title: RNA_T78_SD_T78S4_L

value: SD


title: HS360-Day0-RNA-seq-rep2

status: Public on Jul 01 2024

type: SRA

city: Oslo

first: Mari

last: Spildrejorde

state: OSLO

address: Sognsvannsveien 9

department: Research and Innovation, Neuroscience research unit

country: Norway

institute: Oslo University Hospital

description:
Day 0", "male", "hESCs", "control
344-D0-CTRL-B

library_source: transcriptomic

data_processing:
BBDuk (BBMap v. 34.56) was used to reomve and trim low-quality reads and adaptor sequences with the following configurations: ktrim=r k=23 mink=11 hdist=1 tbo tpe qtrim=r trimq=15 maq=15 minlen=36 forcetrimright=149
Reads were mapped to the human genome/transcriptome ENSEMBL GRCh38 2020-A using hisat2 v2.1.0
FeatureCounts v.1.4.6-p1 was used to count the reads mapping to the features using default configurations
Downstream normalisation and differential expression analysis was performed using R software EdgeR package v3.38.4.
Assembly: ENSEMBL GRCh38 2020-A release-98
Supplementary files format and content: Count file with data matrix with unnormalized counts for each sample. Additionaly, "cpm.csv" contains a normalized count matrix (counts per million) for all samples.

molecule: total RNA

organism: Homo sapiens

growth_protocol: Human embryonic stem cells HS360 (Karolinska Institutet, Sweden, RRID:CVCL_C202) were maintained in Essential 8™ Medium, in feeder-free conditions on Geltrex™ Matrix solution pre-coated culture plates.Culture media were replaced daily and cells were routinely passaged at 75-85% confluency using 0.5 mM EDTA in ratios between 1:3 to 1:6.

extract_protocol:
Total RNA was extracted from cultured cells using Norgen RNA/DNA purification kit or Qiagen RNeasy kit and treated with DNase according to manufacturer´s instructions.
Illumina TruSeq Stranded mRNA Library Prep kit was used to contruct the sequencing library according to manufacturer´s instructions. Libraries were sequenced on an Illumina Novaseq 6000 S1 flow cell with 100bp pair end reads.

treatment_protocol: In brief, at Day 0 HS360 hESCs grown in E8 were collected with Accutase and seeded in Geltrex precoated 12 well dishes. Single-cell suspensions were transferred to E8 medium containing 10 µM Rock inhibitor and at Day 1, the culture medium was switched to neural induction medium (NIM; Advanced DMEM/F12, 1% GlutaMAX, 1% Penicillin/Streptomycin, 1% N2). During days 2 to 6, media were changed daily and the LSX combo (LDN-193189, SB431542, XAV939) was added fresh to NIM. Cells were collected at Day 7 for passaging into the self patterning phase, counted and seeded on 12 well plates sequentially precoated with polyornithine (PO), fibronectin (F) and Geltrex. At Day 7 the Stage II neural self-patterning (NSPM) medium (Advanced DMEM/F12, 1% GlutaMAX, 1% Penicillin/Streptomycin, 1% N2, 1% B27) was supplemented with 10 µM Rock inhibitor. Culture medium was changed daily till day 13.  For cells that were exposed to either 50-400 nM citalopram, fresh media with citalopram was added every day from Day 1 until collection day (Day 6, 10 and 13)

tag: cell line

tag: cell type

value: day 0, hESCs undifferentiated

tag: treatment

value: Day 0 control


title: RNA_T78_SD_T78S3_L

city: Lausanne

first: Maxime

last: Jan

state: Suisse

address: University of Lausanne

department: CIG

country: Switzerland

institute: University of Lausanne

data_processing:
Gene quantification was performed as follow for liver samples: Illumina reads were filtered using fastp to keep high quality reads and remove adapter sequences. Reads were aligned on the mouse reference genome mm10 (GRCm38) using STAR v2.7.0e with default parameters. Read counts was done by STAR using “--quantMode GeneCounts”, taking only reverse strand mapped reads. Genes with low counts (mean counts overall samples < 10) were filtered and normalization was performed with edgeR. Batch effects were corrected by ComBat.
Assembly: mm10
Supplementary files format and content: Gene expression [log2 CPM]

organism: Mus musculus

source_name: Liver

growth_protocol: Mice were housed under standard conditions according to the Swiss Animal Protection Act, under a 12h:12h light/dark cycle, with food accessible ad libitum at all times.

extract_protocol:
Mice were anesthetized with isoflurane prior to decapitation. Liver was rapidly dissected and flash frozen in liquid nitrogen. Frozen Liver of each individual was ground in liquid nitrogen and stored at -140°C until further use.
Total RNA was extracted using the miRNeasy kit (Qiagen; Hilden, Germany) following the manufacturer's instructions. RNA-seq libraries were prepared using 10 ng/μl of total RNA and the Illumina TruSeq Stranded mRNA reagents (Illumina; San Diego, CA, USA). Libraries were sequenced on the Illumina HiSeq 4000 sequencer, producing >24 million mappable single-end reads.

treatment_protocol: Mice for tissue collection were divided into two experimental cohorts, sleep deprived (SD) and non-sleep deprived (controls, Ctr). After a one-week habituation to the experimental setting, at the age of 11-12 weeks, the SD mice were sleep-deprived by gentle handling for 6 hours starting at light onset (zeitgeber time ZT0-ZT6), and allowed to recover according to the tissue collection schedule.

tag: tissue

value: Liver

tag: ztime

tag: time

tag: condition

tag: batch


title: 4T1, Day4, single cell 322

city: Beijing

first: Hanqiu

last: Zheng

address: Haidian District

country: China

institute: Tsinghua university

library_source: transcriptomic single cell

data_processing:
Raw reads were first analyzed for quality control using FastQC (v0.11.7) (Andrews, 2010). Adaptor sequences of raw reads were removed by using TrimGalore (v0.6.6) (https://github.com/FelixKrueger/TrimGalore). Trimmed reads were mapped to a concatenated mouse genome (mm10) with STAR (v2.6.0c) with default parameters to result SAM format files (Dobin et al., 2013). Aligned reads stored in SAM format were transformed to generate BAM files using SAMtools (v1.7) (Danecek et al., 2021). The gene-level read count matrix was summarized from BAM files using FeatureCounts program (v1.6.2) (Liao et al., 2014). Subsequent data analysis was carried out in R 3.6.2 and the Seurat package (v3.1.2) (Stuart et al., 2019).
The gene counts per cell, the percentage of mitochondrial transcripts, the percentage of ERCC RNA spike-in, the percentage of α and β-globin genes were computed using the functions of the Seurat package. Quality controls were performed following: a. Cells with luciferase or GFP sequence detected were kept for further analysis. b. Cells with transcripts counts lower than 5 × 105 or higher than 1 ×107 were discarded. c. Single cell libraries with number of detected gene lower than 5,000, mapping rate lower than 40% or the percentage of mitochondrial transcripts higher than 10% were discarded before further analysis. d. Libraries with the percentage of α and β-globin genes higher than 1% were also discarded. 424 single cells passed quality controls, and were used for further analysis. The gene expression level was normalized as log2(TPM/10 + 1), in which TPM is the abbreviation for transcripts per million, and adding one to avoid negative expression values.
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

molecule: polyA RNA

extract_protocol:
Reverse transcription and cDNA amplification were carried out using a modified Smart-seq2 protocol (Picelli et al., 2014). Single cells were sorted by FACS as described above into 96-well plates containing 0.1 μl of RNase inhibitor (Clontech, Cat# 2313A), 1.9 μl of 0.2% Triton X-100 (Sigma, Cat# T9284), 1 μl of 10 µM oligo-dT primer (5′-AAGCAGTGGTATCA ACGCAGAGTAC T30VN-3′) and 1 μl of dNTP mix (10 mM each; Fermentas, Cat# R0192) in each well. Plates were either stored at -80 °C or processed immediately. Reverse transcription, PCR preamplification, PCR purification were performed following Picelli’s protocol (Picelli et al., 2014). As mRNA quality control, 1 ul of each PCR product was used as template for qPCR detection of mCherry expression and samples with Ct value higher than 30 will be discard. PCR products were purified with 1 × Agencourt Ampure XP beads (Beckman Coulter, Cat# A63881) and the final product was reconstituted in 20 µl TE buffer. The concentration of cDNA was measured by Qubit™ 1× dsDNA High Sensitivity (HS) Assay Kit (Invitrogen, Cat# Q33230). Tagmentation and NGS library was carried out by using TruePrep DNA Library Prep Kit V2 for Illumina (Vazyme, Cat# TD503) following the manufacturer’s instructions. The purified library was qualify controlled by measuring the fragment size distribution with an Agilent HS DNA BioAnalyzer Chip and the concentration of library was measured with Qubit™ 1× dsDNA High Sensitivity (HS) Assay Kits following the manufacturer’s instructions. Single cell cDNA libraries were sequenced on an Illumina HiSeq X Ten platform to obtain paired-end 150-bp reads.
SMART-Seq2 (Picelli et al., 2014)

tag: host

value: Female BALB/c mice

value: metastatic tumor cells


title: RNA_T78_SD_T78S2_L


title: HS360-Day6-CIT200-RNA-seq-rep4

description:
Day 6", "male", "neural rosettes", "neural induction", "citalopram", "CIT200", "200 nM citalopram
337-D6-CIT200-D

value: day 6, neural induction, exposed to 200 nM citalopram

value: Day 6 200 nM citalopram


title: S14_Control_Male [198_1_S14]

city: Houston

first: Tina

middle: Oak

last: Findley

state: TX

address: 6431 Fannin Street, MSB 3.224

department: Pediatrics

country: USA

institute: University of Texas Health Science Center at Houston

data_processing:
Cutadatp
Raw mRNA sequence reads were processed usingCutadatpand the bases with quality scores less than 20 were removed.
Filtered RNA-sequence reads were aligned to the human reference genome (GRCh38.102) and gene read counts were generated by STAR.
Assembly: GRCh38.102
Supplementary files format and content: tab-delimited text file includes raw counts for each sample

source_name: Blood

extract_protocol:
RNA-stabilized samples were thawed and incubated for a minimum of 2 hours at room temperature to allow for complete lysis of blood cells.
Total RNA extraction was performed using RNeasy®blood kits in accordance with themanufacturer’s protocol (Qiagen, Germantown, Maryland).

value: Blood

tag: gender

value: Male

tag: group

value: Control


title: S13_Hypoxic_Male  [195_2_S13]

value: Hypoxic


title: 4T1, Day4, single cell 317


title: 4T1, Day4, single cell 316


title: RNA_T72_SD_T72S4_L


title: 4T1, Day4, single cell 321


title: S12_Hypoxic_Male  [157_1_S12]


title: HS360-Day6-CIT100-RNA-seq-rep5

description:
Day 6", "male", "neural rosettes", "neural induction", "citalopram", "CIT100", "100 nM citalopram
335-D6-CIT100-E

value: day 6, neural induction, exposed to 100 nM citalopram

value: Day 6 100 nM citalopram


title: 4T1, Day4, single cell 315


title: RNA_T72_SD_T72S3_L


title: 4T1, Day4, single cell 314


title: RNA_T72_SD_T72S2_L


title: HS360-Day6-CIT100-RNA-seq-rep4

description:
Day 6", "male", "neural rosettes", "neural induction", "citalopram", "CIT100", "100 nM citalopram
334-D6-CIT100-D


title: S11_Hypoxic_Female [150_1_S11]

value: Female


title: S10_Hypoxic_Female  [131_2_S10]


title: HS360-Day6-CIT50-RNA-seq-rep6

description:
Day 6", "male", "neural rosettes", "neural induction", "citalopram", "CIT50", "50 nM citalopram
333-D6-CIT50-F

value: day 6, neural induction, exposed to 50 nM citalopram

value: Day 6 50 nM citalopram


title: RNA_T66_SD_T66S5_L

value: SD


title: 4T1, Day4, single cell 312


title: HS360-Day6-CIT50-RNA-seq-rep5

description:
Day 6", "male", "neural rosettes", "neural induction", "citalopram", "CIT50", "50 nM citalopram
332-D6-CIT50-E


title: S9_Hypoxic_Female  [114_1_S9]


title: HS360-Day6-CIT50-RNA-seq-rep4

description:
Day 6", "male", "neural rosettes", "neural induction", "citalopram", "CIT50", "50 nM citalopram
331-D6-CIT50-D


title: HS360-Day6-CIT100-RNA-seq-rep6

description:
Day 6", "male", "neural rosettes", "neural induction", "citalopram", "CIT100", "100 nM citalopram
336-D6-CIT100-F


title: S8_Control_Female [111_1_S8]


title: HS360-Day6-RNA-seq-rep6

description:
Day 6", "male", "neural rosettes", "neural induction
330-D6-CTRL-F

value: day 6, neural induction

value: Day 6 control


title: 4T1, Day4, single cell 310


title: S6_Control_Male [99_1_S6]


title: RNA_T60_SD_T60S2_L

value: Liver


title: HS360-Day6-RNA-seq-rep5

description:
Day 6", "male", "neural rosettes", "neural induction
329-D6-CTRL-E


title: 4T1, Day4, single cell 308

value: Female BALB/c mice


title: 4T1, Day4, single cell 307

value: metastatic tumor cells


title: RNA_T6_NSD_T6N3_L

value: NSD


title: 4T1, Day4, single cell 313


title: RNA_T6_NSD_T6N2_L


title: RNA_T6_NSD_J76N1_L


title: HS360-Day6-CIT400-RNA-seq-rep3

description:
Day 6", "male", "neural rosettes", "neural induction", "citalopram", "CIT400", "400 nM citalopram
327-D6-CIT400-C

value: day 6, neural induction, exposed to 400 nM citalopram

value: Day 6 400 nM citalopram


title: 4T1, Day4, single cell 306


title: HS360-Day6-CIT400-RNA-seq-rep2

description:
Day 6", "male", "neural rosettes", "neural induction", "citalopram", "CIT400", "400 nM citalopram
326-D6-CIT400-B


title: 4T1, Day4, single cell 311


title: S3_Control_Male [80_1_S3]

value: Blood

value: Male


title: RNA_T54_SD_T54S4_L


title: RNA_T66_SD_T66S3_L


title: RNA_T60_SD_T60S4_L


title: HS360-Day6-CIT400-RNA-seq-rep1

description:
Day 6", "male", "neural rosettes", "neural induction", "citalopram", "CIT400", "400 nM citalopram
325-D6-CIT400-A


title: S2_Control_Female [50_1_S2]

value: Control


title: S7_Control_Male [100_1_S7]


title: 4T1, Day4, single cell 304


title: RNA_T54_SD_T54S2_L


title: 4T1, Day4, single cell 303


title: 4T1, Day4, single cell 309


title: RNA_T54_SD_T54S1_L


title: S5_Control_Male [83_1_S5]


title: S1_Hypoxic_Female  [11_1_S1]

value: Hypoxic


title: HS360-Day6-CIT200-RNA-seq-rep3

description:
Day 6", "male", "neural rosettes", "neural induction", "citalopram", "CIT200", "200 nM citalopram
324-D6-CIT200-C

value: day 6, neural induction, exposed to 200 nM citalopram

value: Day 6 200 nM citalopram


title: HS360-Day6-CIT200-RNA-seq-rep1

description:
Day 6", "male", "neural rosettes", "neural induction", "citalopram", "CIT200", "200 nM citalopram
322-D6-CIT200-A


title: HS360-Day6-CIT200-RNA-seq-rep2

description:
Day 6", "male", "neural rosettes", "neural induction", "citalopram", "CIT200", "200 nM citalopram
323-D6-CIT200-B


title: HS360-Day6-RNA-seq-rep4

description:
Day 6", "male", "neural rosettes", "neural induction
328-D6-CTRL-D


title: 4T1, Day4, single cell 302


title: 4T1, Day4, single cell 300


title: RNA_T48_SD_T48S4_L


title: S4_Hypoxic_Male  [81_1_S4]


title: RNA_T48_SD_T48S3_L


title: MiaGR_Rep3

city: Loma Linda

first: Nathan

middle: R

last: Wall

state: California

address: 11234 Anderson St, Loma Linda LLUMC B Level Room B125, CA 92354,

institute: Loma Linda University

description: miRNA-seq

data_processing:
All sequencing data were demultiplexed and converted to fastq files using bcl2fastq. Read length was set to 78bp single-end
After quality control with the FastQC tool, fastq files were processed using the QIAseq miRNA Quantification feature provided by Qiagen’s GeneGlobe Data Analysis Center.
Adaptors from read sequences were trimmed and low-quality bps were removed by Cutadapt.
Reads with less than 16bps and 10 assigned index counts were excluded from the analysis. Reads were aligned to miRbase (v21) using Bowtie with no more than 2 mismatches.
Reads with more than 20 assigned index counts were used for differential expression analysis by R/Bioconductor software package, DESeq2.
Assembly: miRbase (v21)
Supplementary files format and content: processed file includes miRNA spectral counts from Mia_repX (parental) and MiaGR_repX (resistant). miRNA listed includes all miRNA recorded in miRbase (v21)

source_name: pancreas

growth_protocol: cells cultured at 37c in 5%co2 with standard growth media. GR cells were cultured with 500nm Gem in addition to standard growth media.

extract_protocol:
Basic Trizol reagent (Invitrogen) extraction
QIAseq miRNA library was used for library construction. Amplified cDNA fragments were double size selected by using QIAseq magnetic beads for fragments of cDNA with 150~200 bp. Libraries were quantified by the Qubit 3.0 HS dsDNA assay. Library size and quality were examined using the TapeStation 2200
miRNA-seq /  enriched >200nt RNA-seq

treatment_protocol: Gem resistance was conveyed through incrementally increasing GR concentrations over time. Briefly, we started with 16 nm Gem until death decreased and growth increased, at which point we scaled resistance by small dose increases up to 500nm Gem, where cells were maintained in from then on.

value: pancreas

value: MIA-PaCa-2 Gem Resistant

value: Adapted Resistance MIA PaCa-2 CRL-1420

tag: genotype

value: Treated (GEM)

value: continuous 500nm Gemcitabine


title: RNA_T42_SD_T42S4_L

value: Liver

value: SD


title: MiaGR_Rep1

description: miRNA-seq


title: Mia_Rep2

description: miRNA-seq

value: MIA PaCa-2 CRL-1420

value: WT


title: RNA_T48_SD_T48S1_L


title: MiaGR_Rep2

description: miRNA-seq


title: 4T1, Day4, single cell 299

value: Female BALB/c mice

value: metastatic tumor cells


title: HS360-Day6-CIT100-RNA-seq-rep3

description:
Day 6", "male", "neural rosettes", "neural induction", "citalopram", "CIT100", "100 nM citalopram
321-D6-CIT100-C

value: day 6, neural induction, exposed to 100 nM citalopram

value: Day 6 100 nM citalopram


title: 4T1, Day4, single cell 305


title: 4T1, Day4, single cell 301


title: HS360-Day6-CIT100-RNA-seq-rep2

description:
Day 6", "male", "neural rosettes", "neural induction", "citalopram", "CIT100", "100 nM citalopram
320-D6-CIT100-B


title: RNA_T42_SD_T42S2_L


title: 4T1, Day4, single cell 298


title: HS360-Day6-CIT50-RNA-seq-rep3

description:
Day 6", "male", "neural rosettes", "neural induction", "citalopram", "CIT50", "50 nM citalopram
318-D6-CIT50-C

value: day 6, neural induction, exposed to 50 nM citalopram

value: Day 6 50 nM citalopram


title: HS360-Day6-CIT100-RNA-seq-rep1

description:
Day 6", "male", "neural rosettes", "neural induction", "citalopram", "CIT100", "100 nM citalopram
319-D6-CIT100-A


title: Mia_Rep3

description: miRNA-seq

value: Control


title: Mia_Rep1

description: miRNA-seq


title: RNA_T36_SD_T36S2_L


title: RNA_T36_SD_T36S4_L


title: 4T1, Day4, single cell 297


title: (-Glc) KO2 RNAseq exp2

city: Los Angeles

first: Cunyu

last: Wang

state: CA

address: 10833 Le Conte Ave

department: School of Dentistry

institute: university of California, Los Angeles

description: Low Glucose condition

data_processing:
FASTQ sequences were mapped to human genome hg38(GRCh38) by Hisat2.
For the uniquely mapped reads, FeatureCounts were used to count the reads mapped to each gene
Supplementary files format and content: raw gene count

source_name: SCC23 HNSCC cells

growth_protocol: Human HNSCC cell line SCC23 was obtained from the University of Michigan, SCC46 and SCC74A cells were from Dr. Zhong Chen’s lab (National Institutes of Health) with permission from Dr. Thomas E. Carey (University of Michigan). These cell lines were maintained in high glucose DMEM (Thermo Fisher Scientific, Cat#11995065) containing 10% FBS and 1% antibiotics at 37°C in a 5% CO2 atmosphere.

extract_protocol:
RNA was extracted by RNAeasy kit(Thermo)
Neb UTRL2 RNAseq with PolyA mRNA

treatment_protocol: To generate KMT2D knockout cell lines, SCC23 and SCC1 cells were transfected with pSpCas9(BB)-2A-GFP plasmid (Addgene, Cat#48138) containing sgRNA targeting either LacZ or KMT2D for 24 hours.

value: SCC23 HNSCC cells

value: HNSCC

value: KMT2D Knockout

value: KO


title: HS360-Day6-CIT50-RNA-seq-rep2

description:
Day 6", "male", "neural rosettes", "neural induction", "citalopram", "CIT50", "50 nM citalopram
317-D6-CIT50-B


title: RNA_T30_SD_T30S4_L


title: HS360-Day6-RNA-seq-rep3

description:
Day 6", "male", "neural rosettes", "neural induction
315-D6-CTRL-C

value: day 6, neural induction

value: Day 6 control


title: 4T1, Day4, single cell 296


title: HS360-Day6-CIT50-RNA-seq-rep1

description:
Day 6", "male", "neural rosettes", "neural induction", "citalopram", "CIT50", "50 nM citalopram
316-D6-CIT50-A


title: RNA_T30_SD_T30S3_L

value: Liver


title: (-Glc) KO1 RNAseq exp1

description: Low Glucose condition


title: (-Glc) KO1 RNAseq exp2

description: Low Glucose condition


title: (-Glc) KO2 RNAseq exp1

description: Low Glucose condition


title: HS360-Day6-RNA-seq-rep2

description:
Day 6", "male", "neural rosettes", "neural induction
314-D6-CTRL-B


title: 4T1, Day4, single cell 294


title: (-Glc) WT2 RNAseq exp2

description: Low Glucose condition

value: control


title: 4T1, Day4, single cell 293


title: RNA_T3_NSD_T3N4_L

value: NSD


title: 4T1, Day4, single cell 295


title: HS360-Day13-CIT400-RNA-seq-rep6

description:
Day 13", "male", "self-patterning", "NPCs", "citalopram", "CIT400", "400 nM citalopram
312-D13-CIT400-F

value: day 13, end of self-pattering stage, exposed to 400 nM citalopram

value: Day 13 400 nM citalopram


title: RNA_T30_SD_T30S1_L

value: SD


title: 4T1, Day4, single cell 292

value: Female BALB/c mice

value: metastatic tumor cells


title: HS360-Day6-RNA-seq-rep1

description:
Day 6", "male", "neural rosettes", "neural induction
313-D6-CTRL-A


title: (-Glc) WT1 RNAseq exp2

description: Low Glucose condition

value: WT


title: 4T1, Day4, single cell 291


title: RNA_T3_NSD_T3N3_L


title: (-Glc) WT RNAseq exp1

description: Low Glucose condition


title: RNA_T27_SD_T27S5_L


title: HS360-Day13-CIT200-RNA-seq-rep5

description:
Day 13", "male", "self-patterning", "NPCs", "citalopram", "CIT200", "200 nM citalopram
311-D13-CIT200-E

value: day 13, end of self-pattering stage, exposed to 200 nM citalopram

value: Day 13 200 nM citalopram


title: 4T1, Day4, single cell 290


title: (+Glc) KO2 RNAseq exp1

description: High glucose condition

value: SCC23 HNSCC cells


title: RNA_T27_SD_T27S3_L


title: HS360-Day13-CIT100-RNA-seq-rep5

description:
Day 13", "male", "self-patterning", "NPCs", "citalopram", "CIT100", "100 nM citalopram
310-D13-CIT100-E

value: day 13, end of self-pattering stage, exposed to 100 nM citalopram

value: Day 13 100 nM citalopram


title: (+Glc) KO1 RNAseq exp1

description: High glucose condition

value: HNSCC

value: KMT2D Knockout

value: KO


title: 4T1, Day4, single cell 289


title: HS360-Day13-CIT400-RNA-seq-rep5

description:
Day 13", "male", "self-patterning", "NPCs", "citalopram", "CIT400", "400 nM citalopram
309-D13-CIT400-E


title: RNA_T27_SD_T27S2_L

value: Liver


title: HS360-Day13-CIT400-RNA-seq-rep4

description:
Day 13", "male", "self-patterning", "NPCs", "citalopram", "CIT400", "400 nM citalopram
308-D13-CIT400-D


title: 4T1, Day4, single cell 288


title: RNA_T24_NSD_T0N3_L


title: 4T1, Day4, single cell 287


title: 4T1, Day4, single cell 286


title: HS360-Day13-CIT400-RNA-seq-rep3

description:
Day 13", "male", "self-patterning", "NPCs", "citalopram", "CIT400", "400 nM citalopram
307-D13-CIT400-C


title: HS360-Day13-CIT400-RNA-seq-rep2

description:
Day 13", "male", "self-patterning", "NPCs", "citalopram", "CIT400", "400 nM citalopram
306-D13-CIT400-B


title: RNA_T198_SD_J76S2_L


title: 4T1, Day4, single cell 285


title: RNA_T198_SD_J76S3_L


title: RNA_T198_SD_J76S1_L


title: HS360-Day13-CIT400-RNA-seq-rep1

description:
Day 13", "male", "self-patterning", "NPCs", "citalopram", "CIT400", "400 nM citalopram
305-D13-CIT400-A


title: (+Glc) WT RNAseq exp1

description: High glucose condition

value: control


title: 4T1, Day4, single cell 284


title: HS360-Day13-CIT200-RNA-seq-rep4

description:
Day 13", "male", "self-patterning", "NPCs", "citalopram", "CIT200", "200 nM citalopram
304-D13-CIT200-D


title: 4T1, Day4, single cell 283


title: HS360-Day13-CIT200-RNA-seq-rep3

description:
Day 13", "male", "self-patterning", "NPCs", "citalopram", "CIT200", "200 nM citalopram
303-D13-CIT200-C


title: RNA_T192_SD_J70S1_L


title: 4T1, Day4, single cell 282


title: 4T1, Day4, single cell 280


title: RNA_T18_NSD_T18N8_L

value: NSD


title: HS360-Day13-CIT100-RNA-seq-rep4

description:
Day 13", "male", "self-patterning", "NPCs", "citalopram", "CIT100", "100 nM citalopram
300-D13-CIT100-D


title: 4T1, Day4, single cell 279


title: HS360-Day13-CIT100-RNA-seq-rep3

description:
Day 13", "male", "self-patterning", "NPCs", "citalopram", "CIT100", "100 nM citalopram
299-D13-CIT100-C


title: RNA_T192_SD_J70S3_L


title: 4T1, Day4, single cell 278


title: HS360-Day13-CIT100-RNA-seq-rep2

description:
Day 13", "male", "self-patterning", "NPCs", "citalopram", "CIT100", "100 nM citalopram
298-D13-CIT100-B


title: RNA_T192_SD_J70S2_L


title: HS360-Day13-CIT200-RNA-seq-rep2

description:
Day 13", "male", "self-patterning", "NPCs", "citalopram", "CIT200", "200 nM citalopram
302-D13-CIT200-B


title: 4T1, Day4, single cell 277


title: HS360-Day13-CIT100-RNA-seq-rep1

description:
Day 13", "male", "self-patterning", "NPCs", "citalopram", "CIT100", "100 nM citalopram
297-D13-CIT100-A


title: SPARC-/- TRAMP -/-, S9

type: RNA

city: Milan

first: Annamaria

last: Piva

address: via Amadeo, 42

country: Italy

institute: Fondazione IRCCS Istituto Nazionale dei Tumori

hyb_protocol: Hybridization was performed according to manufacturer's standard protocols.

scan_protocol: Gene microarrays were scanned with the Gene Chip System 3000 scanner.

data_processing: Raw data were normalized with Robust Multichip Average (RMA) method as implemented in oligo R package.

label: biotin

source_name: prostate tumors from 18-weeks-old SPARC-/- TRAMP -/- mouse

label_protocol: RNA was labeled according to manufacturer's recommended protocols.

extract_protocol: Total RNA was extracted using Qiazol reagent and purified with the RNeasy kit on a QIAcube automated station (Qiagen) according to the manufacturer instructions.

value: SPARC-/- TRAMP -/-

tag: age (weeks)

tag: ID

value: prostate tumors


title: 4T1, Day4, single cell 281


title: SPARC-/- TRAMP -/-, S12


title: SPARC-/- TRAMP -/-, S10


title: SPARC-/- TRAMP -/-, S7


title: RNA_T12_NSD_T12N6_L


title: SPARC-/- TRAMP -/-, S5

source_name: prostate tumors from 25-weeks-old SPARC-/- TRAMP -/- mouse


title: SPARC-/- TRAMP -/-, S8


title: SPARC-/- TRAMP -/-, S11


title: HS360-Day13-CIT200-RNA-seq-rep1

description:
Day 13", "male", "self-patterning", "NPCs", "citalopram", "CIT200", "200 nM citalopram
301-D13-CIT200-A


title: SPARC-/- TRAMP -/-, S6


title: SPARC-/- TRAMP -/-, S2

source_name: prostate tumors from 27-weeks-old SPARC-/- TRAMP -/- mouse


title: 4T1, Day4, single cell 276


title: SPARC-/- TRAMP -/-, S3


title: RNA_T18_NSD_T18N4_L


title: RNA_T18_NSD_T18N3_L


title: HS360-Day13-CIT50-RNA-seq-rep6

description:
Day 13", "male", "self-patterning", "NPCs", "citalopram", "CIT50", "50 nM citalopram
296-D13-CIT50-F

value: day 13, end of self-pattering stage, exposed to 50 nM citalopram

value: Day 13 50 nM citalopram


title: RNA_T12_NSD_T12N5_L


title: 4T1, Day4, single cell 275

value: Female BALB/c mice

value: metastatic tumor cells


title: RNA_T18_NSD_T18N2_L


title: 4T1, Day4, single cell 274


title: RNA_T12_NSD_T12N4_L


title: 4T1, Day4, single cell 273


title: HS360-Day13-RNA-seq-rep5

description:
Day 13", "male", "self-patterning", "NPCs", "control
293-D13-CTRL-E

value: day 13, end of self-pattering stage

value: Day 13 control


title: RNA_T12_NSD_T12N2_L


title: HS360-Day13-RNA-seq-rep6

description:
Day 13", "male", "self-patterning", "NPCs", "control
294-D13-CTRL-F


title: HS360-Day13-CIT50-RNA-seq-rep5

description:
Day 13", "male", "self-patterning", "NPCs", "citalopram", "CIT50", "50 nM citalopram
295-D13-CIT50-E


title: RNA_T12_NSD_T12N1_L


title: 4T1, Day4, single cell 272


title: HS360-Day13-RNA-seq-rep4

description:
Day 13", "male", "self-patterning", "NPCs", "control
292-D13-CTRL-D


title: HS360-Day13-CIT50-RNA-seq-rep4

description:
Day 13", "male", "self-patterning", "NPCs", "citalopram", "CIT50", "50 nM citalopram
291-D13-CIT50-D


title: RNA_T0_NSD_T0N8_L


title: 4T1, Day4, single cell 271


title: 4T1, Day4, single cell 270


title: RNA_T0_NSD_T0N1_L


title: OPN-/-TRAMP -/-, O11

source_name: prostate tumors from 17-weeks-old OPN-/-TRAMP -/- mouse

value: OPN-/-TRAMP -/-


title: HS360-Day13-CIT50-RNA-seq-rep3

description:
Day 13", "male", "self-patterning", "NPCs", "citalopram", "CIT50", "50 nM citalopram
290-D13-CIT50-C


title: SPARC-/- TRAMP -/-, O12

source_name: prostate tumors from 16-weeks-old SPARC-/- TRAMP -/- mouse


title: 4T1, Day4, single cell 269


title: HS360-Day13-CIT50-RNA-seq-rep2

description:
Day 13", "male", "self-patterning", "NPCs", "citalopram", "CIT50", "50 nM citalopram
289-D13-CIT50-B


title: RNA_T0_NSD_J70N1_L


title: 4T1, Day4, single cell 268


title: GMP_KO_40764

city: Marseille

first: Michel

last: Aurrand-Lions

address: 27 Bd Leï Roure

country: France

institute: Cancer Research Center of Marseille (CRCM)

data_processing:
Image analysis and base calling were performed using RTA 2.7.3 and bcl2fastq 2.17.1.14.
Supplementary files format and content: tab delimited text file with counts for each sample
Supplementary files format and content: tab delimited text file with counts for each sample

source_name: bone marrow

extract_protocol:
HSC (Lin-Sca-1+CD117+CD135-CD48-) and GMP (Lin-CD117+CD16/32+, CD34+) were directly sorted by flow cytometry using a BD ARIA3  in RLT buffer from mRNA purification kit using the RNeasy micro kit (QIAGEN). Samples were sent to the GenomEast platform (http://genomeast.igbmc.fr/ Illkirch, France). Libraries were paired-end sequenced (2 x 100bp) on a Hiseq4000 system (Illumina)..
RNA-Seq libraries were generated from 250 ng of total RNA using TruSeq Stranded mRNA Library Prep Kit and TruSeq RNA Single Indexes kits A and B (Illumina, San Diego, CA), according to manufacturer's instructions. Briefly, following purification with poly-T oligo attached magnetic beads, the mRNA was fragmented using divalent cations at 94oC for 2 minutes. The cleaved RNA fragments were copied into first strand cDNA using reverse transcriptase and random primers. Strand specificity was achieved by replacing dTTP with dUTP during second strand cDNA synthesis using DNA Polymerase I and RNase H. Following addition of a single 'A' base and subsequent ligation of the adapter on double stranded cDNA fragments, the products were purified and enriched with PCR (30 sec at 98oC; [10 sec at 98oC, 30 sec at 60oC, 30 sec at 72oC] x 12 cycles; 5 min at 72oC) to create the cDNA library. Surplus PCR primers were further removed by purification using AMPure XP beads (Beckman-Coulter, Villepinte, France) and the final cDNA libraries were checked for quality and quantified using capillary electrophoresis.

treatment_protocol: all mice were treated with doxycyline to induce leukemia, KO mice were treated with Poly I:C 2 weeks prior to leukemia induction

value: bone marrow

value: JAM-C KO

value: Induction leukemia


title: HS360-Day13-CIT50-RNA-seq-rep1

description:
Day 13", "male", "self-patterning", "NPCs", "citalopram", "CIT50", "50 nM citalopram
288-D13-CIT50-A


title: OPN-/-TRAMP -/-, O9


title: GMP_KO_40629


title: 4T1, Day4, single cell 267


title: HS360-Day13-RNA-seq-rep3

description:
Day 13", "male", "self-patterning", "NPCs", "control
287-D13-CTRL-C


title: OPN-/-TRAMP -/-, O10


title: OPN-/-TRAMP -/-, O8


title: HSC_KO_40764


title: SPARC-/- TRAMP +/-, ST16

source_name: prostate tumors from 24-weeks-old SPARC-/- TRAMP +/- mouse

value: SPARC-/- TRAMP +/-


title: SPARC-/- TRAMP -/-, S1


title: OPN-/-TRAMP -/-, O7

source_name: prostate tumors from 24-weeks-old OPN-/-TRAMP -/- mouse


title: SPARC-/- TRAMP +/-, ST15


title: 4T1, Day4, single cell 266


title: OPN-/-TRAMP -/-, O14


title: HS360-Day13-RNA-seq-rep2

description:
Day 13", "male", "self-patterning", "NPCs", "control
286-D13-CTRL-B


title: HSC_KO_40629


title: HS360-Day13-RNA-seq-rep1

description:
Day 13", "male", "self-patterning", "NPCs", "control
285-D13-CTRL-A


title: GMP_WT_45340

value: JAM-C WT


title: HS360-Day10-CIT400-RNA-seq-rep6

description:
Day 10", "male", "self-patterning", "NPCs", "citalopram", "CIT400", "400 nM citalopram
284-D10-CIT400-F

value: day 10, middle of self-pattering stage, exposed to 400 nM citalopram

value: Day 10 400 nM citalopram


title: OPN-/-TRAMP -/-, O2


title: HSC_WT_45340


title: 4T1, Day4, single cell 263


title: HS360-Day10-CIT400-RNA-seq-rep5

description:
Day 10", "male", "self-patterning", "NPCs", "citalopram", "CIT400", "400 nM citalopram
283-D10-CIT400-E


title: HS360-Day10-CIT200-RNA-seq-rep5

description:
Day 10", "male", "self-patterning", "NPCs", "citalopram", "CIT200", "200 nM citalopram
282-D10-CIT200-E

value: day 10, middle of self-pattering stage, exposed to 200 nM citalopram

value: Day 10 200 nM citalopram


title: TRAMP -/-, B11

source_name: prostate tumors from 16-weeks-old TRAMP -/- mouse

value: TRAMP -/-

value: prostate tumors


title: 4T1, Day4, single cell 261


title: 4T1, Day4, single cell 265


title: HSC_KO_45610


title: 4T1, Day4, single cell 260


title: HSC_WT_45790


title: HS360-Day10-CIT200-RNA-seq-rep4

description:
Day 10", "male", "self-patterning", "NPCs", "citalopram", "CIT200", "200 nM citalopram
281-D10-CIT200-D


title: TRAMP -/-, B10


title: OPN-/-TRAMP -/-, O1

source_name: prostate tumors from 16-weeks-old OPN-/-TRAMP -/- mouse


title: GMP_WT_45790


title: HS360-Day10-CIT100-RNA-seq-rep4

description:
Day 10", "male", "self-patterning", "NPCs", "citalopram", "CIT100", "100 nM citalopram
279-D10-CIT100-D

value: day 10, middle of self-pattering stage, exposed to 100 nM citalopram

value: Day 10 100 nM citalopram


title: HS360-Day10-CIT100-RNA-seq-rep5

description:
Day 10", "male", "self-patterning", "NPCs", "citalopram", "CIT100", "100 nM citalopram
280-D10-CIT100-E


title: 4T1, Day4, single cell 262

value: Female BALB/c mice

value: metastatic tumor cells


title: GMP_WT_45789


title: TRAMP -/-, B13


title: GMP_KO_45610


title: 4T1, Day4, single cell 264


title: 4T1, Day4, single cell 258


title: TRAMP -/-, B8


title: 4T1, Day4, single cell 259


title: HS360-Day10-CIT50-RNA-seq-rep6

description:
Day 10", "male", "self-patterning", "NPCs", "citalopram", "CIT50", "50 nM citalopram
278-D10-CIT50-F

value: day 10, middle of self-pattering stage, exposed to 50 nM citalopram

value: Day 10 50 nM citalopram


title: TRAMP -/-, B6

source_name: prostate tumors from 24-weeks-old TRAMP -/- mouse


title: HSC_WT_45789

value: bone marrow


title: TRAMP -/-, B5


title: HS360-Day10-CIT50-RNA-seq-rep5

description:
Day 10", "male", "self-patterning", "NPCs", "citalopram", "CIT50", "50 nM citalopram
277-D10-CIT50-E


title: TRAMP -/-, B4


title: 4T1, Day4, single cell 256


title: Percentile_rank_10_3 [SAM24373083]

city: South San Francisco

first: Sandra

last: Melo

address: 1 DNA Way

institute: Genentech, Inc.

library_source: genomic

data_processing:
library strategy: sgRNA Amplicon
We performed a differential abundance analysis at the gRNA level using the popular limma-voom approach
We fitted a linear model to the log-CPM values for each gRNA, using voom-derived observation and quality weights. We performed robust empirical Bayes shrinkage to obtain shrunken variance estimates for each gRNA, and we used moderated F-tests to compute p-values for each of the two-group comparisons of interest.
Assembly: mm10

molecule: genomic DNA

source_name: BMDMs

extract_protocol:
Genomic DNA was extracted using Gentra Puregene Cell Kit (158388, Qiagen) using extended incubation at 55 oC with Proteinase K (19131, Qiagen) supplemented in the lysis buffer (25 µl per 10 ml) to reduce any DNA-protein cross-links. DNA was allowed to dissolve for 48 h prior to quantification using Qubit dsDNA Quantitation range kit (Q32853, Thermofisher). From the estimated 3 to 6 million cells in each of these bins, 20 to 40 % of genomic DNA was recovered by mass.
sgRNA guide sequences were recovered as amplicons generated by PCR of the genomic DNA using Phusion High-Fidelity PCR Master Mix with GC Buffer (M0531L, NEB) with forward (TCTTGTGGAAAGGACGAGGTACCG) and reverse (TCTACTATTCTTTCCCCTGCACTGT) primers representing complimentary guide flanking sequences. Adapter ligation and indexing PCR was performed on these amplicons using KAPA HTP Library Preparation Kit (KK8234, Kapa biosystems) for multiplexing and sequencing on an Illumina HiSeq5 platform

value: BMDMs

value: gIFN

tag: molecule type

value: synthetic construct


title: HS360-Day10-RNA-seq-rep6

description:
Day 10", "male", "self-patterning", "NPCs", "control
276-D10-CTRL-F

value: day 10, middle of self-pattering stage

value: Day 10 control


title: TRAMP -/-, B3


title: HS360-Day10-RNA-seq-rep5

description:
Day 10", "male", "self-patterning", "NPCs", "control
275-D10-CTRL-E


title: 4T1, Day4, single cell 255


title: HS360-Day10-RNA-seq-rep4

description:
Day 10", "male", "self-patterning", "NPCs", "control
274-D10-CTRL-D


title: Unsorted_3 [SAM24373074]


title: Percentile_rank_10_2 [SAM24373079]


title: Percentile_rank_10_1 [SAM24373075]


title: HS360-Day10-CIT400-RNA-seq-rep4

description:
Day 10", "male", "self-patterning", "NPCs", "citalopram", "CIT400", "400 nM citalopram
273-D10-CIT400-D

value: day 10, middle of self-pattering stage, exposed to 400 nM citalopram

value: Day 10 400 nM citalopram


title: 4T1, Day4, single cell 254


title: HS360-Day10-CIT400-RNA-seq-rep3

description:
Day 10", "male", "self-patterning", "NPCs", "citalopram", "CIT400", "400 nM citalopram
272-D10-CIT400-C


title: 4T1, Day4, single cell 252


title: Unsorted_2 [SAM24373073]


title: Unsorted_1 [SAM24373072]


title: 4T1, Day4, single cell 251


title: HS360-Day10-CIT400-RNA-seq-rep2

description:
Day 10", "male", "self-patterning", "NPCs", "citalopram", "CIT400", "400 nM citalopram
271-D10-CIT400-B


title: Ref_3 [SAM24373071]

value: non


title: 4T1, Day4, single cell 253


title: TRAMP -/-, B1

value: TRAMP -/-


title: 4T1, Day4, single cell 250


title: HS360-Day10-CIT400-RNA-seq-rep1

description:
Day 10", "male", "self-patterning", "NPCs", "citalopram", "CIT400", "400 nM citalopram
270-D10-CIT400-A


title: SPARC-/- TRAMP +/-, ST26

source_name: prostate tumors from 18-weeks-old SPARC-/- TRAMP +/- mouse

value: SPARC-/- TRAMP +/-

value: prostate tumors


title: SPARC-/- TRAMP +/-, ST27


title: 4T1, Day4, single cell 249


title: HS360-Day10-CIT200-RNA-seq-rep3

description:
Day 10", "male", "self-patterning", "NPCs", "citalopram", "CIT200", "200 nM citalopram
269-D10-CIT200-C

value: day 10, middle of self-pattering stage, exposed to 200 nM citalopram

value: Day 10 200 nM citalopram


title: SPARC-/- TRAMP +/-, ST25


title: Ref_1 [SAM24373069]


title: TRAMP -/-, B2


title: SPARC-/- TRAMP +/-, ST24


title: SPARC-/- TRAMP +/-, ST23

source_name: prostate tumors from 19-weeks-old SPARC-/- TRAMP +/- mouse


title: 4T1, Day4, single cell 248

value: Female BALB/c mice

value: metastatic tumor cells


title: 4T1, Day4, single cell 247


title: 4T1, Day4, single cell 246


title: SPARC-/- TRAMP +/-, ST22


title: HS360-Day10-CIT100-RNA-seq-rep3

description:
Day 10", "male", "self-patterning", "NPCs", "citalopram", "CIT100", "100 nM citalopram
266-D10-CIT100-C

value: day 10, middle of self-pattering stage, exposed to 100 nM citalopram

value: Day 10 100 nM citalopram


title: HS360-Day10-CIT200-RNA-seq-rep2

description:
Day 10", "male", "self-patterning", "NPCs", "citalopram", "CIT200", "200 nM citalopram
268-D10-CIT200-B


title: HS360-Day10-CIT200-RNA-seq-rep1

description:
Day 10", "male", "self-patterning", "NPCs", "citalopram", "CIT100", "100 nM citalopram
267-D10-CIT200-A


title: C. elegans gonad, Unknown Worm 11, Early Embryo

city: Charlotte

first: Yangqi

last: Su

state: NC

address: 9201 University City Blvd

department: Bioinformatics

institute: UNC Charlotte

data_processing:
Prior to mapping, raw reads were trimmed with Trim Galore, with parameters (quality >= 10, length > 35bp)
For differential gene expression analysis, trimmed reads were mapped to the genome using HISAT2, raw counts obtained via HTSeq
The trimmed reads were also mapped to the genome using Salmon with default settings to obtain transcript per million (TPM) estimates for both genes and transcripts
Assembly: WBcel235, GCA_000002985.3
Supplementary files format and content: tab delimited file containing HISAT aligned, HTSeq raw counts for all samples/genes
Supplementary files format and content: tab delimited file containing salmon estimated raw counts for all samples/genes
Supplementary files format and content: tab delimited file containing mapping and quality control metrics for all samples

organism: Caenorhabditis elegans

source_name: gonad

extract_protocol:
a cut was made across the vulva using a 26G subcutaneous needle controlled by a micromanipulator (ROE-200, Sutter) under an inverted microscope (Olympus 1X71). This would release fertilized eggs and early-stage embryos from the uterus as well as sperms and at least portions of the two sides of the gonad. Each end of the gonad wrapped around by five pairs of sheath cells was completely isolated by pushing its distal end. The distal proliferative zone (S1) was cut off around the transition zone and harvested in about 10 nl bath solution by suction using a patch clamp pipette under controlled of another micromanipulator (ROE-200, Sutter). The pachytene zone (S2), the loop corresponding to the diplotene zone (S3) and diakinesis zone (S4) were sequentially cut off and similarly harvested. The -3 (F3), -2 (F2), and -1 (F1) oocytes were also isolated by cutting through their boundaries and similarly harvested. The zygote (fertilized oocyte) also known as P0 was similarly harvested when the two pronuclei were fused at its center.
We prepare a RNA-seq library for each harvested sample for Illumina platforms using a modified scRNA-seq method based on Tang et al or using the Smart-seq2 protocol

treatment_protocol: a well-fed gravid hermaphrodite was immobilized in the egg salt solution (ESS) with 10% tetramisole (Sigma, St. Louis)

value: gonad

tag: section

value: Early Embryo

value: Unknown


title: C. elegans gonad, Unknown Worm 10, Early Embryo


title: C. elegans gonad, Unknown Worm 12, Early Embryo


title: 4T1, Day4, single cell 245


title: HS360-Day10-CIT100-RNA-seq-rep2

description:
Day 10", "male", "self-patterning", "NPCs", "citalopram", "CIT100", "100 nM citalopram
265-D10-CIT100-B


title: SPARC-/- TRAMP +/-, ST7

source_name: prostate tumors from 27-weeks-old SPARC-/- TRAMP +/- mouse


title: SPARC-/- TRAMP +/-, ST6

source_name: prostate tumors from 29-weeks-old SPARC-/- TRAMP +/- mouse


title: C. elegans gonad, Unknown Worm 9, Early Embryo


title: Ref_2 [SAM24373070]

value: BMDMs

value: synthetic construct


title: SPARC-/- TRAMP +/-, ST5


title: SPARC-/- TRAMP +/-, ST4


title: HS360-Day10-CIT100-RNA-seq-rep1

description:
Day 10", "male", "self-patterning", "NPCs", "citalopram", "CIT100", "100 nM citalopram
264-D10-CIT100-A


title: 4T1, Day4, single cell 244


title: 4T1, Day4, single cell 243


title: C. elegans gonad, Unknown Worm 8, Early Embryo


title: 4T1, Day4, single cell 242


title: C. elegans gonad, Unknown Worm 7, Early Embryo


title: SPARC-/- TRAMP +/-, ST3


title: HS360-Day10-CIT50-RNA-seq-rep3

description:
Day 10", "male", "self-patterning", "NPCs", "citalopram", "CIT50", "50 nM citalopram
262-D10-CIT50-C

value: day 10, middle of self-pattering stage, exposed to 50 nM citalopram

value: Day 10 50 nM citalopram


title: HS360-Day10-CIT50-RNA-seq-rep2

description:
Day 10", "male", "self-patterning", "NPCs", "citalopram", "CIT50", "50 nM citalopram
261-D10-CIT50-B


title: C. elegans gonad, Unknown Worm 6, Zygote

value: Zygote


title: 4T1, Day4, single cell 240


title: C. elegans gonad, Unknown Worm 5, Zygote


title: 4T1, Day4, single cell 241


title: HS360-Day10-CIT50-RNA-seq-rep1

description:
Day 10", "male", "self-patterning", "NPCs", "citalopram", "CIT50", "50 nM citalopram
260-D10-CIT50-A


title: C. elegans gonad, Worm28, Diakinesis

value: Diakinesis


title: 4T1, Day4, single cell 239


title: SPARC-/- TRAMP +/-, ST2

value: SPARC-/- TRAMP +/-


title: HS360-Day10-CIT50-RNA-seq-rep4

description:
Day 10", "male", "self-patterning", "NPCs", "citalopram", "CIT50", "50 nM citalopram
263-D10-CIT50-D


title: OPN-/-TRAMP +/-, OT14

source_name: prostate tumors from 17-weeks-old OPN-/-TRAMP +/- mouse

value: OPN-/-TRAMP +/-

value: prostate tumors


title: SPARC-/- TRAMP +/-, ST1


title: OPN-/-TRAMP +/-, OT12

source_name: prostate tumors from 16-weeks-old OPN-/-TRAMP +/- mouse


title: OPN-/-TRAMP +/-, OT13


title: HS360-Day10-RNA-seq-rep2

description:
Day 10", "male", "self-patterning", "NPCs", "control
258-D10-CTRL-B

value: day 10, middle of self-pattering stage

value: Day 10 control


title: 4T1, Day4, single cell 238

value: Female BALB/c mice

value: metastatic tumor cells


title: C. elegans gonad, Worm28, -2 Oocyte

value: -2 Oocyte


title: C. elegans gonad, Worm28, -3 Oocyte

value: gonad

value: -3 Oocyte


title: 4T1, Day4, single cell 237


title: 4T1, Day4, single cell 236


title: HS360-Day10-RNA-seq-rep3

description:
Day 10", "male", "self-patterning", "NPCs", "control
259-D10-CTRL-C


title: HS360-Day10-RNA-seq-rep1

description:
Day 10", "male", "self-patterning", "NPCs", "control
257-D10-CTRL-A


title: HBV-specific CD8+ T cells, sample 2, HTO-derived library

city: Freiburg

first: Sagar

address: Hugstetter Straße 55

department: Department of Internal Medicine II

country: Germany

institute: University Medical Center Freiburg

description: Hashtag-derived oligonucleotide (HTO)

library_source: other

data_processing:
Pre-processing of sequencing results to generate count matrices (gene expression and HTO barcode counts) was performed using the 10x genomics Cell Ranger pipeline.
Further processing was done with Seurat (cell and gene filtering, hashtag identification, clustering, differential gene expression analysis based on gene expression).
Assembly: Alignment was performed using prebuilt Cell Ranger human reference GRCh38 (GENCODE v32/Ensembl 98).
Supplementary files format and content: RNA counts (HBV1_RNA_counts.csv.gz and HBV2_RNA_counts.csv.gz) and HTO counts (HBV1_HTO_counts.csv.gz and HBV2_HTO_counts.csv.gz) are in zipped csv format.
Supplementary files format and content: Datasets were merged and analyzed by Seurat and the analyzed object is in rds format (seurat_object_combined.rds).
Library strategy: CITE-seq

molecule: protein

source_name: Peripheral blood

extract_protocol:
HBV-specific CD8+ T cells were enriched by magnetic bead-based enrichment, and surface staining was performed. Cells were stained with barcoded antibodies together with the surface staining solution. The antibody concentrations used were 1 µg per million cells, as recommended by the manufacturer (BioLegend). After staining, cells were washed three times in PBS containing 2% BSA and 0.01% Tween 20, followed by centrifugation (300 x g 5 min at 4 °C) and supernatant exchange. After the final wash, the cells were resuspended in PBS, filtered through 40 µm cell strainers and processed for sorting. Live HBV-specific CD8+ T cells were sorted in 1,5mL microcentrifuge tubes (Eppendorf, Germany) containing 20µl PBS using BD Aria Fusion (BD, Germany). The 1,5mL microcentrifuge tubes were coated with 5% BSA over night and rinsed twice with 1mL PBS before usage. Naive, CD45RA+CCR7+, T cells were excluded.
Single-cell RNA sequencing was performed using 10x Genomics with feature barcoding technology to multiplex cells from different donors so that they could be loaded on one well to reduce costs and minimize technical variability. Hashtag oligos were obtained as purified and already oligo-conjugated in TotalSeq-C (5’ chemistry) format from BioLegend. Sorted cells were processed through the 10x Genomics V(D)J single-cell workflow according to the manufacturer’s instructions. Libraries were pooled to desired quantities to obtain appropriate sequencing depths as recommended by 10x Genomics and sequenced on a NovaSeq 6000 flow cell.

value: Peripheral blood

value: HBV-specific CD8+ T cells

tag: library type

value: HTO

tag: antibodies/tags

value: TotalSeq™-C0251 anti-human Hashtag 1 Antibody for patient 1 - HBeAg- cHBV infection (Hu.Hashtag_1); TotalSeq™-C0252 anti-human Hashtag 2 Antibody for patient 2 - Acute HBV (Hu.Hashtag_2); TotalSeq™-C0255 anti-human Hashtag 5 Antibody for patient 3 - Acute resolved HBV (Hu.Hashtag_5); TotalSeq™-C0265 anti-human Hashtag 15 Antibody for patient 4 - HBeAg- cHBV infection (Hu.Hashtag_15)


title: HBV-specific CD8+ T cells, sample 2, mRNA-derived library

description: poly A RNA

data_processing:
Pre-processing of sequencing results to generate count matrices (gene expression and HTO barcode counts) was performed using the 10x genomics Cell Ranger pipeline.
Further processing was done with Seurat (cell and gene filtering, hashtag identification, clustering, differential gene expression analysis based on gene expression).
Assembly: Alignment was performed using prebuilt Cell Ranger human reference GRCh38 (GENCODE v32/Ensembl 98).
Supplementary files format and content: RNA counts (HBV1_RNA_counts.csv.gz and HBV2_RNA_counts.csv.gz) and HTO counts (HBV1_HTO_counts.csv.gz and HBV2_HTO_counts.csv.gz) are in zipped csv format.
Supplementary files format and content: Datasets were merged and analyzed by Seurat and the analyzed object is in rds format (seurat_object_combined.rds).

tag: cell type

value: mRNA


title: C. elegans gonad, Worm28, -1 Oocyte

value: -1 Oocyte


title: 4T1, Day4, single cell 234

tag: cell line


title: HBV-specific CD8+ T cells, sample 1, HTO-derived library

description: Hashtag-derived oligonucleotide (HTO)

tag: tissue

value: TotalSeq™-C0251 anti-human Hashtag 1 Antibody for patient 1 - HBeAg- cHBV infection (Hu.Hashtag_1); TotalSeq™-C0253 anti-human Hashtag 3 Antibody for patient 2 - Acute HBV (Hu.Hashtag_3); TotalSeq™-C0254 anti-human Hashtag 4 Antibody for patient 3 - Acute HBV (Hu.Hashtag_4); TotalSeq™-C0257 anti-human Hashtag 7 Antibody for patient 4 - Acute resolved HBV (Hu.Hashtag_7)


title: C. elegans gonad, Worm28, Mitotic Region and Transition Zone

value: Mitotic Region and Transition Zone


title: C. elegans gonad, Worm28, Diplotene Loop

value: Diplotene Loop


title: 4T1, Day4, single cell 233


title: OPN-/-TRAMP +/-, OT8

value: OPN-/-TRAMP +/-

value: prostate tumors


title: HBV-specific CD8+ T cells, sample 1, mRNA-derived library

description: poly A RNA


title: C. elegans gonad, Worm27, -3 Oocyte


title: OPN-/-TRAMP +/-, OT11


title: OPN-/-TRAMP +/-, OT9


title: OPN-/-TRAMP +/-, OT6

source_name: prostate tumors from 24-weeks-old OPN-/-TRAMP +/- mouse


title: 4T1, Day4, single cell 232


title: OPN-/-TRAMP +/-, OT3

source_name: prostate tumors from 27-weeks-old OPN-/-TRAMP +/- mouse


title: C. elegans gonad, Worm28, Pachytene Zone

value: Pachytene Zone


title: 4T1, Day4, single cell 235

value: Female BALB/c mice


title: 4T1, Day4, single cell 230

value: metastatic tumor cells


title: TRAMP +/-, T14

source_name: prostate tumors from 16-weeks-old TRAMP +/- mouse

value: TRAMP +/-


title: C. elegans gonad, Worm29, Diakinesis

value: gonad

value: Diakinesis


title: Human mix library

city: xiamen

first: Qingxiang

last: Gao

address: Xiang'an south way

institute: Xiamen University

data_processing:
The raw data were filtered by bbduk2. Using the picard merge the reward and forward sequence
Using the dropseq and STAR to mapping counting the gene count
Supplementary files format and content: tab-delimited  text file includes raw counts for each Sample

source_name: Monocyte

extract_protocol:
RNA was extracted by Trizol method
Using the primer-seq protocols build the RNA-seq library

treatment_protocol: Monocytes in  peripheral blood mononuclear cells (PBMCs) from patients diagnosed with atopic dermatitis and urticaria were collected for RNA-seq.

value: Monocyte

tag: treatment

value: Health


title: 4T1, Day4, single cell 229


title: C. elegans gonad, Worm29, -1 Oocyte


title: C. elegans gonad, Worm29, Pachytene Zone


title: TRAMP +/-, T13


title: 4T1, Day4, single cell 228


title: T002BK, treatment, CD3+ cells, blood and kidney, GEX, ADT, HTO

city: Hamburg

first: Darius

last: Schaub

state: Hamburg

address: Billhorner Kanalstraße 22

department: Center for Biomedical AI

institute: University Medical Center Hamburg

description: polyA RNA, Antibody-derived oligonucleotide (ADT), Hashtag-derived oligonucleotide (HTO)

data_processing:
The Cell Ranger software (v5.0.1 and v7.1.0, 10x Genomics) was used to demultiplex cellular barcodes and map reads to the reference genome GRCh38-3.0.0 and GRCh38-2020-A. All quality control and preprocessing steps were performed in Seurat (v4.0.4) and R (v4.1.1). The Seurat demultiplexing function HTODemux was used to demultiplex the hash-tag samples.
Assembly: refdata-cellranger-GRCh38-3.0.0 and refdata-gex-GRCh38-2020-A
Supplementary files format and content: barcodes.tsv.gz:  list of cell barcodes
Supplementary files format and content: features.tsv.gz:  list of gene IDs
Supplementary files format and content: matrix.mtx.gz:  gene expression count data (and protein count data) in Matrix Market Exchange Format
Library strategy: CITE-seq

molecule: other

source_name: Blood and Kidney

extract_protocol:
Single cell suspensions were obtained from human kidney biopsies by enzymatic digestion in RPMI 1640 medium with collagenase D at 0.4 mg/ml (Roche, 11088858001) and deoxyribonuclease I (DNase I; 10 μg/ml; Sigma-Aldrich, 10104159001) at 37°C for 30 min followed by dissociation with gentle MACS (Miltenyi Biotec). Leukocytes from blood samples were separated using Leucosep tubes (Greiner Bio-One, 10349081). Cells were stained with fluorochrome-conjugated antibodies from BioLegend and BD Biosciences, CD45 BV510 (HI30), CD3 BV785 (OKT3), CD4 BV650 (RPA-T4), CD8 APC-R700 (RPA-T8), CXCR3 Pe/Dazzle (G025H7), CCR6 PerCP-Cy5-5 (G034E3). Cells were also stained with a dead cell stain (Molecular Probes, L10119) to exclude dead cells from analysis. FACS was performed on a FACSAria Fusion cell sorter (BD Biosciences). ScRNA-seq of human samples from the kidney and peripheral blood was performed from FACS-sorted CD3 positive T cells using the Chromium Next GEM Single Cell 5' Kit v2 (10x Genomics) according to manufacturer's instructions. Libraries were sequenced aiming at 50,000 reads per cell on an Illumina NovaSeq™ (P150).
libaries were constructed according to manufacturer specifications

treatment_protocol: Ustekinumab (90 mg) in in combination with low-dose cyclophosphamide and steroids, following the RITUXVAS trial approach

value: Blood and Kidney

value: FACS-sorted CD3+ cells

value: mRNA+ADT+HTO

tag: cellranger version

tag: reference genome

tag: feature reference


title: OPN-/-TRAMP +/-, OT2


title: C. elegans gonad, Worm29, Mitotic Region and Transition Zone


title: 4T1, Day4, single cell 231

tag: host


title: TRAMP +/-, T11


title: TRAMP +/-, T10


title: T004K, treatment, CD3+ cells, kidney, GEX, ADT, HTO

source_name: Kidney

value: Kidney

value: Ustekinumab (90 mg) in in combination with low-dose cyclophosphamide and steroids, following the RITUXVAS trial approach


title: TRAMP +/-, T12


title: T001B, treatment, CD3+ cells, blood, GEX, ADT, HTO

source_name: Blood

value: Blood


title: C. elegans gonad, Worm34, Diakinesis


title: T004B, treatment, CD3+ cells, blood, GEX, ADT, HTO


title: 4T1, Day4, single cell 227


title: C. elegans gonad, Worm29, Diplotene Loop

value: Diplotene Loop


title: 4T1, Day4, single cell 224


title: 4T1, Day4, single cell 257


title: C. elegans gonad, Worm34, Mitotic Region and Transition Zone

value: Mitotic Region and Transition Zone


title: E027K, exploratory, CD3+ cells, kidney, GEX, ADT, HTO


title: E023K, exploratory, CD3+ cells, kidney, GEX, ADT, HTO


title: TRAMP +/-, T9

value: prostate tumors


title: 4T1, Day4, single cell 226


title: TRAMP +/-, T8


title: C. elegans gonad, Worm34, Pachytene Zone

value: Pachytene Zone


title: C. elegans gonad, Worm33, -3 Oocyte

value: -3 Oocyte


title: T001K, treatment, CD3+ cells, kidney, GEX, ADT, HTO


title: 4T1, Day4, single cell 225

value: Female BALB/c mice

value: metastatic tumor cells


title: 4T1, Day4, single cell 222


title: TRAMP +/-, T7

source_name: prostate tumors from 24-weeks-old TRAMP +/- mouse

value: TRAMP +/-


title: 4T1, Day4, single cell 223


title: C. elegans gonad, Worm33, -2 Oocyte

value: gonad

value: C. elegans gonad, Worm33, -2 Oocyte


title: TRAMP +/-, T6


title: C. elegans gonad, Worm33, Diplotene Loop


title: E023B, exploratory, CD3+ cells, blood, GEX, ADT, HTO


title: E027B, exploratory, CD3+ cells, blood, GEX, ADT, HTO


title: 4T1, Day4, single cell 221


title: E020BK, exploratory, CD3+ cells, blood and kidney, GEX, ADT, HTO


title: E019BK, exploratory, CD3+ cells, blood and kidney, GEX, ADT, HTO


title: 4T1, Day4, single cell 220


title: C. elegans gonad, Worm33, Mitotic Region and Transition Zone


title: C. elegans gonad, Worm33, Zygote

value: Zygote


title: TRAMP +/-, T4


title: 4T1, Day4, single cell 219


title: TRAMP +/-, T5


title: E018K, exploratory, CD3+ cells, kidney, GEX

description: polyA RNA

value: mRNA


title: E018B, exploratory, CD3+ cells, blood, GEX

description: polyA RNA

value: FACS-sorted CD3+ cells


title: C. elegans gonad, Worm32, Diakinesis

value: Diakinesis


title: 4T1, Day4, single cell 218


title: E017K, exploratory, CD3+ cells, kidney, GEX

description: polyA RNA

value: Kidney


title: TRAMP +/-, T2


title: C. elegans gonad, Worm32, Diplotene Loop


title: TRAMP +/-, T1

source_name: prostate tumors from 25-weeks-old TRAMP +/- mouse


title: 4T1, Day4, single cell 217


title: 4T1, Day4, single cell 216


title: E017B, exploratory, CD3+ cells, blood, GEX

description: polyA RNA


title: C. elegans gonad, Worm32, Pachytene Zone


title: E015K, exploratory, CD3+ cells, kidney, GEX, ADT, HTO

value: mRNA+ADT+HTO


title: C. elegans gonad, Worm32, Mitotic Region and Transition Zone


title: 12W-TTg_1

city: Shinjuku

first: Taketaro

last: Sadahiro

state: Tokyo

address: 35 Shinanomachi

country: Japan

institute: Keio University School of Medicine

hyb_protocol: Fragmented and labeled ss-cDNA were hybridized for 16 hr at 45°C on GeneChip Clariom S Array. GeneChips were washed and stained in the GeneChip Fluidics Station 450.

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

data_processing: Raw data were processed with Transcriptome Analysis Console software version 4.0 for normalization.

source_name: Whole heart

label_protocol: Biotinylated ss-cDNA were prepared according to the standard Affymetrix protocol from 100ng total RNA (GeneChip WT PLUS Reagent Kit User Guide , Thermo Fisher Scientific Applied Biosystems).Biotinylated ss-cDNA yield were checked with the NanoDrop ND-2000c Spectrophotometer.

extract_protocol: RNA was extracted from Ctrl-MI and TTg-MI hearts using the ReliaPrep RNA Cell Miniprep System (Promega, Z6012). The RNA quality was determined by the RNA Integrity Number (RIN) value with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA)). Only specimens with RIN>7.0 were used in this study.

treatment_protocol: Experiments were performed in 8-week-old randomly allocated male mice. To generate the mouse MI model, mice were intubated and anesthetized with isoflurane gas. The chest cavity was exposed by cutting the intercostal muscle and then the left coronary artery was ligated with a 7-0 silk suture. The mouse surgeon was blinded to the study. Transthoracic echocardiography was performed after 2 days of MI, and mice with an ejection fraction (EF) > 45% were removed from the study.

value: tissue:Heart was harvested 3 months after MI

tag: gender

value: male


title: 4T1, Day4, single cell 215


title: E015B, exploratory, CD3+ cells, blood, GEX, ADT, HTO

value: Blood


title: 4T1, Day4, single cell 214


title: TRAMP +/-, T3

value: prostate tumors


title: E011BK, exploratory, CD3+ cells, blood and kidney, GEX, ADT, HTO

value: Blood and Kidney


title: C. elegans gonad, Worm32, -1 Oocyte

value: -1 Oocyte

tag: group


title: 4T1, Day4, single cell 213

value: Female BALB/c mice


title: C. elegans gonad, Worm32, -2 Oocyte

value: -2 Oocyte


title: Bonetti_RNASeq_KO_NAC_3

city: Esch-sur-Alzette

first: Joseph

last: Longworth

state: Luxembourg

address: 29, rue Henri Koch

department: Department of Infection and Immunity

country: Luxembourg

institute: LIH

data_processing:
RNA-seq transcript alignment was performed with Salmon (Patro et al., 2017) against the Mouse Transcriptome from Genecode v.M32
Tximeta (Love et al., 2020) was used to assign transcripts to genes
differential analysis with DESeq2 (Love, Huber and Anders, 2014)
Assembly: Genecode release M32 assembly GRCm39
Supplementary files format and content: CSV reporting normalized abundance measurements from DESeq

source_name: TH17 cells

growth_protocol: Naive CD4+ T cells were isolated from mouse spleen and lymph nodes by magnetic bead sorting using the Naive CD4+ T cell isolation kit (Miltenyi Biotec) following the manufacturer’s protocol. Negative magnetic bead sorting was performed using the autoMACSR pro Separator (Miltenyi Biotec). Cell numbers were determined using a CASY cell counter (Omni Life Science). To induce in vitro differentiation, naive T cells were cultured at 2x106 cells/mL for 3 days in medium consisting of IMDM (Westburg) supplemented with 10% FBS (Biochrom GmbH), 1% penicillin/streptomycin (Gibco) and 55μM 2-mercaptoethanol (Gibco), and in the presence of Th cell subtype-specific cytokine mixes.  For the induction of conventional Th17 cells, naive T cells were cultured in the presence of TGF-β (2ng/μL; Bio-Techne), IL-6 (30ng/mL; Miltenyi Biotec), anti-IFN-γ (5μg/mL; BD Biosciences), soluble anti-CD28 (1μg/mL; Biolegend) and plate-bound anti-CD3 antibody (5 μg/mL; Biolegend).

extract_protocol:
RNA was extracted using a NucleoSpin RNA Kit according to the manufacturer’s protocol.
The TruSeq Stranded mRNA Library Prep kit was used for library preparation.

treatment_protocol: For the induction of conventional Th17 cells, naive T cells were cultured in the presence of TGF-β (2ng/μL; Bio-Techne), IL-6 (30ng/mL; Miltenyi Biotec), anti-IFN-γ (5μg/mL; BD Biosciences), soluble anti-CD28 (1μg/mL; Biolegend) and plate-bound anti-CD3 antibody (5 μg/mL; Biolegend). For the induction of IL-22-expressing Th17 cells, naive T cells were cultured in the presence of IL-6 (30ng/mL; Miltenyi Biotec), soluble anti-CD28 (1μg/mL; Biolegend), plate-bound anti-CD3 antibody (5μg/mL; Biolegend or BD), IL-1β (50ng/1189 mL; Miltenyi Biotec) and IL-23 (20ng/mL; Miltenyi Biotec).

value: TH17 cells

tag: genotype

value: Cd4Cre Gclc fl/fl

value: 10mM NAC


title: 12W-TTg_2


title: Bonetti_RNASeq_KO_NAC_2


title: E009K, exploratory, CD3+ cells, kidney, GEX, ADT, HTO


title: 8W-Ctrl_2

value: tissue:Heart was harvested 2 months after MI


title: C. elegans gonad, Worm31, Diakinesis

source_name: gonad

value: gonad


title: 4T1, Day4, single cell 211

value: metastatic tumor cells


title: 4T1, Day4, single cell 212


title: E009B, exploratory, CD3+ cells, blood, GEX, ADT, HTO

value: FACS-sorted CD3+ cells


title: C. elegans gonad, Worm31, -2 Oocyte


title: 8W-Ctrl_1


title: Bonetti_RNASeq_KO_UT_3

value: Untretated


title: C. elegans gonad, Worm31, Pachytene Zone

value: Pachytene Zone


title: E007BK, exploratory, CD3+ cells, blood and kidney, GEX, ADT, HTO

value: mRNA+ADT+HTO


title: Bonetti_RNASeq_KO_NAC_1


title: Bonetti_RNASeq_KO_UT_2


title: 12W-Ctrl_1

value: tissue:Heart was harvested 3 months after MI

value: male


title: C. elegans gonad, Worm31, Mitotic Region and Transition Zone

value: Mitotic Region and Transition Zone


title: E006K, exploratory, CD3+ cells, kidney, GEX, ADT, HTO

value: Kidney


title: 4T1, Day4, single cell 209


title: C. elegans gonad, Worm30, Diplotene Loop

value: Diplotene Loop


title: 4T1, Day4, single cell 208

value: Female BALB/c mice


title: E006B, exploratory, CD3+ cells, blood, GEX, ADT, HTO

value: Blood


title: C. elegans gonad, Worm30, -2 Oocyte

value: -2 Oocyte


title: Bonetti_RNASeq_KO_UT_1

value: TH17 cells

value: Cd4Cre Gclc fl/fl


title: E003K, exploratory, CD3+ cells, kidney, GEX

description: polyA RNA

value: mRNA


title: 4T1, Day4, single cell 207


title: 12W-Ctrl_2


title: Bonetti_RNASeq_WT_UT_3

value: Gclc fl/fl


title: C. elegans gonad, Worm30, -1 Oocyte

value: gonad

value: -1 Oocyte


title: 4T1, Day4, single cell 206

value: metastatic tumor cells


title: Bonetti_RNASeq_WT_UT_2

value: Untretated


title: E003B, exploratory, CD3+ cells, blood, GEX

description: polyA RNA

value: FACS-sorted CD3+ cells


title: 1132-D-HF

city: New Haven

first: Eduardo

middle: Gabriel

last: Gonzalez Santiago

state: Connnecticut

address: 375 Congress Ave Rm 407

institute: Yale University

data_processing:
Human genome assembly GRCh38 was used for reads alignment with STAR package
Counts tables were generated with featureCounts.
Assembly: GRCh38.110
Supplementary files format and content: comma-separated values (CSV) with raw counts for each sample.

source_name: small intestine

extract_protocol:
RNA was harvested using RNEasy Mini Plus Kit (Qiagen). 100ug of RNA was used for library preparation.
RNA libraries were prepared utilizing the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (New England Biolabs).

value: small intestine

tag: condition

value: Differentiation

value: Hydrolyzed Formula


title: 4T1, Day4, single cell 205


title: 4T1, Day4, single cell 210


title: C. elegans gonad, Worm30, Pachytene Zone

value: Pachytene Zone


title: 1132-D-DHM

value: Donor Human Milk


title: C. elegans gonad, Worm30, Mitotic Region and Transition Zone

value: Mitotic Region and Transition Zone


title: Bonetti_RNASeq_WT_UT_1


title: 4T1, Day4, single cell 204

value: Female BALB/c mice


title: C. elegans gonad, Worm26, -2 Oocyte

value: -2 Oocyte


title: 4T1, Day4, single cell 203


title: 1132-D-ODM

value: Control


title: C. elegans gonad, Worm26, Diakinesis

value: Diakinesis


title: 4T1, Day4, single cell 202


title: 1132-G-SF

value: Growth

value: Standard Formula


title: 1132-G-HF


title: C. elegans gonad, Worm26, -1 Oocyte

value: gonad


title: H7_Sample 86

city: Tehran

first: Sima

last: Rafati

state: Tehran

address: Pasteur Ave

department: Immunotherapy and Leishmania Vaccine Research

country: Iran

institute: Pasteur Institute of Iran

description:
Healthy
Sample 86

data_processing:
Trace data were analyzed using GeneMapper software 5 package (Applied Biosystems, Bleiswijk, The Netherlands).  assigned the threshold value.
The areas of each assigned peak (in arbitrary units) were exported for further analysis in Microsoft Excel.
Data were normalized to GAPDH, and signals below the threshold value for noise cutoff in GeneMapper (Log2-transformed peak area of 7.64) were assigned the threshold value. The normalized data were Log2-transformed for statistical analysis.

label: MLPA reagents (MRC-Holland)

source_name: Skin

label_protocol: A specific reverse transcription (RT) primer was designed for each target-specific sequence (see PMID 21956656 ; Supplementary Table 1), located immediately downstream of the left- and right-hand half-probe target sequence. The left- and right-hand half-probes were hybridized to the cDNA at 60°C overnight after reverse transcription of the RNA. After being ligated by ligase and amplified by PCR (33 cycles of 30 s/95°C, 30 s/58°C, and 60 s/72°C, followed by 1 cycle of 20 min/72°C), annealed half-probes were subjected to amplification. The Netherlands' Zwijndrecht-based Sigma-Aldrich Chemie provided the primers and probes, and MRC-Holland provided the MLPA reagents (Amsterdam, The Netherlands). The Department of Infectious Diseases at Leiden University Medical Center created reverse transcription primers and half-probes.

extract_protocol: Skin biopsies in RNAlater were homogenized in QIAzol Lysis buffer using stainless steel beads and TissueLyser II (Qiagen, GmbH, Hilden, Germany). Total RNA was isolated using miRNeasy Mini Kit (Qiagen, GmbH, Hilden, Germany), according to the manufacturer’s protocol.

treatment_protocol: Fourteen Moroccan patients with skin lesions suggestive of CL were taken from three hospitals: (i) Department of Dermatology - Ibn Rochd Hospital, Casablanca; (ii) Bougafer Hospital in Ouarzazate; (iii) Tinghir Hospital Center. After the positive diagnosis, a 3mm diameter skin biopsy was taken under sterile conditions from the edge of the active skin lesions. Normal skin samples were taken from four volunteers living in non-endemic areas and with no history of cutaneous leishmaniasis. The patients had been referred to the CL special clinic at Mashhad Medical School in Mashhad, a highly endemic area in Iran for L. tropica.                                                                                The skin biopsies of sixteen Iranian CL patients with L. tropica were taken from the Mashhad Medical School’s CL special clinic, which is located in Mashhad, Iran (a highly endemic area for this species). All CL patients had an active lesion for a maximum of 1 year and had no prior anti-leishmanial treatment. A total of 16 CL patients were enrolled in the study. Healthy skin samples were taken from six volunteers undergoing esthetical surgery at the Noor Eye hospital in Tehran, Iran with no history of leishmaniasis or other skin disorders. The criteria for patient enrolment include clinically verified characteristics of CL skin lesion and a positive result from the diagnostic L. tropica specific PCR using samples obtained from a non-invasive, tape disc-based  sampling method. The genomic DNA was used for a PCR, targeting the ITS1 region of  Leishmania, followed by RFLP for species-specific identification.

value: skin

tag: disease state

value: healthy

tag: patient group

value: Iran


title: H5_Sample 85

description:
Healthy
Sample 85


title: H4_Sample 84

description:
Healthy
Sample 84


title: 1132-G-DHM


title: 1132-G-MM

value: Maternal Milk


title: 4T1, Day4, single cell 201

value: metastatic tumor cells


title: H3_Sample 83

description:
Healthy
Sample 83


title: C. elegans gonad, Worm25, -2 Oocyte

tag: section


title: C. elegans gonad, Worm25, Diakinesis


title: H2_Sample 82

description:
Healthy
Sample 82


title: 1132-G-OGM

value: small intestine


title: C. elegans gonad, Worm25, -1 Oocyte

value: -1 Oocyte


title: 4T1, Day4, single cell 198


title: 1081-D-HF

value: Differentiation

value: Hydrolyzed Formula


title: C. elegans gonad, Worm25, Pachytene Zone

value: Pachytene Zone


title: Q_Sample 80

description:
CL due to L. tropica
Sample 80

value: acute stage


title: C. elegans gonad, Worm25 NA


title: 4T1, Day4, single cell 196

value: Female BALB/c mice


title: 1081-D-DHM

value: Donor Human Milk


title: 1081-D-ODM

value: Control


title: C. elegans gonad, Worm24, Mitotic Region and Transition Zone

value: Mitotic Region and Transition Zone


title: C. elegans gonad, Worm23, Diplotene Loop

value: Diplotene Loop


title: 4T1, Day4, single cell 199


title: 4T1, Day4, single cell 200


title: C. elegans gonad, Worm23, -1 Oocyte

value: gonad


title: 4T1, Day4, single cell 197


title: 1081-G-DHM

value: Growth


title: 1081-G-HF


title: 4T1, Day4, single cell 193


title: H1_Sample 81

description:
Healthy
Sample 81

value: skin

value: healthy


title: M_Sample 77

description:
CL due to L. tropica
Sample 77

value: Iran


title: O_Sample 78

description:
CL due to L. tropica
Sample 78


title: 4T1, Day4, single cell 192

value: metastatic tumor cells


title: L_Sample 76

description:
CL due to L. tropica
Sample 76


title: C. elegans gonad, Worm23, Pachytene Zone


title: 1081-D-SF

value: small intestine

value: Standard Formula


title: K_Sample 75

description:
CL due to L. tropica
Sample 75


title: J_Sample 74

description:
CL due to L. tropica
Sample 74


title: P_Sample 79

description:
CL due to L. tropica
Sample 79


title: C. elegans gonad, Worm23, -2 Oocyte

value: -2 Oocyte


title: 1081-G-OGM


title: I_Sample 73

description:
CL due to L. tropica
Sample 73


title: 4T1, Day4, single cell 194


title: 4T1, Day4, single cell 190


title: C. elegans gonad, Worm23, Mitotic Region and Transition Zone


title: 4T1, Day4, single cell 195


title: 4T1, Day4, single cell 189


title: C. elegans gonad, Worm22, Pachytene Zone


title: 1042-G-DHM


title: H_Sample 72

description:
CL due to L. tropica
Sample 72


title: C. elegans gonad, Worm22, Diplotene Loop


title: 4T1, Day4, single cell 188


title: G_Sample 71

description:
CL due to L. tropica
Sample 71


title: C. elegans gonad, Worm21, -1 Oocyte

value: -1 Oocyte


title: 1042-G-OGM


title: 4T1, Day4, single cell 191


title: 1038-G-HF

value: Hydrolyzed Formula


title: 1042-G-HF


title: 4T1, Day4, single cell 187


title: C. elegans gonad, Worm21 NA


title: F_Sample 70

description:
CL due to L. tropica
Sample 70

value: acute stage


title: D_Sample 68

description:
CL due to L. tropica
Sample 68


title: 1038-G-SF


title: 4T1, Day4, single cell 185

value: Female BALB/c mice


title: C. elegans gonad, Worm20, -3 Oocyte

value: -3 Oocyte


title: C_Sample 67

description:
CL due to L. tropica
Sample 67


title: C. elegans gonad, Worm20, Diakinesis

value: Diakinesis


title: 4T1, Day4, single cell 183


title: C. elegans gonad, Worm20, -2 Oocyte


title: 1038-G-DHM

value: Donor Human Milk


title: 1081-G-MM

value: Maternal Milk


title: B_Sample 66

description:
CL due to L. tropica
Sample 66


title: 1038-G-OGM

value: Control


title: 4T1, Day4, single cell 182


title: C. elegans gonad, Worm20, -1 Oocyte

value: gonad


title: 4T1, Day4, single cell 186


title: A_Sample 65

description:
CL due to L. tropica
Sample 65

value: skin


title: 4T1, Day4, single cell 181


title: R_Sample 64

description:
CL due to L. major
Sample 64

value: Morocco


title: C. elegans gonad, Worm19, Diplotene Loop

value: Diplotene Loop


title: E_Sample 69

description:
CL due to L. tropica
Sample 69

value: Iran


title: C. elegans gonad, Worm19, Pachytene Zone

value: Pachytene Zone


title: PEO1_shCBX2_1

city: Denver

first: Benjamin

last: Bitler

state: CO

department: OB-GYN

institute: The University of Colorado

data_processing:
FASTQ files generated with bcl2fastq (version 2.20.0.422) were processed using the nf-core/rnaseq pipeline (version 3.9, https://nf-co.re/rnaseq/3.9).
Sequencing adapters were removed using Cutadapt (version 3.4) as part of the trimgalore package (version 0.6.7).
Reads were aligned using STAR (version 2.7.10a) to the human transcriptome (GRCh38, gene annotation from Ensembl release 104).
Gene quantification was performed using Salmon (version 1.5.2).
Tables with transcript and gene counts and TPM were generated by the tximport R package (version 1.18.0) under R version 4.0.3.
Assembly: GRCh38
Supplementary files format and content: *_quant.sf: Salmon transcript quantification file (tab-sparated text, https://salmon.readthedocs.io/en/latest/file_formats.html); to be used together with salmon_tx2gene.tsv (from supplemental file) by software accepting Salmon datary
Supplementary files format and content: salmon_gene-transcript_counts-TPM.tar.gz: gzipped tar ball of tab-separated text tables with counts/TPM (transcripts per million) for genes/transcripts, as well as transcript-to-gene translation table

growth_protocol: Cells were cultured in RPMI1640 with 10% Heat Inactivated FBS with 1% Penn/Strp

extract_protocol:
Total RNA was extracted using the Quick-RNA Miniprep Plus Kit (Zymo Research, Cat. #D4209).
Ribosome depletion and library preparation was performed using the Qiagen Fast-select (Cat. #334375) and KAPA BioSystems mRNA HyperPrep Kit (Cat. #KK8581) according to the manufacturer’s protocols. Briefly, 500ng of RNA was used as input, and KAPA BioSystems single-index adapters were added at a final concentration of 1.5mM. Purified, adapter-ligated library was amplified following the manufacturer’s protocol. The final libraries were pooled and sequenced on an Illumina NovaSeq 6000 (University of Colorado Genomics Core; RRID:SCR_021984) as 150 bp paired-end reads.

treatment_protocol: No Treatment

value: High grade serous carcinoma


title: PEO1_shCtrl_2

value: shControl


title: Q_Sample 63

description:
CL due to L. major
Sample 63


title: 4T1, Day4, single cell 180

data_processing:
Raw reads were first analyzed for quality control using FastQC (v0.11.7) (Andrews, 2010). Adaptor sequences of raw reads were removed by using TrimGalore (v0.6.6) (https://github.com/FelixKrueger/TrimGalore). Trimmed reads were mapped to a concatenated mouse genome (mm10) with STAR (v2.6.0c) with default parameters to result SAM format files (Dobin et al., 2013). Aligned reads stored in SAM format were transformed to generate BAM files using SAMtools (v1.7) (Danecek et al., 2021). The gene-level read count matrix was summarized from BAM files using FeatureCounts program (v1.6.2) (Liao et al., 2014). Subsequent data analysis was carried out in R 3.6.2 and the Seurat package (v3.1.2) (Stuart et al., 2019).
The gene counts per cell, the percentage of mitochondrial transcripts, the percentage of ERCC RNA spike-in, the percentage of α and β-globin genes were computed using the functions of the Seurat package. Quality controls were performed following: a. Cells with luciferase or GFP sequence detected were kept for further analysis. b. Cells with transcripts counts lower than 5 × 105 or higher than 1 ×107 were discarded. c. Single cell libraries with number of detected gene lower than 5,000, mapping rate lower than 40% or the percentage of mitochondrial transcripts higher than 10% were discarded before further analysis. d. Libraries with the percentage of α and β-globin genes higher than 1% were also discarded. 424 single cells passed quality controls, and were used for further analysis. The gene expression level was normalized as log2(TPM/10 + 1), in which TPM is the abbreviation for transcripts per million, and adding one to avoid negative expression values.
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

value: metastatic tumor cells


title: P_Sample 62

description:
CL due to L. major
Sample 62


title: 4T1, Day4, single cell 179


title: 4T1, Day4, single cell 184


title: 1038-G-MM

value: small intestine

value: Growth


title: C. elegans gonad, Worm18, -1 Oocyte

value: -1 Oocyte


title: PEO1_shCtrl_1


title: C. elegans gonad, Worm21, Pachytene Zone


title: 4T1, Day4, single cell 178

value: Female BALB/c mice


title: O_Sample 61

description:
CL due to L. major
Sample 61

value: acute stage


title: OV4_CBX2-OE_2

value: CBX2 Overexpression


title: C. elegans gonad, Worm18, Diplotene Loop


title: PEO1_shCBX2_2


title: N_Sample 60

description:
CL due to L. major
Sample 60


title: 4T1, Day4, single cell 177


title: OV4_CBX2-OE_1


title: C. elegans gonad, Worm18, Pachytene Zone


title: M_Sample 59

description:
CL due to L. major
Sample 59


title: OV4_Ctrl_OE-control_2

value: Parental


title: 4T1, Day4, single cell 176


title: C. elegans gonad, Worm17, -2 Oocyte

value: -2 Oocyte


title: OV4_Ctrl_OE-control_1


title: 4T1, Day4, single cell 175


title: OV4_CBX2-KO_C4

value: CBX2 Knockout


title: C. elegans gonad, Worm17, Pachytene Zone

value: gonad


title: C. elegans gonad, Worm17, Diplotene Loop


title: 4T1, Day4, single cell 173


title: L_Sample 58

description:
CL due to L. major
Sample 58

value: skin

value: Morocco


title: J_Sample 56

description:
CL due to L. major
Sample 56


title: C. elegans gonad, Worm17, Mitotic Region and Transition Zone

value: Mitotic Region and Transition Zone


title: K_Sample 57

description:
Healthy
Sample 57

value: healthy


title: OV4_CBX2-KO_B4

value: High grade serous carcinoma


title: I_Sample 55

description:
CL due to L. major
Sample 55


title: 4T1, Day4, single cell 171


title: 4T1, Day4, single cell 172


title: C. elegans gonad, Worm16, Mitotic Region and Transition Zone


title: H_Sample 54

description:
CL due to L. major
Sample 54


title: C. elegans gonad, Worm15, -1 Oocyte


title: OV4_Ctrl_KO-control_1


title: 4T1, Day4, single cell 170


title: HUVEC C with vehicle

city: New York

first: Yang

last: Lin

state: NY

address: 455 Main Street 06W

institute: Weill Cornell Medicine

description: HUVEC from patient C, treated with DMSO

data_processing:
Paired-end reads were aligned to the human genome GRCh38 using the STAR aligner
Raw gene counts for each sample were generated from the subsequent bam files using featureCounts
Downstream analysis including filtering, normalization, and differential expression of the RNA-Seq counts was performed in edgeR
Assembly: GRCh38
Supplementary files format and content: FPKM value of each gene from each sample. Excel file
Supplementary files format and content: Significantly differential expression genes, p value, FDR from paired analysis using edgeR pipline.

source_name: Umbilical cord derived cells

extract_protocol:
RNA was extracted with Rneasy Mini kit with on column DNAse treatment
TruSeq Stranded mRNA Library Preparation (Poly-A selection and Stranded RNA-Seq)

treatment_protocol: Cells were cultured in media contains 1: 10, 000 DMSO with or without 0.5uM SR1

value: Umbilical cord derived cells

value: Primary cell line

value: Endothelial cells

value: WT


title: C. elegans gonad, Worm15, Pachytene Zone

value: Pachytene Zone


title: 4T1, Day4, single cell 169

city: Beijing

first: Hanqiu

institute: Tsinghua university

extract_protocol:
Reverse transcription and cDNA amplification were carried out using a modified Smart-seq2 protocol (Picelli et al., 2014). Single cells were sorted by FACS as described above into 96-well plates containing 0.1 μl of RNase inhibitor (Clontech, Cat# 2313A), 1.9 μl of 0.2% Triton X-100 (Sigma, Cat# T9284), 1 μl of 10 µM oligo-dT primer (5′-AAGCAGTGGTATCA ACGCAGAGTAC T30VN-3′) and 1 μl of dNTP mix (10 mM each; Fermentas, Cat# R0192) in each well. Plates were either stored at -80 °C or processed immediately. Reverse transcription, PCR preamplification, PCR purification were performed following Picelli’s protocol (Picelli et al., 2014). As mRNA quality control, 1 ul of each PCR product was used as template for qPCR detection of mCherry expression and samples with Ct value higher than 30 will be discard. PCR products were purified with 1 × Agencourt Ampure XP beads (Beckman Coulter, Cat# A63881) and the final product was reconstituted in 20 µl TE buffer. The concentration of cDNA was measured by Qubit™ 1× dsDNA High Sensitivity (HS) Assay Kit (Invitrogen, Cat# Q33230). Tagmentation and NGS library was carried out by using TruePrep DNA Library Prep Kit V2 for Illumina (Vazyme, Cat# TD503) following the manufacturer’s instructions. The purified library was qualify controlled by measuring the fragment size distribution with an Agilent HS DNA BioAnalyzer Chip and the concentration of library was measured with Qubit™ 1× dsDNA High Sensitivity (HS) Assay Kits following the manufacturer’s instructions. Single cell cDNA libraries were sequenced on an Illumina HiSeq X Ten platform to obtain paired-end 150-bp reads.
SMART-Seq2 (Picelli et al., 2014)

value: Female BALB/c mice

value: metastatic tumor cells


title: 4T1, Day4, single cell 174


title: F_Sample 52

description:
CL due to L. major
Sample 52

value: acute stage


title: G_Sample 53

description:
CL due to L. major
Sample 53


title: 4T1, Day4, single cell 168


title: HUVEC B with vehicle

description: HUVEC from patient B, treated with DMSO


title: 4T1, Day4, single cell 167


title: E_Sample 51

description:
CL due to L. major
Sample 51


title: C. elegans gonad, Worm15, Mitotic Region and Transition Zone


title: HUVEC B with Canonical AHR Inhibitor SR1

description: HUVEC from patient B, treated with SR1


title: D_Sample 50

description:
CL due to L. major
Sample 50


title: HUVEC C with Canonical AHR Inhibitor SR1

description: HUVEC from patient C, treated with SR1


title: C. elegans gonad, Worm14, Pachytene Zone


title: C. elegans gonad, Worm14, Diplotene Loop

value: Diplotene Loop


title: 4T1, Day4, single cell 166


title: HUVEC A with vehicle

description: HUVEC from patient A, treated with DMSO


title: C_Sample 49

description:
Healthy
Sample 49


title: OV4_Ctrl_KO-control_2

value: Parental


title: HUVEC A with Canonical AHR Inhibitor SR1

description: HUVEC from patient A, treated with SR1


title: B_Sample 48

description:
Healthy
Sample 48


title: 4T1, Day4, single cell 165


title: 4T1, Day4, single cell 164


title: A_Sample 47

description:
Healthy
Sample 47


title: C. elegans gonad, Worm13, Pachytene Zone


title: Donor 32_CD4 T cells, Activated+TB-PE

city: Westmead

first: Gabriel

last: Duette

state: NSW

address: 176 Hawkesbury Road

department: Centre for Virus Research

country: Australia

institute: The Westmead Institute for Medical Research

data_processing:
Library sequencing quality was determined using FastQC (Babraham Bioinformatics: www.bioinformatics.babraham.ac.uk/). Illumina adaptor sequence and low quality read trimming (read pair removed if < 20 base pairs) was performed using Trim Galore (BabrahamBioinformatics). STAR was used to align reads to human genome hg38 using ENSEMBL gene annotations as a guide. Read counts data corresponding to ENSEMBL gene annotations were generated the STAR flag --quantMode GeneCounts. Multiqc was used to verify quality metrics. All analyses were performed in the R Statistical Environment (http://www.Rproject.org) with the Tidyverse package. EdgeR was used to perform background correction and normalize count data by library size.
Assembly: hg38
Supplementary files format and content: STAR was used to align reads to human genome hg38 using ENSEMBL gene annotations as a guide. Read counts data corresponding to ENSEMBL gene annotations were generated the STAR flag --quantMode GeneCounts. Multiqc was used to verify quality metrics. All analyses were performed in the R Statistical Environment (http://www.Rproject.org) with the Tidyverse package. EdgeR was used to perform background correction and normalize count data by library size.

growth_protocol: Peripheral blood mononuclear cells (PBMCs) were obtained by Ficoll-Hypaque density gradient centrifugation from buffy coats of healthy donors. CD4+ primary T cells were isolated and purified from PBMCs by negative selection using a CD4+ T cell isolation kit (MiltenyiBiotec). Cells were cultured in cRF10: RPMI (Lonza) supplemented with 10% fetal bovine serum (FBS, Gibco),1X GlutaMAX (Gibco), 100 U/ml penicillin (Gibco), 100 μg/ml streptomycin (Gibco), and 100 U/ml IL-2 (MiltenyiBiotec).

extract_protocol:
RNA from CD4+ T cells (2x106 cells per condition) was extracted by using the RNeasy Plus Mini kit (QIAGEN). Extracted total RNA was quantified using the Qubit broad range RNA assay, and RNA quality was assessed using the Agilent 4200 Tapestation system
Library preparation was performed using 400ng of total RNA as input and the Illumina stranded mRNA Prep kit. Short read sequencing was performed on the Novaseq 6000 platform where a minimum of 20 million paired-end 50bp reads per sample were generated

treatment_protocol: Primary CD4+ T cells were obtained as described above. A group of isolated CD4+ T cells were activated using anti-CD3/CD28 antibodies in the presence or absence of TB-PE, and after 20 hours, the cells were harvested to perform bulk RNAseq

value: Blood

value: CD4 T cell

tag: donor

value: anti-CD3/CD28 + TB-PE


title: C. elegans gonad, Worm13, Mitotic Region and Transition Zone

value: gonad


title: Donor 32_CD4 T cells, Activated


title: 4T1, Day4, single cell 163

last: Zheng

address: Haidian District


title: C. elegans gonad, Worm11, Diplotene Loop


title: 4T1, Day4, single cell 162


title: Donor 32_CD4 T cells, TB-PE

value: TB-PE


title: A375-BRAFV600E/NRASQ61_MELTF_KO_A18_2

city: Tucson

first: Georg

middle: Thomas

last: Wondrak

state: Arizona

address: UA Cancer Center, 1515 N Campbell Ave, Room 3971

department: Pharm/Tox

institute: University of Arizona

hyb_protocol: All samples were run targeting 100 ng of total RNA (19 h at 65°C) prior to being processed on the nCouner FLEX Analysis System.

scan_protocol: Samples were run on the nCounter Prep Station with high sensitivity settings followed by imaging on the Digital Analyzer with FOV (Field of View) data resolution set to 555.

data_processing: Raw data files were uploaded (RCC files) to the NanoString nSolver Analysis 4.0 software.

label: reporter probe: fluorescent barcode; capture probe: biotin

source_name: malignant melanoma cell line

label_protocol: NanoString nCounter gene expression assay protocol was followed (https://www.nanostring.com/wp-content/uploads/2021/03/MAN-10056-05-Gene-Expression-Hybridization-Protocol.pdf).

growth_protocol: All isogenic malignant melanoma cell lines were grown in DMEM media supplemented with 10% FBS at 37°C, 5%CO2 (analysis occurred no later than 5 population doublings after thawing).

extract_protocol: Total RNA was extracted from cell lysates using Qiagen RNeasy Mini kit according to manufacturer instructions.

treatment_protocol: No special treatment was performed;  isogenic malignant melanoma cell lines differing in MELTF expression [MELTF_WT (wildtype) and MELTF_KO (knockout; two clones A7 and A18)] were compared.

tag: ATCC

value: cell line (ATCC  CRL-1619-LUC2)

value: MELTF knockout (clone A18)


title: C. elegans gonad, Worm11, Pachytene Zone


title: 4T1, Day4, single cell 161

tag: cell type


title: A375-BRAFV600E/NRASQ61_MELTF_KO_A18_3

tag: cell line


title: 4T1, Day4, single cell 160


title: C. elegans gonad, Worm14, Mitotic Region and Transition Zone

tag: tissue

value: Mitotic Region and Transition Zone


title: C. elegans gonad, Worm12, Diplotene Loop


title: A375-BRAFV600E/NRASQ61_MELTF_KO_A18_1


title: Donor 31_CD4 T cells, Activated

tag: treatment


title: Donor 31_CD4 T cells, Activated+TB-PE


title: C. elegans gonad, Worm12, Mitotic Region and Transition Zone


title: 4T1, Day4, single cell 159


title: 4T1, Day4, single cell 158


title: C. elegans gonad, Worm11, Mitotic Region and Transition Zone


title: Donor 31_CD4 T cells, TB-PE


title: 4T1, Day4, single cell 157


title: A375-BRAFV600E/NRASQ61_MELTF_KO_A7_1

value: MELTF knockout (clone A7)


title: A375-BRAFV600E/NRASQ61_MELTF_KO_A7_3


title: A375-BRAFV600E/NRASQ61_WT_3

value: MELTF wildtype


title: Donor 31_CD4 T cells, Control

value: Control


title: A375-BRAFV600E/NRASQ61_MELTF_KO_A7_2


title: C. elegans gonad, Worm10, Zygote

value: Zygote


title: 4T1, Day4, single cell 155

value: Female BALB/c mice


title: C. elegans gonad, Worm8, Zygote


title: Donor 30_CD4 T cells, Activated+TB-PE


title: C. elegans gonad, Worm12, Diakinesis

value: Diakinesis


title: C. elegans gonad, Worm9, Zygote


title: A375-BRAFV600E/NRASQ61_WT_2


title: Donor 30_CD4 T cells, TB-PE


title: C. elegans gonad, Worm7, Diplotene Loop


title: C. elegans gonad, Worm7, -1 Oocyte

value: -1 Oocyte


title: Donor 30_CD4 T cells, Control


title: Donor 32_CD4 T cells, Control


title: A375-BRAFV600E/NRASQ61_WT_1


title: 4T1, Day4, single cell 154

value: metastatic tumor cells


title: 4T1, Day4, single cell 153


title: MSC, H3K9me3, DFO treatment

city: Shenzhen

first: Yunshu

last: Che

address: NO.3025 shennan road

institute: Sun Yat-sen University

data_processing:
Raw reads were filtered and trimmed to remove sequencing adaptors and low-quality reads
Clean reads were mapped to the human genome version hg38 using Bowtie2 (v2.5.1)
Peaks were called using MACS2 (v.2.1.1) and normalization (reads per kilobase per million or RPKM) of the CUT&Tag-seq data and heatmap plotting were performed using deepTools (v2.3.6.0)
The normalized CUT&Tag-seq data were visualized on Integrative Genomics Viewer (IGV)
Assembly: hg18
Supplementary files format and content: bw files were generated by deepTools (v2.3.6.0)
Library strategy: CUT&Tag

source_name: bone marrow

growth_protocol: MSCs were seeded in 6-well plates at a density of 1×105/well and cultured with DMEM (1000 mg/L glucose) without FBS to induce quiescence

extract_protocol:
The DNA fragments were extracted using phenol chloroform.
The CUT&Tag assay was performed using NovoNGS® CUT&Tag 2.0 High-Sensitivity Kit (for Illumina®) (Novoprotein Scientific Inc., Cat# N259-YH01-01A) according to the manufacturer’s instructions. Briefly, cells were harvested with trypsin and enriched by ConA-magnetic beads. A total of 50,000 cells were re-suspended and washed twice with 100 μL Dig-wash Buffer (20 mM HEPES pH 7.5; 150 mM NaCl; 0.5 mM spermidine; 1× protease inhibitor cocktail; 0.05% digitonin). The samples were incubated with primary BRD4 antibody (1:100, 4°C, 18 h) and secondary antibody (1:200, 25°C, 1 h). After incubation, the beads were washed three times in Dig-Hisalt Buffer (0.05% digitonin, 20 mM HEPES, pH 7.5, 300 mM NaCl, 0.5 mM spermidine, 1× protease inhibitor cocktail). Cells were incubated with the protein A-Tn5 transposome at 25°C for 1 h and washed three times in Dig-Hisalt buffer to remove unbound protein A-Tn5. The cells were re-suspended in 50 μL Tagmentation buffer (10 mM MgCl2 in Dig-Hisalt Buffer) and incubated at 37°C for 1 h. The tagmentation was terminated with the addition of 1 μL of 10% SDS at 55°C for 10 min.
Cleavage under targets and tagmentation (CUT&Tag)

treatment_protocol: quiescent MSC was mobilized

value: bone marrow

value: Mesenchymal stem cells

value: DFO treatment

tag: growth state

value: quiescent MSC mobilization

tag: antibody


title: 4T1, Day4, single cell 152


title: 4T1, Day4, single cell 156


title: 4T1, Day4, single cell 151


title: C. elegans gonad, Worm6, Pachytene Zone

value: gonad

value: Pachytene Zone


title: C. elegans gonad, Worm5, Diplotene Loop

value: Diplotene Loop


title: MSC, KDM4D, DFO treatment


title: Donor 30_CD4 T cells, Activated

value: Blood

value: CD4 T cell


title: 4T1, Day4, single cell 150


title: C. elegans gonad, Worm5, Pachytene Zone


title: SKMEL28 cells, shIRF4, day 3,  biological replicate 3

city: Istanbul

first: Tolga

last: Emre

address: Bogazici University, Kuzey Kampus, Kuzey Park Binasi, No 203

country: Turkey

institute: Bogazici University

data_processing:
Reads were aligned with TopHat V2.0.8 and selection of uniquely mapped reads were done with samtools
To quantify mapped reads and determine differentially expressed gene Cuffdiff v2.1.1 software was used.
cuffdiff output was visualized using CummeRbund R package with R v3.0.1
Assembly: GRCh37/hg19 (Feb. 2009 )
Supplementary files format and content: tab-delimited text files include normalized counts for each sample

growth_protocol: SKMEL28 and SKMEL5 cells were maintained in DMEM supplied with 10% FBS, non-essential amino acids, and antibiotics in an incubator at 37°C and 5% CO2

extract_protocol:
RNA was extracted using the Roche High Pure RNA Isolation kit. 1.1 mg total RNA  was used for generating RNA-seq libraries
TruSeq RNA Sample Preparation Kit was used for library preparation step. Briefly, library preparation starts with purification of mRNA by poly-A selection using oligo-dT attached magnetic beads. Following purification, mRNAs are fragmented and copied into first strand cDNA by using random hexamers. Then second strand cDNA synthesis is performed. End repair and addition of adenine base follows the procedure. At the end, adaptors with barcodes are ligated and products are enriched with PCR.

value: melanoma

value: lentiviral transduction


title: MSC, H3K9me3, untreated

value: untreated


title: SNU668 vs CAF5

city: Suwon

first: Tae Hoon

last: Kim

address: 206, World cup-ro, Yeongtong-gu

department: surgery

country: South Korea

institute: Ajou university

description: Gene expression data from human gastric cancer cells co-cultured with CAFs

hyb_protocol: Approximately 5.5 μg of labeled DNA target was hybridized to the Affymetrix GeneChip Array at 45°C for 16hour.

scan_protocol: Hybridized arrays were washed and stained on a GeneChip Fluidics Station 450 and scanned on a GCS3000 Scanner (Affymetrix).

data_processing: The probe cell intensity data computation and a CEL file generation was performed using Affymetrix® GeneChip Command Console® Software (AGCC).

label: biotin-labeled with TdT

source_name: Human gastric cancer cell

label_protocol: The sense cDNA was then fragmented and biotin-labeled with TdT (terminal deoxynucleotidyl transferase) using the GeneChip WT Terminal labeling kit.

growth_protocol: SNU668 cells were maintained in RPMI supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37°C. CAFs were maintained in DMEM supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37°C.

extract_protocol: RNA was harvested using Rneasy mini kit (Qiagen). 1ug of total RNA was used for the construction of sequencing libraries.

treatment_protocol: SNU668 cells were treated with recombinant human GAS6 protein.

value: human gastric cancer cell

value: co-cultured with CAFs


title: SNU668 vs recombinant human GAS6 protein

description: Gene expression data from human gastric cancer cells treated with recombinant human GAS6 protein


title: 4T1, Day4, single cell 149

value: Female BALB/c mice


title: SKMEL28 cells, shIRF4, day 3,  biological replicate 2


title: SNU668 vs CAF51


title: 4T1, Day4, single cell 148


title: MSC, KDM4D, untreated


title: SNU668 vs CAF98


title: SKMEL28 cells, shIRF4, day 3,  biological replicate 1


title: 4T1, Day4, single cell 147


title: SKMEL28 cells, shLuc, day 3,  biological replicate 3

value: shLuc(Control)


title: C. elegans gonad, Worm4, Zygote

data_processing:
Prior to mapping, raw reads were trimmed with Trim Galore, with parameters (quality >= 10, length > 35bp)
For differential gene expression analysis, trimmed reads were mapped to the genome using HISAT2, raw counts obtained via HTSeq
The trimmed reads were also mapped to the genome using Salmon with default settings to obtain transcript per million (TPM) estimates for both genes and transcripts
Assembly: WBcel235, GCA_000002985.3
Supplementary files format and content: tab delimited file containing HISAT aligned, HTSeq raw counts for all samples/genes
Supplementary files format and content: tab delimited file containing salmon estimated raw counts for all samples/genes
Supplementary files format and content: tab delimited file containing mapping and quality control metrics for all samples

value: Zygote


title: 4T1, Day4, single cell 146

value: metastatic tumor cells


title: SKMEL28 cells, shLuc, day 3,  biological replicate 2