title: Aged_ENR_rep3 [AE3]

description:
L27363_DG_1Y-E144
Methylated cytosines converted to uracil by treatment with sodium bisulfite

source_name: Aged_ENR_dentate gyrus


title: Aged_STD_rep6 [AS6]

status: Public on Dec 31 2020

type: SRA

city: Dresden

first: Gerd

last: Kempermann

state: Saxony

address: Tatzberg 41

country: Germany

institute: German Center for Neurodegenerative Diseases (DZNE)

description:
L37122_s6_199f_STD
Methylated cytosines converted to uracil by treatment with sodium bisulfite

library_source: genomic

data_processing:
Trimming: Fastq reads were trimmed using Trim Galore 0.4.0 and the function Cutadapt 1.8.1. To remove cytosines that were filled in during ends preparation, an additional 2 bp were cut off from every sequence with detected adapter.
Alignment: Trimmed reads were mapped against mm10 using Bismark 0.16.1
Base-calling: MethylKit 1.5.2.
Genome_build: mm10
Supplementary_files_format_and_content: Methylation percentages of cytosines for individual samples. Txt file exported from Methylkit.

molecule: genomic DNA

organism: Mus musculus

source_name: Aged_STD_dentate gyrus

growth_protocol: Mice housed in 12:12 light:dark cycle under SPF conditions and given ad libitum access to mouse chow and water.

extract_protocol:
Micro-dissection of the hippocampal dentate gyrus
Genomic DNA was isolated using the QIAamp DNA Micro Kit or the Allprep DNA/RNA Micro Kit (both QIAGEN) following the manufacturer’s manuals. RRBS libraries were prepared using the Premium RRBS Kit (Diagenode) and purified twice using Agencourt AMPure XP beads (Beckman Coulter; 1X bead volume). Quality and concentration of RRBS libraries were determined using the High Sensitivity NGS Fragment Analysis Kit (Advanced Analytical) and a fragment analyzer with capillary size of 33 cm (Advanced Analytical).

treatment_protocol: Mice were housed in either standard cages or in an enriched environment.

tag: strain

tag: age

value: 14 months

tag: Sex

value: Female

tag: housing

value: Standard housing

tag: tissue

value: Dentate gyrus


title: Aged_ENR_rep7 [AE7]

description:
L37124_s8_201_ENR
Methylated cytosines converted to uracil by treatment with sodium bisulfite

value: Environmental enrichment


title: Aged_STD_rep2 [AS2]

description:
L27361_DG_1Y-S28
Methylated cytosines converted to uracil by treatment with sodium bisulfite


title: Aged_ENR_rep1 [AE1]

description:
L27356_DG_1Y-E151
Methylated cytosines converted to uracil by treatment with sodium bisulfite


title: Aged_ENR_rep2 [AE2]

description:
L27355_DG_1Y-E104
Methylated cytosines converted to uracil by treatment with sodium bisulfite


title: Aged_STD_rep3 [AS3]

description:
L27358_DG_1Y-S193
Methylated cytosines converted to uracil by treatment with sodium bisulfite


title: Aged_ENR_rep4 [AE4]

description:
L27359_DG_1Y-E39
Methylated cytosines converted to uracil by treatment with sodium bisulfite


title: Aged_ENR_rep6 [AE6]

description:
L37121_s5_37h_ENR
Methylated cytosines converted to uracil by treatment with sodium bisulfite


title: Aged_STD_rep7 [AS7]

description:
L37123_s7_79a_STD
Methylated cytosines converted to uracil by treatment with sodium bisulfite


title: Young_ENR_rep3 [YE3]

description:
L27353_DG_4d-E3
Methylated cytosines converted to uracil by treatment with sodium bisulfite

source_name: Young_ENR_dentate gyrus

value: 1.5 months


title: Aged_ENR_rep5 [AE5]

description:
L37118_s2_100f_ENR
Methylated cytosines converted to uracil by treatment with sodium bisulfite


title: Aged_STD_rep5 [AS5]

description:
L37120_s4_108g_STD
Methylated cytosines converted to uracil by treatment with sodium bisulfite


title: Young_ENR_rep5 [YE5]

description:
L37116_s4d_ENR5
Methylated cytosines converted to uracil by treatment with sodium bisulfite


title: Young_STD_rep4 [YS4]

description:
L37113_s4d_STD4
Methylated cytosines converted to uracil by treatment with sodium bisulfite

source_name: Young_STD_dentate gyrus


title: Young_STD_rep1 [YS1]

description:
L27348_DG-4d-S1
Methylated cytosines converted to uracil by treatment with sodium bisulfite


title: Young_STD_rep2 [YS2]

description:
L27349_DG_4d-S2
Methylated cytosines converted to uracil by treatment with sodium bisulfite


title: Young_STD_rep5 [YS5]

description:
L37114_s4d_STD5
Methylated cytosines converted to uracil by treatment with sodium bisulfite


title: Young_STD_rep3 [YS3]

description:
L27350_DG_4d-S3
Methylated cytosines converted to uracil by treatment with sodium bisulfite


title: Middle_aged_ENR_rep2 [ENR2]

description:
L13666_Track-37618
Methylated cytosines converted to uracil by treatment with sodium bisulfite

source_name: Middle_aged_ENR_dentate gyrus

value: 4.5 months


title: Middle_aged_ENR_rep3 [ENR3]

description:
L13667_Track-37619
Methylated cytosines converted to uracil by treatment with sodium bisulfite


title: Young_ENR_rep2 [YE2]

description:
L27352_DG_4d-E2
Methylated cytosines converted to uracil by treatment with sodium bisulfite


title: Middle_aged_STD_rep3 [STD3]

description:
L13664_Track-37616
Methylated cytosines converted to uracil by treatment with sodium bisulfite

source_name: Middle_aged_STD_dentate gyrus


title: Middle_aged_STD_rep2 [STD2]

description:
L13663_Track-37615
Methylated cytosines converted to uracil by treatment with sodium bisulfite


title: Middle_aged_ENR_rep1 [ENR1]

description:
L13665_Track-37617
Methylated cytosines converted to uracil by treatment with sodium bisulfite


title: Middle_aged_STD_rep1 [STD1]

description:
L13662_Track-37614
Methylated cytosines converted to uracil by treatment with sodium bisulfite


title: SF9301 (RNA-seq)

status: Public on Dec 10 2020

city: San Francisco

first: Aaron

last: Diaz

state: CA

department: Neurological Surgery

country: USA

institute: University of California, San Francisco

library_source: transcriptomic

data_processing:
Paired-end sequencing was done on the Illumina NovaSeq platform yielding over 277million read-pairs per sample. Sequenced reads were aligned with HISAT2 to grCh38. Gene expression was quantified using the ENSEMBL reference with featureCounts  from subreads version 2.0.0. Only correctly paired, uniquely mapped reads were retained.
Genome_build: hg38
Supplementary_files_format_and_content: feature count tables. Txt files.

molecule: total RNA

organism: Homo sapiens

source_name: Brain

extract_protocol:
FFPE blocks were reviewed by a pathologist to identify regions of high tumor purity. Total RNA was purified from freshly punched cores via a Qiagen RNeasy FFPE purification column. RNA and DNA were quantified via both Bioanalyzer and Qubit to ensure sample quality. All samples yielded over 100ng RNA with DV200>30% and negligible DNA contamination.
We used the Illumina TruSeq RNA Exome kit according to the manufacturer's instructions.

tag: sample id

tag: sf#

tag: primary/recurrent

value: Primary

tag: patient id

value: M

tag: idh mutation

value: WT

tag: disease state

value: Glioblastoma


title: SF6587 (RNA-seq)

value: F


title: ATAC_mTOR_WT

status: Public on Dec 24 2020

city: Cincinnati

first: Yi

last: Zheng

state: OH

address: 3333 Burnet Ave MLC7013

department: Experimental Hematology and Cancer Biology

institute: CINCINNATI CHILDRENS HOSP MED CTR

data_processing:
Illumina Casava software used for basecalling.
Sequenced reads were trimmed for adaptor sequence.
Peak calling was performed using MACS1.4 with a default p value cut off.
bed files were generated by MACS1.4
Genome_build: mm10

source_name: mTOR WT HSC cells

extract_protocol:
50,000 sorted HSC cells from poly(I:C)-treated WT control and mTOR KO mice were lysed in a cold lysis buffer. Transposase reaction were performed for 30 min at 37 °C immediately after the nuclei preparation. The samples were purified using a Qiagen MinElute kit.
The ATAC-seq libraries were amplified using NEBnext PCR master mix followed by purified using Qiagen MinElute PCR Purification Kit (Qiagen, 28004), and then run on the Illumina sequencer HiSeq 2500.

tag: group

value: Control

value: Adult

tag: genotype


title: SF10064 (RNA-seq)

value: Recurrent


title: SF11094 (RNA-seq)


title: Aged_STD_rep4 [AS4]

description:
L27362_DG_1Y-S130
Methylated cytosines converted to uracil by treatment with sodium bisulfite


title: RNAseq__mTOR_KO_2

data_processing:
Illumina Casava software used for basecalling.
Sequenced reads were trimmed for adaptor sequence.
Reads mapped to mm10 whole genome by Tophat with default options
Fragment Per Kilobase of exon per Megabase of library size (FPKM) were calculated using Cufflinks with default options. Outputs from Cufflinks are provided as supplementary files as a tab-delimited text file.
format:fpkm_traking ; Contain the estimated expression values produced by Cufflinks.
Genome_build: mm10

source_name: mTOR KO HSC cells

extract_protocol:
HSC cells from poly(I:C)-treated WT control and mTOR KO mice were sorted by FACS. RNA were extracted using miRNeasy Micro Kit (Qiagen, 217084).
RNA-seq libraries were prepared using Illumina TruSeq Stranded Total RNA Sample Preparation Kit (Illumina, 20020597)

value: KO Mutant


title: RNAseq__mTOR_KO_1


title: RNAseq_Ctr_mTOR_WT_3

source_name: mTOR WT Control HSC cells


title: RNAseq__mTOR_KO_3


title: RNAseq_Ctr_mTOR_WT_4


title: SF10127 (RNA-seq)


title: SF6136 (RNA-seq)


title: RNAseq_Ctr_mTOR_WT_1


title: SF6953 (RNA-seq)


title: SF11587 (RNA-seq)


title: ATAC_mTOR_KO


title: RNAseq__mTOR_KO_4


title: SF10770 (RNA-seq)


title: SF10750 (RNA-seq)


title: SF6839 (RNA-seq)


title: SF11780 (RNA-seq)


title: SF11248 (RNA-seq)


title: SF12243 (RNA-seq)


title: SF8963 (RNA-seq)

value: MT


title: SF7196 (RNA-seq)


title: SF12165 (RNA-seq)


title: SF8642 (RNA-seq)


title: SF9490 (RNA-seq)


title: RNAseq_Ctr_mTOR_WT_2


title: SF10228 (RNA-seq)


title: SF9135 (RNA-seq)


title: SF10931 (RNA-seq)


title: SF4324 (RNA-seq)


title: SF4209 (RNA-seq)


title: SF9259 (RNA-seq)


title: SF11082 (RNA-seq)


title: SF11215 (RNA-seq)


title: IMX_sample00086

city: Burlingame

first: Yehudit

last: Hasin-Brumshtein

address: 863 Mitten Road

department: Computational Biology

institute: Inflammatix

data_processing:
A total of 86 RNA-seq libraries generated above were pooled and sequenced on a NovaSeq 6000 Sequencing System (Illumina) in a pair-ended fasion (2 x 100 cycles). 41 M to 124 M paired-end reads were obtained for each sample. FastQ files were used as input for RNA-Seq data processing. Library prep and sequencing were performed at TBseq (Palo Alto, CA).
Quality control assessment of the reads was done using FastQC.
Trimming:  The adapter sequence and 3 bases on the 3’ end of the reads was trimmed using Cutadapt as a commonly used procedure.
Alignment: Trimmed reads were mapped to a reference genome index generated based on the human genome, GRCh38, and a transcriptome reference, GENCODE v32 primary assembly gtf with the sjdbOverhang option set to 100 (default), using STAR aligner (v2.7.3a).
Quantitation: Mapped reads were finally quantitated per Ensembl transcript ID as defined in GENCODE v32 annotation. Reads were summed up across Ensembl transcript IDs mapping to Entrez gene IDs on order to compare them readily with other viral data assayed by microarrays (AnnotationDbi from Bioconductor)
Genome_build: GRCh38
Supplementary_files_format_and_content: csv count matrix of entrez id X sample, raw counts

source_name: Healthy control_whole blood

extract_protocol:
Prior to processing, samples in PAXgene Blood RNA tubes from 76 COVID-19 patients and 24 healthy controls were removed from -80C to thaw at room temperature for two hours. The samples were then inverted several times to achieve homogeneity, after which 3 mL aliquots were removed for processing. RNA was extracted from these samples using a modified version of the RNeasy Mini Kit (QIAgen) protocol executed on a QIAcube automated workstation. PAXgene samples comprised of whole blood in PAXgene stabilizing solution were diluted with PBS, then centrifuged at 3,000 x g to pellet precipitated nucleic acids. Pellets were washed with water and again pelleted via centrifugation at 3,000 x g. Pelleted material was resuspended in Buffer RLT (QIAgen). Using the automated QIAcube, samples were then subjected to treatment by Proteinase K and gDNA elimination via columns (QIAgen). Flow-through was mixed with isopropanol and passed over a MinElute (QIAgen) spin column. The column was washed with 80% ethanol and purified nucleic acid was eluted in RNase-free water. Purified RNA was heat denatured at 55° C for 5 minutes, then snap-cooled on ice. RNA was quantitated using a Qubit fluorimeter with the Quant-iT RNA Assay kit (Thermo-Fisher). Samples with an RNA integrity number (RIN) below 7 (BioAnalyzer, Agilent) did not proceed to sequencing, resulting in 62 COVID-19 samples and 24 HC samples for sequencing.
Total RNA samples were depleted of globin RNA using the GLOBINclear kit (Invitrogen) as described by the manufacturer. Globin-depleted RNA was quantified using the Qubit RNA High Sensitivity kit (Life Technologies). 10 ng of globin-depleted RNA was used for rRNA depletion and RNA-seq library preparation using the SMARTer Stranded Total RNA-seq kit v2 Pico Input Mammalian (Takara Bio) following the manufacturer’s protocol. RNA-seq libraries were then quantified using the Qubit dsDNA High Sensitivity kit (Life Technologies) and their quality and size evaluated by a Fragment Analyzer High Sensitivity Small Fragment kit (Agilent Technologies).

tag: disease

value: Healthy control

value: Whole blood

value: Male


title: SF6996 (RNA-seq)


title: IMX_sample00082


title: IMX_sample00083


title: IMX_sample00084


title: IMX_sample00078

source_name: COVID19_whole blood


title: IMX_sample00076

value: Female


title: IMX_sample00077


title: IMX_sample00081


title: IMX_sample00079


title: IMX_sample00075


title: IMX_sample00080


title: IMX_sample00073


title: IMX_sample00074


title: IMX_sample00072


title: IMX_sample00071


title: SF9640 (RNA-seq)


title: IMX_sample00069


title: IMX_sample00067


title: IMX_sample00085


title: IMX_sample00066


title: IMX_sample00065


title: IMX_sample00068


title: IMX_sample00064


title: IMX_sample00062


title: IMX_sample00063


title: IMX_sample00061


title: IMX_sample00059


title: IMX_sample00057


title: IMX_sample00056


title: IMX_sample00055


title: IMX_sample00051


title: IMX_sample00050


title: IMX_sample00052


title: IMX_sample00049


title: IMX_sample00044


title: IMX_sample00054


title: IMX_sample00070


title: IMX_sample00053


title: IMX_sample00048


title: IMX_sample00045


title: IMX_sample00043


title: IMX_sample00046


title: IMX_sample00047


title: IMX_sample00041


title: IMX_sample00042


title: IMX_sample00040


title: IMX_sample00039


title: IMX_sample00038


title: IMX_sample00060


title: IMX_sample00036


title: IMX_sample00037


title: IMX_sample00035


title: IMX_sample00058


title: IMX_sample00033


title: IMX_sample00031


title: IMX_sample00032


title: IMX_sample00028


title: IMX_sample00030


title: IMX_sample00023


title: IMX_sample00024


title: IMX_sample00025


title: IMX_sample00026


title: IMX_sample00019


title: IMX_sample00020


title: IMX_sample00017


title: IMX_sample00018


title: IMX_sample00016


title: IMX_sample00021


title: IMX_sample00029


title: IMX_sample00027


title: IMX_sample00013


title: IMX_sample00014


title: IMX_sample00012


title: IMX_sample00011


title: IMX_sample00010


title: IMX_sample00034


title: IMX_sample00008


title: IMX_sample00007


title: IMX_sample00006


title: IMX_sample00009


title: IMX_sample00005


title: IMX_sample00004


title: IMX_sample00003


title: IMX_sample00002


title: IMX_sample00022


title: IMX_sample00001


title: Liver patient 138

status: Public on Dec 03 2020

city: Newcastle

first: Simon

last: Cockell

address: Framlington Place

country: United Kingdom

institute: Newcastle University

data_processing:
Reads were cropped to 75bp using Trimmomatic
Reads were mapped to GRCh38 (ensembl release 78) using STAR (v2.4.2a)
Gene count tables were produced using HTSeq-count (v0.11.2) with -r pos -s reverse
Genome_build: GRCh38, Ensembl release 78
Supplementary_files_format_and_content: txt files with gene-level counts

source_name: NAFLD_moderate_liver biopsy

extract_protocol:
Frozen tissue samples were lysed using Trizol (Sigma-Aldrich) and mRNA was extracted with the Allprep DNA/RNA Micro kit (Qiagen). Concentrations and quality were assessed using the Agilent Pico 6000 kit on the Bioanalyzer 2100.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: nas score

tag: fibrosis stage

tag: group in paper

value: NAFLD

tag: Stage

value: moderate


title: IMX_sample00015

tag: age


title: Liver patient 136

source_name: NAFLD_early_liver biopsy

value: early


title: Liver patient 137


title: Liver patient 135


title: Liver patient 126


title: Liver patient 133


title: Liver patient 125


title: Liver patient 129


title: Liver patient 131


title: Liver patient 128


title: Liver patient 132


title: Liver patient 165


title: Liver patient 161


title: Liver patient 163


title: Liver patient 164


title: Liver patient 160


title: Liver patient 157

value: NAFL


title: Liver patient 158


title: Liver patient 159


title: Liver patient 155


title: Liver patient 156


title: Liver patient 162


title: Liver patient 154


title: Liver patient 153


title: Liver patient 151


title: Liver patient 152


title: Liver patient 150


title: Liver patient 134


title: Liver patient 148


title: Liver patient 147


title: Liver patient 130


title: Liver patient 146


title: Liver patient 145


title: Liver patient 144


title: Liver patient 142


title: Liver control sample 4

source_name: Control_control_liver biopsy

value: control


title: Liver patient 140


title: Liver patient 139


title: Liver patient 143


title: Liver patient 141


title: Liver patient 91


title: Liver patient 4


title: Liver patient 27


title: Liver patient 191


title: Liver patient 190


title: Liver patient 185


title: Liver patient 149


title: Liver patient 206


title: Liver control sample 1


title: Liver patient 45


title: Liver patient 193


title: Liver patient 65


title: Liver patient 67


title: Liver patient 180


title: Liver patient 192


title: Liver patient 62


title: Liver patient 66


title: Liver patient 99


title: Liver patient 53


title: Liver patient 104


title: Liver patient 100


title: Liver patient 41


title: Liver patient 107


title: Liver patient 18


title: Liver patient 26


title: Liver patient 93


title: Liver patient 69


title: Liver patient 181


title: Liver patient 19


title: Liver patient 179


title: Liver patient 201


title: Liver patient 16


title: Liver patient 60


title: Liver patient 1


title: Liver patient 20


title: Liver patient 96


title: Liver patient 200


title: Liver patient 17


title: Liver patient 194


title: Liver patient 199


title: Liver patient 94


title: Liver patient 68


title: Liver patient 56


title: Liver patient 47


title: Liver patient 64


title: Liver patient 55


title: Liver patient 111


title: Liver patient 103


title: Liver patient 95


title: Liver patient 61


title: Liver patient 182


title: Liver patient 92


title: Liver patient 52


title: Liver patient 49


title: Liver patient 22


title: Liver patient 109


title: Liver patient 25


title: Liver patient 11


title: Liver patient 122


title: Liver patient 48


title: Liver patient 50


title: Liver patient 183


title: Liver patient 37


title: Liver patient 76


title: Liver patient 35


title: Liver patient 33


title: Liver patient 43


title: Liver patient 31


title: Liver patient 184


title: Liver patient 39


title: Liver patient 38


title: Liver patient 186


title: Liver patient 42


title: Liver patient 34


title: Liver patient 29


title: Liver patient 63


title: Liver patient 28


title: Liver patient 54


title: Liver patient 13


title: Liver patient 188


title: Liver patient 187


title: Liver patient 59


title: Liver patient 58


title: Liver patient 24


title: Liver patient 113


title: Liver patient 40


title: Liver patient 30


title: Liver patient 44


title: Liver patient 57


title: Liver patient 88


title: Liver patient 87


title: Liver patient 204


title: Liver patient 86


title: Liver patient 80


title: Liver patient 5


title: Liver patient 85


title: Liver patient 189


title: Liver patient 89


title: Liver patient 36


title: Liver patient 73


title: Liver patient 70


title: Liver patient 72


title: Liver patient 74


title: Liver patient 82


title: Liver patient 81


title: Liver patient 121


title: Liver patient 32


title: Liver patient 202


title: Liver patient 75


title: Liver patient 79


title: Liver patient 77


title: Liver patient 90


title: Liver patient 51


title: Liver patient 46


title: Liver patient 23


title: Liver patient 21


title: Liver patient 198


title: Liver control sample 7


title: Liver control sample 5


title: Liver control sample 3


title: Liver control sample 9


title: Liver patient 196


title: Liver control sample 8


title: Liver control sample 2


title: Liver patient 124


title: Liver patient 176


title: Liver control sample 6


title: Liver patient 127


title: Liver control sample 10


title: Liver patient 123


title: Liver patient 177


title: Liver patient 173


title: Liver patient 195


title: Liver patient 174


title: Liver patient 175


title: Liver patient 170


title: Liver patient 169


title: Liver patient 171


title: Liver patient 168


title: Liver patient 172


title: Liver patient 166


title: Liver patient 167


title: Liver patient 205


title: Liver patient 2


title: Liver patient 203


title: Liver patient 84


title: Liver patient 78


title: Liver patient 3


title: Liver patient 178


title: Liver patient 10


title: Liver patient 9


title: Liver patient 83


title: Liver patient 12


title: Liver patient 14


title: Liver patient 8


title: Liver patient 15


title: Liver patient 6


title: Liver patient 71


title: Liver patient 119


title: Liver patient 7


title: Liver patient 118


title: Liver patient 197


title: Liver patient 116


title: Liver patient 117


title: Liver patient 120


title: Liver patient 115


title: Liver patient 112


title: Liver patient 110


title: Liver patient 108


title: Liver patient 105


title: Liver patient 102


title: Liver patient 101


title: Liver patient 106


title: Liver patient 97


title: Teff1_HiC

status: Public on Nov 30 2020

city: Beijing

first: Jingzhe

last: Lu

state: Beijing

address: No.30 shuangqing road

department: School of medicine

country: China

institute: Tsinghua University

data_processing:
Hi-C data was aligned to the mm10 genome assembly using BWA with parameters mem -t 16
Hi-C reads were filtered by the Juicer preprocessing protocol
The chromatin interactions were detected by Chrom-Lasso from preprocessed Hi-C data.
RNA-seq data was aligned to the mm10 genome assembly using Hisat2 with parameters -p 16 --mm --dta -x
The raw read counts were called by HTseq with parameters -count -s no -i gene_name after mapping
The normalized gene expression level were called by R package DESeq2 rlog function using the raw read counts from all samples
Genome_build: mm10
Supplementary_files_format_and_content: Preprocessed files including preserved reads after filtering are used as the input files for Chrom-Lasso to call interactions
Supplementary_files_format_and_content: The result files include interactions called by Chrom-Lasso for each Hi-C sample with the interacting loci information and P value showing significance level
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every RNA-seq sample
Supplementary_files_format_and_content: Matrix table with normalized gene expression level for every gene and every RNA-seq sample

source_name: CD8+ T cells

growth_protocol: Naïve CD8+ T cells were isolated from single-cell suspensions of splenocytes using EasySep™ Mouse Naïve CD8+ T Cell Isolation Kit (STEMCELL technologies, 19858 ) according to the manufacturer’s instructions.

extract_protocol:
The biotin labelled DNA was pulled down with 75μl Dynabeads M-280 Streptavidin (Thermo Fisher Scientific, 11205D).
Sequencing library preparation was performed on beads, including end repair, dATP tailing, adaptor ligation and PCR amplification. 12 cycles of PCR amplification were performed with Q5® High-Fidelity DNA Polymerase (NEB, M0491S). Finally, size selection was done with AMPure XP beads and fragments ranging from 200 bp to 1,000 bp were selected.
in situ Hi-C

treatment_protocol: Freshly purified naïve CD8+ T cells were stimulated with anti-mouse CD3e ( 10μg/ml ) (BioLegend, 100314 )and anti-mouse CD28 ( 10μg/ml ) (BioLegend, 102112). Overnight, recombinant mouse IL-2 (PeproTech, AF212-12-20) was added to the culture at 300U/ml. T cells were used for further experiments after 2d or 5d of in vitro activation.

tag: strain

tag: cell type

value: CD8+ T cells

tag: time

value: day 2 of culture

tag: sorting criteria


title: Tn_HiC

value: day 0 of culture


title: Liver patient 98


title: Teff2_HiC

value: day 5 of culture


title: Tex_HiC


title: Week 10 anti-RANKL

status: Public on Nov 24 2020

city: Aurora

first: Kristen

last: Wells

state: CO

address: 1775 Aurora Ct,

department: Barbara Davis Center

institute: University of Colorado Anschutz

description: GSM4085093_RANKL_wk10.csv.gz contains normalized UMI counts. GSE137699_allSamples.csv.gz contains normalized UMI counts of all samples in this study. Meta data can be found on the associated github https://github.com/kwells4/mtec_analysis

data_processing:
Sequences from scRNA-seq were processed using Cellranger v2.2.0 software. For the anti-RANKL experiment, sequences were processed using the cellranger mm10-1.2.0 genome and gtf file. For the Aire lineage trace experiment, the sequence for the zsGreen transcript was added to the fasta and the gtf file. A complete reference was made running cellranger mkref with the updated fasta and gtf files as arguments. For each sample, cell ranger mkfastq and cellranger count were run with the transcriptome argument pointing to the mm10 reference for the anti-RANKL experiment and the mm10 + zsGreen reference for the lineage trace experiment.
Raw data generated by Cellranger were then read into the Seurat v2.3.4 R package with at least 200 genes per cell and at least 3 cells. Cells were further filtered based on the number of genes per cell (between 200-7500) and the percent of mitochondrial reads per cell (0% – 10%). The remaining cells  and genes were used for downstream analysis. The data were normalized by using “LogNormalize” method and data scaled with “scale.factor = 1000” from Seurat. For each sample, variable genes were found by using “FindVariableGenes” with the following options mean.function=ExpMean, dispersion.function = LogVMR, x.low.cutoff=0.0125, x.high.cutoff = 3, y.cutoff = 0.5.
For the Aire lineage trace sample, the returned variable genes were used as the gene list given to the RunPCA function. Clusters were determined using the “FindClusters” function with the following options reduction.type = “pca”, dims_use = 1:12, resolution = 0.6, random.seed = 0. FindClusters embeds cells in a k-nearest neighbor graph with edges drawn between cells with similar gene expression. These are these partitioned into highly inter connected communities ased on Euclidean distance in PCA space. Further dimensionality reduction was performed by using RunUMAP using the options reduction.type = “pca”, dims_use = 1:12. Markers of each cluster were found using the “FindMarkers” command and highly similar clusters were merged. A small cluster of cells resembling t-cells based on gene expression were removed from further analysis. Clusters were classified based on common marker genes previously described for each mTEC population. Clusters highly expressing Aire were further characterized by their expression of ZsGreen. Differential gene expression was performed by running FindMarkers on all pair-wise clusters (so that differentially expressed genes could be shared between clusters). The FindMarkers command uses a non-parametric Wilcoxon rank sum test. Genes were called differentially expressed if the adjusted p value was less than 0.5 and the log fold change was greater than 2. Differentially expressed genes were filtered to include only transcription factors using a list of mouse transcription factors (http://genome.gsc.riken.jp/TFdb/tf_list.html) and chromatin modifying factors (H2afz, Hmgb1, Hmgn1, H2afx). These genes were manually searched for previous connections to mTEC development and Aire expression.
Cell cycle state was determined using cyclone from scran v1.10.1 which uses a list of known cell cycle genes to determine each cell a score for G2/M and G1 phase. Pairs of genes that change between cell cycle phases (from Scialdone et al. (2015)) are provided to cyclone. Scores are based on which gene within each pair is more highly expressed in each cell. These scores are used to assign each cell to G2/M, G1, or S phase.
The week 2 and week 10 control samples were initially analyzed as explained in the section “Initial analysis of scRNA-seq data”. After initial processing, the two samples were merged using the MergeSeurat function. Variable genes were again found for the combined object as described above. The returned variable genes were used as the gene list given to the RunPCA function. Clusters were determined using the “FindClusters” function with the following options reduction.type = “pca”, dims_use = 1:13, resolution = 0.6, random.seed = 0. Further dimensionality reduction was performed by using RunUMAP using the options reduction.type = “pca”, dims_use = 1:13. Markers of each cluster were found using the “FindMarkers” command and highly similar clusters were merged. A small cluster of cells resembling t-cells based on gene expression were removed from further analysis.  Clusters were classified based on similarity of marker genes to the populations in the Aire lineage trace experiment. Differential gene expression was performed by running FindMarkers on all pair-wise clusters (so that differentially expressed genes could be shared between clusters). Genes were called differentially expressed if the adjusted p value was less than 0.5 and the log fold change was greater than 2. Cell cycle state was again determined using cyclone from scran v1.10.1.
Single cell velocity trajectory analysis was performed in python using scvelo v0.1.16 from the Theis lab. First, a loom file were generated using run10x from velocyto5. The loom file was than loaded into python. Normalization and filtering was done using filter_and_normalize with the options min_counts = 20, min_counts_u=10, n_top_genes=3000. Next the moments were calculated using 30 PCs and 30 neighbors. Finally, velocity and the velocity graph were calculated. UMAP coordinates and cluster identification from the Seurat object were then added to the RNA velocity object. The velocity was plotted on the UMAP coordinates and colored by the cluster id. The scvelo output was used to determine lineage relationships and common progenitor populations. Plots of RNA velocity were made using the command pl. velocity_embedding_stream from scvelo.
Pseudotime scores were determined using slingshot  v1.1.0 with the “Early Aire” cluster as the argument for start.clus. TSA genes were determined using the Fantom database and filtering out genes that were seen in five tissues or less. Genes were further filtered to only keep protein coding genes as described previously. Aire-dependent genes were defined based on the 2014 Sansom et al. list of Aire-dependent genes. Fezf2 dependent genes were identified by determining genes with a 2-fold enrichment in the control mouse vs. the Fezf2 knockout mouse.
All samples were processed as described in the “Initial analysis of scRNA-seq data”. The top 1000 most highly variable genes from each sample were merged, keeping only genes that were present in all samples were used for CCA analysis. The 7 Seurat objects and the variable genes found above were used to generate a new Seurat object with the RunMiltiCCA function, using num.ccs = 30. The canonical correlation strength were calculated using num.dims = 1:30 and the samples were aligned using dims..align = 1:20. Clusters were found using the “FindClusters” function based on the aligned CCA with the following options reduction.type = “cca.aligned”, resolution = 0.6, dims.use = 1:20, random.seed = 0). Further dimensionality reduction was performed by using RunUMAP using the options reduction.type = “cca.aligned”, dims_use = 1:20, seed.use = 0. The cluster identities were assigned based on the Aire trace experiment. The Aire trace cluster identities were added to the Seurat object containing all samples. For each cluster, the identity was assigned based on which Aire trace population it shared the most cells with (Figure 3b). There was a clear majority of cells aligning with the Aire trace populations for all clusters. Population assignments were checked based on gene expression of marker genes such as Ackr4, Ccl21a, Aire, Krt10, and Trpn5 (Supplementary Figure 3b), by plotting expression of marker genes on the UMAP dimensional reduction (Supplementary Figure 4), and by plotting heatmaps of marker genes separated by population for each sample (Supplementary Figure 7). A small cluster of cells resembling t-cells based on gene expression were removed from further analysis. Cell cyc

molecule: polyA RNA

source_name: 100ug anti-RANKL_thymus

extract_protocol:
Mouse thymi were isolated, cleaned of fat and transferred to DMEM (UCSF Cell Culture Facility) containing 2% FBS (Atlanta Biologics) on ice. For each scRNA-seq sample, three thymi were pooled. Thymi were minced with a razor blade and tissue pieces were moved with a glass Pasteur pipette to 15 ml tubes and vortexed briefly in 10 ml of media. Fragments were allowed to settle before removing the media and replacing it with 4 ml of digestion media containing 2% FBS, 100 ug/ml DNase I (Roche), and 100 ug/ml Liberase TM (Sigma-Aldrich) in DMEM. Tubes were moved to a 37°C water bath and fragments were triturated through a glass Pasteur pipette at 0 min and 6 min to mechanically aid digestion. At 12 min tubes were spun briefly to pellet undigested fragments and the supernatant was moved to 20 ml of 0.5% BSA (Sigma-Aldrich), 2 mM EDTA (TekNova), in PBS (MACS buffer) on ice to stop the enzymatic digestion. This was repeated twice for a total of three 12 min digestion cycles, or until there were no remaining tissue fragments. The single cell suspension was then pelleted and washed once in MACS Buffer. Density-gradient centrifugation using a three-layer Percoll gradient (GE Healthcare) with specific gravities of 1.115, 1.065, and 1.0 was used to enrich for stromal cells. Cells isolated from the Percoll-light fraction, between the 1.065 and 1.0 layers, were then resuspended in 0.5% BSA (Sigma-Aldrich), 2 mM EDTA (TekNova) (FACS buffer) and counted.
To prepare the cells for droplet-based sequencing, mTECs were flow-sorted into tubes containing 750ul DMEM + 10%FBS (50,000 cells were sorted for the Aire trace experiment, 60,000 cells were sorted for the week 2 control, 37,000 cells were sorted for the week 2 experiment, 44,000 cells were sorted for the week 4 experiment, 32,000 cells were sorted for the week 6 experiment, 50,000 cells were sorted for the week 10 experiment, and 24,000 cells were sorted for the week 10 control). Cells were spun down at 300g for 5 minutes and all but 50-100ul of supernatant was removed to aim for a final concentration of 700-1000 cells/ul.
10x genomics single-cell isolation and RNA sequencing

value: 12 weeks

tag: treatment

value: 100ug anti-RANKL, 3 treatments in 1 week

tag: tissue

value: Thymus


title: Week 6 anti-RANKL

description: GSM4085092_RANKL_wk6.csv.gz contains normalized UMI counts. GSE137699_allSamples.csv.gz contains normalized UMI counts of all samples in this study. Meta data can be found on the associated github https://github.com/kwells4/mtec_analysis

value: 8 weeks


title: IMQ+XYF3

status: Public on Nov 13 2020

city: Shanghai

first: Xilin

last: Zhang

state: Shanghai

address: No. 1278#, Baode Rd, Jingan District

department: Dermatology

institute: Shanghai Skin Disease Hospital

data_processing:
The raw data was checked by FastQC v
Clean reads were aligned to the human genome using STAR 2.5
The expression of the transcript was calculated by FPKM using Cuffnorm
Differentially expression transcripts were determined using DESeq v1.22.1
Function and signaling pathway enrichment analysis using GO and KEGG database
Genome_build: Mus_musculus.GRCm38.90,ftp://ftp.ensembl.org/pub/release-90/gtf/mus_musculus/ Mus_musculus.GRCm38.90.chr.gtf.gz
Supplementary_files_format_and_content: gene_sample_count_with_symbol dermis.txt

source_name: Dermis

extract_protocol:
RNA was isolated using the standard TRIzol protocol.
Stand-specific libraries were constructed using the TruSeq RNA sample prepartion kit (Illumina).

treatment_protocol: Mice were randomly allocated into the following groups: control group, model group, and XYF group. 200 μl of XYF decoction (23.3 mg/g) or ddH2O was administered once daily by gavage 5 days before the application of vasaline or imiquimod cream, which continued for 10 successive days.

value: Dermis

value: wide type

value: Imiquimod application for 5 days with XYF administeration by gavage for 10 days


title: Aire trace

description: GSM4085087_aireTrace.csv.gz contains normalized UMI counts. GSE137699_allSamples.csv.gz contains normalized UMI counts of all samples in this study. Meta data can be found on the associated github https://github.com/kwells4/mtec_analysis

source_name: 2mg Tamoxifen_thymus

value: 6 weeks

value: 2mg Tamoxifen, every other day for 10 days


title: IMQ+H2O1

value: Imiquimod application for 5 days with ddH2O administeration by gavage for 10 days


title: IMQ+H2O2


title: IMQ+H2O3


title: VAS+H2O2

value: Vaseline application for 5 days with ddH2O administeration by gavage for 10 days


title: VAS+H2O3


title: Week 2 isotype control

description: GSM4085088_isoCtl_wk2.csv.gz	 contains normalized UMI counts. GSE137699_allSamples.csv.gz contains normalized UMI counts of all samples in this study. GSE137699_combinedControl.csv.gz contains normalized UMI counts of the control samples. Meta data can be found on the associated github https://github.com/kwells4/mtec_analysis

source_name: 100ug Isotype control_thymus

value: 4 weeks

value: 100ug Isotype control, 3 treatments in 1 week


title: Week 10 isotype control

description: GSM4085089_isoCtl_wk10.csv.gz contains normalized UMI counts. GSE137699_allSamples.csv.gz contains normalized UMI counts of all samples in this study. GSE137699_combinedControl.csv.gz contains normalized UMI counts of the control samples. Meta data can be found on the associated github https://github.com/kwells4/mtec_analysis


title: IMQ+XYF2


title: Week 2 anti-RANKL

description: GSM4085088_isoCtl_wk2.csv.gz contains normalized UMI counts. GSE137699_allSamples.csv.gz contains normalized UMI counts of all samples in this study. Meta data can be found on the associated github https://github.com/kwells4/mtec_analysis


title: Week 4 anti-RANKL

description: GSM4085091_RANKL_wk4.csv.gz contains normalized UMI counts. GSE137699_allSamples.csv.gz contains normalized UMI counts of all samples in this study. Meta data can be found on the associated github https://github.com/kwells4/mtec_analysis


title: IMQ+XYF1


title: Liver patient 114

value: NAFLD

value: early


title: VAS+H2O1


title: T4984A1

status: Public on Nov 11 2020

type: RNA

city: MIAMI

first: Xi

last: CHEN

state: FL

address: 1120 NW 14th Street

institute: University of Miami

hyb_protocol: Standard Affymetrix protocols for hybridization to the Affy HGU133 2.0 plus array were used.

scan_protocol: GeneChip Scanner was used for scanning and generating the raw .CEL files.

data_processing: RMA normalisation (Bioconductor R affy package) + ComBat (R sva package)

label: biotin

source_name: Moffitt Cancer Center

label_protocol: Standard Affymetrix protocols were used

growth_protocol: Samples stored at -80 C

extract_protocol: RNA was extracted using the Qiagen RNeasy kit.

treatment_protocol: Total RNA was performed according to the manufacturer's instructions.

value: Frozen tissue of primary colorectal adenocarcinoma

value: stage 4


title: T4975A1


title: T4956A1


title: T5102A1


title: T4926A1


title: T5536C4


title: T4750A1


title: T3277B


title: T3650A


title: T2419A1


title: T3263B


title: T5063A


title: T4148A2.2


title: T3437A


title: T3289A


title: T2528C


title: T3426B1


title: T5573A1


title: T3779A


title: T2759A


title: T3025B1


title: T3072A1


title: T6190A1


title: T2404A1


title: T3734A1


title: T4354H


title: T3159B


title: T5513A1.1


title: T2369A


title: T2057A


title: T1792A1


title: T1700A


title: T1356B


title: T1889A1


title: T1535A


title: T1311B


title: T5565A1

value: stage 3


title: T220A


title: T288C


title: T4644B1


title: T4695A1


title: T4452A2


title: T4920A1


title: T377A


title: T5133A


title: T5139A1


title: T4373B3


title: T4448A


title: T4948A2


title: T4111A


title: T5811A1


title: T4550B


title: T4475A1


title: T4489A1


title: T4174A


title: T1094A1


title: T4088A


title: T4110A


title: T4060A


title: T2926B


title: T3087B


title: T3351B


title: T2916A


title: T1612C


title: T3287B


title: T3254B


title: T3040A


title: T3216A


title: T2567B1


title: T3701A1


title: T4449E1


title: T2651C


title: T2130A


title: T3804A


title: T2875A1


title: T2421A


title: T1954A


title: T2660A


title: T2465G


title: T694C


title: T2307A1


title: T3552B


title: T2549C


title: T2638B


title: T3085B


title: T4080A


title: T1204A


title: T1282B


title: T1479A


title: T1430C


title: T1213A


title: T1197A


title: T1102A


title: T625A


title: T451A


title: T949B


title: T672A


title: T771A


title: T1600A


title: T372A


title: T573A


title: T324A


title: T5389A1

value: stage 2


title: T251A


title: T223B


title: T5107B1


title: T4980A1


title: T5024A1


title: T4834A1


title: T5376A1


title: T5164A1


title: T5261B1


title: T5162A1


title: T4701A1


title: T801A1


title: T4612A1


title: T3463A


title: T4508A1


title: T4257A


title: T3912A


title: T4091A


title: T3702A


title: T4660A1


title: T3258A


title: T4555A1


title: T3688A


title: T4541A1


title: T3764A


title: T3778A


title: T2631A


title: T4491A1


title: T2551A


title: T3884A


title: T3541A


title: T2004A


title: T2002B


title: T2183A1


title: T2725C


title: T2746A


title: T2965B


title: T3599A


title: T2976A


title: T2466A


title: T2511B


title: T2367A


title: T1979A


title: T1483C


title: T1923A


title: T1662A


title: T1369A


title: T1359B


title: T433A


title: T379D


title: T789A


title: T1150A


title: T1621B


title: T1129A


title: T1249A


title: T1403D


title: T740A


title: T3737A

value: stage 1


title: T74A


title: T1053B


title: T5589B1


title: T4573A1


title: T5287A1


title: T165A


title: T420A


title: T4015A


title: T402B


title: T826A

value: NNA


title: T4919A1


title: T3566A


title: T5266A1


title: T3686A


title: T2149A


title: T2688A


title: T2011A


title: T3123A


title: T1239A


title: T866D


title: T1558A


title: T1498A


title: T462A


title: T940A


title: RDBCJ17

source_name: Vanderbilt University Medical Center


title: T1856A


title: T3201B


title: T552G


title: T981A


title: T773A1


title: RDBCJ9


title: RDBCJ54


title: T1418A


title: T521B


title: T129A


title: 197RDB1


title: T656A


title: RDBCJ29


title: RDBCJ5


title: RDBCJ59


title: RDBCJ61


title: RDBCJ56


title: T309A


title: RDBCJ12


title: 197RDB6


title: 197RDB5


title: 197RDB7


title: RDBCJ27


title: 197RDB4


title: RDBCJ6


title: RDBCJ16


title: 197RDB2


title: RDBCJ32


title: 197RDB10


title: 197RDB12


title: RDBCJ53


title: 197RDB14


title: 197RDB3


title: RDBCJ57


title: RDB89


title: RDBCJ30


title: RDBCJ43


title: RDB99


title: RDB93


title: RDB79


title: RDB83


title: RDBCJ58


title: RDBCJ18


title: RDBCJ52


title: RDB97


title: RDB85


title: RDBCJ13


title: RDB87


title: RDBCJ64


title: ko_rep3_gtf2i_chip

city: St Louis

first: Joseph

middle: D

last: Dougherty

state: Missouri

address: 4566 Scott Ave, box 8232

department: Genetics and Psychiatry

institute: Washington University

description:
gtf2i_ChIP_DNA
ko_gtf2i_v_input_rep3_peaks.narrowPeak

data_processing:
Trimmed reads with Trimmomatic
aligned with bowtie2
samtools filter reads with q <10
PICARD remove duplicates
MACS2
Genome_build: mm10
Supplementary_files_format_and_content: MACS2 output for IP compared to input

source_name: E13.5 whole brain

extract_protocol:
E13.5 whole brains were dissected and frozen in liquid nitrogen until ChIP experiment was performed. The whole brain was homogenized and crosslinked in formaldehyde. Cells were lysed and nuclei were sonicated in a Covaris to a size of 200-500bp. Chromatin was precleared using Streptavidin coated Protein G beads. 80ul was taken as input control. 400ul of pre-cleared lysate was incubated with 10ug of Gtf2i BD sciences primary antibody or 10ug of Gtf2ird1 Novas primary antibody over night. The IP samples were eluted and de crosslinked at 65 degrees . The input and IP DNA samples were prepared into libraries using the Swift Biosciences Accel 2S plus kit. the libraries were enriched by 13 rounds of PCR.
Swift Biosciences Accel 2S plus DNA library kit

value: whole brain

tag: developmental stage

value: FVB/ANTJ


title: ko_rep4_gtf2i_chip

description:
gtf2i_ChIP_DNA
ko_gtf2i_v_input_rep4_peaks.narrowPeak


title: 197RDB8


title: ko_rep3_input (for gtf2i comparison)

description: genomic DNA


title: 197RDB11


title: RDBCJ47


title: ko_rep4_input (for gtf2i comparison)

description: genomic DNA


title: wt_rep4_gtf2i_chip

description:
gtf2i_ChIP_DNA
wt_gtf2i_v_input_rep4_peaks.narrowPeak

value: wt


title: ko_rep2_gtf2i_chip

description:
gtf2i_ChIP_DNA
ko_gtf2i_v_input_rep2_peaks.narrowPeak


title: RDB91


title: 197RDB9


title: ko_rep2_input (for gtf2i_comparison)

description: genomic DNA


title: RDB95


title: RDB107


title: wt_rep4_input (for gtf2i comparison)

description: genomic DNA


title: RDB105


title: RDBCJ65


title: RDB103


title: wt_rep2_input (for gtf2i comparison)

description: genomic DNA


title: wt_rep3_gtf2i_chip

description:
gtf2i_ChIP_DNA
wt_gtf2i_v_input_rep3_peaks.narrowPeak


title: wt_rep1_gtf2i_chip

description:
gtf2i_ChIP_DNA
wt_gtf2i_v_input_rep1_peaks.narrowPeak


title: wt_rep2_gtf2i_chip

description:
gtf2i_ChIP_DNA
wt_gtf2i_v_input_rep2_peaks.narrowPeak


title: wt_rep3_input (for gtf2i comparison)

description: genomic DNA


title: RDB81


title: RDB101


title: ko_rep1_gtf2i_chip

description:
gtf2i_ChIP_DNA
ko_gtf2i_v_input_rep1_peaks.narrowPeak


title: ird1_rep3_input

description: genomic DNA


title: ko_rep3_input, also used as input for ko_rep1_gtf2i

description: genomic DNA


title: wt_rep3_ird1_chip

description:
ird1_ChIP_DNA
wt_ird1_v_input_rep5_peaks.narrowPeak


title: wt_rep1_ird1_chip

description:
ird1_ChIP_DNA
wt_ird1_v_input_rep1_peaks.narrowPeak


title: ird1_rep3_ird1_chip

description:
ird1_ChIP_DNA
ird1_ird1_v_input_rep5_peaks.narrowPeak


title: wt_rep2_ird1_chip

description:
ird1_ChIP_DNA
wt_ird1_v_input_rep2_peaks.narrowPeak


title: wt_rep2_input

description: genomic DNA


title: wt_rep3_input, also used as input for wt_rep1_gtf2i

description: genomic DNA


title: ko_rep2_ird1_chip

description:
ird1_ChIP_DNA
ko_ird1_v_input_rep2_peaks.narrowPeak


title: ko_rep2_input

description: genomic DNA


title: ko_rep1_ird1_chip

description:
ird1_ChIP_DNA
ko_ird1_v_input_rep1_peaks.narrowPeak


title: ko_rep3_ird1_chip

description:
ird1_ChIP_DNA
ko_ird1_v_input_rep5_peaks.narrowPeak


title: ko_rep1_input

description: genomic DNA


title: ird1_rep2_ird1_chip

description:
ird1_ChIP_DNA
ird1_ird1_v_input_rep2_peaks.narrowPeak


title: 11610-11

data_processing:
Trimmed reads with Trimmomatic
aligned with STAR
count per feature using HT-seq count
Genome_build: mm10
Supplementary_files_format_and_content: counts per feature for each sample

extract_protocol:
E13.5 whole brains were dissected and homogenized in 500ul of RIPA buffer with RNAse inhibitors. 250ul of homogenate was added to 750ul of Trizol LS and stored at -80C until RNA extraction. RNA was extracted using the Zymo clean and concentrator-5 kit with on column DNAse digestion and eluted in 30ul of RNAse free water.
1ug of RNA was used as input for the rRNA depelition kit (human/mouse/rat) (NEB#E6310) and then libraries were prepped using the NEBNext Ultra II RNA Library prep kit for Illumina (E7770L)

value: wt (for ird1 comparison)


title: ird1_rep2_input

description: genomic DNA


title: 11619-4


title: 12419-7

value: wt (for gtf2i comparison)


title: 12419-8


title: 11619-2


title: 12301-7


title: 12301-6


title: 12419-6


title: 11610-2


title: 12301-5


title: 11902-8


title: 11902-5


title: 11610-3


title: 11902-6


title: 11610-1


title: 11610-12


title: 11619-6


title: E12_PFL_wt_ChIP_H3K27ac

status: Public on Nov 10 2020

city: Geneva

first: Eddie

last: Rodríguez-Carballo

address: 4, Boulevard d'Yvoy

department: Department of Genetics and Evolution

country: Switzerland

institute: Université de Genève

description: Proximal forelimb mouse E12_wt_ChIP_H3K27ac

data_processing:
Analyses were performed using the facilities of the Scientific IT and Application Support Center of EPFL. Sequences were filtered and adapters were removed using cutadapt (v1.16) with parameters -m 15 -q 30 -a CTGTCTCTTATACACATCTCCGAGCCCACGAGAC. Reads were mapped on mm10 using bowtie2 (v2.3.4.1) using default parameters. Only reads with a mapping quality above 30 were kept. A profile was obtained with macs2 (version 2.1.1.20160309 option –extsize 300). Bedgraphs were normalized to their number of million tags used in the profile (bedtools v2.27).
Genome_build: mm10
Supplementary_files_format_and_content: bedgraph

source_name: Proximal forelimb

extract_protocol:
For E9.5 ChIP samples, 15 to 17 pairs of forelimb buds were used for each experiment. For the E12.5 H3K27ac ChIP sample, proximal forelimbs were dissected from wild-type mice. For E12.5 CTCF ChIP samples, the four whole limbs were micro-dissected from one mouse embryo either from wild type or mutant lines (del CTCF(CS38), delCTCF(CS38;CS40), inv(CS38-40)). All samples were taken from homozygous crosses.Tissues were dissected, fixed in 1% formaldehyde (in PBS) for 10 min at room temperature and the reaction was quenched with Stop Solution from the ChIP-IT High sensitive kit (Active Motif). Samples were then washed 3 times with working Washing Solution (ChIP-IT, Active Motif) and then snap-frozen in liquid nitrogen and stored at -80ºC until further processing. Limb tissues were disrupted with a polytron device, lysed in RIPA buffer or Prep Buffer (ChIP-IT, Active Motif) and sonicated in Diagenode Bioruptor Pico. All experiments were processed following the ChIPmentation protocol (Schmidl et al., 2015) as in (Rodríguez-Carballo et al., 2019). Around 0.6 million cells were used for each IP on a final volume of 800 to 1000ul of RIPA-LS buffer (10mM Tris-HCl pH8, 140mM NaCl, 1mM EDTA pH8, 0.1% SDS, 0.1% sodium deoxycholate, 1% Triton x-100 and proteinase inhibitors). They were incubated overnight with the respective antibodies (CTCF Active Motif 61311; H3K27ac Diagenode C15410196; RAD21 abcam ab992) and precipitated after a 2h long incubation with magnetic beads (Dynabeads Protein A, Invitrogen 10001D) rotating at 4ºC. Washes were performed as follows: two times RIPA-LS, two times RIPA-HS (10mM Tris-HCl pH8, 500mM NaCl, 1mM EDTA pH8, 0.1% SDS, 0.1% sodium deoxycholate, 1% Triton x-100 and proteinase inhibitors), two times RIPA-LiCl (10mM Tris-HCl pH8, 250mM LiCl, 1mM EDTA pH8, 0.5% NP-40, 0.5% sodium deoxycholate and proteinase inhibitors) and once with 10mM Tris-HCl pH8. Beads were resuspended in 24ul of tagmentation buffer (10mM Tris pH8, 5mM MgCl2, 10% dimethylformamide). They were incubated at 37ºC for either 2 minutes (CTCF, RAD21), or 10 minutes (H3K27ac) with 1 µl of Tn5 transposase (Illumina 15027865, from Nextera DNA Library Prep Kit 15028212). Samples were then resuspended and washed twice in 1ml of RIPA-LS and twice in 1ml TE buffer (10mM Tris-Hcl pH8, 1mM EDTA pH8). Beads were magnetised, DNA was eluted in ChIP elution buffer (10mM Tris-HCl pH8, 5mM EDTA pH8, 300mM NaCl, 0.4% SDS) with 2ul of proteinase K (20mg/ml stock) and then incubated for 1 hour at 55ºC and 6 hours to overnight at 65ºC. After de-crosslinking, the supernatant was recovered and beads were resuspended again in 19ul ChIP elution buffer with 1ul of proteinase K and left 1 hour at 55ºC. The two supernatants were combined and purified with MinElute kit (Qiagen) in 22ul of EB buffer. Relative quantitation was performed using SYBR-green as in (Schmidl et al, 2015; PMID:26280331) using 2ul of DNA. Libraries were amplified according to the Cq values obtained in the previous step, purified and size selected with CleanNGS magnetic beads (CleanNA) and eluted in 15ul of water. DNA was sequenced in a HiSeq 4000 machine as 50 bp or 100 bp reads.
Libraries of ChIP experiments were generated following the ChIPmentation protocol (Schmidl et al, 2015; PMID:26280331).

value: wild-type

tag: embryonic day

tag: chip antibody


title: E12_WL_invCS3840_ChIP_CTCF

description: Whole limb mouse E12_invCS3840_ChIP_CTCF

source_name: Whole forelimb bud

value: CTCF


title: E12_WL_delCTCFs_ChIP_CTCF

description: Whole limb mouse E12_delCTCFs(CS38;CS40)_ChIP_CTCF

value: delCTCFs


title: E12_WL_delCTCF-CS38_ChIP_CTCF

description: Whole limb mouse E12_delCTCF-CS38_ChIP_CTCF


title: ird1_rep1_input

description: genomic DNA


title: E12_WL_wt_ChIP_CTCF

description: Whole limb mouse E12_wt_ChIP_CTCF


title: 11610-10


title: E9_FLB_20-28s_wt_ChIP_CTCF

description: Forelimb bud mouse E9_wt_20-28s_ChIP_CTCF


title: E9_FLB_20-28s_wt_ChIP_RAD21

description: Forelimb bud mouse E9_wt_20-28s_ChIP_RAD21


title: E9_FLB_18-22s_wt_ChIP_H3K27ac

description: Forelimb bud mouse E9_wt_18-22s_ChIP_H3K27ac


title: E9_FLB_24-29s_wt_ChIP_H3K27ac

description: Forelimb bud mouse E9_wt_24-29s_ChIP_H3K27ac


title: Epidermis, IMQ+XYF3

data_processing:
The raw data was checked by FastQC v
Clean reads were aligned to the mouse genome using STAR 2.5
The expression of the transcript was calculated by FPKM using Cuffnorm
Differentially expression transcripts were determined using DESeq v1.22.1
Function and signaling pathway enrichment analysis using GO and KEGG database
Genome_build: Mus_musculus.GRCm38.90,ftp://ftp.ensembl.org/pub/release-90/gtf/mus_musculus/ Mus_musculus.GRCm38.90.chr.gtf.gz
Supplementary_files_format_and_content: gene_sample_count_with_symbol epidermis.txt

source_name: Epidermis

treatment_protocol: Mice were randomly allocated into the following groups: control group, model group, and XYF group. 200 μl of XYF decoction (23.3 mg/g) or ddH2O was administered once daily by gavage 5 days before the application of Vaseline or imiquimod cream, which continued for 10 successive days.

value: Epidermis

value: 8 weeks

value: wild type

value: Imiquimod application for 5 days with XYF administeration by gavage for 10 days

tag: group

value: XYF


title: Epidermis, IMQ+XYF1

tag: genotype


title: Epidermis, IMQ+XYF2


title: Epidermis, IMQ+H2O3

value: Imiquimod application for 5 days with ddH2O administeration by gavage for 10 days

value: model


title: Epidermis, VAS+H2O2

value: Vaseline application for 5 days with ddH2O administeration by gavage for 10 days

value: control


title: Epidermis, VAS+H2O3


title: Epidermis, IMQ+H2O1


title: Epidermis, VAS+H2O1


title: Gtpbp2_2_Ribo

status: Public on Oct 26 2020

city: Farmington

first: Scott

last: Adamson

state: CT

address: 10 Discovery Drive

institute: The Jackson Laboratory

description: Ribosome protected RNA fragments

data_processing:
Cerebellum RNA-seq was quantified using kallisto version 0.42.4 and psuedo-aligned to the Gencode vM20 transcript reference.
Cerebellum ribosome profiling data were adaptor trimmed with fastx_clipper using -a CTGTAGGCACCATCAAT and rRNA was removed using bowtie2 version 2.2.3 using the parameter -L 13.
Remaining ribosome profiling reads were mapped to the mm10 genome with a Gencode vM20 transcript annotation using hisat2 version 2.1.0.
Cerebellum ribosome profiling reads were counted at the gene-level using featureCounts for reads overlapping CDS features.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include kallisto estimated counts and TPM values for each forebrain RNA-seq sample at the transcript level.
Supplementary_files_format_and_content: tab-delimited text files include featureCounts estimated gene counts ribosome profiling samples.

source_name: Cerebellum

extract_protocol:
Cerebella from various strains were isolated from 3-week-old mice and immediately frozen in liquid nitrogen.
RNA-Seq libraries were prepared using the TruSeq v2 mRNA kit (Illumina). Briefly, total cerebellar RNA was isolated and RNA quality was assessed on Agilent TapeStation. mRNA was purified using biotin-tagged polydT oligonucleotides and streptavidin-coated magnetic beads. After fragmentation of mRNA, libraries were prepared according to manufacturer’s instructions. Paired end reads (2x100bp) were obtained using the HiSeq 4000 (Illumina). Ribosome profiling libraries were generated as previously described (Ingolia et al., 2012; Ishimura et al., 2014) and sequenced on an Illumina HiSeq 4000.

value: Cerebellum

value: 3 weeks old

value: Gtpbp2 -/-

tag: batch

value: Batch 2


title: TAL1 G1E-ER4+E2 [707]

status: Public on Oct 14 2020

city: University Park

first: Ross

last: Hardison

state: PA

address: 303 Wartik Lab

institute: Pennsylvania State University

description:
707
707.mm10.broadpeak.gz

data_processing:
Basecalls using bcl2fastq-1.8.4, and parameters --no-eamss --mismatches 1
Mapping to reference genome mm10 canon with Bowtie 1.0.0 using parameters --chunkmbs 1024 -y -n 2 --best -k 1 --maxbts 800 -l 28 -e 80 --sam-nohead --sam
Wiggle and peaks called using MACS with parameters --format BAM --gsize 1870000000 --tsize 36 --bw 120 --mfold 12 --wig --space 1
Filter blacklist regions from peaks, and convert the *peaks.xls file from MACs to broadpeak format (see UCSC Genome Browser for format specs).
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: bigWigs, signal from MACS.
Supplementary_files_format_and_content: broadpeaks, peak calls by MACS.

source_name: G1E-ER4+E2 cells

growth_protocol: G1E-ER4 cells were grown in IMDM media + 15% FBS, kit ligand, and erythropoietin in a standard tissue culture incubator at 37°C with 5% CO2.

extract_protocol:
Lysates were prepared from sonicated nuclei and protein-DNA complexes were isolated with antibody.
ChIP-seq samples were prepared by end repair, 3’ adenylation, and adaptor ligation using Illumina’s TruSeq ChIP-seq Sample Preparation Kit.

treatment_protocol: To induce erythroid maturation, G1E-ER4 cells were treated with 10-8 mol/L β-estradiol for 24 hours (G1E-ER4+E2).

value: ES-derived erythroid progenitor cells

value: TAL1 (Santa Cruz sc12984)

tag: average chromatin size as measured between a 100-500 bp window using the agilent bioanalyzer 7500 chip

tag: subjective quality assessment (pass, low pass, fail)

value: Pass


title: TAL1 G1E-ER4+E2 [584]

description:
584
584.mm10.broadpeak.gz

value: Low pass


title: TAL1 G1E-ER4+E2 [581]

description:
581
581.mm10.broadpeak.gz

value: Fail


title: TAL1 G1E-ER4+E2 [583]

description:
583
583.mm10.broadpeak.gz


title: wt_rep1_input

description: genomic DNA

value: whole brain

value: wt

value: FVB/ANTJ


title: TAL1 G1E-ER4+E2 [585]

description:
585
585.mm10.broadpeak.gz


title: TAL1 G1E-ER4+E2 [580]

description:
580
580.mm10.broadpeak.gz


title: TAL1 G1E-ER4+E2 [582]

description:
582
582.mm10.broadpeak.gz


title: CTCF G1E-ER4+E2 [335]

description:
335
335.mm10.broadpeak.gz

value: CTCF (Millipore 07-729)


title: CTCF G1E-ER4+E2 [366]

description:
366
366.mm10.broadpeak.gz


title: CTCF G1E-ER4+E2 [369]

description:
369
369.mm10.broadpeak.gz


title: TAL1 G1E-ER4+E2 [705]

description:
705
705.mm10.broadpeak.gz


title: RDBCJ15

value: Frozen tissue of primary colorectal adenocarcinoma

value: stage 2


title: CTCF G1E-ER4+E2 [485]

description:
485
485.mm10.broadpeak.gz


title: TAL1 G1E-ER4+E2 [704]

description:
704
704.mm10.broadpeak.gz


title: TAL1 G1E-ER4+E2 [703]

description:
703
703.mm10.broadpeak.gz


title: TAL1 G1E-ER4+E2 [674]

description:
674
674.mm10.broadpeak.gz


title: Epidermis, IMQ+H2O2

value: Epidermis

value: 8 weeks

value: wild type

value: Imiquimod application for 5 days with ddH2O administeration by gavage for 10 days

value: model


title: TAL1 G1E-ER4+E2 [673]

description:
673
673.mm10.broadpeak.gz


title: TAL1 G1E-ER4+E2 [706]

description:
706
706.mm10.broadpeak.gz


title: ird1_rep1_ird1_chip

description:
ird1_ChIP_DNA
ird1_ird1_v_input_rep1_peaks.narrowPeak


title: TAL1 G1E-ER4+E2 [671]

description:
671
671.mm10.broadpeak.gz


title: TAL1 G1E-ER4+E2 [670]

description:
670
670.mm10.broadpeak.gz


title: CTCF G1E-ER4+E2 [735]

description:
735
735.mm10.broadpeak.gz


title: TAL1 G1E-ER4+E2 [672]

description:
672
672.mm10.broadpeak.gz


title: CTCF G1E-ER4+E2 [733]

description:
733
733.mm10.broadpeak.gz


title: CTCF G1E-ER4+E2 [736]

description:
736
736.mm10.broadpeak.gz


title: CTCF G1E-ER4+E2 [732]

description:
732
732.mm10.broadpeak.gz


title: CTCF G1E-ER4+E2 [693]

description:
693
693.mm10.broadpeak.gz


title: CTCF G1E-ER4+E2 [692]

description:
692
692.mm10.broadpeak.gz


title: CTCF G1E-ER4+E2 [695]

description:
695
695.mm10.broadpeak.gz


title: CTCF G1E-ER4+E2 [694]

description:
694
694.mm10.broadpeak.gz


title: CTCF iMK [1910]

description:
1910
1910.mm10.broadpeak.gz

source_name: iMK cells

value: bone marrow derived progenitor cells

tag: facs cell isolation sort markers


title: CTCF iMk [1908]

description:
1908
1908.mm10.broadpeak.gz

source_name: iMk cells


title: CTCF GMP [1977]

description:
1977
1977.mm10.broadpeak.gz

source_name: GMP cells

value: Low Pass


title: TAL1 G1E-ER4+E2 [702]

description:
702
702.mm10.broadpeak.gz

value: ES-derived erythroid progenitor cells

value: TAL1 (Santa Cruz sc12984)


title: CTCF CFUMk [1979]

description:
1979
1979.mm10.broadpeak.gz

source_name: CFUMk cells

value: Pass


title: CTCF ERY [1926]

description:
1926
1926.mm10.broadpeak.gz

source_name: ERY cells


title: CTCF ERY [1909]

description:
1909
1909.mm10.broadpeak.gz


title: CTCF MEP [1978]

description:
1978
1978.mm10.broadpeak.gz

source_name: MEP cells


title: CTCF CFUE [1980]

description:
1980
1980.mm10.broadpeak.gz

source_name: CFUE cells

value: CD4-, CD8-, IL7Ra-, CD11b-, Ly6g-, CD45R-, Ter119+, CD44+, FSCHigh


title: CTCF LSK [1927]

description:
1927
1927.mm10.broadpeak.gz

source_name: LSK cells


title: CTCF G1E-ER4+E2 [789]

description:
789
789.mm10.broadpeak.gz


title: CTCF G1E-ER4+E2 [788]

description:
788
788.mm10.broadpeak.gz

value: Fail


title: CTCF G1E-ER4+E2 [787]

description:
787
787.mm10.broadpeak.gz


title: CTCF G1E-ER4+E2 [786]

description:
786
786.mm10.broadpeak.gz

value: not detected


title: CTCF G1E-ER4+E2 [734]

description:
734
734.mm10.broadpeak.gz


title: CTCF G1E-ER4+E2 [785]

description:
785
785.mm10.broadpeak.gz


title: TAL1 G1E-ER4+E2 [505]

description:
505
505.mm10.broadpeak.gz


title: CTCF G1E-ER4+E2 [696]

description:
696
696.mm10.broadpeak.gz


title: Human fetal liver sample (14 week EGA) XHF007

status: Public on Sep 24 2020

city: Singapore

first: Ankur

last: Sharma

state: Singapore

address: 60 Biopolis Street, Genome, #02-01

country: Singapore

institute: Genome Institute Of Singapore

data_processing:
cellranger-3.1.0 is used for alignment, filtering barcode counting, and UMI counting. Raw count matrix is output from this pipeline
Raw count matrix is processed using scanpy (version 1.4.0) and seurat (version 3.0) for downstream analyses
Genome_build: Human reference (GRCh38), Mouse reference (mm10)
Supplementary_files_format_and_content: Matrix table with log normalized expression count.
Supplementary_files_format_and_content: Tab delimited file of gene names and barcodes metadata
Supplementary_files_format_and_content: *barcodes.tsv, *genes.tsv/*features.tsv, *matrix.mtx
Supplementary_files_format_and_content: *.h5ad: scanpy object
Supplementary_files_format_and_content: HCCF_integrated.Rdata: R object (Seurat object)

source_name: Human fetal liver sample (14 week EGA)

extract_protocol:
Tissue samples were treated with Collagenase IV digestion with DNAseI in RPMI media for 30-40 minutes at 37oC. Cells were washed with 1% BSA PBS solution and filtered using 70um and 40um filters. RBC lysis was performed using 1X RBC lysis buffer incubated with cells on ice.
All libraries were constructed using Chromium 3' v2 (Cat# CG00052) or 3' v3 (Cat# CG000183) chemistry kits by 10x Genomics

value: Human fetal liver

tag: bam id


title: Human fetal liver sample (18 week EGA) XHL100

source_name: Human fetal liver sample (18 week EGA)


title: Human fetal liver sample (18 week EGA) XHL099


title: Human fetal liver sample (14 week EGA) XHF006


title: Human fetal liver sample (21 week EGA) XHF002

source_name: Human fetal liver sample (21 week EGA)


title: Human fetal liver sample (21 week EGA) XHF003


title: Human fetal liver sample (16 week EGA) XHL090

source_name: Human fetal liver sample (16 week EGA)


title: Hepatocellular Carcinoma sample MUX7512

source_name: Hepatocellular Carcinoma sample

value: Human liver

value: Tumor Section 4 and 5


title: CTCF CMP [1976]

description:
1976
1976.mm10.broadpeak.gz

source_name: CMP cells

value: CTCF (Millipore 07-729)


title: Hepatocellular Carcinoma sample MUX7510

value: Tumor Section 2


title: Hepatocellular Carcinoma sample MUX7509

value: Tumor Section 1


title: Hepatocellular Carcinoma sample MUX7511

value: Tumor Section 3


title: Hepatocellular Carcinoma sample MUX7508

value: Adjacent Normal


title: Hepatocellular Carcinoma sample MUX7507


title: Hepatocellular Carcinoma sample MUX7506


title: Hepatocellular Carcinoma sample MUX7505


title: Hepatocellular Carcinoma sample MUX7500


title: Hepatocellular Carcinoma sample MUX7502


title: CTCF LSK [1295]

description:
1295
1295.mm10.broadpeak.gz


title: Hepatocellular Carcinoma sample MUX7400

value: Tumor Section 2 and 3


title: Hepatocellular Carcinoma sample MUX7496

value: Tumor Section 4


title: Hepatocellular Carcinoma sample MUX7398

value: Tumor Section 5


title: Hepatocellular Carcinoma sample MUX7497


title: Hepatocellular Carcinoma sample MUX7399


title: Hepatocellular Carcinoma sample MUX7397


title: Hepatocellular Carcinoma sample MUX7273


title: Hepatocellular Carcinoma sample MUX7272


title: Hepatocellular Carcinoma sample MUX7270


title: Human fetal liver sample (16 week EGA) XHL089


title: Hepatocellular Carcinoma sample MUX7269


title: Hepatocellular Carcinoma sample MUX7267


title: Hepatocellular Carcinoma sample MUX7271


title: Hepatocellular Carcinoma sample MUX7265


title: Hepatocellular Carcinoma sample MUX7266


title: Hepatocellular Carcinoma sample MUX7264


title: Hepatocellular Carcinoma sample MUX7263


title: Hepatocellular Carcinoma sample MUX7503


title: Hepatocellular Carcinoma sample MUX7094


title: Hepatocellular Carcinoma sample MUX7093


title: Hepatocellular Carcinoma sample MUX7095


title: Hepatocellular Carcinoma sample MUX6880


title: Hepatocellular Carcinoma sample MUX6879


title: Mouse liver sample from Ms4a3cre-RosaTdT mouse model (Partial hepatectomy Day 28) day30_Tom_pos

value: Mouse liver

value: Tomato positive


title: Hepatocellular Carcinoma sample MUX7499


title: RDB109

source_name: Vanderbilt University Medical Center

value: Frozen tissue of primary colorectal adenocarcinoma

tag: Stage

value: stage 2

tag: age


title: Hepatocellular Carcinoma sample MUX6877

tag: cell type


title: Hepatocellular Carcinoma sample MUX6874


title: Mouse liver sample from Ms4a3cre-RosaTdT mouse model (Partial hepatectomy Day 28) day30_CD45_neg


title: Mouse liver sample from Ms4a3cre-RosaTdT mouse model (Partial hepatectomy Day 14) day14_Tom_pos


title: Hepatocellular Carcinoma sample MUX6873


title: Hepatocellular Carcinoma sample MUX6872


title: Mouse liver sample from Ms4a3cre-RosaTdT mouse model (Partial hepatectomy Day 14) day14_CD45_neg


title: Hepatocellular Carcinoma sample MUX7268


title: Healthy normal liver sample MUX6736

source_name: Healthy normal liver sample

value: Healthy Normal Liver


title: Mouse liver sample from Ms4a3cre-RosaTdT mouse model (Partial hepatectomy Day 7) day7_Tom_neg

value: Tomato negative


title: Hepatocellular Carcinoma sample MUX6691


title: Hepatocellular Carcinoma sample MUX6690


title: Mouse liver sample from Ms4a3cre-RosaTdT mouse model (Partial hepatectomy Day 7) day7_CD45_neg


title: Mouse liver sample from Ms4a3cre-RosaTdT mouse model (Partial hepatectomy Day 7) day7_Tom_pos


title: Hepatocellular Carcinoma sample MUX6445


title: Hepatocellular Carcinoma sample MUX6443


title: Hepatocellular Carcinoma sample MUX6689


title: Hepatocellular Carcinoma sample MUX6440


title: Mouse liver sample from Ms4a3cre-RosaTdT mouse model (Partial hepatectomy Day 28) day30_Tom_neg


title: Hepatocellular Carcinoma sample MUX6196


title: Mouse liver sample from Ms4a3cre-RosaTdT mouse model (Partial hepatectomy Day 0) Control_CD45_neg


title: Mouse liver sample from Ms4a3cre-RosaTdT mouse model (Partial hepatectomy Day 0) Control_Tom_pos


title: Mouse liver sample from Ms4a3cre-RosaTdT mouse model (Partial hepatectomy Day 14) day14_Tom_neg


title: Hepatocellular Carcinoma sample MUX6195


title: Hepatocellular Carcinoma sample MUX6446


title: Hepatocellular Carcinoma sample MUX6198


title: Hepatocellular Carcinoma sample MUX6194


title: Hepatocellular Carcinoma sample MUX6442


title: Hepatocellular Carcinoma sample MUX6191


title: Hepatocellular Carcinoma sample MUX6189


title: Hepatocellular Carcinoma sample MUX6192


title: Hepatocellular Carcinoma sample MUX6193


title: Hepatocellular Carcinoma sample MUX6190


title: Mouse liver sample from Ms4a3cre-RosaTdT mouse model (Partial hepatectomy Day 0) Control_Tom_neg


title: Hepatocellular Carcinoma sample MUX6444


title: H9_treated_bio_2

status: Public on Sep 09 2020

city: singapore

first: Aw

last: Jong Ghut Ashley

address: 60 Biopolis St

institute: Genome Institute of Singapore

data_processing:
Basecall samples with Albacore version 2.3.3 no filtering
Aligned samples with Graphmap 0.5.2
Aligned raw signal to sequence with Nanopolish 10.2
Calculated reactivity with PORE-cupine
Genome_build: GRCh38
SRA_file_format: Fast5
Processed_files_format_and_content: CSV files were generated, higher peaks represent a higher possibiilty for single stranded regions

source_name: NAI_N3 treated

extract_protocol:
Purified with columns or extracted with TRIzol with or without RNA with poly A tail
Purified RNA was ligated with a adpator at the 3' end and followed by a motor protein or adaptors were ligated at the 5' end and 3' end of the product from fragmented reversed transcribed RNA
Oxford Nanopore direct RNA sequencing or RNA-seq

treatment_protocol: single transcripts unmodified samples are folded in vitro and treated with DMSO

tag: modifications

value: NAI N3


title: TPP_NAI_N3_lig_750nM

organism: Bacillus subtilis

source_name: NAI_N3 treated IVT with ligand


title: Training_NAI_N3

organism:
Bacillus subtilis
Saccharomyces cerevisiae
Dengue virus
Oceanobacillus iheyensis

source_name: NAI_N3 treated IVT

treatment_protocol: Purified with columns or Total RNA was extracted with TRIzol and ligated with a adpator at the 3' end and followed by a motor protein


title: TPP_NAI_N3_lig_250nM


title: Hepatocellular Carcinoma sample MUX6188

value: Human liver


title: TPP_NAI_N3_li


title: TPP_NAI_N3_no_li

source_name: NAI_N3 treated IVT no ligand


title: LYC_unmod

source_name: Unmodified IVT


title: LYC NAI_N3


title: tetra_CMCT

data_processing:
Basecall samples with Albacore version 2.3.3 no filtering
Aligned samples with Graphmap 0.5.2
Aligned raw signal to sequence with Nanopolish 10.2
Calculated reactivity with PORE-cupine
Genome_build: GRCh38
SRA_file_format: Fastq
Processed_files_format_and_content: CSV files were generated, higher peaks represent a higher possibiilty for single stranded regions

organism: Tetrahymena thermophila

source_name: CMCT treated IVT

value: CMCT


title: tetra_unmod

source_name: Unmodifed IVT

treatment_protocol: Purified with columns and ligated with a adpator at the 3' end and followed by a motor protein


title: 16s_NAI_N3


title: TPP_unmod

source_name: Unmodified


title: tetra_NAI_N3


title: tetra_NMIA

source_name: NMIA treated IVT

value: NMIA


title: MUT-input_SC

status: Public on Aug 25 2020

city: Blacksburg

first: Chang

state: VA

address: 235 Goodwin Hall, 635 Prices Fork Road, Virginia Tech

department: Chemical Engineering

institute: Virginia Tech

data_processing:
Raw reads were trimmed with TrimGalore 0.4.1
Trimmed reads were aligned using bowtie 1.1.2
Aligned reads that overlapped ENCODE blacklist were removed
Reads were extended to 250bp
Sample was normalized to sequencing depth and normalized input was subtracted
Sample was converted to BigWig format
Genome_build: hg19
Supplementary_files_format_and_content: Normalized ChIP-seq signal in BigWig format

source_name: Breast stromal cells

extract_protocol:
Sorted samples containing 100K – 3M cells were used as the starting material and centrifuged at 1,600 g for 5 min and washed twice with 1 ml cold PBS. Cells were resuspended in 1 ml freshly made 1% formaldehyde and incubated at room temperature for 5 min on a shaker. Crosslinking was quenched by adding 50 µl of 2.5 M glycine and shaking for 5 min. The pellet was resuspended in 130 μl sonication buffer (10 mM Tris-HCl, pH 8.1, 1 mM EDTA, 0.1% SDS and 1× protease inhibitor cocktail) and sonicated with 105 W peak incident power, 5% duty factor, and 200 cycles per burst for 16 min using a Covaris S220 sonicator. The sheared sample was centrifuged in a 4 oC centrifuge at 16,100g for 10 min, and the supernatant was transferred to a new tube. Sheared chromatin was diluted with IP buffer (20 mM Tris-HCl, pH 8.0, 140 mM NaCl, 1 mM EDTA, 0.5 mM EGTA, 0.1% (w/v) sodium deoxycholate, 0.1% SDS, 1% (v/v) Triton X-100, with 1% freshly added PMSF and PIC) and diluted to contain chromatin from 50,000 cells (H3K27ac) or 10,000 cells (H3K4me3) in 50µL
Library preparation was performed using the Accel-NGS 2S Plus DNA Library Kit (Swift Biosciences) using 8 μl of purified DNA per sample. 2.5 μl of the low EDTA TE buffer in the 50 μl amplification cycle reaction mix was replaced with 2.5 μl of 20x EvaGreen, and amplification was terminated after samples saw a >3000 RFU increase (BioRad CFX Connect). Amplified DNA was then eluted into 10 μl low EDTA TE buffer where 2 μl could be used in qPCR for preliminary quality control analysis, Kappa DNA quantification, and Tapestation fragment size analysis with the other 8 μl for library pooling. Libraries were pooled at 10 nM for sequencing by Illumina HiSeq 4000 with single-end 50 nt read.

value: BRCAmut/+

value: Breast stromal cells


title: RDBCJ45


title: tetra_DMS

source_name: DMS treated IVT

value: DMS


title: MUT-input_ML

source_name: Breast mature luminal cells

value: Breast mature luminal cells


title: NC-input_ML

value: BRCA+/+


title: NC-input_SC


title: NC-input_LP

source_name: Breast luminal progenitors

value: Breast luminal progenitors


title: MUT-input_BC

source_name: Breast basal cells

value: Breast basal cells


title: H9_treated_bio_1


title: Training_unmod


title: NC-input_BC


title: H9_unmodifed

treatment_protocol: Total RNA was extracted with TRIzol, RNA with poly A tail was enriched, adaptors were ligated at the 5' end and 3' end of the product from fragmented reversed transcribed RNA


title: MUT-3_SC_H3K4me3


title: 16s_unmod


title: NC-5_SC_H3K4me3


title: MUT-3_ML_H3K4me3


title: NC-5_ML_H3K4me3


title: tetra_NAI

source_name: NAI treated IVT

value: NAI


title: MUT-2_ML_H3K4me3


title: MUT-3_LP_H3K4me3


title: MUT-input_LP


title: NC-5_LP_H3K4me3


title: MUT-2_LP_H3K4me3


title: MUT-2_BC_H3K4me3


title: NC-5_BC_H3K4me3


title: MUT-2_SC_H3K27ac


title: NC-2_SC_H3K27ac


title: NC-1_SC_H3K27ac


title: MUT-3_SC_H3K27ac


title: MUT-2_ML_H3K27ac


title: MUT-1_ML_H3K27ac


title: NC-3_ML_H3K27ac


title: NC-4_ML_H3K27ac


title: MUT-3_ML_H3K27ac


title: NC-1_ML_H3K27ac


title: MUT-2_LP_H3K27ac


title: MUT-3_LP_H3K27ac


title: NC-4_SC_H3K27ac


title: NC-2_ML_H3K27ac


title: NC-3_LP_H3K27ac


title: MUT-1_LP_H3K27ac


title: NC-4_LP_H3K27ac


title: MUT-1_SC_H3K27ac


title: MUT-1_BC_H3K27ac


title: MUT-2_BC_H3K27ac


title: NC-1_LP_H3K27ac


title: NC-4_BC_H3K27ac


title: MUT-3_BC_H3K27ac


title: NC-1_BC_H3K27ac


title: NC-2_BC_H3K27ac


title: scRNAseq_olig2_eGFP_48hpf

status: Public on Aug 11 2020

first: Bruce

last: Appel

institute: University of Colorado School of Medicine

data_processing:
Raw sequencing reads were demultiplexed, mapped to the zebrafish reference genome and summarized into gene-expression matrices using CellRanger (version 3.0.1)
Count matrices were further filtered in Seurat 3.1.0 (https://satijalab.org/seurat/) to remove cell barcodes with fewer than 250 detectable genes, more than 5% of UMIs derived from mitochondrial genes, or more than 50,000 UMIs (to exclude putative doublets)
Standard Seurat normalization and PCA was run using the 1,291 most variable genes
Applied Harmony (https://doi.org/10.1038/s41592-019-0619-0) alignment (theta = 2) to correct for inter-sample variation, chose 20 Harmony dimensions and applied Seurat UMAP reduction
Genome_build: GRCz11
Supplementary_files_format_and_content: gzipped csv file of matrix of normalized gene expression by cell for merged 3 scRNAseq samples
Supplementary_files_format_and_content: gzipped csv file of metadata for cells

organism: Danio rerio

source_name: spinal cord cells

growth_protocol: Embryos were raised at 28.5°C in E3 media (5 mM NaCl, 0.17 mM KCl, 0.33 mM CaCl2, 0.33 mM MgSO4 at pH 7.4, with sodium bicarbonate), sorted for good health and staged accordingly to developmental morphological features and hours post-fertilization

extract_protocol:
24, 36, and 48 hpf Tg(olig2:EGFP) euthanized embryos were collected in 1.7 ml microcentrifuge tubes and deyolked in 100 μl of pre-chilled Ca free Ringers solution (116 mM NaCl, 2.6 mM KCl, 5 mM HEPES, pH 7.0) on ice. Embryos were pipetted intermittently with a p200 micropipettor for 15 minutes and left for 5 min. 500 μl of protease solution (10 mg/ml BI protease, 125 U/ml DNase, 2.5 mM EDTA, 1X PBS) was added  to microcentrifuge tubes on ice for 15 min and embryos were homogenized every 3 min with a p100 micropipettor for 15 min. 200 μl of STOP solution (30% FBS, 0.8 mM CaCl2, 1X PBS) was then mixed into the tubes. Samples were then spun down at 400g for 5 min at 4°C and supernatant was removed. On ice, 1 ml of chilled suspension media (1% FBS, 0.8 mM CaCl2, 50 U/ml Penicillin, 0.05 mg/ml Streptomycin) was added to samples and then spun down again at 400g for 5 min at 4°C. Supernatant was removed, and 400 μl of chilled suspension media was added and solution was filtered through a 35 μm strainer into a collection tube. Cells were FAC sorted to distinguish EGFP+ cells using a MoFlo XDP100 cell sorter at the CU-SOM Cancer Center Flow Cytometry Shared Resource and collected in 1.7 ml FBS coated microcentrifuge tubes in 200 μl of 1X PBS.
The Chromium Box from 10X Genomics was used to capture cells using Chromium Single Cell 3' Reagent Kit part no. PN-1000075.  Libraries were sequenced on the Illumina NovaSEQ6000 Instrument.

treatment_protocol: No treatment was applied to the samples.

value: 48 hours post fertilization

tag: strain

value: Tg(olig2:EGFP) ZFIN ID:ZDB-ALT-041129-8


title: EdU-seq in GCPs-LT531_shh

status: Public on Jul 20 2020

city: Montreal

first: Frederic

last: Charron

state: Quebec

address: 110 Avenue des Pins Ouest

country: Canada

institute: IRCM

description: EdU-substituted (nascent) DNA

data_processing:
Sequence reads were trimmed for adapter sequences.
The resulting 50bp  reads were trimmed to obtain high quality reads and then mapped to the mm10 mouse genome build using Bowtie2 with the following parameter: -q --fr --no-mixed --no-unal --local
Genome_build: mm10
Supplementary_files_format_and_content: bigwig

source_name: Postnatal day 7 cerebellum

growth_protocol: GCPs were grown in 60mml plates in serum-free Neurobasal media supplemented with B27, Glutamax and Sodium Pyruvate for 24hrs. Cells were incubated  in presence of vehicle (Ctl), Shh or Shh+1µM PHA767491 (Cdc7i). Cdc7i was added 4h before harvesting.

extract_protocol:
After DNA labeling (Biotin-azide), total gDNA was isolated using column purification, sonicated and captured using MyOne Streptavidin C1 beads (ThermoFisher (#65001) according to protocol
Libraries were prepared using the Kappa HyperPrep Kit according to manufacturer instructions, using 12 amplification cycles. Library quality control and sequencing were performed as described for RNAseq. The resulting reads were aligned to the mm10 mouse reference genome using Bowtie v2.3.1
EdU-seq

treatment_protocol: GCPs were pulsed with 100µM EdU (Sigma, Cat No. 900584) for 15min, washed in warm PBS for 3 min, harvested and processed as described (Ref 41). Azide-PEG3-Biotin Conjugate was obtained from Sigma (Cat. No. Sigma  762024). We used 1.5x107 GCPs/condition and two different experiments were performed as replicates. Inputs correspond to biotinylated DNA before the streptavidin capture of EdU-substituted DNA.

value: Primary neural progenitors

tag: passages

tag: cell line

value: GCPs

tag: treatment

value: Shh

value: Streptavidin-capture


title: scRNAseq_olig2_eGFP_36hpf

tag: developmental stage

value: 36 hours post fertilization


title: scRNAseq_olig2_eGFP_24hpf

value: 24 hours post fertilization


title: EdU-seq in GCPs-LT531_shh-cdc7i

description: EdU-substituted (nascent) DNA


title: NC-2_LP_H3K27ac

tag: chip antibody


title: EdU-seq in GCPs-LT530_input

description: EdU-substituted (nascent) DNA

value: Input


title: RNAseq in GCPs Shh experiment 3

data_processing:
Sequence reads were trimmed for adapter sequences.
The resulting 50bp reads were trimmed to obtain high quality reads and then mapped to the GRCm38 mouse genome build using STAR
gene expression raw count was performed with HTSeq-count
Differential gene expression analysis was performed with DESeq2
Genome_build: mm10

growth_protocol: 3x10^6 GCPs/well were grown in 6-well plates in serum-free Neurobasal media supplemented with B27, Glutamax and Sodium Pyruvate for 24hrs

extract_protocol:
Total RNA was extracted using the RNeasy Plus Mini Kit (Qiagen, Cat. No. 74134). 400-450ng total RNA were used for RNAseq
Stranded RNA-Seq (chemical fragmentation, cDNA-dsDNA, library) was performed using the KAPA Stranded RNA-Seq Library Preparation Kit (Illumina Platforms). Library quality control and quantitation were performed using the Agilent High Sensitivity DNA kit on a Bioanalyzer and the NEBNext Library Quant Kit for Illumina. Paired-End 50 reads were sequenced on a HiSeq 2500 with v4 chemistry (Illumina)

treatment_protocol: Murine Igf1 (PreproTech, Cat. No. 250-19) was used at 100ng/ml, and Shh (R&D Systems, Cat. No. 1845-SH) at 10nM.

value: Primary GCPs

value: 10nM Shh

tag: mrna enrichment protocol

value: rRNA-depleted


title: EdU-seq in GCPs-LT530_shh

description: EdU-substituted (nascent) DNA


title: RNAseq in GCPs Igf1 experiment 2

value: 100ng/ml Igf1


title: RNAseq in GCPs Ctrl experiment 3

value: Control


title: RNAseq in GCPs Igf1 experiment 3


title: RNAseq in GCPs Ctrl experiment 2


title: EdU-seq in GCPs-LT531_input

description: EdU-substituted (nascent) DNA


title: MUT-2_SC_H3K4me3

tag: genotype

value: BRCAmut/+

value: Breast stromal cells


title: RNAseq in GCPs Igf1 experiment 1


title: RNAseq in GCPs Shh experiment 1


title: RNAseq in GCPs Ctrl experiment 1


title: Healthy_CD4_replicate_3

status: Public on Jun 01 2020

first: David

last: Oh

address: 513 Parnassus Ave, HSE301, Box 0519

institute: University of California, San Francisco

description: DEPOSITION OF RAW FILES PENDING IRB REVIEW

data_processing:
scRNA-seq reads were aligned to the hg19 genome assembly using 10X Cell Ranger pipeline (version 1.1) with default settings
Data were filtered using the scanpy toolkit (Wolf et. Al. 2018) following specifications: 1. Genes that were detected in less than three cells. 2. Cells with greater than then percent of mitochondrial genes. 3. Cells with fewer than 100 or greater than 1,200 detected genes. 4. Cells that were annotated as red blood cells (HBB) or macrophage (CD14, CD68, CD163)
Gene expression values were log2 plus one transformed and normalizaed to 10,000 counts per cell
scTCR-seq  reads were demultiplexed by matching 10X cell barcodes after first pass filter in the Cell Ranger pipeline
Demultiplexed TCR sequences were aligned and assembled into clonotype families using miXCR.
The most abundant TRA or TRB clonotype in a given cell were kept for further downstream analysis
Unpaired TRA and TRB cells were filtered from further analysis
Genome_build: hg19
Supplementary_files_format_and_content: Processed and filtered gene expression matrix and TCR matrix for downstream analysis.

source_name: Peripheral Blood

extract_protocol:
10X Genomics
Droplet-based single-cell RNA sequencing (dscRNA-seq) was performed using the 10X Genomics Chromium Single Cell 3’ platform, version 1, according to manufacturer’s instructions. RNA libraries were prepared for sequencing using standard Illumina protocols. TCR libraries were generated using consensus primers to amplify the human TCR alpha and beta loci along with droplet- and sample-specific barcodes from the barcoded cDNA generated during 10X RNAseq library preparation.

tag: tissue type

value: PBMC

tag: cell sort

tag: disease

value: healthy


title: Healthy_CD8_replicate_3


title: Healthy_CD8_replicate_2


title: RNAseq in GCPs Shh experiment 2


title: Healthy_CD4_replicate_2


title: Untreated_B_Tumor_CD4

source_name: Bladder Tissue

value: Tumor

value: bladder cancer


title: Untreated_B_Normal_CD8

value: Normal


title: Healthy_CD4_replicate_1


title: Untreated_B_Normal_CD4


title: Untreated_A_Tumor_CD8


title: EdU-seq in GCPs-LT531_ctrl

description: EdU-substituted (nascent) DNA

value: Primary neural progenitors

value: GCPs


title: Untreated_A_Tumor_CD4


title: Healthy_CD8_replicate_1


title: EdU-seq in GCPs-LT530_ctrl

description: EdU-substituted (nascent) DNA

value: Streptavidin-capture


title: Untreated_B_Tumor_CD8


title: Untreated_A_Normal_CD4


title: Chemo_Normal_CD8

value: Chemo


title: Chemo_Tumor_CD8


title: MUT-3_BC_H3K4me3

value: Breast basal cells


title: Chemo_Tumor_CD4


title: Anti-PD-L1_D_Tumor_CD8

value: Atezo


title: Chemo_Normal_CD4


title: Anti-PD-L1_D_Normal_CD4


title: Anti-PD-L1_D_Tumor_CD4


title: Anti-PD-L1_C_Tumor_CD8


title: Anti-PD-L1_B_Tumor_CD8


title: Anti-PD-L1_C_Normal_CD4


title: Anti-PD-L1_C_Tumor_CD4


title: Anti-PD-L1_B_Tumor_CD4


title: Anti-PD-L1_B_Normal_CD4


title: CRPC_01-002N1_LN

city: Seattle

first: Ilsa

last: Coleman

state: WA

address: 1100 Fairview Ave N, E2-112

department: Human Biology

institute: Fred Hutchinson Cancer Center

description:
01-002N1_LN
CRPC lymph node (LN) metastasis
01-002N1_LN

data_processing:
Image analysis and base calling were performed using Illumina's Real Time Analysis v1.18.X software, followed by 'demultiplexing' of indexed reads and generation of FASTQ files, using Illumina's bcl2fastq Conversion Software v1.8.4
Reads were mapped to the hg38 human genome build using TopHat v2.X and bowtie2 v2.2.X.
Mean and standard deviation of fragment size were calculated with picard-tools v2.18.X
Transcript abundance was determined from the TopHat alignments in R using the Genomic Alignments Bioconductor package using the summarizeOverlaps function with mode=IntersectionStrict, counting reads mapping to the exonic regions of genes.
Genome_build: hg38
Supplementary_files_format_and_content: Processed files are tab-delimited text files. Each file contains 7 columns: Entrez Gene ID, gene symbol, gene name, mRNA size, raw fragment count (by gene), FPM (fragments per million reads mapped) and FPKM (fragments per kilobase per million reads mapped).

source_name: CRPC lymph node (LN) metastasis

extract_protocol:
Total RNA was isolated from 138 CRPC metastases frozen in Optimal Cutting Temperature compound (OCT; Tissue-Tek) from 72 patients with RNA STAT-60 (Tel-Test). Using an H&E stained slide for each metastatic site for orientation, one millimeter core punches of tumor were obtained, or where appropriate multiple sections enriched for tumor were cut using a Leica CM3050S cryostat. Total RNA was isolated from cell line samples using the RNeasy Mini Kit (Qiagen, cat#74134) with DNase digestion.
RNA-seq libraries were constructed from 1 ug total RNA using the Illumina TruSeq Stranded mRNA LT Sample Prep Kit according to the manufacturer’s protocol.
Barcoded libraries were pooled and sequenced on the Illumina HiSeq 2500 generating 50-71 bp paired end reads.

tag: gender

value: male

value: prostate cancer

tag: tumor site

value: lymph node (LN)

tag: patient

tag: molecular phenotype


title: Anti-PD-L1_A_Tumor_CD4

city: San Francisco


title: musAd002_UrF

status: Public on May 19 2020

city: Dallas

first: Gervaise

middle: H.

last: Henry

state: Texas

address: 5323 Harry Hines Blvd, Mail Code:9110

department: Urology

institute: UT Southwestern Medical Center

description:
Bam files are a combination of sequence data from the Illumina NextSeq 500 and Illumina NovaSeq 6000
Cells from one normal mouse urethral tissue

data_processing:
Illumina's RTA version 1.18.66.3 was used for basecalling
10x Genomics’ cellranger mkfastq version 3.1.0 was used to demultiplex fastqs using default settings
10x Genomics’ cellranger count version 3.1.0 was used to generate mapped bam files using default settings combining fastq's from NextSeq 500 and NovaSeq 6000
Genome_build: mm10
Supplementary_files_format_and_content: Genes-by-cells matrix in Hierarchical Data Format 5 File (H5)

source_name: Viable mouse urethra

extract_protocol:
Single-cell suspensions containing ~17400 cells were loaded on 10x Genomics Chromium single-cell Controller with 3’ library and gel bead kit v2 and v3  according to manufacture’s recommendations
According to 10x Genomics’ protocol, sequenced (R1=26cycles R2=58cycles, i7=8cycles on NextSeq 500) OR (PE150 on NovaSeq 6000)

treatment_protocol: Single-cells were dissociated from health adult mouse urethra

tag: digestion enzyme

value: 10mg/mL Cold Protease 1hr

tag: number of mice pooled

tag: macs strategy


title: musAd004n5_UrF

description:
Bam files are a combination of sequence data from the Illumina NextSeq 500 and Illumina NovaSeq 6000
Cells from two mouse urethral tissue


title: musAd003_PrF_St

description:
Bam files are a combination of sequence data from the Illumina NextSeq 500 and Illumina NovaSeq 6000
Cells from normal mouse prostate tissue anterior, ventral, and dosi-lateral prostate

data_processing:
Illumina's RTA version 1.18.66.3 was used for basecalling
10x Genomics’ cellranger mkfastq version 3.1.0 was used to demultiplex fastqs using default settings
10x Genomics’ cellranger count version 3.1.0 was used to generate mapped bam files using default settingscombining fastq's from NextSeq 500 and NovaSeq 6000
Genome_build: mm10
Supplementary_files_format_and_content: Genes-by-cells matrix in Hierarchical Data Format 5 File (H5)

source_name: Viable mouse prostate

treatment_protocol: Single-cells were dissociated from health adult mouse prostates

tag: prostatic lobe

value: AP + VP + DLP


title: musAd002_PrF


title: musAd007_PrFcol_GEX

value: 1.5mg/mL Collagenase I 1hr


title: D17PrTzF_Via 2

status: Public on Apr 28 2020

description:
Samples were sequenced on the Illumina NextSeq 500 and the Illumina NovaSeq 6000
Viable cells from normal human prostate tissue transition zone including prostatic urethra

data_processing:
Illumina's RTA version 1.18.66.3 was used for basecalling
10x Genomics’ cellranger mkfastq version 3.1.0 was used to demultiplex fastqs using default settings
10x Genomics’ cellranger count version 3.1.0 was used to generate mapped bam files using default settings combining fastq's from NextSeq 500 and NovaSeq 6000
Genome_build: GRCh38
Supplementary_files_format_and_content: Genes-by-cells matrix in Hierarchical Data Format 5 File (H5)

source_name: Viable human prostate transition zone

extract_protocol:
Single-cell suspensions containing ~17400 cells were loaded on 10x Genomics Chromium single-cell Controller with 3’ library and gel bead kit v2 according to manufacture’s recommendations
According to 10x Genomics’ protocol, sequenced (R1=26cycles R2=58cycles, i7=8cycles on NextSeq 500) OR (PE150 on NovaSeq 6000)

treatment_protocol: Populations of single-cells dissociated from health prostates from organ donors were isolated by FACS

tag: patient phenotype

value: Donor (Normal)

tag: prostatic zone

value: Transition Zone + Urethra

value: 5mg/mL Collagenase I 4hr

tag: facs ab profile

value: Via-


title: D35PrTzF_Via 2


title: BPH340PrGF_Via

description:
Samples were sequenced on the Illumina NextSeq 500 and the Illumina NovaSeq 6000
Viable cells from normal human prostate tissue transition zone

treatment_protocol: Populations of single-cells dissociated from diseased prostates from BPH patients were isolated by FACS

value: BPH Glandular Nodule

value: Transition Zone


title: D27PrPzF_Via 2

description:
Samples were sequenced on the Illumina NextSeq 500 and the Illumina NovaSeq 6000
Viable cells from normal human prostate tissue peripheral zone

source_name: Viable human prostate peripheral zone

value: Peripheral Zone


title: BPH327PrGF_Via


title: D27PrTzF_Via 2


title: Anti-PD-L1_A_Tumor_CD8

value: Tumor

tag: treatment

value: bladder cancer


title: D17PrPzF_Via 2


title: cSCC_03

status: Public on Apr 22 2020

city: Salzburg

first: Roland

last: Zauner

state: Salzburg

address: Muellner Hauptstrasse 48

department: University Hospital of Dermatology  Salzburger Landeskliniken (SALK) | Paracelsus Medical University Salzburg (PMU)

country: Austria

institute: EB House Austria

hyb_protocol: Affymetrix  miRNA 4.1 array plates were washed, stained and scanned according to the protocol described in GeneTitan®Instrument User Guide for Expression Arrays Plates (P/N 702933)

scan_protocol: Scanning was done on an Affymetrix GeneTitan (Single Channel ), software AGCC 3.2.4.1515W

data_processing: Raw data from .CEL files was RMA background corrected, normalized and summarized (Bioconductor oligo package v1.46.0) in statistical software R (v3.5.1). Probesets were filtered for sequence.type==miRNA and Species.Scientific.Name==Homo sapiens. Only probesets with log2 signals > 2.5 in more than 3 samples were further used in downstream analysis. Latent sources of noise and batch effects were corrected by surrogate variable analysis (Bioconductor sva package v3.30.1).

label: Biotin

source_name: cutaneous (non-EB) squamous cell carcinom; primary cultured cells derived from tumor resections

label_protocol: 500ng of total RNA were labeled using the FlashTag™ Biotin HSR RNA Labeling Kit (Catalog Number  901911, Affymetrix, Santa Clara, CA)

growth_protocol: Primary cells were cultured to subconfluency in defined, serum-free CnT-Prime Epithelial Culture Medium (CELLnTEC) at 37°C / 5% CO2 in a humidified incubator.

extract_protocol: For total RNA isolation from cell cultures, we used miRNeasy Mini Kit (Qiagen, 217004), according to manufacturer’s protocol. RNA quality was assessed by Bioanalyzer.

treatment_protocol: no treatment

tag: group

value: cutanous (non-EB) SCC


title: cSCC_01


title: cSCC_02


title: RDEB-SCC_03

source_name: recessive dystrophic epidermolysis bullosa squamous cell carcinoma; primary cultured cells derived from tumor resections

value: RDEB-SCC


title: RDEB-SCC_02

hyb_protocol: Affymetrix human Clariom D arrays were washed, stained and scanned according to the protocol described in GeneChip® WT PLUS Reagent User Manual (Fluidics Protocol FS450_0001)

scan_protocol: Scanning was done on an Affymetrix GeneChip Scanner 3000 7G, software AGCC 3.1.1

data_processing: Raw data from .CEL files was RMA background corrected, normalized and summarized (Bioconductor oligo package v1.46.0) in statistical software R (v3.5.1). Dataset was filtered for category==main and (locus.type==Multiple_Complex or Coding) and ressource==RefSeq to focus on mRNA. Further, genes listed as LINC or MIR or SNORD were discarded.

label_protocol: 100ng of total RNA were amplified and labeled using the GeneChip® WT PLUS Reagent Kit (Catalog Number 902281, Affymetrix, Santa Clara, CA)

extract_protocol: For total RNA isolation from cell cultures, we used miRNeasy Mini Kit (Qiagen, 217004), according to manufacturer’s protocol. miRNeasy kit was used to extract miRNAs from same sample. RNA quality was assessed by Bioanalyzer.

tag: cell type


title: RDEB-SCC_03


title: DDEB-KC_02

source_name: dominant dystrophic epidermolysis bullosa keratinocytes; primary cultured cells derived from skin biopsies

value: DDEB keratinocytes


title: RDEB-SCC_01


title: RDEB-SCC_02


title: RDEB-KC_05

source_name: recessive dystrophic epidermolysis bullosa keratinocytes; primary cultured cells derived from skin biopsies

value: RDEB keratinocytes


title: RDEB-SCC_04


title: RDEB-SCC_01


title: RDEB-KC_03


title: musAd001_PrF


title: RDEB-KC_02


title: RDEB-KC_01


title: RDEB-KC_04


title: RDEB-KC_01


title: HC-KC_05

source_name: healty control keratinocytes; primary cultured cells derived from skin biopsies

value: healthy control keratinocytes


title: RDEB-KC_03


title: RDEB-KC_05


title: RDEB-KC_06


title: RDEB-KC_04


title: DDEB-KC_01


title: D35PrPzF_Via 2


title: RDEB-KC_02


title: RDEB-KC_06


title: RDEB-SCC_04


title: HC-KC_04


title: HC-KC_03


title: HC-KC_01


title: HC-KC_02