


title: Tumor_43


title: H1-C3ACF-2-Resub

value: passage 6 in TM4


title: H1-C3ACF-1

value: passage 2 in TM4


title: E11-1001000356-TPO-1

description: Single cell from HSC


title: H9-C3ACF-4

source_name: H9 hTESCs

value: passage 11 in TM4


title: Tumor_42

value: Breast


title: G1-1001000356-TPO-1

description: Single cell from HSC


title: H9-C3ACF-3


title: C10-1001000356-TPO-1

description: Single cell from HSC


title: Tumor_49

value: primary triple negative cancer


title: H1-C3ACF-3-Resub


title: Tumor_37


title: Tumor_47


title: Tumor_34


title: Tumor_36


title: H9-C3ACF-1


title: B9-1001000356-TPO-1

description: Single cell from HSC


title: H1-C3BSd3-4

description: H1 and H9 hESCs were differentiated by treatment with CYM5541 (2 µM), SB431542 (25 µM), BMP4 (20 ng/ml) in TeSR-E7 medium for 3 days

source_name: H1 day 3 differentiation to trophoblast

value: Differentiation medium

value: passage 22 (original frozen stock)+44 used for differentiation


title: Tumor_3


title: Tumor_33


title: Tumor_26


title: Tumor_28


title: Tumor_27


title: Tumor_24


title: H1-C3BSd3-3

value: passage 22 (original frozen stock)+43 used for differentiation


title: Tumor_38


title: H8-1001000355-AK113-1

description: Single cell from HSC


title: H1-C3BSd3-2


title: Tumor_23


title: A10-1001000355-AK113-1

description: Single cell from HSC


title: Tumor_22


title: H9-C3ACF-2

value: passage 16 in TM4


title: H1-C3BSd3-1

value: passage 22 (original frozen stock)+42 used for differentiation


title: D10-1001000356-TPO-1

description: Single cell from HSC


title: B10-1001000355-AK113-1

description: Single cell from HSC


title: Tumor_168


title: Tumor_169


title: Tumor_17


title: Tumor_165


title: H9-C3BSd3-4

source_name: H9 day 3 differentiation to trophoblast

value: passage 29 (original frozen stock)+40 used for differentiation


title: H5-1001000357-TPO_AB-1

description: Single cell from HSC


title: Tumor_164


title: Tumor_163


title: H9-C3BSd3-3


title: A9-1001000356-TPO-1

description: Single cell from HSC


title: Tumor_16


title: C10-1001000355-AK113-1

description: Single cell from HSC


title: Tumor_156


title: Tumor_21


title: Tumor_158


title: H9-C3BSd3-1-Resub

value: passage 29 (original frozen stock)+45 used for differentiation


title: Tumor_154


title: E3-1001000357-TPO_AB-1

description: Single cell from HSC


title: Tumor_153


title: CT29-TSCM-LAA-4

description: Primary derived hTSCs - CT30 (female) and CT29 (male) were a kind gift from Dr. Hiroaki Okae (Cell Stem Cell. 2018 Jan 4;22(1):50-63). Cells were cultured in a 6-well plate pre-coated with 3 µg/ml of vitronectin and 1 µg/ml of Laminin 521 in TSCM (DMEM/F12 supplemented with 0.1 mM 2-mercaptoethanol, 0.2% FBS, 0.5% Penicillin-Streptomycin, 0.3% BSA, 1% ITS-X supplement, 1.5 µg/ml L-ascorbic acid, 50 ng/ml EGF, 2 µM CHIR99021, 0.5 µM A83-01, 1 µM SB431542, 0.8 mM VPA and 5 µM Y27632). hTSCs were cultured in 2 ml of culture medium at 37C in 5% CO2.  Culture medium was replaced every 2 days. When hTESCs or hTSCs reached 70-90% confluence, they were dissociated with TrypLE at 37°C for 5-10 minutes and passaged to a new 6-well plate pre-coated with 3 µg/ml of vitronectin and 1 µg/ml of Laminin 521 at a 1:4-1:6 split ratio. Cells were routinely passaged approximately every 4-6 days.

source_name: CT29 primary hTSCs

value: TSCM

value: passage 12 (original frozen stock)+7


title: F4-1001000357-TPO_AB-1

description: Single cell from HSC

source_name: CD34+ CD38- CD90+ CD45RA- HSC


title: Tumor_152


title: Tumor_146


title: Tumor_151


title: Tumor_15


title: CT29-TSCM-LAA-3

value: passage 12 (original frozen stock)+6


title: D3-1001000357-TPO_AB-1

description: Single cell from HSC


title: Tumor_145


title: D10-1001000355-AK113-1

description: Single cell from HSC


title: CT29-TSCM-LAA-2

value: passage 12 (original frozen stock)+8


title: G4-1001000357-TPO_AB-1

description: Single cell from HSC

value: HSC


title: CT29-TSCM-LAA-1

value: passage 12 (original frozen stock)+17


title: H9-C3BSd3-2-Resub


title: B3-1001000357-TPO_AB-1

description: Single cell from HSC


title: CT30-TSCM-LAA-4

source_name: CT30 primary hTSCs

value: passage 14 (original frozen stock)+6


title: Tumor_143


title: Tumor_144


title: Tumor_142


title: Tumor_141


title: CT30-TSCM-LAA-3

value: passage 14 (original frozen stock)+8


title: Tumor_14

value: Breast


title: A2-1001000357-TPO_AB-1

description: Single cell from HSC


title: Tumor_139

value: primary triple negative cancer


title: CT30-TSCM-LAA-2

value: passage 14 (original frozen stock)+7


title: F7-1001000355-AK113-1

description: Single cell from HSC


title: Tumor_137


title: Tumor_132


title: CT30-TSCM-LAA-1

value: passage 14 (original frozen stock)+14


title: Tumor_130


title: Tumor_131


title: H1-hESC-4

description: H1 and H9 hESCs were cultured on plates coated with vitronectin (5 µg/ml) at room temperature for at least one hour.  Cells were cultured in 2 ml of TeSR-E8 medium at 37°C in 5% CO2 in 6-well plates and culture medium was replaced every day.  When cells reached confluency, they were passaged using ReLeSR according to the manufacturer’s protocol, at a 1:10 split ratio.

source_name: undifferentiated H1 hESCs

value: passage 22 (original frozen stock)+44


title: G7-1001000355-AK113-1

description: Single cell from HSC


title: E10-1001000355-AK113-1

description: Single cell from HSC


title: H1-hESC-3

value: passage 22 (original frozen stock)+43


title: Tumor_13


title: E7-1001000355-AK113-1

description: Single cell from HSC


title: Tumor_127


title: C3-1001000357-TPO_AB-1

description: Single cell from HSC


title: Tumor_122


title: F10-1001000355-AK113-1

description: Single cell from HSC


title: Tumor_126


title: H1-hESC-1


title: Tumor_12


title: Tumor_121


title: D7-1001000355-AK113-1

description: Single cell from HSC


title: Tumor_119


title: Tumor_116


title: Tumor_117


title: H9-hESC-4

source_name: undifferentiated H9 hESCs

value: passage 29 (original frozen stock)+40


title: C7-1001000355-AK113-1

description: Single cell from HSC


title: Tumor_133


title: H9-hESC-3

value: passage 29 (original frozen stock)+39


title: B7-1001000355-AK113-1

description: Single cell from HSC


title: H9-hESC-2

value: passage 29 (original frozen stock)+37


title: Tumor_114


title: H1-1001000356-TPO-1

description: Single cell from HSC

value: TPO


title: Tumor_113


title: H1-hESC-2

value: passage 22 (original frozen stock)+42


title: Tumor_107


title: Tumor_109


title: G10-1001000355-AK113-1

description: Single cell from HSC


title: Tumor_106


title: Tumor_105


title: A7-1001000355-AK113-1

description: Single cell from HSC


title: A5-1001000357-TPO_AB-1

description: Single cell from HSC


title: EOfAD-like/+_F_40

city: Adelaide

first: Karissa

last: Barthelson

state: South Australia

address: North Terrace Campus

country: Australia

institute: The University of Adelaide

description:
The _I1.fastq.gz files contain the UMIs
16_KB_C12_HTVLLDRXX_CTCGAACA-TTCGTTGG_merged

data_processing:
UMIs were added to headers of each read using fastp (v0.20.1)
Reads were aligned to GRCz11 using STAR v2.5.3 with default parameters.
PCR duplicates were deduplicated using the dedup function of umi_tools (version 1.0.1)
Aligned, deduplicated data was summarised at the gene-level with featureCounts from the Subread package v1.5.2
Genome_build: GRCz11
Supplementary_files_format_and_content: Estimated raw counts in tab delimited file format.

organism: Danio rerio

source_name: whole brain

growth_protocol: An EOfAD-like/+ fish was mated with a fHS-like/+ fish. The progeny of a single spawning event were raised together in a single tank until 6 months of age, at which time their brains were removed, their sex was confirmed by dissection, and their genotype was determined by allele-specific PCRs.

extract_protocol:
Total RNA was extracted from individual entire brains using the mirVana miRNA Isolation Kit following the manufacturer’s protocol. The resulting RNA was DNaseI treated using the DNA-free kit by Life Technologies to remove any contaminating genomic DNA.
Libraries were prepared using the Nugen Universal Plus library kit including unique molecular identifiers.

value: whole brain

tag: psen1 genotype

value: EOfAD-like/+

tag: gender

value: Female

tag: age

value: 6 months old


title: WT_M_37

description:
The _I1.fastq.gz files contain the UMIs
14_KB_C10_HTVLLDRXX_CCAACACT-AGTTCGTC_merged

value: WT

value: Male


title: fAI-like/+_F_45

description:
The _I1.fastq.gz files contain the UMIs
15_KB_C11_HTVLLDRXX_TCTAGGAG-CGTTGCAA_merged

value: fAI-like/+


title: Normal_9

value: Breast

value: normal


title: Tumor_115

value: primary triple negative cancer


title: Normal_7


title: Normal_8


title: F12-1001000356-TPO-1

description: Single cell from HSC

value: HSC


title: Normal_6


title: Tumor_110


title: B8-1001000356-TPO-1

description: Single cell from HSC


title: H9-hESC-1


title: E10-1001000356-TPO-1

description: Single cell from HSC


title: Normal_58


title: WT_F_36

description:
The _I1.fastq.gz files contain the UMIs
23_KB_C7_HTVLLDRXX_TACATCGG-TGATCGGA_merged


title: Normal_57


title: B6-1001000357-TPO_AB-1

description: Single cell from HSC


title: EOfAD-like/+_F_30

description:
The _I1.fastq.gz files contain the UMIs
22_KB_C6_HTVLLDRXX_CGACCTAA-CAGGTTAG_merged


title: Normal_56


title: Tumor_100


title: fAI-like/+_M_49

description:
The _I1.fastq.gz files contain the UMIs
21_KB_C5_HTVLLDRXX_ACGAGAAC-CGAACTGT_merged


title: Normal_54


title: Normal_52


title: WT_M_35

description:
The _I1.fastq.gz files contain the UMIs
20_KB_C4_HTVLLDRXX_GTACACCT-TTGGTCTC_merged


title: fAI-like/+_M_44

description:
The _I1.fastq.gz files contain the UMIs
24_KB_C8_HTVLLDRXX_ATCGTCTC-GTCCTTCT_merged


title: Normal_51


title: Normal_50


title: Normal_59


title: EOfAD-like/+_M_29

description:
The _I1.fastq.gz files contain the UMIs
19_KB_C3_HTVLLDRXX_AACTTGCC-GAAGTTGG_merged


title: C6-1001000357-TPO_AB-1

description: Single cell from HSC


title: A8-1001000356-TPO-1

description: Single cell from HSC


title: Normal_5


title: Normal_49


title: Normal_48


title: Normal_47


title: fAI-like/+_F_47

description:
The _I1.fastq.gz files contain the UMIs
18_KB_C2_HTVLLDRXX_CGTCCATT-AGGAGGAA_merged


title: Normal_46


title: Normal_55


title: H7-1001000355-AK113-1

description: Single cell from HSC


title: Normal_45


title: WT_M_34

description:
The _I1.fastq.gz files contain the UMIs
17_KB_C1_HTVLLDRXX_ACCATCCT-GTTCATGG_merged


title: D6-1001000357-TPO_AB-1

description: Single cell from HSC


title: Normal_53


title: EOfAD-like/+_F_27

description:
The _I1.fastq.gz files contain the UMIs
7_KB_B12_HTVLLDRXX_CTTCCTTC-ACCTGGAA_merged


title: E7-1001000357-TPO_AB-1

description: Single cell from HSC


title: fAI-like/+_M_26

description:
The _I1.fastq.gz files contain the UMIs
6_KB_B11_HTVLLDRXX_ACTCCTAC-AGTTACGG_merged


title: Normal_43


title: C9-1001000356-TPO-1

description: Single cell from HSC


title: Normal_42


title: Normal_44


title: Normal_41


title: WT_M_54

description:
The _I1.fastq.gz files contain the UMIs
13_KB_B9_HTVLLDRXX_GACTACGA-GTCGGTAA_merged


title: Normal_40


title: fAI-like/+_F_22

description:
The _I1.fastq.gz files contain the UMIs
12_KB_B8_HTVLLDRXX_TCTTCGAC-GAGCAGTA_merged


title: Normal_4


title: WT_M_55

description:
The _I1.fastq.gz files contain the UMIs
11_KB_B7_HTVLLDRXX_CTCCTAGT-AGATGAGG_merged


title: F7-1001000357-TPO_AB-1

description: Single cell from HSC


title: Normal_37


title: Normal_38


title: Normal_39


title: EOfAD-like/+_M_50

description:
The _I1.fastq.gz files contain the UMIs
10_KB_B6_HTVLLDRXX_GCACACAA-GATTGCTC_merged


title: Normal_36


title: G3-1001000357-TPO_AB-1

description: Single cell from HSC


title: E2-1001000357-TPO_AB-1

description: Single cell from HSC


title: Normal_35


title: Normal_34


title: Normal_33


title: F3-1001000357-TPO_AB-1

description: Single cell from HSC


title: fAI-like/+_M_21

description:
The _I1.fastq.gz files contain the UMIs
9_KB_B5_HTVLLDRXX_ATGACAGG-TGGCATGT_merged


title: H4-1001000357-TPO_AB-1

description: Single cell from HSC


title: EOfAD-like/+_F_46

description:
The _I1.fastq.gz files contain the UMIs
8_KB_B3_HTVLLDRXX_ACAACAGC-TTGTCGGT_merged


title: Normal_32


title: G7-1001000357-TPO_AB-1

description: Single cell from HSC


title: Normal_31


title: fAI-like/+_F_12

description:
The _I1.fastq.gz files contain the UMIs
2_KB_A11_HTVLLDRXX_GTCGAGAA-GCTGTAAG_merged


title: A1-1001000357-TPO_AB-1

description: Single cell from HSC


title: Normal_30


title: WT_F_25

description:
The _I1.fastq.gz files contain the UMIs
1_KB_A10_HTVLLDRXX_AACTCGGA-GTCTTGCA_merged


title: Normal_29


title: C2-1001000357-TPO_AB-1

description: Single cell from HSC


title: WT_F_19

description:
The _I1.fastq.gz files contain the UMIs
5_KB_A7_HTVLLDRXX_CGTCTAAC-ACTCGTTG_merged


title: Normal_28


title: D2-1001000357-TPO_AB-1

description: Single cell from HSC


title: EOfAD-like/+_M_9

description:
The _I1.fastq.gz files contain the UMIs
4_KB_A6_HTVLLDRXX_AATCCAGC-TAGGATGC_merged


title: B2-1001000357-TPO_AB-1

description: Single cell from HSC


title: G6-1001000355-AK113-1

description: Single cell from HSC


title: F6-1001000355-AK113-1

description: Single cell from HSC


title: WT_F_4

description:
The _I1.fastq.gz files contain the UMIs
3_KB_A1_HTVLLDRXX_CGCTACAT-CGTAGGTT_merged


title: Normal_26


title: Normal_25


title: Normal_27


title: Normal_24


title: Normal_23


title: Normal_3


title: Normal_20


title: Normal_22


title: E6-1001000355-AK113-1

description: Single cell from HSC


title: B6-1001000355-AK113-1

description: Single cell from HSC


title: C6-1001000355-AK113-1

description: Single cell from HSC


title: Normal_19


title: Normal_17


title: Normal_2


title: Normal_16


title: Normal_18


title: D6-1001000355-AK113-1

description: Single cell from HSC


title: Normal_21


title: A6-1001000355-AK113-1

description: Single cell from HSC


title: Normal_14


title: F11-1001000356-TPO-1

description: Single cell from HSC


title: Normal_12


title: Normal_11


title: Normal_1


title: Mets_9

source_name: Lymph node

value: Lymph Node

value: Metastatic


title: Normal_10


title: E9-1001000356-TPO-1

description: Single cell from HSC


title: G12-1001000356-TPO-1

description: Single cell from HSC


title: Mets_8


title: Mets_7


title: Normal_15


title: articular cartilage-derived cells_3D with atelocollagen_2

city: Suita Osaka

first: Takashi

last: Kanamoto

address: 2-2 Yamadaoka

institute: Osaka University

hyb_protocol: 0.6 μg of Cy3-labelled cRNA was fragmented at 60ｰC for 30 minutes in a reaction volume of 25 μμl containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturer’s instructions. On completion of the fragmentation reaction, 25 μμl of 2xAgilent hybridization buffer was added to the fragmentation mixture and hybridized to SurePrint G3 Human GE 8x60K Microarray Ver3.0 (Agilent Technologies) for 17 hours at 65ｰC in a rotating Agilent hybridization oven.After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent Technologies) and 1 minute with 37ｰC GE Wash buffer 2 (Agilent Technologies).

scan_protocol: Slides were scanned immediately after washing on the Agilent SureScan Microarray Scanner (G2600D) using one color scan setting for 8x60k array slides (Scan Area 61x21.6 mm, Scan resolution 3um, Dye channel is set to Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software(Agilent Technologies) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities.Processed signal intensities were normalized by the global scaling method. A trimmed mean probe intensity was determined by removing 2% of the lower and the higher end of the probe intensities in order to calculate the scaling factor. Normalized signalintensities were then calculated from the target intensity on each array using the scaling factor, so that the trimmed mean target intensity of each array was arbitrarily set to 2500.

source_name: articular cartilage-derived cells_3D culture with atelocollagen

label_protocol: Cyanine3 (Cy3) labeled cRNA was prepared from 0.1 μμg Total RNA using the Low Input Quick Amp Labeling Kit(Agilent Technologies) according to the manufacturer's instructions, followed by RNeasy column purification (QIAGEN).Dye incorporation and cRNA yield were checked with the NanoDrop ND-2000 Spectrophotometer.

extract_protocol: Total RNA was extracted using Trizol (Invitgrogen) and PureLink RNA Purification kit (Thermo Fisher Scientific), and reverse transcribed into cDNA using High-Capacity RNA-to-cDNA kit (Thermo Fisher Scientific).The RNA quantity and quality were assayed by measuring the absorbance with NanoDrop-2000 spectrophotometer and electrophoresis.RNA was quantified using a NanoDrop-2000 spectrophotometer and quality was monitored with the Agilent TapeStation (Agilent Technologies, Santa Clara, CA).

treatment_protocol: Knee articular cartilage-derived cells from osteoarthritis patients were cultured with growth medium (DMEM supplemented with 10% heat-inactivated fetal bovine serum). For 3D cell culture, Cells were seeded on atelocollagen sponges using two methods (with or without atelocollagen). For 3D cell culture with atelocollagen, cells were suspended in a growth medium and then mixed with an equal volume of 1% atelocollagen gel to produce a cell suspension in 0.5% collagen solution. The solution was carefully dripped onto the sponge and allowed to soak into. For 3D cell culture without atelocollagen, cells suspended in a growth medium were seeded in the sponge by the same procedure.

value: female

value: articular cartilage

value: articular cartilage-derived cells

tag: growth condition

value: Cells on day 4 of 3D culture with atelocollagen


title: articular cartilage-derived cells_3D with atelocollagen_3


title: articular cartilage-derived cells_3D with atelocollagen_1


title: articular cartilage-derived cells_3D without atelocollagen_1

source_name: articular cartilage-derived cells_3D culture without atelocollagen

value: Cells on day 4 of 3D culture without atelocollagen


title: articular cartilage-derived cells_3D without atelocollagen_2


title: articular cartilage-derived cells_3D without atelocollagen_3


title: C8-1001000356-TPO-1

description: Single cell from HSC

value: TPO


title: articular cartilage-derived cells_2D_3

source_name: articular cartilage-derived cells_2D culture

value: Cells in the growth phase of flat culture


title: D8-1001000356-TPO-1

description: Single cell from HSC


title: Mets_54


title: Mets_52


title: Mets_6


title: Normal_13

source_name: Breast tissue


title: Mets_53


title: B7-1001000356-TPO-1

description: Single cell from HSC


title: Mets_5


title: A7-1001000356-TPO-1

description: Single cell from HSC


title: articular cartilage-derived cells_2D_2


title: Mets_51


title: Mets_50


title: H6-1001000355-AK113-1

description: Single cell from HSC


title: Mets_47


title: Mets_46


title: Mets_49


title: Mets_48


title: D9-1001000355-AK113-1

description: Single cell from HSC


title: A4-1001000357-TPO_AB-1

description: Single cell from HSC


title: Mets_45


title: articular cartilage-derived cells_2D_1


title: SW948, siRHOA, rep2

city: Shinjukuku, Tokyo

first: Naoki

last: Ikari

address: 8-1 Kawadacho

department: Department of Surgery

institute: Institute of Gastroenterology, Tokyo Women's Medical University

hyb_protocol: 1.65 ug of Cy3-labelled cRNA (Cy3-CTP incorporation > 6 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 55 ul containing 1x Agilent Fragmentation Buffer and 2x Agilent Blocking Agent according to the manufacturer's instructions. On completion of the fragmentation reaction, 55 ul of 2x GE Hybridization Buffer HI-RPM (Agilent) was added to the fragmentation mixture and hybridized to Agilent SurePrint G3 Human GE Microarray 8x60k Ver3.0 (G4851C) for 17 hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash Buffer 2 (Agilent), then dried immediately.

scan_protocol: Slides were scanned immediately after washing on the Agilent SureScan (G4900DA) using one color scan setting for 8x60k array slides (Scan Area 61x21.6 mm, Scan resolution 3um, Dye channel is set to Green, Green PMT is set to 100% and TIFF file dynamic range is 20bit).

data_processing: The scanned images were analyzed with Feature Extraction Software 11.5.1.1 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities.

source_name: Cancer cell line, SW948

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 100ng RNA using the Low Input Quick Amp Labeling Kit (Agilent) according to the manufacturer's instructions, followed by RNeasy column purification (QIAGEN).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: The cells were cultured in a humidified incubator at 37°C and maintained in 2D growth according to recommended condition, respectively.

extract_protocol: Total RNA was isolated from collected cells using RNeasy Mini kit (Qiagen, Hilden, Germany) according to the manufacturer’s instruction.

treatment_protocol: Knockdown of the RHOA expression using short interference RNA was conducted as previously reported elsewhere (Kakiuchi, M. et al. Recurrent gain-of-function mutations of RHOA in diffuse-type gastric carcinoma. Nat Genet 46, 583-587, doi:10.1038/ng.2984 (2014)). Cells were seeded after RHOA knockdown in 6 Well Clear Flat Bottom Ultra Low Attachment Multiple Well Plates (CORNING).

value: Colon

tag: rhoa status

value: heterozygous RHOA^p.G17E


title: Mets_43


title: Mets_44


title: Mets_42


title: SW948, siRHOA, rep1


title: G9-1001000355-AK113-1

description: Single cell from HSC

tag: cell type


title: Mets_39


title: F9-1001000355-AK113-1

description: Single cell from HSC

tag: treatment


title: SW948, Negative control, rep1


title: Mets_41


title: Mets_40


title: Mets_4


title: A9-1001000355-AK113-1

description: Single cell from HSC

tag: days in culture


title: Mets_38

tag: tissue


title: Mets_37


title: Mets_36


title: SW948, Negative control, rep2


title: C9-1001000355-AK113-1

description: Single cell from HSC

tag: date sequencing


title: Mets_35


title: CCK81, siRHOA, rep2

source_name: Cancer cell line, CCK81

value: trans-compound heterozygous RHOA^p.R5Q and RHOA^p.Y42C


title: CCK81, siRHOA, rep1


title: CCK81, Negative control, rep2


title: Mets_34


title: CCK81, Negative control, rep1


title: B5-1001000357-TPO_AB-1

description: Single cell from HSC


title: AGS, siRHOA, rep2

source_name: Cancer cell line, AGS

value: Stomach

value: heterozygous RHOA^p.E64del


title: Mets_33


title: AGS, siRHOA, rep1


title: H3-1001000357-TPO_AB-1

description: Single cell from HSC


title: AGS, Negative control, rep2


title: Mets_31


title: Mets_30


title: F2-1001000357-TPO_AB-1

description: Single cell from HSC


title: G2-1001000357-TPO_AB-1

description: Single cell from HSC


title: H11-1001000355-AK113-1

description: Single cell from HSC


title: Mets_3


title: Mets_26


title: Mets_28


title: Mets_25


title: Mets_27


title: Mets_29


title: Mets_32


title: D1-1001000357-TPO_AB-1

description: Single cell from HSC


title: E1-1001000357-TPO_AB-1

description: Single cell from HSC


title: Mets_23


title: Mets_21


title: AGS, Negative control, rep1


title: Mets_20


title: Mets_22


title: Day 4 rep 3 IP

city: Chicago

first: Bryan

middle: T

last: Harada

state: IL

address: 929 E 57th St

department: Chemistry

institute: University of Chicago

data_processing:
Library strategy: m6A-seq
HISAT2 (version 2.1.0) was used to align the sequence reads to reference genome and transcriptome (mm10).
The exomePeak R/Bioconductor package (version 3.7) was used to find m6A peaks.
The QNB package (version 1.1.11) was used to identify differentially methylated regions
Differential gene expression was calculated using DESeq2 (version 1.18.1) using the sequencing reads from input samples.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files listing genes significantly differentially expressed between the Day 0 and Day 4 samples
Supplementary_files_format_and_content: tab-delimited text files listing genes significantly differentially methylated between the Day 0 and Day 4 samples
Supplementary_files_format_and_content: tab-delimited text files listing significant m6A peaks in each condition

organism: Mus musculus

source_name: Primary keratinocytes

growth_protocol: Primary mouse keratinocytes were isolated from the epidermis of newborn mice using trypsin, after prior separation of the epidermis from the dermis by an overnight dispase treatment. Keratinocytes were plated on mitomycin C–treated 3T3 fibroblast feeder cells until passage 3. Cells were cultured in E-media supplemented with 15% serum with a final concentration of 0.05 mM Ca2+.

extract_protocol:
Total RNA was isolated from primary mouse keratinocyte with or without calcium-shift induced differentiation. Polyadenylated RNA was further enriched from total RNA using a Dynabeads® mRNA purification kit (Invitrogen). RNA was fragmented using a Bioruptor ultrasonicator (Diagenode) with 30s on/off for 30 cycles.  m6A-IP was performed using the Epimark N6-methyladenosine enrichment kit (New England Biolabs)
Library preparation was performed using the Illumina TruSeq Stranded mRNA Sample Prep Kit according to previously published protocols (Dominissini et al., 2012)

value: differentiated

tag: antibody

value: anti-m6A (NEB E1610S)

tag: time point

value: Day 4


title: HGC27, siRHOA, rep1

source_name: Cancer cell line, HGC27

value: Wild-type


title: Day 4 rep 2 IP


title: HGC27, siRHOA, rep2


title: HGC27, Negative control, rep2


title: C1-1001000357-TPO_AB-1

description: Single cell from HSC

data_processing:
Sequencing reads were trimmed, adapter sequences removed and the reads aligned using STAR with default parameters.
Duplicate reads were removed using picard. Transcript counts were obtained using HT-Seq and hg19 UCSC exon/transcript annotations.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample

extract_protocol:
Single-cells were collected  in lysis buffer in 96-well plates, followed by reverse transcription with template-switch using an LNA-modified template switch oligo to generate cDNA. After 21 cycles of pre-amplification, DNA was purified and analyzed on an automated Fragment Analyzer (Advanced Analytical).
Each cells cDNA fragment profile was individually inspected and only wells with successful amplification products (concentration higher than 0.06 ng/ul) and with no detectable RNA degradation were selected for final library preparation. Tagmentation assays and barcoded sequencing libraries were prepared using Nextera XT kit (FC-131-1024; Illumina) according to the manufacturers instructions. Barcoded libraries were pooled and subjected to 75 bp paired-end sequencing on the Illumina NextSeq instrument.

value: HSC


title: HGC27, Negative control, rep1


title: Mets_2

value: Lymph Node

value: Metastatic


title: Mets_19


title: B1-1001000357-TPO_AB-1

description: Single cell from HSC


title: Day 0 rep 3 IP

value: undifferentiated

value: Day 0


title: Mets_18


title: H11-1001000356-TPO-1

description: Single cell from HSC


title: Day 0 rep 2 IP


title: Mets_24


title: Day 0 rep 1 IP


title: A12-1001000356-TPO-1

description: Single cell from HSC


title: Mets_16


title: E5-1001000355-AK113-1

description: Single cell from HSC


title: Mets_17


title: Mets_15


title: Mets_14


title: Day 4 rep 3 input

data_processing:
HISAT2 (version 2.1.0) was used to align the sequence reads to reference genome and transcriptome (mm10).
The exomePeak R/Bioconductor package (version 3.7) was used to find m6A peaks.
The QNB package (version 1.1.11) was used to identify differentially methylated regions
Differential gene expression was calculated using DESeq2 (version 1.18.1) using the sequencing reads from input samples.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files listing genes significantly differentially expressed between the Day 0 and Day 4 samples
Supplementary_files_format_and_content: tab-delimited text files listing genes significantly differentially methylated between the Day 0 and Day 4 samples
Supplementary_files_format_and_content: tab-delimited text files listing significant m6A peaks in each condition


title: Day 4 rep 1 IP


title: C1-1001000356-TPO-1

description: Single cell from HSC


title: Day 4 rep 2 input


title: Mets_13


title: Mets_11


title: G5-1001000355-AK113-1

description: Single cell from HSC


title: Day 4 rep 1 input


title: D5-1001000355-AK113-1

description: Single cell from HSC


title: Day 0 rep 2 input


title: C5-1001000355-AK113-1

description: Single cell from HSC


title: Day 0 rep 1 input


title: Mets_12


title: A5-1001000355-AK113-1

description: Single cell from HSC


title: G11-1001000356-TPO-1

description: Single cell from HSC


title: B5-1001000355-AK113-1

description: Single cell from HSC


title: Mets_1


title: Klf2KO/Ring1bKD_rep1_RNA-seq

city: Daejeon

first: Lin

last: Seo

address: Basic Science Bld Rm414, 291 Daehak-ro, Yuseong-gu, KAIST

department: Department of Biological Sciences

country: South Korea

institute: KAIST

data_processing:
Reads were aligned to mm9 using TopHat v2.1.1
Genome_build: mm9
Supplementary_files_format_and_content: Bigwig files were generated using deeptools2 bamCoverage

growth_protocol: E14TG2a cells were cultured in 0.1% gelatin coated dishes with KnockOut DMEM (Gibco) with 15% FBS, NEAA, L-glutamine, 2-mercaptoethanol, and 1,000 U/ml LIF (ESGRO, EMD Millipore).

extract_protocol:
RNA samples were lyesed with RNA-spin™ Total RNA Extraction Kit (iNtRON).
Libraries were prepared according to Illumina's instructions.

treatment_protocol: From HEK 293T cells, shRing1b lentiviruses were harvested. Lentiviral particles (MOI 10) with hexadimethrine bromide were infected in E14TG2a and selected with 2 ug/ml puromycin.

tag: strain background

value: Embryonic stem cells (ESCs)

tag: genotype/variation


title: Ring1bKD_rep2_RNA-seq

tag: cell line


title: Klf2KO/Ring1bKD_rep2_RNA-seq


title: Day 0 rep 3 input


title: D1-1001000356-TPO-1

city: Stanford

first: Gerlinde

last: Wernig

institute: Institute for Regenerative Medicine and Stem Cell Research, Stanford University School of Medicine

description: Single cell from HSC

value: TPO


title: Mets_10

tag: status


title: P4_WNT5A/PEG-SOD

city: Oxford

first: Nadia

last: Akawi

address: Headley Way

country: United Kingdom

institute: John Radcliffe Hospital

hyb_protocol: Samples were hybridized using the Affymetrix GeneChip WT PLUS Reagent kit (Affymetrix) according to the manufacturer’s instructions

scan_protocol: Gene expression array was scanned using the Affymetrix GeneTitan instrument.

data_processing: Data processing, normalisation, quality control (QC) and gene level differential expression analysis was performed in the Affymetrix Transcriptome Analysis Console (TAC 4.0) Software

source_name: VSMCs from patient 4, treated with WNT5A/PEG-SOD

label_protocol: Samples were enzymatically fragmented and biotinylated using the Affymetrix GeneChip WT PLUS Reagent kit (Affymetrix).

growth_protocol: Human saphenous vein explants were washed in PBS and the adventitia layer was removed. The vessels were cut longitudinally to expose the endothelial layer, which was removed using a scalpel. The tissue was washed in PBS and digested with 0.25% trypsin for 10 min. The digested tissue  was then diced into 1mm2 sections and seeded in DMEM + 20% FBS. Vascular smooth muscle cells (VSMCs) were then grown in appropriate media.

extract_protocol: RNA was extracted from VSMCs using the MagMAX mirVana total RNA isolation kit (Thermo Fischer Scientific). RNA was reverse-transcribed to cDNA by using SuperScript VILO mastermix (Thermo Fischer Scientific) following the Manufacturer’s instructions

treatment_protocol: VSMCs isolated from five individual patients were seeded in 6 well plate (200000cell/well) in the appropriate culture media 24 h before treatment. Then they were incubated 8 hours with Wnt5a or PEG-SOD or a combination of both.

value: Primary vascular smooth muscle cells (VSMCs)

tag: ID

value: Patient 4


title: E1-1001000356-TPO-1

address: 265 Campus Drive

description: Single cell from HSC

growth_protocol: Human bone marrows were obtained from Stanford Medical Center with informed consent, according to Institutional Review Board (IRB)-approved protocols (Stanford IRB 39881). CD34+ progenitors from each sample were isolated by Ficoll separation and CD34+ progenitors were isolated by a positive selection using an immunomagnetic cell sorting system (AutoMacs; Miltenyi Biotec,Bergisch Gladbach, Germany). 56,000 cells were incubated in IMDM media supplemented with 10% BSA, 1% L-glutamine, 450 µM MTG, 1% ITG, liposomes (composition and concentration???), 1% penicillin/streptomycin, in the presence SCF 20 ng/ml and different diabodies at 100 nM for 12 days, with change medium every other day, and addition of new cytokines 3 times per day. After 12 days, cells were pelleted and resuspended in PBS 2% FCS. Fc block was performed for 20 min and the mononuclear cells were stained with directly conjugated anti-mouse CD34, CD38, CD45RA, CD90 and HSC were isolated as DAPI-CD34+CD38-CD45RA-CD90+ cells on a BD FACS ARIA sorter.


title: P4r_PEG-SOD

source_name: VSMCs from patient 4, treated with PEG-SOD, bilogical replicate

value: PEG-SOD


title: P4_PEG-SOD

source_name: VSMCs from patient 4, treated with PEG-SOD


title: P1_WNT5A/PEG-SOD

source_name: VSMCs from patient 1, treated with WNT5A/PEG-SOD

value: Patient 1


title: P3_WNT5A/PEG-SOD

source_name: VSMCs from patient 3, treated with WNT5A/PEG-SOD

value: Patient 3


title: P4_WNT5A

source_name: VSMCs from patient 4, treated with WNT5A


title: P2_WNT5A/PEG-SOD

source_name: VSMCs from patient 2, treated with WNT5A/PEG-SOD

value: Patient 2


title: P3_PEG-SOD

source_name: VSMCs from patient 3, treated with PEG-SOD


title: P3_WNT5A

source_name: VSMCs from patient 3, treated with WNT5A


title: P2_WNT5A

source_name: VSMCs from patient 2, treated with WNT5A


title: Ring1bKD_rep1_RNA-seq


title: F2-1001000356-TPO-1

description: Single cell from HSC

source_name: CD34+ CD38- CD90+ CD45RA- HSC


title: P5_WNT5A/PEG-SOD

source_name: VSMCs from patient 5, treated with WNT5A/PEG-SOD

value: Patient 5


title: P2_PEG-SOD

source_name: VSMCs from patient 2, treated with PEG-SOD


title: G5-1001000356-TPO-1

description: Single cell from HSC


title: Klf2KO_rep2_RNA-seq

value: untreated


title: WT_rep2_RNA-seq


title: Klf2KO_rep1_RNA-seq


title: A11-1001000355-AK113-1

description: Single cell from HSC


title: P5_WNT5A

source_name: VSMCs from patient 5, treated with WNT5A


title: P1_WNT5A

source_name: VSMCs from patient 1, treated with WNT5A


title: C2C12 at D4, biological rep3

city: Shenzhen

first: Yong Sheng

last: Zhang

address: pengfei road 7

country: China

institute: CAAS AGIS

description: Gene expression data from C2C12 cells at D4

hyb_protocol: For hybridization per probe, denature 1 ml Cot1 DNA (1mg/ml) (Gibco 18440-016) and 250 m l tRNA (as above) at 95° C for 10 min first. For washing: 100 ml of 2X SSC 0.5% SDS RT 20 min. Move each membrane into a new polypuropylen tube and do the last 4 repeated washes as follows: 3 ml each of 2X SSC 0.5% SDS 65° C 30 min(Tanaka et al., 2000).

scan_protocol: RNA quality and quantity was measured by using nanodrop spectrophotometer (ND-2000C, Nanodrop Technologies) .  Scanned images were imported into GenePix Pro 6.0 software (Axon) for grid alignment and data extraction.

data_processing: After normalization, significant differentially expressed miRNAs between two groups were identified through Fold change and P-value(|Fold changed|≥2.0 and p≤0.05). Finally, hierarchical clustering was performed to show distinguishable miRNA expression profiling among samples.

source_name: C2C12 cells at 4 days after differentiation

label_protocol: RNA Integrity was determined by gel electrophoresis. Agilent mouse miRNA microarray was used in detecting profiling of the miRNAs expression. Replicated miRNAs were averaged and miRNAs that intensities ≥30 in all samples were chosen for calculating normalization factor.

growth_protocol: C2C12 were cultured in Dulbecco’s Modified Eagle’s Medium (DMEM, Gibco) supplement with 10% fetal bovine serum and 1% Penicillin-streptomycin (PS, Thermo Scientific) at 37℃ in a 5% CO2 incubator.

extract_protocol: Total RNA was extracted from C2C12 cells at D0 and D4 after differentiation using 2% horse serum and purified with RNeasy minit kit (QIAGEN) according to manufacturer’s instructions.

treatment_protocol: To induce myogenic differentiation, the culture medium of C2C12 cells was replaced with DMEM supplemented with 2% pregnant mare serum (Gibco) and 1% PS at 80% confluence. And the cells were collected at the undifferentiated stages and at 4 days of differentiation.

tag: days after differentiation


title: WT_rep1_RNA-seq


title: B11-1001000355-AK113-1

description: Single cell from HSC


title: C11-1001000355-AK113-1

description: Single cell from HSC


title: C2C12 at D0, biological rep3

description: Gene expression data from C2C12 cells at D0

source_name: C2C12 cells at 0 day after differentiation


title: P4_control

source_name: VSMCs from patient 4, untreated

value: Control


title: C2C12 at D4, biological rep1


title: C2C12 at D4, biological rep2


title: P1_control

source_name: VSMCs from patient 1, untreated


title: P3_control

source_name: VSMCs from patient 3, untreated


title: P5_control

source_name: VSMCs from patient 5, untreated


title: D11-1001000355-AK113-1

description: Single cell from HSC


title: C2C12 at D0, biological rep2


title: Chow_3

city: Rochester

first: Mrunal

middle: Kishor

last: Dehankar

state: MN

address: 200 First St. SW

department: Computational genomics

institute: Mayo Clinic

data_processing:
Base calling was performed with the Illumina bcl2fastq
QC was performed on the FASTQ files using RSeQC software (http://rseqc.sourceforge.net/)
The paired end reads were aligned by TopHat (https://ccb.jhu.edu/software/tophat/index.shtml)
Gene counts were generated using Subread featureCounts (http://subread.sourceforge.net/)
Genome_build: mm10
Supplementary_files_format_and_content: Tab-delimited text file includes Raw counts and FPKM values for each gene per sample

source_name: mouse liver RNA

extract_protocol:
Liver total RNA was extracted using RNeasy-Mini kit (Qiagen) according to manufacturer's instruction.
RNA libraries were prepared using 200 ng of total RNA according to the manufacturer’s instructions for the TruSeq RNA Sample Prep Kit v2 (Illumina).
The concentration and size distribution of the completed libraries was determined using an Agilent Bioanalyzer DNA 1000 chip and Qubit fluorometry.

treatment_protocol: Eight-week-old C57BL/6J mice were fed either chow or a diet rich in fat, fructose, and cholesterol (FFC) for 30 weeks. Liver was harvested for RNA extraction.

tag: strain

value: liver

tag: treatment group

value: Chow

tag: disease state

value: Pair-fed control


title: Chow_2


title: P1_PEG-SOD

source_name: VSMCs from patient 1, treated with PEG-SOD


title: C2C12 at D0, biological rep1


title: Chow_1


title: P2_control

source_name: VSMCs from patient 2, untreated


title: H1-1001000357-TPO_AB-1

description: Single cell from HSC

value: HSC