title: Control Parotid - donor 6 [s06_PAR]


title: Kat5 knockout clone 1

status: Public on Mar 23 2023

type: SRA

city: Erlangen

first: Michael

last: Wegner

state: Bavaria

address: Fahrstr. 17

department: Institut of Biochemistry

country: Germany

description:
raw_counts.tsv
normalized_counts_Kat5.csv

library_source: transcriptomic

data_processing:
Demultiplexing of the sequencing reads was performed with Illumina bcl2fastq (2.20).
Adapters were trimmed with Skewer (version 0.2.2) (Jiang et al. 2014).
Quality trimming of the reads has not been performed.
Trimmed raw reads were aligned to mm10 using STAR (version 2.7.3) (Dobin et al. 2013).
Normalized counts have been calculated with DESeq2 (version 1.36.0) (Love et al. 2014) in R (version 4.2.1).
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes the number of aligned fragments for each gene; 1st column: ENSEMBL gene id, 2nd: column gene name, column 3-12: samples
Supplementary files format and content: comma-separated values (CSV) file of normalized read counts for WT and knockout samples

molecule: total RNA

organism: Mus musculus

growth_protocol: O9-1 cells were maintained at 37°C under 5% CO2 on 1/100 Matrigel coated dishes in preconditioned O9-1 medium (Nguyen et al. 2018).

extract_protocol:
RNA was harvested using Rneasy micro kit (Qiagen). 100 ng of total RNA was used for the construction of sequencing libraries.
Library preparation kit: TruSeq Stranded mRNA (Illumina)

tag: cell line

tag: cell type

value: murine cranial neural crest

tag: genotype

value: Kat5 knockout


title: 17-CL1_shTUT47_0hpi_3

city: DURHAM

first: ANKIT

last: GUPTA

address: TW 111 ALEXANDER DRIVE

department: RDBL

country: USA

institute: NIEHS

data_processing:
Base calling was done with Guppy version 5.0.10.
Demultiplexing of barcoded oligos was done with Deeplexicon.
The alignment to the reference transcriptome was done with Minimap2 version 2.20.
The poly (A) tail length was determined with Nanopolish version 0.13.3.
Differential gene expression analysis was performed using DESeq2.
Supplementary files format and content: Comma separated value file wih polyA tail length, mapping transcript and replicate information for each read.

source_name: 17-CL1 cells

growth_protocol: Mouse 17-CL1 cells were cultured in DMEM (Life Technologies) media supplemented with 10% Fetal Bovine Serum (FBS, Gemini Bio-Products), L-glutamine (Invitrogen), and Sodium pyruvate (Invitrogen). The 17-CL1 cells were cultured at 37ºC and in 5% CO2.

extract_protocol:
Total RNA was isolated with RNeasy Mini Kit (Cat. No. 74104, Qiagen)
5 µg of total RNA from 17-CL1 shCTL and shTUT4/7 knowckdown cells were used for each sample. Poly (A) containing mRNAs were enriched with Oligo(dT)25 Dynabead™ (61002, Thermo Fisher Scientific) and libraries were prepared using the Direct RNA Sequencing Kit (SQK-RNA002, Oxford Nanopore Technologies). All the libraries were multiplexed using the DeePlexiCon adapters, loaded to Nanopore R9 Flow Cells (FLO-MIN106D, Oxford Nanopore Technologies) and run on a MinION sequencer.

treatment_protocol: Cells were infected with 10 M.O.I. of MHV for different timepoints

tag: treatment

value: Non-infected with mouse hepatitis virus

tag: viral strain

tag: duration

value: 0 hours


title: 17-CL1_shCTL_24hpi_1

value: shCTL

value: Infected with mouse hepatitis virus

value: MHV-S (ATCC_VR-766)

value: 24 hours


title: Control SMG - donor 4 [s04_SMG]

city: San Francisco

first: Alejandro

last: Martinez Chibly

state: CALIFORNIA

address: 330A Guerrero Street

institute: Genentech

data_processing:
Basecalls performed using Illumina’s RTA  2.0.12
Sequenced reads were mapped to GRCh38.v25human genome using STAR v2.5.2a in  single-pass mode with the following parameters:  --outFilterMultimapNmax 10 –outFilterType BySJout --alignSJoverhangMin 5 --alignSJDBoverhangMin 3 --outFilterMismatchNmax 10 --outFilterMismatchNoverLmax 0.3 --alignIntronMin 21 --alignIntronMax 0 --alignMatesGapMax 0  --outSAMtype BAM SortedByCoordinate --bamRemoveDuplicatesType UniqueIdentical --quantMode GeneCounts
Gene counts were generated with STAR v2.5.2a built-in counting option --quantMode GeneCounts against a customized Gencode GRCm38 vM11 genome annotation GTF which included ERCCs.
A expression matrix was assembled using R. Genes with less than 5 reads in at least one of the samples were filtered out before differential gene expression analysis.
Differential expression was performed using the DESeq2, EdgeR and Limma-Voom R packages.
Assembly: hg38
Supplementary files format and content: Raw counts expression matrix.
Supplementary files format and content: Filtered counts expression matrix. Genes with less than 5 counts in at least one sample were removed.
Supplementary files format and content: TMM-normalized Counts Per Million expression matrix.

organism: Homo sapiens

source_name: Submandibular Gland

extract_protocol: Library preparation was performed according to the manufacturer’s instructions for the Illumina Nextera XT unstranded library kit. The libraries were then pooled and sequenced on a HiSeq2500 sequencer (Illumina).

tag: tissue

value: Submandibular Gland

value: Control


title: 17-CL1_shTUT47_0hpi_2


title: O9-1 WT biol rep 3

value: WT


title: Control Parotid - donor 4 [s04_PAR]

source_name: Parotid Gland

value: Parotid Gland


title: human_moDC_D2_t=0

city: Amsterdam

first: PETROS

last: DIMITRIADIS

email: p.dimitriadis@nki.nl, d.rao@nki.nl

state: Noord-Holland

address: Plesmanlaan 121

country: Netherlands

institute: NETHERLANDS CANCER INSTITUTE - NKI

data_processing:
The samples were mapped with STAR (v2.7.3a) to mouse reference genome Homo_sapiens.GRCh38.dna.primary_assembly using default settings.
 The read counts were computed with HTseq-count (v0.12.4) and were analyzed with DESeq2 (v1.30.1)

source_name: monocyte derived dendritic cells

growth_protocol: Human moDCs were generated from healthy donor buffy coats, as described by Ali et al. (48). In brief, buffy coats from healthy donors were obtained from Sanquin Amsterdam. Next, peripheral blood mononuclear cells (PBMCs) were isolated through Ficoll (Fisher Scientific) gradient separation and cells were stored at -80 °C. After thawing, monocytes were isolated with positive bead labeling using CD14 MicroBeads (Miltenyi Biotec) following manufacturer’s instructions. Isolated CD14+ cells were resuspended at 1 x 106 cells/ml in DC medium (GMP DC medium (CellGenix®) supplemented with 1% human serum (Sigma-Aldrich) and 1% P/S) with the addition of 50 IU/ml human recombinant IL-4 (Peprotech) and 800 IU/ml human recombinant GM-CSF (Peprotech) in a six-well plate (Corning). After 48 hours, DC medium with 200 IU/ml IL-4 and 3200 IU/ml GM-CSF was added and incubated for an additional 24 hours at 37 °C. The next day, DC medium was added with 50 IU/ml IL-4 and 800 IU/ml GM-CSF, in the presence of 0.5 μM AZD5582 or corresponding volume of control. After 24 hours, adherend DCs were dislodged from the plate and used for sequencing.

extract_protocol: Total RNA samples having RIN>8 were subjected to library generation. The library was prepared using TruSeq Stranded mRNA kit (Illumina) according to manual and analyzed using the Fragment analyzer.

value: monocyte derived dendritic cells

value: human moDC

value: No

tag: dose

tag: timepoint


title: human_moDC_D1_AZD

value: Yes


title: Irradiated SMG - donor 1 [s01_SMG_IR]

value: Irradiated


title: Control SMG - donor 3 [s03_SMG]


title: Control SMG - donor 7 [s07_SMG]


title: 17-CL1_shTUT47_0hpi_1


title: RNA-seq_PAF1AID-DLD1_NT_Rep3

city: Chicago

first: Ali

last: Shilatifard

state: IL

address: 320 E Superior St

department: Department of Biochemistry and Molecular Genetics

institute: Northwestern University Feinberg School of Medicine

data_processing:
Basecalls were performed using bcl2fastq v2.19 for Novaseq output.
ChIP-seq: low-quality bases were removed using Trimmomatic v0.33, with parameters TRAILING:30 MINLEN:20. Reads were aligned with bowtie v1.1.2 with parameters -m 1 -v 2, to human GRCh38 genome assembly with Ensembl gene annotation GRCh38 release 78. J-LAT 5a8 cells were aligned to the concatenated hg38/HIV-1 genome, using the same parameters as for the human samples. After alignment, HIV-1 reads were filtered out and normalized by the mapped read counts. Bigwig files were generated using an in-house R script utilizing bam2bw function, with a parameter to extend reads length -extLen=150 and scaled to reads-per-million (rpm).
RNA-seq:low-quality bases were removed using Trimmomatic v0.33, with parameters TRAILING:30 MINLEN:20. Reads were aligned to human GRCh38 genome assembly with Ensembl gene annotation GRCh38 release 78 using TopHat2 v2.1.0 (Kim et al., 2013), with parameters --no-novel-juncs --read-mismatches 2 --read-edit-dist 2 --max-multihits 20. Reads with non-primary alignment and low mapping quality were discarded. Reads were quantified using HTSeq v0.6.1.
PRO-seq: Low-quality bases and adapters from 30 ends of reads were removed using cutadapt 1.14 requiring a read length of 16–36 bp. Reads derived from ribosomal RNA were filtered out by mapping reads on human and fly ribosomal DNA. The remaining reads were aligned using bowtie 2.2.6 with option --very-sensitive, to a concatenated genome comprised of human hg38 (sample) and fly dm6 (spike-in) assemblies. The 5’ ends of aligned reads with MAPQ 30 were processed using bedtools genomecov v2.25.0 with paremeters -strand, -bg, and -5 to calculate coverage of 5’ ends. Read counts were normalized with total reads aligned to the spike-in genome (dm6), final bigwig files were scaled 10 to reads-per-million (rpm).
Assembly: hg38
Supplementary files format and content: bigWig files contain strand-specific, spike-in normalized PRO-seq signal.

molecule: polyA RNA

source_name: colon

growth_protocol: DLD1 and HCT116 cells were maintained in DMEM supplemented with 10% FBS. J-LAT 5a8, 11.1, and 6.3 were cultured in RPMI-1640 supplemented with 5 mM HEPES, 50 μg/mL P/S, 5 mM sodium pyruvate, and 10% FBS. Cells were cultured at 37°C in humidified incubator with 5% CO2. For RNA interference, cells were infected with a lentivirus containing shRNA against PAF1 using 8 μg/ml polybrene for 24hrs followed by 2 μg/ml puromycin for 2 days.

extract_protocol:
Extraction of total RNA was performed using RNeasy Mini kit (Qiagen, Cat# 74106). Briefly, 1million of DLD1_PAF1_AID cells were plated in a 6-well plate 24 hrs prior to treatment with 20μM iPAF1C versus DMSO or 500 μM auxin versus non-treated cells.
ChIP-seq: ChIP-seq was performed according to a previously published protocol (Lee et al., 2006). For RNA Pol II, and PAF1 ChIP-seq, the chromatin was sonicated using Covaris E220 for 4 min using the following sonication conditions: 10% duty cycle, 140 peak intensity power, 200 cycles per burst. Successively, pulldown of chromatin was carried out overnight at 4°C using the specific antibodies (Rpb1 NTD (D8L4Y) rabbit mAb for RNA Pol II and PAF1 (D9G9X) Rabbit mAb). DNA libraries were prepared by the HTP Library Preparation Kit for Illumina (KAPA). RNA-seq: Extraction of total RNA was performed using RNeasy Mini kit (Qiagen, Cat# 74106). Briefly, 1million of DLD1_PAF1_AID cells were plated in a 6-well plate 24 hrs prior to treatment with 20μM iPAF1C versus DMSO or 500 μM auxin versus non-treated cells. For performing RNA-seq polyadenylated RNA was isolated using NEBNext Poly(A) mRNA Magnetic Isolation Module (NEB, Cat# E7490L). This isolated poly(A)+ RNA was used to prepare libraries using NEBNext Ultra II Directional RNA Library Prep Kit (NEB, Cat# E7760L). PRO-seq: PRO-seq was performed according to the previously published protocol with minor modifications (Mahat et al., 2016a). Reverse transcription was performed with SuperScript III (ThermoFisher, Cat#18080044). cDNA was amplified using Phusion Hot Start II DNA polymerase (ThermoFisher, Cat#F549). DNA Libraries were purified using Beckman Coulter AMpure XP (Fisher Scientific, Cat#NC9959336).

treatment_protocol:
ChIP-seq: HCT116 and DLD1 cells were treated with 20μM of iPAF1C or DMSO as a control. Knocking down PAF1 was achieved by transducing cells with a lenti-viral vector expressing shRNA against PAF1.
RNA-seq: 1million of DLD1_PAF1_AID cells were plated in a 6-well plate 24 hrs prior to treatment with 20μM iPAF1C versus DMSO or 500 μM auxin versus non-treated cells.
Heat shock of mammalian cells was performed using ∼70%–80% confluent DLD1 cells by 15 adding pre-heated (42°C) conditioned media collected from identically growing cells (Mahat et al., 2016b). The heat shock cells were incubated at 42°C for 1.5 hour.
J-Lat 5a8, 11.1, and 6.3 cell lines were plated in 96-well flat bottom plates at a density of 150,000 cells/250 μL supplemented RPMI. Cells were DMSO-treated or treated with iPAF1C (12.5 μM), JQ1 (1μM), PHA (0.5 μg/mL), and PMA (1 nM) for 48 hours.

value: colon

value: colorectal adenocarcinoma

value: untreated


title: HC, Female 20 months control (CFO3)

city: Fort Collins

first: Devin

last: Wahl

state: Colorado

address: 1582 Campus Delivery, Moby Reception

institute: Colorado State University

data_processing:
Adapters trimmed & file QC by Fastp
Reads aligned with STAR and quantified using TEtranscripts
Differential expression analyzed with DESeq2
Assembly: mm10
Supplementary files format and content: Raw counts

source_name: Hippocampus

extract_protocol:
RNA for total RNA-seq extracted using Trizol and Zymo spin columns.
Libraries were prepared according to manufacturer's instructions using the Illumina TruSeq kit

value: Hippocampus

tag: strain

tag: age

value: 20 months

tag: Sex

value: Female

value: control


title: Control Parotid - donor 3  [s03_PAR]


title: O9-1 WT biol rep 1

value: murine cranial neural crest


title: RNA-seq_PAF1AID-DLD1_NT_Rep2


title: HC, Female 20 months control (CFO2)


title: human_moDC_D1_DMSO


title: human_moDC_D2_AZD


title: Irradiated SMG - donor 2 [s02_SMG_IR]

value: Submandibular Gland


title: human_moDC_D2_DMSO


title: 17-CL1_WT_48hpi_2

description: Direct RNA-seq as method described by nanopore

data_processing:
Base calling was done with Guppy version 5.0.10.
Demultiplexing of barcoded oligos was done with Deeplexicon.
The alignment to the reference transcriptome was done with Minimap2 version 2.20.
The poly (A) tail length was determined with Nanopolish version 0.13.3.
Supplementary files format and content: Comma separated value file wih polyA tail length, mapping transcript and replicate information for each read.

extract_protocol:
Total RNA was isolated using RNeasy Mini Kit (Cat. No. 74104, Qiagen)
5 µg of total RNA isolated from 17-CL1 wild-type cells was used for each sample. Poly (A) containing mRNAs were enriched with Oligo(dT)25 Dynabead™ (61002, Thermo Fisher Scientific) and libraries were prepared using the Direct RNA Sequencing Kit (SQK-RNA002, Oxford Nanopore Technologies). All the libraries were multiplexed using the DeePlexiCon adapters, loaded to Nanopore R9 Flow Cells (FLO-MIN106D, Oxford Nanopore Technologies) and run on a MinION sequencer.

value: Wild-type

value: Infected with mouse hepatitis virus

value: MHV-S (ATCC_VR-766)

value: 48 hours


title: YZ6_ESR2SUZ12E3N, input

city: new haven

first: Yuping

last: Zhou

state: CT

address: 310 cedar street

department: OB/GYN

institute: Yale

library_source: genomic

data_processing:
Data generated during sequencing runs are simultaneously transferred to the YCGA high-performance computing cluster
Supplementary files format and content: bedGraph

molecule: genomic DNA

source_name: Ishikawa

growth_protocol: Ishikawa cells were maintained in MEM (Sigma-Aldrich, MO) both containing 10% Fetal Bovine Serum (FBS) and 1% penicillin/streptomycin

extract_protocol:
Lysates were clarified from sonicated nuclei and Protein-DNA complexes were isolated with antibody.
Samples are sequenced using 100bp paired-end sequencing on an Illumina HiSeq 4000 according to Illumina protocols.Briefly, approximately 5-10ng of DNA is cleaned up using Ampure XP SPRI beads (Beckman Coulter Genomics).  The DNA is then end-repaired, A-tailed, adapter ligated and PCR enriched (8 -10 cycles). Indexed libraries that meet appropriate cut-offs are quantified by both RT-qPCR using a commercially available kit (KAPA Biosystems) and insert size distribution determined with the LabChip GX. Samples with a yield of ≥0.5 ng/µl are used for sequencing.  Flow Cell Preparation and Sequencing: Sample concentrations are normalized to 1 nM and loaded onto an Illumina HiSeq4000 flow cell at a concentration that yields 25 - 50 million passing filter clusters per sample. Samples are sequenced using 100bp paired-end sequencing on an Illumina HiSeq 4000 according to Illumina protocols.

treatment_protocol: Ishikawa cells (~70% confluence) were transfection  with 40ug of either pcDNA 3.1(+)/Flag-ERα or pcDNA /Flag-ERβ for 18 hours and subsequently treated with E3 for another 24 hours .

value: endometrial adenocarcinoma

tag: fraction

value: input


title: 17-CL1_WT_48hpi_3


title: YZ8_ESR2SUZ12E3Y, input

value: Treated with Estriol for 24 hours


title: RNA-seq_PAF1AID-DLD1_DMSO_Rep3

value: DMSO


title: O9-1 WT biol rep 4

value: WT


title: HC, Male 20 months control (CMO1)

value: Male


title: HC, Male 20 months control (CMO6)


title: human_moDC_D1_t=0

value: monocyte derived dendritic cells

value: human moDC

value: No


title: O9-1 WT biol rep 2


title: 17-CL1_WT_48hpi_1


title: HC, Male 20 months control (CMO3)

value: Hippocampus

value: 20 months


title: 17-CL1_WT_24hpi_3

value: 24 hours


title: YZ3_ESR1SUZ12E3Y, input


title: HC, Female 20 months control (CFO1)

value: Female

value: control


title: 17-CL1_WT_24hpi_2

value: Wild-type

value: Infected with mouse hepatitis virus


title: HC, Female 20 months treated with 3TC (DFO5)


title: RNA-seq_PAF1AID-DLD1_DMSO_Rep2

value: colon

value: colorectal adenocarcinoma


title: RNA-seq_PAF1AID-DLD1_DMSO_Rep1


title: YZ8_ESR2SUZ12E3Y

value: endometrial adenocarcinoma

value: ChIP


title: 17-CL1_WT_24hpi_1

value: MHV-S (ATCC_VR-766)


title: YZ6_ESR2SUZ12E3N


title: HC, Female 20 months treated with 3TC (DFO8)


title: YZ3_ESR1SUZ12E3Y


title: RNA-seq_PAF1AID-DLD1_Auxin_Rep3

value: Auxin 500uM


title: RNA-seq_PAF1AID-DLD1_NT_Rep1

value: untreated


title: TNFa_4

city: Montréal

first: Theo

last: Crosson

state: Quebec

address: 2900 Boulevard Edouard Montpetit

country: Canada

institute: Université de Montréal

data_processing:
Demultiplexing
For analysis, sequences were trimmed for sequencing adapters and low quality 3' bases using Trimmomatic version 0.35 and aligned to the reference mouse genome version GRCm38 (gene annotation from Gencode version M25, based on Ensembl 100) using STAR version 2.7.1. Gene expressions were obtained from STAR as readcounts and computed using RSEM in order to obtain normalized gene and transcript level expression in FPKM.
Assembly: GRCm38
Supplementary files format and content: STAR readcount
Supplementary files format and content: FPKM

source_name: jugular nodose complex ganglia (JNC)

extract_protocol:
RNA was separated from protein and DNA by mixing 500μL sample in Trizol with 100μL chloroform before ultracentrifugation (15min, 16000g, 4°). The upperphase was mixed with a half volume of 100° isopropanol, transferred to a purification column, and the RNA purified using the kit PureLink™ RNA Micro Scale (Thermofisher #12183016) following manufacturer’s instructions.
RNA from all samples were extracted using the the kit PureLink™ RNA Micro Scale (Thermofisher #12183016), quality controlled, before mRNA library preparation mRNA KAPA mRNA HyperPrep Kit (KapaBiosystems #KR1352). All barcoded samples were then sequenced with a Nextseq500 (Illumina) with 75-cycle single-end read.

treatment_protocol: NaV1.8cre::tdTomatofl/wt mice were sacrificed and their jugular nodose complex ganglia (JNC) harvested. For each replicate, JNC from males and females were pooled and enzymatically dissociated, seeded at 10000 neurons per well, and cultured for 24 hours with BDNF (50 ng/mL), IL-1β (100 ng/mL), TNF-α (100 ng/mL), or vehicle (Neurobasal medium supplemented with B27 (2%), AraC (0.01 mM), L-Glutamine (200 nM), penicillin (100 U/mL) and streptomycin (100 μg/mL)). Cells were then mechanically detached with a cell scraper, the nociceptors sorted by flow cytometry (tdTomatohi) and collected into Trizol.

value: jugular nodose complex ganglia (JNC)

value: Nociceptors (Nav1.8+)

value: TNFa


title: RNA-seq_PAF1AID-DLD1_Auxin_Rep2


title: HC, Male 20 months treated with 3TC (DMO1)

value: Hippocampus

value: Male


title: TNFa_3


title: YZ1_ESR1SUZ12E3N


title: RNA-seq_PAF1AID-DLD1_Auxin_Rep1


title: AIGA hidrotic lesion [654-1]

city: nagasaki

first: Naoya

last: Murayama

state: nagasaki

country: Japan

institute: Nagasaki  University

data_processing:
An Illumina Casava1.8.2 software was used for base-calling.
Sequenced reads were mapped to the human reference genome sequences (hg19) using a TopHat v2.0.13 software in combination with Bowtie2 ver. 2.2.3 and SAMtools ver. 0.1.19 softwares.
The fragments per kilobase of exon per million mapped fragments (FPKMs) were calculated using a Cuffnorm version 2.2.1 software.
Genome_build: hg19
Supplementary_files_format_and_content: Excel

source_name: AIGA hidrotic lesion

growth_protocol: Skin tissues were taken by skin punch biopsies (diameter of 4-5 mm) from anhidrotic and hidrotic areas, and were fixed in a 10% formalin neutral buffer solution at room temperature overnight, and then paraffin-embedded.

extract_protocol:
Paraffin-embedded (FFPE)-skin tissues were cut into 10 µm thick sections, then sweat glands were isolated by laser micro-dissection (LMD 7000, Leica).
Total RNAs were extracted from the cells with an miRNeasy FFPE kit (QIAGEN)
NGS library preparation was conducted using a SMARTer ® Stranded Total RNA Sample Prep Kit-Pico Input Mammalian (Clontech, TaKaRa) kit
Sequencing was performed on an Illumina HiSeq 2500 platform in a 75-base single-end mode.

treatment_protocol: No treatement

tag: subject status

value: Acquired idiopathic generalized anhidrosis (AIGA) patient

tag: subject id

value: sweat gland

tag: tissue type

value: hidrotic lesion/skin


title: RNA-seq_PAF1AID-DLD1_iPAF1C_Rep2

value: iPAF1C 20uM


title: IL1b_4


title: TNFa_2


title: HC, Male 20 months treated with 3TC (DMO2)

value: 20 months


title: AIGA anhidrotic lesion [654-2]

source_name: AIGA anhidrotic lesion

value: anhidrotic lesion/skin


title: RNA-seq_PAF1AID-DLD1_iPAF1C_Rep3

value: colon

value: colorectal adenocarcinoma


title: RNA-seq_PAF1AID-DLD1_iPAF1C_Rep1


title: IL1b_3


title: TNFa_1


title: HC, Male 20 months treated with 3TC (DMO5)


title: YZ1_ESR1SUZ12E3N, input

value: endometrial adenocarcinoma

value: input


title: AIGA anhidrotic lesion [340-1]


title: HC, Female 9 months (YF8)

value: 9 months

value: Female


title: ChIP-seq_PolII_PAF1AID-DLD1_Auxin

value: Auxin 500uM

tag: chip antibody

value: Rpb1 NTD (D8L4Y)


title: HC, Female 9 months (YF2)


title: HC, Female 20 months treated with 3TC (DFO4)


title: AIGA hidrotic lesion [448-1]


title: HC, Female 9 months (YF3)


title: BDNF_4

value: jugular nodose complex ganglia (JNC)

value: Nociceptors (Nav1.8+)

value: BDNF


title: AIGA hidrotic lesion [340-2]

value: Acquired idiopathic generalized anhidrosis (AIGA) patient


title: IL1b_2


title: ChIP-seq_PolII_PAF1AID-DLD1_NT

tag: cell line

value: untreated


title: ChIP-seq_PolII_PAF1AID-DLD1_iPAF1C_Rep1

tag: cell type


title: AIGA hidrotic lesion [172-2]

value: sweat gland

value: hidrotic lesion/skin


title: ChIP-seq_PolII_PAF1AID-DLD1_iPAF1C_Rep2

tag: genotype

value: iPAF1C 20uM


title: ChIP-seq_PolII_PAF1AID-DLD1_DMSO_Rep2

tag: treatment

value: DMSO


title: ChIP-seq_PolII_PAF1AID-DLD1_DMSO_Rep3

value: colon


title: LRS4 deletion replicate3

city: charlottesville

first: Jeffrey

middle: S

last: Smith

state: VIRGINIA

address: 1340 jpa pinn hall

department: Biochemistry and Molecular Genetics

institute: University of Virginia

data_processing:
Barcoded DNA was sequenced on an Illumina Nextseq 500 and Nextseq 2000. For samples run on Nextseq 500, individual lanes were pooled together for unique samples.
Micro-C sequencing reads were filtered and mapped using Bowtie2.
HiC-Pro pipeline was used to generate iteratively corrected genome matrix. Differential interaction contacts were analysed using BART3D.
Using R package HiTC the contact maps were created.
Assembly: sacCer3
Supplementary files format and content: Text files for every sample
Library strategy: Micro-C seq

organism: Saccharomyces cerevisiae

source_name: yeast cells

growth_protocol: All cells were grown in YPD medium with 2% glucose.

extract_protocol:
Micro-C XL was performed following standard protocol from Hsieh et al., 2016. Briefly, exponential yeast cells were dual crosslinked with 3% formaldehyde and EGS and digested with appropriate amount of MNase to get >95% mononucleosomes. The chromatin pellet obtained was dephosphorylated, end-repaired and biotinylated through ligation, followed by isolation of dinucleosomal DNA from an agarose gel. The isolated DNA was processed for library preparation according to Illumina NEBNext protocol and paired-end sequencing was performed on an Illumina Nextseq 500 and Nextseq 2000 in the UVA Genome Analysis and Technology Core.
Illumina sequencing protocol

treatment_protocol: No treatment done.

tag: collection time point

value: Log

value: No treatment

value: LRS4 deletion

value: yeast cells


title: BDNF_2


title: BDNF_1


title: HC, Male 9 months (YM1)

value: Hippocampus

value: 9 months

value: Male


title: LRS4 deletion replicate2


title: IL1b_1

value: jugular nodose complex ganglia (JNC)


title: HC, Male 9 months (YM2)


title: AIGA anhidrotic lesion [172-1]

value: anhidrotic lesion/skin


title: FOB1 deletion replicate1

value: FOB1 deletion


title: tumor Treg-PBS

city: New York

first: Ning

last: Yang

state: NY

institute: MSKCC

data_processing:
The sequencing data were primarily analyzed by the 10X cellranger pipeline (v6.1.1)
cellranger mkfastq was used for sample demultiplexing and fastq generation.
cellranger count was used to align reads to the 10X pre-built mouse reference genome (refdata-gex-mm10-2020-A) and to extract gene expression UMI counts matrix.
Assembly: mm10
Supplementary files format and content: UMI counts matrix generated by 10X cellranger count; matrix.mtx.gz stores UMI counts per gene per cell; features.tsv.gz stores gene annotations; barcodes.tsv.gz stores cell barcodes.

source_name: tumor Treg

extract_protocol:
RNA was harvested using Chromium Single Cell V(D)J Solution from 10x Genomics according to the manufacturer’s instructions
Cell-barcoded 5′ gene expression libraries were sequenced on an Illumina No-vaSeq6000 system with pair-end reads (28 bp for read 1 and 91 bp for read 2).

value: tumor Treg

value: PBS


title: ChIP-seq_Input_PAF1AID-DLD1

value: colorectal adenocarcinoma

value: untreated


title: HC, Male 9 months (YM8)


title: tumor Treg-rMVA

value: rMVA


title: Vehicle_3

value: Nociceptors (Nav1.8+)

value: Vehicle


title: Vehicle_2


title: ChIP-seq_PolII_PAF1AID-DLD1_DMSO_Rep1

value: colon

value: DMSO

value: Rpb1 NTD (D8L4Y)


title: LRS4 deletion replicate1

value: Log

value: No treatment

value: LRS4 deletion

value: yeast cells


title: BDNF_3

value: jugular nodose complex ganglia (JNC)

value: BDNF


title: kdrl:mCherry-, sele:GFP+ 72 hpf, rep3

city: Boston

first: Leonard

last: Zon

state: MA

address: 1 Blackfan Circle

department: Oncology/Hematology

institute: Boston Children's Hospital

description:
Any cells from whole embryos that were GFP + and mCherry -
S_danRer7_peaks.narrowPeak

data_processing:
All zebra ATAC-Seq datasets were aligned to build version danRer7 of the zebrafish genome using Bowtie2 (version 2.2.1)  (Langmead et al., 2012) with the following parameters: --end-to-end, -N0, -L20. We used the MACS2 version 2.1.0 (Zhang et al., 2008) peak finding algorithm to identify regions of ATAC-Seq peaks, with the following parameter --nomodel --shift -100 --extsize 200. A q-value threshold of enrichment of 0.05 was used for all datasets.
Assembly: danRer7
Supplementary files format and content: bed file of called peaks

organism: Danio rerio

source_name: kdrl:mCherry, sele:GFP transgenic zebrafish embryos (wild-type)

growth_protocol: Double transgenic kdrl:mCherry and sele:GFP zebrafish embryos were grown under standard conditions at 28C in E3 buffer until 72 hpf.  Embryos were screened for transgene expression and then homogenized, filtered, and sorted using FACS into PBS, collecting up to 50,000 cells.

extract_protocol:
Approximately 12,000 to 50,000 kdrl:mCherry and sele:GFP double positive cells, sele:GFP single positive cells, kdrl:mCherry single positive cells, and double negative cells were lysed and nuclei subjected to Tn5 transposase (Corces et al., 2017). Libraries were prepared for sequencing as previously described.
Libraries were prepared as previously described (Corces et al., 2017) and sequenced on an Illumina Hiseq 2500

treatment_protocol: No treatments

value: wild-type

value: embryos


title: Wild-type replicate2

value: Wild type


title: ChIP-seq_PAF1_DLD1_NuiPAF-22R-26

value: colorectal adenocarcinoma

value: WT

value: NUiPAF-22 20uM

value: PAF1 (D9G9X, Rabbit mAb).


title: Vehicle_1

value: Nociceptors (Nav1.8+)

value: Vehicle


title: ChIP-seq_PAF1_DLD1_iPAF1C

value: colon

value: iPAF1C 20uM


title: kdrl:mCherry-, sele:GFP- 72 hpf, rep3

description:
Any cells from whole embryos that were GFP - and mCherry -
N_danRer7_peaks.narrowPeak


title: kdrl:mCherry-, sele:GFP- 72 hpf, rep2


title: WT, Ctf3-myc, IP, replicate1

data_processing:
Barcoded DNA was sequenced on an Illumina Nextseq 500. Individual lanes were pooled together for unique samples.
Sequencing reads were mapped to the sacCer3 genome using bowtie2 with default settings.
The aligned reads were filtered, indexed using SAMtools to generate bam files which were converted to bedtools.
MACS was used for enriched peaks and then analysed the differential binding in R using DiffBind.
Assembly: sacCer3
Supplementary files format and content: BigWig files for every sample

growth_protocol: All cells were grown in YPD medium with 2% glucose

extract_protocol:
Exponential yeast cells were crosslinked with 1% formaldehyde and lysed in a Mini-beadbeater. The chromatin was sonicated, quantified and incubated with anti-myc antibody overnight followed by 2 hr incubation with Protein G-Dynabeads. The non-specific binding was removed by washing and DNA was eluted by reverse crosslinking and Proteinase K digestion, followed by processing for Illumina DNA sequencing libraries. Libraries were sequenced on an Illumina NextSeq 500 by the UVA Genome Analysis and Technology Core.
Libraries were made according to Illumina's TrueSeq protocol

value: Log

value: anti-myc


title: kdrl:mCherry+, sele:GFP+ 72 hpf, rep3

description:
Any cells from whole embryos that were GFP + and mCherry +
FS_danRer7_peaks.narrowPeak


title: WT, Ctf3-myc, IP, replicate2

value: No treatment


title: kdrl:mCherry+, sele:GFP- 72 hpf, rep3

description:
Any cells from whole embryos that were GFP - and mCherry +
F_danRer7_peaks.narrowPeak


title: ChIP-seq_PAF1_DLD1_DMSO

value: untreated


title: ChIP-seq_PolII_HCT116_NUiPAF-22

value: colorectal carcinoma

value: Rpb1 NTD (D8L4Y)


title: kdrl:mCherry+, sele:GFP- 72 hpf, rep2

value: wild-type


title: ChIP-seq_PolII_HCT116_shPAF1

value: PAF1 knockdown


title: WT, Lrs4-myc, IP, replicate2

value: yeast cells


title: ChIP-seq_Input_DLD1

value: colorectal adenocarcinoma


title: kdrl:mCherry+, sele:GFP+ 72 hpf, rep2

value: embryos


title: WTPKP2M05257903

city: Leiden

first: Sebastiaan

middle: Johannes

last: van Kampen

address: Sylviusweg 62

institute: LUMC

data_processing:
STAR_2.4.2a mapping to reference genome
read count analysis HTSeq 0.6.1
Assembly: GRCm38/mm10
Supplementary files format and content: raw read counts in matrix table

source_name: Cardiac tissue

growth_protocol: Mice were kept under standard housing conditions.

extract_protocol:
Trizol reagent (Thermo Fisher)
Truseq RNA stranded polyA

value: Ventrical - mix of left and right

value: PKP2 WT/WT

value: 8 weeks


title: ChIP-seq_PolII_HCT116_iPAF1C

value: WT


title: Wild-type replicate1

value: Wild type


title: kdrl:mCherry-, sele:GFP- 72 hpf, rep1


title: LRS4 deletion, Brn1-myc, IP, replicate2

value: Brn1-myc in LRS4 deletion


title: WTPKP2M01254701


title: WTPKP2M01258004


title: kdrl:mCherry-, sele:GFP+ 72 hpf, rep2


title: WT, Lrs4-myc, IP, replicate1

value: Log


title: HETPKP2M04254707

value: PKP2 c.1755A/WT


title: Irradiated parotid gland

library_source: transcriptomic single cell

data_processing:
Basecalls performed using Illumina’s RTA  2.0.12
Sample demultiplexing, alignment and gene counts were performed using the 10X Genomics CellRanger v3.0.1 pipeline using default settings.
Secondary analysis was performed using Seurat v3
Assembly: mm10
Supplementary files format and content: 10X Genomics Cell Ranger v3.0.1 filtered gene counts matrices.

source_name: parotid gland

extract_protocol: Library preparation was performed according to the manufacturer’s instructions for the 10× Chromium single-cell kit (10x Genomics). The libraries were then pooled and sequenced on four lanes on a NextSeq500 sequencer (Illumina).

value: parotid gland

value: Irradiated


title: Control parotid gland

value: Non-Irradiated


title: kdrl:mCherry-, sele:GFP+ 72 hpf, rep1


title: WT, Brn1-myc, IP, replicate2

value: No treatment

value: anti-myc


title: HETPKP2M03254706


title: ChIP-seq_Input_HCT116

value: colon

value: colorectal carcinoma

value: untreated


title: ChIP-seq_PolII_HCT116_DMSO

value: DMSO

value: Rpb1 NTD (D8L4Y)


title: LRS4 deletion, Brn1-myc, IP, replicate1

value: yeast cells


title: kdrl:mCherry+, sele:GFP- 72 hpf, rep1

value: wild-type

value: embryos


title: HETPKP2M02257908

value: Ventrical - mix of left and right

value: 8 weeks


title: WT, Brn1-myc, IP, replicate1

value: Log


title: WTPKP2M03257902

value: PKP2 WT/WT


title: HETPKP2M02254705

value: PKP2 c.1755A/WT


title: 64_2_2

city: West Haven

first: Francesc

last: Lopez

department: Department of Genetics

institute: Yale University

description: replicate 2

data_processing:
According to Illumina protocol, the libraries underwent 101-bp paired-end sequencing using an Illumina NovaSeq (S4). Basecalls performed using CASAVA version 1.8.2
Trimming of the reads for the presence of adapters and low quality bases was performed with fastp with default parameters.
Trimmed reads were mapped to the Neurospora crassa OR74A reference genome (FungiDB release 43) with hisat2 v2.1.0 indicating that reads correspond to the reverse complement of the transcripts. Alignments with quality score below 20 were excluded from further analysis.
Gene counts were produced with stringtie v1.3.3b and the python script “prepde.py” provided in the package. Stringtie was limited to reads matching the reference annotation.
LOX v1.4 was applied to the tallies for each sample for each gene to estimate gene expression levels and credible intervals across developmental stages. LOX provides relative gene expression levels standardized by the lowest sample, with credible intervals
Assembly: Neurospora crassa OR74A (FungiDB release 43)
Supplementary files format and content: Tab delimited and CSV text files including raw counts and LOX output, respectively. LOX provides relative gene expression levels standardized by the lowest sample, with credible intervals

organism: Neurospora crassa

source_name: crossed mutant protoperithecia

growth_protocol: Conidia of N. crassa mat 1-2-1 mutant (FGSC#4564, mat a[m1]s-3B cyh-1) were  harvested from cultures on Bird medium. 2 ml filtrate conidia spore was plated out on cellophane membrane covering solid SCM in petri dish (9cm in diameter) and incubated were incubated in a refrigerated incubator (VWR Signature™ Diurnal Growth for 6 days until abundant protoperithecia appear.

extract_protocol:
Cellophane membranes with fungal tissues were collected at protoperithecial stage (0 time point right before the crossing) and 2h after crossing. Tissue samples were flash frozen in liquid nitrogen and stored at ﹣80 C. All tissues/perithecia that were collected from a single plate were counted as one biological replicate. At least three biological replicates were prepared for each sampled time-point.
Total RNA was extracted from homogenized tissue with TRI REAGENT (Molecular Research Center) as in Clark et al. (2008).
Sequencing libraries were produced from purified total RNA samples by the Illumina TruSeq stranded protocol. The libraries underwent 101 bp paired-end sequencing.

treatment_protocol: Protoperithecia from mat 1-2-1 muant were crossing with conidia from wild type FGSC#2489

value: FGSC#4564, mat a[m1]s-3B cyh-1

tag: time point

value: 2 hr after crossing

tag: morphology

value: crossed protoperithecia

tag: Stage


title: 64_2_1

description: replicate 1


title: iPSC-derived neuron (monolayer), day 66, biol rep 1

city: Kawasaki

first: Waka

last: Lin

state: Kanagawa

address: 3-25-22, Tonomachi

institute: Ricoh Company, Ltd.

data_processing:
The libraries were sequenced as paired-end 75 bp reads on the NextSeq 550 system (Illumina).
Low-quality and low-complexity reads were removed using PRINSEQ++ version 1.2 (Ho and Patrizi, 2021) (parameters -trim_tail_left 10 -trim_tail_right 10 -trim_qual_left 30 -trim_qual_right 30 -ns_max_n 0 -min_len 30 -threads 8)
The reads were mapped to the human reference genome GRCh38 and the GENCODE 34 annotations, including the ERCC spike-in references using HISAT2 version 2.1.0 with default parameters (Kim et al., 2019).
The mRNA expression levels were estimated as transcripts per million (TPM) using StringTie version 2.0.6 (Kovaka et al., 2019).
Assembly: Human GENCODE genome assembly GRCh38.p13

source_name: CIRM line CW50065

extract_protocol:
The cells were washed once in PBS, collected by centrifugation, and frozen for storage in a -150 °C freezer. Total RNA were extracted using the RNeasy Micro Kit (Qiagen) following the manufacturer’s user manuals.
1 ng of RNA per sample for cDNA library preparation according to the Smart-seq 2 method (Picelli et al., 2014).

value: CIRM line CW50065

tag: donor type

value: Healthy

value: iPSC-derived neuron

tag: culture type

value: monolayer

tag: treatment for_differentiation

value: Quick-Neuron Excitatory

tag: culture time

value: Day 66


title: kdrl:GFP -, 72 hpf

description:
cells that were not GFP+
EH1-2.expression.xlsx

data_processing:
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence using cutadapt, then mapped to UCSC danRer7 whole genome using Tophat 2.0.11 without novel splicing form calls
Transcript abundance and differential expression were calculated with Cufflinks 2.2.1. FPKM values were used to normalize and quantify each transcript
Genome_build: Ensembl Zv9 (UCSC danRer7)
Supplementary_files_format_and_content: excel files include RPKM values for each Sample

source_name: kdrl:GFP transgenic zebrafish embryos (wild-type)

growth_protocol: Transgenic zebrafish stocks (kdrl:GFP or kdrl:mCherry; sele:GFP double positive) were incrossed and embryos were grown under standard conditions at 28C in E3 buffer until 72 hpf.  Embryos were screened for transgene expression and then homogenized, filtered, and sorted using FACS into PBS, collecting at least 10,000 cells per group (max 300,000).

extract_protocol:
Total RNA was collected using Trizol LS and GenElute LPA carrier per manufacturer instructions
Libraries were prepared using Ribogone kit (Clontech) and the SMARTer Universal Low input RNA Kit (Clontech; input was 50 ng total RNA for each sample) and sequenced on the Illumina Hiseq 2500

tag: developmental stage

value: 72 hpf

tag: genotype/variation

value: kdrl:GFP -

tag: tissue

value: whole embryos


title: kdrl:GFP+, 72 hpf

description: Any cells from whole embryos that were GFP +

data_processing:
the inDrops single-cell RNA-seq analysis follows the instruction as descriibed in https://github.com/indrops/indrops. inDrops Library v3 requires manual demultiplex raw bcl into different samples. Zebrafish Bowtie transcriptome index was build based on Ensembl GRCz10 genome sequenc and gene annotation.
Genome_build: GRCz10
Supplementary_files_format_and_content: The output data matrix contains the raw count of each gene for each cell barcode

growth_protocol: Transgenic kdrl:GFP zebrafish were incrossed and embryos were grown under standard conditions at 28C in E3 buffer until 72 hpf.  Embryos were screened for transgene expression and then homogenized, filtered, and sorted using FACS into PBS, collecting at least 25,000 cells.

extract_protocol:
Approximately 2,000 kdrl:GFP+ cells were encapsulated using the inDrops method (Zilionis et al., 2017). Libraries were prepared for sequencing as previously described.
Libraries were prepared as previously described (Zilionis et al., 2017) and sequenced on an Illumina Hiseq 2500
Single cell RNA-seq (inDrops)

value: whole embryo


title: Tomo-seq_zebrafish tail at 72 hpf

description: 40 cryosections were collected along the dorsal-ventral axis of the frozen tail tissue

data_processing:
Library strategy: RNA-tomography (tomo-seq)
Paired end reads were aligned to the transcriptome using bwa (version 0.6.2) with default parameters. The zebrafish transcriptome was based on genome release zv9 (and contained improved gene annotations as described in the Junker, et al., 2014). The right mate of each read pair was mapped to the ensemble of all transcripts and to the set of 92 ERCC spike-ins in sense direction. Reads mapping equally to multiple loci were discarded.
Mapped reads were assigned to sections based on barcodes according to the CEL-seq protocol (Hashimshony et al., Cell Reports, 2012) Mapping and demultiplexing were done as described in Grün et al., Validation of noise models for single-cell transcriptomics, Nature Methods, 2014. The script needed to process the data is available in https://www.dropbox.com/sh/7s59vvocwtn2ct4/AAAR6pWte8xOzObCYONAFPvIa?dl=0 , where script_tomo.sh is an example for how to run the mapping scripts.
Genome_build: zv9

source_name: mpx:GFP transgenic zebrafish embryo (wild-type, Casper background)

growth_protocol: mpx:GFP transgenic zebrafish were incrossed and embryos were grown under standard conditions at 28C in E3 buffer until 72 hpf.  Embryos were screened for transgene expression and then euthanized by tricaine overdose. The region of the tail containing the CHT was isolated using a scalpel and then snap-frozen on dry ice.

extract_protocol:
The total RNA from individual cryosections (40 in total, each 8 µm-thick) was extracted using Trizol reagent.
The RNA from individual cryosections was barcoded during a reverse transcription step prior to library synthesis according to the method previously described (Junker et al., 2014).

treatment_protocol: No treatment

value: tail


title: iPSC-derived neuron (monolayer), day 88, biol rep 1

value: Day 88


title: Severe  3

type: RNA

city: Cincinnati

first: Ameet

last: Chimote

state: Ohio

address: 231 Albert Sabin Way, ML 0585, CARE 6884

department: Internal Medicine- Nephrology

institute: University of Cincinnati

hyb_protocol: 100 ng RNA from each sample was used for hybridization.Hybridization was performed at 65°C for 16 hours using PCR

scan_protocol: Post hybridization steps and scanning were performed on the nCounter Prep Station and nCounter Flex instrument

data_processing: RCC files containing raw counts for 770 genes provided from nanostring were loaded into nSolver Analysis Software 4.0 and then imported into the nSolver Advanced Analysis plug-in (version 2.0) for cell type profiling, pathway score analysis, and differential gene expression; and Rosalind software (OnRamp Bio) for normalized gene expression data. The counts were normalized for housekeeping genes and positive controls.

source_name: peripheral blood mononuclear cells

label_protocol: No label used in NanoString

extract_protocol: RNA isolation from PBMCs was performed using the E.Z.N.A. total RNA isolation kit (Omega Bio-tek) and quantified using a NanoDrop 2000 spectrophotometer (ThermoFisher Scientific). The RNA quality was analyzed using an Agilent 2100 Bioanalyzer (Agilent); and concentrated using the RNA Clean and Concentrator kit (Zymo Corp.)

tag: patient cohort

value: Severe COVID-19

tag: age

tag: Sex

value: Male


title: Dexa 2

value: Severe COVID-19+ Dexa

value: Female


title: Dexa 3


title: 64_2_3

description: replicate 3

tag: strain

value: FGSC#4564, mat a[m1]s-3B cyh-1

value: 2 hr after crossing

value: crossed protoperithecia


title: Dexa 4


title: Dexa 1


title: 64_1_3

description: replicate 3

source_name: mutant protoperithecia

value: 6-day of protoperithecial production

value: protoperithecia


title: Severe  2


title: cotreated biol rep C

city: High Point

first: Heather

middle: Bennett

last: Miller

state: NC

address: One University Parkway

department: Chemistry

institute: High Point University

data_processing:
Quality control of resulting reads included removing adapter-containing reads, removing reads where “N” was > 10%, and removing low-quality reads where the quality value of over 50% of the bases was ≤ 5.
The remaining reads were mapped to the reference genome (ATCC 43300) using Bowtie2.
Gene expression levels were quantified as fragments per kilobase of transcript sequence per million base pairs sequenced (FPKM) and averaged among biological triplicate samples.
Pearson correlation analysis quantified the correlation among biological triplicates. Only one sample out of twelve did not meet the correlation criteria of 0.92 (cotreated biol rep A) and it was removed from subsequent analysis.
Assembly: ATCC 43300 https://genomes.atcc.org/genomes/79691302ed634fef
Supplementary files format and content: An Excel spreadsheet for all treatment comparison groups that contain all analyzed replicates, gene information, read counts, fpkm, log2fold change and adjusted pvalues

organism: Staphylococcus aureus

growth_protocol: S. aureus 43300 was purchased from the American Type Culture Collection. Cultures were grown overnight in CAMHB at 37 °C with shaking. Mid-log-phase cultures were diluted to 5 × 10^5 CFU mL–1 in CAMHB.

extract_protocol:
Total RNA was purified from 3mL of culture using a Qiagen RNeasy kit and Thermo's Turbo DNase kit.
RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: The cell suspension (3 mL) was aliquoted into sterile culture tubes, and loratadine was added to the appropriate concentration (≤25% of the compound MIC = 50 uM). Oxacillin was added to a separate culture tube at 4 ug/mL. Cotreatment consisted of both oxacillin (4 ug/mL) and loratadine (50uM). Untreated cultures served as negative controls. These treatments continued for 1 hour while in the shaking incubator.

tag: cell line

tag: cell type

value: bacterial cells

value: cotreated w/oxacillin and loratadine


title: loratadine treated biol rep C

tag: treatment

value: loratadine treated, 50 uM


title: iPSC-derived neuron, day 88, biol rep 3

value: CIRM line CW50065

value: Healthy

value: iPSC-derived neuron

value: spheroid

value: Quick-Neuron Excitatory


title: kdrl:mCherry+, sele:GFP+ 72 hpf, rep1

tag: genotype

value: wild-type

value: embryos


title: kdrl:mCherry-mrc1a:GFP-_Rep 3

description:
cells that were neither mCherry + nor GFP +
N_danRer7_peaks.narrowPeak

data_processing:
All zebrafish ATAC-Seq datasets were aligned to UCSC build version danRer7 of the zebrafish genome using Bowtie2 (version 2.2.1)  (Langmead et al., 2012) with the following parameters: --end-to-end, -N0, -L20. We used the MACS2 version 2.1.0 (Zhang et al., 2008) peak finding algorithm to identify regions of ATAC-Seq peaks, with the following parameter --nomodel --shift -100 --extsize 200. A q-value threshold of enrichment of 0.05 was used for all datasets.
Genome_build: danRer7
Supplementary_files_format_and_content: bed file of called peaks

source_name: kdrl:mCherry; mrc1a:GFP transgenic zebrafish embryos (wild-type)

growth_protocol: Transgenic zebrafish (kdrl:mCherry; mrc1a:GFP double positive) were incrossed and embryos were grown under standard conditions at 28C in E3 buffer until 72 hpf.  Embryos were screened for transgene expression and then homogenized, filtered, and sorted using FACS into PBS, collecting at least 12,000 cells per group (max 50,000).

extract_protocol:
FACS-isolated cells were spun at 500 x g for 5 min at 4° C. Cells were washed once with 50 uL of cold 1X PBS and spun down at 500 x g for 5 min at 4° C. After discarding supernatant, cells were lysed using 50 uL cold lysis buffer (10 mM Tris-HCl pH 7.4, 10 mM NaCl, 3 mM MgCl2, 0.1% IGEPAL CA-360). Nuclei were spun down at 500 x g for 10 mins at 4° C. Nuclei were kept on ice and subsequently resuspended in 25 uL 2X TD Buffer (Illumina Nextera kit), 2.5 uL Transposase enzyme (Illumina Nextera kit, 15028252) and 22.5 uL Nuclease-free water in a total of 50 uL reaction. Transposase reaction was continued for 1 hr at 37° C. Immediately following the reaction, DNA was purified using Qiagen MinElute PCR purification kit (28004) in a final volume of 10 uL.
Libraries were purified according to Illumina protocol using the transposed DNA, NEB PCR master mix, Sybr green, universal and library-specific Nextera index primers. First round of PCR cycles was performed with the following cycles: 72° C, 5 min; 98° C, 30 sec; [98°C, 10 sec; 63 °C, 30 sec; 72 °C, 1 min] X 5 cycles; hold at 4°C. Reactions were kept on ice and using a 5 uL reaction aliquot, appropriate number of additional cycles required for further amplification were determined in a side qPCR reaction with the following procedure: 98 °C , 30 sec; [98 °C, 10 sec; 63 °C, 30 sec; 72 °C, 1 min] X 20 cycles; hold at 4 °C. Upon determining the additional number of PCR cycles required further for each sample, library amplification was conducted using the following conditions: 98°C, 30 sec; [98°C,10 sec; 63°C, 30 sec; 72 °C, 1 min] X appropriate number of cycles; hold at 4°C. Libraries prepared went through quality control analysis using an Agilent Bioanalyzer. Samples with appropriate nucleosomal laddering profiles were selected for next generation sequencing using Illumina Hiseq 2500 platform

value: Combined, remaining transgene negative portion of the embryo


title: untreated biol rep C

value: untreated


title: kdrl:GFP +, 72 hpf

description:
cells that were GFP +
EH1-2.expression.xlsx

value: 72 hpf

value: kdrl:GFP +

value: whole embryos


title: Severe  1

value: Severe COVID-19

value: Male


title: iPSC-derived neuron, day 57, biol rep 3

value: Day 57


title: iPSC-derived neuron, day 88, biol rep 1

value: Day 88


title: iPSC-derived neuron, day 32, biol rep 2

value: Day 32


title: kdrl:mCherry-mrc1a:GFP+_Rep 3

description:
cells that were GFP+ only
M_danRer7_peaks.narrowPeak

value: Mesenchymal cells in tail fin


title: Mild  4

value: Mild COVID-19


title: kdrl:mCherry-mrc1a:GFP-_Rep 2


title: Healthy 5

description:
Healthy control: demographic info not available
D300

value: Healthy Control


title: Mild  2


title: oxacillin treated biol rep C

value: bacterial cells

value: oxacillin treated, 4 ug/mL


title: kdrl:mCherry+;sele:GFP+, 72 hpf

description:
cells that were GFP+ and mCherry+
EH-JP-7.expression.xlsx

source_name: kdrl:mCherry; sele:GFP transgenic zebrafish embryos (wild-type)


title: oxacillin treated biol rep B


title: iPSC-derived neuron, day 32, biol rep 1

value: CIRM line CW50065

value: Healthy

value: iPSC-derived neuron

value: spheroid

value: Quick-Neuron Excitatory


title: Healthy 4

description:
Healthy control: demographic info not available
D354


title: Mild  3

value: Female


title: iPSC-derived neuron, day 57, biol rep 2


title: kdrl:mCherry-mrc1a:GFP-_Rep 1

value: Combined, remaining transgene negative portion of the embryo


title: 64_1_1

description: replicate 1

value: FGSC#4564, mat a[m1]s-3B cyh-1

tag: time point

value: 6-day of protoperithecial production

tag: morphology

value: protoperithecia


title: cotreated biol rep A

value: cotreated w/oxacillin and loratadine


title: iPSC-derived neuron, day 10, biol rep 3

tag: donor type

value: Day 10


title: iPSC-derived neuron, day 57, biol rep 1

tag: culture type

value: Day 57


title: cotreated biol rep B


title: iPSC-derived neuron, day 88, biol rep 2

tag: treatment for_differentiation

value: Day 88


title: iPSC-derived neuron, day 32, biol rep 3

tag: culture time

value: Day 32


title: Mild  1

value: Mild COVID-19


title: loratadine treated biol rep A

value: bacterial cells

value: loratadine treated, 50 uM


title: loratadine treated biol rep B


title: kdrl:mCherry-mrc1a:GFP+_Rep 1

value: Mesenchymal cells in tail fin


title: kdrl:mCherry-mrc1a:GFP+_Rep 2


title: kdrl:mCherry+mrc1a:GFP-_Rep 3

description:
cells that were mCherry + only
F_danRer7_peaks.narrowPeak

value: Endothelial cells


title: untreated biol rep B

value: untreated


title: kdrl:mCherry+mrc1a:GFP+_Rep 3

description:
cells that were GFP+ and mCherry+
FM_danRer7_peaks.narrowPeak


title: kdrl:mCherry+mrc1a:GFP+_Rep 2


title: FOB1 deletion replicate2

tag: collection time point

value: Log

value: No treatment

value: FOB1 deletion

value: yeast cells


title: untreated biol rep A

value: untreated, DMSO only


title: kdrl:mCherry+mrc1a:GFP-_Rep 2

tag: genotype/variation


title: Healthy1

description:
Healthy control: demographic info not available
D287

value: Healthy Control


title: kdrl:mCherry+mrc1a:GFP+_Rep 1


title: Healthy3

description:
Healthy control: demographic info not available
D325


title: iPSC-derived neuron, day 10, biol rep 1

value: CIRM line CW50065

value: Healthy

value: iPSC-derived neuron

value: spheroid

value: Quick-Neuron Excitatory


title: oxacillin treated biol rep A

value: oxacillin treated, 4 ug/mL


title: Control iPSC, lot 2, day 0, biol rep 3

value: undifferentiated iPSC

value: monolayer

value: Day 0


title: PTEN SHAM [BLVD3]

city: Illkirch

first: Julie

last: Terzic

address: 1 rue Laurent Fries

department: Génomique fonctionnelle et cancer

country: France

institute: IGBMC

description: pool of 3 mice

data_processing:
Image analysis, base calling and demultiplexing were performed using RTA 2.7.7 and Cell Ranger 3.0.2 mkfastq.
Alignment, barcode and UMI filtering and counting were performed using Cell Ranger 6.0.2 count and mouse reference mm10-2020-A (GRCm38 Ensembl release 98 and Gencode release M23).
Assembly: mm10
Supplementary files format and content: Filtered (contains only detected cellular barcodes) feature-barcode matrix (each element of the matrix is the number of UMIs associated with a feature (row) and a barcode (column)) in Market Exchange Format (MEX) and gzipped.
Supplementary files format and content: Gzipped tsv files with feature and barcode sequences corresponding respectively to row and column indices from the matrix.

source_name: prostate tumor

extract_protocol:
Mice prostates were dissociated into single cells after enzymatic (collagenase 1, trypsine and DNAse I) and mechanic digestion.
Cell number and viability were determined by a Trypan Blue exclusion assay on a Buerker Chamber. Samples consisted of at least 90 and 80 percent viable cells were processed on the Chromium Controller from 10X Genomics (Leiden, The Netherlands). 16500 total cells were loaded per well to yield approximately 10000 captured cells into nanoliter-scale Gel Beads-in-Emulsion (GEMs). Single cell 3 prime mRNA seq library were generated using Chromium Next GEM Single Cell 3 prime Reagent Kits v3.1 (10X Genomics). Briefly, GEMs were generated by combining barcoded gel beads, a RT master mix containing cells, and partitioning oil onto Chromium Chip G. Following full length cDNA synthesis and barcoding from poly-adenylated RNAs, GEM were broken and pooled before cDNA amplification by PCR using 11 cycles. After enzymatic fragmentation and size selection, sequencing library were constructed by adding P5 and P7 primers (Illumina, San Diego, USA) as well as sample index via end-repair, A-tailing, adaptor ligation and PCR amplification with 12 cycles. Library quantification and quality control was performed using Bioanalyzer 2100 (Agilent Technologies, Santa Clara CA).

tag: tissue

value: prostate tumor

value: Pten(i)pe-/-

value: SHAM-OPERATION


title: PTEN CTX [BLVD4]

description: pool of 3 mice

value: CASTRATION


title: Control iPSC, lot 2, day 0, biol rep 1


title: Healthy2

description:
Healthy control: demographic info not available
D341

tag: patient cohort


title: iPSC-derived neuron, day 10, biol rep 2

value: Day 10


title: Control iPSC, lot 2, day 0, biol rep 2


title: Estriol teatment [E3-CT]

type: genomic

hyb_protocol: Samles hybridization using NimbleGen Hybridization Kit, brifely adding solution to each sample Incubate at +95°C for 5 minutes, protected from light. Then place tubes at 42°C for at least 5 minutes.

scan_protocol: NimbleGen MS 200 Microarray Scanner

data_processing:
Data were analyzed by using Roche NimbleGen Software DEVA
normalized_ratio, ks_test, Genes presenting a peak score greater than 3 were identified

source_name: UTERUS

label_protocol: Samles labeled in parallel using the NimbleGen Dual-Color Labeling Kits. Cy3 Random and Cy5 Random Nonamers fromCy5-labeled experimental (IP) sample and Cy3-labeled control (input) sample.

growth_protocol: Eight-week-old CD-1 female mice were bred to male mice of the same strain and examined every 12 hours until the presence of a vaginal plug was detected. Detection of a vaginal plug was considered day 0.5 of pregnancy.

extract_protocol: Genomic DNA was extracted using the Qiagen DNeasy Kit, following the manufacturer’s protocol including the RNase A treatment.The DNA was then sonicated on ice to a chromatin size range of 100 to 2,000 bp, with 700 bp average. Sonication efficiency was optimized and tested on agarose gel before performing Methylated DNA immunoprecipitation (MeDIP).Genomic DNA was extracted using the Qiagen DNeasy Kit, following the manufacturer’s protocol including the RNase A treatment.The DNA was then sonicated on ice to a chromatin size range of 100 to 2,000 bp, with 700 bp average. Sonication efficiency was optimized and tested on agarose gel before performing Methylated DNA immunoprecipitation (MeDIP).For MeDIP, DNA was incubated with 5 μg of a 5-methylcytosine antibody (Eurogentec, BI-MECY-0100) to immunoprecipitate methylated DNA fragments overnight, with agitation at 4 °C.

treatment_protocol: Pregnant CD-1 mice were then housed individually and continuously treated with E3 (50µl of 0.46mg/ml in DMSO to approximate human exposure) via a mini-osmotic pump (Alzet model # 1002) beginning on Day 9 of gestation.At the age of 6 weeks of offspring, the female offspring (N=12 per group) were ovariectomized; after 2 weeks they were treated with a single intraperitoneal injection of  vehicle control (DMSO).

tag: agent

value: Estriol teatment

tag: fraction

value: experimental (IP)

value: control, input


title: Virion_2

city: DURHAM

first: ANKIT

last: GUPTA

institute: NIEHS

description: Direct RNA-seq as method described by nanopore

data_processing:
Base calling was done with Guppy version 5.0.10.
Demultiplexing of barcoded oligos was done with Deeplexicon.
The alignment to the reference transcriptome was done with Minimap2 version 2.20.
The poly (A) tail length was determined with Nanopolish version 0.13.3.
Supplementary files format and content: Comma separated value file wih polyA tail length, mapping transcript and replicate information for each read.

organism: Murine hepatitis virus

source_name: virion

growth_protocol: Murine hepatitis virus strain S (MHV) was obtained from ATCC (Cat# VR-766) and cultured according to the manufacture instructions

extract_protocol:
Total RNA was isolated with the Trizol method
1 µg of total RNA isolated from MHV was used for each sample. Libraries for direct RNA-seq were prepared using the Direct RNA Sequencing Kit (SQK-RNA002, Oxford Nanopore Technologies). All the libraries were multiplexed using the DeePlexiCon adapters, loaded to Nanopore R9 Flow Cells (FLO-MIN106D, Oxford Nanopore Technologies) and run on a MinION sequencer.

value: Wild-type

tag: strain

value: MHV-S (ATCC_VR-766)


title: Wild-type replicate3

data_processing:
Barcoded DNA was sequenced on an Illumina Nextseq 500 and Nextseq 2000. For samples run on Nextseq 500, individual lanes were pooled together for unique samples.
Micro-C sequencing reads were filtered and mapped using Bowtie2.
HiC-Pro pipeline was used to generate iteratively corrected genome matrix. Differential interaction contacts were analysed using BART3D.
Using R package HiTC the contact maps were created.
Assembly: sacCer3
Supplementary files format and content: Text files for every sample
Library strategy: Micro-C seq

extract_protocol:
Micro-C XL was performed following standard protocol from Hsieh et al., 2016. Briefly, exponential yeast cells were dual crosslinked with 3% formaldehyde and EGS and digested with appropriate amount of MNase to get >95% mononucleosomes. The chromatin pellet obtained was dephosphorylated, end-repaired and biotinylated through ligation, followed by isolation of dinucleosomal DNA from an agarose gel. The isolated DNA was processed for library preparation according to Illumina NEBNext protocol and paired-end sequencing was performed on an Illumina Nextseq 500 and Nextseq 2000 in the UVA Genome Analysis and Technology Core.
Illumina sequencing protocol

value: Log

value: No treatment

value: Wild type

value: yeast cells


title: methylome_Obir_WT_rep2

city: Athens

first: Robert

middle: J

last: Schmitz

state: GA

address: B416 Davison Life Sciences

department: Genetics

institute: University of Georgia

data_processing:
MethylC-seq: MethylC-seq analysis was performed as described in (Schmtiz et al. 2013)
Genome_build: Obir v5.4 genome
Supplementary_files_format_and_content: tab delimited text file, see "allc_header_descriptions.txt" for column headers

organism: Ooceraea biroi

source_name: genomic DNA

growth_protocol: We injected freshly laid eggs with Cas9 enzyme and a CRISPR guide RNA (DNMT1g2) designed to target exon 11 of DNMT1, just upstream of a conserved residue in the catalytic domain that is essential for enzyme function in mice.

extract_protocol: MethylC-seq libraries were constructed using the MethylC-seq protocol (Urich et al., 2015). Briefly, genomic DNA was sonicated to around 200 bp using a Covaris S-series focused ultrasonicator, and end-repaired with an End-It DNA end-repair kit (Epicentre). The end-repaired DNA was subjected to A-tailing using Klenow 3′–5′ exo− (NEB) and ligated to methylated adapters using T4 DNA ligase (NEB). The ligated DNA was treated with sodium bisulfite reagent using the EZ DNA methylation-Gold kit and amplified using KAPA HiFi uracil + Readymix Polymerase. Sequencing was performed on an Illumina NextSeq500 instrument.

value: WT

value: whole bodies (minus ovaries and brains)


title: Estradiol and Estriol treatment [E3-E2]

treatment_protocol: Pregnant CD-1 mice were then housed individually and continuously treated with E3 (50µl of 0.46mg/ml in DMSO to approximate human exposure) via a mini-osmotic pump (Alzet model # 1002) beginning on Day 9 of gestation.At the age of 6 weeks of offspring, the female offspring (N=12 per group) were ovariectomized; after 2 weeks they were treatedwith a single intraperitoneal injection of  300ng of estradiol (E2).

value: Estradiol and Estriol treatment


title: kdrl:mCherry+mrc1a:GFP-_Rep 1

value: Endothelial cells


title: methylome_Obir_DNMT1g2_rep1


title: Control iPSC, lot 1, day 0, biol rep 3

tag: cell line

value: CIRM line CW50065

value: Healthy

value: undifferentiated iPSC

value: monolayer

value: Day 0


title: methylome_Obir_DNMT1g2_rep2


title: methylome_Obir_WT_rep1


title: vehicle control [CT-CT]

treatment_protocol: Pregnant CD-1 mice were then housed individually and continuously treated with vehicle control (DMSO) via a mini-osmotic pump (Alzet model # 1002) beginning on Day 9 of gestation.At the age of 6 weeks of offspring, the female offspring (N=12 per group) were ovariectomized; after 2 weeks they were treated with a single intraperitoneal injection of  vehicle control (DMSO).

value: vehicle control

value: experimental (IP)


title: Virion_1

value: Wild-type


title: Control iPSC, lot 1, day 0, biol rep 2

tag: cell type


title: NaCl_OE1_01

status: Public on Mar 22 2023

city: Taipei

first: MenChi

last: Chang

state: Taiwan (R.O.C.)

address: No. 1, Sec. 4, Roosevelt Rd.

department: Agronomy

country: Taiwan

institute: National Taiwan University

data_processing:
The original data obtained by high-throughput sequencing were transformed into raw sequenced reads by CASAVA base recognition (Base Calling).
Paired-end raw sequenced reads were filtered and trimmed using Trimmomatic V.0.38.
Paired-end clean reads were aligned to the rice genome (IRGSP-1.0) using HISAT2 V2.1.0
To identify differentially expressed genes (DEGs), the RNA-seq data were analyzed with the DEGseq R package.
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

organism: Oryza sativa

source_name: roots

growth_protocol: The seeds were treated with 1.5% (v/v) commercial bleach for 30 minutes, rinsed twice with sterile water for 30 minutes each time, and subsequently subjected to imbibition at 37°C for 3 days in the dark. After imbibition, the germinating seeds were grown on a wire stand in a plastic basin at 28/24°C (day/night) under long-day (16-h light/8-h dark) conditions with a light intensity of approximately 100 µE s-1 m2

extract_protocol:
Total RNA was extracted from two different tissues (shoot and root) of rice using an RNeasy Plant Mini Kit (Qiagen) according to the manufacturer’s instructions.
Sequencing libraries were generated with 1.0 µg of RNA input using the KAPA mRNA HyperPrep Kit (Roche) according to the manufacturer’s instructions.

tag: cultivar

value: Tainung 67

value: roots

tag: treatment

value: 150 mM NaCl

tag: time

value: 24 hrs


title: ctrl_OE1_03

tag: genotype

value: 0 mM NaCl


title: Estradiol teatment [CT-E2]

treatment_protocol: Pregnant CD-1 mice were then housed individually and continuously treated with vehicle control (DMSO) via a mini-osmotic pump (Alzet model # 1002) beginning on Day 9 of gestation.At the age of 6 weeks of offspring, the female offspring (N=12 per group) were ovariectomized; after 2 weeks they were treatedwith a single intraperitoneal injection of  300ng of estradiol (E2).

value: Estradiol teatment

value: control, input


title: Control iPSC, lot 1, day 0, biol rep 1

tag: donor type


title: NaCl_67_02

value: WT


title: NaCl_OE1_03


title: ctrl_OE1_01


title: NaCl_67_01


title: NaCl_67_03


title: Lmgp66_TCR_2

first: Herman

last: Gudjonson

address: 417 E 68th St

department: Computational and Systems Biology Program, SKI

institute: Memorial Sloan Kettering Cancer Center

description:
5' RNA + TCR
Lmgp66_TCR_2_CD4_T_cell_metadata_2717x16.tsv.gz
Lmgp66_TCR_2_CD4_T_counts_normalized_2717x10573.tsv.gz
Lmgp66_TCR_2_CD4_T_counts_imputed_2717x10573.tsv.gz
Lmgp66_TCR_2_CD4_T_raw_counts.tsv.gz
Lmgp66_TCR_2_CD4_T_raw_contig_annotations.tsv.gz

data_processing:
Library strategy: 5' RNA-seq + TCR-seq
Single-cell RNA seq samples were individually processed using the SEQC v0.2.1 pipeline (Azizi et al., 2018) using the package provided mm38 mouse genome reference and default parameters for the 10X platform. The SEQC pipeline performs read alignment, multi-mapping read resolution, as well as cell barcode and UMI correction to generate a (cells x genes) count matrix. The pipeline filters empty droplets from true cells based on total molecule counts, filters cells with >20% mitochondrial molecule fraction and filters cells with low library complexity. Data from D7 gp66:I-Ab+ single-cell TCR-seq were individually processed with the CellRanger (v3.1.0) 5’ RNA-seq and V(D)J pipeline, aligned to mm10-3.0.0 for genomic libraries and vdj_GRCm38_alts_ensembl-3.1.0 for TCR libraries. For each sample, an additional library size filter was used to remove any remaining low quality cell libraries. Genes that were expressed in more than 10 cells were retained for further analysis.
The filtered count matrix was normalized for library size. This normalized matrix was then multiplied by the median of the total molecule count across all cells for numerical stability and log2 transformed with a pseudocount of 0.1 for downstream analysis.
To perform an integrated analysis of naïve CD4 T cell samples, we selected the top 1000 highly variable genes based on normalized dispersion. We then batch corrected expression in naïve CD4 T cell samples using mnnCorrect (Haghverdi et al., 2018).
For naïve C7 and LmESAT C7 timecourse samples, we enhanced connectivity between time-adjacent using the data integration technique Harmony (github.com/dpeerlab/Harmony).
Phenograph was used to cluster PCA reduced expression data for cell type identification. Imputed gene expression was calculated using MAGIC (van Dijk et al., 2018). Putative cell doublets were identified using Scrublet (Wolock et al., 2019) and removed from further analysis.
Genome_build: mm38
Supplementary_files_format_and_content: Tab-delimited text files containing raw counts generated by the SEQC or CellRanger pipeline for each sample, library-size normalized log2-transformed counts for each experiment, MAGIC imputed gene expression data for each experiment and associated cell metadata containing per-cell annotations as presented in the publication.
Supplementary_files_format_and_content: naive_CD4_T_cell_metadata_28146x12.tsv: cell metadata
Supplementary_files_format_and_content: naive_CD4_T_counts_normalized_28146x11488.tsv: normalized abundance measurements
Supplementary_files_format_and_content: naive_CD4_T_counts_imputed_28146x11488.tsv: imputed abundance measurements
Supplementary_files_format_and_content: naive_CD4_T_B6_Naive_raw_counts.tsv: raw count abundance measurements
Supplementary_files_format_and_content: naive_CD4_T_C7_Naive_1_raw_counts.tsv: raw count abundance measurements
Supplementary_files_format_and_content: naive_CD4_T_C7_Naive_2_raw_counts.tsv: raw count abundance measurements
Supplementary_files_format_and_content: naive_CD4_T_SMARTA_Naive_1_raw_counts.tsv: raw count abundance measurements
Supplementary_files_format_and_content: naive_CD4_T_SMARTA_Naive_2_raw_counts.tsv: raw count abundance measurements
Supplementary_files_format_and_content: LmESAT_C7_CD4_T_cell_metadata_11403x11.tsv: cell metadata
Supplementary_files_format_and_content: LmESAT_C7_CD4_T_counts_normalized_11403x12044.tsv: normalized abundance measurements
Supplementary_files_format_and_content: LmESAT_C7_CD4_T_counts_imputed_11403x12044.tsv: imputed abundance measurements
Supplementary_files_format_and_content: LmESAT_C7_CD4_T_LmESAT_C7_16hr_1_raw_counts.tsv: raw count abundance measurements
Supplementary_files_format_and_content: LmESAT_C7_CD4_T_LmESAT_C7_16hr_2_raw_counts.tsv: raw count abundance measurements
Supplementary_files_format_and_content: LmESAT_C7_CD4_T_LmESAT_C7_40hr_raw_counts.tsv: raw count abundance measurements
Supplementary_files_format_and_content: Lmgp66_TCR_1_CD4_T_cell_metadata_2964x16.tsv: cell metadata
Supplementary_files_format_and_content: Lmgp66_TCR_1_CD4_T_counts_normalized_2964x10857.tsv: normalized abundance measurements
Supplementary_files_format_and_content: Lmgp66_TCR_1_CD4_T_counts_imputed_2964x10857.tsv: imputed abundance measurements
Supplementary_files_format_and_content: Lmgp66_TCR_1_CD4_T_raw_counts.tsv: raw count abundance measurements
Supplementary_files_format_and_content: Lmgp66_TCR_1_CD4_T_raw_contig_annotations.tsv: raw TCR contig annotations
Supplementary_files_format_and_content: Lmgp66_TCR_2_CD4_T_cell_metadata_2717x16.tsv: cell metadata
Supplementary_files_format_and_content: Lmgp66_TCR_2_CD4_T_counts_normalized_2717x10573.tsv: normalized abundance measurements
Supplementary_files_format_and_content: Lmgp66_TCR_2_CD4_T_counts_imputed_2717x10573.tsv: imputed abundance measurements
Supplementary_files_format_and_content: Lmgp66_TCR_2_CD4_T_raw_counts.tsv: raw count abundance measurements
Supplementary_files_format_and_content: Lmgp66_TCR_2_CD4_T_raw_contig_annotations.tsv: raw TCR contig annotations

source_name: spleen

extract_protocol:
Splenic CD4+ T cells were enriched with the CD4 T cell negative isolation kit (Miltenyi). Cells were incubated with anti-CD16/32 in sorting buffer (2% FBS in PBS) for 10 min at 4°C to block binding to Fc receptors. Extracellular antigens were stained for 30 min at 4°C in sorting buffer. Cells were washed and resuspended in sorting buffer with SYTOX blue (Invitrogen) for exclusion of dead cells. Cells were sorted into cRPMI, pelleted and resuspended in RPMI-2% FBS.
The TCR libraries were prepared following the Chromium Single Cell Immune Profiling Solution protocol. Sorted gp66:I-Ab tetramer-positive cells (>80% viability) were encapsulated at a final concentration of ~120 cells/uL. After the reverse transcription step the barcoded-cDNA was released from droplets and purified with DynaBeads, followed by 14 PCR cycles (98°C for 45 s; [98°C for 20 s, 67°C for 30 s, 72°C for 1 min] x 14; 72°C for 1 min). The resulting cDNA library was used to construct single cell 5` gene expression and TCR VDJ enriched libraries. The library was fragmented, double-size selected with SPRI beads (avg. size 450 bp), reamplified and sequenced on Illumina NextSeq platform (R1 – 26 cycles, R2 – 98 cycles, i7 – 8 cycles) at depth of ~50.000 reads per cell. To construct TCR libraries, 10 ng of barcoded material was amplified by 2-step nested-PCR (10-cycles of PCR (98°C for 45 s; [98°C for 20 s, 67°C for 30 s, 72°C for 1 min] x 10; 72°C for 1 min) followed by an additional 10 cycles of PCR (98°C for 45 s; [98°C for 20 s, 67°C for 30 s, 72°C for 1 min] x 10; 72°C for 1 min) using DNA primers provided in the kit. VDJ region-enriched libraries with average size of 600 bp were sequenced on an Illumina HiSeq 2500 instrument (R1 – 150 cycles, R2 – 150 cycles, i7 – 8 cycles) to obtain ~5000 reads per cell.

treatment_protocol: Mice were injected intravenously with 1 x 10^7 colony forming units (CFU) of L. monocytogenes-gp66. Spleens were harvested 7 days post infection.

tag: purification

value: CD4+ gp66:I-Ab tetramer+

tag: condition

value: 7d post Lm-gp66 infection


title: Lmgp66_TCR_1

description:
5' RNA + TCR
Lmgp66_TCR_1_CD4_T_cell_metadata_2964x16.tsv.gz
Lmgp66_TCR_1_CD4_T_counts_normalized_2964x10857.tsv.gz
Lmgp66_TCR_1_CD4_T_counts_imputed_2964x10857.tsv.gz
Lmgp66_TCR_1_CD4_T_raw_counts.tsv.gz
Lmgp66_TCR_1_CD4_T_raw_contig_annotations.tsv.gz


title: ctrl_67_02


title: ctrl_67_03


title: NaCl_OE1_02


title: ctrl_67_01


title: PM9_D28_5F-O_RNAseq

city: Loma Linda

first: Charles

last: Wang

state: CA

address: 11021 Campus Street

institute: Loma Linda University

description: RNA-seq

data_processing:
Basecalling, fastq files were generated using Illumina bcl2fastq package v1.8.4 with default settings.
For RNA-seq, the raw reads were trimmed using TrimGalore (v.0.4.5), and then aligned to the human reference genome (GRCh38) for gene counts using STAR (--quantMode GeneCounts).
For ATAC-seq, the raw reads were mapped to human reference genome (GRCh38) using the bioinformatics pipeline snakePipes with the ATAC-seq mode. In the pipeline, fastq files were trimmed using TrimGalore, aligned with Bowtie2, and peaks are called with MACS2.
For ATAC-seq, a consensus peak set was defined by taking the intersection of peaks from both biological replicates using soGGi (v.1.18) package and regions intersecting with blacklisted regions and ChrY were excluded. The ATAC-seq count matrix was computed by counting the reads that fell into the consensus peaks using Rsubread v2.0.1.
For RRBS analysis, raw fastq reads were trimmed using TrimGalore (v.0.4.5) and Nugen RRBS trimming script (trimRRBSdiversityAdaptCustomers.py). After trimming, reads were aligned to the human reference genome (GRCh38) with Bismark54 by default parameter settings, and PCR duplicates were removed by Nugen script (nudup.py).
The methylation call files (Bismark files) including the location of each CpG sites and the methylation percentage were generated by the bismark_methylation_extractor function.
Assembly: NCBI GRCh38
Supplementary files format and content: For ATAC-seq datasets, narrowpeak files were generated. For RRBS datasets, CpG coverage report in text format were generated.

source_name: PBMC reprogrammed iMSCs

growth_protocol: After reprogramming, the cells were seeded onto fibronectin-coated plates in the mixture of erythroid medium and MSC medium (50:50 ratio) supplemented with small molecules including 3 μM CHIR99021, 10 μM Forskolin, 10 μM ALK inhibitor (SB431542), and 5 μM Tranylcypromine hydrochloride for two days, and replaced with MSC medium thereafter.

extract_protocol:
QIAGEN AllPrep DNA/RNA/miRNA Universal Kit protocol
RNA-seq libraries was constructed using the NuGEN Ovation universal RNA-seq kit (TECAN). RRBS libraries were constructed following standard protocols of the NuGEN Ovation Ultralow Methyl-seq Library Systems. ATAC-seq libraries were constructed by following the improved protocol as described by Corces et al., 2017.

tag: reprogram factors

tag: reprogram day

value: day 28


title: ctrl_OE1_02


title: H1975_His+osim+alp

city: Koto-ku

first: Hitomi

last: Shirahama

state: Tokyo

address: Ariake 3-8-31

institute: Japanese Foundation for Cancer Research

description: NCI-H1975 cells treated with combination of osimertinib and alpelisib (osim+alp) under L-histidinol (His)-condtitions for 24h

hyb_protocol: Following fragmentation, 15 µg of cRNA were hybridized for 16 hours at 45℃ on Affymetrix GeneChip Human Genome U133 Plus 2.0 Array (Thermo Fisher Scientific, MA, USA). GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the GeneChip Scanner 3000 (Thermo Fisher Scientific).

data_processing: Normalization of microarray data was carried out by the Robust Multichip Average (RMA) method using R software with affy package.

label: biotin

label_protocol: Biotinylated cRNA was prepared according to the standard Affymetrix protocol (Expression Analysis Technical Manual) from 100 ng total RNA.

growth_protocol: Cells were cultured in RPMI1640 supplemented with 10% fetal bovine serum and 100 µg/ml kanamycin.

extract_protocol: Total RNA was extracted from cultured cells using QIAshredder and RNeasy Mini Kit (QIAGEN, CA, USA).

treatment_protocol: NCI-H1975 cells were treated with DMSO, osimertinib (10 nM), alpelisib (1 µM), or a combination of these in the presence or absence of L-histidinol (2 mM) for 24 hours.

value: 2 mM L-histidinol, 10 nM osimertinib, and 1 μM alpelisib 24h


title: H1975_osim+alp

description: NCI-H1975 cells treated with combination of osimertinib and alpelisib (osim+alp) for 24 h

value: 10 nM osimertinib and 1 µM alpelisib 24h


title: 839_H3K9me3

first: Tao

last: YE

institute: IGBMC (CNRS/INSERM/UDS)

data_processing:
Image analysis and base calling were performed using RTA 2.7.3 and bcl2fastq 2.17.1.14.
Sequence reads were mapped to reference genome hg19 using Bowtie 1.0.0 with the following parameters -m 1 --strata --best -y -S -l 40 -p 2.
Genome_build: hg19
Supplementary_files_format_and_content: Bigwig files were generated using Homer software makeUCSCfile script with default parameters and scaled to 1e7 reads.

source_name: ChIPseq from slices of frozen human samples

extract_protocol:
OCT-compount frozen blocks from CIT cohort () were frozen-sectioned and stained with hematoxylin and eosin. Pathology review was performed to confirm the tumour stage and to select tumour areas, in order to enhance neoplastic content (estimated at 30 to 95%, median tumour cell content = 65%). For tumours with sufficient material, tumour-enriched areas were macrodissected from the frozen block and manually finely ground in a mortar. Frozen ground tumour tissue was further homogenized using a tube pestle or the TissueLyser II system (Qiagen). Disrupted tissue was then processed using the reagents from the iDeal ChIP-seq Kit for Histones (Diagenode), according to the manufacturer’s instructions. Tumour samples with optimal chromatin fragment size (200-500 bp) were immunoprecipitated using the iDeal ChIP-seq Kit for Histones (Diagenode).Magnetic immunoprecipitation of sheared DNA-chromatin complexes (500ng) was performed overnight using a rabbit polyclonal histone H3K27acetyl ChIP Grade antibody (ab4729, Abcam), H3K27me3 (Active Motif, ref. 39155), and H3K9me3 (Active Motif, ref. 39161). DNA purification was performed using iPure magnetic beads.
ChIP samples were purified using Agencourt AMPure XP beads (Beckman Coulter) and quantified with the Qubit (Invitrogen). ChIP-seq libraries were prepared from 10 ng of double-stranded purified DNA using the MicroPlex Library Preparation kit v2 (C05010014, Diagenode s.a., Seraing, Belgium), according to manufacturer's instructions. In the first step, the DNA was repaired and yielded molecules with blunt ends. In the next step, stem-loop adaptors with blocked 5 prime ends were ligated to the 5 prime end of the genomic DNA, leaving a nick at the 3 prime end. The adaptors cannot ligate to each other and do not have single-strand tails, avoiding non-specific background. In the final step, the 3 prime ends of the genomic DNA were extended to complete library synthesis and Illumina compatible indexes were added through a PCR amplification (7cycles ONLY). Amplified libraries were purified and size-selected using Agencourt AMPure XP beads (Beckman Coulter) to remove unincorporated primers and other reagents.

value: tumors

tag: antibody


title: H1975_His

description: NCI-H1975 cells without drug treatment (DMSO) under stress conditions by L-histidinol (His) for 24h

value: 2 mM L-histidinol 24h


title: HDF_vitro_young_rep2

city: Lübeck

first: Hauke

last: Busch

state: Schleswig-Holstein

address: Ratzeburger Allee 160

department: Lübeck Institute of Experimental Dermatology

institute: University of Lübeck

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: All arrays were normalized together using quantile normalization algorithm.

source_name: human dermal fibroblast

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

growth_protocol: Skin sampling was conducted according to the principles of the Declaration of Helsinki. Skin samples were obtained from surgical excisions that were not required for histological diagnostics. The patients signed the informed consent in the respective Departments of Dermatology. These were approved by the Institutional Commission of Ethics of the University of Heidelberg (103/2001) or the University of Freiburg (42/2005). NHDF were isolated (explant cultures) as described (Boehnke, K., Mirancea, N., Pavesio, A., Fusenig, N.E.,Boukamp, P., and Stark, H.J. Effects of fibroblasts and microenvironment on epidermal regeneration and tissue function in long-term skin equivalents. Eur J Cell Biol 86,731, 2007).

extract_protocol: RNA was extracted with the QIAGEN RNeasy Plus Mini Kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser.

treatment_protocol: NHDF were cultured in high glucose and l-glutamine containing Dulbecco’s modified Eagle’s medium (DMEM; Lonza) supplemented with 10% fetal calf serum (FCS; Invitrogen) and 1% antibiotics (Lonza) and incubated at 37°C, 5% CO2 and 5% O2.

tag: tissue

value: skin

tag: replicate

tag: passage

tag: donor age

tag: Sex

value: male

tag: arrayid


title: H1975_DMSO

description: NCI-H1975 cells without drug treatment (DMSO)

tag: cell line

value: Vehicle (DMSO) 24h


title: PM9_D28_5F_RNAseq

description: RNA-seq


title: 1025_Input

value: Input


title: HDF_vitro_young_rep1


title: HDF_vitro_old_rep2


title: HDF_vivo_old_rep3

value: female


title: HDF_vivo_young_rep1


title: HDF_vivo_young_rep2


title: HDF_vivo_young_rep3


title: HDF_vitro_young_rep3


title: HDF_vivo_old_rep2


title: HDF_vivo_old_rep1


title: H1975_His+alp

description: NCI-H1975 cells treated with alpelisib (alp) under His-conditions for 24h

value: 2 mM L-histidinol and 1 µM alpelisib 24h


title: H1975_osim

description: NCI-H1975 cells treated with osimertinib (osim) for 24 h

value: 10 nM osimertinib 24h


title: HDF_vitro_old_rep3


title: H1975_alp

description: NCI-H1975 cells treated with alpelisib (alp) for 24 h

value: 1 μM alpelisib 24h


title: HDF_vitro_old_rep1


title: H1975_His+osim

description: NCI-H1975 cells treated with osimertinib (osim) under His-conditions for 24h

value: 2 mM L-histidinol and 10 nM osimertinib 24h


title: 1211-2_Input


title: 839_H3K27ac


title: 839_H3K27me3


title: 877_H3K9me3


title: 839_Input


title: 877_H3K27me3


title: 877_H3K27ac


title: PM9_D28_5F-K_RNAseq

description: RNA-seq


title: 877_Input


title: 1025_H3K9me3


title: 447_H3K27ac


title: 1025_H3K27me3


title: 447_H3K27me3


title: 447_H3K9me3


title: 447_Input


title: 1025_H3K27ac


title: 1175_Input


title: 1211-2_H3K9me3


title: 791-Input_b

value: b


title: 1211-2_H3K27me3


title: 1087-Input_b


title: 1175_H3K27me3


title: 1175_H3K27ac


title: 1211-2_H3K27ac


title: 791-2_H3K27me3


title: 791-2_H3K9me3


title: 391_Input_b


title: 1175_H3K9me3


title: 1087-1_H3K9me3


title: 791-2_H3K27ac


title: 1087-1_H3K27me3


title: 1087-1_H3K27ac


title: 391_H3K9me3


title: 2542_H3K27ac


title: 391_H3K27ac


title: 813-1_H3K9me3


title: 3395_H3K27me3


title: 1033_H3K27ac


title: 813-1_H3K27ac


title: 924-1_H3K9me3


title: 2542_H3K27me3


title: 2542_Input


title: 924-1_H3K27me3


title: 813-1_H3K27me3


title: 813-1_Input


title: 1156_H3K27me3


title: 1156_H3K27ac


title: 1156_H3K9me3


title: 3395_Input


title: 3395_H3K27ac


title: 1033_Input


title: 1156_Input


title: 3395_H3K9me3


title: 1033_H3K9me3


title: 1033_H3K27me3


title: SD48_H3K9me3_rep2

data_processing:
Image analysis and base calling were performed using RTA 2.7.3 and bcl2fastq 2.17.1.14.
Sequence reads were mapped to reference genome hg19 using Bowtie 1.0.0 with the following parameters -m 1 --strata --best -y -S -l 40 -p 2.
Genome_build: hg19
Supplementary_files_format_and_content: Wig files were generated using with an in-house script (Variable step, span=25, reads were elongated to 200b).

source_name: Bladder cancer cell lines, ChIP for 6 Histones marks, CTCF and FOXA1

growth_protocol: DMEM +10% FBS

extract_protocol: Fixation in 10% Formaldehyde. ChIP using Active Motif High sensitivity ChIP kit


title: SD48_H3K27me3_rep2


title: 391_H3K27me3


title: 924-1_H3K27ac


title: SD48_Input_rep2


title: SD48_FOXA1


title: 2542_H3K9me3


title: SD48_H3K27ac


title: SD48_CTCF

value: CTCF


title: SD48_H3K4me1


title: SD48_H3K9ac


title: 924-1_Input


title: SCaBER_Input

source_name: Bladder cancer cell lines, ChIP for Histones marks

extract_protocol:
Fixation in 10% Formaldehyde. ChIP using Active Motif High sensitivity ChIP kit
ChIP samples were purified using Agencourt AMPure XP beads (Beckman Coulter) and quantified with the Qubit (Invitrogen). ChIP-seq libraries were prepared from 10 ng of double-stranded purified DNA using the MicroPlex Library Preparation kit v2 (C05010014, Diagenode s.a., Seraing, Belgium), according to manufacturer's instructions. In the first step, the DNA was repaired and yielded molecules with blunt ends. In the next step, stem-loop adaptors with blocked 5 prime ends were ligated to the 5 prime end of the genomic DNA, leaving a nick at the 3 prime end. The adaptors cannot ligate to each other and do not have single-strand tails, avoiding non-specific background. In the final step, the 3 prime ends of the genomic DNA were extended to complete library synthesis and Illumina compatible indexes were added through a PCR amplification (7 cycles). Amplified libraries were purified and size-selected using Agencourt AMPure XP beads (Beckman Coulter) to remove unincorporated primers and other reagents.


title: SCaBER_H3K27ac


title: SD48_Input


title: NHU11_CTCF

description: ureter derived Normal Urothelial cells

source_name: ureter derived Normal Urothelial cells

growth_protocol: KSFM supplemented with  EGF 1-53 and Bovine pituitary extract (BPE)

tag: sample type

value: Healthy donor for kidney graft

tag: age

tag: gender


title: SCaBER_H3K27me3


title: NHU11_H3K9ac

description: ureter derived Normal Urothelial cells


title: NHU11_H3K27ac

description: ureter derived Normal Urothelial cells


title: NHU11_H3K27me3

description: ureter derived Normal Urothelial cells


title: NHU11_H3K4me3

description: ureter derived Normal Urothelial cells


title: NHU12_CTCF

description: ureter derived Normal Urothelial cells


title: NHU12_H3K27ac

description: ureter derived Normal Urothelial cells


title: NHU12_H3K27me3

description: ureter derived Normal Urothelial cells


title: NHU12_H3K9ac

description: ureter derived Normal Urothelial cells


title: NHU12_H3K9me3

description: ureter derived Normal Urothelial cells


title: NHU12_H3K4me1

description: ureter derived Normal Urothelial cells


title: NHU12_Input

description: ureter derived Normal Urothelial cells


title: NHU12_H3K4me3

description: ureter derived Normal Urothelial cells


title: MGHU3_Input


title: MGHU3_H3K27ac


title: MGHU3_H3K27me3


title: KK47_Input


title: SD48_H3K4me3


title: 5637_FOXA1

growth_protocol: RPMI +10% FBS


title: KK47_H3K27ac


title: 5637_H3K27ac


title: 5637_H3K4me1


title: 5637_H3K27me3


title: 5637_H3K9ac


title: NHU11_H3K4me1

description: ureter derived Normal Urothelial cells


title: CFG2355-seq2 PM10_D28_5F-O_PEF_RRBS

data_processing:
Basecalling, fastq files were generated using Illumina bcl2fastq package v1.8.4 with default settings.
For RNA-seq, the raw reads were trimmed using TrimGalore (v.0.4.5), and then aligned to the human reference genome (GRCh38) for gene counts using STAR (--quantMode GeneCounts).
For ATAC-seq, the raw reads were mapped to human reference genome (GRCh38) using the bioinformatics pipeline snakePipes with the ATAC-seq mode. In the pipeline, fastq files were trimmed using TrimGalore, aligned with Bowtie2, and peaks are called with MACS2.
For ATAC-seq, a consensus peak set was defined by taking the intersection of peaks from both biological replicates using soGGi (v.1.18) package and regions intersecting with blacklisted regions and ChrY were excluded. The ATAC-seq count matrix was computed by counting the reads that fell into the consensus peaks using Rsubread v2.0.1.
For RRBS analysis, raw fastq reads were trimmed using TrimGalore (v.0.4.5) and Nugen RRBS trimming script (trimRRBSdiversityAdaptCustomers.py). After trimming, reads were aligned to the human reference genome (GRCh38) with Bismark54 by default parameter settings, and PCR duplicates were removed by Nugen script (nudup.py).
The methylation call files (Bismark files) including the location of each CpG sites and the methylation percentage were generated by the bismark_methylation_extractor function.
Genome_build: NCBI GRCh38
Supplementary_files_format_and_content: For ATAC-seq datasets, narrowpeak files were generated. For RRBS datasets, CpG coverage report in text format were generated.

value: day 28


title: 5637_Input


title: NHU11_H3K9me3

description: ureter derived Normal Urothelial cells


title: NHU11_Input

description: ureter derived Normal Urothelial cells


title: 5637_CTCF


title: CFG2354-seq2 PM10_D28_5F_PEF_RRBS


title: 5637_H3K4me3


title: CFG2351-seq2 PM18_D28_5F_PEF_RRBS


title: CFG2352-seq2 PM18_D28_5F-O_PEF_RRBS


title: CFG2355 PM10_D28_5F-O_PEF_RRBS


title: CFG2356 PM10_D28_5F-K_PEF_RRBS


title: 5637_H3K9me3


title: CFG2353 PM18_D28_5F-K_PEF_RRBS


title: CFG2334 PM18_D28_5F-K_RNAseq


title: KK47_H3K27me3


title: CFG2337 PM10_D28_5F-K_RNAseq


title: CFG2354 PM10_D28_5F_PEF_RRBS


title: CFG2351 PM18_D28_5F_PEF_RRBS


title: CFG2295 PM18_D28_5F_RNAseq


title: CFG2352 PM18_D28_5F-O_PEF_RRBS


title: CFG2338 PM10_D28_5F-O_RNAseq


title: CFG2336 PM10_D28_5F_RNAseq


title: CFG2356-seq2 PM10_D28_5F-K_PEF_RRBS


title: Lung cancer celll-H1299-hyperoxia 2

city: shanghai

first: Xiucheng

last: Liu

address: zhengmin road 557

country: China

institute: Shanghai pulmonary hospital

data_processing:
The ribosomal RNA (rRNA) was removed from the total RNA using the NEBNext® rRNA Depletion Kit (New England Biolabs, Inc., Ipswich, MA, 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.
Then, HTSeq software (v0.9.1) was used to obtain the transcript level (lncRNA) raw count as the expression profiling, and edgeR (v3.16.5) was used to perform normalization, and differentially expressed mRNAs were identified by p-value and fold change.
Genome_build: mm9
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample:
Column A: gene_id, the Ensembl gene identifier.
Column B: gene, the gene name.
Column C: gene description.
Column D: Length, the length of the locus. It equals to end-start of the locus.
Column E~I:Statistical results, statistical results by edgeR.
Column J ~ U: raw counts, raw counts of all samples of the gene by HTSeq.
Column V, W: Trans Per Million.
Column X ~ AG: annotation information, including dbXrefs (other database ID), chromosome, map_location, description, pathway and GO annotations.

source_name: H1299 cells

extract_protocol:
H1299 cells were flash frozen on dry ice, and RNA was harvested using Trizol reagent. 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: Smartor118-three gas incubator (China Innovation Instrument, Ningbo, China) was used to mimic protocols of supplemental oxygen delivery in vitro. H1299 cells were treated with hyperoxia (60% O2 / 5%CO2 / 35%N2) for 24.

tag: tissue/cell type

value: Lung adenocarcinoma (LUAD)

tag: treatment


title: Lung cancer celll-H1299-hyperoxia 6


title: Lung cancer celll-H1299-hyperoxia 4


title: Lung cancer celll-H1299-hyperoxia 3


title: CFG2353-seq2 PM18_D28_5F-K_PEF_RRBS


title: Lung cancer celll-H1299-hyperoxia 1


title: Lung cancer celll-H1299-normoxia 6


title: Lung cancer celll-H1299-normoxia 2


title: Lung cancer celll-H1299-normoxia 5


title: Lung cancer celll-H1299-normoxia 3


title: Lung cancer celll-H1299-normoxia 4


title: Lung cancer celll-H1299-hyperoxia 5


title: CFG2296 PM18_D28_5F-O_RNAseq