title: Interferon receptor dosage-normalized (Dp16^2xIFNRs); sample 6 (E18.5 heart)

source_name: embryonic heart

value: embryonic heart

tag: age in_days_post_conception


title: ddm1 progeny of high CO2

status: Public on Mar 20 2023

type: SRA

city: St. Louis

first: R. Keith

last: Slotkin

state: Missouri

address: 975 North Warson Road

country: USA

institute: Donald Danforth Plant Science Center

library_source: genomic

data_processing:
Adapters were trimmed from paired-end raw reads using Fastp (Chen et. al., PMID: 30423086). The reads were mapped to the genome and DNA methylation was called for each cytosine using methylpy (Schultz et. al., PMID: 26030523). The output of this tool - allC file is provided as a processed fle.
Assembly: TAIR10
Supplementary files format and content: Output of methylpy tool - allC files are provided as processed data files. “allC” stands for all cytosine (C). Each row corresponds to one cytosine in the genome. The columns are as described in the tool’s github page (https://github.com/yupenghe/methylpy)

molecule: genomic DNA

organism: Arabidopsis thaliana

source_name: leaves from 25 day old plants

growth_protocol: All plants were grown at 22℃ under 16-hour day conditions in a growth chamber. 25 days after planting, whole leaves were collected and stored at -80℃.

extract_protocol:
Genomic DNA was isolated from frozen leaf tissue using the Qiagen DNAEasy prep kit. Quality was assessed by gel electrophoresis.
NEBNext Enzymatic Methyl-seq kit was used at the Genomics Technology Core at University of Missouri to construct the EM-Seq libraries.
Multiplexed libraries were sequenced on Illumina NovaSeq with paired-end 150 bp strategy.

treatment_protocol: Control plants were grown at ambient CO2 levels (which ranged between 450-500 ppm CO2) and the experimental plants were grown at high CO2 (set to 1,000 ppm). The progeny of high CO2 plants were grown at ambient CO2 levels.

tag: ecotype

value: Columbia

tag: genotype

tag: tissue

value: leaves from 25 day old plants

tag: treatment

value: high CO2


title: T21, HTP0330A

city: Aurora

first: Matthew

middle: D

last: Galbraith

state: CO

department: Department of Pharmacology; Linda Crnic Institute for Down Syndrome

institute: University of Colorado Anschutz Medical Campus

description: globin-depleted, poly(A)+ RNA from whole blood

library_source: transcriptomic

data_processing:
Signal processing, base-calling, and quality scoring was carried out automatically by the NovaSeq 6000 software (Illumina).
Demultiplexing and conversion to FASTQ format was carried out using bcl2fastq (Illumina).
Data quality was assessed using FASTQC (v0.11.5) (https://www.bioinformatics.babraham.ac.uk/projects/fastqc/) and FastQ Screen (v0.11.0, https://www.bioinformatics.babraham.ac.uk/projects/fastq_screen/).
For some samples, FASTQ files from multiple sequencing runs were merged to obtain ≥40x10^6 raw reads.
Trimming and filtering of low-quality reads was performed using bbduk from BBTools (v37.99) and fastq-mcf from ea-utils (v1.05, https://expressionanalysis.github.io/ea-utils/).
Alignment to the human reference genome (GRCh38) was carried out using HISAT2 (v2.1.0) in paired, spliced-alignment mode with a GRCh38 index with a Gencode v33 annotation GTF.
Alignments were sorted and filtered for mapping quality (MAPQ>10) using Samtools (v1.5).
Gene-level count data were quantified using HTSeq-count (v0.6.1) with the following options (--stranded=reverse –minaqual=10 –type=exon --mode=intersection-nonempty) using a Gencode v33 GTF annotation file.
Genome_build: GRCh38
Supplementary_files_format_and_content: Tab-delimited text files containing per gene strand-specific fragment counts or normalized fragments-per-kilobase-per-million-mapped (FPKM).

molecule: polyA RNA

organism: Homo sapiens

source_name: whole blood

extract_protocol:
Whole blood samples were collected into PAXgene Blood RNA Tubes (PreAnalytiX/Qiagen) and RNA purified using a PAXgene Blood RNA Kit (Qiagen). RNA quality was assessed using an Agilent 2200 TapeStation and quantified by Qubit (Life Technologies).
Globin RNA depletion, poly-A(+) RNA enrichment, and strand-specific library preparation were carried out using a GlobinClear kit, NEBNext® Poly(A) mRNA Magnetic Isolation Module, and NEBNext Ultra™ II Directional RNA Library Prep Kit for Illumina. Paired-end 150 bp sequencing was carried out on an Illumina NovaSeq 6000 instrument by Novogene Co., Ltd.

value: whole blood

tag: karyotype

tag: Sex

value: Male

tag: age

tag: sample source

value: A

tag: library type

value: strand-specific


title: Interferon receptor dosage-normalized (Dp16^2xIFNRs); sample 5 (E18.5 heart)

data_processing:
Signal processing, base-calling, and quality scoring was carried out automatically by the NovaSeq 6000 software (Illumina).
Demultiplexing and conversion to FASTQ format was carried out using bcl2fastq (Illumina).
Data quality was assessed using FASTQC (v0.11.5) (https://www.bioinformatics.babraham.ac.uk/projects/fastqc/) and FastQ Screen (v0.11.0, https://www.bioinformatics.babraham.ac.uk/projects/fastq_screen/).
Trimming and filtering of low-quality reads was performed using bbduk from BBTools (v37.99) and fastq-mcf from ea-utils (v1.05, https://expressionanalysis.github.io/ea-utils/).
Alignment to the mouse reference genome (GRCm38) was carried out using HISAT2 (v2.1.0) in paired, spliced-alignment mode with a GRCm38 index with a Gencode M24 annotation GTF.
Alignments were sorted and filtered for mapping quality (MAPQ>10) using Samtools (v1.5).
Gene-level count data were quantified using HTSeq-count (v0.6.1) with the following options (--stranded=reverse –minaqual=10 –type=exon --mode=intersection-nonempty) using a Gencode M24 GTF annotation file.
Assembly: GRCm38
Supplementary files format and content: Tab-delimited text files containing per gene strand-specific fragment counts, normalized fragments-per-kilobase-per-million-mapped (FPKM), or normalized transcripts-per-million-mapped (TPM).

organism: Mus musculus

extract_protocol:
Total RNA from tissue samples was extracted using TRIzol reagent (Invitrogen) following the manufacture’s protocol. RNA quality was assessed using an Agilent 2200 TapeStation and quantified by Qubit (Life Technologies).
Poly-A(+) RNA enrichment, and strand-specific library preparation were carried out using a Tecan/Nugen Universal Plus mRNA Kit. Paired-end 150 bp sequencing was carried out on an Illumina NovaSeq 6000 instrument by the University of Colorado Cancer Center Genomics Shared Resource.


title: Wt progeny of high CO2

value: Wild type


title: T21, HTP0329A2

value: Female


title: PH calf 204

type: RNA

first: R.

middle: Dale

last: Brown

state: Colorado

address: 12700 East 19th Ave

hyb_protocol: Sample labeling, hybridization, and scanning was performed by University of Colorado Cancer Center Genomics Core Lab according to manufacturer specifications (Affymetrix).

data_processing:
Data processing was performed by University of Colorado Cancer Center Genomics Core Lab using R/Bioconductor. Affymetrix gene arrays were RMA normalized with a GC content adjustment. Summarized probes converted into genes, log2 signal values.
Differential gene expression between PH and CO animals was determined bywith Fisher's Exact Test with correction for false discovery rate = 0.1.

label: biotin

molecule: total RNA

organism: Bos taurus

source_name: RV

growth_protocol: Calves (postnatal day 3-7) were subjected to hypobaric hypoxia or ambient normoxia for 14d. Animals were maintained according to standard husbandry and veterinary practices.

extract_protocol: Total RNA was extracted with Trizol reagent (Invitrogen) and re-purified with RNAEasy spin columns.

treatment_protocol: RV tissues were collected immediately post mortem and snap frozen in liquid N2 for storage until tissue processing.

tag: group

value: 14d hypobaric hypoxia

value: male

tag: breed

value: Holstein


title: Wt high CO2 Rep 2


title: PH calf 178

scan_protocol: Sample labeling, hybridization, and scanning was performed by University of Colorado Cancer Center Genomics Core Lab according to manufacturer specifications (Affymetrix).


title: PH calf 192

label_protocol: Sample labeling, hybridization, and scanning was performed by University of Colorado Cancer Center Genomics Core Lab according to manufacturer specifications (Affymetrix).


title: PH calf 199


title: T21, HTP0328A


title: Control calf 195

value: ambient normoxic controls


title: Wt high CO2 Rep 1


title: PH calf 173


title: T21, HTP0327A


title: Wt ambient CO2 Rep 3

value: ambient CO2


title: Interferon receptor dosage-normalized (Dp16^2xIFNRs); sample 2 (E18.5 heart)


title: Interferon receptor dosage-normalized (Dp16^2xIFNRs); sample 3 (E18.5 heart)


title: Interferon receptor dosage-normalized (Dp16^2xIFNRs); sample 1 (E18.5 heart)


title: T21, HTP0326A


title: Wt ambient CO2 Rep 1


title: T21, HTP0324A2


title: T21, HTP0325A


title: Wt ambient CO2 Rep 2


title: Trim75-OE-rep1_FKDL210225702-1a

city: Wenzhou

first: LIjun

last: Chen

state: Other

address: Wenzhou Medical University, Wenzhou City, Zhejiang Rrovince,China

country: China

institute: Wen Zhou Medical University

description:
mRNA
Trim75-OE-rep1

data_processing:
FastQC was performed for Illumina reads.
Sequence reads were trimmed for adaptor sequence/low-quality sequence using Trim Galore software.
Trimmed sequence reads were mapped to CRCm38.p6 using HISAT2.
Read count extraction and normalization were performed using featureCounts tool.
Assembly: mm10
Supplementary files format and content: COUNTS_FPKM.xlsx: Excel file includes counts and FPKM values for each Sample.

source_name: 2-cell embryo

extract_protocol:
RNA was harvested using mMACHINE Kit (Invitrogen).
RNA libraries for RNA-seq were prepared using the TruePrep DNA Library Prep Kit V2 for Illumina (Vazyme, TD501) according to the  manufacturer's protocols.

tag: cell type

value: 2-cell embryo

value: Trim75 OE

tag: condition

value: in vitro culture

tag: time

value: Day 2


title: Trim75-OE-rep2_FKDL210225703-1a

description:
mRNA
Trim75-OE-rep2


title: Interferon receptor dosage-normalized (Dp16^2xIFNRs); sample 4 (E18.5 heart)

value: embryonic heart


title: Dp16; sample 6 (E18.5 heart)

description: Dp16; sample 6


title: T21, HTP0323A


title: L2C-con-rep2_FKDL210218072-1a

description:
mRNA
L2C-con-rep2

value: WT


title: Dp16; sample 5 (E18.5 heart)

description: Dp16; sample 5


title: Control calf 177


title: Control calf 181


title: Control calf 180


title: Dp16; sample 4 (E18.5 heart)

description: Dp16; sample 4


title: Control, HTP0322B

value: whole blood

value: Control


title: L2C-con-rep1_FKDL210218071-1a

description:
mRNA
L2C-con-rep1


title: Dp16; sample 3 (E18.5 heart)

description: Dp16; sample 3

value: Male


title: adult male arcuate nucleus of the hypothalamus, DOCA-salt, rep 2

city: Wauwatosa

first: Valerie

middle: A

last: Wagner

state: Wisconsin

address: 8701 W Watertown Plank Road

department: Physiology

institute: Medical College of Wisconsin

description: 10X Genomics

library_source: transcriptomic single cell

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation was done using Cell Ranger software v3.0.1 (10X Genomics)
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: arcuate nucleus of the hypothalamus punches

extract_protocol:
ARC brain punches were homogenized using a pestle mixer (Argos Technologies) in Nuclei EZ lysis buffer (Sigma-Aldrich). Homogenates were then filtered through a 70 μm cell strainer (Sigma-Aldrich) and collected in a fresh Eppendorf tube, followed by two rounds of centrifugation at 500 g for 5 mins at 4°C in Nuclei EZ lysis buffer. After removal of supernatant, 500 μL of Nuclei Wash and Resuspension buffer (NWR, 1.0% bovine serum albumin, 0.2 U/μl RNase inhibitor in phosphate buffered saline) was added to the pellets and incubated on ice for 5 mins without pellet disruption. Pellets were then resuspended in an additional volume of 500 μL NWR. An additional three rounds of centrifugation were carried out in the presence of NWR. After the last centrifugation step, the pellets were resuspended in 50 μL of NWR and the number of isolated intact nuclei was counted using a hemocytometer.
Sequencing libraries were constructed following the manufacter’s instructions using the Chromium Signle Cell3' GEM, Library & Gel Bead Kit v3 (10X Genomics; https://cdn.10xgenomics.com/image/upload/v1660261285/support-documents/CG000204_ChromiumNextGEMSingleCell3_v3.1_Rev_D.pdf). Briefly, GEMs are generated by combining barcoded Single Cell  3ʹ v3.1 Gel Beads, a Master Mix containing cells, and Partitioning Oil onto Chromium Next GEM Chip G. Immediately following GEM generation, the Gel Bead is dissolved, primers are released, and any copartitioned cell is lysed. Primers are mixed with the cell lysate and a Master Mix containing reverse transcription (RT) reagents. Incubation of the GEMs produces barcoded, full-length cDNA from poly-adenylated mRNA. GEMs are then broken and pooled fractions are recovered. Silane magnetic beads are used to purify the first-strand cDNA from the post GEM-RT reaction mixture, which includes leftover biochemical reagents and primers. Barcoded, full-length cDNA is amplified via PCR to generate sufficient mass for library construction. Enzymatic fragmentation and size selection are used to optimize the cDNA amplicon size. TruSeq Read  1 (read 1 primer sequence) is added to the molecules during GEM incubation. P5, P7, a sample index, and TruSeq Read  2 (read  2 primer sequence) are added via End Repair, A-tailing, Adaptor Ligation, and PCR. The final libraries contain the P5 and P7 primers used in Illumina bridge amplification.

value: wildtype

tag: strain

value: 10 weeks old

value: DOCA-salt, 3 weeks


title: T21, HTP0321A

value: Female

value: A

value: strand-specific


title: Control calf 176

value: ambient normoxic controls

value: male

value: Holstein


title: Dp16; sample 2 (E18.5 heart)

description: Dp16; sample 2


title: adult male arcuate nucleus of the hypothalamus, sham, rep 2

description: 10X Genomics

value: arcuate nucleus of the hypothalamus punches

value: sham, 3 weeks


title: Dp16; sample 1 (E18.5 heart)

description: Dp16; sample 1


title: Cnp_5xFAD_16_bulkRNA

city: Göttingen

first: Ting

last: Sun

state: Germany (DEU)

address: Hermann-Rein-Straße 3

department: Neurogenetics

country: Germany

institute: Max Planck Institute for Multidisciplinary Sciencesi

data_processing:
raw data was recovered in fastq format and accessed for quality using FASTQC v0.72
raw data was aligned to mouse genome GRCm38 using STAR v2.5.2b-2
gene counts were extracted using featureCounts v1.6.3
Genome_build: GRCm38
Supplementary_files_format_and_content: comma-delimited matrix include raw counts of genes for each Sample
Supplementary_files_format_and_content: comma-delimited matrix include TPM values for each Sample

source_name: Brain

extract_protocol:
Mice brain hemispheres (without cerebellum and olfactory bulb) were enzymatically and mechanically dissociated using Miltenyi adult brain dissociation kit under 37 °C for 30 min. Dissociated tissue suspensions were purified with Miltenyi RBC lysis and debris removal reagents. The acquired single-cell suspensions were stained by CD11b beads and passed through the Miltenyi magnetic field for microglia cell enrichment. Further, total RNA was extracted from sorted microglia cells using the RNeasy Micro kit (Qiagen).
mRNA libraries were prepared using illumina TruSeq protocol and sequenced by illumina HiSeq 4000

value: Cnp-/- x 5xFAD

value: Microglia

value: Brain

tag: mouse model

value: Alzheimer’s disease (AD)


title: DC.DC6.123+.Bl#1

city: Boston

first: Liang

last: Yang

state: MA

address: 77 Avenue Louis Pasteur

department: Pathology

institute: Harvard Medical School

description: Sorted as HLA.DR+ CD141- CD16- CD14- AXL- SIGLEC6- CD123+ CD11c- PBMCs

data_processing:
Reads were mapped to the mouse reference genome (mm10) with STAR 2.7.3a
Non-uniquely mapped reads were discarded.
The uniquely mapped reads were assigned to genes using featureCounts with GENCODE annotation (vM25)
Supplementary files format and content: mm10
Supplementary files format and content: tab-delimited text files include raw read counts for each Sample

source_name: Blood

extract_protocol:
For each sample, 1000 cells were sorted directly into the lysis buffer [5uL TCL buffer (Qiagen) supplemented with 1% 2-mercaptoethanol (Sigma)]. Total RNA was purified using RNAClean XP beads (Beckman Coulter). Polyadenylated mRNA was selected using an anchored oligo(dT) primer (5′–AAGCAGTGGTATCAACGCAGAGTACT30VN-3) and then reverse transcribed to cDNA. First-strand cDNA was subjected to limited PCR amplification followed by Tn5 transposon-based fragmentation using the Nextera XT DNA Library Preparation Kit (Illumina).
Libraries were constructed following the Smart-seq2 RNA-seq library preparation protocol.

value: Blood

value: Dendritic cells

tag: organ

tag: organ fraction

value: PBMC (Ficoll)

value: 20 years old

tag: ethnicity

value: East Asian

tag: donor status

value: Live

tag: disease


title: DC.DC5.AXL+SIGLEC6+.Bl#2

description: Sorted as HLA.DR+ CD141- CD16- CD14- AXL+ SIGLEC6+ PBMCs

tag: tissue

tag: genotype

value: Male


title: Cnp_5xFAD_15_bulkRNA

tag: age


title: adult male arcuate nucleus of the hypothalamus, sham, rep 1

description: 10X Genomics

value: wildtype

tag: Sex

value: 10 weeks old

tag: treatment


title: Control, HTP0316B

value: whole blood

tag: karyotype

value: Control

value: Female

tag: sample source

value: A

tag: library type

value: strand-specific


title: Cnp_5xFAD_14_bulkRNA

value: Cnp-/- x 5xFAD

tag: cell type

value: Microglia


title: Wild-type; sample 6 (E18.5 heart)

description: Wild-type; sample 6

value: embryonic heart

value: wild-type C57/BL6

tag: age in_days_post_conception


title: Wild-type; sample 5 (E18.5 heart)

description: Wild-type; sample 5


title: T21, HTP0318A3


title: Wild-type; sample 4 (E18.5 heart)

description: Wild-type; sample 4


title: DC.DC1.141+.Bl#1

description: Sorted as HLA.DR+ CD141+ CD16- CD14- PBMCs

value: Blood

value: Dendritic cells


title: T21, HTP0310A


title: DC.DC6.123+.Bl#2

value: PBMC (Ficoll)

value: 20 years old


title: DC.DC1.141+.Bl#2

value: East Asian

value: Live


title: Cnp_5xFAD_13_bulkRNA

tag: strain

value: Brain

value: Alzheimer’s disease (AD)


title: T21, HTP0312A2

value: whole blood


title: adult male arcuate nucleus of the hypothalamus, DOCA-salt, rep 1

description: 10X Genomics

value: arcuate nucleus of the hypothalamus punches

value: wildtype

value: male

value: 10 weeks old

value: DOCA-salt, 3 weeks


title: Wild-type; sample 2 (E18.5 heart)

description: Wild-type; sample 2

value: Female


title: Mo.14+.Bl#2

description: Sorted as HLA.DR+ CD16lo CD14hi PBMCs

value: Monocytes

value: 26 years old


title: 5xFAD_11_bulkRNA

value: Microglia

tag: mouse model


title: T21, HTP0320A2

value: A

value: strand-specific


title: T21, HTP0306A

value: Male


title: Wild-type; sample 3 (E18.5 heart)

description: Wild-type; sample 3

value: embryonic heart

value: wild-type C57/BL6


title: 5xFAD_12_bulkRNA

value: Brain


title: 5xFAD_10_bulkRNA

value: Alzheimer’s disease (AD)


title: Mo.14+.Bl#1

description: Sorted as HLA.DR+ CD16lo CD14hi PBMCs

value: Blood

tag: organ

value: PBMC (Ficoll)

value: East Asian

value: Live


title: Wild-type; sample 1 (E18.5 heart)

description: Wild-type; sample 1


title: DC.DC5.AXL+SIGLEC6+.Bl#1

value: Dendritic cells

tag: organ fraction

value: 20 years old


title: Control, HTP0302B

value: whole blood

value: Control

value: Female


title: T21, HTP0301A3


title: 5xFAD_9_bulkRNA

value: Microglia


title: Mo.16+.Bl#1

description: Sorted as HLA.DR+ CD16hi CD14lo PBMCs

value: Monocytes

tag: ethnicity


title: Cnp_ko_8_bulkRNA

value: Cnp-/-


title: T21, HTP0300A

value: A

value: strand-specific


title: Interferon receptor dosage-normalized (Dp16^2xIFNRs); sample 6 (E12.5 heart)

value: embryonic heart

value: Male


title: Cnp_ko_7_bulkRNA

value: Brain

value: Alzheimer’s disease (AD)


title: T.Treg.act.Bl#1

description: Sorted as CD19- CD4+ CD25+ CD127- CD45RA- PBMCs

value: Blood

value: T cells

value: PBMC (Ficoll)

tag: donor status


title: T.Treg.act.Bl#2

value: East Asian

value: Live

tag: disease


title: T21, HTP0296A

tag: tissue

value: whole blood


title: Cnp_ko_6_bulkRNA

tag: genotype


title: Interferon receptor dosage-normalized (Dp16^2xIFNRs); sample 5 (E12.5 heart)


title: Interferon receptor dosage-normalized (Dp16^2xIFNRs); sample 3 (E12.5 heart)


title: T21, HTP0298A

tag: age


title: Interferon receptor dosage-normalized (Dp16^2xIFNRs); sample 4 (E12.5 heart)

tag: Sex


title: T.Treg.rest.Bl#2

description: Sorted as CD19- CD4+ CD25+ CD127- CD45RA+ PBMCs

value: 20 years old


title: T21, HTP0295A


title: Mo.16+.Bl#2

description: Sorted as HLA.DR+ CD16hi CD14lo PBMCs


title: Control, HTP0294B

value: Control


title: WT_4_bulkRNA

value: WT

value: Microglia


title: T.MAIT.8+.Bl#2

description: Sorted as CD19- CD3+ CD4- CD8+ Va7.2+ CD161dull PBMCs


title: T21, HTP0293A


title: Interferon receptor dosage-normalized (Dp16^2xIFNRs); sample 1 (E12.5 heart)

value: Female

tag: treatment


title: WT_3_bulkRNA


title: Dp16; sample 6 (E12.5 heart)

description: Dp16; sample 6


title: T.MAIT.8+.Bl#1


title: WT_2_bulkRNA


title: Dp16; sample 5 (E12.5 heart)

description: Dp16; sample 5


title: Control, HTP0289B

tag: karyotype

value: A


title: T.MAIT.4+.Bl#2

description: Sorted as CD19- CD3+ CD4+ CD8- Va7.2+ CD161dull PBMCs


title: Dp16; sample 4 (E12.5 heart)

description: Dp16; sample 4


title: WT_1_bulkRNA


title: T.MAIT.4+.Bl#1


title: T.Treg.rest.Bl#1


title: Dp16; sample 3 (E12.5 heart)

description: Dp16; sample 3


title: Control, HTP0288B

tag: sample source

value: strand-specific


title: T.NKT.Va24+.Bl#2

description: Sorted as CD19- CD3+ TCRVa24+ PBMCs


title: Cnp_ko_5_bulkRNA

value: Cnp-/-


title: Dp16; sample 2 (E12.5 heart)

description: Dp16; sample 2

value: embryonic heart


title: T.NKT.Va24+.Bl#1

description: Sorted as CD19- CD3+ TCRVa24+ PBMCs

value: Male


title: Control, HTP0290B

tag: library type


title: Dp16; sample 1 (E12.5 heart)

description: Dp16; sample 1


title: CPW18: CISPCN(CPW) rep2

city: Dalian

first: Zhilin

last: Luan

state: China

address: 9 W., S. Lvshun Blvd.

institute: Advanced Institute for Medical Sciences, Dalian Medical University

data_processing:
Quality control: Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts. In this step, clean data (clean reads) were obtained by removing read containing adapter, reads containing ploy-N and low quality reads from raw data. At the same time, Q20, Q30 and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality.
Reads mapping to the reference genome: Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using Hisat2 v2.0.5 and paired-end clean reads were aligned to the reference genome using Hisat2 v2.0.5. We selected Hisat2 as the mapping tool for that Hisat2 can generate a database of splice junctions based on the gene model annotation file and thus a better mapping result than other non-splice mapping tools.
Quantification of gene expression level: featureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene. FPKM, expected number of Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced, considers the effect of sequencing depth and gene length for the reads count at the same time, and is currently the most commonly used method for estimating gene expression levels.
Differential expression analysis: (For DESeq2 with biological replicates) Differential expression analysis of two conditions/groups (two biological replicates per condition) was performed using the DESeq2 R package (1.16.1). DESeq2 provide statistical routines for determining differential expression in digital gene expression data using a model based on the negative binomial distribution. The resulting P-values were adjusted using the Benjamini and Hochberg’s approach for controlling the false discovery rate. Genes with an adjusted P-value <0.05 found by DESeq2 were assigned as differentially expressed. (For edgeR without biological replicates) Prior to differential gene expression analysis, for each sequenced library, the read counts were adjusted by edgeR program package through one scaling normalized factor. Differential expression analysis of two conditions was performed using the edgeR R package (3.18.1). The P values were adjusted using the Benjamini & Hochberg method. Corrected P-value of 0.05 and absolute foldchange of 2 were set as the threshold for significantly differential expression.
GO and KEGG enrichment analysis of differentially expressed genes: Gene Ontology (GO) enrichment analysis of differentially expressed genes was implemented by the clusterProfiler R package, in which gene length bias wascorrected. GO terms with corrected Pvalue less than 0.05 were considered significantly enriched by differential expressed genes. KEGG is a database resource for understanding high-level functions and utilities of the biological system, such as the cell, the organism and the ecosystem, from molecular-level information, especially large-scale molecular datasets generated by genome sequencing and other high-through put experimental technologies (http://www.genome.jp/kegg/). We used clusterProfiler R package to test the statistical enrichment of differential expression genes in KEGG pathways.
Genome_build: mm8
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample.

source_name: Kidney

extract_protocol:
Male C57BL/6 wild-type mice (8 week old) were randomly divided into 4 groups with 6~8 animals each: corn oil + saline (CON), PCN + saline (PCN), corn oil + cisplatin (CIS) and PCN + cisplatin (CIS+PCN). Two groups of mice (CIS and CIS+PCN) were pretreated via oral gavage daily with PCN (40 mg/kg) for 4 days and the additional two groups (CON and CIS) were administrated with equal volume of corn oil for 4 days. A single nephrotoxic dose of cisplatin (20 mg/kg) was administrated intraperitoneally (i.p.) to CIS and CIS+PCN groups on Day 4, and then the daily corn oil or PCN treatment was continued for 3 days in all groups. Mice were sacrificed 4 days after cisplatin injection.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: kidney

value: 8 weeks

value: wild type


title: Wild-type; sample 6 (E12.5 heart)

description: Wild-type; sample 6

value: wild-type C57/BL6


title: CIS15: CIS rep3


title: CPW17: CISPCN(CPW) rep1


title: T21, HTP0263A2

value: C


title: T21, HTP0261A2


title: T.8EffMem.CD3+8+RA-62L-.Bl#2

description: Sorted as DR- CD3+ CD4- CD8+ CD127+ CD45RA- CD62L- PBMCs

value: Blood

tag: cell type

value: T cells

value: PBMC (Ficoll)

value: East Asian

value: Live


title: T.8Nve.CD3+8+RA+62L+.Bl#2

description: Sorted as DR- CD3+ CD4- CD8+ CD127+ CD25- CD45RAhi CD62Lhi PBMCs

value: 20 years old


title: CIS11: CIS rep1


title: T21, HTP0277A3

value: whole blood

value: Female

value: D


title: Wild-type; sample 4 (E12.5 heart)

description: Wild-type; sample 4

tag: age in_days_post_conception


title: Wild-type; sample 5 (E12.5 heart)

description: Wild-type; sample 5


title: T21, HTP0259A2

value: A

value: strand-specific


title: T21, HTP0254A2

value: Male


title: Interferon receptor dosage-normalized (Dp16^2xIFNRs); sample 2 (E12.5 heart)

value: embryonic heart


title: T21, HTP0262A2


title: T.8Nve.CD3+8+RA+62L+.Bl#1


title: PCN7: PCN rep3

tag: strain

value: kidney

value: 8 weeks


title: T.4EffMem.CD3+4+RA-62L-.Bl#1

description: Sorted as DR- CD3+ CD4+ CD8- CD127+ CD45RA- CD62L- PBMCs


title: Wild-type; sample 3 (E12.5 heart)

description: Wild-type; sample 3

value: wild-type C57/BL6


title: CIS13: CIS rep2

value: wild type


title: PCN6: PCN rep2


title: PCN5: PCN rep1


title: CPW21: CISPCN(CPW) rep3


title: T.8EffMem.CD3+8+RA-62L-.Bl#1

value: Blood


title: Wild-type; sample 1 (E12.5 heart)

description: Wild-type; sample 1


title: T.4Nve.CD3+4+RA+62L+.Bl#1

description: Sorted as DR- CD3+ CD4+ CD8- CD127+ CD25- CD45RAhi CD62Lhi PBMCs

value: T cells


title: T.4Nve.CD3+4+RA+62L+.Bl#2

value: PBMC (Ficoll)


title: T21, HTP0247A2

value: C


title: T21, HTP0251A2


title: T.4EffMem.CD3+4+RA-62L-.Bl#2

value: East Asian

value: Live


title: Control2: Control rep2


title: Wild-type; sample 2 (E12.5 heart)

description: Wild-type; sample 2


title: Control1: Control rep1


title: Control3: Control rep3


title: ILC.NKmem.56lo16hi57hi.Bl#2

description: Sorted as CD19- CD56mid CD16+ CD57+ PBMCs

value: Innate lymphoid cells

value: 20 years old


title: Interferon receptor dosage-normalized (Dp16^2xIFNRs); sample 2 (embryonic facial mesenchyme)

source_name: whole brain

value: whole brain


title: Control, HTP0242B3

value: whole blood

value: Control

value: Female

value: D


title: Interferon receptor dosage-normalized (Dp16^2xIFNRs); sample 1 (embryonic facial mesenchyme)


title: Dp16; sample 3 (embryonic facial mesenchyme)

description: Dp16; sample 3

value: Male


title: ILC.NKmem.56lo16hi57hi.Bl#1


title: ILC.NKmat.56lo16hi57-.Bl#2

description: Sorted as CD19- CD56mid CD16+ CD57- PBMCs


title: T21, HTP0243A3

value: strand-specific


title: ILC.NKmat.56lo16hi57-.Bl#1


title: T21, HTP0236A2


title: T21, HTP0238A3


title: T21, HTP0230A2


title: ILC.NKimm.56hi16-.Bl#1

description: Sorted as CD19- CD56hi PBMCs


title: Dp16; sample 2 (embryonic facial mesenchyme)

description: Dp16; sample 2


title: ILC.NKimm.56hi16-.Bl#2

description: Sorted as CD19- CD56hi PBMCs


title: Squamous epithelium 2

first: Hongmei

last: Mou

address: 55 Fruit Street, Jackson 1402

department: The Mucosal Immunology & Biology Research Center

institute: Massachusetts General Hospital

data_processing:
none provided
Supplementary files format and content: Excel files include Mean and SD values for each Sample

source_name: Squamous epithelium

growth_protocol: Human airway basal cells were propagated in Small Airway Epithelial Cell Medium (Promocell medium, C-21170) with 5-10 mM ROCKi (Tocris, 1254), 1 mM A-83-01 (Tocris, 2939) and 0.5 mM CHIR99021 (Tocris, 4423) on plates pre-coated with laminin-enriched 804G-conditioned medium. Human airway basal cells were trypsinized and seeded onto 0.4 um transwell membranes pre-coated with 804G-conditioned medium with a density of >6000 cells/mm2. The airway stem cells were 100% confluent after attachment at this density. Following cell attachment for >12 hours, excess cells were removed, and the medium was replaced with complete Pneumacult-ALI medium (StemCell Technology, Cat. 05001) filling both the upper and lower chambers. The next day, ALI medium was added only in the lower chamber to initiate airway-liquid interface. The ALI medium was changed every 2 days until differentiation was well established. We culture ALI for 14-21 days as a standard protocol.

extract_protocol:
RNA was harvested using RNeasy mini kit (Qiagen, 74104).
RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacturer's protocols.

treatment_protocol: For squmous group, duiring ALI differentiation, add  2 uM CHIR99021 in Pneumacult-ALI medium.

value: Squamous epithelium

value: 2 uM CHIR99021

tag: time

value: Whole ALI differentiation


title: T21, HTP0249A2


title: Squamous epithelium 1


title: Normal airway epithelium 2

source_name: Normal airway epithelium

value: Normal airway epithelium


title: T21, HTP0226A3


title: B.TransIgD+27+.Bl#2

description: Sorted as CD19+IgD+CD27+ PBMCs

value: Blood

value: B cells

tag: organ

value: PBMC (Ficoll)


title: T21, HTP0219A2

value: C


title: B.TransIgD+27+.Bl#1

description: Sorted as CD19+IgD+CD27+ PBMCs

tag: organ fraction

value: East Asian

value: Live


title: Control, HTP0216B2


title: Wild-type; sample 2 (embryonic facial mesenchyme)

description: Wild-type; sample 2

value: whole brain

value: wild-type C57/BL6


title: Wild-type; sample 1 (embryonic facial mesenchyme)

description: Wild-type; sample 1


title: Squamous epithelium 3


title: Normal airway epithelium 1


title: G263, P3, inflamed

city: Sao Paulo

first: Tiago

middle: da Silva

last: Medina

state: SP

address: 440 Tagua Street

department: International Research Center

country: Brazil

institute: A. C. Camargo Cancer Center

description: 10x Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v2.1.1 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: GRCh38
Supplementary files format and content: Count matrix (tab-separated values)

source_name: Inflamed biopsy

extract_protocol:
CD161-Vα24Jα18-CD8-CD4+ T cells were isolated from biopsies of CD patients. The surface markers CD161 and Vα24Jα18 were used to exclude possible contamination with NK and NKT cells.
Library was performed according to the manufacter’s instructions (single cell 3’ v2 protocol, 10x Genomics). Briefly, ~1000 cells per sample were resuspended in PBS + 0.4% BSA and loaded together with partitioning oil and gel beads into the chip to generate the gel bead-in-emulsion (GEM). The poly-A RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA, which contains an Ilumina R1 primer sequence, Unique Molecular Identifier (UMI) and the 10x Barcode. The pooled barcoded cDNA was then cleaned up with Silane DynaBeads, amplified by PCR and the apropiated sized fragments were selected with SPRIselect reagent for subsequent library construction. During the library construction Ilumina R2 primer sequence, paired-end constructs with P5 and P7 sequences and a sample index were added. Samples were sequenced on a HiSeq 2500 (Illumina)

tag: patient

tag: patient gender

tag: patient age

tag: disease state

value: Crohn’s disease

value: Inflamed biopsy

value: CD4 T cells


title: B.MemIgD-27+38-.Bl#2

description: Sorted as CD19+ IgD- CD27+ CD38- PBMCs

tag: tissue

tag: genotype

value: 20 years old

value: Male

tag: ethnicity

tag: donor status

tag: disease


title: G262, P3, noninflamed

description: 10x Genomics

source_name: Non-inflamed biopsy

value: Female

value: Non-inflamed biopsy


title: Wild-type; sample 3 (embryonic facial mesenchyme)

description: Wild-type; sample 3

tag: Sex

tag: treatment


title: Control, HTP0214B2

value: whole blood

tag: karyotype

value: Control

tag: age

tag: sample source

tag: library type

value: strand-specific


title: Interferon receptor dosage-normalized (Dp16^2xIFNRs); sample 7 (adult brain)

tag: age in_days_post_conception


title: B.MemIgD-27+38-.Bl#1

description: Sorted as CD19+ IgD- CD27+ CD38- PBMCs

value: Blood

tag: cell type

value: B cells

tag: organ

tag: organ fraction


title: G08, P2, inflamed

description: 10x Genomics

tag: patient

tag: patient gender

tag: patient age


title: Interferon receptor dosage-normalized (Dp16^2xIFNRs); sample 6 (adult brain)

tag: tissue

tag: genotype


title: T21, HTP0213A3

value: D


title: T21, HTP0211A3


title: Interferon receptor dosage-normalized (Dp16^2xIFNRs); sample 4 (adult brain)


title: B.NveIgD+27-.Bl#4

description: Sorted as CD19+ IgD+ CD27- PBMCs

value: PBMC (Ficoll)

tag: ethnicity

value: East Asian

tag: donor status


title: T21, HTP0207A4

tag: Sex

value: A


title: G06, P1, inflamed

description: 10x Genomics

tag: disease state


title: Interferon receptor dosage-normalized (Dp16^2xIFNRs); sample 5 (adult brain)

value: whole brain

tag: treatment


title: B.NveIgD+27-.Bl#3

description: Sorted as CD19+ IgD+ CD27- PBMCs

tag: age

value: Live

tag: disease


title: G07, P2, noninflamed

description: 10x Genomics

value: Crohn’s disease


title: B.NveIgD+27-.Bl#2

description: Sorted as CD19+ IgD+ CD27- PBMCs


title: G05, P1, noninflamed

description: 10x Genomics

value: CD4 T cells


title: Interferon receptor dosage-normalized (Dp16^2xIFNRs); sample 2 (adult brain)


title: Interferon receptor dosage-normalized (Dp16^2xIFNRs); sample 3 (adult brain)


title: B.NveIgD+27-.Bl#1

description: Sorted as CD19+ IgD+ CD27- PBMCs

value: 20 years old


title: Control, HTP0206B

tag: karyotype

value: Male

tag: sample source

tag: library type


title: JAR, DMSO, DMF, 3

city: Bonn

first: Kai

last: Funke

state: NRW

address: Venusberg-Campus 1

department: Pathology, Developmental Pathology

institute: University Hospital Bonn

description:
DE11NGSUKBR116666
Control sample to "JAR, MLN4924, Cisplatin"
MLN_CP_stringtie_raw_counts.csv

data_processing:
QC of raw sequencing reads and trimming were performed in Trim Galore! 0.4.5 (Brabraham Bioinformatics, http://www.bioinformatics.babraham.ac.uk/projects/trim_galore), using a phred score cutoff of 30 and minimum sequence length of 30 after trimming.
Mapping was done using HISAT2 2.1
Transcript quantification and annotation was done using StringTie 1.3.3. Gene annotation information was retrieved from the Ensembl FTP server (ftp://ftp.ensembl.org) for the human genome (GRCh38.p13). We used the python script (preDE.py) included in the StringTie package to prepare gene-level count matrices for analysis of differential gene expression.
Differential expression was tested with DESeq2 1.16.1. Pseudogenes were removed from the count matrices based on “biotype” annotation information extracted from Biomart (R-package biomaRt). Low counts were removed by the independent filtering process implemented in DESeq2.
Assembly: human genome GRCh38.p13
Supplementary files format and content: comma-separated text files include raw counts
Supplementary files format and content: tab-delimited text files include DEseq2 normalized counts and DESeq2 differential expression analysis outputs for each comparison

source_name: JAR

growth_protocol: 2102EP and JAR cells were cultured in Dulbecco’s modified Eagle’s medium (DMEM) supplemented with 10% fetal bovine serum (FBS), 1% penicillin/streptomycin (pen/strep) and 200 mM L-glutamine (L-glu). All cells were kept at 37 °C and 7.5 % CO2.

extract_protocol:
RNA was isolated using the RNeasy Mini Kit (Qiagen, Hilden, Germany)
The RNA quality control, library preparation (QuantSeq 3'-mRNA Library Prep (Lexogen, USA)) and RNA sequencing were performed by the Core Facility Next Generation Sequencing (University of Bonn, Germany).

treatment_protocol: Cells were treated for 48 h with MLN4924/cisplatin/combination of MLN4924 and cisplatin, or corresponsding  control DMSO/DMF/ combination of DMSO and DMF.

tag: cell line

value: JAR

tag: cell type

value: Choriocarcinoma


title: Control, HTP0205B

value: whole blood

value: Female


title: Interferon receptor dosage-normalized (Dp16^2xIFNRs); sample 1 (adult brain)

tag: age in_days_post_conception


title: T21, HTP0241A2

value: C

value: strand-specific


title: Dp16; sample 5 (adult brain)

description: Dp16; sample 5


title: T21, HTP0204A


title: JAR, DMSO, DMF, 1

description:
DE65NGSUKBR116664
Control sample to "JAR, MLN4924, Cisplatin"
MLN_CP_stringtie_raw_counts.csv


title: JAR, MLN4924, Cisplatin, 3

description:
DE92NGSUKBR116663
MLN_CP_stringtie_raw_counts.csv
JAR_MLN_CP_vs_DMSO_DMF_DESeq2_counts.txt
JAR_MLN_CP_vs_DMSO_DMF_DESeq2_DE.txt

value: MLN4924, Cisplatin, 1µM, 4µM, 48h


title: Dp16; sample 3 (adult brain)

description: Dp16; sample 3


title: T21, HTP0198A3

description: globin-depleted, poly(A)+ RNA from whole blood


title: Dp16; sample 4 (adult brain)

description: Dp16; sample 4


title: T21, HTP0151A


title: JAR, DMSO, DMF, 2

description:
DE38NGSUKBR116665
Control sample to "JAR, MLN4924, Cisplatin"
MLN_CP_stringtie_raw_counts.csv


title: JAR, MLN4924, Cisplatin, 1

description:
DE49NGSUKBR116661
MLN_CP_stringtie_raw_counts.csv
JAR_MLN_CP_vs_DMSO_DMF_DESeq2_counts.txt
JAR_MLN_CP_vs_DMSO_DMF_DESeq2_DE.txt


title: CCR6int_D2 (scRNA-seq)

city: Bethesda

first: Timothy

middle: G

last: Myers

state: MD

address: 50 South Drive, Room 5509

department: Research Technologies Branch

institute: National Institute of Allergy and Infectious Diseases

description: 5-prime RNA expression library from cell suspension AB4041

data_processing:
The raw data were downloaded using Python Run Downloader (Illumina) and analyzed using Cell Ranger (Illumina).
Cell ranger 3.1.0 (STAR_2.5.1b, samtools 1.7)
Assembly: GRCh38
Supplementary files format and content: contig and clonotype assignment files from v(d)j sequencing
Supplementary files format and content: h5 format matrix file (unfiltered) for 5' expression sequencing

source_name: PBMC

extract_protocol:
Purified CD4+ T cells were FACS sorted into CCR6neg, CCR6low, CCR6int and CCR6high subgroups, counted for cell viability, and immediately used for library preparation using ChromiumTM Single Cell V (D) J, and 5-prime gene expression Reagent Kit (10X Genomics) according to the manufacturer’s instructions
The single-cell 5’ gene expression libraries were sequenced on Illumina NextSeq500 to a minimum sequencing depth of 50,000 reads per cell using pair-end sequencing as follows: read length of 150 bp read 1, 8 bp i7 index, 150 bp read 2.
The single-cell TCR libraries were sequenced on an Illumina NextSeq500 to a minimum sequencing depth of 5,000 reads per cell using paired-end sequencing with single indexing as follows: read length of 150 bp read 1, 8 bp i7 index, 150 bp read 2

value: PBMC

tag: cell suspension id

tag: library

value: CD4 T-cell

tag: cell subset

tag: human donor

tag: single cell barcoded cdna

value: 5-prime RNA

tag: reactor

value: 10x Genomics


title: CCR6high-D1 (scRNA-seq)

description: 5-prime RNA expression library from cell suspension AB4038

tag: tissue


title: Wild-type; sample 6 (adult brain)

description: Wild-type; sample 6

value: whole brain

tag: genotype

value: wild-type C57/BL6

tag: Sex


title: JAR, MLN4924, Cisplatin, 2

description:
DE22NGSUKBR116662
MLN_CP_stringtie_raw_counts.csv
JAR_MLN_CP_vs_DMSO_DMF_DESeq2_counts.txt
JAR_MLN_CP_vs_DMSO_DMF_DESeq2_DE.txt

tag: treatment


title: Control, HTP0149B

value: Control

tag: age

value: A


title: CCR6low_D2 (scRNA-seq)

description: 5-prime RNA expression library from cell suspension AB4040


title: Dp16; sample 2 (adult brain)

description: Dp16; sample 2


title: CCR6neg_D2 (scRNA-seq)

description: 5-prime RNA expression library from cell suspension AB4039


title: CCR6low_D1 (scRNA-seq)

description: 5-prime RNA expression library from cell suspension AB4036


title: Control, HTP0147B

tag: karyotype


title: Dp16; sample 1 (adult brain)

description: Dp16; sample 1


title: CCR6high_D2 (scRNA-seq)

description: 5-prime RNA expression library from cell suspension AB4042


title: Control, HTP0202B

tag: sample source


title: CCR6int-D1 (scRNA-seq)

description: 5-prime RNA expression library from cell suspension AB4037


title: Control, HTP0148B2

tag: library type


title: CCR6neg_D1 (scRNA-seq)

description: 5-prime RNA expression library from cell suspension AB4035


title: Control, HTP0146B


title: JAR, DMF, 2

description:
DE06NGSUKBR116659
Control sample to "JAR, Cisplatin"
MLN_CP_stringtie_raw_counts.csv

tag: cell line


title: CCR6high_D2 (scTCR-seq)

description: TCR V(D)J library from cell suspension AB4042

data_processing:
The raw data were downloaded using Python Run Downloader (Illumina) and analyzed using Cell Ranger (Illumina).
Cell ranger 3.1.0 (STAR_2.5.1b, samtools 1.7)
Assembly: GRCh38
Supplementary files format and content: contig and clonotype assignment files from v(d)j sequencing
Supplementary files format and content: h5 format matrix file (unfiltered) for 5' expression sequencing
Library strategy: scTCR-seq

tag: cell type

value: TCR V(D)J


title: Wild-type; sample 4 (adult brain)

description: Wild-type; sample 4

tag: age in_days_post_conception


title: JAR, DMF, 3

description:
DE76NGSUKBR116660
Control sample to "JAR, Cisplatin"
MLN_CP_stringtie_raw_counts.csv


title: Control, HTP0127B2


title: Control, HTP0126B2


title: JAR, Cisplatin, 2

description:
DE87NGSUKBR116656
MLN_CP_stringtie_raw_counts.csv
JAR_Cisplatin_vs_DMF_DESeq2_counts.txt
JAR_Cisplatin_vs_DMF_DESeq2_DE.txt

value: Cisplatin, 4µM, 48h


title: Wild-type; sample 1 (adult brain)

description: Wild-type; sample 1


title: T21, HTP0119A


title: JAR, Cisplatin, 1

description:
DE17NGSUKBR116655
MLN_CP_stringtie_raw_counts.csv
JAR_Cisplatin_vs_DMF_DESeq2_counts.txt
JAR_Cisplatin_vs_DMF_DESeq2_DE.txt

value: JAR


title: JAR, DMSO, 2

description:
DE71NGSUKBR116653
Control sample to "JAR, MLN4924"
MLN_CP_stringtie_raw_counts.csv

value: Choriocarcinoma


title: T21, HTP0116A2

description: globin-depleted, poly(A)+ RNA from whole blood

value: whole blood

value: Male


title: Control, HTP0118B


title: JAR, Cisplatin, 3

description:
DE60NGSUKBR116657
MLN_CP_stringtie_raw_counts.csv
JAR_Cisplatin_vs_DMF_DESeq2_counts.txt
JAR_Cisplatin_vs_DMF_DESeq2_DE.txt


title: Wild-type; sample 3 (adult brain)

description: Wild-type; sample 3


title: JAR, DMF, 1

description:
DE33NGSUKBR116658
Control sample to "JAR, Cisplatin"
MLN_CP_stringtie_raw_counts.csv


title: CCR6int_D2 (scTCR-seq)

description: TCR V(D)J library from cell suspension AB4041

tag: cell suspension id


title: Wild-type; sample 5 (adult brain)

description: Wild-type; sample 5

value: Female


title: Wild-type; sample 2 (adult brain)

description: Wild-type; sample 2


title: JAR, DMSO, 3

description:
DE44NGSUKBR116654
Control sample to "JAR, MLN4924"
MLN_CP_stringtie_raw_counts.csv


title: CCR6low_D2 (scTCR-seq)

description: TCR V(D)J library from cell suspension AB4040

tag: library


title: CCR6neg_D2 (scTCR-seq)

description: TCR V(D)J library from cell suspension AB4039

tag: cell subset


title: CCR6high-D1 (scTCR-seq)

description: TCR V(D)J library from cell suspension AB4038

tag: human donor


title: Interferon receptor dosage-normalized (Dp16^2xIFNRs); sample 5 (adult heart)

source_name: adult heart

value: adult heart

tag: age in_weeks


title: Interferon receptor dosage-normalized (Dp16^2xIFNRs); sample 4 (adult heart)


title: T21, HTP0112A3

value: strand-specific


title: CCR6low_D1 (scTCR-seq)

description: TCR V(D)J library from cell suspension AB4036

value: PBMC

tag: single cell barcoded cdna

tag: reactor


title: Control, HTP0111B2

tag: tissue


title: JAR, DMSO, 1

description:
DE98NGSUKBR116652
Control sample to "JAR, MLN4924"
MLN_CP_stringtie_raw_counts.csv


title: Interferon receptor dosage-normalized (Dp16^2xIFNRs); sample 3 (adult heart)

tag: genotype

tag: Sex


title: JAR, MLN4924, 3

description:
DE28NGSUKBR116651
MLN_CP_stringtie_raw_counts.csv
JAR_MLN4924_vs_DMSO_DESeq2_counts.txt
JAR_MLN4924_vs_DMSO_DESeq2_DE.txt

tag: treatment


title: CCR6int-D1 (scTCR-seq)

description: TCR V(D)J library from cell suspension AB4037

value: CD4 T-cell


title: Interferon receptor dosage-normalized (Dp16^2xIFNRs); sample 2 (adult heart)


title: JAR, MLN4924, 2

description:
DE55NGSUKBR116650
MLN_CP_stringtie_raw_counts.csv
JAR_MLN4924_vs_DMSO_DESeq2_counts.txt
JAR_MLN4924_vs_DMSO_DESeq2_DE.txt


title: T21, HTP0109A3

tag: karyotype

tag: age


title: T21, HTP0107A3

tag: sample source

tag: library type


title: 2102EP, DMSO, DMF, 3

description:
DE12NGSUKBR116648
Control sample to "2102EP, MLN4924, Cisplatin"
MLN_CP_stringtie_raw_counts.csv

tag: cell line

tag: cell type

value: Embryonal Carcinoma


title: Control, HTP0105B3


title: JAR, MLN4924, 1

description:
DE82NGSUKBR116649
MLN_CP_stringtie_raw_counts.csv
JAR_MLN4924_vs_DMSO_DESeq2_counts.txt
JAR_MLN4924_vs_DMSO_DESeq2_DE.txt


title: Dp16; sample 6 (adult heart)

description: Dp16; sample 6


title: 2102EP, DMSO, DMF, 2

description:
DE39NGSUKBR116647
Control sample to "2102EP, MLN4924, Cisplatin"
MLN_CP_stringtie_raw_counts.csv


title: CCR6int-CMV_D2

description: V(D)J targeted sequencing of CMV selected T-cells

data_processing:
The raw data were downloaded using Python Run Downloader (Illumina) and analyzed using Cellranger (Illumina).
cellranger vdj (3.1.0)
Assembly: GRCh38
Supplementary files format and content: contig and clonotype assignment files from cellranger vdj
Library strategy: scTCR-seq

extract_protocol:
Purified CD4+ T cells were FACS sorted into CCR6neg, CCR6low, CCR6int and CCR6high subgroups, loaded with CFSE, and cultured with autologous dodecyldimethylamine oxide (DDAO)-loaded, irradiated PBMCs in the presence of an extract of CMV-infected cells (EastCoast Bio, North Berwick, ME). On day 7, the proliferated, CFSElow T cells were sorted, counted for cell viability, and immediately used for library preparation
using ChromiumTM Single Cell V (D) J Reagent Kit (10X Genomics) according to the manufacturer’s instructions.
The single-cell TCR libraries were sequenced on an Illumina NextSeq500 to a minimum sequencing depth of 5000 reads per cell using paired-end sequencing with single indexing as follows: read length of 150 bp read 1, 8 bp i7 index, 150 bp read 2.

tag: sampleID

value: 10x Genomics


title: CCR6high-CMV_D4


title: Control, HTP0104B2

description: globin-depleted, poly(A)+ RNA from whole blood


title: Dp16; sample 4 (adult heart)

description: Dp16; sample 4


title: T21, HTP0103A2


title: 2102EP, DMSO, DMF, 1

description:
DE66NGSUKBR116646
Control sample to "2102EP, MLN4924, Cisplatin"
MLN_CP_stringtie_raw_counts.csv


title: Dp16; sample 3 (adult heart)

description: Dp16; sample 3


title: Dp16; sample 2 (adult heart)

description: Dp16; sample 2


title: CCR6high-CMV-D3


title: CCR6neg_D1 (scTCR-seq)

description: TCR V(D)J library from cell suspension AB4035

tag: cell suspension id

tag: library


title: Interferon receptor dosage-normalized (Dp16^2xIFNRs); sample 1 (adult heart)


title: CCR6int-CMV-D4

tag: cell subset

tag: human donor


title: T21, HTP0101A2


title: 2102EP, MLN4924, Cisplatin, 2

description:
DE23NGSUKBR116644
MLN_CP_stringtie_raw_counts.csv
2102EP_MLN_CP_vs_DMSO_DMF_DESeq2_counts.txt
2102EP_MLN_CP_vs_DMSO_DMF_DESeq2_DE.txt

value: MLN4924, Cisplatin, 0.25µM, 2.5µM, 48h


title: Dp16; sample 5 (adult heart)

description: Dp16; sample 5

tag: age in_weeks


title: Dp16; sample 1 (adult heart)

description: Dp16; sample 1


title: CCR6low-CMV_D3

tag: reactor


title: Control, HTP0098B2

tag: tissue


title: Wild-type; sample 5 (adult heart)

description: Wild-type; sample 5

tag: genotype

value: wild-type C57/BL6


title: Control, HTP0100B2

value: Control

tag: Sex


title: CCR6neg-CMV_D3


title: Control, HTP0096B2

value: A


title: Wild-type; sample 4 (adult heart)

description: Wild-type; sample 4

tag: treatment


title: CCR6low-CMV_D4


title: 2102EP, MLN4924, Cisplatin, 1

description:
DE50NGSUKBR116643
MLN_CP_stringtie_raw_counts.csv
2102EP_MLN_CP_vs_DMSO_DMF_DESeq2_counts.txt
2102EP_MLN_CP_vs_DMSO_DMF_DESeq2_DE.txt


title: 2102EP, DMF, 3

description:
DE77NGSUKBR116642
Control sample to "2102EP, Cisplatin"
MLN_CP_stringtie_raw_counts.csv


title: Control, HTP0095B2

tag: karyotype


title: Dp16; sample 1 (embryonic facial mesenchyme)

description: Dp16; sample 1

value: whole brain

tag: age in_days_post_conception


title: 2102EP, DMF, 2

description:
DE07NGSUKBR116641
Control sample to "2102EP, Cisplatin"
MLN_CP_stringtie_raw_counts.csv


title: Interferon receptor dosage-normalized (Dp16^2xIFNRs); sample 3 (embryonic facial mesenchyme)


title: Wild-type; sample 3 (adult heart)

description: Wild-type; sample 3


title: 2102EP, MLN4924, Cisplatin, 3

description:
DE93NGSUKBR116645
MLN_CP_stringtie_raw_counts.csv
2102EP_MLN_CP_vs_DMSO_DMF_DESeq2_counts.txt
2102EP_MLN_CP_vs_DMSO_DMF_DESeq2_DE.txt


title: Normal airway epithelium 3

value: Normal airway epithelium


title: Midbrain organoid Line 15 SARS-CoV-2 infection biol rep 4 [C19-MB-15_V1_R4C19OR_DVB_S8]

city: Esch-sur-Alzette

first: Javier

last: Jarazo

address: 6A, avenue des Hauts-Fourneaux

country: Luxembourg

institute: OrganoTherapeutics

data_processing:
The raw RNA sequencing data was pre-processed using the software package Rsubread of R
Gene-level differential expression analysis was conducted in R using the software package DESeq2
Filtering out genes with low expression counts (sum of counts < 10 across all samples)
Assembly: Hg38
Supplementary files format and content: Thefile feature_counts_covid19_data.csv has the counts of all in samples (each column corresponds to one library name)

source_name: Midbrain organoid

growth_protocol: Midbrain organoids generated in successive batches were cultured in N2B27 differentiation media for 30-33 days

extract_protocol:
Five organoids were pooled per line per batch, and RNA was extracted using the QIAshredder (Qiagen, 79654) and the RNeasy Mini kit (Qiagen, 74104) after 4 dpi following manufacturer’s protocol
A total of 750 ng of RNA was used for library preparation using TruSeq stranded mRNA library preparation kit (Illumina, 20020594) as per the protocol provided. The libraries were quantified using Qubit dsDNA HS assay kit (Thermo Fisher Scientific, Q32851) and the size distribution was determined using Agilent 2100 Bioanalyzer (RRID:SCR_019389)

treatment_protocol: Either SARS-CoV-2 infection or mock treatment was done to the organoids. The organoids were kept for 4 days post infection until RNA was extracted

value: Midbrain organoid

value: hiPSC

value: Wild type

value: SARS-CoV-2 infection


title: 2102EP, DMF, 1

description:
DE34NGSUKBR116640
Control sample to "2102EP, Cisplatin"
MLN_CP_stringtie_raw_counts.csv


title: Control, HTP0092B2

value: whole blood

value: Female

tag: age

tag: sample source


title: Midbrain organoid Line 15 SARS-CoV-2 infection biol rep 2 [C19-MB-15_V1_R2C19OR_DVB_S6]

tag: cell line


title: Wild-type; sample 2 (adult heart)

description: Wild-type; sample 2

value: adult heart


title: Control, HTP0090B2

value: Male

tag: library type

value: strand-specific


title: 2102EP, Cisplatin, 3

description:
DE61NGSUKBR116639
MLN_CP_stringtie_raw_counts.csv
2102EP_Cisplatin_vs_DMF_DESeq2_counts.txt
2102EP_Cisplatin_vs_DMF_DESeq2_DE.txt

tag: cell type

value: Embryonal Carcinoma

value: Cisplatin, 2.5µM, 48h


title: Wild-type; sample 1 (adult heart)

description: Wild-type; sample 1


title: Control, HTP0087B2


title: Midbrain organoid Line 15 SARS-CoV-2 infection biol rep 1 [C19-MB-15_V1_R1C19OR_DVB_S5]


title: mir-125b-2 P0 mKO

city: Taipei

first: Hsien-Sung

last: Huang

address: Rm. 1547, 15F., No. 1, Sec. 1, Ren'ai Rd., Zhongzheng Dist

country: Taiwan

institute: National Taiwan University College of Medicine

description: Six mKO extracted total RNA were pooled together as one, equally.

data_processing:
The bcl2fastq conversion software v2.20 was used to convert BCL files from sequencing platforms into FASTQ reads.
Both adaptor clipping and sequence quality trimming were performed using Trimmomatic v0.36 with a sliding-window approach.
Reads were mapped to refenrence by HISAT2 v2.1.0.
Differential exprssion was analyzed by cuffdif v2.2.1 with P-value <0.05, KO/WT log2 ratio>1, and FPKM of one of the subject>0.3. P-value was calculated by cuffdiff with non-grouped sample used "blind mode", which all samples were treated as replicates of a single global "condition" and used to build one model for statistic test. The q-value of a test measures the proportion of false positives incurred (called the false discovery rate) when that particular test is called significant. Without enough replicates for a test, q-value might over-estimate the FDR, so we would not set a cutoff of q-value in our data by defalut.
Assembly: GRCm38.p5 GCA_000001635.7
Supplementary files format and content: Matrix table with expression for every gene and filtered diffential expression genes

extract_protocol:
Mice hippocampus was isolated and digested by QIAzol, and then extracted by Qiagen miRNeasy Micro kit (# 217084). Six WT or six maternal KO total RNA samples were pooled together equally as one to get pooled WT and pooled maternal KO sample.
Before libray, perform rRNA depletion with Ribo-Zero Gold rRNA Removal Kit(#MRZG126). Then, Library were preparaed according to the Illumina's official protocol by Agilent's SureSelect Strand-Specific RNA Library Preparation Kit(#G9691A).

tag: strain

value: maternal mir-125-2 KO

tag: developmental stage

value: post-natal day 0


title: Control, HTP0085B2

value: Control


title: Midbrain organoid Line 15 Mock infection biol rep 4 [C19-MB-15_Un_R4C19OR_DVB_S4]

value: Mock infection


title: 2102EP, Cisplatin, 1

description:
DE18NGSUKBR116637
MLN_CP_stringtie_raw_counts.csv
2102EP_Cisplatin_vs_DMF_DESeq2_counts.txt
2102EP_Cisplatin_vs_DMF_DESeq2_DE.txt


title: mir-125b-2 P0 WT

description: Six WT extracted total RNA were pooled together as one, equally.

value: whole brain

value: Wildtype


title: T21, HTP0084A2

value: A


title: T21, HTP0080A2


title: CCR6neg-CMV_D2

value: PBMC

tag: sampleID

value: CD4 T-cell

tag: cell subset

value: 10x Genomics


title: Midbrain organoid Line 15 SARS-CoV-2 infection biol rep 3 [C19-MB-15_V1_R3C19OR_DVB_S7]

value: Midbrain organoid

value: hiPSC

value: Wild type

value: SARS-CoV-2 infection


title: 2102EP, DMSO, 2

description:
DE72NGSUKBR116635
Control sample to "2102EP, MLN4924"
MLN_CP_stringtie_raw_counts.csv


title: Midbrain organoid Line 15 Mock infection biol rep 1 [C19-MB-15_Un_R1C19OR_DVB_S1]


title: 2102EP, DMSO, 1

description:
DE02NGSUKBR116634
Control sample to "2102EP, MLN4924"
MLN_CP_stringtie_raw_counts.csv


title: IR_17Gy_5M_2

city: Paris

first: Charles

last: Fouillade

address: 25 rue d'Ulm

country: France

institute: Institut Curie

description: 10x Genomics

data_processing:
Fastq files were generated with mkfastq as part of CellRanger pipeline (10x Genomics).
Reads were aligned on mm10 reference genome and raw count matrix files was generated using the CellRanger pipeline.
Raw data was filtered with CellRanger V3.0.2 pipeline to generate processed count matrix in Market Exchange Format (MEX) supplemented with TSV files with genes and barcode sequences corresponding to rows and columns respectively.
Assembly: mm10
Supplementary files format and content: Each sample contains filtered gene-barcode matrix containing the number of UMIs associated with a gene and barcode in Market Exchange Format (MEX) generated by CellRanger V3.0.2 pipeline (10x Genomics). It also contains TSV files with genes and barcode sequences corresponding to row and column indices, respectively.

source_name: Lung

growth_protocol: C57BL/6J female mice, 10-12 weeks old, were maintained at Institut Curie animal facility under normal day-night cycle.

extract_protocol:
Lungs were resected and single cell suspensions were prepared by enzymatic dissociation (dispase and elastase) and sequential filtering (100 and 40 µm) before red blood cell lysis and cell counting. Single-cell 3’-RNA-Seq samples were prepared using single cell 3'V3 or 3'V3 NextGem reagent kit and Chromium controller (10x Genomics, PN-120237). cDNA quality control was assessed by capillary electrophoresis (Bioanalyzer, Agilent).
Single-cell RNA-Seq libraries were prepared using Chromium Single Cell 3'V3 or 3'V3 NextGem Reagent Kit (10X Genomics) according to manufacturer’s protocol. Read 1 (26 cycles) corresponds to cell barcode and UMI, Read 2 (98 cycles) corresponds to 3'-end of RNA molecules.

treatment_protocol: Isoflurane anesthesized C57BL/6J female mouse received thoracic irradiation with a 4.5 MeV electron LINAC at a dose of 10 Gy or 17 Gy.

value: Lung

value: female

value: IR 17 Gy

tag: time point_after_ir

value: WT


title: IR_17Gy_5M_1

description: 10x Genomics


title: 2102EP, MLN4924, 3

description:
DE29NGSUKBR116633
MLN_CP_stringtie_raw_counts.csv
2102EP_MLN4924_vs_DMSO_DESeq2_counts.txt
2102EP_MLN4924_vs_DMSO_DESeq2_DE.txt

value: Embryonal Carcinoma


title: Midbrain organoid Line 11 SARS-CoV-2 infection biol rep 4 [C19-MB-11_V1_R4C19OR_DVB_S8]


title: Midbrain organoid Line 11 SARS-CoV-2 infection biol rep 3 [C19-MB-11_V1_R3C19OR_DVB_S7]


title: Control, HTP0078B2

data_processing:
Signal processing, base-calling, and quality scoring was carried out automatically by the NovaSeq 6000 software (Illumina).
Demultiplexing and conversion to FASTQ format was carried out using bcl2fastq (Illumina).
Data quality was assessed using FASTQC (v0.11.5) (https://www.bioinformatics.babraham.ac.uk/projects/fastqc/) and FastQ Screen (v0.11.0, https://www.bioinformatics.babraham.ac.uk/projects/fastq_screen/).
For some samples, FASTQ files from multiple sequencing runs were merged to obtain ≥40x10^6 raw reads.
Trimming and filtering of low-quality reads was performed using bbduk from BBTools (v37.99) and fastq-mcf from ea-utils (v1.05, https://expressionanalysis.github.io/ea-utils/).
Alignment to the human reference genome (GRCh38) was carried out using HISAT2 (v2.1.0) in paired, spliced-alignment mode with a GRCh38 index with a Gencode v33 annotation GTF.
Alignments were sorted and filtered for mapping quality (MAPQ>10) using Samtools (v1.5).
Gene-level count data were quantified using HTSeq-count (v0.6.1) with the following options (--stranded=reverse –minaqual=10 –type=exon --mode=intersection-nonempty) using a Gencode v33 GTF annotation file.
Genome_build: GRCh38
Supplementary_files_format_and_content: Tab-delimited text files containing per gene strand-specific fragment counts or normalized fragments-per-kilobase-per-million-mapped (FPKM).

source_name: whole blood

value: whole blood

value: Control

value: Male

value: strand-specific


title: Control, HTP0077B2

value: A


title: 2102EP, MLN4924, 2

description:
DE56NGSUKBR116632
MLN_CP_stringtie_raw_counts.csv
2102EP_MLN4924_vs_DMSO_DESeq2_counts.txt
2102EP_MLN4924_vs_DMSO_DESeq2_DE.txt


title: Control, HTP0079B2

description: globin-depleted, poly(A)+ RNA from whole blood


title: IR_17Gy_4M_2

description: 10x Genomics


title: IR_17Gy_4M_1

description: 10x Genomics


title: 2102EP, Cisplatin, 2

description:
DE88NGSUKBR116638
MLN_CP_stringtie_raw_counts.csv
2102EP_Cisplatin_vs_DMF_DESeq2_counts.txt
2102EP_Cisplatin_vs_DMF_DESeq2_DE.txt

value: Cisplatin, 2.5µM, 48h


title: Midbrain organoid Line 11 SARS-CoV-2 infection biol rep 2 [C19-MB-11_V1_R2C19OR_DVB_S6]


title: IR_17Gy_3M_2

description: 10x Genomics


title: Midbrain organoid Line 15 Mock infection biol rep 3 [C19-MB-15_Un_R3C19OR_DVB_S3]

value: Mock infection


title: T21, HTP0073A2


title: 2102EP, MLN4924, 1

description:
DE83NGSUKBR116631
MLN_CP_stringtie_raw_counts.csv
2102EP_MLN4924_vs_DMSO_DESeq2_counts.txt
2102EP_MLN4924_vs_DMSO_DESeq2_DE.txt


title: Midbrain organoid Line 11 SARS-CoV-2 infection biol rep 1 [C19-MB-11_V1_R1C19OR_DVB_S5]


title: Midbrain organoid Line 15 Mock infection biol rep 2 [C19-MB-15_Un_R2C19OR_DVB_S2]


title: 2102EP, DMSO, 3

description:
DE45NGSUKBR116636
Control sample to "2102EP, MLN4924"
MLN_CP_stringtie_raw_counts.csv


title: IR_17Gy_3M_1

description: 10x Genomics


title: T21, HTP0070A3


title: IR_17Gy_2M_2

description: 10x Genomics


title: TWIST2 KD_RD_3

city: Dallas

first: Lei

last: Guo

state: TX

address: 5323 Harry Hines Blvd

department: Department of Population and Data Sciences

institute: University of Texas Southwestern Medical Center

description: RNAseq_RD_Control_TWIST2 KD.txt

data_processing:
Adapters were trimmed using trimgalore v0.6.4.
Fastq files were aligned to the GRCH38 human genome using Star v2.7.3a.
Data quality was examined using multiqc v1.7.
Gene expression matrix was generated using Subread v1.6.3.
Assembly: GRCH38
Supplementary files format and content: Tab-delimited raw counts table

source_name: RD

growth_protocol: Control and TWIST2 KD cells were cultured in in DMEM (Sigma-Aldrich), supplemented with 100 U/mL penicillin/streptomycin, 2 mmol/L l-glutamine, and 10% Tet System Approved FBS (Takara) in 5% CO2 at 37°C. 1 μg/mL of Puromycin added to culture media to maintain stable cell line.

extract_protocol:
RNA was extracted from cells using the RNeasy mini kit (QIAGEN, 74104) according to the manufacturer's protocol.
Stranded mRNA-Seq libraries were generated using the KAPA mRNA HyperPrep Kit (Roche, KK8580) following manufacturer’s protocol.

treatment_protocol: The cells were treated with 10 ng/mL of Doxycycline (Sigma) for 4 days (TWIST2 KD) prior to analysis. Control cells were left untreated.

value: RD

value: fusion-negative rhabdomyosarcoma

value: TWIST2 KD


title: Control, HTP0067B2

extract_protocol:
Whole blood samples were collected into PAXgene Blood RNA Tubes (PreAnalytiX/Qiagen) and RNA purified using a PAXgene Blood RNA Kit (Qiagen). RNA quality was assessed using an Agilent 2200 TapeStation and quantified by Qubit (Life Technologies).
Globin RNA depletion, poly-A(+) RNA enrichment, and strand-specific library preparation were carried out using a GlobinClear kit, NEBNext® Poly(A) mRNA Magnetic Isolation Module, and NEBNext Ultra™ II Directional RNA Library Prep Kit for Illumina. Paired-end 150 bp sequencing was carried out on an Illumina NovaSeq 6000 instrument by Novogene Co., Ltd.


title: IR_17Gy_2M_1

description: 10x Genomics


title: Midbrain organoid Line 11 Mock infection biol rep 3 [C19-MB-11_Un_R3C19OR_DVB_S3]

value: Midbrain organoid

value: hiPSC

value: Wild type


title: T21, HTP0066A2

description: Re-analysis of GSM5097130


title: TWIST2 KD_RD_1

description: RNAseq_RD_Control_TWIST2 KD.txt


title: Control, HTP0062B2

value: Female


title: TWIST2 KD_RD_2

description: RNAseq_RD_Control_TWIST2 KD.txt


title: Control_RD_3

description: RNAseq_RD_Control_TWIST2 KD.txt


title: Midbrain organoid Line 11 Mock infection biol rep 1 [C19-MB-11_Un_R1C19OR_DVB_S1]


title: IR_17Gy_1M_1

description: 10x Genomics

value: Lung

value: female

value: IR 17 Gy


title: Control_RD_1

description: RNAseq_RD_Control_TWIST2 KD.txt

value: WT


title: Control, HTP0059B2

value: whole blood

value: Control


title: Control, HTP0058B2

value: Male

value: strand-specific


title: Control, HTP0061B2

value: A


title: IR_10Gy_5M

description: 10x Genomics

value: IR 10 Gy


title: BeWo, INPUT, rep3

city: London

first: Stephen

middle: James

last: Renaud

state: Ontario

address: 1151 Richmond St

country: Canada

institute: Western University

data_processing:
Raw sequence reads that passed quality control filtering were mapped onto the hg38 human reference genome using BWA version 0.7.17.
Blacklisted regions, PCR duplicates, and multimapping reads with a MAPQ quality score below 20 were then filtered out.
Peaks were called using MACS2 version 2.1.1.2. in paired-end mode using default parameters.
A single set of reproducible peaks from three biological replicates were then generated using ChIP-R version 1.1.0.
RPKM normalized coverage tracks were generated from aligned reads using the bamCoverage tool in deepTools version 3.3.2.
Assembly: hg38
Supplementary files format and content: Bed files contain peaks called for each biological replicate using MACS2, or a set of reproducible peaks from all three replicates generated using ChIP-R ("output_optimal.bed").
Supplementary files format and content: bigWig files contain coverage tracks for each biological replicate generated from aligned reads using deepTools bamCoverage.

source_name: BeWo

extract_protocol:
Cells were fixed with 0.7% formaldehyde for 10 min, lysed, and sonicated using a Bioruptor (Diagenode). Approximately 1% of sonicated nuclear lysate was removed to serve as an input control. Sonicated nuclear lysate was incubated with ARNT antibody overnight, and the next day, immunoprecipitated chromatin fragments were captured using protein G-conjugated Sepharose beads. Control (input) and immunoprecipitated DNA fragments were then eluted and purified.
Libraries were generated using the NEBNext Ultra II DNA Library Prep Kit (New England Biolabs).

value: BeWo

value: Trophoblast

tag: chip antibody

value: none (input)

value: Cells were cultured under 1% O2 for 24 h.


title: Midbrain organoid Line 11 Mock infection biol rep 4 [C19-MB-11_Un_R4C19OR_DVB_S4]

tag: tissue

value: Midbrain organoid

value: hiPSC

value: Mock infection


title: BeWo, INPUT, rep2


title: BeWo, INPUT, rep1


title: grf10Δ strain, replicate C, 4-hr

city: Washington

first: Ronda

middle: Joan

last: Rolfes

state: DC

address: 3700 O Street NW

department: Biology

institute: Georgetown University

description: arg4Δ/arg4Δ leu2Δ/leu2Δ his1Δ/his1Δ URA3/ura3Δ IRO1/iro1Δ grf10Δ::CdHIS1/grf10Δ::CmLEU2

data_processing:
FASTQ files were paired, trimmed using BBDuk
Mapping to the reference genome used the Geneious software and default settings.
Raw reads from the two alleles were combined and expression differences determined using DESeq2 (v1.30.1) in R
Assembly: Reference genome: the phased C_albicans_SC5314 Assembly 22 from Candida genome database (online)
Supplementary files format and content: The "Reads mapped Y1 raw expression" file has the mapping to the phased genome (assembly 22) from RNA at 1-hr
Supplementary files format and content: the "allGenes_GRF10vWT_Y1_LFCshrink_padj" is the differential expression comparing grf10 mutant to WT at 1-hr
Supplementary files format and content: The "Reads mapped Y4 raw expression" file has the mapping to the phased genome (assembly 22) from RNA at 4-hr
Supplementary files format and content: the "allGenes_GRF10vWT_Y4_LFCshrink_padj" is the differential expression comparing grf10 mutant to WT at 4-hr

organism: Candida albicans

source_name: yeast

growth_protocol: Triplicate cultures of the two strains were inoculated into YPD medium and grown for 1-hr or 4-hr, and pelleted by centrifugation.

extract_protocol:
Ribopure Yeast Kit (Ambion) following instructions; RNA quality was assessed on an Agilent Bioznalyzer
cDNA libraries were made using TruSeq Stranded mRNA sample prep kit (Illumina, RS-122-2101 Set A). cDNA library quality assessed by Aubit.
RNAsequencing was performed on a MiSeq instrument

value: yeast

tag: strain background

value: SN152-TF mutant

tag: genotype

value: arg4{delta}/arg4{delta} leu2{delta}/leu2{delta} his1{delta}/his1{delta} URA3/ura3{delta} IRO1/iro1{delta} grf10{delta}::CdHIS1/grf10{delta}::CmLEU2

value: 4-hr growth post inoculation


title: IR_10Gy_4M

description: 10x Genomics

value: Lung

tag: Sex

value: female

tag: treatment

value: WT


title: Control, HTP0057B2

first: Matthew

last: Galbraith

value: whole blood

tag: karyotype

value: Control

value: Female

value: strand-specific


title: grf10Δ strain, replicate B, 4-hr


title: BeWo, ARNT, rep3

value: BeWo

value: Trophoblast


title: IR_10Gy_2M

description: 10x Genomics

value: IR 10 Gy


title: grf10Δ strain, replicate A, 4-hr


title: Control, HTP0055B2

value: Male

tag: age

value: A


title: IR_10Gy_1M

description: 10x Genomics


title: Midbrain organoid Line 11 Mock infection biol rep 2 [C19-MB-11_Un_R2C19OR_DVB_S2]

value: Midbrain organoid

value: hiPSC

value: Wild type

value: Mock infection


title: IR_10Gy_3M

description: 10x Genomics


title: BeWo, ARNT, rep2

value: Cells were cultured under 1% O2 for 24 h.


title: IR_17Gy_1M_2

description: 10x Genomics

value: Lung

value: IR 17 Gy


title: WT strain, replicate C, 4-hr

description: arg4Δ/arg4Δ leu2Δ/leu2Δ::CmLEU2  his1Δ /his1Δ::CdHIS1 URA3/ura3Δ  IRO1/iro1Δ

value: yeast

value: arg4{delta}/arg4{delta} leu2{delta}/leu2{delta}::CmLEU2  his1{delta} /his1{delta}::CdHIS1 URA3/ura3{delta}  IRO1/iro1{delta}

value: 4-hr growth post inoculation


title: T21, HTP0054A2

value: whole blood

tag: sample source


title: Control_RD_2

description: RNAseq_RD_Control_TWIST2 KD.txt

tag: cell line

value: RD

value: fusion-negative rhabdomyosarcoma

value: WT


title: Ctrl_5

description: 10x Genomics

value: female

value: Non-Irradiated Control

value: NI


title: BeWo, ARNT, rep1

value: BeWo

value: Trophoblast


title: WT strain, replicate B, 4-hr


title: TWIST2 KD_SMSCTR_3

description: RNAseq_SMSCTR_Control_TWIST2 KD.txt

source_name: SMS-CTR

value: SMS-CTR

value: TWIST2 KD


title: Ctrl_4

description: 10x Genomics


title: Ctrl_3

description: 10x Genomics


title: WT strain, replicate A, 4-hr


title: T21, HTP0052A2

value: Female

value: A

tag: library type

value: strand-specific


title: Ctrl_2

description: 10x Genomics

value: Lung


title: TWIST2 KD_SMSCTR_1

description: RNAseq_SMSCTR_Control_TWIST2 KD.txt

tag: cell type


title: T21, HTP0050A3


title: grf10Δ strain, replicate C, 1-hr

value: yeast

value: SN152-TF mutant

value: arg4{delta}/arg4{delta} leu2{delta}/leu2{delta} his1{delta}/his1{delta} URA3/ura3{delta} IRO1/iro1{delta} grf10{delta}::CdHIS1/grf10{delta}::CmLEU2

value: 1-hr growth post inoculation


title: grf10Δ strain, replicate B, 1-hr


title: Control_SMSCTR_3

description: RNAseq_SMSCTR_Control_TWIST2 KD.txt

value: fusion-negative rhabdomyosarcoma


title: Ctrl_1

description: 10x Genomics

tag: strain

value: WT


title: Control, HTP0047B2

value: whole blood

value: Control

value: Male


title: grf10Δ strain, replicate A, 1-hr


title: Control_SMSCTR_2

description: RNAseq_SMSCTR_Control_TWIST2 KD.txt


title: Control, HTP0043B2


title: HFD, 104616-001-016

city: Rijswijk

first: Eveline

last: Gart

state: Zuid-Holland

address: Van vredenburchweg 659

country: Netherlands

institute: TNO

data_processing:
Quality filtering and adapter-trimming of the Illumina NovaSeq6000 fastq files was performed by TRIMMOMATIC software
Trimmed Fastq files were merged (in case of Paired-end reads) and aligned to the reference genome using the STAR 2.5 algorithm with default settings (https://github.com/alexdobin/STAR).
Based on the mapped read locations and the genome annotation, Htseq-count 0.6.1p1 was used to count the read mapping frequency/gene (transcript region) resulting in count.files.
Assembly: Mus_musculus.GRCm38.gencode.vM19
Supplementary files format and content: The count files contain the # reads mapped per gene (not normalized per sample). These counts serve as input for the statistical analysis using DEseq2 package.

source_name: liver

growth_protocol: Male Ldlr-/-.Leiden mice were bred and housed in the AAALAC-accredited animal facility at TNO (Leiden, the Netherlands). These animals were used herein for a time course experiment in accordance with the rules and regulations set forward by the Animal Care and Use Committee and ethical approval by an independent Animal Welfare Body (IVD TNO; approval number 3682/TNO-245). At starting point all mice (n=103) were fed a standard laboratory low-fat control diet (chow; Sniff-R/M-V1530, Uden, the Netherlands).

extract_protocol:
5h-fasted blood samples for EDTA plasma isolation were collected from the tail vein at set intervals. Also body weight and food intake measurements were acquired repeatedly. A few days before sacrifice a functional gut permeability test was performed. Mice were sacrificed after a 5-h fast. At sacrifice blood for EDTA plasma and serum was collected via heart puncture, organs were isolated and weighed, and mucosal microbiota from ileum and colon was collected.
Next Generation Sequencing was performed at Genome Scan (Leiden, the Netherlands). For this, strand-specific cDNA libraries were generated from RNA using oligo-dT magnetic beads, mRNA fragmentation, NEBNext Ultra II Directional RNA Library Prep Kit from Illumina, NEB #E7760S/L resulting in 300–500 bp amplified libraries/sample. Libraries (1.1nM) were multiplexed, clustered, and sequenced on a NovaSeq6000 system for Illumina, (New England Biolabs, Inc. Ipswich, MA, USA), with a paired-end, 150 bp sequencing protocol, 20-35 million reads per sample).
Clustering and DNA sequencing using the NovaSeq6000 v1.5 was performed according to manufacturer's protocols. A concentration of 1.1 nM of DNA was used yielding paired end reads (2x 150bp). NovaSeq control software NCS v1.7 was used. Image analysis, base calling, and quality check was performed with the Illumina data analysis pipeline RTA3.4.4 and Bcl2fastq v2.20.

treatment_protocol: A group of these mice (n=6) was sacrificed as a starting reference group (t=0) with 14-16 weeks of age. The remaining mice were divided into two different treatment arms, one part remained on chow while others were fed an energy-dense high-fat diet (HFD; D12451, Research Diets Inc.; 20 kcal% protein, 35 kcal% carbohydrate, 45 kcal% lard fat) up to 38 weeks to induce NAFLD. Groups of n=6 chow and n=15 HFD fed mice were sacrificed after 8, 16 and 28 weeks, and groups of n=15 chow and n=15 HFD fed mice were sacrificed after 38 weeks.

value: liver

value: HFD

tag: time

tag: mouse nr


title: HFD, 104616-001-015


title: T21, HTP0053A2

institute: University of Colorado Anschutz Medical Campus


title: HFD, 104616-001-014


title: RD-2_Input_TWIST2 KD_2

data_processing:
Fastq files were aligned to the GRCH37 human genome using Bowtie2 v2.3.4.3 with default parameters. The aligned reads were subsequently filtered for quality and uniquely mappable reads were retained for further analysis using Samtools version 0.1.19 and Sambamba version 0.6.6.
Bam files were filtered using bedtools (v. 2.29.2) to remove any ENCODE blacklisted regions (ENCFF001TDO.bed).
ChIP-Seq peaks were identified using the findPeaks function in Hypergeometric Optimization of Motif EnRichment (HOMER v4.4, http://homer.ucsd.edu/homer/) with the parameter "-style factor" for transcription factor ChIP-seq data and "-style histone" for histone marker ChIP-seq data.
FDR adjusted P < 10-3  and fold change > 4 were used as the threshold during peak calling.
BigWig files were generated using the makeUCSCfile function in the Homer package with the parameter “-bigWig”.
Assembly: hg19
Supplementary files format and content: bigWig, narrowPeak (except for Input sample)

extract_protocol:
Cells were fixed with 4% formaldehyde for 10 minutes. After quenching and cell lysis, chromatin was sheared on a Bioruptor Pico (Diagenode) for 20 cycles (30 sec on/ 30 sec off for each cycle) at 4°C
ChIP-seq libraries were prepared using the NEBNext Ultra II DNA Library Preparation Kit complemented with NEBNext Multiplex Oligos for Illumina from NEB. 10 ng of DNA was used as starting material for input samples and 1 ng for ip samples. Libraries were amplified using 15 cycles for ip samples and 12 cycles for input on the thermocycler. Post amplification libraries were size selected at 250-450bp in length using SPRISelect beads from Beckman Coulter. Libraries were validated using the Agilent D1000 ScreenTape.

value: RD


title: Control_SMSCTR_1

description: RNAseq_SMSCTR_Control_TWIST2 KD.txt

value: SMS-CTR


title: WT strain, replicate A, 1-hr

value: arg4{delta}/arg4{delta} leu2{delta}/leu2{delta}::CmLEU2  his1{delta} /his1{delta}::CdHIS1 URA3/ura3{delta}  IRO1/iro1{delta}


title: Control, HTP0044B2

value: A


title: HFD, 104616-001-013


title: TWIST2 KD_SMSCTR_2

description: RNAseq_SMSCTR_Control_TWIST2 KD.txt

value: TWIST2 KD


title: Control, HTP0048B2

value: Female

value: strand-specific


title: RD-2_Input_TWIST2 KD_1


title: T21, HTP0036A2


title: TC-1 untreated (Z4)

city: Brussels

first: Benoit

last: Van den Eynde

state: Please Select

address: Avenue Hippocrate, 75 - Bte B1.74.10

country: Belgium

institute: de Duve Institute

data_processing:
Cells were processed with the CellRanger platform
Barcodes, features and count matrix for valid cells were imported and further processed with Scanpy and R/Bioconductor
We performed clustering with PhenoGraph
Cluster identities were assigned with known markers
Assembly: GRCm38.96
Supplementary files format and content: archived 10X counts directory (mtx counts and feature/sample csv files)

source_name: Tumour

extract_protocol:
Standard 10x Genomics protocol
The DNA libraries was paired end sequenced on an Illumina Novaseq S4, with a 2x150 bp Illumina kit.

value: 10 weeks

value: untreated

value: wild type


title: RD-2_Input_Control_2

value: fusion-negative rhabdomyosarcoma

value: control


title: HFD, 104616-001-011


title: WT strain, replicate C, 1-hr

value: yeast

value: 1-hr growth post inoculation


title: RD-2_Input_Control_1


title: RD-2_SMARCA4_TWIST2 KD_2

value: BRG1 (Abcam, ab110641)


title: HFD, 104616-001-010

value: liver


title: Control, HTP0035B3

city: Aurora

value: whole blood

value: Control


title: High_Pi_4

first: Eugene

last: Rhee

address: 165 Cambridge Street

department: Endocrinology

institute: MGH

data_processing:
Raw data containing reads of low quality, reads with adaptor sequences and reads with high levels of N base were filtered before the data analysis
We used HISAT to align the clean reads to the reference genome
We used Bowtie2 to align the clean reads to the reference genes
Assembly: GCF_000001635.26_GRCm38.p6
Supplementary files format and content: Processed data are formatted for Microsoft Excel (.xls extension).  Files contain fragments per kilobase of per million mapped fragments (FPKM) reads of samples of interest.

source_name: Kidney

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen, REF: 74104, LOT: 57202853). At least 3 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared by BGI using a proprietary process that inserts two known synthetic DNA sequences (adaptors) into each DNA fragment

value: Kidney

value: High phosphate diet (1.2%)


title: Control, HTP0034B3

value: A


title: Control, HTP0026B2


title: HFD, 104616-001-009

value: HFD


title: High_Pi_3


title: WT strain, replicate B, 1-hr

value: arg4{delta}/arg4{delta} leu2{delta}/leu2{delta}::CmLEU2  his1{delta} /his1{delta}::CdHIS1 URA3/ura3{delta}  IRO1/iro1{delta}


title: Control, HTP0042B2

value: Male

value: strand-specific


title: RD-2_SMARCA4_TWIST2 KD_1

value: RD

value: TWIST2 KD


title: HFD, 104616-001-008


title: T21, HTP0025A3

value: Female


title: RD-2_SMARCA4_Control_2

value: fusion-negative rhabdomyosarcoma

value: control


title: High_Pi_1


title: HFD, 104616-001-007


title: High_Pi_2


title: T21, HTP0023A2


title: TC-1 treated (Z6)

value: 10 weeks

value: clonidine

value: wild type


title: HFD, 104616-001-012

value: liver


title: Ctrl_WT_4

value: Normal phosphate diet (0.6%)


title: Control, HTP0040B3

value: whole blood

value: Control


title: chow, 104616-001-006

value: chow


title: RD-1_Input_3xTy1-TWIST2_2


title: Ctrl_WT_3

value: Kidney


title: RD-2_SMARCA4_Control_1

value: BRG1 (Abcam, ab110641)


title: chow, 104616-001-005


title: Control, HTP0019B2

value: A


title: RD-1_Input_3xTy1-TWIST2_1


title: Control, HTP0022B2

value: strand-specific


title: Ctrl_WT_2


title: chow, 104616-001-004


title: RD-1_Ty1_3xTy1-TWIST2_2

value: RD

value: Ty1 (Diagenode, C15200054)


title: chow, 104616-001-002


title: chow, 104616-001-003


title: T21, HTP0015A4

value: Male


title: chow, 104616-001-001


title: RD-1_Input_TWIST2 KD_2

value: fusion-negative rhabdomyosarcoma

value: TWIST2 KD


title: T21, HTP0012A2

value: Female


title: RD-1_Ty1_3xTy1-TWIST2_1


title: RD-1_Input_TWIST2 KD_1


title: RD-1_Input_Control_2

value: control


title: T21, HTP0005A3


title: RD-1_Input_Control_1


title: Control, HTP0001B2


title: Control, HTP0018B3


title: T21, HTP0017A4


title: RD-1_MYOD_TWIST2 KD_2

value: MYOD G1 Clone (Santa Cruz, sc-377460 X)


title: TWIST2 KD_Xenograft_3

data_processing:
Adapters were trimmed using trimgalore v0.6.4.
Fastq files were aligned to the GRCH38 human genome using Star v2.7.3a.
Data quality was examined using multiqc v1.7.
Gene expression matrix was generated using Subread v1.6.3.
Assembly: GRCm39
Supplementary files format and content: Tab-delimited raw counts table

organism: Mus

source_name: RD-Xenograft

value: RD-Xenograft


title: 5xFAD1_6m_snRNA

first: Ting

last: Sun

institute: Max Planck Institute for Multidisciplinary Sciencesi

data_processing:
raw data was aligned to reference profile refdata-gex-mm10-2020-A using 10x genomics toolkit CellRanger v6.1.2
Single-nuclei UMI matrices were extracted and nuclei with less then 300 detected genes or less than 500 total transcripts were filtered out
Potential doublets were filtered based on individual sample’s sequencing depth
Assembly: refdata-gex-mm10-2020-A
Supplementary files format and content: Tab-delimited matrix include raw UMI counts for single-cells collected from all samples
Supplementary files format and content: Tab-delimited matrix of single-cell meta data which includes cell basic information and annotation during analysis
Supplementary files format and content: Tab-delimited matrix include raw UMI counts for microglia cells
Supplementary files format and content: Tab-delimited matrix of microglia meta data which includes cell basic information and annotation during analysis

source_name: brain hemisphere

extract_protocol:
Frozen tissue was transferred into 2ml of pre-chilled homogenization buffer (320mM sucrose, 0.1% NP40, 0.1mM EDTA, 5mM CaCl2, 3mM Mg(Ac)2, 10mM pH 7.8 Tris, 167uM β-mercaptoethanol and 1x protease inhibitor (Roche)). Tissue was carefully homogenized and filtered through a 80um strainer, and further centrifuged for 1min under 100 rcf. For each sample, 400 ul supernatant was collected into a pre-chilled 2ml eppendorf low-binding eppendorf tube, followed by adding 400ul 50% iodixanol solution (in 1x homogenization buffer containing 480mM sucrose) to reach a 25% iodixanol concentration. By layering 600ul of 29% iodixanol underneath the 25% iodixanol mixture, then 600ul of 35% iodixanol underneath the 29% iodixanol, two clear interfaces between different concentrations of buffers were created, and the tube was centrifuged for 20 min under 3000 rcf. After centrifuge, nuclei were collected from the band between the 29% and the 35% iodixanol layers and transferred to a fresh pre-chilled tube. The isolated nuclei were washed and resuspended in pre-chilled resuspension buffer (1xPBA, 1% BSA, 0.1U/ul RNase inhibitor).
Single-nucleus RNA libraries were prepared using 10x genomics chromium single-cell 3’ protocol and sequenced by Illumina Novaseq 6000


title: 5xFAD2_6m_snRNA


title: THP-1_OPA [RNA-seq]

city: Hangzhou

first: Jun

last: Lu

state: Zhejiang

address: 866 Yuhangtang Road

institute: Zhejiang University

data_processing:
Illumina 4000 sequence platform used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence,
Using HISAT packagealigned reads of sample to the UCSC (http://genome.ucsc.edu/) homo sapiens reference genome , which initially remove a portion of the reads based on quality information accompanying each read and then maps the reads to the reference genome.
The mapped reads of each sample were assembled using StringTie. Then, all transcriptomes from Samples were merged to reconstruct a comprehensive transcriptome using perl scripts. After the final transcriptome was generated, StringTie and edgeR was used to estimate the expression levels of all transcripts. StringTie was used to perform expression level for mRNAs by calculating FPKM. The differentially expressed mRNAs and genes were selected with log2 (fold change) >1 or log2 (fold change) <-1 and with statistical significance (p value < 0.05) by R package.
Genome_build: hg19
Supplementary_files_format_and_content: FPKM

growth_protocol: THP-1 cells were cultured in RPMI-1640 medium (Gibco, Grand Island, NY, USA), supplemented with 10% FBS (Gibco) and penicillin-streptomycin.

extract_protocol:
The total RNA was extracted from cells with Trizol.
RNA libraries were prepared for sequencing using standard Illumina RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: THP-1 cells were treated with 2 μM OPA1 or DMSO control for 48 hrs.

value: AML cell line

value: 2 μM OPA1 for 48hrs


title: CnpKO_5xFAD1_6m_snRNA

address: Hermann-Rein-Straße 3

value: Cnp-/- 5xFAD


title: THP-1_CTRL [RNA-seq]

value: DMSO for 48hrs


title: CnpKO_5xFAD2_6m_snRNA


title: Ctrl_WT_1

value: Kidney

value: Normal phosphate diet (0.6%)


title: TWIST2 KD_Xenograft_2


title: THP-1_OPA-input

data_processing:
library strategy: 5hmC-Seal
Basecalls performed using HiSEQ4000 sequencer (Illumina)
Off-Line Basecaller (OLB V1.8) was used to recognize the image files generated by sequencing to obtain sequence files, and the data was preliminarily filtered by Solexa CHASTITY. Data quality was identified using FastQC (v0.11.7).
5hmC reads were deeper filtered with Trimmomatic and were mapped to Ensembl GRCh37 human reference genome using HISAT2. The identification of 5hmC peaks in each sample was performed using MACS v249, and an IDR cutoff of 0.05 was used to filter high confident peaks.
DiffBind was used to determine the differences in 5hmC density according to the peak numbers at the same gene locus of different samples.
5hmC-seq reads were aligned to the hg19 genome assembly using IGV_2.8.0
Genome_build: hg19

extract_protocol:
Genomic DNA was obtained from 5x10^6 cells with Cell/Tissue DNA Isolation Mini Kit (Vazyme)
50 ng genomic DNA extracted from THP-1 cell was fragmented into 300 bp reads by use of Ultrasonic Bioruptor sonicator (Diagenode Bioruptor). Then, the selective 5hmC chemical labeling was performed. The above fragmented DNA was added into 60 μl reaction buffer containing 6 μl of 10×β-GT reaction buffer, 2 μl of N3-UDP-Glc (3 mM), and 3 μl of β-GT (40 mM), and incubated at 37°C for 2 hr. The reaction product was purified with magnetic beads and DNA was eluted with 60 μl ddH2O. DMCO-S-S-PEG-Biotin (1 mM) was added into the DNA solution to reach a final concentration as 150 μM, and incubated at 37°C for 2 hr. The biotin labeled DNA was pulled down by 50 µl Dynabeads MyOne Streptavidin C1 beads (Life Technologies) for 30 min at room temperature. Next, the captured DNA fragments were subjected to 18 cycles of PCR amplification using Genomic DNA Sample Prep Kit (Illumina). The input library was prepared from fragmented DNA through direct PCR, without chemical labeling or capture. The libraries were denatured with 0.1 M NaOH to generate single-strand DNA (ssDNA) molecules and were added to the flow cell channel at a concentration of 8 pM. The libraries were quantified with a Qubit fluorometer (Life Technologies) and sequenced on a HiSEQ4000 sequencer (Illumina) with paired-end 50-bp reads.


title: THP-1_OPA-5hmC-seq


title: circAAGAB_O/E_A2

first: Liang-Chuan

last: Lai

state: Taiwan

address: 1 Jen-Ai Road, Sec 1

institute: National Taiwan University

description: replicate 2

hyb_protocol: Standard Affymetrix hybridization protocol

scan_protocol: Standard Affymetrix scanning protocol

data_processing: The data were normalized using Robust Multi-array Average (RMA) method

label: Biotin

label_protocol: Single-stranded cDNA was generated from the amplified cRNA with the WT Plus cDNA Synthesis Kit (Affymetrix) and then fragmented and labeled with the WT Terminal Labeling Kit (Affymetrix).

growth_protocol: MDA-MB-231 cells were cultured in Dulbecco's Modified Eagle's Medium (DMEM)  (GIBCO; Thermo Fisher, Waltham, MA, USA) with 10% fetal bovine serum (FBS) (Millipore, US Origin, Korea Eligible) and 1% penicillin-streptomycin (GIBCO)

extract_protocol: Total RNA was extracted from cultured cells using NucleoZOL reagent (Machery-Nagel, Düren, Germany) according to the manufacturer's protocol

treatment_protocol: Cells were transfected with circAAGAB expressing plasmids and control plasmid by TransIT-X2® Dynamic Delivery System (Mirus Bio, U.S.) according to the manufacturer's protocol.

value: breast

value: MDA-MB-231 breast cancer cell line

value: circAAGAB overexpression


title: TWIST2 KD_Xenograft_1


title: RD-1_MYOD_Control_2

value: RD


title: circAAGAB_O/E_A3

description: replicate 3


title: circAAGAB_O/E_A1

description: replicate 1


title: circAAGAB_Empty_E3

description: replicate 3


title: RD-1_MYOD_Control_1


title: circAAGAB_Empty_E1

description: replicate 1


title: circAAGAB_Empty_E2

description: replicate 2


title: WT2_6m_snRNA

value: WT


title: CnpKO2_6m_snRNA

value: Cnp-/-


title: RD-1_H3K27Ac_TWIST2 KD_2

value: fusion-negative rhabdomyosarcoma

value: H3K27Ac (Diagenode, C15410196)

value: TWIST2 KD


title: Control_Xenograft_3


title: CnpKO1_6m_snRNA


title: RD-1_MYOD_TWIST2 KD_1

value: MYOD G1 Clone (Santa Cruz, sc-377460 X)


title: THP-1_CTRL-input


title: WT1_6m_snRNA


title: RD-1_H3K27Ac_TWIST2 KD_1


title: Control_Xenograft_2

value: RD-Xenograft


title: THP-1_CTRL-5hmC-seq

value: AML cell line


title: Dorsal Root Ganglion, MOCK, 31dpi, 3

city: New York

first: Justin

middle: J

last: Frere

state: NY

address: Alexandria Center for Life Sciences, West Tower, 430 E 29th St.

department: Microbiology

institute: NYU Langone Health

description: PolyA enriched and prepared using TruSeq Stranded mRNA library prep

data_processing:
Base calling and sample deconvolution performed via Illumina BaseSpace
Reads aligned to MesAur1.0 genome assembly using Ensembl GTF file and quantified using Salmon as made available in Illumina BaseSpace "RNA-Seq Alignment" application
Assembly: Mesocricetus Auratus MesAur1.0
Supplementary files format and content: .quant.genes.sf Salmon files (show raw and normalized read counts by gene)

organism: Mesocricetus auratus

source_name: Dorsal Root Ganglion

extract_protocol:
Trizol Phenol Chloroform
Poly A tail enrichment and preparation using True Strand RNA-seq Prep

value: Dorsal Root Ganglion

value: Mock (PBS-treated) --- 31 dpi


title: Control_Xenograft_1


title: Dorsal Root Ganglion, MOCK, 31dpi, 2


title: Foxg1Cre_MbpKO2

city: Göttingen

data_processing:
raw data was aligned to reference profile pre-mRNA mm10 using 10x genomics toolkit CellRanger v3.0.2
Single-nuclei UMI matrices were extracted and nuclei with less then 200 detected genes or less than 500 total transcripts were filtered out
Assembly: premRNA_mm10
Supplementary files format and content: Tab-delimited matrix include raw UMI counts for single-cells collected from all samples
Supplementary files format and content: Tab-delimited matrix of single-cell meta data which includes cell basic information and annotation during analysis
Supplementary files format and content: Tab-delimited matrix include raw UMI counts for microglia cells
Supplementary files format and content: Tab-delimited matrix of microglia meta data which includes cell basic information and annotation during analysis

source_name: Cortex and corpus callosum

value: Foxg1Cre Mbpfl/fl


title: Foxg1Cre_MbpKO1


title: RD-1_H3K27Ac_Control_1

value: control


title: Cnp_ko_2_snRNA

data_processing:
raw data was aligned to reference profile pre-mRNA mm10 using 10x genomics toolkit CellRanger v3.0.2
Single-nuclei UMI matrices were extracted and nuclei with less then 200 detected genes or less than 500 total transcripts were filtered out
Genome_build: premRNA_mm10
Supplementary_files_format_and_content: Tab-delimited matrix include raw UMI counts for single-cells collected from all samples
Supplementary_files_format_and_content: Tab-delimited matrix of single-cell meta data which includes cell basic information and annotation during analysis
Supplementary_files_format_and_content: Tab-delimited matrix include raw UMI counts for microglia cells
Supplementary_files_format_and_content: Tab-delimited matrix of microglia meta data which includes cell basic information and annotation during analysis

value: Cortex and corpus callosum

tag: mouse model

value: Alzheimer’s disease (AD)


title: RD-1_H3K27Ac_Control_2


title: HPASMCs, IgG2

city: Incheon

first: Hara

last: Kang

address: 119 Academy-ro

country: South Korea

institute: Incheon National University

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence(using fastx_trimmer), then mapped to hsa (mirbase) whole genome using Bowtie2
Read count extraction using bedtools.
Genome_build: miRBase hsa version 21
Supplementary_files_format_and_content: tab-delimited text files include read count values for each Sample

source_name: Human pulmonary artery smooth muscle cell

extract_protocol:
RNA was harvested using Trizol reagent (Invitrogen). Total RNA was used for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using NEBNext Multiplex Small  RNA Library Prep kit (New England BioLabs, Inc., USA) according to the manufacturer’ instructions.

tag: growth protocol

value: Cultured smooth muscle cell

value: Control

tag: rip antibody

value: rabbit IgG (Cell Signaling Technology, #2729)


title: Cnp_ko_1_snRNA

tag: tissue


title: Dorsal Root Ganglion, SARS-CoV-2, 31dpi, 3

value: WT


title: HPASMCs, NCL2

value: Human pulmonary artery smooth muscle cell

value: anti-nucleolin antibody (Abcam, #ab22758)


title: HPASMCs, IgG1


title: Dorsal Root Ganglion, SARS-CoV-2, 31dpi, 2


title: P3 fermentation, S0, 4d, rep2

city: Beijing

first: Keqian

last: Yang

address: NO.1 Beichen West  Road, Chaoyang District

institute: IMCAS

data_processing:
Illumina Casava1.8 software used for basecalling.
Genomic localization analysis of sequence using Bowtie 2.2.3
Expected number of Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced (FPKM) were estimation of gene expression level (Trapnell, Cole, et al., 2010)
Assembly: PRJNA939387
Supplementary files format and content: tab-delimited text files include counts and FPKM values for each sample

organism: Streptomyces avermitilis

source_name: Streptomyces avermitilis S0

extract_protocol:
The mycelia were collected,flash frozen on liquid nitrogen, and RNA was harvested using Trizol reagent.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: mycelia

value: P3 fermentation


title: P3 fermentation, S0, 8d, rep1


title: P3 fermentation, S0, 8d, rep2


title: Dorsal Root Ganglion, MOCK, 31dpi, 1


title: P3 fermentation, S0, 4d, rep1


title: Dorsal Root Ganglion, SARS-CoV-2, 31dpi, 1


title: HPASMCs, NCL1


title: WT1_snRNA