title: GFPhESc,NRP1+

city: Edinburgh

first: Nadine

last: Bestard-Cuche

address: 5 Little France Drive

country: United Kingdom

institute: University of Edinburgh

data_processing:
CellRanger v7.0.0
QC - scater v 1.26.1 and manual filtering
scran normalisation - v. 1.26.2
scran dimred and variance estimation v 1.26.2
Seurat clustering v 4.3.0.1
Assembly: refdata-gex-GRCh38-2020-A
Supplementary files format and content: metadata_17105x42.csv contains information from each cell. Special relevance the "Oligodendroglia" column that indicates if the cell is oligodendroglia (only those were used for the differential expression analysis) and the "Genotype" column, that indicates if the cells are NRP1+ or NRP1-
Supplementary files format and content: counts_29820x17105.csv. Contains the raw counts from all the cells after QC.

source_name: GFPhESc from RC17f

growth_protocol: GFP, NRP1+/+ and NRP1-/- hESCs were cultured on human recombinant laminin-521 coated plates (5 μg/ml, Biolamina) in StemMACS™ iPS-Brew XF, human medium (Miltenyi Biotec Inc.) with 1% Antibiotic Antimycotic Solution (Sigma). Once confluent, hESCs were differentiated into oligodendroglia using a previously published protocol - Livesey, M.R., et al., Maturation and electrophysiological properties of human pluripotent stem cell-derived oligodendrocytes. STEM CELLS, 2016. 34(4): p. 1040-1053..  Membrane tagged GFP+ hESCs were generated using zinc-finger recombinase in the RC17 line as in van Erp, S., et al., Age-related loss of axonal regeneration is reflected by the level of local translation. Experimental neurology, 2021. 339: p. 113594.

extract_protocol:
Cells were lifted with accutase and resuspended in PBS
Single cells were processed through the Chromium Single Cell Platform using a Chromium Next GEM Single Cell 3′ GEM Library and Gel Bead kit and a Chromium Next GEM Chip G kit (PN-1000120) and processed following the manufacturer’s instructions.

treatment_protocol: Generation of NRP1-/- knockout line was performed using Alt-R™ CRISPR-Cas9 genome editing system

tag: cell line

value: GFPhESc from RC17f

value: NRP1 WT

value: differentiation  to oligodendroglia


title: PRL_9 (PRL, HA_T2, Sample 3)

status: Public on Aug 23 2023

type: SRA

city: Chicago

first: Terry

last: Moore

state: IL

address: 833 S Wood St

department: Pharmaceutical Sciences

country: USA

institute: University of Illinois at Chicago College of Pharmacy

description:
fpkm_genename.txt
fpkm_group.txt
fpkm_sample.txt
readcount_genename.txt
readcount.txt

library_source: transcriptomic

data_processing:
RNA sequencing data was analyzed by Novogene as follows, per the provided methods report (Novogene, USA): Analysis was performed using a combination of programs including STAR, HTseq, Cufflink and Novogene?s wrapped scripts. Alignments were parsed using Tophat program and differential expression was determined through DESeq2/edgeR. GO and KEGG enrichment analyses were implemented by the ClusterProfiler. Gene fusion and differences of alternative splicing were detected by Star-fusion and rMATS software. Reference genome and gene model annotation files were downloaded directly from NCBI/UCSC/Ensembl. Indexes of the reference genome were built and paired-end clean reads were aligned to the reference genome using STAR (v2.5), with the Maximal Mappable Prefix method. HTSeq v0.6.1 was used to count the read numbers mapped of each gene. FPKM of each gene was calculated based on the length of the gene and read count. Differential expression analysis was performed using the DESeq2 R package (2_1.6.3) using a model based on the negative binomial distribution. The resulting P-values were adjusted using the Benjamini and Hochberg approach for controlling the False Discovery Rate (FDR). Genes with an adjusted P-value <0.05 found by DESeq2 were assigned as differentially expressed. To allow for log adjustment, genes with 0 FPKM were assigned a value of 0.001. Correlations were determined using the cor.test function in R with options set alternative =?greater? and method = ?Spearman?. To identify the correlation between differences, samples were clustered by FPKM using the hierarchical clustering distance method with the heatmap, self-organization mapping, and kmeans functions in R. GO enrichment and KEGG pathway analyses were implemented using the clusterProfiler R package, with gene length bias corrected. GO, KEGG, DO, and Reactome terms with corrected p value less than 0.05 were considered significantly enriched by differential expressed genes. PPI analysis of differentially expressed genes was based on the STRING database. Star-fusion(0.8.0) as used to detect of fusion genes. rMATS(3.2.1) software was used to analyze the AS event. Bam alignment results of each sample were handled using picard tools(v1.111) and samtools(v0.1.18). Single nucleotide polymorphisms were called using HaplotypeCaller in GATK3.4, and Annovar was used to annotate them against the dbSNP database. TFCat and COSMIC databases were used to annotate the differentially expressed genes.
Assembly: Homo sapiens hg38
Supplementary files format and content: fpkms and readcounts for all samples

molecule: total RNA

organism: Homo sapiens

source_name: skin

growth_protocol: Cells were cultured in Dulbecco’s Modified Eagle Medium (DMEM) containing L-glutamine, sodium pyruvate, and phenol red, without HEPES (N-2-hydroxyethylpiperazine-N'-2-ethanesulfonic acid) buffer.

extract_protocol:
Total RNA was extracted using the Qiagen RNEasy Plus Mini kit.
RNA sequencing and data analysis, including library preparation, quality control, mapping, quantification, differential gene expression analysis, and enrichment analyses were conducted by Novogene USA (Sacramento, CA). Detailed descriptions are available in the Novogene methods report.
Analysis was performed using a combination of programs including STAR, HTseq, Cufflink and Novogene’s wrapped scripts. Alignments were parsed using Tophat program and differential expression was determined through DESeq2/edgeR. GO and KEGG enrichment analyses were implemented by the ClusterProfiler. Gene fusion and differences of alternative splicing were detected by Star-fusion and rMATS software. Reference genome and gene model annotation files were downloaded directly from NCBI/UCSC/Ensembl. Indexes of the reference genome were built and paired-end clean reads were aligned to the reference genome using STAR (v2.5), with the Maximal Mappable Prefix method. HTSeq v0.6.1 was used to count the read numbers mapped of each gene. FPKM of each gene was calculated based on the length of the gene and read count. Differential expression analysis was performed using the DESeq2 R package (2_1.6.3) using a model based on the negative binomial distribution. The resulting P-values were adjusted using the Benjamini and Hochberg approach for controlling the False Discovery Rate (FDR). Genes with an adjusted P-value <0.05 found by DESeq2 were assigned as differentially expressed. To allow for log adjustment, genes with 0 FPKM were assigned a value of 0.001. Correlations were determined using the cor.test function in R with options set alternative =”greater” and method = “Spearman”. To identify the correlation between differences, samples were clustered by FPKM using the hierarchical clustering distance method with the heatmap, self-organization mapping, and kmeans functions in R. GO enrichment and KEGG pathway analyses were implemented using the clusterProfiler R package, with gene length bias corrected. GO, KEGG, DO, and Reactome terms with corrected p value less than 0.05 were considered significantly enriched by differential expressed genes. PPI analysis of differentially expressed genes was based on the STRING database. Star-fusion(0.8.0) as used to detect of fusion genes. rMATS(3.2.1) software was used to analyze the AS event. Bam alignment results of each sample were handled using picard tools(v1.111) and samtools(v0.1.18). Single nucleotide polymorphisms were called using HaplotypeCaller in GATK3.4, and Annovar was used to annotate them against the dbSNP database. TFCat and COSMIC databases were used to annotate the differentially expressed genes.

treatment_protocol: Cells were treated with either 1% DMSO (Control), 250 nM CDDO-Me, or 10uM PRL-295 for 14 hours.

tag: group

tag: tissue

value: skin

value: HaCaT

tag: cell type

value: keratinocyte

tag: treatment

value: 10 uM PRL-295 in DMEM

tag: time

value: 14 hours


title: GFPhESc,NRP1-

library_source: transcriptomic single cell

molecule: polyA RNA

source_name: GFPhESc from RC17

value: GFPhESc from RC17

tag: genotype

value: NRP1 KO

value: differentiation  to oligodendroglia, KO NRP1


title: genomic DNA from peripheral blood leukocytes_control 4

type: genomic

city: Seongnam-si

first: Hwa Young

last: Kim

state: Gyeonggi-do

address: 82, Gumi-ro 173 Beon-gil

country: South Korea

institute: Seoul National University Bundang Hospital

description: normal peripheral blood leukocytes sample

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium MethylationEpic Beadchip kits using standard Illumina protocol

scan_protocol: Standard Illumina procedures using Ilumina iScan scanner

data_processing:
Illumina GenomeStudio v2011.1
Average Beta, Unmethylated and methylated signal intensities in supplementary file

label: Cy5 and Cy3

molecule: genomic DNA

source_name: peripheral blood leukocytes 4

label_protocol: Standard Illumina Protocol

extract_protocol: genomic DNA was extracted and purified from peripheral blood samples using Qiagen DNeasy Kit according to standard instructions

tag: gender

value: Male

value: peripheral blood leukocytes

tag: disease state

value: normal


title: PRL_8 (PRL, HA_T2, Sample 2)


title: NU00408 SYC128

first: Wei

last: Zhang

address: 680 N Lake Shore Drive, Suite 1400

department: Preventive Medicine

institute: Northwestern University

description:
NU00408
Ribo-Zero Transcriptome

data_processing: Raw sequencing reads were trimmed and filtered for low-quality bases and reads (quality score  20 for a minimum of 90% bases) using the FASTX Toolkit (v 0.0.14), followed by alignment to the human genome reference (GRCh37/hg19 without chromosome X, Y and Mitochondria) using the spliced aligner Tophat (v 2.1.0) with the default paired-end mode. Read pairs were concordantly aligned with ≤ 2 mismatches. Aligned read pairs with mapping quality score ≥ 20 were counted for genomic features according to the start and end coordinates derived from the ENCODE-derived annotation files (hg19) using FeatureCounts from Subread (v 1.6.1) with strand information.

source_name: Tissue

extract_protocol:
Total RNA was isolated (~1 ug/sample ) , followed by treatment with the Ribo-Zero Gold rRNA Removal Kit (Illumina, Inc., USA) . The cDNA libraries were prepared using the TrueSeq Stranded Total RNA Library Prep Kit (Illumina, Inc., USA).
The next-generation sequencing (NGS) was performed on the Illumina HiSeq 4000 platform (PE50) at the University of Chicago Genomics Facility. Approximately 24 million read pairs were generated from each library.

tag: tissue type

value: GBM

tag: population

value: White


title: BMDM, LPS, 4hr, biol rep 1

city: Nashville

first: Margaret

middle: Ann

last: Mcbride

state: Tennessee

address: 1211 Medical Center Drive

department: Anesthesiology

institute: Vanderbilt University Medical Center

data_processing:
The clustering of the index-coded samples was performed on a cBot Cluster Generation System using PE Cluster Kit cBot-HS (Illumina) according to the manufacturer’s instructions. After cluster generation, the library preparations were sequenced on an Illumina platform and paired-end reads were generated. STAR-software was used to align reads to the reference genome. Expression levels were quantified using FPKM.
Reads that met the following citeria were removed. 1. reads containing adapters; 2., reads containing N > 10% (N represents base that could not be determined); 3. low quality reads: The Qscore (Quality value) of over 50% bases of the read is <= 5.
Assembly: mm10
Supplementary files format and content: excel file including raw counts for each sample
Supplementary files format and content: excel file including FPKM  for each sample

organism: Mus musculus

source_name: bone marrow-derived macrophage

growth_protocol: Murine bone marrow-servied macrophages were cultured from whole bone marrow and maintained in RPMI 1640 supplemented with 10% FBS, 1% antibiotic/anitbmycotic solution, and 10ug/mL murine macrophage colony stimulating factor

extract_protocol:
Total RNA was isolated under an RNase-free environment using the RNeasy Mini Kit (Qiagen, Hilden, Germany) which included a DNAse treatment step. Total RNA quality and concentration were verified with a Thermo Scientific NanoDrop 2000 spectrophotometer.
Sequencing libraries were prepared using NEBNext® UltraTM RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s protocol.

treatment_protocol: BMDM were treated with β-glucan (5μg/mL), MPLA (1μg/mL), or lactated Ringers solution or DMSO (1uL/mL) in supplemnted RPMI for 4h, 24h, or 3 days (3dp) prior to RNA harvest. The 3dp groups were treated as specifiec for 24 hours, after which the BMDM were washed with PBS and the supplemented RPMI without the treatment was replaced.  The BMDM then rested for 3 additional days prior to RNA harvest.

value: bone marrow-derived macrophage

tag: strain

tag: Sex

value: WT

value: 4hrs post 100ng/mL LPS


title: Scgb1a1+,CD24low single cell 74

city: Suita

first: Katsuyuki

last: Shiroguchi

state: Osaka

address: 6-2-3 Furuedai

department: Center for Biosystems Dynamics Research (BDR)

country: Japan

institute: RIKEN

data_processing:
Basecalls performed by Illumina MiSeq
Sequenced reads were trimmed for adaptor sequence, and were sorted by indexes in Illumina MiSeq
Reads were aligned to the mm10 genome assebly using STAR
Mapped reads seperated by genes, and the reads mapped for each gene were clusterd by molecular barcode
The number of cluteres for each gene was counted, which provides the number of molecules detected for each gene
Genome_build: mm10
Supplementary_files_format_and_content: The detected number of RNA moelcules per well (i.e., single cell)  for each gene is listed.

source_name: Scgb1a1+,CD24low cell

extract_protocol:
RNAs from cell lysate in each well was directly used for library preparation without purification
Libraries were prepared by using molecular barcoding technique. First, for control, the same amount of spike-in RNAs, a known number of External RNA Controls Consortium (ERCC) RNA molecules, was added into every tube which contains an isolated cell. Then, the cells were lysed and RNA molecules were fragmentated by temperature elevation. cDNAs were generated by reverse transcription using a reverse transcription primer, in which the first common primer sequence, molecular barcode, fourteen T bases, and one V (A or G or C) base are tandemly arranged from 5' end. In the reverse transcription, the second common primer sequence was also attached to 3' end of each generated cDNA molecule by template switching. Subsequently, cDNAs were amplified by PCR using two primers; one primer contains an illumina adapter sequence, sample index, and the first common primer sequence, and the other primer has another illumina adapter sequence, sample index, and the second common primer sequence.

treatment_protocol: Single cells were isolated in wells respectively

tag: age

value: 4 month


title: Scgb1a1+,CD24low single cell 73


title: Scgb1a1+,CD24low single cell 79


title: NU00387 SYC126

description:
NU00387
Ribo-Zero Transcriptome


title: NU00400 SYC127

description:
NU00400
Ribo-Zero Transcriptome

value: Unknown


title: BMDM, β-glucan, 3dp, biol rep 3

value: 3 days post 5microg/mL Beta-Glucan for 24 hours


title: PRL_7 (PRL, HA_T2, Sample 1)

value: skin

value: HaCaT

value: keratinocyte


title: Scgb1a1+,CD24low single cell 72


title: BMDM, β-glucan, 3dp, biol rep 2


title: CDDO_6 (CDDO, HA_T1, Sample 3)

value: HA_T1 (CDDO-Me)

value: 250 nM CDDO-Me in DMEM

value: 14 hours


title: NU00382 SYC125

description:
NU00382
Ribo-Zero Transcriptome


title: Scgb1a1+,CD24low single cell 71


title: CDDO_5 (CDDO, HA_T1, Sample 2)


title: BMDM, β-glucan, 3dp, biol rep 1

value: Male


title: Scgb1a1+,CD24low single cell 70


title: NU00351 SYC122

description:
NU00351
Ribo-Zero Transcriptome


title: NU00348 SYC121

description:
NU00348
Ribo-Zero Transcriptome


title: CDDO_4 (CDDO, HA_T1, Sample 1)


title: BMDM, β-glucan, 24h, biol rep 3

value: 24hrs post 5microg/mL Beta-Glucan


title: Scgb1a1+,CD24low single cell 69


title: BMDM, β-glucan, 24h, biol rep 2


title: DMSO_3 (DMSO, Control, Sample 3)

value: HA_C (Control)

value: 1% DMSO in DMEM


title: Scgb1a1+,CD24low single cell 68


title: NU00334 SYC119

description:
NU00334
Ribo-Zero Transcriptome

value: GBM

value: Refused, not reported


title: BMDM, β-glucan, 24h, biol rep 1

value: bone marrow-derived macrophage

value: WT


title: DMSO_2 (DMSO, Control, Sample 2)


title: Scgb1a1+,CD24low single cell 67

value: 4 month


title: NU00328 SYC118

description:
NU00328
Ribo-Zero Transcriptome

value: White


title: BMDM, β-glucan, 4h, biol rep 3

value: 4hrs post 5microg/mL Beta-Glucan


title: DMSO_1 (DMSO, Control, Sample 1)

value: skin


title: Scgb1a1+,CD24low single cell 66


title: BMDM, β-glucan, 4h, biol rep 2


title: NU00318 SYC116

description:
NU00318
Ribo-Zero Transcriptome


title: BMDM, β-glucan, 4h, biol rep 1


title: NU00323 SYC117

description:
NU00323
Ribo-Zero Transcriptome


title: BMDM, NS control, 3dp, biol rep 3

value: 3 days post 0.1% NS for 24 hrs


title: Scgb1a1+,CD24low single cell 64


title: LS8817 cycling replicate 1

city: New York

first: Andrew

last: Koff

state: NY

address: 1275 York Avenue

institute: Memorial Sloan Kettering Cancer Center

description: 10X genomics

data_processing:
The demultiplexing, barcoded processing, gene counting, and aggregation were made using Cellranger v3.0.2
Sequence reads were aligned to GRCH37/hg19 human genome reference using STAR as implemented in the Cellranger v3.0.2 pipeline
The resulting BAM file was analyzed with velocyto to obtain read counts.  Merged treatment and control spliced read counts were used for clustering with Seurat implementing the SCTransform pipeline with 20 dimensions.
Differential expression analysis between cell samples, trated and control, were carried out with Monocle3, excluding high mitochondrial clusters.
Assembly: alignment was made to GRCh37/hg19 human genome reference using STAR
Supplementary files format and content: HDF format values containing gene read-count matrices for treatment and control
Supplementary files format and content: .RDA file containing final seurat object

source_name: cell line

growth_protocol: cells were grown in DME supplemented with 10% fetal bovine serum, 2 mM glutamine, and penicillin and streptomycin at 37C in 5% CO2

extract_protocol:
Cells were collected by trypsinization and suspensions prepared according to guidelines from 10X genomics.  Suspensions were adjusted to a concentration of 1000 cells per microliter and loaded to one capture well to obtain 10,000 cells.
Construction of the library was perfomed according to manufacturers instructions.  10X genomics libfraries were prepared using v3 chemistry
Libraries were sequenced to an average of 23000 reads per cell quantifying expression for a median of 1509 and 2733 transcripts per cell for palbociclib treated and control, respectively

treatment_protocol: asynchronously growing cells were treated with 1 uM palbociclib and media replaced every three days

value: cell line

value: dedifferentiated liposarcoma

value: wild type


title: LS8817 1 uM palbociclib treated replicate 1

description: 10X genomics

value: 1 uM palbociclib


title: BMDM, NS control, 3dp, biol rep 2

value: Male


title: NU00295 SYC114

description:
NU00295
Ribo-Zero Transcriptome


title: NU00280 SYC113

description:
NU00280
Ribo-Zero Transcriptome

value: Unknown


title: BMDM, NS control, 3dp, biol rep 1


title: NU00341 SYC120

description:
NU00341
Ribo-Zero Transcriptome


title: Scgb1a1+,CD24low single cell 62


title: CC2 liver tissues,RNA-seq

city: Shenzhen

first: Bin

last: Wang

state: Guangdong

address: Department of General Surgery, Shenzhen Children’s Hospital, 7019 Yitian Road, Futian District, Shenzhen 518000, Guangdong, China

country: China

institute: Shenzhen Children’s Hospital

data_processing:
Raw sequencing data were processed using the 10x Genomics Space Ranger pipeline to generate FASTQ files
Sequences were aligned to mm10 genome to gene expression count using Space Ranger's default settings
Gene expression level of Refseg coding genes were quantified using 5pace Ranger's default settings
Assembly: mm10
Supplementary files format and content: tab-delimited test file includes TPM values for each sample

source_name: choledochal cyst

extract_protocol:
TRIzol reagent (Invitrogen, USA) was employed to extract total RNA from BA liver tissues as well as CC tissues. The concentration and purity of RNA were detected by Nanodrop-1000 and Qubit, then the yield and quality were evaluated by Agilent 2100 Bioanalyzer, and the integrity of RNA was accurately tested.
Before the construction of the library, rRNA was removed by a Ribo-zero kit, and RNA fragmentation was realized by the interaction of high temperature and metal ions. Following the manufacturer's instructions, rRNA-depleted RNAs were used as the material for library preparation. Then, an Agilent 2100 Bioanalyzer was employed to analyze the inserted fragments of the library. According to the manufacturer's instructions for performing a sample cluster on the cBot Cluster Generation System using the TruSeq PE Cluster Kit v3-cBot-HS (Illumina, San Diego, USA), paired-end sequencing of 125-bp reads was performed on the Illumina HiSeq 2500 platform.
Each sample had 3 μg of RNA as the input material of the small RNA library. NEBNextR Multiplex Small RNA Library PrepSet was used to generate a sequencing library. To map the sequence to each sample, we needed to add a barcode. Then, the quality of the library was examined by a DNA high sensitivity chip on an Agilent Biological Analyzer 2100 system. In accordance with expectations, the ABI Step One Plus Real-Time PCR system was employed to accurately quantify the effective concentration of the library. TruSeqSRClusterKitv3-CBOT-HS (Illumina) was used to perform a cluster of barcode samples on the CBOT cluster generation system. After the cluster was generated, the library was sequenced on the Illumina HiSeq2500 platform, and a single-ended read of 50 bp was generated.

value: choledochal cyst


title: CC1 liver tissues,RNA-seq


title: BA2 liver tissues,RNA-seq

source_name: biliary atresia

value: biliary atresia


title: NU00266 SYC110

description:
NU00266
Ribo-Zero Transcriptome

value: GBM


title: Scgb1a1+,CD24low single cell 61


title: D-Red+

city: Würzburg

first: Milas

last: Ugur

state: Bayern

address: Versbacherstr. 9

department: Institute of Systems Immunology

country: Germany

institute: Universität Würzburg

description: 10X Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v7.1.0.
Assembly: mm10-2020-A
Supplementary files format and content: Tab-separated values files and matrix files

source_name: lymph node

extract_protocol:
Single cell suspensions were generated in 1 % v/v FCS in PBS by meshing fresly isolated lymph nodes, incubated with fluorochrome labelled antibodies for 20 minutes on ice and sorted with a BD FACSAria Fusion sorter.
Library construction was performed according to manufacturer's instructions (Single Cell 5' R2-only protocol, 10x Genomics). Briefly, single cells were encapsulated into droplets with the ChromiumTM Controller (10x Genomics) and processed following manufacturer’s specifications. Transcripts captured in all the cells encapsulated with a bead were uniquely barcoded using a combination of a 16 bp 10x Barcode and a 10 bp unique molecular identifier (UMI). cDNA libraries were generated using the Chromium™ Next GEM Single Cell 5’ Reagent Kit v2 (10x Genomics) following the detailed protocol provided by the manufacturer.

value: lymph node

value: T cell


title: Scgb1a1+,CD24low single cell 65


title: Scgb1a1+,CD24low single cell 60


title: NU00273 SYC111

description:
NU00273
Ribo-Zero Transcriptome


title: NU00265 SYC108

description:
NU00265
Ribo-Zero Transcriptome


title: BA3 liver tissues,RNA-seq


title: Brown adipose tissue, TG5

city: Baltimore

first: Meng

last: Ding

state: Maryland

address: 733 n broadway

institute: Johns Hopkins University

data_processing:
bcl2fastq software used for basecalling.
Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts. In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data.
Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using Hisat2 v2.0.5 and paired-end clean reads were aligned to the reference genome using Hisat2 v2.0.5.
featureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene.
Assembly: mm10
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

source_name: Brown adipose tissue

extract_protocol:
Brown adipose tissue were removed, flash frozen on dry ice, and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Brown adipose tissue

value: TG (CLCF1-ATG)


title: Brown adipose tissue, TG3


title: NU00252 SYC107

description:
NU00252
Ribo-Zero Transcriptome

value: White


title: CC3 liver tissues,RNA-seq


title: BA1 liver tissues,RNA-seq


title: NU00313 SYC115

description:
NU00313
Ribo-Zero Transcriptome

value: More than one race


title: Scgb1a1+,CD24low single cell 58

value: 4 month


title: Scgb1a1+,CD24low single cell 57


title: Scgb1a1+,CD24low single cell 63


title: Brown adipose tissue, TG2


title: TCR UPN82

city: Freiburg im Breisgau

first: Andreas

last: Hecht

address: Stefan-Meier-Str. 17

department: Institute of Molecular Medicine and Cell Research

institute: Albert Ludwig University of Freiburg

description: 10x Genomics

data_processing: none provided

source_name: Blood

growth_protocol: 12 day in vitro expansion

extract_protocol:
Sorted cells were washed and counted according to the 10x Genomics Cell Preparation Guide. Shortly, cells were washed three times in 1 ml 1X PBS 0.5% BSA, 2 mmol EDTA using wide-bore pipette tips for low-shear mixing and centrifuged at 300 rcf for 5 min. After final centrifugation step, cells were resuspended in 50 µl 1X PBS 0.5% BSA, 2 mmol EDTA and cell numbers were obtained by using a Neubauer chamber. Cells were adjusted to a final stock concentration of 1000 cells/µl and 10000 cells were loaded to the Chromium Next GEM Chip for each sample.
Library construction was performed according to the manufacture's protocol (single cell 5' v2 (dual index) + human TCR amplification). To generate gel beads-in-emulsion (GEMs), cells were loaded to Chromium Next GEM Chip K together with master mix, gel beads and partitioning oil. After GEM generation, poly-A RNA was retrotranscripted to cDNA and Illumina R1 primer sequence, Unique Molecular Identifier (UMI) and a 10x Barcode were included. For final library construction, pooled cDNA was cleaned up with Silane DynaBeads, further amplified by PCR and size-restricted by using SPRIselect reagent. To generate TCR libraries, a part of the amplified cDNA was used for V(D)J amplification followed by SPRIselect cleanup steps. During final libarary construction and V(D)J amplification, Illumina R2 primer, paired-end constructs and induvidual sample indeces were included.
scRNA-seq and TCR seq

treatment_protocol: peptide-stimulated followed by cell sorting based on IFN-g secretion

value: Blood

value: T cells

value: in vitro peptide-stimulated followed by single cell sort based on IFN-gamma secretion


title: TCR UPN120

description: 10x Genomics


title: NU00210 SYC106

description:
NU00210
Ribo-Zero Transcriptome


title: Scgb1a1+,CD24low single cell 56


title: Brown adipose tissue, TG1


title: NU00184 SYC105

description:
NU00184
Ribo-Zero Transcriptome

value: Black


title: TCR UPN114

description: 10x Genomics


title: Scgb1a1+,CD24low single cell 55


title: D-Red-

description: 10X Genomics


title: Scgb1a1+,CD24low single cell 59


title: UPN82

description: 10x Genomics


title: NU00153 SYC102

description:
NU00153
Ribo-Zero Transcriptome

value: Refused, not reported


title: Scgb1a1+,CD24low single cell 54


title: Brown adipose tissue, WT3

value: WT


title: UPN120

description: 10x Genomics


title: Scgb1a1+,CD24low single cell 53


title: NU00140 SYC101

description:
NU00140
Ribo-Zero Transcriptome


title: Brown adipose tissue, WT2


title: UPN114

description: 10x Genomics


title: Brown adipose tissue, WT1


title: Scgb1a1+,CD24low single cell 52


title: Scgb1a1+,CD24low single cell 51


title: NU00123 SYC95

description:
NU00123
Ribo-Zero Transcriptome


title: SHL2-sh3-IP

city: hongkong

first: Yasi

last: PAN

address: Rm701, LiKS Med Sci Bldg, PWH, Shatin

country: Hong Kong

institute: the Chinese University of Hong Kong

data_processing:
Sequencing was carried out using an Illumina NovaSeq 6000 platform
Assembly: hg38
Supplementary files format and content: bw
Library strategy: m6A-seq

source_name: HKCI2 cell line

extract_protocol:
Total RNAs from HKCI2 cell lines were extracted with TRIzol (Invitrogen). Then, mRNA sequencing and m6A sequencing were simultaneously performed (Shanghai Jiayin Biotechnology Ltd, Shanghai, China).
The amount of 2 μl of 14 μl eluted RNA was reverse transcribed with High-Capacity cDNA Reverse Transcription Kit (Thermo Fisher Scientific). Once successfully immunoprecipitated methylated RNA was confirmed, further transcriptome-wide interrogation was pursued by deep sequencing using SMARTer Stranded Total RNA-Seq Kit version 2 (Pico Input Mammalian; 634413; Takara/Clontech, Japan) according to the manufacturer's protocol. A purified library was quantified using a Qubit Fluorometer (Thermo Fisher Scientific), and the size distribution was checked using the Bioanalyzer 2100 system (Agilent Technologies). The library preparations were sequenced on an Illumina Novaseq 6000 platform and 150 bp paired-end reads were generated.

value: HKCI2 cell line

value: NAFLD-HCC


title: NU00121 SYC94

description:
NU00121
Ribo-Zero Transcriptome


title: SHL2-sh3-input


title: WR24

city: La Jolla

first: Olivia

last: Osborn

state: CA

address: 9500 Gilman Drive

department: Medicine

institute: UCSD

data_processing:
Quality control of fastq file using FastQC v0.11.8
Sequence trimming using Trimmomatic V0.38
Alignment using STAR aligner v2.5.1a
Data quantification using RSEM v1.3.0 and Ensembl release 98 notation
limma-voom method for differential expression analaysis using edgeR and limma
Assembly: GRCm38p6
Supplementary files format and content: differential genes.xlsm

source_name: perigonadal adipose tissue

extract_protocol:
RNA extraction using Qiagen RNAeasy and RNA integrity using Tapestation 2200
TruSeq library preparation kit

treatment_protocol: Frozen perigonadal adipose tissue

value: perigonadal adipose tissue

value: female

value: C57b/6J wild-type

value: Weight restored


title: WR23


title: SHL2-sh2-IP


title: NU00119 SYC93

description:
NU00119
Ribo-Zero Transcriptome

value: GBM


title: Scgb1a1+,CD24low single cell 49


title: WR22


title: SHL2-sh2-input


title: NU00118 SYC92

description:
NU00118
Ribo-Zero Transcriptome


title: Brown adipose tissue, WT5

value: Brown adipose tissue


title: NU00160 SYC103

description:
NU00160
Ribo-Zero Transcriptome


title: WR21


title: NU00109 SYC86

description:
NU00109
Ribo-Zero Transcriptome

value: White


title: SHL2-nc-2-IP


title: HU13260 SYC66

description:
HU13260
Ribo-Zero Transcriptome

value: Normal


title: Scgb1a1+,CD24low single cell 47

value: 4 month


title: WR18


title: SHL2-nc-2-input


title: Scgb1a1+,CD24low single cell 46


title: WR17


title: HU13144 SYC81

description:
HU13144
Ribo-Zero Transcriptome


title: SHL2-nc-1-IP


title: AN8

value: ABA


title: Scgb1a1+,CD24low single cell 45


title: SHL2-nc-1-input


title: Scgb1a1+,CD24low single cell 44


title: Scgb1a1+,CD24low single cell 50


title: HU13062 SYC64

description:
HU13062
Ribo-Zero Transcriptome


title: 82370 SYC73

description:
82370
Ribo-Zero Transcriptome


title: Scgb1a1+,CD24low single cell 43


title: pH1N1_7101_3

city: Beijing

first: Rui-Ting

last: Li

state: Beijing

address: No.20 Dongda Street, Fengtai District

department: State Key Laboratory of Pathogen and Biosecurity

institute: Beijing Institute of Microbiology and Epidemiology

data_processing:
Clean reads were aligned to the human genome (hg19) using HISAT2 (v2.1.0). The number of reads mapped to each gene for each sample was counted by HTSeq v0.6.0.
Assembly: hg19
Supplementary files format and content: tab-delimited text files include FPKM values for each sample

extract_protocol:
Total RNA was extracted at 48 hpi by using TRIzol reagent (ThermoFisher, Cat no. 15596026) according to the manufacturer’s instructions
Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® (#E7530L, NEB, USA) following the manufacturer’s recommendations

value: drug+pH1N1 infected

value: 48 dpi


title: AN4


title: pH1N1_7101_2


title: Scgb1a1+,CD24low single cell 48


title: AN3


title: Scgb1a1+,CD24low single cell 42


title: 5482 SYC68

description:
5482
Ribo-Zero Transcriptome


title: pH1N1_7101_1


title: AN2


title: Scgb1a1+,CD24low single cell 41


title: 7101_3

value: drug


title: 5427 SYC67

description:
5427
Ribo-Zero Transcriptome


title: AN1


title: 5246 SYC78

description:
5246
Ribo-Zero Transcriptome


title: 7101_2


title: Scgb1a1+,CD24low single cell 39


title: Scgb1a1+,CD24low single cell 40


title: CON15

value: Control


title: AN7


title: 7101_1


title: NONPWT, Control, 0hr, Full, animal 1195

city: Kansas City

first: Sumedha

middle: S

last: Gunewardena

state: Kansas

address: 2146 West 39th Avenue

department: Dept. of Molecular and Integrative Physiology

institute: University of kansas medical center

data_processing:
RNA-Sequencing was performed at a strand specific (fr-secondstrand) 100 cycle paired-end resolution in biological duplicates with samples obtained from different regions subject to different treatments from each animal.
The read quality was assessed using the FastQC software. The reads were mapped to the sus scrofa genome (Sscrofa11.1; Ensembl release 105) using the STAR software, version 2.6.1c2.
Transcript abundance estimates were calculated using the featureCounts software. Expression normalization and differential gene expression calculations were performed in DESeq2 software.
Assembly: Sscrofa11.1; Ensembl release 105
Supplementary files format and content: Excel file containing raw read counts

organism: Sus scrofa

growth_protocol: Animals were allowed to acclimate for 14 days in an AAALAC accredited facility at KUMC. Animals were provided with food, water, and social enrichment ad libitum.

extract_protocol:
RNAlater preserved wound samples were stratified into four groups for each wound, Full/Bulk, epidermis, dermis, and subcutaneous. For processing, the previously bisected wound samples (two equal mirror halves of same wound) were thawed from −80°C on ice. Epidermis and Subcutaneous Layers. Epidermis and subcutaneous isolates from the pig wound channel were suspended in 1ml of 4⁰C Invitrogen Trizol Reagent (Fisher Scientific 15-596-026) in a 5ml tissue culture tube on ice. The tissue was homogenized using a Power Gen 35 Tissue Homogenizer employing a medium shark’s tooth probe – 6mm diameter (Fisher Scientific) for 20 seconds on ice. The 1ml lysate is transferred to a Andwin Scientific 5Prime Phase Lock Gel – Heavy 2ml tube (Fisher Scientific) and the Phase Lock gel purification is performed according to manufacturer’s protocol until the separation centrifugation of the aqueous phase and organic phase is complete. The aqueous phase is transferred to a microcentrifuge tube and the volume is determined. An equal volume of 70% ethanol in nuclease free water is added to the aqueous phase. The ethanol adjusted aqueous phase (with guanidinium salts) is applied directly to a RNeasy Mini kit (Qiagen 74104) purification column and the RNA Clean-up protocol is performed using an on-column DNase treatment with the RNase-Free DNase Set (Qiagen 79254) according to manufacturer’s instruction. DNase treated RNA isolates are quality controlled and quantified using a TapeStation 4200 running the RNA ScreenTape assay (Agilent Technologies). RNA Integrity Number (RIN) of ≥8.0 are targeted for proceeding to stranded mRNA library preparation.  Dermis and “Full/Bulk” Layers. Dermis and full tissue isolates (with skin) from the pig wound channel were suspended in 500ul of 4⁰C Invitrogen Trizol Reagent (Fisher Scientific 15-596-026) in a 5ml tissue culture tube on ice. The tissue was homogenized using a Power Gen 35 Tissue Homogenizer employing a medium shark’s tooth probe – 6mm diameter (Fisher Scientific) for 20 seconds on ice. The lysate was removed to a new 5ml tissue culture tube on ice. 500ul of additional chilled Trizol Reagent was added to the remaining un-lysed tissue (mainly skin) and homogenized an additional 20 seconds on ice leaving ~10% of the original skin undisrupted. The lysate was pooled with the first lysate for 1ml total. The 1ml lysate is transferred to an Andwin Scientific 5 Prime Phase Lock Gel – Heavy 2ml tube (Fisher Scientific) and the Phase Lock gel purification is performed according to manufacturer’s protocol until the separation centrifugation of the aqueous phase and organic phase is complete. The aqueous phase is transferred to a microcentrifuge tube and the volume is determined. An equal volume of 70% ethanol in nuclease free water is added to the aqueous phase. The ethanol adjusted aqueous phase (with guanidinium salts) is applied directly to a RNeasy Mini kit (Qiagen 74104) purification column and the RNA Clean-up protocol is performed using an on-column DNase treatment with the RNase-Free DNase Set (Qiagen 79254) according to manufacturer’s instruction. DNase treated RNA isolates are quality controlled and quantified using a TapeStation 4200 running the RNA ScreenTape assay (Agilent Technologies). RNA Integrity Number (RIN) of ≥8.0 are targeted for proceeding to stranded mRNA library preparation. and removed prior to complete thaw so that the tissue was still hard but RNAlater had melted. Samples were immediately transported to the Genomics Core facility in fresh RNAlater (on ice) for RNA processing and isolation.
Total RNA was enriched for messenger RNA (mRNA) by oligo dT capture using the NuGEN Universal Plus mRNA-seq + UDI library kit (NuGEN 9144-96). Captured mRNAs were fragmented, reverse transcribed into cDNA and ligated with unique dual indexed (UDI) sequence adapters and PCR amplified to generate indexed libraries. Validation of library preparations was performed using the Agilent Bioanalyzer. Prior to pooling, quantification of the indexed libraries was performed using the Roche LightCycler96 RealTime PCR system.

treatment_protocol: Animals were inflicted with a 2cm incisional wound that was 2.5cm in depth and dressing materails were inserted into the wounds for 0, 2, 4, 8 hours in duration.

value: skin

tag: npwt (negative_pressure_wound_therapy)

value: NONPWT

tag: dressing

tag: layer

value: Full


title: Scgb1a1+,CD24low single cell 38


title: CON13

value: perigonadal adipose tissue


title: 5511 SYC69

description:
5511
Ribo-Zero Transcriptome


title: pH1N1_3

tag: cell line

value: pH1N1 infected


title: Scgb1a1+,CD24low single cell 37


title: NONPWT, Control, 0hr, SubQ, animal 1195

value: SubQ


title: Scgb1a1+,CD24low single cell 36


title: CON12

value: female

value: C57b/6J wild-type


title: NONPWT, Control, 0hr, Dermis, animal 1195

value: Dermis


title: CON10


title: CON11


title: pH1N1_1


title: NPWT, Granufoam, 8hr, Full, animal 1195

value: NPWT

value: Granufoam


title: Scgb1a1+,CD24low single cell 35

value: 4 month


title: Scgb1a1+,CD24low single cell 34


title: NONPWT, Control, 0hr, Epidermis, animal 1195

value: Epidermis


title: mock_2

value: mock


title: mock_3

value: 48 dpi


title: Ube2i cKO GV oocyte 17 [6322c_SB40]

city: Houston

first: Peixin

last: Jiang

state: TX

address: One Baylor Plaza

institute: Baylor College of Medicine

data_processing:
Raw sequencing reads were preprocessed using BBDuk for quality-trimming and filtering, adapter-trimming.
Reads were aligned to reference genome using STAR Aligner.
The gene count table was generated from from subreads using featureCounts.
The raw counts were filtered, normalized, and analyzed using DESeq2.
Assembly: GRCm38
Supplementary files format and content: tab-delimited text files include normalized gene counts for each Sample

source_name: GV stage Oocyte

extract_protocol:
RNA-seq library was generated according to SMART-seq v4 Ultra low input RNA kit (Takara). In brief, isolated cells were lysed in lysis buffer, 3-SMART-seq CDS primer II and V4 oligonucleotide were added for first stranded cDNA synthesis.  cDNA was amplified using PCR Primer II A, and subsequently purified using Ampure XP beads (Beckman).
Illumina library was prepared using Nextera XT DNA library preparation kit (Illumina) and sequenced using Illumina Novaseq.

value: GV stage Oocyte

value: Ube2i(loxp/loxp) Zp3-cre(+)


title: NPWT, Granufoam, 8hr, SubQ, animal 1195

value: skin


title: Ube2i cKO GV oocyte 16 [6322b_SB39]


title: Scgb1a1+,CD24low single cell 33


title: Scgb1a1+,CD24low single cell 32


title: CON9

value: Control


title: NPWT, Granufoam, 8hr, Dermis, animal 1195


title: Scgb1a1+,CD24low single cell 31


title: PBMC, expanded GZMB+Bregs, rep3, HTO

city: Nantes

first: Nicolas

last: Sailliet

address: 30 Boulevard Jean Monnet

country: France

institute: Nantes université

description:
Cell Hashing library: read1 file contains cell barcode and UMI; read2 file contains Hashtag Antibody Derived Tag reads
Hashtag-derived oligonucleotide (HTO)

library_source: other

data_processing:
Pre-processing of sequencing results to generate count matrices (gene expression, ADT and HTO barcode counts) was performed using the 10x genomics Cell Ranger pipeline where ADT and HTO sequences were concatenated and treated as Custom library with default settings (v4.0.2) and aligning to the GRCh38 genome.
Further processing steps were done with Seurat4.0.2
Assembly: GRCh38
Supplementary files format and content: 10x Genomics output files: barcodes.tsv.gz, features.tsv.gz, matrix.mtx.gz
Library strategy: CITE-seq (Cellular Indexing of Transcriptomes and Epitopes by sequencing)

molecule: protein

source_name: PBMC

growth_protocol: negatively sorted B cells (human B cell isolation kit II, Miltenyi) were either stimulated with CpG ODN 2006 [1µg/mL] (Invivogen), soluble rhCD40L [50ng/mL] (R&D systems), rhIL-2 [50IU/mL] (Proleukine – Novartis), rhIL-21 [10ng/mL] (R&D systems), anti-human IgG/A/M F(ab)’2 [5µg/mL] (Jackson ImmunoResearch)) in complete RPMI1640 (containing 10% Fetal Calf Serum, 2mM L-Glutamine, 100U/mL penicillin / streptomycin.) in 6-well plates at 10^6 cells/mL for 72h at 37°C 5%CO2 or left unstimulated in complete RPMI1640 in 6-well plates at 10^6 cells/mL for 72h at 37°C 5%CO2.

extract_protocol:
Living cells were sorted on an ARIA III (BD Biosciences) and marked with anti-β2-microglobulin or anti-CD293 conjugated DNA sequences (HashTag Oligonucleotide, HTO) specific of the donor and the experimental condition. Extraction was performed following CITE-seq protocols
scRNA-seq libraries were produced with the Chromium Single Cell 3′ Library and Gel Bead Kit v3 (10X Genomics, San Francisco, CA) following supplier's protocols.
CITE-seq library: amplification was performed at 95°C for 3’ followed by ten cycles at 95°C for 20’’; 60°C for 30’’; 72°C for 20’’ and final elongation 72°C for 5’ with 5’-CAAGCAGAAGACGGCATACGAGATCGTGATGTGACTGGAGTTCCTTGGCACCCGAGAATTCCA-3’ Small RNA RPI1 primer as i7 primer (Illumina).
Following the final bead purification, all three libraries were pooled as 90% mRNA library, 10% HTO library before sequencing.

value: PBMC

value: B cells

tag: library type

value: HTO

tag: antibodies/tags

value: anti-β2-microglobulin or anti-CD293:Ech3-GZMB+Bregs :TotalSeqB-0254; Ech4-GZMB+Bregs :TotalSeqB-0256; Ech3-nonBregs :TotalSeqB-0253; Ech4-nonBregs :TotalSeqB-0255; NA :TotalSeqB-0251; TotalSeqB-0252; TotalSeqB-0257; TotalSeqB-0258


title: NPWT, Granufoam, 8hr, Epidermis, animal 1195

tag: tissue


title: pH1N1_2

tag: treatment

value: pH1N1 infected


title: Ube2i cKO GV oocyte 15 [6322a_SB38]

tag: cell type


title: PBMC, expanded GZMB+Bregs, rep3, RNA

description:
3' mRNA library: read1 file contains cell barcode and UMI; read2 file contains transcript
poly A RNA

value: mRNA


title: NONPWT, Control, 8hr, Full, animal 1195

value: NONPWT

tag: time

value: Full


title: Ube2i cKO GV oocyte 14 [6302d_SB32]

tag: genotype


title: Scgb1a1+,CD24low single cell 29


title: Ube2i cKO GV oocyte 13 [6302c_SB31]


title: NONPWT, Control, 8hr, SubQ, animal 1195

value: SubQ


title: PBMC, expanded GZMB+Bregs, rep2, RNA


title: Ube2i cKO GV oocyte 12 [6302b_SB30]


title: Scgb1a1+,CD24low single cell 28

value: 4 month


title: NONPWT, Control, 8hr, Epidermis, animal 1195

value: Epidermis


title: Ube2i cKO GV oocyte 11 [6302a_SB29]


title: mock_1

value: mock


title: Scgb1a1+,CD24low single cell 27


title: PBMC, expanded GZMB+Bregs, rep1, HTO

value: anti-β2-microglobulin or anti-CD293:Ech1-GZMB+Bregs :HTO2-TotalSeqB; Ech1-nonBregs :HTO1-TotalSeqB; NA :HTO5-TotalSeqB; NA:HTO6-TotalSeqB; NA:HTO7-TotalSeqB; NA :HTO8-TotalSeqB


title: PBMC, expanded GZMB+Bregs, rep1, RNA


title: NONPWT, Control, 0hr, Full, animal 1157


title: Scgb1a1+,CD24low single cell 30


title: Ube2i cKO GV oocyte 9 [6301b_SB26]

value: GV stage Oocyte


title: PBMC, B/T cocultures, HTO

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 where  HTO sequences were concatenated and treated as Custom library with default settings (v4.0.2) and aligning to the GRCh38 genome.
Further processing steps were performed with Seurat4.0.2
Assembly: GRCh38
Supplementary files format and content: 10x Genomics output files: barcodes.tsv.gz, features.tsv.gz, matrix.mtx.gz
Library strategy: CITE-seq (Cellular Indexing of Transcriptomes and Epitopes by sequencing)

growth_protocol: negatively sorted B cells (human B cell isolation kit II, Miltenyi) were either stimulated with CpG ODN 2006 [1µg/mL] (Invivogen), soluble rhCD40L [50ng/mL] (R&D systems), rhIL-2 [50IU/mL] (Proleukine – Novartis), rhIL-21 [10ng/mL] (R&D systems), anti-human IgG/A/M F(ab)’2 [5µg/mL] (Jackson ImmunoResearch)) in complete RPMI1640 (containing 10% Fetal Calf Serum, 2mM L-Glutamine, 100U/mL penicillin / streptomycin.) in 6-well plates at 10^6 cells/mL for 24h at 37°C 5%CO2 or left unstimulated in complete RPMI1640 in 6-well plates at 10^6 cells/mL for 24h at 37°C 5%CO2. The next day, negatively sorted CD4+CD25- T cells (two subsequent negative isolations with the human CD4+T cell isolation kit and the human CD25 microbeads, miltenyi) were activated with CD3/CD28 coated dynabeads (1:1 beads to T cell ratio) for 3 days alone, with GZMB+enriched B cells or unstimulated B cells at 37°C5%CO2.

value: Lymphocytes

value: anti-CD293 + anti-B2-microglobulin :Ech1-LT/GZMB+Bregs :antihumanH12; Ech2-LT/GZMB+Bregs:antihumanH13; Ech1-LT/nonBregs:antihumanH14; Ech2-LT/nonBregs:antihumanH15; Ech1-LT:antihumanH7; Ech2-LT:antihumanH8


title: NONPWT, Control, 0hr, SubQ, animal 1157

value: skin

value: Control


title: PBMC, B/T cocultures, RNA

value: PBMC


title: PBMC, expanded GZMB+Bregs, rep2, HTO

value: B cells

value: HTO

value: anti-β2-microglobulin or anti-CD293:Ech2-GZMB+Bregs :HTO2-TotalSeqB; Ech2-nonBregs :HTO1-TotalSeqB; NA :HTO3-TotalSeqB; NA:HTO4-TotalSeqB; NA:HTO5-TotalSeqB; NA :HTO6-TotalSeqB


title: Scgb1a1+,CD24low single cell 25


title: NONPWT, Control, 0hr, Dermis, animal 1157

value: Dermis


title: Ube2i cKO GV oocyte 8 [6301a_SB25]

value: Ube2i(loxp/loxp) Zp3-cre(+)


title: NONPWT, Control, 0hr, Epidermis, animal 1157

value: NONPWT


title: Ube2i cKO GV oocyte 7 [6300e_SB24]


title: NONPWT, Control, 8hr, Dermis, animal 1195


title: TC71_48h-3

city: Iowa City

first: David

middle: Jon

last: Gordon

state: Iowa

address: 25 S Grand Ave

department: Pediatric Hematology/Oncology

institute: University of Iowa

data_processing:
FastQC was used to assess the quality of the sequencing reads. Reads were then mapped against the human reference genome (version hg38) using the STAR aligner.
The raw counts were normalized and transformed using the rlog function and principal components analysis (PCA) was performed to visualize sample clusters. No outlier samples were identified or removed from the analysis.
Assembly: hg38
Supplementary files format and content: Matrix table with raw gene counts for each gene and sample

source_name: TC71 Ewing sarcoma cell line

growth_protocol: The cell lines were cultured in DMEM with 10% FBS.

extract_protocol:
RNA was isolated from cell lines using RNeasy Plus Mini Kit (Qiagen).
RNA libraries were prepared for sequencing using standard Illumina TruSeq Stranded mRNA protocols.

tag: time (hrs)


title: Scgb1a1+,CD24low single cell 24


title: Scgb1a1+,CD24low single cell 23


title: NPWT, Granufoam, 8hr, Full, animal 1157

source_name: skin

value: NPWT

value: Granufoam

value: Full


title: Scgb1a1+,CD24low single cell 22

value: 4 month


title: TC71_48h-1


title: TC71_48h-2


title: NPWT, Granufoam, 8hr, SubQ, animal 1157

value: SubQ


title: Scgb1a1+,CD24low single cell 26


title: Ube2i cKO GV oocyte 5 [6300c_SB22]

value: GV stage Oocyte


title: Scgb1a1+,CD24low single cell 21


title: Ube2i cKO GV oocyte 10 [6301c_SB27]


title: Scgb1a1+,CD24low single cell 20


title: TC71_0h-3


title: NPWT, Granufoam, 8hr, Dermis, animal 1157


title: NPWT, Granufoam, 8hr, Epidermis, animal 1157

value: Epidermis


title: TC71_0h-2


title: NONPWT, Control, 8hr, Full, animal 1157


title: TC71_0h-1


title: Scgb1a1+,CD24low single cell 19


title: EW8_48h-3

source_name: EW8 Ewing sarcoma cell line


title: NONPWT, Control, 8hr, SubQ, animal 1157


title: Scgb1a1+,CD24low single cell 18


title: EW8_48h-2


title: Ube2i cKO GV oocyte 1 [6299a_SB17]


title: Ube2i cKO GV oocyte 3 [8300a_SB20]


title: NONPWT, Control, 8hr, Dermis, animal 1157


title: Control GV oocyte 17 [6323d_SB36]


title: Scgb1a1+,CD24low single cell 17


title: Scgb1a1+,CD24low single cell 16


title: Ube2i cKO GV oocyte 2 [6299b_SB18]


title: Ube2i cKO GV oocyte 6 [6300d_SB23]


title: EW8_48h-1


title: NONPWT, Control, 8hr, Epidermis, animal 1157


title: Scgb1a1+,CD24low single cell 15


title: Control GV oocyte 16 [6323c_SB35]


title: EW8_0h-3


title: Ube2i cKO GV oocyte 4 [6300b_SB21]


title: Scgb1a1+,CD24low single cell 14


title: 3DRAM-seq (RNA) mESC rep2

city: Neuherberg

first: Boyan

last: Bonev

state: Deutschland

address: Ingolstädter Landstr. 1

institute: Helmholtz Zentrum München

data_processing:
Reads were aligned using the STAR and FPKM calculated using Deseq2.
Supplementary files and format and content:  Compressed tab: Table with reads per gene

source_name: E14 mESC

growth_protocol: E14 mESC were cultured at 37˚C (5% CO2) on 0.1% Gelatin (Millipore, Cat. N: ES-006-B) coated 10cm dishes (Falcon, Cat. N.: 35300) in sterile-filtered (Millipore, Cat. N.: SCGPS05RE) Glutamax DMEM media (Gibco, Cat. N.: 31966047) supplemented with 15% heat inactivated FBS (ThermoFisher, Cat. N:16141079), 1% Pen-strep (Gibco, Cat. N.: 15140122), 1% MEM (Gibco, Cat. N.: 11140035), 0.2% b-mercaptoethanol (Gibco, Cat. N: 31350010) and 0.1% LIF (Merck, Cat. N.: ESG1106). Media was changed every day and cells were splitted using Accutase (ThermoFisher, Cat. N.: A1110501) every second.

extract_protocol:
RNA was isolated from 2.5x104 (10% of the sample) fixed mESC using the Quick-RNA FFPE Miniprep (Zymo Research, Cat. N: R1008) in combination with Zymo-Spin IC Columns (Zymo Research, Cat. N: C1004-250) according to the manufacturing instructions starting from the tissue dissociation step.
RNA libraries were generated using the NEBNext® Single Cell/Low Input RNA Library Prep Kit (NEB, Cat. N: E6420S) according to the manufacturing instructions.

treatment_protocol: mESC were harvested and fixed at a concentration of 1x106 cells/mL with 1% formaldehyde (ThermoFisher, Cat. N.:28906) in PBS for 10min. at RT and subsequently quench for 5min. at RT with Glycine (ThermoFisher, Cat. N.: 15527-013) in a final concentration of 0.2M. Thereafter, cells were spun down with 500g for 5min. at 4˚C and washed once with PBS containing 1% BSA (Sigma, Cat. N.: B6917) and 0.1% RNAsin plus RNase inhibitor (Promega, Cat. N.: N261A).

value: E14 mESC

tag: technique

tag: genome build


title: EW8_0h-2


title: Control GV oocyte 14 [6323a_SB33]


title: Scgb1a1+,CD24low single cell 13

tag: strain


title: 3DRAM-seq (RNA) mESC rep1

data_processing:
Reads were aligned using the STAR and FPKM calculated using Deseq2.
Supplementary files format and content: Compressed tab: Table with reads per gene


title: EW8_0h-1


title: Control GV oocyte 13 [6297d_SB16]


title: Scgb1a1+,CD24low single cell 12


title: 3DRAM-seq (RNA) mESC rep3


title: Control GV oocyte 12 [6297c_SB15]


title: Scgb1a1+,CD24low single cell 11


title: RNA immunoMPRA human NEG rep2

data_processing:
150xbp paired-end reads from the DNA or RNA libraries were trimmed using cutadapt with the following parameters: -m 12:10 -e 0.4 -u 1 -a GAATTCTCATTAC -A TCGACCGCAAGTTGG --discard-untrimmed. Subsequently read 1 was addtionally trimmed with -l 12. Count tables for RNA and DNA reads were generated using MPRAflow (--bc-length 12 and –mpranalyze).
Supplementary files and format and content:  Compressed tarball archive containing DNA/RNA read counts and annotations for both replicates.
Library strategy: Targeted barcode amplification from RNA/DNA

source_name: Electroporated negative cells from the day 47 human cortical organoids

growth_protocol: Human iPSCs were cultured following the technical manual of the mTeSR plus medium (StemCell Technologies, Cat. N.: 100-0276) and then used to derive 3D-hCOs according to modified Yoon and Cederquist protocols (Yoon et al., 2019: Cederquist et al., 2019). In brief, 80-90% confluent hiPSCs were dissociated to single cells, and 1x104 single cells were seeded in one well of an AggreWell 800 plate (StemCell Technologies, Cat. N.: 34815) to promote embryo body aggregation. Neural induction was then prompted with 2.5µM Dorsomorphin (StemCell Technologies, Cat. N.: 72102), 10µM SB-431542 (StemCell Technologies, Cat. N.: 72232), and 2.5µM XAV-939 (Tocris, Cat. N.: 3748). Once the neuroepithelium started to be generated (day 7 of the neural induction), embryo bodies were embedded in a drop of Matrigel (Corning, Cat. N.: 354234), and cultured in differentiation media minus Vitamin A for the first 4 days, and plus Vitamin A afterwards to enhance brain tissue growth (1:1 mixture of DMEM/F-12 (Gibco, Cat. N.: 11330-032) and Neurobasal medium (Gibco, Cat. N.: 21103-049) supplemented with 0.5% N2 Supplement (Life Technologies, Cat. N.: 17502-048), 0.025% Insulin (Sigma, Cat. N.: I9278), 1% B-27 Supplement minus/plus Vitamin A (Life Technologies, Cat. N.: 12587010/17504044), 1% GlutaMAX Supplement (Life Technologies, Cat. N.: 35050-061), 0.5% MEM-NEAA (Life Technologies, Cat. N.: 1140-050), 1% Pen-strep (Gibco, Cat. N.: 15140122), and 0.1% b-mercaptoethanol (Gibco, Cat. N.: 31350010)).

extract_protocol:
RNA and DNA were extracted from sorted cells using the Quick-DNA/RNA Microprep Plus Kit (Zymo Research; Cat. N: D7005). Purified RNA was treated with TURBO DNase (Thermo Fisher; Cat. N: AM1907) and reverse transcribed with Maxima H Minus RT (Thermo Fisher; Cat. N: EP0753) using Oligo(dT)18 Primer (Thermo Fisher; Cat. N: SO131). cDNA was purified with 1.5X vol. AMPure XP magnetic beads (Agencourt, Cat. N: A63881) and stored at -20 °C for later use.
Libraries from DNA and cDNA were prepared in the same way. Briefly, UMIs were added (98°C 30s; {98°C 10s, 65°C 30s, 72°C 1min} x3; 72°C 3min; Hold at 4°C) using the primers RV_univ_MPRA (CGACGCTCTTCCGATCT) and FWD_mScar_Tn7_10UMI_3 (0.5 µM each; GTCTCGTGGGCTCGGAGATGTGTATAAGAGACAG NNNNNNNNNN TCGACCGCAAGTTGGAC). P7 and P5 sequencing adapters were attached in two separate PCRs (98°C 30s; {98°C 10s, 65°C 90s} x(10+X); 72°C 5min; Hold at 4°C) using indexed Ad2.X(CAAGCAGAAGACGGCATACGAGAT XXXXXXXX GTCTCGTGGGCTCGGAGATGT) and P5NEXT_SXXX primers (0.1 µM each; AATGATACGGCGACCACCGAGATCTACAC NNNNNNNN ACACTCTTTCCCTACACGACGCTCTTCCG*A*T*C*T ). Required PCR cycle numbers were estimated by qPCR and using 1/10 of the second PCR product as input. All PCRs were performed in 1X NEBNext® Ultra™ II Q5® Master Mix (New England Biolabs; Cat. N: M0544), and PCR products were purified with 0.8X - 1.2X vol. of AMPure XP magnetic beads.

treatment_protocol: Electroporation of the MPRA library was carried out two days after the first slicing on day 45 of organoid culture. MPRA library at a final concentration of 1 µg/µl diluted in 0.1 % Fast Green Solution were injected into up to 5 ventricular structures per organoid. After injection, organoids were transferred into an electroporation chamber containing Tyrode’s solution and electroporated with 5 pulses applied at 38 V for 50 ms each at intervals of 1 seconds (Harvard Bioscience, BTX ECM 830) followed by a incubation for 72 hours. Depending on size and structure up to 40 organoids per replicate were microdissected for the electroporated area and dissociated using the papain-based neural dissociation kit (Miltenyi Biotec, Cat. N: 130-092-628) with reduced incubation times. Dissociated cells were fixed at a concentration of 1x106 cells/mL with 1% formaldehyde (ThermoFisher, Cat. N.:28906) in PBS for 10min. at RT and subsequently quench for 5min. at RT with Glycine (ThermoFisher, Cat. N.: 15527-013) in a final concentration of 0.2M. To isolate human neuronal stem cells (NSC) and intermediate progenitors (IPC), dissociated and fixed cells were first incubated in permeabilization buffer consistent of 0.1% freshly prepared Saponin (Sigma-Aldrich, Cat. N.: SAE0073), 0.2% BSA (Sigma, Cat. N.: B6917) and 0.1% RNAsin plus RNase inhibitor (Promega, Cat. N.: N261A) in PBS for 15min. at 4˚C. The permeabilization buffer was removed by centrifuging the cells with 2500g for 5min. at 4˚C followed by staining against SOX2-PE (1:20; BD Biosciences, Cat. N.: 562195), PAX6-AlexaFluor488 (1:40; BD Bioscience, Cat. N.: 561664), and EOMES-eFluor660 (1:20; BD Bioscience, Cat. N.: 566749) in staining buffer consistent of 0.1% freshly prepared Saponin, 1% BSA and 0.1% RNAsin plus RNase inhibitor in PBS for 1 hour at 4˚C under slow rotation. Cells were washed twice for 5min. in PBS containing 1% BSA and 0.1% RNAsin plus RNase inhibitor and incubated for 10min. at 4°C with slow rotation in PBS containing 0.5% BSA, 0.1% RNAsin plus RNase inhibitor and DAPI (1:1000; ThermoFischer, Cat. N.: D1306).Cells were sorted for SOX2+/PAX6+ for NSC; SOX2-/EOMES+ for IPC; SOX2-/EOMES- for double negative cells.

value: NEG (PAX6-, SOX2- and EOMES-)

value: immunoMPRA


title: NH_X_5_s2

city: Meguro-ku

first: Tatsuo

last: Michiue

address: 3-8-1, Komaba

institute: The University of Tokyo

data_processing:
Sequences were aligned by HISAT2.
Samtools was used to convert SAM files to indexed, sorted, and merged BAM files.
Transcripts were assembled and quantified using StringTie.
Assembly: X. tropicalis v10.0 genome assembly
Supplementary files format and content: tab-delimited text files include gene counts for each Sample

organism: Xenopus tropicalis

extract_protocol:
Tumor tissues and skin of the leg and flank were surgically collected and subsequently crushed using a bead crusher (MS-100R, TOMY) with 6 mm diameter beads. The beads and samples were placed in a tube together and crushed five times (3000 rpm, 1 min, 2°C). RNA was then purified using the ReliaPrep RNA Cell Miniprep System (Promega).
RNA libraries for RNA-seq were performed at Novogene, the analysis contractor.

value: skin


title: DNA immunoMPRA human NEG rep2

library_source: genomic


title: Control GV oocyte 11 [6297b_SB14]


title: Scgb1a1+,CD24low single cell 10

data_processing:
Basecalls performed by Illumina MiSeq
Sequenced reads were trimmed for adaptor sequence, and were sorted by indexes in Illumina MiSeq
Reads were aligned to the mm10 genome assebly using STAR
Mapped reads seperated by genes, and the reads mapped for each gene were clusterd by molecular barcode
The number of cluteres for each gene was counted, which provides the number of molecules detected for each gene
Genome_build: mm10
Supplementary_files_format_and_content: The detected number of RNA moelcules per well (i.e., single cell)  for each gene is listed.


title: NH_X_5_n2


title: Scgb1a1+,CD24low single cell 9


title: NH_X_5_n1


title: Control GV oocyte 10 [6297a_SB13]


title: Scgb1a1+,CD24low single cell 8


title: DNA immunoMPRA human NEG rep1


title: RNA immunoMPRA human NEG rep1


title: Control GV oocyte 9 [6296d_SB12]


title: NH_X_4_s


title: Control GV oocyte 8 [6296c_SB11]


title: Scgb1a1+,CD24low single cell 7


title: RNA immunoMPRA human IPC rep2

source_name: Electroporated IPC from the day 47 human cortical organoids

value: IPC (EOMES+)


title: NH_X_4_n


title: Control GV oocyte 15 [6323b_SB34]


title: DNA immunoMPRA human IPC rep2


title: Scgb1a1+,CD24low single cell 6

source_name: Scgb1a1+,CD24low cell


title: Control GV oocyte 7 [6296b_SB10]


title: RNA immunoMPRA human IPC rep1


title: NH_VIII_7_s


title: Control GV oocyte 6 [6296a_SB9]


title: NH_VIII_7_n

source_name: tumor tissue

value: tumor tissue


title: Scgb1a1+,CD24low single cell 4


title: DNA immunoMPRA human IPC rep1


title: RNA immunoMPRA human NSC rep2

source_name: Electroporated NSC from the day 47 human cortical organoids

value: NSC (PAX6+/SOX2+)


title: Scgb1a1+,CD24low single cell 3


title: Control GV oocyte 5 [6295c_SB8]


title: NH_X_5_s1


title: NH_V_1_n


title: NH_III_4_s


title: DNA immunoMPRA human NSC rep2


title: RNA immunoMPRA human NSC rep1


title: Scgb1a1+,CD24low single cell 2


title: NH_III_4_n


title: Control GV oocyte 3 [6295a_SB6]


title: DNA immunoMPRA human NSC rep1


title: Control GV oocyte 1 [6292a_SB2]


title: NH_V_1_s


title: Negative control 2

organism: metagenome

source_name: medium


title: 3DRAM-seq (DNA) IPC rep2

data_processing:
100bp paired-end reads where first trimmed using Trim Galore with the following parameters: --nextseq 30 --clip_R1 1 --clip_R2 15 --length 20. Subsequently reads where aligned using Bismarck (Krueger and Andrews, 2011) with Bowtie2 in PE mode and the post-bisulfite adapter tagging option (--pbat) for the reverse read. To recover chimeric reads resulting for the proximity ligation, and thus are not aligned during the previous step, unmapped reads where split at adjacent DpnII cutting sites (GATTGATT, GATTGATC for forward and AATCAATC, GATCAATC for reverse strand), separately aligned and subsequently merged with the non-chimeric reads. The unique read pairs were transformed into restriction fragment end (fend) coordinates, converted into ‘misha’ tracks and imported into the corresponding genomic database (mm10 or hg38). Methylation levels in both, CpG and GpC context, were calculated on uniquely mapped reads using the bismark methylation extractor and coverage2cytosine function. Only cytosine with a 5x coverage for individual replicates or 10x coverage for merged replicates were considered for further analysis.
Supplementary files and format and content:  Bigwig: Measured CpG and GpC methylation levels with min. 5x coverage. Compressed txt: Coordinates of paired fragments

source_name: human cortical organoids

growth_protocol: Human iPSCs were cultured following the technical manual of the mTeSR plus medium (StemCell Technologies, Cat. N.: 100-0276) and then used to derive 3D-hCOs according to modified Yoon and Cederquist protocols (Yoon et al., 2019: Cederquist et al., 2019). In brief, 80-90% confluent hiPSCs were dissociated to single cells, and 1x104 single cells were seeded in one well of an AggreWell 800 plate (StemCell Technologies, Cat. N.: 34815) to promote embryo body aggregation. Neural induction was then prompted with 2.5µM Dorsomorphin (StemCell Technologies, Cat. N.: 72102), 10µM SB-431542 (StemCell Technologies, Cat. N.: 72232), and 2.5µM XAV-939 (Tocris, Cat. N.: 3748). Once the neuroepithelium started to be generated (day 7 of the neural induction), embryo bodies were embedded in a drop of Matrigel (Corning, Cat. N.: 354234), and cultured in differentiation media minus vitamin A for the first 4 days, and plus vitamin A afterwards to enhance brain tissue growth (1:1 mixture of DMEM/F-12 (Gibco, Cat. N.: 11330-032) and Neurobasal medium (Gibco, Cat. N.: 21103-049) supplemented with 0.5% N2 Supplement (Life Technologies, Cat. N.: 17502-048), 0.025% Insulin (Sigma, Cat. N.: I9278), 1% B-27 Supplement minus/plus vitamin A (Life Technologies, Cat. N.: 12587010/17504044), 1% GlutaMAX Supplement (Life Technologies, Cat. N.: 35050-061), 0.5% MEM-NEAA (Life Technologies, Cat. N.: 1140-050), 1% Pen-strep (Gibco, Cat. N.: 15140122), and 0.1% b-mercaptoethanol (Gibco, Cat. N.: 31350010)).

extract_protocol:
Between 1.5-2x105 immunoFAC-sorted human NSCs and IPCs were first lysed with 0.2% Igepal-CA630 (Sigma-Aldrich, Cat. N: I3021) for 10min. at RT, washed once with 1x GpC buffer (New England Biolabs, Cat. N.: M0227S) containing 1% BSA (Sigma, Cat. N.: B6917) and subsequently incubated for 3h at 37˚C in a reaction mix containing 60U M.CviPI (New England Biolabs, Cat. N.: M0227S) and 0.6mM SAM (New England Biolabs, Cat. N.: B9003). During the incubation the reaction was substitution with 8U M.CviPI and 1µl of 32mM SAM every hour. Nuclei were washed, permeabilized with 0.5% SDS (Invitrogen, Cat. N:AM9823) followed by a quenching of the SDS with SDS ~1.5% Triton-X-100 (Sigma Aldrich, Cat. N: X100) and a digested with 400U DpnII (New England Biolabs, Cat. N: R0543) overnight at 37˚C. Subsequently, sticky ends were filled by incubating the nuclei for 4h at RT with DNA Polymerase I (New England Biolabs, Cat. N: M0210) and a biotin-14-dATP (Life Technologies, Cat. N: 195245016) containing nucleotide mix in DpnII buffer. Proximity ligation was performed at least for 6h at 16˚C using the T4 DNA Ligase (New England Biolabs, Cat. N.: M0202). Thereafter nuclei and chromatin were digested using 200µg Proteinase K (New England Biolabs, Cat. N: P8107) with 1% SDS followed by reverse crosslinking overnight at 68˚C with 0.5M NaCl, purification by ethanol precipitation and shearing to ~550 bp DNA fragments using a Covaris S220 sonicator. End repaired was performed using the T4 DNA Polymerase (New England Biolabs, Cat. N: M0203) and non-biotinylated nucleotides for 4h at 20˚C. Approximately 0.01% of biotinylated methylation controls are added to the sample and bisulfite conversion was performed using the EZ DNA Methylation-Gold kit (Zymo Research, Cat. N: D5005).
For library constructed the Accel-NGS® Methyl-Seq DNA Library kit (Swift Bioscience, Cat. N: 30024) was used according to the manufacturing instructions until the adapter ligation step. After this step, biotin pulldown was performed using MyOne Streptavidin T1 beads (ThermoFisher, Cat. N: 65602) followed by 5 washes with washing buffer containing 0.05% Tween-20 (Sigma-Aldrich, Cat. N: P9416) and two additional washes with low-TE water. Final library amplification was performed in 5 separate reactions using the EpiMark Hot Start Taq (New England Biolabs, Cat. N: M0490) with Methyl-Seq Indexing Primers (Swift Bioscience, Cat. N: 36024) with the following PCR program: 95˚C 30s; {95˚C 15s, 61˚C 30s, 68˚C 80s} x10-11; 68˚C 5min; Hold at 10˚C. The different reactions were pooled, Streptavidin T1 beads were pelleted on a magnetic rack and the prepared libraries within the supernatant were purified using 0.65x AMPure XP beads (Agencourt, Cat. N: A63881) to reach an average fragment size of approximately 500bp.

treatment_protocol: 3D-hCOs were harvested after 45 days and dissociated using the Papain-based Neural Tissue Dissociation Kit (Miltenyi Biotec, Cat. N.: 130-092-628) following the manual dissociation protocol. Dissociated cells were fixed at a concentration of 1x106 cells/mL with 1% formaldehyde (ThermoFisher, Cat. N.:28906) in PBS for 10min. at RT and subsequently quench for 5min. at RT with Glycine (ThermoFisher, Cat. N.: 15527-013) in a final concentration of 0.2M. To isolate human neuronal stem cells (NSC) and intermediate progenitors (IPC), dissociated and fixed cells were first incubated in permeabilization buffer consistent of 0.1% freshly prepared Saponin (Sigma-Aldrich, Cat. N.: SAE0073), 0.2% BSA (Sigma, Cat. N.: B6917) and 0.1% RNAsin plus RNase inhibitor (Promega, Cat. N.: N261A) in PBS for 15min. at 4˚C. The permeabilization buffer was removed by centrifuging the cells with 2500g for 5min. at 4˚C followed by staining against SOX2-PE (1:20; BD Biosciences, Cat. N.: 562195), PAX6-AlexaFluor488 (1:40; BD Bioscience, Cat. N.: 561664), and EOMES-eFluor660 (1:20; BD Bioscience, Cat. N.: 566749) in staining buffer consistent of 0.1% freshly prepared Saponin, 1% BSA and 0.1% RNAsin plus RNase inhibitor in PBS for 1 hour at 4˚C under slow rotation. Cells were washed twice for 5min. in PBS containing 1% BSA and 0.1% RNAsin plus RNase inhibitor and incubated for 10min. at 4°C with slow rotation in PBS containing 0.5% BSA, 0.1% RNAsin plus RNase inhibitor and DAPI (1:1000; ThermoFischer, Cat. N.: D1306). Cells were sorted for SOX2+/PAX6+ for NSC and SOX2-/EOMES+ for IPC.


title: Control GV oocyte 2 [6292b_SB3]


title: Scgb1a1+,CD24low single cell 5

extract_protocol:
RNAs from cell lysate in each well was directly used for library preparation without purification
Libraries were prepared by using molecular barcoding technique. First, for control, the same amount of spike-in RNAs, a known number of External RNA Controls Consortium (ERCC) RNA molecules, was added into every tube which contains an isolated cell. Then, the cells were lysed and RNA molecules were fragmentated by temperature elevation. cDNAs were generated by reverse transcription using a reverse transcription primer, in which the first common primer sequence, molecular barcode, fourteen T bases, and one V (A or G or C) base are tandemly arranged from 5' end. In the reverse transcription, the second common primer sequence was also attached to 3' end of each generated cDNA molecule by template switching. Subsequently, cDNAs were amplified by PCR using two primers; one primer contains an illumina adapter sequence, sample index, and the first common primer sequence, and the other primer has another illumina adapter sequence, sample index, and the second common primer sequence.


title: 3DRAM-seq (DNA) IPC rep1


title: Hex_3_D

city: Munich

first: Adam

last: Burton

address: Marchioninistr. 25

department: IES

institute: Helmholtz Munchen

data_processing:
Paired-end sequencing reads were mapped to the reference genome (version GRCm38, primary assembly fasta) using STAR (version 2.7.6a) with the parameter quantMode GeneCounts and the gtf annotation (version GRCm38.101) and ERCC92 (Thermofisher). Raw read counts files (ReadsPerGene.out.tab) generated by STAR were used for downstream analysis.
Assembly: GRCm38
Supplementary files format and content: TAB format with read counts per gene

source_name: 2-cell stage

growth_protocol: incubation KSOM

extract_protocol:
single embryo
Smartseq2

treatment_protocol: 3.5% 1,6-Hexanediol

value: 2-cell stage

value: F1:C57BL/6J x CBA/H

value: 3.5% 1,6-Hexanediol 1 hour


title: Control GV oocyte 4 [6295b_SB7]


title: Hex_3_C


title: Hex_3_B


title: Scgb1a1+,CD24low single cell 1


title: 3DRAM-seq (DNA) NSC rep1

value: NSC (PAX6+)


title: Hex_3_A


title: 3DRAM-seq (RNA) IPC rep2

extract_protocol:
RNA was isolated from fixed and sorted NSC or IPC using the Quick-RNA FFPE Miniprep (Zymo Research, Cat. N: R1008) in combination with Zymo-Spin IC Columns (Zymo Research, Cat. N: C1004-250) according to the manufacturing instructions starting from the tissue dissociation step.
RNA libraries were generated using the NEBNext® Single Cell/Low Input RNA Library Prep Kit (NEB, Cat. N: E6420S) according to the manufacturing instructions.


title: Control_3_D

value: no treatment


title: 3DRAM-seq (RNA) IPC rep1


title: Negative control 1


title: 3D_WT-TH_24h_3

type: RNA

city: Pathum Thani

first: Papon

last: Muangsanit

state: Pathum Thani

address: 113 Thailand Science Park Phahonyothin Road Khlong Nueng, Khlong Luang, BIOTEC building, Room 345

department: BIOTEC

country: Thailand

institute: NSTDA

hyb_protocol: Purified total RNA samples were analyzed using the NanoString nCounter XT gene expression assay following the manufacturer’s protocol. Briefly, 5 µl of 50 ng of total RNAs were mixed with 2 μl of the Capture Probe set and 8 µl of hybridization buffer containing the Reporter CodeSet and mixtures were allowed to hybridize by incubation at 65 °C in a thermal cycler for 16 hours.

scan_protocol: Post-hybridization processing and data collection were performed using the nCounter Analysis System.

data_processing: Raw data were pre-processed using the nSolverTM 4.0 software according to nCounter gene expression data analysis guidelines. Data pre-processing included sample quality control (QC), background and normalization. Probes against 14 external RNA control consortiums (ERCC) consisted of 6 synthetic DNA positive and 8 negative controls. The geometric mean of positive control counts in each sample was applied to QC to evaluate overall assay efficiency, assay linearity and limit of detection (LOD). A correlation value higher than 0.95 indicated high assay efficiency. Negative controls were used to estimate non-specific binding of probes within the samples being run and background correction. Reference housekeeping genes were used for data normalization according to the nSolverTM 4.0 software.

label: Reporter CodeSet

source_name: 3D culture

label_protocol: One hundred nanograms of purified total RNA were analyzed using the nCounter Analysis System (NanoString Technologies, WA, USA), according to the manufacturer’s instructions. The assay is based on direct detection of targets using molecular barcodes, without the necessity of reverse transcription and mRNA amplification.

growth_protocol: 10-day pre-differentiated neurons from hiPSC were plated in 24-well plates at a density of 1×10^5 cells/well to generate 2D cultures, while 3D cultures were prepared at a density of 1×10^6 cells/ml of collagen-Matrigel hydrogel (400 µl/well of 24-well plates). The NB medium was changed every 2-3 days and cells remained in culture for 7 days before virus adsorption.

extract_protocol: Total RNA was isolated using TRIzol following the manufacturer's instructions. Rabies virus-infected 2D and 3D samples were collected at 0, 8 and 24 hours post-infection. In 24-well plates, 2D samples were homogenized in 500 µl of TRIzol and 3D samples were homogenized in 1,000 µl of TRIzol by pipetting up and down several times until the homogenates appeared consistent with no visible clumping. RNA from TRIzol-lysed samples was purified using the Direct-zol RNA Microprep kit, treated with DNase I, eluted in 35 µl RNase-free water, and stored at -80 °C until used. The quality of the purified RNA was measured using the Nanodrop 2000 spectrophotometer. Gel electrophoresis was run to confirm there was no cellular DNA contamination of the purified total RNA.

treatment_protocol: 2D and 3D neuronal cultures were adsorbed with TH or CVS-11 at a multiplicity of infection of 0.5 for 2 hours. Cells were washed twice with PBS before adding fresh media.

tag: virus strain

value: WT-TH

tag: time point

value: 24 hour

value: hiPSC-derived neurons


title: Control_3_B


title: 3D_WT-TH_24h_1


title: 3D_WT-TH_24h_2


title: 3D_CVS11_24h_3


title: PKO cells, biological rep 2

city: Boston

first: Chen

last: Chu

state: MA

address: 450 Brookline Ave, Smith 914

institute: Dana-Farber Cancer Institute

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G2500A.

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100.

label: biotin

source_name: PKO cells

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: PKO cells and Myc-Cap cells were cultured in 10% FBS, 1% Pen/Strep-containing DMEM.

extract_protocol: A Qiagen RNA extraction kit was applied to extract total RNA according to the manufacturer's instructions.

treatment_protocol: PKO cells and Myc-Cap cells were collected at log phase, and washed with PBS three times before RNA extraction.

value: PKO

value: prostate cancer cell

tag: phenotype

value: androgen-independent


title: 3DRAM-seq (RNA) NSC rep2


title: PKO cells, biological rep 3


title: PKO cells, biological rep 1


title: Control_3_A


title: ADSC single-cell RNA-seq from 1 DM patient (Tag04) and 2 healthy control (Tag05 & Tag06)

city: Taipei

first: Chia-Lang

last: Hsu

address: No. 7, Zhongshan S. Rd.

department: Department of Medical Research

country: Taiwan

institute: National Taiwan University Hospital

description: BD Rhapsody™ Single-Cell Analysis System with multiplex

data_processing:
FASTQ files were processed to demultiplex and gene expression quantification using the Seven Bridges Genomics cloud server with the BD Rhapsody WTA Analysis Pipeline.
Assembly: GRCh38
Supplementary files format and content: .st: read count, UMI count, RSEC corrected count for cell-gene pairs
Supplementary files format and content: *.csv: UMI count per cell matrices with recursive substation error correction (RSEC)

source_name: Adipocyte

growth_protocol: Dulbecco’s modified Eagle’s medium/Nutrient Mixture F-12 (DMEM/F-12), supplemented with 10% FBS, 1% penicillin-streptomycin, and 1 ng/mL FGF2. Cells were cultured at 37C at 5% CO2.

extract_protocol: Library was performed according to the manufacter's instructions (BD Rhapsody WTA kit).

value: Adipocyte

value: Adipose-derived stem cells

tag: sampleplex


title: Myc-Cap cells, biological rep 3

source_name: Myc-Cap cells

value: Myc-Cap

value: androgen-dependent


title: Myc-Cap cells, biological rep 4


title: Myc-Cap cells, biological rep 2


title: 3DRAM-seq (RNA) NSC rep1


title: Myc-Cap cells, biological rep 1


title: 3DRAM-seq (DNA) NSC rep2


title: Hex_2_F


title: ADSC single-cell RNA-seq from 2 DM patients (Tag01 & Tag03) and 1 healthy control (Tag02)


title: shNC_3

city: Dalian

first: Wenzhe

last: Duan

address: Shahekou Zone, Zhongshan Road 467

institute: Second hospital of Dalian Medical University

data_processing:
Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts. In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing N base and low quality reads from raw data.
Index of the reference genome was built using Hisat2 v2.0.5 and paired-end clean reads were aligned to the reference genome using Hisat2 v2.0.5.
featureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene.
Assembly: Hisat2 v2.0.5
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

source_name: lung cancer

growth_protocol: All cells were routinely cultured in Roswell Park Memorial Institute medium-1640 (RPMI1640) supplemented with 10% fetal bovine serum (FBS), 100 U/mL penicillin and streptomycin (all these reagents were obtained from Gibco, Invitrogen, Inc, California, USA) and maintained in a humidified atmosphere with 5% CO2 at 37°C.

extract_protocol:
RNA was harvested using Trizol (Transgen, China) and RNA integrity was assessed using the RNA Nano 6000 Assay Kit of the Bioanalyzer 2100 system (Agilent Technologies, CA, USA).
Fragmentation was carried out using divalent cations under elevated temperature in First Strand Synthesis Reaction Buffer(5X). First strand cDNA was synthesized using random hexamer primer and M MuLV Reverse Transcriptase, then use RNaseH to degrade the RNA. Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and dNTP. Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. After adenylation of 3’ ends of DNA fragments, Adaptor with hairpin loop structure were ligated to prepare for hybridization. In order to select cDNA fragments of preferentially 370~420 bp in length, the library fragments were purified with AMPure XP system (Beckman Coulter, Beverly, USA). Then PCR was performed with Phusion High-Fidelity DNA polymerase, Universal PCR primers and Index (X) Primer. At last, PCR products were purified (AMPure XP system) and library quality was assessed on the Agilent Bioanalyzer 2100 system.

value: lung cancer

value: lung cancer cell line

value: WT

value: routine culture


title: nAchRβ3 knockdown, biological rep4

city: South San Francisco

first: Nadja

middle: Sandra

last: Katheder

address: 1 DNA

department: Regenerative Medicine

institute: Genentech

data_processing:
Sequencing reads were filtered and aligned using HTSeqGenie v4.2.2
GSNAP v2013-11-01 was used for alignment, through the HTSeqGenie wrapper, against the Drosophila reference genome (BDGP6).
Read counts were scaled by library size, quantile normalized and precision weights were calculated using the voom R package
Differential expression analysis was performed using the limma package
Assembly: BDGP6
Supplementary files format and content: tab-delimited text files include nRPKM values for each Sample
Supplementary files format and content: tab-delimited text files include raw counts for each Sample

organism: Drosophila melanogaster

source_name: adult midgut

growth_protocol: flies were raised at 18C on standard corn-meal based fly food (Bloomington recipe)

extract_protocol:
RNA was isolated using the RNeasy Plus Mini Kit (Qiagen).
Total RNA was quantified with Qubit RNA HS Assay Kit (Thermo Fisher Scientific) and quality was assessed using RNA ScreenTape on 4200 TapeStation (Agilent Technologies).  For sequencinglibrary generation, the Truseq Stranded mRNA kit (Illumina) was used with an input of 100 nanograms of total RNA. Libraries were quantified with Qubit dsDNA HS Assay Kit (Thermo Fisher Scientific)  and the average library size was determined using D1000 ScreenTape on 4200 TapeStation (Agilent Technologies).Libraries were pooled and sequenced on  NovaSeq 6000 (Illumina) to generate 30 millions single-end 50-base pairreads for each sample

treatment_protocol: Adult mated female flies were shifted to a 29C incubator for 3 days

value: adult midgut

value: w;  NP1::Gal4, tubGa80ts /  w; UAS-nAchRBeta3-RNAi

value: 3 days at 29 degreeCC


title: Hex_2_D

value: 2-cell stage

value: F1:C57BL/6J x CBA/H

value: 3.5% 1,6-Hexanediol 1 hour


title: nAchRβ3 knockdown, biological rep3


title: Hex_2_C


title: 3D_CVS11_24h_1

value: 24 hour

value: hiPSC-derived neurons


title: shNC_2


title: shNC_1


title: nAchRβ3 knockdown, biological rep2


title: 3D_Mock_24h_2

value: Non-infected


title: Hex_2_B


title: shAKR1B10_3

value: AKR1B10 knockdown


title: 3D_Mock_24h_1


title: 3D_CVS11_24h_2


title: nAchRβ3 knockdown, biological rep1


title: Hex_2_A


title: 2D_WT-TH_24h_3

source_name: 2D culture

value: WT-TH


title: shAKR1B10_2


title: Control_2_G

value: no treatment


title: nAchRβ1 knockdown, biological rep4

value: w;  NP1::Gal4, tubGa80ts /  w; UAS-nAchRBeta1-RNAi


title: 2D_WT-TH_24h_2


title: nAchRβ1 knockdown, biological rep3


title: Control_2_F


title: shAKR1B10_1

value: lung cancer


title: 2D_WT-TH_24h_1


title: MM1.S cells, Dex+Spi, rep3

city: Gent

first: Karolien

last: De Bosscher

address: Technologiepark-Zwijnaarde 75

country: Belgium

institute: VIB-UGent Center for Medical Biotechnology

data_processing:
Sequencing reads were trimmed using Trim-Galore (version 0.6.6-0) to remove low-quality ends (phred score <30) as well as adapters.
Reads were pre-mapped to PhiX genome using STAR (version 2.7.6a) and the resulting PhiX-unmapped reads were aligned to the human genome GRCh38.
The position-sorted output BAM files were converted to count data using HTSeq (version 0.12.4) in the ‘union’ mode.
Assembly: GRCh38
Supplementary files format and content: tab-delimited text files include read counts for each Sample

source_name: Peripheral blood

growth_protocol: MM1.S cells were cultured in RPMI1640 GlutaMAX, supplemented with 10% fetal bovine serum (FBS), 100U/mL penicillin and 0.1mg/mL streptomycin, and grown at 5% CO2 and 37°C.

extract_protocol:
Total RNA was isolated using the RNeasy mini kit (Qiagen).
The RNA-seq library was prepared using the Illumina TruSeq stranded mRNA library kit, followed by single-end 100 bp sequencing on a Illumina NOVASeq 600 instrument, yielding 19-27 million reads per sample.

treatment_protocol: MM1.S cells were treated with Dex (10E-6 M), Spi (10E-5 M), a Dex/Spi combination or solvent control (EtOH) for 6h.

value: Peripheral blood

value: multiple myeloma

value: Spi+Dex


title: Control_2_E


title: 2D_CVS11_24h_3


title: 2D_CVS11_24h_2


title: MM1.S cells, Dex+Spi, rep2


title: Control_2_D


title: nAchRβ1 knockdown, biological rep1

value: adult midgut


title: MM1.S cells, Dex+Spi, rep1


title: 2D_CVS11_24h_1


title: mCherry knockdown, biological rep4

value: w;  NP1::Gal4, tubGa80ts /  y,sc,sev; UAS-mCherry-RNAi


title: nAchRβ1 knockdown, biological rep2

value: 3 days at 29 degreeCC


title: Hex_1_H

value: 2-cell stage


title: 2D_Mock_24h_1


title: MM1.S cells, Spi, rep2

value: Spi


title: mCherry knockdown, biological rep2


title: 2D_Mock_24h_2


title: 3D_WT-TH_8h_3

value: 8 hour


title: mCherry knockdown, biological rep1


title: Hex_1_G

value: F1:C57BL/6J x CBA/H

value: 3.5% 1,6-Hexanediol 1 hour


title: MM1.S cells, Spi, rep1


title: ChAT knockdown, biol rep4

value: w; UAS::GFP, tubGal80ts; ProsV1::Gal4 /   w1118; UAS-ChAT-RNAi

value: 3 days at 29 degreeC


title: 3D_WT-TH_8h_2

value: WT-TH

value: hiPSC-derived neurons


title: Hex_1_F


title: 3D_WT-TH_8h_1


title: MM1.S cells, Dex, rep2

value: Dex


title: ChAT knockdown, biol rep3


title: Hex_1_E


title: 3D_CVS11_8h_3


title: Control_2_A

value: no treatment


title: Hex_1_D


title: ChAT knockdown, biol rep2


title: Control_2_C


title: MM1.S cells, Dex, rep1

value: Peripheral blood


title: MM1.S cells, EtOH, rep3

value: multiple myeloma

value: EtOH


title: MM1.S cells, Spi, rep3


title: mCherry knockdown, biological rep3

value: adult midgut


title: ChAT knockdown, biol rep1


title: Hex_1_B


title: MM1.S cells, EtOH, rep2


title: mCherry knockdown, biol rep4

value: w; UAS::GFP, tubGal80ts; ProsV1::Gal4 /  y,sc,sev; UAS-mCherry-RNAi


title: MM1.S cells, Dex, rep3


title: 3D_CVS11_8h_1


title: MM1.S cells, EtOH, rep1


title: Control_1_G


title: mCherry knockdown, biol rep3


title: 3D_Mock_8h_2

value: Non-infected


title: mCherry knockdown,biol rep2


title: Control_1_F

value: 2-cell stage


title: 3D_Mock_8h_1


title: mCherry knockdown, biol rep1


title: 2D_WT-TH_8h_3


title: 2D_WT-TH_8h_2


title: Control_1_B


title: 3D_CVS11_8h_2


title: TetLowProg, low avidity GSW11-specific CD8+ TILs from progressing tumors [TetLow_12]

city: Oxford

first: Doreen

last: Lau

address: Old Road Campus Research Building, Roosevelt Drive, Headington

department: Nuffield Department of Medicine

institute: University of Oxford

data_processing:
The paired-end reads were aligned to the mouse reference genome GRCm39/mm39 with STAR 2.7.6a and the mapped reads were assigned to genomic features using featureCounts.
Assembly: mm39
Supplementary files format and content: tab-delimited text files include reads per gene for each sample

source_name: tumor

growth_protocol: T cells were tetramer-sorted from CT26.WT tumours.

extract_protocol:
RNA was harvested using Zymo Quick RNA Miniprep Kit (Zymo, USA) prior to cDNA synthesis. The purified RNA was quantified using Qubit 4 Fluorometer (Invitrogen) and the quality was determined using the Agilent 2100 Bioanalyzer with the Agilent RNA 6000 nano kit (Agilent Technologies). RNA was reverse transcribed using SuperScript II (Invitrogen) and cDNA pre-amplification was performed using KAPA HiFi HotStart ReadyMix (Roche Molecular Systems) for 22 cycles of amplification. The cDNA libraries were purified with Agencourt AMPure XP beads (Beckman Coulter) according to the manufacturer’s instructions. The cDNA product was then analyzed using the Agilent 2100 Bioanalyzer with the Agilent High Sensitivity DNA kit (Agilent Technologies).
Tagmentation and library preparation was undertaken using the Illumina Nextera XT DNA Library Preparation Kit (Illumina) according to manufacturer's instructions.

treatment_protocol: The schedule adopted in this study involved three intraperitoneal administrations of anti-PD-1 on day 3, 6 and 9 following subcutaneous implantation of CT26 tumors, which resulted in a variable impact on tumor growth rate during early tumor development and a 20-30% curative response rate.

value: tumor

value: mouse-derived

value: T lymphocytes

value: wildtype

value: PD-1 antibodies (Clone RMP1-14)


title: 3DRAM-seq mESC rep3

source_name: E14 mESC

extract_protocol:
Approximately 2.5x105 fixed mESC were first lysed with 0.2% Igepal-CA630 (Sigma-Aldrich, Cat. N: I3021) for 10min. at RT, washed once with 1x GpC buffer (New England Biolabs, Cat. N.: M0227S) containing 1% BSA (Sigma, Cat. N.: B6917) and subsequently incubated for 3h at 37˚C in a reaction mix containing 60U M.CviPI (New England Biolabs, Cat. N.: M0227S) and 0.6mM SAM (New England Biolabs, Cat. N.: B9003). During the incubation the reaction was substitution with 8U M.CviPI and 1µl of 32mM SAM every hour. Nuclei were washed, permeabilized with 0.5% SDS (Invitrogen, Cat. N:AM9823) followed by a quenching of the SDS with SDS ~1.5% Triton-X-100 (Sigma Aldrich, Cat. N: X100) and a digested with 400U DpnII (New England Biolabs, Cat. N: R0543) overnight at 37˚C. Subsequently, sticky ends were filled by incubating the nuclei for 4h at RT with DNA Polymerase I (New England Biolabs, Cat. N: M0210) and a biotin-14-dATP (Life Technologies, Cat. N: 195245016) containing nucleotide mix in DpnII buffer. Proximity ligation was performed at least for 6h at 16˚C using the T4 DNA Ligase (New England Biolabs, Cat. N.: M0202). Thereafter nuclei and chromatin were digested using 200µg Proteinase K (New England Biolabs, Cat. N: P8107) with 1% SDS followed by reverse crosslinking overnight at 68˚C with 0.5M NaCl, purification by ethanol precipitation and shearing to ~550 bp DNA fragments using a Covaris S220 sonicator. End repaired was performed using the T4 DNA Polymerase (New England Biolabs, Cat. N: M0203) and non-biotinylated nucleotides for 4h at 20˚C. Approximately 0.01% of biotinylated methylation controls are added to the sample and bisulfite conversion was performed using the EZ DNA Methylation-Gold kit (Zymo Research, Cat. N: D5005).
For library constructed the Accel-NGS® Methyl-Seq DNA Library kit (Swift Bioscience, Cat. N: 30024) was used according to the manufacturing instructions until the adapter ligation step. After this step, biotin pulldown was performed using MyOne Streptavidin T1 beads (ThermoFisher, Cat. N: 65602) followed by 5 washes with washing buffer containing 0.05% Tween-20 (Sigma-Aldrich, Cat. N: P9416) and two additional washes with low-TE water. Final library amplification was performed in 5 separate reactions using the EpiMark Hot Start Taq (New England Biolabs, Cat. N: M0490) with Methyl-Seq Indexing Primers (Swift Bioscience, Cat. N: 36024) with the following PCR program: 95˚C 30s; {95˚C 15s, 61˚C 30s, 68˚C 80s} x10-11; 68˚C 5min; Hold at 10˚C. The different reactions were pooled, Streptavidin T1 beads were pelleted on a magnetic rack and the prepared libraries within the supernatant were purified using 0.65x AMPure XP beads (Agencourt, Cat. N: A63881) to reach an average fragment size of approximately 500bp.

value: E14 mESC


title: Hex_1_A

value: F1:C57BL/6J x CBA/H

value: 3.5% 1,6-Hexanediol 1 hour


title: 2D_WT-TH_8h_1

value: WT-TH

value: 8 hour

value: hiPSC-derived neurons


title: 3DRAM-seq mESC rep2


title: 2D_CVS11_8h_3


title: TRL 1215-T100-3

city: RTP

first: NIEHS

last: Microarray Core

state: NC

address: 111 T.W. Alexander Drive

department: DIR

institute: NIEHS

hyb_protocol: Five and one-half micrograms (5.5 .g) of amplified biotin-cDNAs were fragmented and hybridized to each array for 16 hours at 45°C in a rotating hybridization oven. Array slides were stained with streptavidin/phycoerythrin utilizing a double-antibody staining procedure and then washed for antibody amplification per the GeneChip Hybridization, Wash and Stain Kit and user manual.

scan_protocol: Arrays were scanned in an Affymetrix Scanner 3000.

data_processing: Data was obtained using TAC Software.

organism: Rattus norvegicus

source_name: 100 µM PFOA treated 38 weeks-3

label_protocol: One hundred nanograms (100 ng) of total RNA were amplified and labeled as directed using the Affymetrix WT Plus Reagent Kit (WT Plus Kit).

growth_protocol: TRL 1215 cells were cultured and passaged once per week in William's E media containing 10% FBS

extract_protocol: Total RNA was isolated from cells by using AllPrep DNA/RNA/Protein Kit (Cat# 80004) from QIAGEN (Germantown, MD) according to the manufacturer's instructions

treatment_protocol: PFOA-treated cells were cultured in the same medium with addition of fresh PFOA each time at 10 µM (T10), 50 µM (T50) or 100 µM (T100) up to 38 weeks.

value: liver

value: 100 µM PFOA treated 38 weeks


title: TetLowProg, low avidity GSW11-specific CD8+ TILs from progressing tumors [TetLow_9]


title: TRL 1215-T100-2

source_name: 100 µM PFOA treated 38 weeks-2


title: 2D_CVS11_8h_2


title: 3DRAM-seq mESC rep1


title: TetLowReg, low avidity GSW11-specific CD8+ TILs from regressing tumors [TetLow_8]


title: TRL 1215-T100-1

source_name: 100 µM PFOA treated 38 weeks-1


title: N2_replicat2

city: Haikou

first: Li

last: WEI

state: Hainan

address: No. 99 Longkun South Road, Haikou City

institute: Hainan normal university

data_processing:
Illumina Casava1.7 software used for basecalling.
The raw data (2×150 bp PE reads) were quality controlled using Trim-Galore! (https://www.bioinformatics.babraham.ac.uk/projects/trim_galore/).
The remaining high quality Illumina reads were aligned to our previously published N. oceanica IMET1 genome (Gong, Kang, Kim, Wang, Wei, Xin, Shen, Wang, You, Lim, Jeong, Park, Oh, Pan, Poliner, Yang, Li-Beisson, Li, Hu, Poetsch, Farre, Chang, Jeong, Jeong, Xu, 2020) with STAR (Dobin, Davis, Schlesinger, Drenkow, Zaleski, Jha, Batut, Chaisson, Gingeras, 2013) with duplication marked using Picard (https://broadinstitute.github.io/picard/).
The abundance of expression was quantified using featureCounts (Liao, Smyth, Shi, 2014) and StringTie (Kovaka, Zimin, Pertea, Razaghi, Salzberg, Pertea, 2019). For each of the mRNA-Seq datasets under each experimental condition, gene expression was measured as the numbers of aligned reads to annotated genes by featureCounts (Liao, Smyth, Shi, 2014) and normalized to CPM, FPKM (fragments per kilobase of exon model per million mapped fragments) and TPM values. Besides, raw counts from featureCounts (Liao, Smyth, Shi, 2014) were used for the differential gene expression analysis with edgeR (R package)
Assembly: Nannochloropsis oceanica IMET1
Supplementary files format and content: Excel files include FPKM values for each Sample

organism: Nannochloropsis oceanica

source_name: Cells

growth_protocol: Nannochloropsis oceanica IMET1 was inoculated into the modified f/2 liquid medium, which was prepared with 35 g L-1 sea salt (Realocean, USA), 1 g L-1 NaNO3, 67 mg L-1 NaH2PO4*H2O, 3.65 mg L-1 FeCl3*6H2O, 4.37 mg l-1 Na2EDTA*2H2O, trace metal mix (0.0196 mg L-1 CuSO4*5H2O, 0.0126 mg L-1 NaMoO4*2H2O, 0.044 mg L-1 ZnSO4*7H2O, 0.01mg L-1 CoCl2, and 0.36 mg L-1 MnCl2*4H2O), and vitamin mix (2.5 µg L-1 VB12, 2.5 µg L-1 biotin, and 0.5 µg L-1 thiamine HCl).The cells were first cultured in f/2 medium at 25°C with 80±5 μmol m-2 s-1 continuous irradiation in a 1 L column reactor (inner diameter: 5cm).

extract_protocol:
Total microalgal RNA was extracted using Trizol reagents (Invitrogen, USA). The concentration and purity of the RNA were determined spectrophotometrically (NanoDrop-1000, Thermo Scientific, USA)
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: The cells were first cultured in f/2 medium at 25°C with 80±5 μmol m-2 s-1 continuous irradiation in a 1 L column reactor (inner diameter: 5cm). The seed cultures were bubbled with air-level CO2. At the logarithmic phase (OD750=2.5), cells were harvested by centrifugation, one was sampled for RNA extraction as control (C0) with three replicates and the other was washed with fresh medium (nitrogen-free) for three times before being used for the following experiments. Cell pellets were inoculated into Nitrogen-free (for sampling of mRNA-seq, ChIP-seq and HiC-seq) and Nitrogen-repletion f/2 medium (for physiological measurement). Cultures started with the same initial cell concentration of OD750 = 2.5 and were exposed to continuous illumination of 50±5 μmol m−2 s−1. Cell aliquots were collected  for sampling of mRNA-seq, ChIP-seq and HiC-seq after being transferred to the designated conditions for one and two days  as nitrogen-deprivation samples (N1 and N2) with three replicates


title: TetLowReg, low avidity GSW11-specific CD8+ TILs from regressing tumors [TetLow_7]


title: N2_replicat1

value: Nitrogen-deprivation