title: IMM6-T3

first: Jia

state: Texas

address: 2121 W HOLCOMBE BLVD

department: CEDP

institute: Guangzhou Medical University

data_processing:
Illumina Casava1.7 software used for basecalling.
Removed the low quality reads; Bowtie2 was used to map RNAseq to hg19 with default parameters.
RPKM was calculated to measure the genes expression level.
DESeq2 was used to call differential expressed genes.
Genome_build: hg19
Supplementary_files_format_and_content: Tab-delimited text file include the RPKM for each gene in each sample

source_name: hESC

growth_protocol: H9 hESCs were maintained on mouse embryonic fibroblast feeder cells in SR medium: Dulbecco’s modified Eagle’s medium (DMEM): Ham’s F12 (1:1), 20% (v/v) KnockOut Serum Replacement (KSR), 2 mM GlutaMAX, 0.1 mM non-essential amino acids (all from Invitrogen, Carlsbad, CA) and 90 mM  b-mercaptoethanol (Sigma-Aldrich, St. Louis, MO), supplemented with 4 ng/ml FGF2 (hFGF2-IS, Miltenyi Biotec, Bergisch Gladbach, Germany) as described (Umeda et al., 2012). Then ESCs were treated with collagenase I (Worthington, Lakewood, NJ) to generate clumps, which were plated onto a low-adhesion dish (Sarstedt, Nümbrecht, Germany) and cultured for 1 day in a chemically defined medium (CDM): Iscove’s modified Dulbecco’s Medium (IMDM) (Sigma): Ham’s F12 (Invitrogen) (1:1), 0.5% (w/v) bovine serum albumin (Sigma), 1% (v/v) synthetic lipid concentrate (Invitrogen), 100  μg/ml human holo-transferrin (Sigma), 20 μg/ml human insulin (Sigma), 0.17 mM ascorbic acid-2-phosphate (AA2P, Sigma), 2 mM GlutaMAX (Invitrogen), and 0.4 mM monothioglycerol (MTG, Sigma), supplemented with 10 µM SB431542 (Tocris) and 5 µM Y27632 (ROCK inhibitor, Tocris, Ellisville MO) at 37oC under 5% CO2/5% O2. The embryoid bodies (EBs) formed were transferred to a plate coated with 0.1% (w/v)  porcine gelatin (Sigma) on day 1 and cultured in CDM with 10 µM SB431542 and 2 µM CHIR99021 (Tocris) till day 5. Then media was changed to CDM with 10 µM SB431542 only. On the day of harvest (usually day 6), a suspension of single cells was prepared using TrypLE Select (Invitrogen), diluted 2.5-fold with 0.5 mM EDTA in D-PBS (without Ca2+ and Mg2+), immunostained with the AlexaFluor647-conjugated mouse anti-CD271 (BD Biosciences, San Jose, CA) and phycoerythrin (PE)-conjugated mouse anti-CD73 (BioLegend, San Diego, CA) monoclonal antibodies, and the CD271hiCD73- cell population was isolated by FACS as described (Umeda et al., 2015). Alternatively, the CD271hi cell population was isolated by magnetic cell sorting using the MACS cell separation system and CD271 microbead kits (Miltenyi Biotec). The sorted cells were transferred to a plate coated with 10 μg/ml human fibronectin (Sigma) and cultured overnight at 4oC in CDM supplemented with 2 µg/ml heparin (Sigma), 2.5 µg/ml catalase (Sigma), 5-10 ng/ml FGF2 and 5-7.5 µM SB431542 (FSb medium), at 37oC under 5% CO2/5% O2. The cells were passaged every 2-3 days at 3-4 x 104 cells/cm2 using the diluted TrypLE Select as described (Umeda et al., 2015). At the desired density, the ectomesenchymal cells were primed with CDM supplemented with 5 ng/ml FGF2 and 10 ng/ml TGFβ3 (hTGFβ3, R&D Systems, Minneapolis, MN) for 3 days prior to chondrogenesis induction, and harvested with TrypLE Select.

extract_protocol:
Cartilage pellets were collected and submerged in liquid N2, manually cracked into small pieces with a liquid N2 cooled mortar and a pellet pestle, and homogenized in the lysis buffer (RLT, Qiagen, Valencia, CA). The cleared lysates were then subjected to DNA, RNA and proteins isolation using the AllPrep DNA/RNA/Protein mini kit (Qiagen).
RNAseq libraries were prepared for sequencing using standard illumina protocols

treatment_protocol: To induce chondrogenesis from hPSC-derived chondroprogenitors, aliquots of 2-3×105 cells were centrifuged in a 15-ml conical tube (BD) to form pellets, and cultured in a 0.5 ml of serum-free chondrogenic media: DMEM (high glucose), 1 mM sodium pyruvate, 1% (v/v) ITS+ (BD), 100 nM dexamethasone (Sigma), 0.17 mM AA2P, 0.35 mM proline, 2 mM GlutaMAX, and 50 μM MTG, supplemented with 40 ng/ml PDGF. On day 6 of pellet culture, 10 ng/ml TGFβ3 was added, and on day 10, hBMP4 was added at 50 ng/ml (PTB pellet) . When necessary the following were added on day 11 or 12: the activator of adenylyl cyclase, forskolin, 30 μM (Tocris) (PTBFk pellet). The pellet cultures were maintained at 37oC under 7.5% CO2 for up to 40 days. When the cartilage pellet became large enough to fill the bottom of the conical tube (larger than 4 mm in diameter), the pellet was transferred to a well of a 24-well tissue culture-untreated plate (BD), and cultured in 1.0-1.5 ml of chondrogenic medium at 37oC under 7.5% CO2/5% O2.

tag: cartilage pellets

value: PTBFk


title: IMM8-T4

status: Public on Jun 01 2020

type: SRA

city: Houston

last: Li

country: USA

library_source: transcriptomic

molecule: total RNA

organism: Homo sapiens


title: IMM7-C4

value: PTB


title: IMM5-C3


title: IMM4-T2


title: IMM3-C2


title: Sample 1345_Single mESC cell

city: Stanford

first: Alina

last: Isakova

state: CA

address: 318 Campus drive

department: Bioengineering

institute: Stanford University

data_processing:
Sequences from the NovaSeq were de-multiplexed using bcl2fastq version 2.19.0.316. Reads were trimmed from polyA tails using cutadapt v 1.18 with the following parameters: -m 18 -j 4 -a AAAAAAAAAA -a TTTTTTTTTT. Reads were then aligned to the human (GRCh38) or mouse genome (GRCm38) using STAR v2.7.0d 37 with the following parameters --outFilterMismatchNoverLmax 0.05 --outFilterMatchNmin 18 --outFilterMatchNminOverLread 0 --outFilterScoreMinOverLread 0  --outMultimapperOrder Random. Reads mapping to multiple locations were assigned either to a location with the best mapping score or, in the case of equal multimapping score – to the genomic location randomly chosen as “primary”.
Genome_build: GRCm38, GRCh38
Supplementary_files_format_and_content: tab-delimited text files of count tables

organism: Mus musculus

source_name: Single mESC cell

growth_protocol: HEK293T cells were cultured in complete DMEM high glucose medium (Gibco, ThermoFisher 11965092) supplemented with 5% Fetal Bovine Serum (ThermoFisher 16000044), 1mM Sodium Pyruvate (ThermoFisher 11360070) and 100 μg/mL Pencillin/Streptomycin (ThermoFisher 15070063). They were collected 2h after passaging and sorted in either 96-well plates with 3uL lysis buffer or 384-well paltes with 0.3 uL of lysis buffer in each well.    Human primary dermal fibroblasts were obtained from ATCC (ATCC® PCS-201-012™). Cells were cultured and passaged four times in Fibroblast Basal Medium (ATCC® PCS-201-030™) supplemented with 5ng/mL rh FGF β, 7.5mM L-glutamine, 50 ug/mL Ascorbic acid, 5ug/mL rh Insulin, and 1% Fetal Bovine Serum (Fibroblast Growth kit- low serum, ATCC® PCS-201-041™).  MCF7 cells (ATCC® HTB¬22™) were cultured in complete DMEM high glucose medium (Gibco, ThermoFisher 11965092) supplemented with 10% Fetal Bovine Serum (ThermoFisher 16000044), 1mM Sodium Pyruvate (ThermoFisher 11360070) and 100 μg/mL Pencillin/Streptomycin (ThermoFisher 15070063).  mESCs were maintained and differentiated as described previously35,36. Briefly, mESCs were grown in serum-free 2i+LIF medium (complete medium: DMEM/F12 glutaMAX (Gibco, ThermoFisher  10565018) , 1% N2 supplement (Gemini Bio), 2% B27 supplement (Gemini Bio), 0.05% BSA fraction V (ThermoFisher, 15260037), 1% MEM-non-essential amino acids (c  11140050), and 110 μM 2-mercaptoethanol (Pierce); supplemeted with MEK inhibitor PD0325901 (0.8 μM), GSK3β inhibitor CHIR99021 (3.3 μM) and 10ng/mL mouse LIF (Gibco, PMC9484) in tissue culture (TC) dishes pretreated with 7.5 μg/ml polyL-ornithine (Sigma) and 5 μg/ml laminine (BD). To induce spontaneous embryoid body formation cells were washed with PBS, dissociated with StemPro Accutase (Gibco, ThermoFisher cat# A1110501), transferred to serum-rich medium (complete medium: DMEM/F12 glutaMAX (Gibco) , 1% N2 supplement (Gemini Bio), 2% B27 supplement (Gemini Bio), 0.05% BSA fraction V, 1% MEM-non-essential amino acids, and 110 μM 2-mercaptoethanol; supplemented with 10% FBS (ThermoFisher 10439001) and diluted to 10^6 cells/mL. Each 10 uL of cell suspension were plated as a hanging drop in 10 cm2 TC dishes (15-20 drops per dish). 10uL of fresh serum-rich media was added to each drop on day 4 of the culture. Primed mESCs were collected 6h after hanging drop culture. Embryoid bodies were collected and dissociated at days 4, 8 and 12 of culture.

extract_protocol:
Lysis plates were prepared by dispensing 0.3μL lysis buffer (4 U Recombinant RNase Inhibitor (RRI) (Takara Bio, 2313B), 0.12% TritonTM X-100 (Sigma, 93443-100ML), 1μM Smart-seq4 oligo-dT primer (5’-Biotin- /5BiosG/CATAGTCTCGTGGGCTCGGAGATGTGTATAAGAGACAGT30VN-3’;IDT) (see Supplementary Table 3 for a full list of oligos used in the present study) into 384-well hard-shell PCR plates (Bio-Rad HSP3901) using Mantis liquid handler (Formulatrix). 96-well lysis plates were prepared with 3 μl lysis buffer. All plates were sealed with AlumaSeal CS Films (Sigma-Aldrich Z722634), spun down and snap-frozen on dry ice.   Cells were stained with calcein-AM and ethidium homodimer-1 (LIVE/DEAD® Viability/Cytotoxicity Kit, ThermoFisher L3224) and individual live cells were sorted in 384 well lysis plates using SONY sorter (SH800S) with 100um nozzle chip. Plates were spun down and stored at -80 degrees immediately after sorting.
Smart-seq-total

tag: cell line

value: Differentiated mESC

tag: day of differentiation

value: day 0


title: Sample 1346_Single mESC cell


title: Sample 1344_Single mESC cell


title: IMM2-T1


title: Sample 1343_Single mESC cell


title: Sample_13015GP37

city: Philadelphia

first: Gregory

middle: Robert

last: Grant

state: PA

address: 3400 Civic Center Blvd.

department: Genetics

institute: University of Pennsylvania

data_processing:
CASAVA was used to demultiplex pooled samples and convert BCL to FASTQ.
RNA-seq data were aligned to the mouse genome build mm9 by STAR-2.4.1d.
Data were normalized using a resampling strategy, the code is available at https://github.com/itmat/Normalization . We performed gene-level normalization using default parameters for the mm9 genome.
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text file from gene-level normalization contains counts from unique reads that only map to one gene.

source_name: liver

growth_protocol: All mice were housed under 12h:12h LD conditions with free access to food and water unless specified. All procedures were approved by the University of Pennsylvania Institutional Animal Care and Use Committee. Bmal1f/f mice (PMID: 25512522) were obtained from C. Bradfield (University of Wisconsin, Madison, WI, USA). The floxed mice were crossed with an aP2 driven Cre (aP2-Cre) mice (Jackson Laboratories, Bar Harbor, ME) to yield Bmal1f/f-aP2-Cre mice.

extract_protocol:
Liver samples were quickly excised every four hour for 20 hours and snap-frozen in liquid nitrogen. Mouse liver (50 - 100 mg) was homogenized using magnetic beads and a TissueLyzer. Total RNA was isolated using Qiagen RNeasy Kit and the RNA integrity was checked using an Agilent Technologies 2100 Bioanalyzer.
Illumina TruSeq RNA Sample Prep v2 was used for library construction, according to manufacturer's instructions. Briefly, poly-A containing mRNA was isolated using poly-T oligo-attached magnetic beads and fragmented during elution. First strand cDNA was reverse transcribed from cleaved RNA fragments primed with random hexamers. Second strand cDNA was synthesized and isolated using Ampure XP beads. Blunt ends were created using 3' to 5' exonuclease activity and polymerase activity. A single "A" nucleotide was added to the 3' end and adapters were subsequently ligated onto the ends of the ds cDNA. Indices for multiplexing were attached during this ligation step. 13 cycles of PCR selectively amplified cDNA with adapter molecules on both ends. Using the molarity from Bioanalyzer (DNA 1000), libraries were diluted to 10nM. Libraries at 10nM were run on Bioanalyzer again (HighSensitivity DNA) and taking the lowest molarity, two samples with distinct barcodes were pooled. Clusters were generated using cBOT, and sequenced in one flow cell lane.

treatment_protocol: Mice were kept under constant darkness for 36 h and then sacrificed. Four aP2-Cre Bmal1 fx/fx mice and four littermate controls were sacrificed in darkness every 4h for 20h (6 time points)

tag: strain

tag: genotype

value: WT

tag: sample collection time

tag: replicate

tag: tissue

value: Liver

tag: cell type

value: Adipocyte


title: IMM1-C1


title: Sample_13015GP29

value: Bmal1 knockout (KO)


title: RNA-seq_D80MP2

city: Utrecht

first: Aridaman

last: Pandit

address: Heidelberglaan 100

country: Netherlands

institute: University Medical Center Utrecht

description:
rawReadsData.csv
VST_normalized_data.csv

data_processing:
Reads were aligned using STAR aligner using the default parameters to the 65,217 annotated genes obtained from the GrCh38 (v79) built of the human genome.
The read counts per gene were quantified by the Python package HTSeq (2) using annotations from the GrCh38 (v79) built of the human genome
Genome_build: GrCh38 (v79)
Supplementary_files_format_and_content: Raw counts and VST normalized data for each sample

source_name: Day8_moDC_24h stimulation_donor2

growth_protocol: PBMCs were isolated from heparinized venous blood using Ficoll PaqueTM Plus (GE Healthcare) density gradient. Monocytes were purified with anti-CD14 magnetic beads-based positive separation using an autoMACS Pro Separator assisted cell sorting (Miltenyi Biotec), according to the manufacture’s protocol. Monocyte purity was above 95% for all the samples (data not shown). For the differentiation of monocyte-derived dendritic cells (moDCs), monocytes were cultured at a density of 1x10^6 cells/ml in culture medium: RPMI 1640 with GlutaMAX (Life Technologies) supplemented with 10% (v/v) heat-inactivated fetal bovine serum (FBS; Biowest) and 1% (v/v) antibiotics (penicillin and streptomycin) (Life Technologies). In order to generate moDCs, GM-CSF (800 U/ml; R&D) and IL-4 (500 U/ml; R&D) were added. For the experiments where we investigated the effects of CXCL4, we added 10 µg/ml of recombinant human CXCL4 (PeproTech) on day 0 and day 3. Medium and cytokines were refreshed on day 3. Differentiated moDCs were obtained after 6 days from monocytes cultured at 37oC in the presence of 5% CO2. After differentiation, cells were washed, plated at a density of 0.5x10^6 cells/ml and left overnight (O/N) in new culture medium. Cells were stimulated with 25 µg/ml of polyinosinic-polycytidylic acid (polyI:C; InvivoGen) for 4 hours or 24 hours, or kept unstimulated, as shown in the Fig. 1A.

extract_protocol:
Cells were lysed in RLTplus buffer (Qiagen) containing 1% (v/v) beta-mercaptoethanol (Sigma). RNA were extracted using the Allprep Universal Kit (Qiagen) following the manufacturer’s instructions.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: For the experiments where we investigated the effects of CXCL4, we added 10 µg/ml of recombinant human CXCL4 (PeproTech) on day 0 and day 3. Medium and cytokines were refreshed on day 3.  After differentiation, cells were washed, plated at a density of 0.5 million cells/ml and left overnight (O/N) in new culture medium. Cells were stimulated with 25 µg/ml of polyinosinic-polycytidylic acid (polyI:C; InvivoGen) for 4 hours or 24 hours, or kept unstimulated.

value: monocyte-derived dendritic cells

tag: donor number

tag: age

tag: Sex

value: F

tag: differentiation day


title: RNA-seq_D80MP4

source_name: Day8_moDC_24h stimulation_donor4

value: M


title: RNA-seq_D80MP1

source_name: Day8_moDC_24h stimulation_donor1


title: Sample_13015GP33


title: RNA-seq_D80MP5

source_name: Day8_moDC_24h stimulation_donor5


title: Sample_13015GP34


title: RNA-seq_D80MP3

source_name: Day8_moDC_24h stimulation_donor3


title: Sample_13015GP26


title: RNA-seq_D80CP5

source_name: Day8_CXCL4-moDC_24h stimulation_donor5


title: Sample_13015GP42


title: Sample 1342_Single mESC cell


title: RNA-seq_D80CP4

source_name: Day8_CXCL4-moDC_24h stimulation_donor4


title: Sample_13015GP19


title: RNA-seq_D80CP3

source_name: Day8_CXCL4-moDC_24h stimulation_donor3


title: Sample 1341_Single mESC cell


title: Sample 1340_Single mESC cell


title: RNA-seq_D80CP1

source_name: Day8_CXCL4-moDC_24h stimulation_donor1


title: RNA-seq_D80CP2

source_name: Day8_CXCL4-moDC_24h stimulation_donor2


title: RNA-seq_D74MP5

source_name: Day7_moDC_4h stimulation_donor5


title: Sample 1339_Single mESC cell


title: Sample_13015GP09


title: RNA-seq_D74MP4

source_name: Day7_moDC_4h stimulation_donor4


title: RNA-seq_D74MP1

source_name: Day7_moDC_4h stimulation_donor1


title: Sample_13015GP03


title: RNA-seq_D74CP3

source_name: Day7_CXCL4-moDC_4h stimulation_donor3


title: RNA-seq_D74MP3

source_name: Day7_moDC_4h stimulation_donor3


title: Sample_13015GP01


title: Sample_13015GP48


title: RNA-seq_D74MP2

source_name: Day7_moDC_4h stimulation_donor2


title: Sample_13015GP45

source_name: liver


title: Sample 1336_Single mESC cell

source_name: Single mESC cell


title: RNA-seq_D74CP4

source_name: Day7_CXCL4-moDC_4h stimulation_donor4


title: RNA-seq_D74CP1

source_name: Day7_CXCL4-moDC_4h stimulation_donor1


title: RNA-seq_D74CP5

source_name: Day7_CXCL4-moDC_4h stimulation_donor5


title: RNA-seq_D70M_5


title: Sample 1337_Single mESC cell


title: RNA-seq_D74CP2

source_name: Day7_CXCL4-moDC_4h stimulation_donor2


title: Sample 1334_Single mESC cell


title: RNA-seq_D70M_4


title: Sample_13015GP12


title: Sample_13015GP24


title: RNA-seq_D70M_3


title: Sample_13015GP27


title: RNA-seq_D70M_2


title: RNA-seq_D70M_1


title: Sample 1335_Single mESC cell


title: Sample 1338_Single mESC cell


title: Sample_13015GP47


title: RNA-seq_D70C_5


title: Sample 1332_Single mESC cell


title: Sample_13015GP21


title: Sample 1333_Single mESC cell


title: Sample 1331_Single mESC cell


title: RNA-seq_D70C_2


title: Sample 1330_Single mESC cell


title: RNA-seq_D70C_3


title: Sample_13015GP31


title: RNA-seq_D60M_5

value: differentiating monocyte


title: RNA-seq_D60M_3


title: RNA-seq_D70C_1


title: Sample_13015GP46


title: Sample 1328_Single mESC cell


title: Sample 1329_Single mESC cell


title: RNA-seq_D60M_4


title: Sample 1327_Single mESC cell


title: Sample_13015GP08


title: RNA-seq_D60C_4

source_name: Day6_differentiation with CXCL4_donor4


title: RNA-seq_D60C_3

source_name: Day6_differentiation with CXCL4_donor3


title: Sample_13015GP38


title: RNA-seq_D60C_5

source_name: Day6_differentiation with CXCL4_donor5


title: Sample 1326_Single mESC cell


title: Sample_13015GP15


title: RNA-seq_D60C_2

source_name: Day6_differentiation with CXCL4_donor2


title: RNA-seq_D60C_1

source_name: Day6_differentiation with CXCL4_donor1


title: RNA-seq_D70C_4


title: RNA-seq_D40M_5


title: Sample 1325_Single mESC cell


title: RNA-seq_D40M_4


title: Sample_13015GP18


title: RNA-seq_D60M_1


title: Sample_13015GP32


title: Sample 1324_Single mESC cell


title: Sample_13015GP35


title: RNA-seq_D40M_3


title: RNA-seq_D60M_2


title: RNA-seq_D40M_2


title: fetal_mature_gd_P3_4

city: Freiburg

first: Sagar

address: Hugstetter Straße 55

department: Department of Internal Medicine II

country: Germany

institute: University Medical Center Freiburg

description: library of 96 cells

data_processing:
For image aquisition, intensity extraction and basecalling HiSeq Control Software  2.0.2, RTA 2.4.11 / Recipe Fragment 2.0.0.2 was used. Conversion of bcl2fastq files was performed using bcl2fastq 2.17.1.14
Paired end reads were aligned to the transcriptome using bwa (version 0.6.2-r126) with default parameters. The transcriptome contained all gene models based on the mouse ENCODE VM9 release downloaded from the UCSC genome browser comprising 57,207 isoforms derived from 57,207 gene loci with 57,114 isoforms mapping to fully annotated chromosomes (1 to 19, X, Y, M). All isoforms of the same gene were merged to a single gene locus. Furthermore, gene loci overlapping by >75% were merged to larger gene groups. This procedure resulted in 34,111 gene groups.
The right mate of each read pair was mapped to the ensemble of all gene loci and to the set of 92 ERCC spike-ins in sense direction. Reads mapping to multiple loci were discarded. The left read contains the barcode information: the first six bases correspond to the cell specific barcode followed by six bases representing the unique molecular identifier (UMI). The remainder of the left read contains a poly(T) stretch. The left read was not used for quantification. For each cell barcode, the number of UMIs per transcript was counted and aggregated across all transcripts derived from the same gene locus.
Based on binomial statistics, the number of observed UMIs was converted into transcript counts (Gruen et al., 2014).
Genome_build: ENCODE VM9
Supplementary_files_format_and_content: CSV files, columns represent each cell barcode (total barcodes used = 192), rows represent the geneid and the values in the file are the quantified number of transcripts.

source_name: Thymus

growth_protocol: WT mice were kept in the animal facility of the Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany. Sox13 KO mice were kept in the animal facility of Institut für Biochemie, Emil-Fischer-Zentrum, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany. Rorc KO mice were kept in the animal facility of Institute of Medical Microbiology and Hygiene, University Medical Center Freiburg, Freiburg, Germany.

extract_protocol:
Thymocytes were isolated using mechanical dissociation of thymus.
As described in mCEL-Seq2 protocol (Hashimshony et al. 2016 and Herman et al. 2018)
Adapted from TruSeq Small RNA Library Preparation Protocol

treatment_protocol: Sox13 Ko and Rorc KO cells were kept frozen in 90 % fetal bovine serum (FBS) and 10 % Dimethyl sulfoxide (DMSO) -80ºC before performing antibody staining, FACS sorting and single cell RNA sequencing.

value: C57BL/6 WT

value: Thymus

value: Embryonic day 17.5-18.5


title: Sample 1323_Single mESC cell


title: Sample 1322_Single mESC cell


title: RNA-seq_D40C_4

source_name: Day4_differentiation with CXCL4_donor4


title: RNA-seq_D40C_5

source_name: Day4_differentiation with CXCL4_donor5


title: fetal_mature_gd_P3_3

description: library of 96 cells


title: Sample 1321_Single mESC cell


title: RNA-seq_D40C_3

source_name: Day4_differentiation with CXCL4_donor3


title: fetal_mature_gd_NEW_12

description: library of 96 cells


title: Sample 1320_Single mESC cell


title: RNA-seq_D40C_1

source_name: Day4_differentiation with CXCL4_donor1


title: RNA-seq_D20M_5


title: RNA-seq_D20M_4


title: Sample 1319_Single mESC cell


title: RNA-seq_D20M_3


title: fetal_mature_gd_NEW_11

description: library of 96 cells


title: RNA-seq_D40C_2

source_name: Day4_differentiation with CXCL4_donor2


title: RNA-seq_D20M_2


title: Sample 1318_Single mESC cell


title: fetal_mature_gd_8

description: library of 96 cells


title: RNA-seq_D20M_1


title: Sample 1317_Single mESC cell


title: RNA-seq_D20C_4

source_name: Day2_differentiation with CXCL4_donor4


title: fetal_mature_gd_7

description: library of 96 cells


title: RNA-seq_D40M_1


title: fetal_mature_gd_4

description: library of 96 cells


title: RNA-seq_D20C_5

source_name: Day2_differentiation with CXCL4_donor5


title: RNA-seq_D20C_3

source_name: Day2_differentiation with CXCL4_donor3


title: RNA-seq_D20C_2

source_name: Day2_differentiation with CXCL4_donor2


title: Sample 1316_Single mESC cell

source_name: Single mESC cell


title: fetal_mature_gd_3

description: library of 96 cells


title: RNA-seq_D20C_1

source_name: Day2_differentiation with CXCL4_donor1


title: Sample 1315_Single mESC cell


title: RNA-seq_D00__5

value: monocyte


title: RNA-seq_D00__4


title: fetal_immature_gd_P3_2

description: library of 96 cells


title: Sample 1314_Single mESC cell


title: fetal_immature_gd_P3_1

description: library of 96 cells


title: RNA-seq_D00__3


title: RNA-seq_D00__2


title: RNA-seq_D00__1


title: Sample 1312_Single mESC cell


title: Sample 1311_Single mESC cell


title: P1_05182016

city: New York

first: Miguel

last: Brown

state: New York

address: 1230 York Ave Box 186

institute: The Rockefeller University

data_processing:
Fastq files are trimmed if needed, such that read1=20bp, read2=50bp;Unaligned BAM file created using picard-tools FastqToSam
Drop-seq_alignment.sh (provided by Steve McCarroll lab) is started, which tags cell and molecular barcodes, trims adaptor and polyA sequences, performs alignment, adds gene annotations
DetectBeadSynthesisErrors.sh (provided by Steve McCarroll lab) is run with NUM_BARCODES=2x expected no of cells, then DGE matrix generated with MIN_NUM_GENES_PER_CELL=250
DGEs for all runs are merged, then normalized, scaled and log transformed. Cell cycle and batch effects are regressed out.Training set created, highly variable gene identified.
A topic model is generated from the training set using the highly variable genes as the vocabulary
a topic distribution is calculated for the cells not included in the training set and cells are assigned to the topic with the highest probability, and clusters with fewer than 50 cells are removed
Pairwise marker genes for each cluster are identified using genes that are expressed in least 10% of the cells in both clusters and have average log fold change >1 between clusters. Clusters that do not have at least 10 unique marker genes are merged
Genome_build: hg19
Supplementary_files_format_and_content: text files

source_name: PDAC derived organoid

growth_protocol: To establish organoid cultures, a piece of subcutaneous PDX tumors was extracted, minced and digested with collagenase type XI and dispase in DMEM and incubated from 0.5-1 h at 37 ºC with gentle shaking. Cells were spin and dissociated with TrypLE Express and DNase I for 10 min at 37 ºC, and washed with DMEM. For culturing organoids, dissociated cells were washed and embedded in growth-factor-reduced (GFR) Matrigel and cultured in complete media (Intesticult, A83-01 0.5 µM, fibroblast growth factor 10 100 ng/ml, Gastrin I 10 nM, N-acetyl-L-cysteine 10 mM. Nicotinamide 10 mM, B27 supplement 1x, Primocin 1 mg/ml and Y-27632 10.5 µM).

extract_protocol:
The single cell RNA-seq dataset is comprised of 15 separate drop-seq runs. For each run, a total of 2000 fully growth organoids were pooled, typsinized with TrypLE in presence of 10 µM Y-27632, strained into a single cell suspension and counted. The final concentration of the cell suspension varied between 100-120 cells/uL depending on the flow rate at which monodisperse droplets were formed. Organoids were always harvested for drop-seq analysis at same growth size to ensure uniformity from run to run.
The droplets were broken and the beads were collected and reverse-transcribed. The cDNA obtained was then PCR amplified and quantified. Finally, the cDNA was fragmented
and amplified using primers that
 allow amplification of only the 3’
ends, processed into RNA-seq
libraries using Illumina Nextera XT library prep kit.
As described in Macosko et al Cell (2015)

tag: patient id

value: Patient 1

value: epithelial

tag: Stage

value: mature

value: PDAC derived organoid


title: fetal_immature_gd_NEW_9

description: library of 96 cells


title: fetal_immature_gd_NEW_10

description: library of 96 cells


title: P1_06222016


title: P1_06022016


title: P1_03252016


title: P1_03082016


title: Sample 1310_Single mESC cell

value: Differentiated mESC

value: day 0


title: fetal_immature_gd_6

description: library of 96 cells


title: Sample 1309_Single mESC cell


title: P1_13


title: fetal_immature_gd_5

description: library of 96 cells


title: P1_10_total


title: P1_12


title: Sample 1308_Single mESC cell


title: Sample 1307_Single mESC cell


title: P1_11


title: fetal_immature_gd_1

description: library of 96 cells


title: P1_9_total


title: Sample 1306_Single mESC cell


title: fetal_immature_gd_2

description: library of 96 cells


title: P1_7_total


title: fetal_DN3_9

description: library of 96 cells


title: P1_6_total


title: fetal_DN3_9_2

description: library of 96 cells


title: Sample 1313_Single mESC cell


title: P1_5_total


title: Sample 1305_Single mESC cell


title: fetal_DN3_8

description: library of 96 cells


title: P1_1_total


title: P1_14


title: fetal_DN3_7

description: library of 96 cells


title: P1_8_total


title: fetal_DN3_12

description: library of 96 cells


title: Sample 1301_Single mESC cell


title: Sample 1302_Single mESC cell


title: fetal_DN3_10_old

description: library of 96 cells


title: fetal_DN3_12_old

description: library of 96 cells


title: Sample 1299_Single mESC cell


title: fetal_DN3_10

description: library of 96 cells


title: fetal_DN3_10_2

description: library of 96 cells


title: Sample 1298_Single mESC cell


title: Sample 1304_Single mESC cell


title: P1_2_total


title: Sample 1303_Single mESC cell


title: Sample 1297_Single mESC cell


title: Sample 1300_Single mESC cell


title: Sample 1296_Single mESC cell


title: fetal_DN2_P3_13

description: library of 96 cells


title: leukemic cell line OCI_AML3 treated with DMSO replicate 3

type: RNA

city: Paris

first: Marc

last: Delord

address: Hopital Saint-Louis, 1 avenue Claude Vellefaux

department: Recherche clinique

country: France

institute: Centre hospitalier de Versailles

hyb_protocol: Incubated with rotation at 60 RPM for 16 hours at 45C

scan_protocol: Scanned with the Affymetrix® GeneChip Scanner 3000 7G using the Command Console software (Affymetrix®)

data_processing:
Analyzed using the Affymetrix® rma-sketch routine.
Log2 rma-sketch values computed with apt Affymetrix software

label: biotin

label_protocol: Biotinylated cRNA were prepared according to the Affymetrix manual target preparation for genechip ®  whole transcript expression array.

extract_protocol: RNA were extracted using a promega extractor according to manufacturer protocol

treatment_protocol: Comparison of drugs ATO+ATRA, ATO, ATRA, JQ1, OTX015 and DMSO in IMS-M2 and OCI AML3 leukemic cell lines

tag: drug

value: DMSO

tag: replicate number


title: leukemic cell line OCI_AML3 treated with ATRA replicate 1

value: ATRA


title: leukemic cell line OCI_AML3 treated with ATRA replicate 2


title: leukemic cell line OCI_AML3 treated with ATO replicate 3

value: ATO


title: leukemic cell line OCI_AML3 treated with ATO replicate 2


title: leukemic cell line OCI_AML3 treated with JQ1 replicate 1


title: fetal_DN2_P3_14

description: library of 96 cells


title: leukemic cell line OCI_AML3 treated with OTX015 replicate 2


title: fetal_DN2_P3_12

description: library of 96 cells


title: fetal_DN2_P3_11

description: library of 96 cells


title: leukemic cell line OCI_AML3 treated with JQ1 replicate 3


title: leukemic cell line OCI_AML3 treated with ATO replicate 1


title: Sample 1295_Single mESC cell


title: leukemic cell line OCI_AML3 treated with DMSO replicate 1


title: leukemic cell line OCI_AML3 treated with DMSO replicate 2


title: leukemic cell line OCI_AML3 treated with OTX015 replicate 1


title: leukemic cell line OCI_AML3 treated with OTX015 replicate 3


title: leukemic cell line OCI_AML3 treated with ATO_ATRA replicate 2


title: Sample 1294_Single mESC cell


title: leukemic cell line OCI_AML3 treated with ATRA replicate 3


title: leukemic cell line OCI_AML3 treated with JQ1 replicate 2


title: leukemic cell line OCI_AML3 treated with ATO_ATRA replicate 1


title: fetal_DN2_P1_4

description: library of 96 cells


title: Sample 1293_Single mESC cell


title: Sample 1292_Single mESC cell


title: fetal_DN2_P1_3

description: library of 96 cells


title: leukemic cell line IMS_M2 treated with OTX015 replicate 3


title: Sample 1290_Single mESC cell


title: fetal_DN2_P1_1

description: library of 96 cells


title: Sample 1291_Single mESC cell


title: fetal_DN2_P1_2

description: library of 96 cells


title: Sample 1289_Single mESC cell


title: fetal_DN1_P3_3

description: library of 96 cells


title: leukemic cell line IMS_M2 treated with OTX015 replicate 2


title: Sample 1287_Single mESC cell


title: Sample 1288_Single mESC cell


title: leukemic cell line OCI_AML3 treated with ATO_ATRA replicate 3


title: leukemic cell line IMS_M2 treated with JQ1 replicate 2


title: leukemic cell line IMS_M2 treated with DMSO replicate 3


title: leukemic cell line IMS_M2 treated with JQ1 replicate 1


title: leukemic cell line IMS_M2 treated with OTX015 replicate 1


title: leukemic cell line IMS_M2 treated with DMSO replicate 1


title: leukemic cell line IMS_M2 treated with ATO replicate 2


title: leukemic cell line IMS_M2 treated with ATO_ATRA replicate 3


title: Sample 1286_Single mESC cell


title: fetal_DN1_P3_4

description: library of 96 cells


title: leukemic cell line IMS_M2 treated with ATO replicate 1


title: leukemic cell line IMS_M2 treated with DMSO replicate 2


title: fetal_DN1_P3_1

description: library of 96 cells


title: leukemic cell line IMS_M2 treated with JQ1 replicate 3


title: Sample 1285_Single mESC cell


title: leukemic cell line IMS_M2 treated with ATRA replicate 2


title: fetal_DN1_P3_2

description: library of 96 cells


title: Sample 1284_Single mESC cell


title: leukemic cell line IMS_M2 treated with ATRA replicate 1


title: leukemic cell line IMS_M2 treated with ATO_ATRA replicate 2


title: leukemic cell line IMS_M2 treated with ATRA replicate 3


title: leukemic cell line IMS_M2 treated with ATO_ATRA replicate 1


title: fetal_DN1_P2_7

description: library of 96 cells


title: fetal_DN1_P2_9

description: library of 96 cells


title: leukemic cell line IMS_M2 treated with ATO replicate 3


title: Sample 1283_Single mESC cell


title: fetal_DN1_P2_8

description: library of 96 cells


title: fetal_DN1_P1_16

description: library of 96 cells


title: fetal_DN1_P2_10

description: library of 96 cells


title: RKO_3

city: Uppsala

first: L.

last: He

address: Dag Hammarskjölds Väg 20

country: Sweden

institute: Uppsala University

description: RKO rep 3

data_processing:
The reads were aligned to the human genome hg19 assembly (https://genome.ucsc.edu) using Tophat2 software (version 2.0.4)
The FPKM summary and statistical tests were performed using the Cufflinks tool (version 2.2.1)
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files with RPKM values for each Sample.

source_name: Cell culture

extract_protocol: Cells were trypsinized and pelleted and total RNA was isolated using the Qiagen RNeasy mini kit with on-column DNAse digestion. The RNA integrity and concentration was determined on a Bioanalyzer 2100 instrument (Agilent) using an RNA 6000 Nano kit.

value: human colorectal cancer cell line

value: RKO, ATCC CRL-2577

tag: genotype/variation

value: control


title: WPMY-1 cells treated with PAO (250μg/ml) repeat1

city: nanjing

first: jiakuan

last: liu

address: 12 xuefu road, pukou district

country: China

institute: nanjing university

hyb_protocol: 1 ug total RNA of each samples was used as input into the procedure as recommended by protocol.(Manual Target Preparation for GeneChip® Whole Transcript (WT) Expression Arrays)

scan_protocol: GeneChips were scanned using the GeneChip®Scanner 3000 7G

data_processing: The data were procesed using the RMA algorithm

source_name: WPMY-1 cells

label_protocol: The 5.5μg cDNA was labeled by terminal deoxynucleotidyl transferase (TdT) using the Affymetrix proprietary DNA Labeling Reagent that was covalently linked to biotin.

growth_protocol: BPH1 and WPMY-1 Cells were respectively maintained in RPMI1640 and DMEM supplemented with 10% FBS, 100 units/ml penicillin and 100 μg/ml streptomycin at 37 ℃ under 5% CO2.

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions.

treatment_protocol: BPH1 and WPMY-1  cells were treated with vehicle or PAO (250μg/ml)  for 48 hours. Then, cells were washed with PBS and lysed with Trizol.

value: prostate stroma

tag: cell line

value: WPMY-1 cells

tag: treatment

value: treated with PAO (250μg/ml)


title: Sample 1281_Single mESC cell

tag: day of differentiation


title: Sample 1282_Single mESC cell


title: RKO KMT2C KI2_2

description: KMT2C KI R-3-8-A11A1_2

value: KMT2C knock-in


title: RKO KMT2C KI1

description: KMT2C KI R-1-D10-B11


title: RKO KMT2C KI2_1

description: KMT2C KI R-3-8-A11A1_1


title: Sample 1280_Single mESC cell


title: RKO_2

description: RKO rep 2


title: RKO_1

description: RKO rep 1


title: HCT116 KMT2C KI3

description: KMT2C KI H-3-5-A5

value: HCT116, ATCC CCL-247


title: HCT116 KMT2C KI2

description: KMT2C KI H-1-7-A6


title: WPMY-1 cells treated with vehicle repeat2

value: treated with vehicle


title: WPMY-1 cells treated with PAO (250μg/ml) repeat2


title: BPH1 cells treated with vehicle repeat2

source_name: BPH1 cells

value: prostate epithelium

value: BPH1 cells


title: fetal_DN1_P1_14

description: library of 96 cells

tag: strain

value: C57BL/6 WT

value: Thymus

value: Embryonic day 17.5-18.5


title: BPH1 cells treated with vehicle repeat1


title: BPH1 cells treated with PAO (250μg/ml) repeat2


title: HCT116 KMT2C KI1

description: KMT2C KI H-1-1-E11


title: fetal_DN1_P1_13

description: library of 96 cells


title: BPH1 cells treated with PAO (250μg/ml) repeat1


title: WPMY-1 cells treated with vehicle repeat1


title: Sample 1278_Single mESC cell

value: Differentiated mESC

value: day 0


title: fetal_CD25posgd_P3_9

description: library of 96 cells


title: Sample 1277_Single mESC cell


title: fetal_CD25posgd_P3_12

description: library of 96 cells


title: Sample 1276_Single mESC cell


title: HCT116_2

description: HCT116 rep 2


title: HCT116_1

description: HCT116 rep 1


title: Sample 1279_Single mESC cell


title: fetal_DN1_P1_15

description: library of 96 cells


title: HCT116_3

description: HCT116 rep 3


title: Sample 1275_Single mESC cell


title: fetal_CD25posgd_P3_10

description: library of 96 cells


title: Microglia cells from brain at 6h after IR from four sham controls (SH) mice

first: Ying

last: Sun

state: Uppsala

address: Dag Hammarskjölds väg 20

department: Department of Immunology, Genetics and Pathology

data_processing:
The raw sequence reads were analyzed by Cell Ranger 2.0 with default parameters
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files with read counts for each sample

source_name: Microglia cells in brain

extract_protocol: Single cell sequencing was performed at the eukaryotic single cell genomics facility(ESCG) using the 10× Genomics Chromium method (Hochgerner et al., 2018)

value: microglia cells in brain


title: Microglia cells from brain at 6h after IR from four irradiated (IR) mice

value: Irradiated


title: Microglia cells from brain at 1 week after IR from four irradiated (IR) mice


title: Sample 1274_Single mESC cell


title: fetal_CD25posgd_P1_8

description: library of 96 cells

source_name: Thymus


title: Stim1fl/fl Cd4Cre pathogenic Th17 cells, rep3

first: Stefan

last: Feske

state: NY

address: 550 First Avenue

institute: New York University School of Medicine

data_processing:
Sequenced reads were mapped to the mm10 reference genome using STAR aligner (v.2.5.0c)
Htseq v0.6.0 was used to generate the matrix of read counts for annotated genomic features
The DESeq2 package (Bioconductor v3.10) in the R statistical programming environment was utilized to normalize counts based on library size factors and perform differential expression analysis
Genome_build: mm10
Supplementary_files_format_and_content: txt file containing the normalized read counts matrix for all features across all samples.

source_name: CD4+ T cells

growth_protocol: CD4+ T Cells; unstimulated and in vitro stimulation with 1 ug/ml plate bound anti-CD3/CD28 in presence of 2 ug/ml anti-IL4 and 2 ug/ml anti-IFN-γ in fully complemented RPMI

extract_protocol:
RNA was extracted using the Quiagen MicroRNAeasy kit with Dnase I digestion
Automated Illumina TruSeq Stranded mRNA Sample Prep Kit (Cat. No. RS-122-2101) was used with 100ng of input RNA for the construction of sequencing libraries

treatment_protocol: in vitro stimulation with 1 ug/ml plate bound anti-CD3/CD28 in presence of 2 ug/ml anti-IL4 and 2 ug/ml anti-IFN-γ cultured in the presence of 20 ng/ml IL6 and 0.5ng/ml hTGFβ1 for 2-3 days or 20 ng/ml IL6, 20 ng/ml IL1β, and 20 ng/ml IL23 for 2-3 days.

value: CD4+IL-6+IL-1<beta>+IL-23+ Th17 cells

tag: genotype

value: Stim1fl/fl Cd4Cre

tag: phenotype

value: pathogenic


title: Sample 1273_Single mESC cell


title: Stim1fl/fl Cd4Cre pathogenic Th17 cells, rep2


title: Microglia cells from brain at 1 week after IR from four sham controls (SH) mice

value: control


title: fetal_CD25posgd_P1_7

description: library of 96 cells

tag: tissue


title: Stim1fl/fl Cd4Cre non-pathogenic Th17 cells, rep3

tag: cell type

value: CD4+IL-6+hTGF<beta>1+ Th17 cells

value: non-pathogenic


title: Sample 1271_Single mESC cell


title: fetal_CD25posgd_P1_6

description: library of 96 cells


title: WT pathogenic Th17 cells, rep3

value: WT


title: Sample 1272_Single mESC cell


title: fetal_CD25posgd_P1_5

description: library of 96 cells


title: Sample 1269_Single mESC cell


title: Stim1fl/fl Cd4Cre non-pathogenic Th17 cells, rep1


title: WT non-pathogenic Th17 cells, rep3


title: Stim1fl/fl Cd4Cre non-pathogenic Th17 cells, rep2


title: Sample 1270_Single mESC cell


title: WT non-pathogenic Th17 cells, rep1


title: fetal_CD25posgd_15_old

description: library of 96 cells


title: fetal_CD25posgd_15

description: library of 96 cells


title: WT pathogenic Th17 cells, rep2


title: WT non-pathogenic Th17 cells, rep2


title: YFP negative single cell RNA-seq

city: St Louis

first: Jeffrey

last: Milbrandt

state: Missouri

address: 660 S Euclid Ave #5101

institute: Washington University School of Medicine

data_processing:
Library sequenced by HiSeq2500
Reads mapped to GRCm38 genome and demultiplexed using cellranger 3.0.2
Raw expression matrix generated by using cellranger 3.0.2
Data cleaning, QC, clustering and visualization performed by using Seurat 2.2.0
Genome_build: GRCm38
Supplementary_files_format_and_content: Sparse matrix format of raw expression data

source_name: sciatic nerves of 19 male mice

extract_protocol:
single cell RNA captured by using 10X genomics single cell RNA-seq platform v2
library construction following 10X genomics single cell RNA-seq v2 protocol
single cell RNA-seq by barcoding

value: YFP negative macrophages

tag: markers

value: Sorted cells based on CD64 and CD45

value: 10-12 weeks

tag: gender

value: male


title: YFP positive single cell RNA-seq

value: YFP positive macrophages

tag: age


title: Sample 1267_Single mESC cell


title: Sample 1268_Single mESC cell


title: fetal_CD25posgd_14_old

description: library of 96 cells

value: C57BL/6 WT

value: Thymus

value: Embryonic day 17.5-18.5


title: Stim1fl/fl Cd4Cre pathogenic Th17 cells, rep1


title: WT pathogenic Th17 cells, rep1


title: Sample 1266_Single mESC cell

value: Differentiated mESC

value: day 0


title: fetal_CD25posgd_13_old

description: library of 96 cells


title: In tube validation of ZipSeq design 2

first: Kenneth

middle: H

last: Hu

address: 7455 Fannin Street

department: Immunology

institute: MD Anderson

data_processing:
Library strategy: ZipSeq
Base-calling using CellRanger v3.0.2 mkfastq
Demultiplexing using i7 index using CellRanger v3.0.2 mkfastq
Alignment using CellRanger v3.0.2 count to mouse reference assembly
Filter out cells below nUMI threshold
Genome_build: mm10 from 10X with added fluorophores
Supplementary_files_format_and_content: Raw count files with cell barcodes and gene names in .tsv and counts in .mtx

source_name: primary mouse immune cells

extract_protocol:
10X Chromium v3 encapsulation and RT
10X recommended library construction

value: primary mouse immune cells

tag: setting

value: In tube validation


title: fetal_CD25posgd_13

description: library of 96 cells


title: Lymph node 4 region assay

source_name: CD45+ immune cells from lymph node

value: CD45+ immune cells from lymph node

value: live lymph node section


title: Lymph node 2 region assay


title: Wound healing 2 region assay

source_name: mouse NIH3T3 fibroblasts

value: mouse NIH3T3 fibroblasts

value: in-vitro wound healing


title: Sample 1265_Single mESC cell


title: In tube validation of ZipSeq design 1


title: Sample 1264_Single mESC cell


title: e175_sox13wt_mature_gd_P2_4

description: library of 96 cells

value: Embryonic day 17.5


title: e175_sox13wt_mature_gd_P2_3

description: library of 96 cells


title: 3-LG-10

city: St. Louis

first: Leslie

middle: Stuart

last: Gewin

state: MO

address: 660 S Euclid Ave, McDonnell Science Building, Rm 718

department: Medicine (Nephrology)

institute: Washington University in St. Louis

description:
RNAseq with Hiseq 2500 with a read length of 100.
Raw data could not be provided for this submission because the files had been previously deleted

data_processing:
RNAseq raw reads were aligned against MM10 reference using TOPHAT2 followed by gene quantification into FPKM using Cufflinks. .
Differential expression analyses were performed using cuffdiff from Cufflink packages.
p values were adjusted using Benjamini-Hochberg method.
Supplementary_files_format_and_content: Processed data are comparisons between different samples in Excel files

source_name: renal proximal tubule cells

growth_protocol: conditionally immortalized proximal tubule cells; isolation, characterization and media components listed in JASN manuscript, PMID: 23160515

extract_protocol:
RNA isolation performed with Qiagen Rneasy Kit plus DNAse step
performed by Vanderbilt VANTAGE Core

treatment_protocol: cells were transfected with siRNA in 33C and then moved to 37 (with interferon gamma removed)

value: Mixed:mice were N2 FVB with TbRII floxed crossed with Immorto-mouse

value: renal proximal tubule cells

tag: sirna used

value: siRNA to FoxO1 and FoxO3

tag: wnt treatment

value: Wnt3a 20ng/mL


title: 3-LG-9

value: siRNA to FoxO3


title: 3-LG-8

value: siRNA to FoxO1


title: Sample 1263_Single mESC cell


title: 3-LG-6


title: 3-LG-7

value: scramble siRNA


title: e175_sox13wt_mature_gd_P1_16

description: library of 96 cells

value: C57BL/6 WT

value: Thymus


title: 3-LG-5


title: Sample 1262_Single mESC cell

value: Differentiated mESC

value: day 0


title: 3-LG-4


title: Sample 1261_Single mESC cell


title: 3-LG-2


title: Sample 1260_Single mESC cell


title: e175_sox13wt_mature_gd_P1_15

description: library of 96 cells


title: e175_sox13wt_immature_gd_P2_2

description: library of 96 cells


title: 3-LG-1

value: Wnt diluting buffer


title: e175_sox13wt_immature_gd_P2_1

description: library of 96 cells


title: Sample 1259_Single mESC cell


title: Pre-B_Cell_Lysate

city: London

first: Ya

last: Guo

address: Faculty of Medicine, Imperial College, Hammersmith Hospital Campus

department: Epigenetics section

country: United Kingdom

institute: MRC London Institute of Medical Sciences

library_source: genomic

data_processing:
Data was processed using RTA version 1.18.64, with default filter and quality settings. The reads were de-multiplexed using CASAVA 1.8.4.
Raw sequencing data was mapped and processed using bowtie 2.3.2 and HiC-Pro 2.7.8 by default setting.
Valid chromatin contacts were normalized by KR matrix balancing algorithm.
Genome_build: mm9
Supplementary_files_format_and_content: hic files were generated using Juicer Pre

molecule: genomic DNA

source_name: pre-B cells

extract_protocol:
Samples were cross-linked in 1% formaldehyde for 10min at RT.
Chromatin was digested with 600 units of HindIII overnight at 37°C with rotation. Digested sticky ends were filled in by DNA polymerase I, large Klenow fragment in the presence of 50nM biotin-14-dATP, 50nM dTTP, 50nM dGTP, and 50nM dCTP for 90min at 37°C with rotation. Chromatin fragment ends were ligated by 4000 units of T4 DNA ligase by incubating at RT for 6h with slow rotation. Proteins were digested by proteinase K and then cross-linked chromatin was reversed by incubating overnight. Rnase A was used to remove RNA after decross-linking. After isolation with phenol/chloroform/isoamyl alcohol (25:24:1 mixture), DNA was precipitated by sodium acetate/ethanol precipitation. DNA was sheared for 9min by Bioruptor sonicator (30sec on and 30sec off per minute using high power setting). DNA fragments in the range of 300-500bp were selected with AMPure XP beads. After biotinylated DNA was captured on Dynabeads MyOne Streptavidin T1, DNA ends were repaired in a mixture of T4 polynucleotide kinase, T4 DNA polymerase I and DNA polymerase I, large Klenow fragment. dATP was then added to the repaired ends using Klenow Fragment (3'→5' exo-). NEBNext adaptors for Illumina were ligated to the dA-tailed ends. After USER enzyme digestion, NEBNext oligos for Illumina were used for library preparation. A PCR titration was performed to determine the minimal number of PCR cycles (8 cycles in this work).

tag: type

value: before sorting

tag: condition

value: cell lysate

tag: restriction enzyme

value: HindIII


title: Sample 1258_Single mESC cell

tag: cell line


title: e175_sox13wt_immature_gd_P1_14

description: library of 96 cells


title: Chromosome_Sorted_Pre-B

value: flow-sorted

value: mitotic chromosomes


title: KO_antiIgM_rep1

city: Suita

first: Daisuke

last: Okuzaki

state: Osaka

address: Yamadaoka 3-1

department: Immunology Frontier Research Center

country: Japan

institute: Osaka univ.

description: Trpm5−/− MZB cells stimulated with 10 µg/mL of anti-IgM antibody for 4 h

data_processing:
Sequencing was performed on an Illumina HiSeq 2500 platform in a 75-base single-end mode.
Illumina Casava1.8.2 software used for basecalling.
Sequenced reads were mapped to the mouse reference genome sequences (mm10) using TopHat v2.0.13 in combination with Bowtie2 ver. 2.2.3 and SAMtools ver. 0.1.19.
The fragments per kilobase of exon per million mapped fragments (FPKMs) was calculated using Cufflinks version 2.2.1.
Genome_build: mm10

source_name: KO antiIgM

extract_protocol:
Total RNA was extracted using the miRNeasy Mini Kit (Qiagen, Hilden, Germany) according to the manufacturer’s protocol.
Full-length cDNA was generated using a SMART-Seq HT Kit (Takara Bio, Mountain View, CA) according to the manufacturer’s instructions. An Illumina library was prepared using a Nextera DNA Library Preparation Kit (Illumina, San Diego, CA) according to SMARTer kit instructions.

value: marginal zone B cells


title: KO_antiIgM_rep2


title: e175_sox13wt_immature_gd_P1_13

description: library of 96 cells

value: Embryonic day 17.5


title: Sample 1257_Single mESC cell


title: KO_LPS_rep1

description: Trpm5−/− MZB cells stimulated with 10 µg/mL of LPS for 4 h

source_name: KO LPS


title: Sample 1256_Single mESC cell

source_name: Single mESC cell


title: e175_sox13ko_mature_gd_p2_5

description: library of 96 cells


title: WT_antiIgM_rep1

description: Wild-type MZB cells stimulated with 10 µg/mL of anti-IgM antibody for 4 h

source_name: WT antiIgM


title: KO_LPS_rep2


title: KO_unstimulated_rep1

description: Trpm5−/− MZB cells stimulated without LPS or anti-IgM antibody for 4 h

source_name: KO unstimulated


title: KO_unstimulated_rep2


title: 3-LG-3

value: Mixed:mice were N2 FVB with TbRII floxed crossed with Immorto-mouse

value: renal proximal tubule cells


title: Sample 1255_Single mESC cell


title: WT_antiIgM_rep2


title: e175_sox13ko_mature_gd_p2_6

description: library of 96 cells


title: Sample 1254_Single mESC cell


title: WT_LPS_rep2

description: Wild-type MZB cells stimulated with 10 µg/mL of LPS for 4 h

source_name: WT LPS


title: Sample 1253_Single mESC cell


title: WT_unstimulated_rep2

description: Wild-type MZB cells stimulated without LPS or anti-IgM antibody for 4 h

source_name: WT unstimulated


title: e175_sox13ko_mature_gd_2

description: library of 96 cells


title: Sample 1252_Single mESC cell


title: e175_sox13ko_mature_gd_5

description: library of 96 cells


title: WT_unstimulated_rep1


title: AT2 ctrl [FGC1649_s_8_TCGGCGTC]

first: G

middle: Scott

last: Worthen

address: 3615 Civic Center Blvd

department: Pediatrics

institute: Children's Hospital of Philadelphia

description:
FGC1649_s_8_1_TCGGCGTC
processed data file:
at2_ctrl_barcodes.tsv.gz
at2_ctrl_genes.tsv.gz
at2_ctrl_matrix.mtx.gz

data_processing:
Fastq files were alignef and quantified using Cell Ranger.
T-SNE clustering and differential expression analysis was done using Seurat.
Genome_build: mm10
Supplementary_files_format_and_content: Raw output from cellranger combines barcodes, genes and the count matrix

source_name: AT2 ctrl

extract_protocol:
Cells captured in 10x platform
scRNA-Seq Library 10x 3' v3 sequenced at 28PE (28x8x91)

treatment_protocol: AT2 cells were sorted from minced Right  lung 24 hrs after Unilateral acid-induced lung injury or after PBS in control mice.

tag: strain background

tag: genotype/variation

value: WT

tag: treatment

value: control

value: lung

value: type II alveolar pneumocytes (AT2)

tag: sorting profile

value: DAPI- EpCAM+ CD45- CD31- Sca1-


title: AT2 inj [FGC1649_s_8_TTTCATGA]

description:
FGC1649_s_8_1_TTTCATGA
processed data file:
at2_inj_barcodes.tsv.gz
at2_inj_genes.tsv.gz
at2_inj_matrix.mtx.gz

source_name: AT2 inj

value: injured


title: AT2 ctrl [FGC1649_s_8_GGTTTACT]

description:
FGC1649_s_8_1_GGTTTACT
processed data file:
at2_ctrl_barcodes.tsv.gz
at2_ctrl_genes.tsv.gz
at2_ctrl_matrix.mtx.gz


title: Sample 1251_Single mESC cell

value: Differentiated mESC

tag: day of differentiation

value: day 0


title: e175_sox13ko_mature_gd_1

description: library of 96 cells

source_name: Thymus

tag: strain

value: C57BL/6 WT

tag: tissue

value: Thymus


title: e175_sox13ko_immature_gd_p2_8

description: library of 96 cells


title: AT2 inj [FGC1649_s_8_GAAGGAAC]

description:
FGC1649_s_8_1_GAAGGAAC
processed data file:
at2_inj_barcodes.tsv.gz
at2_inj_genes.tsv.gz
at2_inj_matrix.mtx.gz

tag: cell type


title: AT2 ctrl [FGC1649_s_8_CTAAACGG]

description:
FGC1649_s_8_1_CTAAACGG
processed data file:
at2_ctrl_barcodes.tsv.gz
at2_ctrl_genes.tsv.gz
at2_ctrl_matrix.mtx.gz


title: Sample 1250_Single mESC cell


title: AT2 inj [FGC1649_s_8_ACGTCCCT]

description:
FGC1649_s_8_1_ACGTCCCT
processed data file:
at2_inj_barcodes.tsv.gz
at2_inj_genes.tsv.gz
at2_inj_matrix.mtx.gz


title: AT2 ctrl [FGC1649_s_8_AACCGTAA]

description:
FGC1649_s_8_1_AACCGTAA
processed data file:
at2_ctrl_barcodes.tsv.gz
at2_ctrl_genes.tsv.gz
at2_ctrl_matrix.mtx.gz


title: e175_sox13ko_mature_gd_6

description: library of 96 cells


title: WT_LPS_rep1


title: AT2 inj [FGC1649_s_8_CGCATGTG]

description:
FGC1649_s_8_1_CGCATGTG
processed data file:
at2_inj_barcodes.tsv.gz
at2_inj_genes.tsv.gz
at2_inj_matrix.mtx.gz


title: Sample 1248_Single mESC cell


title: Microglia Depletion #35

city: Austin

first: Anna

last: Warden

state: TX

address: 2500 Speedway

institute: University of Texas at Austin

description: Microglia Depletion #35 abundance

data_processing:
Adapters were trimmed and filtered using tagseq_clipper.pl and tagseq_trim_launch.pl https://github.com/z0on/tag-based_RNAseq
Raw 3'UTR biased-sequencing files were evaluated for quality control using FastQC (0.11.8).
Reads were mapped to the mouse reference genome (UCSC, mm10) using the alignment tool Bowtie2 (v2.3.4.3).
HTSeq (v.0.11.0), was used for counting mapped sequencing reads.
Quantified read counts were normalized and analyzed for differential expression using DESeq2 (v 1.10.1), between microglia intact and microglia depleted animals, within the R statistical computing environment (v3.5.1)
Genome_build: GRCm38.p6.genome.fa.gz from ftp://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_mouse/release_M17/GRCm38.primary_assembly.genome.fa.gz
Supplementary_files_format_and_content: tab-delimited text files include counts for each Sample

source_name: medial prefrontal cortex

extract_protocol:
medial prefrontal cortex was fresh dissected, flash frozen on dry ice, and RNA was harvested using Trizol reagent and MagMAX-96 Total RNA Isolation Kit . DNA contamination removed using DNA-free kit.  (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA was fragmented then first strand synthesis occurred using majority deoxycytidine nucleotides which served as an anchor for the switch oligos. swOligo used: /5Me-isodC/iisodG/iMeisodC/CCATGCGGCTACACGACGC TCTTCCGATCTNNMWrGrGrG. cDNA strand with portions of adapter were added then amplified, followed by second PCR to add index portion of the adapter.
Samples were then pooled, size selected with Pippin then sequenced on a Single End Run using the HiSeq 2500 for a read depth of ~4 million reads per sample

treatment_protocol: Treated with PLX5622 (1200mg/kg) for 21 days prior to beginning every-other-day drinking procedure (15%) for 44 days, sacrified 24 hours after last ethanol exposure.

value: medial prefrontal cortex

value: post-natal day 100

tag: chow


title: Sample 1249_Single mESC cell

first: Alina

address: 318 Campus drive

data_processing:
Sequences from the NovaSeq were de-multiplexed using bcl2fastq version 2.19.0.316. Reads were trimmed from polyA tails using cutadapt v 1.18 with the following parameters: -m 18 -j 4 -a AAAAAAAAAA -a TTTTTTTTTT. Reads were then aligned to the human (GRCh38) or mouse genome (GRCm38) using STAR v2.7.0d 37 with the following parameters --outFilterMismatchNoverLmax 0.05 --outFilterMatchNmin 18 --outFilterMatchNminOverLread 0 --outFilterScoreMinOverLread 0  --outMultimapperOrder Random. Reads mapping to multiple locations were assigned either to a location with the best mapping score or, in the case of equal multimapping score – to the genomic location randomly chosen as “primary”.
Genome_build: GRCm38, GRCh38
Supplementary_files_format_and_content: tab-delimited text files of count tables

extract_protocol:
Lysis plates were prepared by dispensing 0.3μL lysis buffer (4 U Recombinant RNase Inhibitor (RRI) (Takara Bio, 2313B), 0.12% TritonTM X-100 (Sigma, 93443-100ML), 1μM Smart-seq4 oligo-dT primer (5’-Biotin- /5BiosG/CATAGTCTCGTGGGCTCGGAGATGTGTATAAGAGACAGT30VN-3’;IDT) (see Supplementary Table 3 for a full list of oligos used in the present study) into 384-well hard-shell PCR plates (Bio-Rad HSP3901) using Mantis liquid handler (Formulatrix). 96-well lysis plates were prepared with 3 μl lysis buffer. All plates were sealed with AlumaSeal CS Films (Sigma-Aldrich Z722634), spun down and snap-frozen on dry ice.   Cells were stained with calcein-AM and ethidium homodimer-1 (LIVE/DEAD® Viability/Cytotoxicity Kit, ThermoFisher L3224) and individual live cells were sorted in 384 well lysis plates using SONY sorter (SH800S) with 100um nozzle chip. Plates were spun down and stored at -80 degrees immediately after sorting.
Smart-seq-total


title: e175_sox13ko_immature_gd_p2_7

description: library of 96 cells

tag: age


title: e175_sox13ko_immature_gd_8

description: library of 96 cells


title: e175_sox13ko_immature_gd_7

description: library of 96 cells


title: e175_sox13ko_immature_gd_4

description: library of 96 cells


title: Sample 1247_Single mESC cell


title: Microglia Depletion #32

description: Microglia Depletion #32 abundance


title: Microglia Depletion #34

description: Microglia Depletion #34 abundance


title: Microglia Depletion #31

description: Microglia Depletion #31 abundance


title: e175_sox13ko_immature_gd_3

description: library of 96 cells


title: e175_rorcwt_mature_gd_P2_12

description: library of 96 cells


title: Microglia Depletion #28

description: Microglia Depletion #28 abundance


title: Microglia Depletion #27

description: Microglia Depletion #27 abundance


title: Microglia Depletion #26

description: Microglia Depletion #26 abundance


title: Microglia Depletion #25

description: Microglia Depletion #25 abundance


title: Sample 1244_Single mESC cell


title: Control Diet #11

description: Control Diet #11 abundance

value: Control Diet


title: Control Diet #10

description: Control Diet #10 abundance


title: Sample 1243_Single mESC cell


title: Microglia Depletion #29

description: Microglia Depletion #29 abundance


title: e175_rorcwt_mature_gd_P1_8

description: library of 96 cells


title: Control Diet #08

description: Control Diet #08 abundance


title: Control Diet #09

description: Control Diet #09 abundance


title: e175_rorcwt_mature_gd_P2_11

description: library of 96 cells


title: Sample 1241_Single mESC cell


title: Sample 1242_Single mESC cell


title: Control Diet #05

description: Control Diet #05 abundance


title: Control Diet #04

description: Control Diet #04 abundance


title: e175_rorcwt_mature_gd_P1_7

description: library of 96 cells


title: Control Diet #03

description: Control Diet #03 abundance


title: Control Diet #07

description: Control Diet #07 abundance


title: Sample 1240_Single mESC cell


title: Control Diet #02

description: Control Diet #02 abundance


title: e175_rorcwt_immature_gd_P2_10

description: library of 96 cells


title: Sample 1239_Single mESC cell


title: Sample 1246_Single mESC cell


title: Sample 1245_Single mESC cell


title: e175_rorcwt_immature_gd_P1_6

description: library of 96 cells


title: e175_rorcwt_immature_gd_P1_5

description: library of 96 cells


title: Sample 1236_Single mESC cell


title: Sample 1233_Single mESC cell


title: Sample 1237_Single mESC cell


title: Sample 1238_Single mESC cell


title: Sample 1234_Single mESC cell


title: e175_rorcko_mature_gd_P3_12

description: library of 96 cells


title: e175_rorcko_mature_gd_P2_7

description: library of 96 cells


title: e175_rorcko_mature_gd_P1_4

description: library of 96 cells


title: e175_rorcko_mature_gd_P2_8

description: library of 96 cells


title: Sample 1235_Single mESC cell


title: e175_rorcko_mature_gd_P1_3

description: library of 96 cells


title: fetal_CD25posgd_P3_11

description: library of 96 cells

value: Embryonic day 17.5-18.5


title: Sample 1232_Single mESC cell


title: Sample 1230_Single mESC cell


title: e175_rorcko_mature_gd_P3_11

description: library of 96 cells

value: Embryonic day 17.5


title: Sample 1231_Single mESC cell


title: e175_rorcko_immature_gd_P3_10

description: library of 96 cells


title: e175_rorcko_immature_gd_P2_6

description: library of 96 cells


title: Sample 1229_Single mESC cell


title: e175_rorcko_immature_gd_P2_5

description: library of 96 cells


title: Sample 1228_Single mESC cell


title: rorcko_week6_mature_gd_M2_1

description: library of 96 Rorc KO mature gamma delta T cells

growth_protocol: WT mice were kept in the animal facility of the Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany. Maf KO mice were kept in the animal facility of The Kimmel Center for Biology and Medicine of the Skirball Institute, New York University School of Medicine, New York, USA. Sox13 KO mice were kept in the animal facility of Institut für Biochemie, Emil-Fischer-Zentrum, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany. Rorc KO mice were kept in the animal facility of Institute of Medical Microbiology and Hygiene, University Medical Center Freiburg, Freiburg, Germany.

extract_protocol:
Thymocytes were isolated using mechanical dissociation of thymus. Since double negative (DN) thymocytes are rare, we performed the magnetic enrichment for DN thymocytes.
As described in mCEL-Seq2 protocol (Hashimshony et al. 2016 and Herman et al. 2018)
Adapted from TruSeq Small RNA Library Preparation Protocol

treatment_protocol: Maf KO, Sox13 Ko and Rorc KO cells were kept frozen in 90 % fetal bovine serum (FBS) and 10 % Dimethyl sulfoxide (DMSO) -80ºC before performing antibody staining, FACS sorting and single cell RNA sequencing.

value: Rorc KO

tag: Sex

value: female

tag: age/developemental stage

value: 4-5 weeks

value: mature gamma delta T cells


title: rorcko_week6_mature_gd_21

source_name: library of 96 Rorc KO mature gamma delta T cells


title: rorcko_week6_mature_gd_M1_5


title: rorcko_week6_mature_gd_M1_6


title: rorcko_week6_mature_gd_22


title: rorcko_week6_mature_gd_M2_2


title: e175_rorcko_immature_gd_P3_9

description: library of 96 cells


title: rorcko_week6_mature_gd_M2_9


title: e175_rorcko_immature_gd_P1_2

description: library of 96 cells


title: Sample 1227_Single mESC cell


title: e175_rorcko_immature_gd_P1_1

description: library of 96 cells


title: rorcko_week6_immature_gd_8

description: library of 96 Rorc KO immature gamma delta T cells

value: immature gamma delta T cells


title: rorcko_week6_immature_gd_6

source_name: library of 96 Rorc KO immature gamma delta T cells


title: rorcko_week6_mature_gd_M1_10


title: Sample 1226_Single mESC cell


title: rorcko_week6_immature_gd_5


title: M4 Cell line-derived allograft anti-CTLA4 C54

city: Bethesda

first: Maxwell

last: Lee

state: MD

address: Building 37, Room 5120

department: CCR

institute: National Cancer Institute, NIH

data_processing:
Quality checking (trimming/masking if necessary), alignment/mapping to the reference genome; Variant calling (SNVs and indels) and comparisons between the conditions; IGV visualizations.
Using combination of Galaxy on Helix and Bioconductor /R packages
Single nucleotide variants (SNV) were identified using samtools mpileup or GATK HaplotypeCaller. Mouse germline single nucleotide polymorphisms (SNPs) were filtered out using the Sanger Mouse Genomes Project database
Variants with a Phred-scaled quality score of <30 were removed.  Variants that are present in normal spleen samples (in-house collection) were also removed.
Variants were annotated with Annovar software to identify non-synonymous mutations.
Genome_build: UCSC reference Genome Sequence, mouse mm10
Supplementary_files_format_and_content: vcf files include variants for each sample
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample …

source_name: Melanoma allograft

extract_protocol:
Cell lines were harvested following regular cell culture process. Tumors harvested from mice were homogenized by cryogenic grinding. Genomic DNA and RNA was prepared using Qiagen DNeasy Blood & Tissue Kit and RNeasy Blood & Tissue Kit, respectvely.
Exome and cDNA (RNA) libraries were prepared for sequencing using Agilent SureSelectXT library prep ILM Kit and standard Illumina library prep, respectively.

tag: genotype

value: Hgftg


title: rorcko_week6_immature_gd_7


title: M4 Cell line-derived allograft anti-CTLA4 C51


title: Sample 1224_Single mESC cell

last: Isakova

institute: Stanford University


title: rorcko_week6_immature_gd_24


title: Sample 1223_Single mESC cell


title: M4 Cell line-derived allograft anti-CTLA4 C56


title: Sample 1225_Single mESC cell


title: M4 Cell line-derived allograft anti-CTLA4 C49


title: week6_DN1_2

description: library of 96 WT DN1 cells

source_name: library of 96 WT DN1 cells

value: wild type

value: 5-6 weeks

value: DN1 cells


title: week6_DN1_3

description: library of 96 WT DN1 cells


title: week6_DN1_1

description: library of 96 WT DN1 cells


title: week6_DN1_4

description: library of 96 WT DN1 cells


title: Sample 1222_Single mESC cell

value: Differentiated mESC

value: day 0


title: M4 Cell line-derived allograft anti-CTLA4 C47


title: Sample 1221_Single mESC cell


title: week6_DN1_5

description: library of 96 WT DN1 cells

value: Thymus


title: week6_DN1_7

description: library of 96 WT DN1 cells


title: week6_DN1_8

description: library of 96 WT DN1 cells


title: M4 Cell line-derived allograft Isotype control C58

value: Isotype control


title: rorcko_week6_immature_gd_23


title: week6_DN2_1

description: library of 96 WT DN2 cells

source_name: library of 96 WT DN2 cells

value: DN2 cells


title: Sample 1220_Single mESC cell


title: M4 Cell line-derived allograft Isotype control C40


title: Sample 1219_Single mESC cell


title: M4 Cell line-derived allograft Isotype control C37


title: week6_DN2_2

description: library of 96 WT DN2 cells


title: week6_DN2_11

description: library of 96 WT DN2 cells


title: M4 Cell line-derived allograft Isotype control C36


title: Sample 1218_Single mESC cell


title: week6_DN2_12

description: library of 96 WT DN2 cells


title: week6_DN1_6

description: library of 96 WT DN1 cells


title: week6_DN2_3

description: library of 96 WT DN2 cells


title: week6_DN2_4

description: library of 96 WT DN2 cells


title: M4 Cell line-derived allograft Untreated C59

value: Untreated


title: week6_DN2_9

description: library of 96 WT DN2 cells


title: Sample 1215_Single mESC cell


title: week6_DN3_2

description: library of 96 WT DN3 cells

source_name: library of 96 WT DN3 cells

value: DN3 cells


title: M4 Cell line-derived allograft Untreated C55


title: week6_DN3_5

description: library of 96 WT DN3 cells


title: week6_DN3_1

description: library of 96 WT DN3 cells


title: Sample 1214_Single mESC cell


title: week6_DN3_3

description: library of 96 WT DN3 cells


title: week6_DN2_10

description: library of 96 WT DN2 cells


title: M4 Cell line-derived allograft Untreated C34


title: week6_DN3_6

description: library of 96 WT DN3 cells


title: Sample 1213_Single mESC cell


title: week6_DN3_7

description: library of 96 WT DN3 cells


title: M3 Cell line-derived allograft anti-CTLA4 B8

value: Cdk4R24C; Hgftg


title: Sample 1217_Single mESC cell


title: Sample 1212_Single mESC cell


title: M3 Cell line-derived allograft anti-CTLA4 B7


title: week6_mature_gd_1

description: library of 96 WT mature gamma delta T cells


title: week6_mature_gd_2

source_name: library of 96 WT mature gamma delta T cells


title: Sample 1211_Single mESC cell


title: week6_DN3_4

description: library of 96 WT DN3 cells


title: week6_mature_gd_10


title: Sample 1216_Single mESC cell


title: M3 Cell line-derived allograft anti-CTLA4 B5


title: M4 Cell line-derived allograft Untreated C53


title: week6_mature_gd_3


title: week6_mature_gd_4


title: week6_mature_gd_8


title: M3 Cell line-derived allograft anti-CTLA4 B24


title: week6_mature_gd_7


title: M3 Cell line-derived allograft anti-CTLA4 B21


title: week6_mature_gd_9


title: Sample 1208_Single mESC cell


title: week6_DN3_8

description: library of 96 WT DN3 cells


title: week6_pan_gd_10

description: library of 96 WT pan gamma delta T cells

value: pan gamma delta T cells


title: Sample 1207_Single mESC cell


title: week6_pan_gd_11

source_name: library of 96 WT pan gamma delta T cells

value: female


title: M3 Cell line-derived allograft anti-CTLA4 B15


title: week6_pan_gd_1


title: week6_pan_gd_13


title: Sample 1206_Single mESC cell

source_name: Single mESC cell


title: M3 Cell line-derived allograft Isotype control B29


title: week6_pan_gd_12


title: M3 Cell line-derived allograft Isotype control B26


title: week6_pan_gd_14


title: Sample 1210_Single mESC cell


title: M3 Cell line-derived allograft Isotype control B14


title: Sample 1209_Single mESC cell


title: week6_pan_gd_4


title: Sample 1204_Single mESC cell


title: week6_pan_gd_2


title: week6_pan_gd_5


title: M3 Cell line-derived allograft Untreated B3


title: week6_pan_gd_3


title: week6_pan_gd_8


title: Sample 1202_Single mESC cell


title: week6_pan_gd_7


title: week6_pan_gd_9


title: M3 Cell line-derived allograft Untreated B2


title: week6_postselected_gd_11

description: library of 96 WT postselected gamma delta T cells

value: postselected gamma delta T cells


title: Sample 1201_Single mESC cell


title: M3 Cell line-derived allograft Untreated B16


title: week6_postselected_gd_12

source_name: library of 96 WT postselected gamma delta T cells


title: week6_postselected_gd_5


title: M2 Cell line-derived allograft anti-CTLA4 D98

value: BrafCA/+; Cdkn2aflox/+; Tyr-CreERT2-tg; Hgftg


title: week6_preselected_gd_1

description: library of 96 WT preselected gamma delta T cells

value: preselected gamma delta T cells


title: Sample 1205_Single mESC cell


title: week6_preselected_gd_2

source_name: library of 96 WT preselected gamma delta T cells


title: week6_preselected_gd_3


title: week6_postselected_gd_6


title: week6_pan_gd_6


title: Sample 1203_Single mESC cell


title: week6_preselected_gd_4


title: M3 Cell line-derived allograft Untreated B27


title: 43-2DG

city: Pasadena

first: Boyoung

last: Shin

state: California

address: 1200 E. California Blvd

institute: Californial Institute of Technology

description: 2DG3_0 (column name in processed data file LEH_glycolysis_dataset.txt)

data_processing:
Total RNA was sequenced on Illumina HiSeq 2500 (1x50 base pair, single-read). For the base-calling, Illumina Bal2fastq program, version 1.8.4 was used
Sequence reads were aligned to the mouse mm10 reference genome using TopHat 2.1.0.
Fragments Per Kilobase of transcript per Million mapped reads (FPKM) were calculated with Cufflinks version 2.2.1.0 and normalized expression levels were determined by Cuffnorm version 2.2.1.1
Significant changes in transcript expression were determined with Cuffdiff version 2.2.1.3
Genome_build: mm10
Supplementary_files_format_and_content: FPKMs

growth_protocol: Naïve CD4 T cells were cultured with plate-bound anti-CD3e(10ug/ml) and anti-CD28(1ug/ml) and Th17 polarizing cytokines (IL-6 20ng/ml, TGFb1 2.5ng/ml, IL-23 10ng/ml) for 48h

extract_protocol:
RNeasy Plus Mini Kit (Qiagen)
RNA libraries were prepared for sequencing according to Illumina's instructions

treatment_protocol: vehicle (DMSO) or 2DG (250uM)

value: Naive CD4 T cells differentiated into Th17 cells


title: M2 Cell line-derived allograft Isotype control D115


title: 43-Veh

description: Vehicle3_0 (column name in processed data file LEH_glycolysis_dataset.txt)

value: Veh


title: Sample 1198_Single mESC cell


title: 42-Veh

description: Vehicle2_0 (column name in processed data file LEH_glycolysis_dataset.txt)


title: Sample 1196_Single mESC cell


title: Sample 1197_Single mESC cell


title: 42-2DG

description: 2DG2_0 (column name in processed data file LEH_glycolysis_dataset.txt)


title: Sample 1195_Single mESC cell


title: 17-2DG

description: 2DG1_0 (column name in processed data file LEH_glycolysis_dataset.txt)


title: 17-Veh

description: Vehicle1_0 (column name in processed data file LEH_glycolysis_dataset.txt)


title: Sample 1194_Single mESC cell


title: Sample 1200_Single mESC cell


title: Sample 1199_Single mESC cell


title: M2 Cell line-derived allograft Untreated D95


title: 10060-3

city: Worcester

first: Brian

last: Quattochi

state: MA

address: 364 Plantation Street

department: MCCB

institute: UMass Medical School

description: Small RNA

data_processing:
The 3' adaptor (TGGAATTCTCGGGTGCCAAGG) for sequencing was removed from the raw reads.
Reads with the length less than 10 were excluded.
Reads were mapped to miRbase version 21 using the miRDeep2 algorithm.
Genome_build: mm10
Supplementary_files_format_and_content: Processed data is provided in matrix format in a single XLSX file and contains the reads mappable to miRBase v21 controlled to sequencing depth, which is defined by the number of reads between 10 and 30bp in length.

source_name: Primary murine pancreatic tumor

growth_protocol: Murine pancreatic cancer cell lines were isolated by routine methods, involving mechanical disruption of a tumor sample and plating onto a tissue-culture-treated 10cm plate in DMEM supplemented with fetal bovine serum to 10% and penicillin/streptomycin. Prior to RNA isolation, tumor cells were plated to uniform density and allowed to adhere and grow for 48 hours to uniform 80% confluency.

extract_protocol:
One 10cm plate of confluent cells was scraped into 1mL of TRIzol, mixed with 200ul chloroform, precipitated into 250ul of isopropanol plus 250ul RNA precipitation solution (1.2M NaCl, 0.8M Na-citrate), then incubated at 4 degrees for 3hrs, then -20 degrees overnight. RNA was pelleted at 13,000rpm at 4 degrees celcius for 15 minutes, washed twice with 800ul ethanol and allowed to air dry prior to resolubilization in 100ul nuclease-free water. Total RNA samples were shipped to LC Sciences, who performed the small RNA isolation according to their own standard protocols.
Library construction was performed by LC Sciences according to their own standard protocols for multiplexing all samples in a single lane.

value: Pancreatic adenocarcinoma cell line

tag: dicer status

value: Dicer (wt/wt)

tag: passages


title: M2 Cell line-derived allograft Isotype control D100


title: M2 Cell line-derived allograft anti-CTLA4 D110


title: 1451-2

description: Small RNA


title: Sample 1193_Single mESC cell

value: Differentiated mESC


title: 10086-4

description: Small RNA


title: M2 Cell line-derived allograft Untreated D117


title: M2 Cell line-derived allograft anti-CTLA4 D104


title: 10087-5

description: Small RNA

value: Dicer (flox/wt)


title: 1448-3A

description: Small RNA


title: Sample 1192_Single mESC cell

value: day 0


title: M2 Cell line-derived allograft Isotype control D101

value: Isotype control


title: 1449-2A

description: Small RNA


title: M2 Cell line-derived allograft Untreated D111


title: 10060-1A

description: Small RNA


title: Sample 1191_Single mESC cell


title: M2 Cell line-derived allograft Untreated D108


title: 1447-4B

description: Small RNA


title: 1432-3A

description: Small RNA


title: M1 Cell line-derived allograft anti-CTLA4 A79

value: BrafCA/+; Ptenflox/+; Cdkn2aflox/+; Tyr-CreERT2-tg


title: Sample 1189_Single mESC cell


title: Sample 1190_Single mESC cell


title: Sample 1188_Single mESC cell


title: M1 Cell line-derived allograft Isotype control A88


title: Sample 1186_Single mESC cell


title: Sample 1187_Single mESC cell


title: Sample 1185_Single mESC cell


title: M1 Cell line-derived allograft Isotype control A71


title: M1 Cell line-derived allograft Isotype control A75


title: Sample 1184_Single mESC cell


title: M1 Cell line-derived allograft Untreated A90

value: Untreated


title: M1 Cell line-derived allograft Untreated A84


title: YZM_6475

city: Zhengzhou

first: Zhenyu

last: Zhang

address: Jian She Dong Road 1, Zhengzhou, Henan , China

institute: The First Affiliated Hospital of Zhengzhou University

data_processing:
After the library passed the inspection, the different libraries were pooled according to the requirements of effective concentration and target offline data volume, and then the Illumina PE150 was sequenced.
All RNA-seq data were normalized using the fragments per kilobase transcriptome per million reads (FPKM) method.
Genome_build: hg18
Supplementary_files_format_and_content: FPKM values, raw coutns for each Sample ...
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: Brain tissue

extract_protocol:
Fresh frozen tissues of 17 MB patients with MRI were used for RNA-seq.
Detection of RNA purity by NanoDrop™One/OneC（OD260/280, OD260/230）
Qubit™RNA HS Assay Kit is used for accurate quantification by fluorescence quantitative instrument （Life Invitrogen Qubit® 3.0）
Agilent 4200 Tapestation system accurately detects RNA integrity (RIN value)
After the samples pass the test, construct the library of samples using standard Illumina protocols
After the library was constructed successfully, Kapa qPCR and Agilent 4200 Tapestation were used to detect the library

treatment_protocol: Formalin-fixed paraffin embedded (FFPE) tissues were available in all the MB cases and used for detection of molecular subgroups based on a nanoString assay.

tag: subject status

value: medulloblastoma (MB) patient

tag: sex   male=1;female=2

tag: age at diagnosis

tag: resection extent   complete=1; incompelete=2

tag: radiation therapy    yes=1; no=2

tag: chemotherapy   yes=1; no=2

tag: preoperative kps

tag: postoperative kps

tag: overall survival(months)

tag: event-free survival  (months)

tag: recrudescence  yes=1；no=0

value: operation

value: Brain cell


title: LJQ_7006

tag: molecular subgroup by nanostring assay

value: Group 3

tag: treatment

tag: cell type


title: NYX_7010

value: WNT


title: MZY_7008

value: Group 4


title: YQY_7001


title: M1 Cell line-derived allograft Untreated A80

tag: strain

tag: genotype


title: M1 Cell line-derived allograft anti-CTLA4 A62


title: SYL_6473


title: LJR_7011


title: ZJX_7004


title: YYX_7003


title: ZXY_6999


title: M1 Cell line-derived allograft Untreated A67


title: Sample 1181_Single mESC cell

city: Stanford

tag: cell line

tag: day of differentiation


title: MJY_6998

tag: subject status

tag: sex   male=1;female=2

value: SHH


title: LJR_7012

tag: age at diagnosis

tag: resection extent   complete=1; incompelete=2


title: M1 Cell line-derived allograft anti-CTLA4 A61


title: ZKY_7000

tag: radiation therapy    yes=1; no=2

tag: chemotherapy   yes=1; no=2


title: HQE_6474

tag: preoperative kps

tag: postoperative kps


title: M4 GEM-derived allograft

data_processing:
Library strategy: Exome-seq
Quality checking (trimming/masking if necessary), alignment/mapping to the reference genome; Variant calling (SNVs and indels) and comparisons between the conditions; IGV visualizations.
Using combination of Galaxy on Helix and Bioconductor /R packages
Single nucleotide variants (SNV) were identified using samtools mpileup or GATK HaplotypeCaller. Mouse germline single nucleotide polymorphisms (SNPs) were filtered out using the Sanger Mouse Genomes Project database
Variants with a Phred-scaled quality score of <30 were removed.  Variants that are present in normal spleen samples (in-house collection) were also removed.
Variants were annotated with Annovar software to identify non-synonymous mutations.
Genome_build: UCSC reference Genome Sequence, mouse mm10
Supplementary_files_format_and_content: vcf files include variants for each sample
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample …

value: Hgftg


title: Sample 1179_Single mESC cell


title: Sample 1182_Single mESC cell


title: Sample 1180_Single mESC cell


title: M3 GEM-derived allograft

value: Cdk4R24C; Hgftg


title: Sample 1183_Single mESC cell


title: Sample 1178_Single mESC cell


title: DJL_7005

tag: overall survival(months)

tag: event-free survival  (months)


title: CCY_7007

tag: molecular subgroup by nanostring assay

tag: recrudescence  yes=1；no=0


title: CHY_7002

tag: treatment

tag: cell type


title: M2 GEM-derived allograft

tag: strain

tag: genotype

value: BrafCA/+; Cdkn2aflox/+; Tyr-CreERT2-tg; Hgftg


title: Sample 1177_Single mESC cell

tag: cell line

tag: day of differentiation


title: M1 GEM-derived allograft


title: Sample 1176_Single mESC cell


title: Sample 1175_Single mESC cell


title: M3 Cell line (HCmel1274)

source_name: Melanoma cell line


title: M4 Cell line (B2905)


title: Sample 1173_Single mESC cell


title: Sample 1174_Single mESC cell


title: NSC-CB660-TERT sgTP53 replicate 2

city: Seattle

first: Sonali

last: Arora

state: WA

address: 1100 Fairview Ave N,

institute: FHCRC

description: NSC-CB660-TERT with CRISPR KO of TP53; cell pool; replicate 2

data_processing:
Sequencing was performed using an Illumina HiSeq 2000 in Rapid Run mode and employed a paired-end, 100 base read length (PE100) sequencing strategy.
RNA-seq reads were aligned to the UCSC hg19 assembly using STAR2 and counted for gene associations against the UCSC genes database with HTSeq.
Genome_build: hg19
Supplementary_files_format_and_content: Tab-delimited text files include raw values for each sample.

extract_protocol:
Cells were lysed with Trizol (Thermo Fisher Scientific). Total RNA was then isolated using a Direct-zol RNA kit (Zymo Research) and quality validated on the Agilent 2200 TapeStation. RNA concentration was measured using a NanoDrop 1000 Spectrophotometer (Thermo Fisher Scientific).
RNA libraries were prepared for sequencing using standard Illumina protocols.

value: CRISPR KO of TP53


title: NSC-CB660-TERT sgTP53 + sgCDKN2A + sgPTEN replicate 1

description: NSC-CB660-TERT with CRISPR KO of TP53, CDKN2A, and PTEN; cell pool; replicate 1

value: CRISPR KO of TP53, CDKN2A, and PTEN


title: NSC-CB660-TERT sgTP53 + sgCDKN2A replicate 2

description: NSC-CB660-TERT with CRISPR KO of TP53 and CDKN2A; cell pool; replicate 2

value: CRISPR KO of TP53 and CDKN2A


title: NSC-CB660-TERT sgTP53 + sgCDKN2A + sgPTEN +sgNF1 CLONE 1 replicate 1

description: NSC-CB660-TERT with CRISPR KO of TP53, CDKN2A, PTEN, and NF1; CLONE 1; replicate 1


title: NSC-CB660-TERT sgTP53 + sgCDKN2A replicate 1

description: NSC-CB660-TERT with CRISPR KO of TP53 and CDKN2A; cell pool; replicate 1


title: NSC-CB660-TERT sgTP53 + sgCDKN2A + sgPTEN +sgNF1 replicate 1

description: NSC-CB660-TERT with CRISPR KO of TP53, CDKN2A, PTEN, and NF1; cell pool; replicate 1


title: NSC-CB660-TERT sgTP53 replicate 1

description: NSC-CB660-TERT with CRISPR KO of TP53; cell pool; replicate 1


title: NSC-CB660-TERT sgTP53 + sgCDKN2A + sgPTEN replicate 2

description: NSC-CB660-TERT with CRISPR KO of TP53, CDKN2A, and PTEN; cell pool; replicate 2


title: M2 Cell line (B9013HCB)


title: NSC-CB660-TERT sgTP53 + sgCDKN2A + sgPTEN +sgNF1 replicate 2

description: NSC-CB660-TERT with CRISPR KO of TP53, CDKN2A, PTEN, and NF1; cell pool; replicate 2


title: NSC-CB660-TERT replicate 1

description: NSC-CB660-TERT replicate 1

value: wild type


title: M1 Cell line (Mel114433)


title: NSC-CB660-TERT replicate 2

description: NSC-CB660-TERT replicate 2


title: Sample 1172_Single mESC cell

value: Differentiated mESC

value: day 0


title: Sample 1171_Single mESC cell


title: week6_mature_mafko_gd_M5_8

first: Sagar

address: Hugstetter Straße 55

institute: University Medical Center Freiburg

description: library of 96 Maf KO mature gamma delta T cells

data_processing:
For image aquisition, intensity extraction and basecalling HiSeq Control Software  2.0.2, RTA 2.4.11 / Recipe Fragment 2.0.0.2 was used. Conversion of bcl2fastq files was performed using bcl2fastq 2.17.1.14
Paired end reads were aligned to the transcriptome using bwa (version 0.6.2-r126) with default parameters. The transcriptome contained all gene models based on the mouse ENCODE VM9 release downloaded from the UCSC genome browser comprising 57,207 isoforms derived from 57,207 gene loci with 57,114 isoforms mapping to fully annotated chromosomes (1 to 19, X, Y, M). All isoforms of the same gene were merged to a single gene locus. Furthermore, gene loci overlapping by >75% were merged to larger gene groups. This procedure resulted in 34,111 gene groups.
The right mate of each read pair was mapped to the ensemble of all gene loci and to the set of 92 ERCC spike-ins in sense direction. Reads mapping to multiple loci were discarded. The left read contains the barcode information: the first six bases correspond to the cell specific barcode followed by six bases representing the unique molecular identifier (UMI). The remainder of the left read contains a poly(T) stretch. The left read was not used for quantification. For each cell barcode, the number of UMIs per transcript was counted and aggregated across all transcripts derived from the same gene locus.
Based on binomial statistics, the number of observed UMIs was converted into transcript counts (Gruen et al., 2014).
Genome_build: ENCODE VM9
Supplementary_files_format_and_content: CSV files, columns represent each cell barcode (total barcodes used = 192), rows represent the geneid and the values in the file are the quantified number of transcripts.

tag: strain background

tag: genotype/variation

value: Maf KO

tag: Sex

value: female

tag: age/developemental stage

value: 6-7 weeks

tag: tissue

value: Thymus

value: mature gamma delta T cells


title: iPSC-derived astrocytes, C9-L5

city: Jerusalem

first: Benjamin

last: Reubinoff

state: Jerusalem

address: Kiryat Hadassah

department: The Goldyne Savad Institute of Gene Therapy

country: Israel

institute: Hadassah  University Medical Center

data_processing:
Raw reads were trimmed to length 50 using FASTX (version 0.0.14), then quality-trimmed at their 3' end with threshold 32.
Adapter sequences were removed with Trim Galore (version 0.3.7), using default parameters and keeping reads of at least 15 nt after trimming.
The remaining reads were further filtered to remove very low-quality reads, using the fastq_quality_filter program of the FASTX package, with parameters -q 20 and -p 90.
Processed reads were aligned using TopHat (v2.0.13). Parameters were -N 3, --read-gap-length 5, --read-edit-dist 8, --segment-length 20 and --read-realign-edit-dist 5. Gene annotations from Ensembl release 78 were provided by the -G parameter.
Differential expression was done with Cufflinks package (v2.2.1). The cuffquant program was used for quantification with parameters -b, -u and masking for rRNA (-M). The cuffdiff program was run with default parameters on the cuffquant output.
Significantly differentially expressed genes were defined as ones with at least 0.3 FPKM level of expression in at least one of the conditions and a q-value less than 0.05.
Genome_build: GRCh38
Supplementary_files_format_and_content: Excel table contains the results of differential expression analysis. The first 2 rows are header rows, then data rows for each gene. Columns include general gene details, followed by Cufflinks' FPKMs in each sample, then by columns for the cuffdiff results. The last column is for filtering significantly differentially expressed genes, as defined in this study: genes with at least 0.3 FPKM level of expression in at least one of the conditions and a q-value less than 0.05.

source_name: iPSC-derived astrocytes

growth_protocol: Differentiation of iPSCs into spinal cord astrocytes was performed using a previously published protocol with slight changes directing neural precursor cells to acquire spinal cord specification [25,26]. Briefly, iPSC colonies were detached from the feeder cells using collagenase type IV, collected, centrifuged and re-suspended in NSCR medium (AdDMEM/F12 supplemented with 1% N2 and 0.1% B27, 1% nonessential amino acids, 1% penicillin/streptomycin, 1% GlutaMAX solution (all from Invitrogen) and distributed into 6-12 low cell attachment well plates to avoid adhesion. For neural induction, NSCR medium was supplemented with 10 mM SB431542 (Biogems, Westlake Village, CA, USA), 2.5 mM Dorsomorphin (Calbiochem) and 0.5 mM N-acetylcysteine (Sigma) for the first 4 days. At day 4, 1 mM retinoic acid (RA, Sigma-Aldrich, St. Louis, MO, USA) was added to medium. At day 7, 500 mM Purmorphamine (Biogems) was added to medium. At day 11 SB431542, Dorsomorphin, retinoic acid, and Purmorphamine were omitted. The neurospheres were mechanically chopped at the beginning of the glial enrichment phase and cultured in NSCR medium with addition of 20 ng/mL leukemia inhibitory factor (LIF) and 20 ng/mL epidermal growth factor (EGF)(PeproTech) for 3 weeks. After enrichment, the spheres were propagated in NSCR medium for 3 weeks. After this, monolayer cultures were generated by dissociating the spheres using Accutase (Gibco-BRL) for 10 min/ 37 °C and single cells or small clumps were plated on plates coated with Matrigel (BD Biosciences; 1:80 dilution). The monolayer of astrocyte precursor cells (APC) cultures were propagated in NSCR medium supplemented with 20 ng/mL EGF, 20 ng/mL basic fibroblast growth factor (bFGF, PeproTech) for 3 weeks and passaged when confluent by using Accutase (Sigma, split ratio 1:21:3). Astrocyte populations were obtained by differentiating the APCs for at least 30 days of final differentiation with AstroMED (Neurobasal supplemented with 0.2% B27, 1% nonessential amino acids, 1% penicillin/streptomycin, 1% GlutaMAX solution (all from Invitrogen) with 10 ng/mL ciliary neurotrophic factor (CNTF, PeproTech). Astrocytes were passaged using Try:EDTA solution (1:10) for 2 min to fresh Matrigel every week or two based on confluence. In each of the experiments, the passage number and the time in culture of each line were identical. The passage number in all experiments did not exceed passage 10. All astrocyte lines (C9-mutated and control) went through the same passage scheduling. Until passage 4 all cell lines were split at a ratio of 1:4. A tendency to divide slower with each passage was observed in all lines but was more prominent in the C9-mutated lines. Hence, from passage 5 onward, the split ratio of each line was individualized according to the number of cells that were harvested.

extract_protocol:
Total RNA was extracted using 5 PRIME PerfectPure RNA Purification kit (Gentra Systems, Inc.).
cDNA libraries were produced according to Illumina TruSeq RNA protocol.

tag: days of final differentiation

value: iPSC-derived astrocytes


title: week6_mature_mafko_gd_M5_7

city: Freiburg

source_name: library of 96 Maf KO mature gamma delta T cells


title: iPSC-derived astrocytes, Contr-L3

treatment_protocol: All astrocyte lines (C9-mutated and control) went through the same passage scheduling.

value: control


title: iPSC-derived astrocytes, Contr-L9


title: Sample 1170_Single mESC cell


title: sDFBSLO3L1

city: Madison

first: Ali

last: Fathi

state: WI

address: 1500 Highland Ave. Rm 641D, Waisman Center

department: Waisman Center

institute: University of Wisconsin

data_processing:
The trimming software skewer (Jiang et al. 2014) was used to preprocess raw fastq files. Skewer implements an efficient dynamic programming algorithm designed to remove adapters from Illumina-generated sequence reads.
The trimmed reads are aligned against to hg9 whole genome sequence using STAR (Spliced Transcripts Alignment to a Reference) (Dobin et al. 2013).,  using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: hg9
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample ...

source_name: cortical neuron

growth_protocol: ES cell–derived cortical progenitors at day 14 after differentiation  were routinely generated by re-plating d 14 sphere neural differentiation cultures (typically 2–3 × 106 cells into a 1 well of 6well plates) on PLO/Laminin coated plates in Neurobasal medium (GIBCO) supplemented with B27.

extract_protocol:
All experiments were run three times and RNA was extracted from all samples (3 biological replicates and 3 technical replicates) using the RNeasy Plus Mini kit (Qiagen) following manufacturer’s instructions. RNA quality was assessed using an Agilent RNA NanoChip08 with all samples passing QC.
Sample libraries were prepared using poly-A selection using an Illumina TruSeq RNAv2 kit following manufacturer’s instructions.

treatment_protocol: Cells treated with SLO compounds for five days starting at day 21 (total 26 days from differentiation)

tag: age

value: Embryonic

value: H9 Embryonic stem cell

tag: passage


title: week6_mature_mafko_gd_M5_4_11


title: Sample 1169_Single mESC cell


title: sDFBSLO2L1


title: sDFBSLO1L1


title: week6_mature_mafko_gd_M5_3_10


title: sDFBCTR3L1


title: Sample 1167_Single mESC cell


title: Sample 1168_Single mESC cell


title: sDFBCTR1L1


title: Sample 1165_Single mESC cell


title: Sample 1166_Single mESC cell


title: week6_mature_mafko_gd_M5_2_11


title: RKO KMT2C KI2 H3K4me1

first: Chatarina

last: Larsson

address: Rudbeck Laboratory

department: Immunology, Genetics and Pathology

institute: Uppsala University

description: Raw data for anti-histone H3K4me1 and input provided

data_processing:
ChIP-seq data were aligned using Bowtie 2 (default parameters). BAM files were uploaded into Seqmonk (http://www.bioinformatics.babraham.ac.uk/projects/seqmonk/).
Peak calling was performed with MACS peak builder in Seqmonk.
FANTOM5 enhancers were identified by bidirectional transcription using the capped analysis of gene expression technique and obtained from the FANTOM data resource online (http://enhancer.binf.ku.dk/presets/). H3K4me1 signal was quantified by calculating the log2 of the reads per million for each sample relative to input (ChIP/Input).
Genome_build: GRCh37/hg19
Supplementary_files_format_and_content: Data given are the H3K4me1 ChIP-seq peaks identified with MACS using Seqmonk given in BED file format for GRC37/hg19. Supplementary file contains ChIP/Input scores at human enhancers from the FANTOM 5 project for each sample.

source_name: Cell culture

growth_protocol: The parental and KMT2C knock-in cell lines were cultured in McCoy’s 5 A medium (Gibco, /Life Technologies, cat. no 26600-080) with 10% heat inactivated FBS.

extract_protocol:
Cells were fixed in 1% paraformaldehyde for 8 minutes. Chromatin was analyzed by ChIP-sequencing the Diagenode iDeal ChIP-seq kit for histones according to the manufacturer’s instructions. Chromatin extracts from one million cells were sonicated to yield 100 to 500 bp fragments using a Bioruptor Pico sonication device (Diagenode) on high power for two rounds of 6 cycles with 30 s on 30 s off at 4 °C. ChIP-seq was performed using 1 microgram of H3K4me1 antibody  (ab8895, Abcam) per ChIP. Cross-links were reversed (4 h at 65 °C) and DNA was purified using the Qiagen MinElute PCR purification kit. Samples were quantified using Qubit (HS dsDNA) and 10 ng of DNA was used for library preparation.
Libraries were prepared for sequencing using the NEBNext® ChIP-Seq Library Prep Reagent Set for Illumina® and sequenced on a HiSeq 2500 System (Illumina).

value: RKO ATCC CRL-2577

value: KMT2C KI2

tag: chip antibody

value: Anti-Histone H3K4me1

tag: chip antibody source

value: Abcam ab8895


title: week6_mature_mafko_gd_M2_16


title: HCT116 KMT2C KI1 H3K4me1

value: HCT116 ATCC CCL-247


title: RKO parental H3K4me1

value: parental


title: iPSC-derived astrocytes, C9-L8


title: HCT116 parental H3K4me1


title: sDFBCTR2L1


title: week6_mature_mafko_gd_M2_15


title: Sample 1164_Single mESC cell

value: Differentiated mESC