title: KD553-2

city: Qingdao

first: Yong

last: Zhao

state: Shandong

address: 700 Changcheng Road

department: College of Life Sciences

institute: Qingdao Agricultural University

description: The group information is prefixed with  KD553_1 in the column of processed data file

data_processing:
The 50nt sequence tags from HiSeq sequencing went through the data cleaning first,
which included getting rid of the low quality tags and several kinds of contaminants from the
50nt tags. Length distribution of clean tags was then summarized. Afterwards, the standard
bioinformatics analysis was used to annotate the clean tags into different categories and to take
those which cannot be annotated to any category to predict the novel miRNA and base edit of potential known miRNA
Genome_build: ARS1

organism: Capra aegagrus

extract_protocol:
goat mamamary gland cells were isolated for small RNA. Then small RNA samples were sequenced.
small RNA was used for the library.

tag: breed

value: Lanshan dairy goat

value: mammary gland

tag: molecule subtype

value: small RNA


status: Public on Aug 13 2020

type: SRA

city: Pozzuoli

first: Rossella

last: De Cegli

address: Via Campi Flegrei 34

country: Italy

institute: Tigem

description: Transcriptome profile of a PiZ/Chop-/- mouse livers at 36 weeks of age, biological rep5

library_source: transcriptomic

data_processing:
Sequence reads were trimmed using bbduk software(https://jgi.doe.gov/data-and-tools/bbtools/bb-tools-user-guide/usage-guide/) (bbmap suite 37.31) to remove adapter sequences, poly-A tails and low-quality end bases (regions with average quality below 6).
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include raw counts for each Sample

molecule: total RNA

organism: Mus musculus

source_name: PiZ mouse model deleted for Chop, 36-week old mouse liver

extract_protocol:
RNA was quantified and mixed at 10ng/µl
Total RNA (100 ng) from each sample was prepared using QuantSeq 3'mRNA-Seq Library prep kit  (Lexogen, Vienna, Austria) according to manufacturer's instructions
Libraries were sequenced on a NovaSeq 6000 sequencing system using an S1, 100 cycles flow cell (Illumina Inc.).
Amplified fragmented cDNA of 300 bp in size were sequenced in single-end mode with a read length of 100 bp.

treatment_protocol: Animal procedures were performed in accordance to regulations of the Italian Ministry of Health. All the mice were maintained on a C57/BL6 background.

tag: strain

tag: gender

value: MALE

tag: genotype

value: PiZ mouse model deleted for Chop

tag: age

value: 36-week old

tag: tissue

value: liver


description: Transcriptome profile of a PiZ/Chop-/- mouse livers at 36 weeks of age, biological rep3


title: bulkRNAseq_DamV133A_LMNB1_rep2

city: Berkeley

first: Nicolas

last: Altemose

state: CA

address: 327 Stanley Hall

department: Bioengineering

country: USA

institute: University of California, Berkeley

description:
16
HEK_DamLam_RNA_2
RNAseq_Counts_GeneBySample.csv

data_processing:
Library strategy: DamID
Bulk and single-cell DamID reads were demultiplexed using Illumina’s BaseSpace platform to obtain fastq files for each sample.
DamID and Illumina adapter sequences were trimmed off using trimmomatic (v0.39; Bolger et al. 2014; ILLUMINACLIP:adapters-PE.fa:2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:20, where adapters-PE.fa is:\n>PrefixPE/1\nTACACTCTTTCCCTACACGACGCTCTTCCGATCT\n>PrefixPE/2\nGTGACTGGAGTTCAGACGTGTGCTCTTCCGATCT\n>Dam\nGGTCGCGGCCGAGGA\n>Dam_rc\nTCCTCGGCCGCGACC).
Trimmed reads were aligned to a custom reference (hg38 reference sequence plus the Dam-LMNB1 and m6A-Tracer plasmid sequences) using BWA-MEM (v0.7.15-r1140, Li 2013). Alignments with mapping quality 0 were discarded using samtools (v1.9, Li et al. 2009).
The hg38 reference sequence was split into simulated DpnI digestion fragments by reporting all intervals between GATC sites (excluding the GATC sites themselves), yielding 7180359 possible DpnI fragments across the 24 chromosome assemblies. The number of reads overlapping each fragment was counted using bedtools (v2.28; Quinlan et al. 2010). For single-cell data, the number of DpnI fragments with non-zero coverage was reported within each non-overlapping bin in the genome (28163 total 100 kb bins, after excluding unmappable regions with zero coverage in any cell).
For bulk data, the number of read pairs overlapping each 100 kb bin was reported. For bulk data, Dam-LMNB1 vs DamOnly enrichment was computed using Deseq2 in each 100 kb bin (Love et al. 2014). For single-cell data, the expected background coverage in each bin was computed as n(m/t), where n is the number of unique fragments sequenced from that cell, m is the number of bulk Dam-only read pairs mapping to that bin, and t is the total number of mapped bulk Dam-only read pairs. Single-cell normalization was computed either as a ratio of observed to expected coverage (for browser visualization and comparison to bulk data), or as their difference (for classification and coverage distribution plotting).
For bulk RNA-seq data, adapters were trimmed using trimmomatic (v0.39; Bolger et al. 2014; ILLUMINACLIP:adapters-PE.fa:2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:36, where adapters-PE.fa is:\n>PrefixPE/1\nTACACTCTTTCCCTACACGACGCTCTTCCGATCT\n>PrefixPE/2\nGTGACTGGAGTTCAGACGTGTGCTCTTCCGATCT). Transcript quantification was performed using Salmon (Patro et al. 2017) with the GRCh38 transcript reference. Differential expression analysis was performed using the voom function in limma (Ritchie et al. 2015). Differential expression was called based on logFC significantly greater than 1 and adjusted p-value < 0.01.
Genome_build: hg38 (GRCh38)
Supplementary_files_format_and_content: hg38_100kb_UniqueFragmentCounts.tsv
Supplementary_files_format_and_content: DamMutantComparison_Counts.tsv
Supplementary_files_format_and_content: RNAseq_Counts_GeneBySample.csv

molecule: polyA RNA

organism: Homo sapiens

source_name: HEK293T cells

growth_protocol: HEK293T cells (CRL-3216, ATCC, Manassas, VA; validated by microsatellite typing & mycoplasma tested, at passage number <10) were cultured in DMEM plus 10%FBS and 1X Penicillin-Streptomycin at 37C with 5% CO2.

extract_protocol:
Cells were processed within nanoliter reaction chambers on a custom PDMS microfluidic device, following the reagents and incubation times of the in-tube single-cell DamID protocol (Kind et al. 2015) with minor modifications (addition of 0.2% Tween-20 to prevent enzyme adhesion). Amplified DNA from each individual cell was flushed out of the device and transferred to 0.2 ml tubes, where library preparation took place.
Single-cell sequencing libraries were prepared from the DamID amplified DNA using an NEBnext UltraII DNA Library Prep Kit for Illumina (samples 001-018) or an NEBnext UltraII FS Kit (samples A01-D10).

treatment_protocol: Human HEK293T cells were transiently transfected with Dam-LMNB1 plus m6A-Tracer using FuGene HD, induced using 1 mM Shield-1 ligand for 20 hours prior to harvesting as a single-cell suspension.

tag: cell line

tag: transfection


title: bulkRNAseq_DamV133A_LMNB1_rep1

description:
15
HEK_DamLam_RNA_1
RNAseq_Counts_GeneBySample.csv


title: Lv3NC-2

country: China

description: The group information is prefixed with  Lv3NC_2 in the column of processed data file

tag: treatment


description: Transcriptome profile of a PiZ/Chop-/- mouse livers at 36 weeks of age, biological rep2


title: bulkRNAseq_DamV133A_rep2

description:
14
HEK_Dam_RNA_2
RNAseq_Counts_GeneBySample.csv


title: scDamID_batch2_D10

description:
74
D10
hg38_100kb_UniqueFragmentCounts.tsv

library_source: genomic

molecule: genomic DNA


title: scDamID_batch2_D09

description:
73
D09
hg38_100kb_UniqueFragmentCounts.tsv


title: bulkRNAseq_DamV133A_rep1

description:
13
HEK_Dam_RNA_1
RNAseq_Counts_GeneBySample.csv


title: Lv3NC-1

description: The group information is prefixed with  Lv3NC_1 in the column of processed data file


description: Transcriptome profile of a PiZ/Chop-/- mouse livers at 36 weeks of age, biological rep1


title: OV55666-2

description: The group information is prefixed with OV55666_2 in the column of processed data file


title: scDamID_batch2_D08

description:
72
D08
hg38_100kb_UniqueFragmentCounts.tsv


title: bulkRNAseq_m6ATracer_rep2

description:
18
HEK_mTracer_RNA_2
RNAseq_Counts_GeneBySample.csv


title: bulkDamID_DamV133A_LMNB1_rep2

description:
4
HEK_DamLam_DNA_frag_2
hg38_100kb_UniqueFragmentCounts.tsv


description: Transcriptome profile of a PiZ mouse livers at 36 weeks of age, biological rep5

source_name: PiZ mouse model, 36-week old mouse liver

value: PiZ mouse model


title: scDamID_batch2_D07

description:
71
D07
hg38_100kb_UniqueFragmentCounts.tsv


title: bulkDamID_DamV133A_LMNB1_rep1

description:
3
HEK_DamLam_DNA_frag_1
hg38_100kb_UniqueFragmentCounts.tsv


title: Csm 128 Rep-1

city: Warsaw

first: Cecilia

middle: Lanny

last: Winata

state: Mazovia

address: 4 Ks. Trojdena

country: Poland

institute: International Institute of Molecular and Cell Biology in Warsaw

description:
PolyA RNA
Replicate 1

data_processing:
Base-calling was performed by Illumina RTA 1.18.61. Files were translated into demultiplexed FASTQ files by Illumina bcl2fastq2 2.16.10.
The first 12 nucleotides of read 1, containing the UMI sequence, were extracted and added to the sequence identifier using UMI-tools v. 1.0.0.
Low-quality sequences and adapter content were trimmed with cutadapt v. 2.4.
Reads were aligned to the GRCz11 reference genome supplemented with the EGFP sequence with STAR v. 2.7.2b using the following custom parameters: --outFilterType BySJout --outFilterMultimapNmax 20 --alignSJoverhangMin 8 --alignSJDBoverhangMin 1 --outFilterMismatchNmax 999 --alignIntronMin 20 --alignIntronMax 1000000 --alignMatesGapMax 1000000 --outFilterMismatchNoverLmax 0.6.
Alignments were de-duplicated based on their Unique Molecular Identifier sequence using UMI-tools v. 1.0.0.
De-duplicated alignments were counted per exon on the gene-level with the htseq-count script from the HTSeq v. 0.11.2 package using Ensembl GRCz11 version 97 genome annotation.
Further analysis was performed in R v. 3.6.1 programming language. Differential expression was analyzed using DESeq2 v. 1.24.0 package.
Genome_build: GRCz11
Supplementary_files_format_and_content: HTSeq counts.tsv files were generated with htseq-count script, they contain counts for each gene for each sample in tab-delimited format; normalized_counts files were generated with DESeq2, they contain library-size normalized read counts for each gene for every sample from each time point in tab-delimited format; egfp.fa file contains the EGFP sequence in FASTA format; egfp.gtf file contains the custom EGFP annotation in GTF format; egfp_crrna.fa file contains the crRNA sequence against the EGFP transcript used in the experiment in FASTA format.

organism: Danio rerio

source_name: whole zebrafish embryo

growth_protocol: Zebrafish embryos were maintained according to standard protocol (Westerfield et al., 2000) and staged according to standard morphological criteria (Kimmel et al., 1995).

extract_protocol:
25 embryos each (for both StCsm and mock injected) were pooled at 128 cell stage, 5 hpf and 24 hpf from 3 biological replicates. Total RNA was extracted from the whole embryos with Tri Reagent Solution (Invitrogen) according to the manufacturer’s protocol. RNA was further purified using Zymo RNA Clean and Concentrator-5 kit according to manufacturer's protocol.
1.5 ug of total RNA was subjected to Lexogen poly(A) RNA Selection kit according to company recommendations. Enriched RNA has been used for sequencing library construction with CORALL Total RNA-Seq Library Prep Kit according to the Lexogen manufacturer’s protocol.

treatment_protocol: Zebrafish embryos from three different mating pairs of Tg(ddx4:ddx4-EGFP) females with casper males were pooled during collection. D16A-StCsm(EGFP) was diluted with water for injection (1:1 v/v) up to a concentration of 0.7mg/ml. For mock injection, Tris storage buffer (10mM Tris-HCl pH8.5, 300mM Nacl, 1mM DTT, 0.1mM EDTA, 50% glycerol) was also diluted in the similar manner. 1nl of either StCsm (EGFP) solution (0.7ng) or buffer alone were injected into the yolk of embryos at the 1-cell stage. In total, three independent injections were performed. 25 embryos (for both StCsm and mock injected) per replica set per time point were frozen in liquid nitrogen, stored at -80℃, and processed together.

value: ABTL Tg(ddx4:ddx4-EGFP)

value: whole embryo

tag: condition

value: Csm complex targeted against the EGFP transcript

tag: developmental stage

value: 128 cells


title: scDamID_batch2_D04

description:
69
D04
hg38_100kb_UniqueFragmentCounts.tsv


title: bulkDamID_DamV133A_rep2

description:
2
HEK_Dam_DNA_frag_2
hg38_100kb_UniqueFragmentCounts.tsv


title: bulkDamID_DamV133A_rep1

description:
1
HEK_Dam_DNA_frag_1
hg38_100kb_UniqueFragmentCounts.tsv


description: Transcriptome profile of a PiZ mouse livers at 36 weeks of age, biological rep4


title: KD553-1

description: The group information is prefixed with  KD553_3 in the column of processed data file


title: scDamID_batch2_D03

description:
68
D03
hg38_100kb_UniqueFragmentCounts.tsv


description: Transcriptome profile of a PiZ mouse livers at 36 weeks of age, biological rep3


description: Transcriptome profile of a PiZ mouse livers at 36 weeks of age, biological rep1


title: Blank-2

description: The group information is prefixed with Blank_2 in the column of processed data file

value: Blank


title: scDamID_batch2_D02

description:
67
D02
hg38_100kb_UniqueFragmentCounts.tsv


description: Transcriptome profile of a PiZ mouse livers at 36 weeks of age, biological rep2


title: Blank-1

description: The group information is prefixed with Blank_1 in the column of processed data file


title: scDamID_batch2_D01

description:
66
D01
hg38_100kb_UniqueFragmentCounts.tsv


title: EGF_2: Human epidermal stem cells-EGF-2

city: Beijing

first: Sun

last: Jiachen

address: 51 Fucheng Road, Haidian District

department: Burns

institute: The Fourth Medical Center of PLA General Hospital

data_processing:
Sample quality inspection using Nanodrop 2000 and Agilent 2100
Library construction, detection and sequencing using Qubit 2.0, Agilent 2100 and Illumina HiSeqTM/MiseqTM
Sequencing data quality control and gene structure analysis using STAR 2.6.1a, StringTie 1.3.3b, rMATS 0.9.7
FPKM is used for statistical analysis of expression levels
Genome_build: GRCh38

source_name: Human epidermal stem cells

growth_protocol: Epidermal stem cells extracted from the foreskin of healthy adult men were planted in collagen-coated T75 culture flasks. Epilife medium and HKGS are used for cell culture.

extract_protocol:
Trizol was used to extract total RNA, following the manufacturer's instructions.
Libraries were prepared according to Illumina's instructions. Briefly, after the sample is qualified, use magnetic beads with Oligo (dT) to enrich eukaryotic cell mRNA. After the enrichment is complete, add fragmentation buffer to break the mRNA into short fragments. Subsequently, six-base random primers (random hexamers) were used to reverse transcription to synthesize double-stranded cDNA using mRNA as a template. Then use AMPure XP beads to purify double-stranded cDNA. Perform end repair on the purified double-stranded cDNA, add an A tail, and connect a sequencing adapter. The double-stranded cDNA fragment size is selected by AMPure XP beads, and finally the selected double-stranded cDNA is PCR enriched to construct a cDNA library.

treatment_protocol: EGF-treated group was incubated with 20 ng/ml EGF for 24 h.

tag: cell type

value: Skin-derived epidermal stem cells

value: male

value: EGF treated for 24 h


title: EGF_3: Human epidermal stem cells-EGF-3


title: Germination of ago4-3 in NaCl, rep2

city: Coyoacan

first: V Miguel

last: Palomar

state: Mexico City

address: Circuito Exterior SN

department: Biochemistry

country: Mexico

institute: School of Chemistry, UNAM

description: Bisulfite treated DNA

data_processing:
Reads were adapter trimmed using TrimGalore v 0.4.1
Reads were aligned to TAIR10 genome using Bismark v. 0.16.1, no mismateches were allowed
Reads mapped to one position were kept and regions with at least 10 reads were taken for downstream analyses
Methylation and DMR identification was done using methylKit R package
Genome_build: TAIR 10
Supplementary_files_format_and_content: processed files are formatted for methylKit input in .txt.gz

organism: Arabidopsis thaliana

source_name: Germinating seeds

growth_protocol: Seeds were sown in MS media and germinated under 16/8 light/dark photoperiod at 21ºC and 100uE of light intensity

extract_protocol:
DNA was extracted using the DNEasy Plant DNA isolation kit (#69106)
Librariues were generated using the Zymo pico methylKit

treatment_protocol: MS 1X was used as control medium while for salinity we added 100 mM of NaCl to MS

value: Germinating seeds

value: Salinity

value: AGO4 null mutant


title: EGF_1: Human epidermal stem cells-EGF-1


title: scDamID_batch2_C09

description:
65
C09
hg38_100kb_UniqueFragmentCounts.tsv


description: Transcriptome profile of a wild type mouse at 36 weeks of age, biological rep2

source_name: Wild-type mouse control, 36-week old mouse liver

value: Wild-type


description: Transcriptome profile of a wild type mouse at 36 weeks of age, biological rep3

value: MALE


title: scDamID_batch2_D06

description:
70
D06
hg38_100kb_UniqueFragmentCounts.tsv


title: OV55666-1

description: The group information is prefixed with OV55666_1 in the column of processed data file

value: Lanshan dairy goat

value: mammary gland

value: small RNA


title: Lv5NC-2

description: The group information is prefixed with  Lv5NC_2 in the column of processed data file


title: scDamID_batch2_C08

description:
64
C08
hg38_100kb_UniqueFragmentCounts.tsv


description: Transcriptome profile of a wild type mouse at 36 weeks of age, biological rep1

value: 36-week old

value: liver


title: Germination of ago4-3 in NaCl, rep1

description: Bisulfite treated DNA


title: scDamID_batch2_C07

description:
63
C07
hg38_100kb_UniqueFragmentCounts.tsv


title: Germination of ago4-3 in MS, rep2

description: Bisulfite treated DNA

value: Control


title: Control_2: Human epidermal stem cells-control-2

value: untreated


title: Lv5NC-1

description: The group information is prefixed with Lv5NC_1 in the column of processed data file


description: Transcriptome profile of a PiZ/Chop-/- mouse livers at 6 weeks of age, biological rep5

source_name: PiZ mouse model deleted for Chop, 6-week old mouse liver

value: PiZ mouse model deleted for Chop

value: 6-week old


title: scDamID_batch2_C06

description:
62
C06
hg38_100kb_UniqueFragmentCounts.tsv


title: Germination of ago4-2 in NaCl, rep2

description: Bisulfite treated DNA

value: AGO4 point mutant


title: Control_1: Human epidermal stem cells-control-1

value: Skin-derived epidermal stem cells

value: male


title: Germination of ago4-3 in MS, rep1

description: Bisulfite treated DNA

value: Germinating seeds


description: Transcriptome profile of a wild type mouse at 36 weeks of age, biological rep4


title: scDamID_batch2_C05

description:
61
C05
hg38_100kb_UniqueFragmentCounts.tsv


description: Transcriptome profile of a PiZ/Chop-/- mouse livers at 6 weeks of age, biological rep4


title: Control_3: Human epidermal stem cells-control-3


description: Transcriptome profile of a PiZ/Chop-/- mouse livers at 6 weeks of age, biological rep2


title: scDamID_batch2_C03

description:
59
C03
hg38_100kb_UniqueFragmentCounts.tsv


title: Germination of ago4-2 in MS, rep2

description: Bisulfite treated DNA


title: Patient 02 Normal

city: Los Angeles

first: Linh

middle: My

last: Tran

state: California

department: Medicine - Pulmonary & Critical Care

institute: University of Los Angeles

description: 10X Chromium Single Cell 3' Reagent Kits v3

data_processing:
Fastq files were processed with cellranger (v3.0.2) count pipeline to create feature-barcode matrices for individual samples
The R Seurat package (v.3.0) was used to aggregate non-empty filtered matrices from cellranger outputs.  Poor quality cells were filtered out if (1) their percentage of mitochondrial gene > 15% total UMI counts and (2) number of detected genes < 500
Data of the qualified cells was normalized with LogNormalize (Seurat)
Batched adjusted was done by Seurat recommended Standard Intergration Workflow for 2000 high variance genes among samples
Genome_build: GRCh38
Supplementary_files_format_and_content: batched adjusted data of all samples

source_name: lung distal normal tissue from patient 02

extract_protocol:
Resected tissues were placed on ice in RPMI medium immediately after resection and delivered to the lab for tissue dissociation. Dissociation was performed in RPMI medium supplemented with 10% FBS. Briefly, tissues were sliced to approximately 1 mm3 pieces and dissociated in 1 mg/ml collagenase (Sigma Aldrich, #C9407) and 1000 U/ml DNAse I (Sigma Aldrich, #D4263-1VL) at 37°C for approximately 1 hour until homogeneity followed by passing through a 40 µm strainer to remove cell aggregates and red blood cell lysis with 1 ml of ACK buffer (Sigma Aldrich, #11814389001). Cells were resuspended in 5 ml DPBS + 0.04% BSA, counted and immediately used to prepare the sequencing libraries.
The single-cell capturing and downstream library constructions were performed using the Chromium Single Cell 3’ library preparation kit according to the manufacturer’s protocol (10x Genomics). The libraries were sequenced by Illumina NovaSeq 6000

tag: subject status

value: patient diagnosed with lung adenocarcinoma (LUAD) carrying KRAS mutations

tag: subject id

value: Patient 02

value: female

tag: tumor stage

value: normal

tag: driver mutation

value: lung

tag: tissue subtype

value: lung distal normal tissue


description: Transcriptome profile of a PiZ/Chop-/- mouse livers at 6 weeks of age, biological rep3

value: MALE


title: Germination of ago4-2 in MS, rep1

description: Bisulfite treated DNA


description: Transcriptome profile of a PiZ mouse livers at 6 weeks of age, biological rep5

source_name: PiZ mouse model, 6-week old mouse liver

value: PiZ mouse model


description: Transcriptome profile of a PiZ/Chop-/- mouse livers at 6 weeks of age, biological rep1

value: liver


title: Germination of ago4-2 in NaCl, rep1

description: Bisulfite treated DNA

value: Salinity


description: Transcriptome profile of a PiZ mouse livers at 6 weeks of age, biological rep4


title: scDamID_batch2_C02

description:
58
C02
hg38_100kb_UniqueFragmentCounts.tsv


title: scDamID_batch2_B10

description:
57
B10
hg38_100kb_UniqueFragmentCounts.tsv


title: Patient 01 Normal

description: 10X Chromium Single Cell 3' Reagent Kits v2

source_name: lung distal normal tissue from patient 01

value: Patient 01


title: scDamID_batch2_B09

description:
56
B09
hg38_100kb_UniqueFragmentCounts.tsv


title: scRNA-seq of Homo sapiens: adult male FNA from lymph node d60 [d60_FNA_2]

city: New Haven

first: Steven

last: Kleinstein

state: Ct

address: 300 George St.

department: Pathology

institute: Yale University

data_processing:
Single cell feature counts for a single library were generated using `cellranger count` from Cell Ranger v3.1.0
Single cell feature counts for multiple libraries were pooled by subsampling to the same effective sequencing depth using `cellranger aggr` from Cell Ranger v3.1.0
Genome_build: GRCh38
Supplementary_files_format_and_content:
matrix.mtx.gz contains a gene expression count matrix stored in the Market Exchange Format for sparse matrices
features.tsv.gz contains feature information that correspond to row indices of matrix.mtx.gz
barcodes.tsv.gz contains cellular barcodes that correspond to column indices of matrix.mtx.gz. The trailing dash and number (e.g. -12) indicates the sample from which the cell originated and corresponds the row number for that sample in aggregation.csv.
aggregation.csv contains the sample information. The order of the samples represented as rows in aggregation.cs corresponds to the numbers after the dash (e.g. -12) in barcodes.tsv.gz.

source_name: Lymph node

extract_protocol:
PBMCs were isolated from blood. Fine-needle aspiration was performed on axillary lymph nodes.
Libraries were prepared using 10x Genomics' Chromium Next GEM single cell 5' gene expression workflow

value: Lymph node

tag: time point

tag: isolate


title: Patient 02  Adeno

source_name: lung adenocarcinoma lesion from patient 02

tag: gender

value: stage 1A

value: KRAS G12V

value: lung adenocarcinoma lesion


title: scRNA-seq of Homo sapiens: adult male FNA from lymph node d28 [d28_FNA_3]

value: male


title: Germination of Col-0 in NaCl, rep1

description: Bisulfite treated DNA

value: Germinating seeds

tag: genotype

value: Wild type


title: scRNA-seq of Homo sapiens: adult male FNA from lymph node d28 [d28_FNA_2]


description: Transcriptome profile of a PiZ mouse livers at 6 weeks of age, biological rep2

tag: strain

tag: age

value: 6-week old


title: scDamID_batch2_B08

description:
55
B08
hg38_100kb_UniqueFragmentCounts.tsv

tag: cell line


description: Transcriptome profile of a PiZ mouse livers at 6 weeks of age, biological rep3

tag: tissue


title: Germination of Col-0 in MS, rep2

description: Bisulfite treated DNA

tag: treatment

value: Control


title: Germination of Col-0 in MS, rep1

description: Bisulfite treated DNA


title: scDamID_batch2_C04

description:
60
C04
hg38_100kb_UniqueFragmentCounts.tsv

tag: transfection


title: scRNA-seq of Homo sapiens: adult male PBMC enriched for IgD low B cells d12 [d12_memory_B_PBMC]

source_name: PBMC

value: PBMC


title: scDamID_batch2_B07

description:
54
B07
hg38_100kb_UniqueFragmentCounts.tsv


title: Patient 01  Adeno

source_name: lung adenocarcinoma lesion from patient 01

value: patient diagnosed with lung adenocarcinoma (LUAD) carrying KRAS mutations

value: female

value: KRAS G12F

value: lung


title: Germination of Col-0 in NaCl, rep2

description: Bisulfite treated DNA

tag: developmental stage


title: scDamID_batch2_B06

description:
53
B06
hg38_100kb_UniqueFragmentCounts.tsv


description: Transcriptome profile of a wild type mouse at 6 weeks of age, biological rep5

source_name: Wild-type mouse control, 6-week old mouse liver

value: MALE

value: Wild-type

value: liver


title: scRNA-seq of Homo sapiens: adult male FNA from lymph node d12 [d12_FNA_3]

value: Lymph node


description: Transcriptome profile of a PiZ mouse livers at 6 weeks of age, biological rep1

value: PiZ mouse model


title: scDamID_batch2_B05

description:
52
B05
hg38_100kb_UniqueFragmentCounts.tsv


title: scRNA-seq of Homo sapiens: adult male whole PBMC d28 [d28_PBMC_2]


description: Transcriptome profile of a wild type mouse at 6 weeks of age, biological rep4


title: 93h_bact-2

city: Ithaca

first: Olga

last: Lastovetsky

state: NY

address: 334 Plant Science Building, 236 Tower Rd, Cornell University

institute: Cornell University

description:
processed data file: phys_contact_bacterial.count
processed data file: phys_contact_bacterial_to_atcc11559.edgeR.DE_results

data_processing:
Reads were quality controlled using FASTQ and trimmed with Trimmomatic to eliminate low quality reads and Illumina adapters
reads were aligned to the fungal genomes of R. microsporus ATCC 52813 (GenBank accession JOSV00000000) and R. microsporus ATCC 11559 (GenBank MCOJ00000000) using TopHat with following parameters tophat -p 11 -o outputdirectory -G genome.gff3 --transcriptome-index xxx --no-novel-juncs genomefile xxx_R1_paired.fq xxx_R2_paired.fq. Bacterial reads were aligned to genome of Burkholderia sp. B13 (FTPM01000001-FTPM01000002) using bwa with the following parameters: bwa mem -t 8 GENOME.fa -t 8 xxx.fq > xxx.sam
Fungal transcript abundances were quantified with CuffDiff, bacterial transcript abundances measured with RSEM, and the counts files used for differential expression analysis with EdgeR
Genome_build: R. microsporus ATCC 52813 NCBI accession number: JOSV00000000
Genome_build: R. microsporus ATCC 11559 NCBI accession number: MCOJ00000000
Genome_build: Burkholderia sp. B13 European Nucleotide Archive (ENA) accession FTPM01000001-FTPM01000002
Supplementary_files_format_and_content: tab-delimeted text file with read counts generated by CuffDiff  or RSEM which was then used for differential expression analysis with EdgeR. EdgeR-generated tab-delimited text file with fold change, p- and and false discovery rate-values for all the genes .

organism: Burkholderia sp. b13

source_name: bacterial cells

extract_protocol:
Total RNA was extracted with the Ambion ToTALLY Total RNA Isolation Kit (Life Technologies, Grand Island, NY) and rRNA was removed with RiboZero Magnetic Gold Kit (Epicentre, Madison, WI)
RNA sequencing libraries were prepared using the NEBNext® mRNA Library Prep Reagent Set for Illumina®

tag: cell type

value: bacterial cells

tag: growth stage

value: 93h post inoculation


title: scRNA-seq of Homo sapiens: adult male FNA from lymph node d60 [d60_FNA]

value: male


title: 93h_bact-1


title: scDamID_batch2_B04

description:
51
B04
hg38_100kb_UniqueFragmentCounts.tsv


title: scRNA-seq of Homo sapiens: adult male PBMC enriched for IgD low B cells d0 [d0_memory_B_PBMC]


title: 67h_bact-3

description:
processed data file: phys_contact_bacterial.count
processed data file: phys_contact_bacterial_to_atcc52813.edgeR.DE_results

value: 67h post inoculation


title: scDamID_batch2_B03

description:
50
B03
hg38_100kb_UniqueFragmentCounts.tsv


title: 67h_bact-2


title: scRNA-seq of Homo sapiens: adult male whole PBMC d12 [d12_PBMC_2]


description: Transcriptome profile of a wild type mouse at 6 weeks of age, biological rep3


title: scRNA-seq of Homo sapiens: adult male whole PBMC d5 [d5_PBMC]


description: Transcriptome profile of a wild type mouse at 6 weeks of age, biological rep2


title: scDamID_batch2_B01

description:
48
B01
hg38_100kb_UniqueFragmentCounts.tsv


description: Transcriptome profile of a wild type mouse at 6 weeks of age, biological rep1


title: 67h_bact-1


title: scDamID_batch2_A10

description:
47
A10
hg38_100kb_UniqueFragmentCounts.tsv


title: 56h_bact-3

description:
processed data file: pre-contact_bacterial.count
processed data file: pre-contact_bacterial_to_atcc11559.edgeR.DE_results

value: 56h post inoculation


title: scRNA-seq of Homo sapiens: adult male FNA from lymph node d12 [d12_FNA]


title: control3.input

city: yangzhou

first: zhengchang

last: wu

address: southdaxueroad

institute: yangzhoudaxue

data_processing:
Briefly, Paired-end reads were harvested from Illumina HiSeq 4000 sequencer, and were quality controlled by Q30. After 3’ adaptor-trimming and low quality reads removing by cutadapt software (v1.9.3). First, clean reads of all libraries were aligned to the reference genome (SusScr11)  by Hisat2 software (v2.0.4).
Methylated sites on RNAs (peaks) were identified by MACS software. Differentially methylated sites were identified by diffReps. These peaks identified by both softwares overlapping with exons of mRNA were figured out and choosed by home-made scripts. GO and Pathway enrichment analysis were performed by the differentially methylated protein coding genes.
Paired-end reads were harvested from Illumina HiSeq 4000 sequencer, and were quality controlled by Q30. After 3’ adaptor-trimming and low quality reads removing by cutadapt software (v1.9.3), the high quality clean reads were aligned to the reference genome (SusScr11) with hisat2 software (v2.0.4).
Then, guided by the Ensembl gtf gene annotation file, cuffdiff software (part of cufflinks) was used to get the gene level FPKM as the expression profiles of mRNA, and fold change and p-value were calculated based on FPKM, differentially expressed mRNA were identified. GO and Pathway enrichment analysis were performed based on the differentially expressed mRNAs.
Genome_build: SusScr11
Supplementary_files_format_and_content: Methylated_RNA_sites.mRNA
Supplementary_files_format_and_content: mRNA Expression Profiling.xls
Supplementary_files_format_and_content: peaks bed

organism: Sus scrofa

source_name: IPEC-J2 Cell

growth_protocol: Pig intestinal epithelial cells (IPEC-J2) offered by the University of Pennsylvania (Philadelphia, PA, USA) were cultured at 37 ℃ and 5% CO2 with DMEM/F12 medium supplemented with 10% fetal bovine serum (FBS)

extract_protocol:
Total RNA was used for removing the rRNAs with NEBNext rRNA Depletion Kit (New England Biolabs, Inc., Massachusetts, USA) following the manufacturer's instructions. RNA libraries were constructed by using NEBNext® Ultra™ II Directional RNA Library Prep Kit (New England Biolabs, Inc., Massachusetts,USA) according to the manufacturer’s instructions.
Libraries were controlled for quality and quantified using the BioAnalyzer 2100 system (Agilent Technologies, Inc., USA). Library sequencing was performed on an illumina Hiseq instrument with 150bp paired end reads.
Total RNA was isolated using trizol.Total RNA (1 μg) was used for removing the rRNAs using NEBNext rRNA Depletion Kit (New England Biolabs, Inc., Massachusetts, USA)  following the manufacturer's instructions

treatment_protocol: 1000 ng/mL DON treatment for 48 h

value: IPEC-J2 Cell

tag: agent

value: Normal


title: 93h_bact-3


title: control3.IP

data_processing:
Library strategy: MeRIP-seq
Briefly, Paired-end reads were harvested from Illumina HiSeq 4000 sequencer, and were quality controlled by Q30. After 3’ adaptor-trimming and low quality reads removing by cutadapt software (v1.9.3). First, clean reads of all libraries were aligned to the reference genome (SusScr11)  by Hisat2 software (v2.0.4).
Methylated sites on RNAs (peaks) were identified by MACS software. Differentially methylated sites were identified by diffReps. These peaks identified by both softwares overlapping with exons of mRNA were figured out and choosed by home-made scripts. GO and Pathway enrichment analysis were performed by the differentially methylated protein coding genes.
Paired-end reads were harvested from Illumina HiSeq 4000 sequencer, and were quality controlled by Q30. After 3’ adaptor-trimming and low quality reads removing by cutadapt software (v1.9.3), the high quality clean reads were aligned to the reference genome (SusScr11) with hisat2 software (v2.0.4).
Then, guided by the Ensembl gtf gene annotation file, cuffdiff software (part of cufflinks) was used to get the gene level FPKM as the expression profiles of mRNA, and fold change and p-value were calculated based on FPKM, differentially expressed mRNA were identified. GO and Pathway enrichment analysis were performed based on the differentially expressed mRNAs.
Genome_build: SusScr11
Supplementary_files_format_and_content: Methylated_RNA_sites.mRNA
Supplementary_files_format_and_content: mRNA Expression Profiling.xls
Supplementary_files_format_and_content: peaks bed

extract_protocol:
m6A RNA immunoprecipitation was performed with the GenSeq™ m6A-MeRIP Kit (GenSeq Inc., China) by following the manufacturer’s instructions. Both the input sample without immunoprecipitation and the m6A IP samples were used for RNA-seq library generation with NEBNext® Ultra II Directional RNA Library Prep Kit (New England Biolabs, Inc., USA).
The library quality was evaluated with BioAnalyzer 2100 system (Agilent Technologies, Inc., USA). Library sequencing was performed on an illumina Hiseq instrument with 150bp paired-end reads.
Total RNA was isolated using trizol.Total RNA (1 μg) was used for removing the rRNAs using NEBNext rRNA Depletion Kit (New England Biolabs, Inc., Massachusetts, USA)  following the manufacturer's instructions

tag: antibody


title: 56h_bact-2


title: control2.input


title: scRNA-seq of Homo sapiens: adult male FNA from lymph node d5 [d5_FNA]


title: scRNA-seq of Homo sapiens: adult male whole PBMC d0 [d0_PBMC_2]

value: PBMC


title: 56h_bact-1


title: control2.IP


title: scDamID_batch2_A07

description:
45
A07
hg38_100kb_UniqueFragmentCounts.tsv

source_name: HEK293T cells


title: 50h_bact-3

description:
processed data file: pre-contact_bacterial.count
processed data file: pre-contact_bacterial_to_atcc52813.edgeR.DE_results

value: 50h post inoculation


title: scDamID_batch2_A05

description:
43
A05
hg38_100kb_UniqueFragmentCounts.tsv


title: scRNA-seq of Homo sapiens: adult male FNA from lymph node d5 [d5_FNA_2]


title: 50h_bact-2


title: scDamID_batch2_A06

description:
44
A06
hg38_100kb_UniqueFragmentCounts.tsv


title: scRNA-seq of Homo sapiens: adult male FNA from lymph node d0 [d0_FNA_2]


title: scDamID_batch2_B02

description:
49
B02
hg38_100kb_UniqueFragmentCounts.tsv


title: 50h_bact-1


title: control1.IP


title: scRNA-seq of Homo sapiens: adult male whole PBMC d60 [d60_PBMC]


title: control1.input


title: scDamID_batch2_A04

description:
42
A04
hg38_100kb_UniqueFragmentCounts.tsv


title: DON3.input

value: DON treatment


title: scDamID_batch2_A03

description:
41
A03
hg38_100kb_UniqueFragmentCounts.tsv


title: 72h_C3

city: Brisbane

first: Amin

middle: Roushdy

last: Mohamed

state: Queensland

address: 306 Carmody Rd, University of Queensland

department: Agriculture and Food

country: Australia

institute: CSIRO

data_processing:
Sequenced reads were mapped to Coral reference transcriptome: using bowtie2 with DEFAULT parameters
transcript abundances were estimated from libraries mapped to the refrenece transcriptome using RSEM
Raw counts were analysed to infer differential expression in edgeR package in the R environment. Symbiotic samples at 3, 12, 48 and 72 h were compared to their corresponding control samples.
Gene co-expression network was constructed by application of RIF and PCIT algorithms
Genome_build: Coral reference transcriptome: http://aten.reefgenomics.org/download/
Genome_build: Symbiont reference transcriptome C. goreaui (Levin et al., 2016):  https://www.ncbi.nlm.nih.gov/geo/download/?acc=GSE72763&format=file&file=GSE72763%5FMI%5Ftranscriptome%2Efasta%2Egz
Supplementary_files_format_and_content: tab-delimited text files include expression values in CPM for each Sample

organism: Acropora tenuis

source_name: non-infected coral larvae "control"_72hpi

growth_protocol: Coral larvae were raised in FSW

extract_protocol:
Both infected and non-infected "control" larvae were removed from FSW, flash frozen in liquid Nitrogen and lysed twice for 20s at 4.0 m s−1 in Lysing Matrix D tubes (MP Biomedicals, Australia) containing 960 µL of lysis/binding solution plus 80 µL of the Plant RNA Isolation Aid (Ambion, USA) on a FastPrep®-24 Instrument (MP Biomedicals, Australia). RNA was bound to the columns, washed multiple times, eluted in 40 μL of RNase-free water and stored at -80°C . Illumina TruSeq RNA Sample Prep Kit was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Exposure of symbiont-free larvae to native algal symbionts (normally found in the adult) and sampling larvae at 3, 12, 48 and 72 hours post colonisation

value: Planula larvae

value: non-infected coral larvae "control"

value: 72hr post infection


title: DON3.IP


title: scRNA-seq of Homo sapiens: adult male PBMC enriched for IgD low B cells d60 [d60_memory_B_PBMC]


title: scDamID_batch2_A02

description:
40
A02
hg38_100kb_UniqueFragmentCounts.tsv


title: DON2.input


title: 72h_C2


title: scDamID_batch2_A09

description:
46
A09
hg38_100kb_UniqueFragmentCounts.tsv


title: scDamID_batch2_A01

description:
39
A01
hg38_100kb_UniqueFragmentCounts.tsv


title: DON2.IP


title: scRNA-seq of Homo sapiens: adult male FNA from lymph node d12 [d12_FNA_2]


title: 48h_C3

source_name: non-infected coral larvae "control"_48hpi

value: 48hr post infection


title: bulkDamIDmut_DamV133A_LMNB1_rep2

description:
12
DamV133A_Lam_2
DamMutantComparison_Counts.tsv


title: DON1.input


title: 72h_C1


title: 48h_C2


title: DON1.IP


title: 48h_C1


title: scRNA-seq of Homo sapiens: adult male FNA from lymph node d0 [d0_FNA]


title: 12h_C3

source_name: non-infected coral larvae "control"_12hpi

value: 12hr post infection


title: 6_N1_E_GFF

city: Atlanta

first: Gregory

middle: K

last: Tharp

state: GA

address: 954 Gatewood Dr

department: Developmental and Cognitive Neuroscience

institute: Yerkes National Primate Research Center

data_processing:
Illumina bcl2fastq v2.17.1.14 was used for demultiplexing.
Reads were mapped to the Acinetobacter baumannii AB5075  genomic reference with STAR (v2.5.2b) with default alignment parameters.
Abundance estimation of raw read counts per transcript was done with htseq-count.
Normalized abundance calculation and differential expression analysis was performed with DESeq2.
Genome_build: ASM96381v1 Strain: AB5075-UW GenBank assembly accession: GCA_000963815.1
Supplementary_files_format_and_content: tab-delimited text files with raw or DESeq2 normailzed read count values for each Sample …

organism: Acinetobacter baumannii

source_name: LB media

growth_protocol: Samples were grown at 37 degrees with shaking to an OD of 0.5.

extract_protocol:
RNA was prepared from 1 ml of pelleted culture using the MasterPure RNA Purification kit (Epicentre, Madison, WI)
Libraries were prepared from 2ug of bacterial RNA using the ScriptSeq v2 Complete (Bacteria) kit. After pooling at equimolar ratios, the libraries were sequenced on a HiSeq3000 using a SR100 configuration

tag: od

tag: population

value: LSO


title: bulkDamIDmut_DamV133A_rep2

description:
10
DamV133A_2
DamMutantComparison_Counts.tsv


title: RUNX2 CUT&RUN Msc Experiment #2

city: Odense M

first: Susanne

last: Mandrup

state: Fyn

address: Campusvej 55

department: Department of Biochemistry and Molecular Biologi

country: Denmark

institute: University of Southern Denmark

data_processing:
Library strategy: CUT&RUN
Base calling for all sequencing runs was performed using bcl2fastq (v2.20.0.422).
ChIP-seq: Reads were aligned using STAR (v2.3.1, --outSJfilterIntronMaxVsReadN 0 --outFilterMatchNmin 25 --outFilterMismatchNmax 2 --alignIntronMax 1). Duplicated reads/fragments were removed using Picard (v2.5.0). Reads/fragments were counted using HOMER (v4.10.3) in DNase I hypersensitive regions identified in a previous study (Rauch et al., 2019)
scATAC-seq: Reads (R1 and R2) were trimmed using TrimGalore (v. 0.6.0) and aligned aligned using STAR (v2.3.1, --outSJfilterIntronMaxVsReadN 0 --outFilterMatchNmin 25 --outFilterMismatchNmax 2 --alignIntronMax 1). Only short fragments (< 140bp) were kept , the short fragments were deduplicated using Picard (v2.5.0) and peaks were detected using MACS2 (v. 2.1.2). The cell barcodes (Index1) were quality filtered using FASTX toolkit (v. 0.0.13, -q 30 -p 80). The quality filtered barcodes were matched to the barcode white list (10X Genomics) and only barcodes with more than 10000 reads were kept. The raw aligned reads were split into cell-specific files using the filtered barcodes and individually deduplicated. Count matrices were generated by counting fragments for each cell using featureCounts (v.2.0.0) in peak detected regions. Cells and peaks were quality filtered and co-accessible peaks were identified using Cicero.
CUT&RUN: Reads trimmed with cutadpt and aligned using STAR (v2.3.1, --outSJfilterIntronMaxVsReadN 0 --outFilterMatchNmin 25 --outFilterMismatchNmax 2 --alignIntronMax 1).
RNA-seq: Reads were aligned using STAR (v2.3.1). Reads were counted using iRNA-seq (v1.0).
HiC: Reads were aligned and quality controlled using Hicup (v0.6.1). TADs were identified using HiTAD from TADlib (v0.3.1).
ECHiC: Reads were aligned and quality controlled using Hicup (v0.6.1). Interactions between virtual restriction fragments were detected using Chicago (v1.6.0) using custom weights calculated from high confidence interactions in the data.
Genome_build: hg19
Supplementary_files_format_and_content: ChIP-seq: Tab-delimited txt files containing normalized tag counts for each replicate in DNase I hypersensitive regions identified in a previous study (Rauch et al., 2019). For each replicate, read depth normalized bedGraph files are also supplied for filtered and deduplicated alignments.
Supplementary_files_format_and_content: scATAC-seq: Tab-deliminted txt file containing the peak co-accessibility (estimated with Cicero).
Supplementary_files_format_and_content: CUT&RUN: Tab-delimited txt files containing raw tag counts for each replicate in DNase I hypersensitive regions identified in a previous study (Rauch et al., 2019). For each replicate, read depth normalized bedGraph files are also supplied.
Supplementary_files_format_and_content: RNA-seq: Tab-delimited txt file containing raw tag counts for each replicate for all RefSeq genes . For each replicate, read depth normalized bedGraph files are also supplied.
Supplementary_files_format_and_content: Hi-C: The BED file contains all detected TADs and subTADs (identified using HiTAD).
Supplementary_files_format_and_content: ECHi-C: All interactions identified (using Chicago), as well as counts in all samples and annotation is also supplied in a tab-delimited txt file.

growth_protocol: Telomerase-immortalized human mesenchymal stromal cells of bone marrow (BM-hMSC-TERT4) were grown under standard cell culture conditions in α-MEM supplemented with 10 % fetal calf serum (FCS) and 1 % penicillin/streptomycin (P/S).

extract_protocol:
The CUT&RUN procedure was performed as previously described (Skene and Henikoff, 2017), with some modifications. Briefly, 10 µl concanavalin A–coated magnetic beads (Bangs Laboratories) were washed twice in binding buffer (20 mM HEPES-KOH pH 7.9, 1 mM CaCl2, 1 mM MnCl2, 10 mM KCl), and resuspended in 1 volume binding buffer. Single cell suspensions of mesenchymal stem cells were prepared by detaching the cells using Accutase, resuspending them in culture medium and passed through a 40 µm cell strainer. The cells were pelleted by centrifugation and washed three times in wash buffer (20 mM HEPES pH 7.5, 150 mM NaCl, 0.5 mM Spermidine, 1x Complete (Roche)), and finally, 1 ∙ 106 cells were resuspended 1 mL wash buffer. Bead and cell suspensions were mixed by gently vortexing and split into 4 aliquots. The buffer was changed by clearing the samples on a magnetic rack and resuspending the cell-bead mixture in antibody buffer (20 mM HEPES pH 7.5, 150 mM NaCl, 0.5 mM Spermidine, 1x Complete (Roche), 2 mM EDTA, 0.025% Digitonin). Subsequently, antibodies were added and the samples were incubated overnight rotating at 4°C or for 10 minutes at room temperature. The cell-bead mixture was washed once and resuspended in 50 µl Dig-wash buffer (20 mM HEPES pH 7.5, 150 mM NaCl, 0.5 mM Spermidine, 1x Complete (Roche), 0.025% Digitonin). pA-MNase were added (final concentration: 700 ng/ml) and the samples were incubated 1 h at 4°C rotating or for 10 minutes at room temperature. The cell-bead mixture was washed once and resuspended in 100 µl Dig-wash buffer, chilled to 0°C, 2 µl 100 mM CaCl2 were added, and samples were incubated for 30 minutes at 0°C. 100 µl 2x STOP-buffer (340 mM NaCl, 20 mM EDTA, 4 mM EGTA, 0.025% Digitonin, 50 µg/ml RNase A, 50 µg/ml glycogen, 2 pg/ml yeast spike in DNA) were added and the reactions were incubated at 37°C for 10 minutes. The samples were separated on a magnetic rack, and the supernatant Lo-Bind Eppendorf tube. 2 µl 10% SDS and 1.5 µl Proteinase K (20 mg/ml) were added and the sample was incubated for 10 minutes at 70°C and DNA was purified.
CUT&RUN libraries were constructed from 20 ng of genomic DNA according to the manufacturer's instructions (Illumina).

treatment_protocol: Two days post confluency (day 0), cells were induced to undergo adipocyte differentiation by exposing them to a adipogenic differentiation cocktail (DMEM supplemented with 10% fetal calf serum, 10ug/mL insulin, 1µM rosiglitazone, 100 mM dexamethasone, and 500 µM isobutylmethylxanthine). Medium was replaced on days 2, 4, 7 and 9.

value: Stem cell

tag: Stage

value: Day 0

value: RUNX2 (Cell Signaling, 8486)


title: scRNA-seq of Homo sapiens: adult male PBMC enriched for IgD low B cells d5 [d5_memory_B_PBMC]

value: male

tag: time point

tag: isolate


title: scRNA-seq of Homo sapiens: adult male PBMC enriched for IgD low B cells d28 [d28_memory_B_PBMC]

tag: gender


title: 12h_C2

tag: strain


title: CEBPb CUT&RUN Msc Experiment #2

value: CEBPb (Santa Cruz, sc-7962)


title: bulkDamIDmut_DamWT_LMNB1_rep2

description:
8
DamWT_Lam_2
DamMutantComparison_Counts.tsv


title: 5_AB5075_E_GFF

value: VIR-O


title: bulkDamIDmut_DamV133A_rep1

description:
9
DamV133A_1
DamMutantComparison_Counts.tsv


title: 4_N1_D_GFF


title: 12h_C1

tag: age


title: RUNX2 CUT&RUN Msc Experiment #1


title: CEBPb CUT&RUN Msc Experiment #1


title: 3_AB5075_D_GFF


title: 3hrC_3

source_name: non-infected coral larvae "control"_3hpi

value: 3hr post infection


title: bulkDamIDmut_DamWT_LMNB1_rep1

description:
7
DamWT_Lam_1
DamMutantComparison_Counts.tsv

tag: cell line


title: 2_N1_C_GFF


title: bulkDamIDmut_DamWT_rep2

description:
6
DamWT_2
DamMutantComparison_Counts.tsv

value: DamWT


title: bulkDamIDmut_DamV133A_LMNB1_rep1

description:
11
DamV133A_Lam_1
DamMutantComparison_Counts.tsv


title: 3hrC_2

tag: tissue


title: bulkDamIDmut_DamWT_rep1

description:
5
DamWT_1
DamMutantComparison_Counts.tsv


title: RUNX2 ChIP-seq Msc Experiment #1

data_processing:
Base calling for all sequencing runs was performed using bcl2fastq (v2.20.0.422).
ChIP-seq: Reads were aligned using STAR (v2.3.1, --outSJfilterIntronMaxVsReadN 0 --outFilterMatchNmin 25 --outFilterMismatchNmax 2 --alignIntronMax 1). Duplicated reads/fragments were removed using Picard (v2.5.0). Reads/fragments were counted using HOMER (v4.10.3) in DNase I hypersensitive regions identified in a previous study (Rauch et al., 2019)
scATAC-seq: Reads (R1 and R2) were trimmed using TrimGalore (v. 0.6.0) and aligned aligned using STAR (v2.3.1, --outSJfilterIntronMaxVsReadN 0 --outFilterMatchNmin 25 --outFilterMismatchNmax 2 --alignIntronMax 1). Only short fragments (< 140bp) were kept , the short fragments were deduplicated using Picard (v2.5.0) and peaks were detected using MACS2 (v. 2.1.2). The cell barcodes (Index1) were quality filtered using FASTX toolkit (v. 0.0.13, -q 30 -p 80). The quality filtered barcodes were matched to the barcode white list (10X Genomics) and only barcodes with more than 10000 reads were kept. The raw aligned reads were split into cell-specific files using the filtered barcodes and individually deduplicated. Count matrices were generated by counting fragments for each cell using featureCounts (v.2.0.0) in peak detected regions. Cells and peaks were quality filtered and co-accessible peaks were identified using Cicero.
CUT&RUN: Reads trimmed with cutadpt and aligned using STAR (v2.3.1, --outSJfilterIntronMaxVsReadN 0 --outFilterMatchNmin 25 --outFilterMismatchNmax 2 --alignIntronMax 1).
RNA-seq: Reads were aligned using STAR (v2.3.1). Reads were counted using iRNA-seq (v1.0).
HiC: Reads were aligned and quality controlled using Hicup (v0.6.1). TADs were identified using HiTAD from TADlib (v0.3.1).
ECHiC: Reads were aligned and quality controlled using Hicup (v0.6.1). Interactions between virtual restriction fragments were detected using Chicago (v1.6.0) using custom weights calculated from high confidence interactions in the data.
Genome_build: hg19
Supplementary_files_format_and_content: ChIP-seq: Tab-delimited txt files containing normalized tag counts for each replicate in DNase I hypersensitive regions identified in a previous study (Rauch et al., 2019). For each replicate, read depth normalized bedGraph files are also supplied for filtered and deduplicated alignments.
Supplementary_files_format_and_content: scATAC-seq: Tab-deliminted txt file containing the peak co-accessibility (estimated with Cicero).
Supplementary_files_format_and_content: CUT&RUN: Tab-delimited txt files containing raw tag counts for each replicate in DNase I hypersensitive regions identified in a previous study (Rauch et al., 2019). For each replicate, read depth normalized bedGraph files are also supplied.
Supplementary_files_format_and_content: RNA-seq: Tab-delimited txt file containing raw tag counts for each replicate for all RefSeq genes . For each replicate, read depth normalized bedGraph files are also supplied.
Supplementary_files_format_and_content: Hi-C: The BED file contains all detected TADs and subTADs (identified using HiTAD).
Supplementary_files_format_and_content: ECHi-C: All interactions identified (using Chicago), as well as counts in all samples and annotation is also supplied in a tab-delimited txt file.

extract_protocol:
Chromatin was prepared from 150 mm culture dishes by in 1% formaldehyde in PBS (10 minutes, RT). Cross-linking was stopped by adding glycine to a final concentration of 0.125 M (10 minutes, RT). The cells were washed twice in ice-cold PBS, and harvested in ice-cold lysis buffer (0.1% SDS, 1% Triton X-100, 0.15 M NaCl, 1 mM EDTA, 20 mM Tris pH=8) and sonicated at high setting in a Bioruptor-Twin (Diagenode) at a volume of 1.5 ml in 15-mL tubes for 40 cycles of 30 seconds on and 30 seconds off. The chromatin IPs were performed as described in (Nielsen R, et al. 2014. Methods in Enzymology 537: 261-279).
ChIP-seq libraries were constructed from 10 to 20 ng of genomic DNA according to the manufacturer's instructions (Illumina) as described in (Nielsen R, et al. 2014. Methods in Enzymology 537: 261-279).


title: 1_AB5075_C_GFF


title: RUNX2 ChIP-seq Msc Experiment #2


title: 3hrC_1


title: Control group

status: Public on Aug 12 2020

type: RNA

city: Tianjin

first: Cheng

last: Yang

address: No. 38 Tongyan road

institute: Nankai Universtiy

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalised using quantile normalisation with IlluminaGUI in R

label: biotin

source_name: Intestinal cells

label_protocol: Biotinylated cRNA were prepared with the Ambion MessageAmp kit for Illumina arrays

growth_protocol: Intestinal SMCs were cultured in DMEM and then passaged after enzyme digestion.

extract_protocol: RNA was extracted with Trizol reagent, followed by clean-up and DNase I treatment with QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser.

treatment_protocol: HISMCs (5×106 cells) were collected from Deg-AZM-treated (20 μM, 24h) and control groups.

value: intestinal smooth muscle cells

tag: treatment

value: control


title: Adults B-cell ALL Bone marrow, sample 11, Relapse

type: genomic

city: Salamanca

first: Jesús

middle: Maria

last: Hernández-Rivas

state: Salamanca

address: Paseo San Vicente, 88-182

department: Hematology

country: Spain

institute: Hospital Universitario de Salamanca, Universidad de Salamanca-CSIC

description: Human Genomic DNA: Female, Promega, Madison, WI, USA

hyb_protocol: Hybridization was performed according to the instructions in the NimbleGen Array User Guide

scan_protocol: Scanning was performed according to the instructions in the NimbleGen Array User Guide

data_processing: Arrays were processed using Nimblegen's standard protocol and segmented using the copynumber R package.

source_name: DNA from Bone marrow cells

label_protocol: Samples were denatured and labeled in parallel with Cy3 for the test group and Cy5 for the control group, each through a random priming method, using Klenow fragments (NimbleGen Dual-Color DNA Labeling Kit, Roche NimbleGen, Inc., Madison, WI, USA)

extract_protocol: The genomic DNA was extracted from frozen bone marrow or fixed peripheral blood cell samples with QIAmp DNA Mini Kit (Qiagen,  16 Valencia, CA, USA) following the manufacturer’s instructions

tag: patient id

tag: disease state

value: Relapse

tag: array id

value: Female

tag: disease

value: B-cell acute lymphoblastic leukemia

tag: age group

value: Adults ≥18 years

source_name: genomic DNA

value: Not applicable


title: Adults B-cell ALL Bone marrow, sample 13, Diagnosis

value: Diagnosis


title: Adults B-cell ALL Bone marrow, sample 8, Diagnosis

description: Human Genomic DNA: Male, Promega, Madison, WI, USA

value: Male


title: Adult B-cell ALL Bone marrow, sample 5, Diagnosis


title: Adults B-cell ALL Bone marrow, sample 8, Relapse


title: Adults B-cell ALL Bone marrow, sample 13, Relapse


title: Children B-cell ALL Bone marrow, sample 3, Diagnosis

value: Children <18 years


title: Adults B-cell ALL Bone marrow, sample 9, Relapse


title: Adults B-cell ALL Bone marrow, sample 11, Diagnosis


title: Deg-AZM treated group

tag: cell type

value: DEG-AZM


title: Mock vs D-Tagatose in shoot of rice replicate 3

city: Miki

first: Kazuya

last: Akimitsu

state: Kagawa

address: Ikenobe 2393

department: Faculty of Agriculture

country: Japan

institute: Kagawa University

description: Biological replicate 3 of 3

hyb_protocol: Cy3- and Cy5-labbelled samples (500 μl) were equally mixed and used for hyblidaization. Hybridization was conducted at 65°C, 10 rpm, 17h

scan_protocol: The plate was washed with SSC series, removed excess of buffer with N2 gus and scanned with an Agilent Microarray Scanner (Agilent Technologies).

data_processing:
Feature extraction software (version 9.1; Agilent Technologies) was used to delineate and measure the signal intensity of each spot in the array, and to normalize intensities. The background was measured around each spot as local background, calculated by the Feature Extraction software. Statistical data extraction processes were performed according to the manufacturer’s instructions.
Please note that each processed data file contains the following additional data columns:
NormCH1: Dye-normalized signal intensity of CH1 (rProcessedSignal)
NormCH2: Dye-normalized signal intensity of CH2 (gProcessedSignal)
MeanSignalCH1: Raw mean CH1 signal of feature (rMeanSignal)
MeanSignalCH2: Raw mean CH2 signal of feature (gMeanSignal)

organism: Oryza sativa

source_name: Rice shoot, treated with D-Tagatose at 2-leaf stage

label_protocol: Low RNA Input Linear Amplification/Labeling Kit (Agilent Technologies) according to the manufacturer’s instructions

growth_protocol: Seeds were germinated in 0.2%Benlate for 1 day and deionized water for 1 day at 30°C under dark, and grown for 5 days on water.

extract_protocol: Matufacture's instruction of Qiagen RNeasy Plant Mini Kit

treatment_protocol: Seedlings of two-leaf-stage rice plants were cultured in Kimura-B liquid medium with or without 0.5 mM D-Tagatose for 2 days.

tag: cultivar

value: cv. Nipponbare

value: grown for 5 days with water, then for 2 days with D-Tagatose

tag: tissues

value: shoot

source_name: Rice shoot, non-sugar-treated at 2-leaf stage

value: grown for 5 days with water, then for 2 days with water


title: 367IL17

city: Greenville

first: Weihua

last: Huang

state: North Carolina

address: 600 Moye Blvd, Brody 7S-24

institute: East Carolina University

data_processing:
Kallisto for pseudo-alignment to transcriptome of hg38
DESeq2 for differential gene expression
Genome_build: hg38
Supplementary_files_format_and_content: A .csv file including TPM of each gene for all 32 samples

source_name: interneurons

growth_protocol: interneurons were generated from iPSCs according to previously published protocols (Kim, T.G., et al. Efficient specification of interneurons from human pluripotent stem cells by dorsoventral and rostrocaudal modulation. Stem cells 32, 1789-1804, 2014), and were harvested for RNA preparation after 8 weeks of differentiation with or without treatment.

extract_protocol:
Samples were harvested using Trizol reagent (Invitrogen).
NEBNext Ultra II Directional RNA library Prep Kit for Illumina

value: iPSC-derived interneurons


title: Mock vs D-Tagatose in shoot of rice replicate 2

description: Biological replicate 2 of 3


title: Children B-cell ALL Bone marrow, sample 4, Diagnosis


title: Adults B-cell ALL Bone marrow, sample 6, Diagnosis


title: Adults B-cell ALL Peripheral blood, sample 7, Diagnosis

source_name: DNA from Peripheral blood cells


title: Adults B-cell ALL Bone marrow, sample 12, Diagnosis


title: Adults B-cell ALL Bone marrow, sample 10, Diagnosis


title: Children B-cell ALL Bone marrow, sample 2, Relapse


title: Children B-cell ALL Bone marrow, sample 4, Relapse


title: Children B-cell ALL Bone marrow, sample 3, Relapse


title: Adults B-cell ALL Peripheral blood, sample 7, Relapse


title: Children B-cell ALL Bone marrow, sample 1, Diagnosis


title: Children B-cell ALL Bone marrow, sample 1, Relapse


title: Adults B-cell ALL Bone marrow, sample 12, Relapse


title: Children B-cell ALL Peripheral blood, sample 2, Diagnosis


title: Adults B-cell ALL Bone marrow, sample 6, Relapse


title: Adults B-cell ALL Bone marrow, sample 10, Relapse


title: Adults B-cell ALL Bone marrow, sample 9, Diagnosis


title: Adults B-cell ALL Peripheral blood, sample 5, Relapse


title: 190IL17


title: 272IL17


title: 162IL17


title: 212IL17


title: 128IL17


title: 67IL17


title: 367Nor

value: normal control


title: 272Nor


title: 226Nor


title: 190Nor


title: 162Nor


title: NRVCM, tachycardia + KB-R7934, biol.rep 2,  tech.rep 1,2,3

city: Graz

first: Karin

last: Wagner

state: Styria

address: Stiftingtalstrasse 24

department: Molecular Biology

country: Austria

institute: Medical University Graz

description: Tachycardia + KB 2

hyb_protocol: Affymetrix Rat Gene 2.0 ST Array (Cat No. 902124);  Affymetrix GeneChip® HT hybridization, Wash and Stain Kit (Cat No. 900720);   Affymetrix Genechip®  fluidics station 450: protocol FS450_0002 for Cartridge Arrays

scan_protocol: Affymetrix Scanner: GCS3000; AGCC (Command Console Software  AGCC 4.0.0)

data_processing: Affymetrix Genexpression Console (1.3.1) using Affymetrix default analysis settings for generation of CEL-files

label: Biotin

organism: Rattus norvegicus

source_name: isolated neonatal rat cardiomyocytes

label_protocol: NuGen Ovation Pico WTA System V2, M01224v2 (Cat No. 3302); Encore Biotin Module, M01111v6 (Cat No. 4200);

growth_protocol: Cardiomyocytes were isolated from neonatal rat hearts and kept in cell culture for 3 days untill treatment.

extract_protocol: miRNeasyMICRO (Qiagen CatNo: 74004) incl DNase Treatment on column (RNase-Free DNase Set; Qiagen CatNo: 79254)

treatment_protocol: Cardiomyocytes were subjected to 20% biaxial stretch for 24h with and without 10µM KB-R7934, control dishes were kept unstreatched. High frequency pacing (8 Hz -tachycardia) was applied for 3h duration, the control samples were treated with normal rate 1 Hz frequency for the same duration.

value: tachycardia + KB-R7934

tag: developmental stage

value: neonatal

value: ventricular tissue

value: cardiomyocytes


title: NRVCM, tachycardia + KB-R7934, biol.rep 3, tech.rep 1,2,3,4,5,6

description: Tachycardia + KB 3


title: 67Nor


title: NRVCM, tachycardia + KB-R7934, biol.rep 1, tech.rep 1,2,3,4

description: Tachycardia + KB 1


title: 128Nor


title: 367SD

value: stress delayed


title: NRVCM, tachycardia, biol.rep 3, tech.rep 1,2,3,4,5,6

description: Tachycardia 3

value: tachycardia


title: Mock vs D-Tagatose in shoot of rice replicate 1

description: Biological replicate 1 of 3


title: NRVCM, tachycardia, biol.rep 2, tech.rep 1,2,3

description: Tachycardia 2


title: NRVCM, tachycradia control, biol.rep 3, tech.rep 1,2,3,4,5,6

description: Control tachycardia 3

value: tachycradia control


title: 272SD


title: 226SD


title: NRVCM, tachycradia control, biol.rep 1, tech.rep 1,2,3,4

description: Control tachycardia 1


title: NRVCM, stretch + KB-R7934, biol.rep 3, tech.rep 1,2

description: Stretch + KB 3

value: stretch + KB-R7934


title: 212SD


title: 212Nor


title: NRVCM, stretch + KB-R7934, biol.rep 2, tech.rep 1,2

description: Stretch + KB 2


title: 190SD


title: NRVCM, stretch + KB-R7934, biol.rep 1, tech.rep 1,2

description: Stretch + KB 1


title: 128SD


title: NRVCM, stretch, biol.rep 2, tech.rep 1,2

description: Stretch 2

value: stretch


title: atf6_rep4

city: Quechee

first: Michael

middle: J

last: Steinbaugh

state: VT

address: PO Box 1520

institute: Acid Genomics

data_processing:
RNA-seq alignment was performed using the bcbio-nextgen toolkit v1.0.9a0-3556ceb8. Internally, this called salmon v0.9.1 (used for differential expression) and STAR v2.5.3a (used for quality control) during alignment.
Data was imported into R using bcbioRNASeq v0.2.2 and tximport v1.6.0.
Differential expression was performed with DESeq2 v1.19.51.
Genome_build: WBcel235 (Ensembl 90)
Supplementary_files_format_and_content: Per-sample quant.sf files: salmon transcript-level quantification files used as input for DESeq2 (refer to Bioconductor tximport vignette for usage details).
Supplementary_files_format_and_content: raw_counts.csv: gene-level raw count matrix generated from transcript-level salmon counts used for DESeq2 differential expression analysis.
Supplementary_files_format_and_content: normalized_counts.csv: gene-level size factor adjusted (normalized) counts generated by DESeq2.

organism: Caenorhabditis elegans

source_name: whole organism

growth_protocol: In each of 4 independent biological replicates, roughly 1000 hypochlorite-synchronized L1s were washed onto OP50-1 lawns and allowed to develop for 72 h to day 1 adulthood.

extract_protocol:
Total RNA was isolated after disrupting worms with 5 freeze-thaws with Qiazol extraction and RNeasy mini kit (Qiagen).
cDNA libraries were prepared through TruSeq Stranded mRNA kit (Illumina) and sequenced with an Illumina NextSeq500 over 75 cycles by the Dana Farber Molecular Biology Core.

treatment_protocol: Samples were washed in M9 to remove bacteria, resuspended in Qiazol (Qiagen) and snap-frozen in liquid nitrogen.

tag: genotype

tag: replicate

tag: temperature


title: 67SD


title: 162SD


title: NRVCM, tachycardia, biol.rep 1, tech.rep 1,2,3,4

description: Tachycardia 1


title: wt_rep4

tag: strain

value: N2 (wild-type)

value: wt


title: 367ND

value: control delayed


title: NRVCM, stretch, biol.rep 1, tech.rep 1,2,3,4

description: Stretch 1


title: wt_rep3


title: wt_rep2


title: atf6_rep1


title: atf6_rep3


title: NRVCM, stretch control, biol.rep 3, tech.rep 1,2

description: Control stretch 3

value: stretch control


title: NRVCM, stretch control, biol. rep 1, tech.rep 1,2,3,4

description: Control stretch 1


title: NRVCM, stretch, biol.rep 3, tech.rep 1,2

description: Stretch 3


title: NRVCM, tachycradia control, biol.rep 2, tech.rep 1,2,3

description: Control tachycardia 2


title: 226ND


title: NRVCM, stretch control, biol.rep 2, tech.rep 1,2

description: Control stretch 2


title: 190ND


title: 212ND


title: wt_rep1


title: P11

city: Hangzhou

first: Ningning

last: Xie

address: 1 Xueshi Road

institute: Women’s Hospital, School of Medicine, Zhejiang University

description: processed data file: hypothalamus RNA-seq.xlsx

data_processing:
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence using Trim Galore, then FastQC (v0.11.5) was used to check the quality.
Fragments per kilobase of exon per million reads mapped (FPKM) were calculated using cuffnorm.
Genome_build: GRCh38
Supplementary_files_format_and_content: Tab-delimited text files include FPKM values for each sample.
Supplementary_files_format_and_content: Table with different methylation level of CGI and promoter.

source_name: hypothalamus

extract_protocol:
Isolation of the total RNA was performed using Trizol Reagent (Invitrogen, USA). Total genomic DNA was extracted by TIANamp Genomic DNA Kit (Tiangen Biotech, China).
The libraries for RNA-seq were obtained by TruSeq RNA LT Sample Prep Kit v2 (Illumina, USA). RRBS libraries of genomic DNA were prepared using TruSeq DNA LT Sample Prep Kit v2 (Illumina, USA). The libraries were quantified with Quant-iT PicoGreen dsDNA Assay Kit (Life technologies, USA).

tag: strain background

value: Sprague-Dawley

tag: sample group

value: born to PCOS rats

value: hypothalamus


title: P12

tag: tissue


title: 162ND

value: iPSC-derived interneurons

tag: treatment


title: atf6_rep2


title: 128ND


title: 67ND


title: C12


title: C11


title: 272ND


title: C10


title: G3

city: ChangChun

first: Xiaowei

last: Zhong

address: Xi'an Road

institute: Jilin University

data_processing:
Illumina Casava1.7 software used for basecalling.
Hisat2 was used to compare the quality control sequence with the reference genome.The results were compared by RSeQC.
By comparing the results, the coverage of each transcription site was calculated by BEDTools software.
By using Qualimap software, the proportion of each genome structure in reads, including exon, intron and intergenic, was calculated.
Using BEDTools software to compare and map the sequence of each chromosome in the genome, so as to reflect the distribution of the sequence on each chromosome.
Genome_build: human NCBI genome build 36
Supplementary_files_format_and_content: xlsx files include TPM and FPKM value for each sample

source_name: MHCC97H cells

extract_protocol:
Total RNA from MHCC97H cells was extracted using TRIzol Reagent (Invitrogen). rRNA removal and subsequent purification were performed and with RiboZero Magnetic Gold Kit following the manufacturer’s protocol. RNA-seq was carried out at the Sequencing and Non-Coding RNA Program
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: cell line

value: MHCC97H cells

value: Human hepatoma cell line

value: 100μM Galangin 48h


title: G2


title: P9

description: processed data file: hippocampus RNA-seq.xlsx

source_name: hippocampus

value: hippocampus


title: G1


title: P7


title: P8


title: C9


title: C2


title: C7


title: C3


title: C8


title: C1


title: human-hepatocyte-2

city: Fukuoka

first: Atsushi

last: Suzuki

state: Fukuoka

address: 3-1-1 Maidashi, Higashi-ku

department: Medical Institute of Bioregulation

institute: Kyushu University

data_processing:
The sequence reads were aligned to the human reference genome assembly (Ensemble GRCh38) using bowtie2 (v2.3.1)
UMI count was calculated from raw read count data that were estimated from aligned data by using HTSeq (v0.6.0) as descrived in "CEL-Seq2: sensitive highly-multiplexed single-cell RNA-Seq (PMID: 27121950)".
Genome_build: GRCh38
Supplementary_files_format_and_content: Tab-delimited text files include raw count values of all samples

source_name: human-primary-hepatocyte

growth_protocol: In monolayer culture, hiHepPCs were cultured in DMEM/F12 and Fibrolife mixture medium with 4% FBS, 1 µg/ml insulin, 10-7 M dexamethasone, 10 mM nicotinamide, 2mM L-glutamine, 50 µM 2-mercaptoethanol, and penicillin/streptomycin, containing 20 ng/ml HGF, 1 µM A83-01, 2 µM SB43852, and 5 µM Y27632. In cell aggregation culture, hiHepPCs were cultured in DMEM/F-12 serum-free medium with 1μg/ml insulin, 10mM nicotinamide, 2mM L-glutamine, 50μM 2-mercaptoethanol, penicillin/streptomycin, 1μM A8301, 20μM Y27632, 20ng/ml HGF and 1μM Forskolin. In spheroid culture with Matrigel, hiHepPCs were cultured in advanced DMEM/F-12 with 2 mM GlutaMax, 10 mM HEPES, N-2 supplement(1 × ) , B-27 supplement (1 × ), 1 mM N-acetylcysteine, and penicillin/streptomycin, containing 50 ng/mL human recombinant EGF, 100 ng/mL murine recombinant Noggin, and 500 ng/mL human recombinant R-spondin1, 100 ng/mL murine recombinant Wnt3a, 10μM Forskolin , 100 ng/ml human FGF10, 10 mM Nicotinamide, 10 nM gastrin, 25 ng/ml human HGF, and 5 μM A8301.

extract_protocol:
RNA was extracted using the NucleoSpin RNA II Kit (MACHEREY-NAGEL)
Detailed protocol is described in "CEL-Seq2: sensitive highly-multiplexed single-cell RNA-Seq (PMID: 27121950)".

treatment_protocol: We purchased HUVECs and human liver-derived hepatocytes and cholangiocytes on the market and isolated HPBECs from human peripheral blood samples. To generate hiHepPCs, HUVECs and HPBECs were infected with retroviruses expressing the genes encoding transcription factors indicated above.

value: liver

tag: cell type source

value: Human liver-derived hepatocytes

tag: transfection

value: non-treated

tag: Stage

value: freshly isolated from tissue


title: P10


title: human-hepatocyte-1


title: HPBEC-hiHepPC-spheroid-2

source_name: HPBEC-hiHepPC-spheroid

value: peripheral blood

value: Human peripheral blood-derived endothelial cells

value: transduced with FOXA3, HNF1A, and HNF6

value: in vitro spheroid culture condition


title: human-cholangiocyte-spheroid-culture

source_name: human-cholangiocyte-spheroid

value: Human liver-derived cholangiocytes


title: Ncr1Cre Id2F/F Tcf7F/F cells DKO-3

city: Chicago

first: Barbara

middle: L

last: Kee

state: Illinois

address: 924 E57th st

institute: The University of Chicago

description: Ncr1Cre Id2F/F Tcf7F/F cells

data_processing:
Raw sequence reads were trimmed using Trimmomatic v 0.33 (TRAILING:30 MINLEN:20)
Trimmed reads were aligned to mouse genome assembly mm10 with Tophat v 2.1.0.
Reads were assigned to genes using the htseq-count tool from HTSeq v 0.6.1 and gene annotations from Ensembl release 78.
The R package EdgeR was used to normalize the gene counts and to calculate differential expression statistics for each gene for each pairwise comparison of sample groups. Genes were considered differentially expressed if the |fold change| >= 2 and FDR < 0.05.
Genome_build: mm10
Supplementary_files_format_and_content: normalized abundance measurements provided as edgeR output files

source_name: bone marrow NK cells

extract_protocol:
Total RNA was isolated using RNAeasy MicroKit (Qiagen) according to manufacturer’s recommendations.
Libraries were constructed using Nugen’s Ovation Ultralow Library systems and were subsequently subjected to 76 cycles of NextSeq500 sequencing.

treatment_protocol: NK cells (NK1.1+CD9b+) were sorted from the bone marrow of Ncr1Cre Id2F/F (Id2KO), Ncr1Cre Tcf7F/F (Tcf1KO), Ncr1Cre Id2F/F Tcf7F/F (DKO) and Id2F/F (Ctrl) mice directly into RLT buffer.  Three independent samples per genotype were assessed.

value: bone marrow NK cells

tag: sorting markers


title: Ncr1Cre Tcf7F/F NK cells Tcf1KO_2

description: Ncr1Cre Tcf7F/F NK cells

tag: cell type


title: Ncr1Cre Tcf7F/F NK cells Tcf1KO_3

description: Ncr1Cre Tcf7F/F NK cells


title: HPBEC-hiHepPC-spheroid-1


title: Ncr1Cre Tcf7F/F NK cells Tcf1KO_1

description: Ncr1Cre Tcf7F/F NK cells


title: Ncr1Cre Id2F/F Tcf7F/F cells DKO-2

description: Ncr1Cre Id2F/F Tcf7F/F cells


title: Ncr1Cre Id2F/F NK cells Id2KO_2

description: Ncr1Cre Id2F/F NK cells


title: Ncr1Cre Id2F/F NK cells Id2KO_3

description: Ncr1Cre Id2F/F NK cells


title: Ncr1Cre Id2F/F NK cells Id2KO_1

description: Ncr1Cre Id2F/F NK cells


title: HPBEC-hiHepPC-aggregate-1

source_name: HPBEC-hiHepPC-aggregate

value: in vitro cell-aggregate culture condition


title: Control NK cells Ctrl_3

description: Control NK cells


title: HPBEC-hiHepPC-2D-2

value: in vitro monolayer culture condition


title: HPBEC-hiHepPC-2D-1


title: Control NK cells Ctrl_2

description: Control NK cells


title: HPBEC-1

source_name: HPBEC


title: Control NK cells Ctrl_1

description: Control NK cells


title: HUVEC-hiHepPC-spheroid-3

source_name: HUVEC-hiHepPC-spheroid

value: umbilical vein

value: Human umbilical vein endothelial cells


title: 226IL17

value: iPSC-derived interneurons


title: Ncr1Cre Id2F/F Tcf7F/F cells DKO_1

description: Ncr1Cre Id2F/F Tcf7F/F cells


title: HUVEC-hiHepPC-spheroid-2


title: 20190912_MCA_Treg_positive

city: Rehovot

first: Ido

last: Amit

address: 234 Herzl st.

department: Immunology

country: Israel

institute: Weizmann Institute of Science

data_processing:
bcl2fastq/2.15.0.4
Sequences with RMT of low quality (defined as RMT with minimum Phred score of less than 27) were filtered out.
Pool-barcode and well-barcode-RMT were extracted from the first and second end of the read (respectively) and concatenated to the fastq header, delimited by a underscore i.e. POOL_BARCODE_WELL_BARCODE_RMT while "NNNNNN" was used as a place holders if plate barcode was not used.
Reads were separated by POOL_BARCODE_WELL_BARCODE header data, allowing 1 sequencing error. This process created a single fastq file for each source well.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include mRNA molecule count values for each Sample
Supplementary_files_format_and_content: barcodes.tsv.gz
Supplementary_files_format_and_content: features.tsv.gz
Supplementary_files_format_and_content: matrix.mtx.gz

source_name: 10x run of mouse MCA tumor

extract_protocol:
Bone marrow derived cell culture:  Female mice were sacrificed by cervical dislocation. To isolate the bone marrow, femora and tibiae from one leg were removed, cleaned from flesh, and flushed with C10 culture medium (RPMI-1640 supplemented with 15% serum, 1% x100 non-essential amino acids, 10mM HEPES buffer, 1mM sodium pyruvate, 2mM L-glutamine, and 50μM b-mercaptoethanol) using a G21 needle syringe. Flushed bone marrow was filtered through a 70-μm cell strainer and spun down in a cold centrifuge at 300xg for 5 min. Cells were re-suspended in 250 μl RBC lysis solution (Sigma) per leg and incubated for 5 min at room temperature, washed, and resuspended in pre-warmed C10 medium. Cultures were set by plating 2x106 cells in 10mL C10 supplemented with 20 ng/ml GM-CSF in a 100 mm non-tissue culture plate, and incubated under standard culture conditions (37°C, 5% CO2) (Day 0). On day 2 another 10 ml C10 medium supplemented with 20 ng/ml GM-CSF was added. On day 5, three quarter of the medium was replaced with fresh C10 medium supplemented with 20 ng/ml GM-CSF. On day 7, another 5 ml of C10 medium supplemented with 10 ng/ml GM-CSF. On day 8, non-adherent and loosely adherent cells in the culture supernatant were harvested by gentle washing and re-cultured in a fresh C10 medium supplemented with 10 ng/ml GM-CSF in new non-tissue culture plates and used as starting material for all BMDC experiments.  Tumor cell line  MCA-205 fibrosarcoma cell lines were kindly provided by Sergio Quezada group at UCL cancer institute, London, UK. Cells were cultured in DMEM (41965-039) medium supplemented with 10% heat-inactivated FBS, 1mM sodium pyruvate, 2mM l-glutamine, 1% penicillin-streptomycin (Thermo Fisher Scientific). Cells were cultured in 100 mm tissue culture plates in an incubator with humidified air and 5% CO2 at 37°C. Cell lines were validated for lack of mycoplasma infection using primers for mycoplasma-specific 16S rRNA gene region (EZPCR Mycoplasma Kit; Biological Industries).    Tumor growth measurements  Mice were inoculated intradermally (i.d.) with 5x105 MCA-205 cells suspended in 100μl PBS on their right flank. At day 19, tumors volume was measured using a caliper. Tumor volume was assessed by measuring two diameters and calculated using the formula X2 × Y × 0.52 (where X, smaller diameter and Y, larger diameter).  Isolation of tumor infiltrating leukocytes  Tumor bearing mice were sacrificed at 10 and 19 days after tumor cell inoculation. The tumors underwent mechanical (gentleMACSTM C tube, Miltenyi Biotec Inc., San Diego, CA) and enzymatic digestion (0.1mg/ml DNase type I (Roche), and 1mg/ml Collagenase IV (Worthington) in RPMI-1640) for 15 min at 37°C. Cells then filtered through 100µm cell strainer, washed with ice cold sorting buffer, centrifuged (5 min, 4°C, 300g), and stained with fluorophores conjugated antibodies.  Human peripheral blood of healthy donors and Isolation of peripheral blood PBMC  Blood was taken from 3 healthy peripheral blood donors. The peripheral blood collecting samples is part of the (0220-15-TLV) approval. PBMCs were purified from fresh blood samples by sterile density gradient separation by density centrifugation media (Ficoll-Paque (GE Healthcare Life Sciences)) in a 1:1. Centrifugation (460 g, 25 min,) was performed at 10 °C, and the mononuclear cells were carefully aspirated and washed with ice-cold FACS buffer, followed by red blood lysis (Sigma-Aldrich) for 5min at 4°C and washing with ice cold FACS buffer.      Isolation of T-regulatory cells from mouse tumors and cervical lymph nodes  CD45+, TCR-+, CD11b- and Foxp3+ (by endogenous Foxp3-RFP or anti Foxp3-APC conjugated antibody) cells were isolated from cervical lymph nodes or MCA-205 fiborosarcoma tumors from Foxp3RFP mice.
10x - Fresh or INs-seq-fixed cells were FACS sorted into 0.04% PBS-BSA buffer or INs-seq collection buffer respectively. Cells were stained with trypan blue and counted using light microscopy and then loaded onto a 10x Chromium microfluidics system according to the manufacturer’s guidelines. scRNA-seq 5’ gene expression (GEX) libraries were generated using the 10X Genomics Chromium Single Cell 5' Kit v2 and the 10x Chromium Controller (10x Genomics) according to the 10x Single Cell 5’ v2 protocol guidelines. The 5′ mRNA library was sequenced with Illumina’s NextSeq 500 using 75 paired-end reads.
10x genomics according to the manufacturer protocol
single cell RNA-seq 5'

tag: organ

value: Tumor

tag: selection marker

value: CD45+TCRb+CD4+Foxp3+ FACS gating

value: Treated wit INs-seq fixation method

tag: mouse age

value: 6 weeks


title: HUVEC-hiHepPC-spheroid-1


title: HUVEC-hiHepPC-aggregate-3

source_name: HUVEC-hiHepPC-aggregate


title: 20190912_MCA_Treg_negative

value: CD45+TCRb+CD4+Foxp3- FACS gating


title: HUVEC-hiHepPC-aggregate-2


title: 20190903_MCA-Arg1-Negative

value: CD45+CD11b+Arg1- FACS gating


title: 20190719_Fixed_P38pos

source_name: 10x run of mouse BMDC

value: Bone Marrow

value: CD11c+ Ly6c- phospho-P38+ FACS gating


title: 20190719_Fixed_P38neg

value: CD11c+ Ly6c- phospho-P38- FACS gating


title: HPBEC-hiHepPC-aggregate-2

value: peripheral blood

value: Human peripheral blood-derived endothelial cells

value: transduced with FOXA3, HNF1A, and HNF6


title: HUVEC-hiHepPC-aggregate-1

value: in vitro cell-aggregate culture condition


title: 20190613_Fresh_FOXP3

source_name: 10x run of mouse LN

value: Foxp3RFP (Tg(Foxp3-RFP,-cre)) mice

value: Cervical Lymph node


title: HUVEC-hiHepPC-2D-2

value: umbilical vein

value: Human umbilical vein endothelial cells

value: in vitro monolayer culture condition


title: 20190613_Fixed_FOXP3

value: Fresh, control


title: HUVEC-hiHepPC-2D-3


title: 20190410_Fresh_CD11c

value: CD11c+ Ly6c- FACS gating

value: Treated wit INs-seq fixation method


title: HUVEC-hiHepPC-2D-1


title: HPBEC-2

value: non-treated


title: HUVEC-1

source_name: HUVEC


title: AB8346

data_processing:
bcl2fastq/2.15.0.4
Sequences with RMT of low quality (defined as RMT with minimum Phred score of less than 27) were filtered out.
Pool-barcode and well-barcode-RMT were extracted from the first and second end of the read (respectively) and concatenated to the fastq header, delimited by a underscore i.e. POOL_BARCODE_WELL_BARCODE_RMT while "NNNNNN" was used as a place holders if plate barcode was not used.
Reads were separated by POOL_BARCODE_WELL_BARCODE header data, allowing 1 sequencing error. This process created a single fastq file for each source well.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include mRNA molecule count values for each Sample
Supplementary_files_format_and_content: Meta data file associating each single cell with its amplification batch and index sorting readouts

source_name: MARS seq run of mouse MCA tumor

extract_protocol:
Isolation of tumor infiltrating leukocytes:  Tumor bearing mice were sacrificed at 10 and 19 days after tumor cell inoculation. The tumors underwent mechanical (gentleMACSTM C tube, Miltenyi Biotec Inc., San Diego, CA) and enzymatic digestion (0.1mg/ml DNase type I (Roche), and 1mg/ml Collagenase IV (Worthington) in RPMI-1640) for 15 min at 37°C. Cells then filtered through 100µm cell strainer, washed with ice cold sorting buffer, centrifuged (5 min, 4°C, 300g), and stained with fluorophores conjugated antibodies.
MARS seq 2.0 - Following staining, cells were washed and resuspended in cold washing buffer (0.5% BSA and 2 mM EDTA in PBS), stained with fluorophore conjugated anti-mouse CD45 antibody, and filtered through a 70-µm strainer. Before sorting, cells were stained with propidium iodide to exclude dead/dying cells. Cell sorting was performed using a BD FACSAria Fusion flow cytometer (BD Biosciences), gating for CD45+ cells after exclusion of dead cells and doublets. Single cells were sorted into 384-well capture plates containing 2 ml of lysis solution and barcoded poly(T) reverse-transcription (RT) primers for scRNA-seq as described previously (Keren-Shaul et. al 2019). Immediately after sorting, plates were spun down to ensure cell immersion into the lysis solution, snap-frozen on dry ice and stored at 80C until further processing. Cells were analyzed using BD FACSDIVA software (BD Bioscience) and FlowJo software (FlowJo, LLC).
3' end mRNA libraries were prepared for sequencing using MARS-seq (Jaitin et al, Science 2014)
single cell RNA-seq for gene expression quantitation

value: Tumor

value: Fresh

tag: timepoint

value: Day 19

tag: replicate id

value: total RNA

value: 6 weeks


title: 20190903_MCA-Arg1-Positive

value: CD45+CD11b+Arg1+ FACS gating


title: HUVEC-hiHepPC-2D-P16-1

source_name: Human umbilical vein endothelial cells

value: transduced with FOXA3, HNF1A, and HNF6

value: in vitro monolayer culture condition, passage 16


title: AB8344


title: HUVEC-hiHepPC-2D-P16-2


title: RR057i_00116_E21_S325

city: San Francisco

first: Charles

last: Langelier

address: 499 Illinois St

department: Medicine

institute: University of California San Francisco

data_processing:
Alignment against human genome- Kallisto v 0.46.1
Gene-level counts were generated from the transcript-level abundance estimates using the R package tximport
Fitering to retain samples with 400,000 gene counts
Differential expression with R package limma
Genome_build: HG-38, ENSEMBL v. 99
Supplementary_files_format_and_content: .csv files with genecounts

source_name: NP/OP swab

growth_protocol: Clinical naso/pharyngeal swab specimens

extract_protocol:
Zymo DNA/RNA magbead
NEBnext with Qiagen Fastselect rRNA depletion

treatment_protocol: DNAse

tag: gender

value: F

tag: age

tag: sars-cov-2 rpm

value: NEG

tag: sars-cov-2 pcr

tag: disease state

value: no virus


title: AB8343

tag: strain

tag: treatment


title: RR057i_00067_C05_S67

value: POS


title: HUVEC-hiHepPC-2D-P16-3

tag: tissue

value: umbilical vein


title: AB8341


title: AB8342


title: HUVEC-2

tag: cell type source

value: Human umbilical vein endothelial cells

tag: transfection

value: in vitro monolayer culture condition


title: RR057e_00731_H08_S120


title: AB8339

value: Trem2-/- knock-out (KO) mice


title: AB8345


title: RR057e_00721_L04_S60

value: M


title: AB8338

value: Tumor


title: RR057e_00719_H04_S56


title: RR057i_00158_F15_S230


title: 20190410_Fixed_CD11c

value: Bone Marrow

value: CD11c+ Ly6c- FACS gating

value: Fresh, control


title: AB8335

value: Fresh

value: Day 19

value: total RNA

value: 6 weeks


title: AB8336


title: AB8278


title: AB8337


title: RR057i_00137_L07_S108

value: F


title: RR057i_00156_N13_S206


title: AB8277


title: RR057i_00138_N07_S110


title: AB8276


title: AB8340


title: RR057e_00728_N06_S94


title: AB8275


title: AB8273


title: RR057i_00108_M17_S269


title: AB8271


title: AB8272


title: RR057i_00172_J19_S298


title: RR057i_00114_M19_S301


title: AB8270


title: AB8269


title: RR057i_00141_H09_S136


title: RR057i_00145_D11_S164


title: AB8268


title: AB8267


title: RR057i_00163_D17_S260


title: AB8182


title: RR057i_00175_D21_S324

value: NEG


title: RR057i_00134_F07_S102


title: RR057i_00136_J07_S106


title: RR057i_00132_N05_S78


title: AB8179


title: AB8180


title: RR057i_00133_D07_S100


title: RR057i_00109_C19_S291


title: AB8274


title: AB8178


title: RR057i_00117_G21_S327

value: no virus


title: RR057i_00110_E19_S293

value: POS


title: RR057i_00112_I19_S297


title: AB8176


title: RR057i_00135_H07_S104


title: RR057i_00070_I05_S73


title: AB8177


title: RR057i_00071_K05_S75


title: AB8175


title: RR057i_00069_G05_S71


title: AB7984

value: Day 10


title: AB8174


title: RR057i_00122_F03_S38


title: RR057i_00123_H03_S40


title: AB8181


title: AB7982


title: RR057i_00089_K11_S171


title: AB7983


title: RR057i_00088_I11_S169


title: AB7981


title: RR057i_00169_D19_S292


title: AB7980


title: RR057i_00090_M11_S173


title: AB7979


title: AB7978


title: AB7977


title: RR057i_00082_I09_S137


title: RR057i_00080_E09_S133


title: RR057i_00075_G07_S103


title: AB7976


title: RR057i_00078_M07_S109


title: AB7974


title: RR057i_00118_I21_S329


title: AB7975


title: AB7973


title: AB7967


title: RR057i_00074_E07_S101


title: RR057i_00081_G09_S135


title: AB7968


title: RR057i_00077_K07_S107


title: AB7966


title: AB7965


title: AB7963


title: AB7964


title: RR057i_00115_C21_S323


title: RR057i_00064_I03_S41


title: AB7962


title: RR057i_00101_K15_S235


title: RR057e_00746_N12_S190


title: RR057i_00096_M13_S205


title: embryonic fibroblasts, wt1 (tRNA)

city: Philadelphia

first: Dawei

middle: W

last: Dong

state: Pennsylvania

address: 3620 Hamilton Walk

department: Biomedical Sciences

institute: University of Pennsylvania

data_processing:
Sequencing quality was examined by FastQC software (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/)
Trimmed reads (pass Illumina quality filter, trimmed 3-adaptor bases by cutadapt(1.0)) were aligned to cytoplasmic mature-tRNA sequence getting from GtRNAdb and also including the mitochondrial tRNA sequences from mitotRNAdb using STAR (2.4.2a) software.
The transcript abundances for each sample was estimated with unique matched reads and the count value for tRNAs level were calculated using MATLAB software (6.5.0.180913a).  The differentially expressed tRNAs were screened based on the count value using the R (3.2.1) and the MATLAB routines developed in our lab.
Supplementary_files_format_and_content: CSV format mapped reads for each tRNA and sample

source_name: embryonic fibroblasts

extract_protocol:
Agarose electrophoresis was used to check the integrality of total RNA samples, and NanoDrop ND-1000 instrument was used to measure the concentration of the samples.  NEBNext® Multiplex Small RNA Library Prep Set for Illumina® reagents were used in library preparation. tRNAs were purified from total RNA samples and pretreated according to Hydro-tRNAseq method: a) over 2 µg total RNA was resolved on urea-polyacrylamide gels and recovered within a size window of 60-100 nt for tRNA; b) purified tRNA was subjected to limited alkaline hydrolysis by carbonate buffer; c) the partial hydrolyzed tRNA was dephosphorylated with calf intestinal phosphatase (CIP) and then re-phosphorylated with T4 polynucleotide kinase (T4 PNK).  Partially hydrolyzed and re-phosphorylated tRNAs of each sample was used to construct Hydro-tRNAseq library.  Library preparation procedures included: 1) 3'-adapter ligation; 2) 5'-adapter ligation; 3) cDNA synthesis; 4) PCR amplification; 5) size selection of ~140-155 bp PCR amplified fragments (corresponding to ~19-35 nt tRNA fragments). The completed libraries were quantified by Agilent 2100 Bioanalyzer. Libraries were mixed in equal amounts according to the quantification results, and used for sequencing on the instrument.
The DNA fragments in well mixed libraries were denatured with 0.1M NaOH to generate single-stranded DNA molecules, and loaded onto the reagent cartridge at 1.8 pM concentration.  The sequencing run was performed on Illumina NextSeq 500 system and carried out by running 75 cycles.

value: embryonic fibroblasts

tag: genotype

value: wildtype


title: embryonic fibroblasts, wt2 (tRNA)

tag: cell type


title: RR057i_00106_I17_S265

state: CA


title: RR057i_00094_I13_S201


title: RR057i_00104_E17_S261


title: embryonic fibroblasts, ko2 (tRNA)

value: Ate1 KO


title: embryonic fibroblasts, ko1 (tRNA)


title: embryonic fibroblasts, ko3 (tRNA)


title: RR057i_00099_G15_S231

value: M


title: RR057i_00100_I15_S233


title: RR057i_00103_C17_S259


title: embryonic fibroblasts, wt2 (tRF)

extract_protocol:
Agarose electrophoresis was used to check the integrality of total RNA samples, and NanoDrop ND-1000 instrument was used to measure the concentration of the samples.  NEBNext® Multiplex Small RNA Library Prep Set for Illumina® reagents were used in library preparation. tRF were extracted from total RNA samples and pretreated as following to remove some RNA modifications that interfere with small RNA-seq library construction: 3-aminoacyl (charged) deacylation to 3-OH for 3 adaptor ligation, 3-cP (2,3-cyclic phosphate) removal to 3-OH for 3 adaptor ligation, 5-OH (hydroxyl group) phosphorylation to 5-P for 5-adaptor ligation, m1A and m3C demethylation for efficient reverse transcription.  Pretreated total RNA of each sample was taken for tRF & tiRNA-seq library preparation.  Library preparation procedures included: 1) 3'-adapter ligation; 2) 5'-adapter ligation; 3) cDNA synthesis; 4) PCR amplification; 5) size selection of ~135-160 bp PCR amplified fragments (corresponding to ~15-40 nt small RNAs).  The completed libraries were quantified by Agilent 2100 Bioanalyzer. Libraries were mixed in equal amounts according to the quantification results, and used for sequencing on the instrument.
The DNA fragments in well mixed libraries were denatured with 0.1M NaOH to generate single-stranded DNA molecules, and loaded onto the reagent cartridge at 1.8 pM concentration.  The sequencing run was performed on Illumina NextSeq system using NextSeq 500/550 V2 kit (#FC-404-2005) and carried out by running 50 cycles.


title: embryonic fibroblasts, wt1 (tRF)


title: embryonic fibroblasts, ko3 (tRF)


title: RR057i_00062_E03_S37


title: RR057i_00120_M21_S333


title: embryonic fibroblasts, ko2 (tRF)


title: RR057i_00147_H11_S168


title: embryonic fibroblasts, wt3 (tRNA)


title: embryonic fibroblasts, ko1 (tRF)


title: RR057i_00068_E05_S69


title: RR057i_00098_E15_S229


title: RR057e_00733_L08_S124


title: Fibroblasts AD-HIES1_TNF

city: Bethesda

first: Manfred

last: Boehm

state: MD

address: 9000 Rockbille Pike

institute: NHLBI

data_processing:
RNA-seq data quality was assessed using FastQC
Reads obtained for each sample were aligned to the hg19 human reference genome using Tophat2
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text file include total counts values for all samples

source_name: skin biopsy

growth_protocol: 3 Control and 3 AD-HIES patient-derived fibroblasts lines were generated from 3-4-mm skin biopsies following informed consent under protocols approved by NHLBI IRB. The skin biopsy was cut into 1mm pieces and digested for 1h at 37C in 10ml of 0.1% Collagenase Type II (No.17101-015, Thermo Fisher Scientific) / 0.25 U/ml Dispase (No. 17105-0411, Thermo Fisher Scientific)/PBS solution. The skin pieces were then transferred to 2 wells of a 6 well culture plate, covered with cover slips to facilitate attachment, and cultured in Dulbecco’s modified Eagle medium (DMEM) supplemented with 20% fetal bovine serum and antibiotics in 20% O2, 5% CO2 incubator. Fibroblasts outgrown from the explants were subcultured after 3-4 weeks when they occupied most of the well’s surface. The fibroblasts then were cultured in DMEM medium supplemented with 10% fetal bovine serum (No. S10250, Atlanta biological, Flowery Branch, GA) and antibiotics.

extract_protocol:
Total RNA was isolated using TRIzol Reagent (No. 15596026, ThermoFisher Scientific).
One mg of total RNA was used as input for library preparation using the TruSeqRNA Sample Preparation Kit (Illumina) according to manufacturer’s instructions.

treatment_protocol: The fibroblasts were routinely grown in DMEM medium supplemented with 10% fetal bovine serum and seeded for experiments on six well plates at a density of 250,000 cells per well and switched to serum free medium after they reached confluence. After 24h in serum free medium, media was replaced with fresh serum free media and treated of not with TNFa 50ng/ml for 8h

tag: isolated cells

value: skin fibroblasts

value: TNFa 50ng/ml for 8h

tag: genotype/variation

value: AD-HIES STAT3 mutation


title: RR057i_00177_H21_S328


title: RR057e_00261_G14_S215


title: Fibroblasts CONTROL3_TNF

value: control


title: Fibroblasts AD-HIES3_TNF


title: RR057e_00203_K20_S315


title: RR057e_00130_E16_S245


title: embryonic fibroblasts, wt3 (tRF)


title: Fibroblasts CONTROL2_TNF


title: RR057i_00095_K13_S203


title: Fibroblasts CONTROL1_TNF


title: RR057e_00039_N16_S254


title: Fibroblasts AD-HIES3_NT

value: no treatment


title: RR057e_00058_J18_S282


title: RR057e_00504_K06_S91

value: other virus