title: 120541

description: Gene expression data from nasal brushing of subject 120541.


title: 190502

status: Public on Oct 25 2022

type: RNA

city: Boston

first: Adam

middle: C

last: Gower

state: MA

address: 72 East Concord Street, E632

department: Department of Medicine

country: USA

institute: Boston University School of Medicine

description: Gene expression data from nasal brushing of subject 190502.

hyb_protocol: The labeled, fragmented DNA was hybridized to the GeneChip Human Gene 1.0 ST Array for 18 hours in a GeneChip Hybridization oven 640 at 45oC with rotation (60 rpm). The hybridized samples were washed and stained using an Affymetrix fluidics station 450.

scan_protocol: After staining, microarrays were immediately scanned using an Affymetrix GeneArray Scanner 3000 7G Plus.

data_processing: Raw Affymetrix CEL files were normalized to produce Entrez-Gene-identifier-specific expression values using the implementation of the Robust Multiarray Average (RMA) in the affy Bioconductor package (version 1.54.0), using R version 3.5.1 and the Brainarray hugene10sthsentrezgcdf R package (version 22.0.0).

label: biotin

molecule: total RNA

organism: Homo sapiens

source_name: Brushing of nasal epithelium

label_protocol: Biotin labeling was performed using the Ambion WT Expression Kit (Life Technologies, Grand Island, NY) according to the manufacturer's protocol, followed by the GeneChip WT Terminal Labeling and Controls Kit (Affymetrix, Santa Clara, CA).

extract_protocol: Total RNA isolated using miRNeasy kit from Qiagen, quantified using Nanodrop and quality determined using Bioanalyzer 2100 (Life Technologies). RNA was amplified using Ambion WT expression kit (Life Technologies).

tag: Sex

value: Male

tag: age

tag: smoking status

value: Former smoker

tag: fev1 % predicted

tag: cancer status

value: Cancer


title: MCF12A_E_6

type: SRA

city: London

first: Robin

last: Mesnage

address: Guy's Hospital, 8th Floor, Tower Wing

country: United Kingdom

institute: Kings College London

library_source: transcriptomic

data_processing:
RNA-seq data were first processed with Salmon (Patro et al., 2017). This tool was used to quantify transcript abundance by mapping the reads against a reference transcriptome (Homo sapiens GRCh38 cDNA fasta). The Salmon output was then imported in R using the Bioconductor package tximport.
Genome_build: Homo sapiens GRCh38 cDNA fasta
Supplementary_files_format_and_content: Abundance data (salmon output file)

growth_protocol: The MCF-7 cell line was grown in DMEM (Life Technologies, UK) supplemented with  2-mM glutamine (GE Healthcare Life Sciences), 10 mg/ml penicillin/streptomycin (Life Technologies, UK) and 5% fetal bovine serum (FBS). MCF-10A and MCF-12A cells were cultured in Dulbecco’s modified Eagle’s media F12 (DMEM-F12: Life Technologies, UK) supplemented with 20ng/ml Epidermal Growth Factor (EGF), 0.5 μg/ml ul hydrocortisone (Life Technologies, UK), 100ng/ml cholera toxin, 10 μg/ml insulin (Thermo Fisher scientific), 10 mg/ml penicillin/streptomycin (Life Technologies, UK), 5% horse serum. All cell cultures were grown at 37C (5% CO2) in 75cm2 flasks (Corning, Tewksbury, USA). The cells were detached using 0.05% trypsin EDTA (Life Technologies, UK) and counted using a haemocytometer.

extract_protocol:
After 48 hour exposure, RNA was extracted using the Qiagen RNeasy Mini Kit. The quality of the RNA samples was checked using a Nanodrop instrument (NanoDrop™ One Microvolume UV-Vis Spectrophotometers, Thermo Fisher Scientific, USA). All RNA samples were sent off to Genewiz (Lepizig, Germany) where they were sequenced.
RNA Library Preparation and cDNA Sequencing was performed by Genewiz (Leipzig, Germany). RNA samples were quantified using Qubit 4.0 Fluorometer (Life Technologies, Carlsbad, CA, USA) and RNA integrity was checked with RNA Kit on Agilent 5300 Fragment Analyzer (Agilent Technologies, Palo Alto, CA, USA). RNA sequencing library preparation was prepared using NEBNext Ultra II RNA Library Prep Kit for Illumina following manufacturer’s instructions (NEB, Ipswich, MA, USA). Briefly, mRNAs were first enriched with Oligo(dT) beads. Enriched mRNAs were fragmented. First strand and second strand cDNA were subsequently synthesized. cDNA fragments were end repaired and adenylated at 3’ends, and universal adapter was ligated to cDNA fragments, followed by index addition and library enrichment with limited cycle PCR. Sequencing libraries were validated using NGS Kit on the Agilent 5300 Fragment Analyzer (Agilent Technologies, Palo Alto, CA, USA), and quantified by using Qubit 4.0 Fluorometer (Invitrogen, Carlsbad, CA).
The sequencing libraries were multiplexed and loaded on the flow cell on the Illumina NovaSeq 6000 instrument according to manufacturer’s instructions. The samples were sequenced using a 2x150 Pair-End (PE) configuration v1.5. Image analysis and base calling were conducted by the NovaSeq Control Software v1.7 on the NovaSeq instrument. Raw sequence data (.bcl files) generated from Illumina NovaSeq was converted into fastq files and de-multiplexed using Illumina bcl2fastq program version 2.20. One mismatch was allowed for index sequence identification.

treatment_protocol: BPA, BPAF, BPAP, BPB, BPF, BPS and BPZ, as well as pendimethalin, were purchased from Merck KGaA (Sigma Aldrich®, Gillingham, Dorset, UK). The pendimethalin formulation Stomp aqua (BasF, 455g/L Pendimethalin) was purchased from PestControl Expert S.R.L. To prepare stock solutions the test substances were individually diluted in DMSO. Then the stock solutions were further diluted using media containing self-stripped serums leading to a final volume of 0.1% of DMOS in the test solutions. For the MCF-7 cell line, the media used for diluting the bisphenols consisted of DMEM supplemented with  2-mM glutamine, 10 mg/ml penicillin-streptomycin and 5% charcoal-stripped FBS. For the MCF-10A and MCF-12A cell lines DMEM-F12 supplemented with 20ng/ml EGF, 0.5μg/ml hydrocortisone, 100ng/ml cholera toxin, 10 μg/ml insulin, 10 mg/ml penicillin-streptomycin and 2% charcoal-stripped horse serum were used.

tag: cell line

tag: group

value: E

tag: treatment

value: Mid dose (BPAF, BPAP, BPB, BPF, BPS and BPZ) at 50 nM

tag: batch


title: MCF12A_F_6

value: F

value: Low dose (BPA, BPAF, BPAP, BPB, BPF, BPS and BPZ) at 1 nM


title: ATAC-seq_G3MSen_2

city: Barcelona

first: Eusebio

last: Perdiguero

address: Dr. Aiguader 88

department: Department of Medicine and Life Sciences

country: Spain

institute: UPF

library_source: genomic

data_processing:
Read quality was assessed by FastQC 0.11.8. All adapters were removed by Fastp 0.21.0.
The clean data was then aligned to mouse genome using Bowtie2 2.2.5.
BigWig files were generated using deeptools 3.3.1. Peaks were called using Macs2 2.1.0
Union peak sets were created by Bedtools 2.29.2, reads corresponding to each region were assigned by featureCounts 2.0.0.
Genome_build: mm10
Supplementary_files_format_and_content: Tab-delimited text files with raw read counts for each sample.

molecule: genomic DNA

organism: Mus musculus

source_name: Skeletal muscles (tibialis anterior, gastrocnemius and quadriceps)

growth_protocol: Mice were housed in standard cages under 12-hour light-dark cycles and fed ad libitum with a standard chow diet.

extract_protocol:
Sorted cells were directly processed for ATAC-seq library preparation without in vitro culture.  Sorted cells were centrifuged at 500 × g for 5min at 4°C and lysed using cold ATAC-RSB (10mM Tris-HCl, pH7.4,10mM NaCl, 3mM MgCl2 supplemented in 0.1% NP40, 0.1% Tween20 and 0.1mg/ml Digitonin) on ice for 3min. Next, the lysed cells were added in 50µl of transposition mix (25 µl of 2 × TD buffer (20mM Tris-HCl, pH7.6, 10mM MgCl2, 20% Dimethyl Formamide), 1.5 µl transposase (in house, (Picelli et al., 2014)), 17.5µl of PBS, 0.5µl of 10% Digitonin, 0.5µl of 10% Tween20 and 5µl of nuclease-free water). The transposition reaction was carried out for 30 min at 37°C and placed at 10°C. The transposition sample was purified using a Qiagen MinElute kit and eluted using 21µl of EB buffer.
The transposed fragments were amplified using 50ul of PCR mix (20µl of DNA, 2.5µl of custom Nextera PCR primers 1 and 2, and 25µl of KAPA HiFi HS Ready Mix for a total of 15 cycles. The PCR amplification conditions were 72°C for 5 min and 95°C for 30 sec, followed by 15 cycles at 95 °C for 10 s, 63 °C for 30 s, and 72 °C for 60 s, with a final extension at 72 °C for 5 min. Following PCR amplification, the libraries were purified, and the size was selected from 150 to 800bp using AMPure XP beads.

treatment_protocol: Cells were isolated from skeletal muscle tissue (tibialis anterior, gastrocnemius and quadriceps).

tag: cell type

value: Myeloid cells

tag: strain

tag: spider staining

value: SPiDER+

value: geriatric (28months old)

tag: muscle state

value: 3 days after injury (Cardiotoxin)


title: ATAC-seq_G7MNSen_1

value: SPiDER-

value: 7 days after injury (Cardiotoxin)


title: ATAC-seq_G3MSen_1


title: 4714-036-54

description: Gene expression data from nasal brushing 4714-036-54.

data_processing:
Demultiplexing and creation of FASTQ files were performed using BaseSpace.
Samples were aligned using hg19 and 2-pass STAR alignment (v2.5.2b). Gene-level posterior mean counts were calculated using RSEM (v1.3.0) and Ensembl Gene annotation build 75.
Posterior mean counts were filtered to exclude those that did not have more than one count per million (cpm) in at least 10% of the samples, and then corrected for sequencing batch using ComBat-seq.
Assembly: hg19
Supplementary files format and content: DECAMP_nasal_COVID19_posterior_mean_counts.tsv: a tab-separated value (TSV) file containing the posterior mean counts as computed by RSEM
Supplementary files format and content: DECAMP_nasal_COVID19_normalized_counts.tsv: a tab-separated value (TSV) file containing the ComBat-corrected counts for a subset of features that passed expression filtering.

extract_protocol:
Total RNA was isolated from nasal and bronchial brushings using the miRNeasy Mini Kit [QIAGEN].
Libraries were generated using the Illumina TruSeq Stranded Total RNA kit.

tag: tissue

value: Brushing of nasal epithelium

tag: subject

value: Current smoker

tag: fev1 %_predicted


title: MCF10A_G_1

value: G

value: Pendimethalin at 10 nM


title: MCF12A_D_6

value: D

value: Mid dose (BPA, BPAF, BPAP, BPB, BPF, BPS and BPZ) of 50 nM


title: ATAC-seq_G3MNSen_2


title: ATAC-seq_G3MNSen_1


title: 4714-032-54

description: Gene expression data from nasal brushing 4714-032-54.

value: Male


title: MCF12A_C_6

value: C

value: Mid dose (BPA) of 50 nM


title: 4714-030-54

description: Gene expression data from nasal brushing 4714-030-54.

value: Former smoker


title: ATAC-seq_G3M_2

value: non-injured contralateral muscle at 3 days post injury


title: 10005

description: Gene expression data from nasal brushing of subject 10005.

value: Female

value: Benign


title: 4714-037-55

description: Gene expression data from nasal brushing 4714-037-55.


title: MCF10A_A_6

value: A

value: Negative Control


title: 70015

description: Gene expression data from nasal brushing of subject 70015.


title: 20007

description: Gene expression data from nasal brushing of subject 20007.

value: Cancer


title: 4714-024-54

description: Gene expression data from nasal brushing 4714-024-54.


title: ATAC-seq_Y7MSen_4

value: Myeloid cells

value: SPiDER+

value: young (3-6 months old)

value: 7 days after injury (Cardiotoxin)


title: 4714-022-54

description: Gene expression data from nasal brushing 4714-022-54.

value: Brushing of nasal epithelium


title: MCF10A_H_6

value: H

value: Stomp Aqua at 10 nM pendimethalin


title: 210512

description: Gene expression data from nasal brushing of subject 210512.


title: MCF10A_G_6

value: G

value: Pendimethalin at 10 nM


title: 60012

description: Gene expression data from nasal brushing of subject 60012.

value: Male


title: MCF10A_F_6

value: F

value: Low dose (BPA, BPAF, BPAP, BPB, BPF, BPS and BPZ) at 1 nM


title: ATAC-seq_Y7MSen_3


title: 10023

description: Gene expression data from nasal brushing of subject 10023.

value: Former smoker


title: 4714-021-54

description: Gene expression data from nasal brushing 4714-021-54.


title: 140015

description: Gene expression data from nasal brushing of subject 140015.

value: Benign


title: MCF12A_B_6

value: B

value: High dose (BPA) of 250 nM


title: ATAC-seq_Y7MSen_2


title: 4714-025-54

description: Gene expression data from nasal brushing 4714-025-54.

value: Current smoker


title: ATAC-seq_Y7MSen_1

value: Myeloid cells


title: 4714-019-54

description: Gene expression data from nasal brushing 4714-019-54.


title: ATAC-seq_G3M_1

value: SPiDER-

value: geriatric (28months old)

value: non-injured contralateral muscle at 3 days post injury


title: 4714-018-54

description: Gene expression data from nasal brushing 4714-018-54.

value: Brushing of nasal epithelium


title: ATAC-seq_Y7MNSen_2

value: young (3-6 months old)

value: 7 days after injury (Cardiotoxin)


title: ATAC-seq_Y7MNSen_1


title: 4714-017-54

description: Gene expression data from nasal brushing 4714-017-54.


title: 4714-016-54

description: Gene expression data from nasal brushing 4714-016-54.


title: 10112

description: Gene expression data from nasal brushing of subject 10112.


title: ATAC-seq_Y3MSen_3

value: SPiDER+

value: 3 days after injury (Cardiotoxin)


title: MCF10A_C_6

value: C

value: Mid dose (BPA) of 50 nM


title: MCF10A_E_6

value: E

value: Mid dose (BPAF, BPAP, BPB, BPF, BPS and BPZ) at 50 nM


title: MCF10A_D_6

value: D

value: Mid dose (BPA, BPAF, BPAP, BPB, BPF, BPS and BPZ) of 50 nM


title: 140016

description: Gene expression data from nasal brushing of subject 140016.

value: Female

value: Former smoker

value: Benign


title: MCF10A_F_1

value: F

value: Low dose (BPA, BPAF, BPAP, BPB, BPF, BPS and BPZ) at 1 nM


title: 50530

description: Gene expression data from nasal brushing of subject 50530.

value: Male


title: 70008

description: Gene expression data from nasal brushing of subject 70008.

value: Cancer


title: 4714-033-54

description: Gene expression data from nasal brushing 4714-033-54.

value: Brushing of nasal epithelium

value: Current smoker


title: 70014

description: Gene expression data from nasal brushing of subject 70014.


title: 4714-015-54

description: Gene expression data from nasal brushing 4714-015-54.


title: ATAC-seq_Y3MSen_2

value: Myeloid cells

value: SPiDER+

value: young (3-6 months old)


title: 4714-014-54

description: Gene expression data from nasal brushing 4714-014-54.


title: ATAC-seq_Y3MSen_1

value: 3 days after injury (Cardiotoxin)


title: 90019

description: Gene expression data from nasal brushing of subject 90019.


title: MCF10A_B_6

value: B

value: High dose (BPA) of 250 nM


title: MCF7_A_6

value: A

value: Negative Control


title: 150502

description: Gene expression data from nasal brushing of subject 150502.


title: MCF7_H_6

value: H

value: Stomp Aqua at 10 nM pendimethalin


title: 4714-011-54

description: Gene expression data from nasal brushing 4714-011-54.

value: Former smoker


title: MCF7_G_6

value: G

value: Pendimethalin at 10 nM


title: 4714-010-54

description: Gene expression data from nasal brushing 4714-010-54.

value: Male


title: 70503

description: Gene expression data from nasal brushing of subject 70503.

value: Female

value: Cancer


title: ATAC-seq_Y3MNSen_1

value: SPiDER-


title: 120510

description: Gene expression data from nasal brushing of subject 120510.


title: 4714-006-54

description: Gene expression data from nasal brushing 4714-006-54.

value: Brushing of nasal epithelium


title: MCF7_E_6

value: E

value: Mid dose (BPAF, BPAP, BPB, BPF, BPS and BPZ) at 50 nM


title: 140058

description: Gene expression data from nasal brushing of subject 140058.

value: Current smoker


title: ATAC-seq_Y3M_2

value: Myeloid cells

value: young (3-6 months old)

value: non-injured contralateral muscle at 3 days post injury


title: ATAC-seq_Y3MNSen_2

value: 3 days after injury (Cardiotoxin)


title: MCF7_F_6

value: F

value: Low dose (BPA, BPAF, BPAP, BPB, BPF, BPS and BPZ) at 1 nM


title: ATAC-seq_Y3M_1


title: MCF7_D_6

value: D

value: Mid dose (BPA, BPAF, BPAP, BPB, BPF, BPS and BPZ) of 50 nM


title: 4494-004-54

description: Gene expression data from nasal brushing 4494-004-54.

value: Former smoker


title: ATAC-seq_G7SSen_1

value: Satellite cells

value: SPiDER+

value: geriatric (28months old)

value: 7 days after injury (Cardiotoxin)


title: 4714-003-55

description: Gene expression data from nasal brushing 4714-003-55.

value: Brushing of nasal epithelium

value: Male


title: 220502

description: Gene expression data from nasal brushing of subject 220502.

value: Cancer


title: 4438-121-54

description: Gene expression data from nasal brushing 4438-121-54.

value: Current smoker


title: ATAC-seq_G7SSen_2


title: 10126

description: Gene expression data from nasal brushing of subject 10126.

value: Benign


title: ATAC-seq_G7SNSen_2

value: SPiDER-


title: MCF7_B_6

value: B

value: High dose (BPA) of 250 nM


title: MCF12A_A_5

value: A

value: Negative Control


title: 110019

description: Gene expression data from nasal brushing of subject 110019.


title: 4438-118-54

description: Gene expression data from nasal brushing 4438-118-54.


title: MCF10A_E_1

value: E

value: Mid dose (BPAF, BPAP, BPB, BPF, BPS and BPZ) at 50 nM


title: ATAC-seq_G7SNSen_1


title: 4438-111-54

description: Gene expression data from nasal brushing 4438-111-54.


title: 50504

description: Gene expression data from nasal brushing of subject 50504.

value: Female


title: 120545

description: Gene expression data from nasal brushing of subject 120545.

value: Former smoker


title: 4714-004-54

description: Gene expression data from nasal brushing 4714-004-54.


title: 210509

description: Gene expression data from nasal brushing of subject 210509.


title: MCF7_C_6

value: C

value: Mid dose (BPA) of 50 nM


title: 60002

description: Gene expression data from nasal brushing of subject 60002.


title: ATAC-seq_G3SSen_3

value: Satellite cells

value: SPiDER+

value: geriatric (28months old)

value: 3 days after injury (Cardiotoxin)


title: ATAC-seq_G3SSen_2


title: MCF12A_H_5

value: H

value: Stomp Aqua at 10 nM pendimethalin


title: 4438-082-54

description: Gene expression data from nasal brushing 4438-082-54.

value: Brushing of nasal epithelium

value: Male


title: MCF12A_G_5

value: G

value: Pendimethalin at 10 nM


title: 4438-060-54

description: Gene expression data from nasal brushing 4438-060-54.


title: MCF12A_F_5

value: F

value: Low dose (BPA, BPAF, BPAP, BPB, BPF, BPS and BPZ) at 1 nM


title: 4438-093-54

description: Gene expression data from nasal brushing 4438-093-54.

value: Current smoker


title: MCF12A_E_5

value: E

value: Mid dose (BPAF, BPAP, BPB, BPF, BPS and BPZ) at 50 nM


title: 4438-053-54

description: Gene expression data from nasal brushing 4438-053-54.

value: Former smoker


title: ATAC-seq_G3SSen_1


title: ATAC-seq_G3SNSen_2

value: SPiDER-


title: ATAC-seq_G3SNSen_3

value: Satellite cells


title: MCF12A_D_5

value: D

value: Mid dose (BPA, BPAF, BPAP, BPB, BPF, BPS and BPZ) of 50 nM


title: 120524

description: Gene expression data from nasal brushing of subject 120524.

value: Female

value: Benign


title: ATAC-seq_G3SNSen_1

value: geriatric (28months old)

value: 3 days after injury (Cardiotoxin)


title: 120555

description: Gene expression data from nasal brushing of subject 120555.

value: Cancer


title: 70513

description: Gene expression data from nasal brushing of subject 70513.


title: 4238-041-54

description: Gene expression data from nasal brushing 4238-041-54.

value: Brushing of nasal epithelium


title: ATAC-seq_G3S_3

value: non-injured contralateral muscle at 3 days post injury


title: MCF12A_C_5

value: C

value: Mid dose (BPA) of 50 nM


title: 4238-021-54

description: Gene expression data from nasal brushing 4238-021-54.

value: Male

value: Current smoker


title: ATAC-seq_G3S_2


title: 120043

description: Gene expression data from nasal brushing of subject 120043.


title: MCF10A_A_5

value: A

value: Negative Control


title: ATAC-seq_G3S_1

value: SPiDER-


title: 4202-035-54

description: Gene expression data from nasal brushing 4202-035-54.

value: Former smoker


title: 120041

description: Gene expression data from nasal brushing of subject 120041.


title: 4202-034-54

description: Gene expression data from nasal brushing 4202-034-54.


title: CD45PosSen_2

data_processing:
Sequences were aligned to mouse reference genome with STARsolo 2.7.3a.
Datasets were processed following Seurat 2.3.4 standard integration protocol as per tutorial instructions.
Genes expressed in < 3 cells and cells with < 500 features, < 2000 transcripts and > 20% reads mapping to mitochondrial genes as well as cells identified as doublets by DoubletFinder 2.0 were removed.
PCA was performed for dimensionality reduction and the first 30 components were used for UMAP embedding and clustering.
Genome_build: mm10
Supplementary_files_format_and_content: Single R object with data processed by Seurat.

extract_protocol:
Sorted cells were directly processed for scRNA-seq library preparation.
scRNA-seq libraries were prepared using the Chromium Single Cell Gene Expression kit (10X Genomics, PN-1000121) according to the manufacturer's instruction and targeting a recovery of 5000 cells/dataset. Libraries were sequenced by a MGI DNBSEQ-Tx sequencer with following strategy: read 1, 28 bp, read 2, 100 bp.

value: CD45+ cells

value: SPiDER+

value: young (3-6 months old)


title: MCF10A_G_5

value: G

value: Pendimethalin at 10 nM


title: ATAC-seq_Y7SSen_1

value: Satellite cells

value: 7 days after injury (Cardiotoxin)


title: 4202-032-54

description: Gene expression data from nasal brushing 4202-032-54.

value: Brushing of nasal epithelium


title: 4438-042-54

description: Gene expression data from nasal brushing 4438-042-54.


title: CD45PosSen_1

value: 3 days after injury (Cardiotoxin)


title: 4202-031-54

description: Gene expression data from nasal brushing 4202-031-54.

value: Female


title: ATAC-seq_Y7SNSen_2


title: CD45NegSen_2

value: CD45- cells


title: MCF10A_D_1

value: D

value: Mid dose (BPA, BPAF, BPAP, BPB, BPF, BPS and BPZ) of 50 nM


title: 120523

description: Gene expression data from nasal brushing of subject 120523.

value: Male

value: Current smoker

value: Cancer


title: 140069

description: Gene expression data from nasal brushing of subject 140069.


title: 130121

description: Gene expression data from nasal brushing of subject 130121.

value: Former smoker


title: ATAC-seq_Y7SNSen_1

value: SPiDER-


title: MCF12A_B_5

value: B

value: High dose (BPA) of 250 nM


title: MCF10A_F_5

value: F

value: Low dose (BPA, BPAF, BPAP, BPB, BPF, BPS and BPZ) at 1 nM


title: 120032

description: Gene expression data from nasal brushing of subject 120032.

value: Benign


title: CD45NegSen_1

value: SPiDER+

value: young (3-6 months old)


title: MCF10A_E_5

value: E

value: Mid dose (BPAF, BPAP, BPB, BPF, BPS and BPZ) at 50 nM


title: MCF10A_H_5

value: H

value: Stomp Aqua at 10 nM pendimethalin


title: 4202-020-54

description: Gene expression data from nasal brushing 4202-020-54.

value: Brushing of nasal epithelium


title: ATAC-seq_Y3SSen_3

value: Satellite cells

value: 3 days after injury (Cardiotoxin)


title: MCF10A_D_5

value: D

value: Mid dose (BPA, BPAF, BPAP, BPB, BPF, BPS and BPZ) of 50 nM


title: ATAC-seq_Y7SSen_2

value: 7 days after injury (Cardiotoxin)


title: 4202-018-54

description: Gene expression data from nasal brushing 4202-018-54.

value: Female

value: Former smoker


title: CD45PosNSen_2

value: CD45+ cells

value: SPiDER-


title: ATAC-seq_Y3SSen_2


title: CD45PosNSen_1


title: 4202-014-54

description: Gene expression data from nasal brushing 4202-014-54.


title: ATAC-seq_Y3SSen_1


title: 4202-008-54

description: Gene expression data from nasal brushing 4202-008-54.

value: Male

value: Current smoker


title: MCF10A_C_5

value: C

value: Mid dose (BPA) of 50 nM


title: MCF10A_B_5

value: B

value: High dose (BPA) of 250 nM


title: CD45NegNSen_2

value: CD45- cells

value: young (3-6 months old)


title: 4202-030-54

description: Gene expression data from nasal brushing 4202-030-54.

value: Brushing of nasal epithelium


title: ATAC-seq_Y3SNSen_3

value: Satellite cells

value: 3 days after injury (Cardiotoxin)


title: CD45NegNSen_1


title: MCF7_A_5

value: A

value: Negative Control


title: ATAC-seq_Y3SNSen_2


title: MCF7_H_5

value: H

value: Stomp Aqua at 10 nM pendimethalin


title: 4202-007-54

description: Gene expression data from nasal brushing 4202-007-54.


title: ATAC-seq_Y3SNSen_1


title: miRNA_T48Gs2

city: Lanzhou City

first: lu

last: zhao

state: Gansu Province

address: Yintan Road Street

country: China

institute: Gansu Agricultural University

data_processing:
Raw reads were further filtered according to the following rules: 1) Removing low quality reads containing more than one low quality (Q-value≤20) base or containing unknown nucleotides(N); 2) Removing reads without 3’adapters; 3) Removing reads containing 5’adapters; 4) Removing reads containing 3’ and 5’ adapters but no small RNA fragment between them; 5) Removing reads containing ployA in small RNA fragment; 6) Removing reads shorter than 18nt (not include adapters).
Low-quality raw reads and clean tags were identified as tRNA, rRNA, snoRNA, snRNA and scRNA using GenBank and Rfam database were removed and enriched clean tags were compared with the reference genome USDA_OmykA_1.1 and the reads mapped to exons, introns and repeat sequences were removed.
The expression profiles of miRNAs were calculated and normalized to transcripts per million (TPM), and the formula was TPM = Actual miRNA counts/Total counts of clean tags ×10 ^ 6, obtained the expression profiles of all miRNA of all samples.
Assembly: Oncorhynchus mykiss USDA_OmykA_1.1
Supplementary files format and content: tab-delimited text files include TPM values for each Sample …

organism: Oncorhynchus mykiss

source_name: gill tissues

extract_protocol:
The samples were collected immediately, then flash-frozen in liquid nitrogen,and total RNA was extracted using Trizol reagent.
miRNA libraries were prepared for sequencing using standard Illumina protocols

value: gill tissues

value: IHNV infection

tag: genotype

value: wild-type


title: ATAC-seq_Y3S_3

value: SPiDER-

value: non-injured contralateral muscle at 3 days post injury


title: MCF7_G_5

value: G

value: Pendimethalin at 10 nM


title: miRNA_T48Gs1


title: miRNA_T48Gs3


title: MCF7_F_5

value: F

value: Low dose (BPA, BPAF, BPAP, BPB, BPF, BPS and BPZ) at 1 nM


title: ATAC-seq_Y3S_2

value: young (3-6 months old)


title: miRNA_C48Gs3

value: control


title: ATAC-seq_Y3S_1

value: Satellite cells


title: 32D_Nup98Nsd1_3

city: Kyoto

first: Kenji

last: Okamoto

state: Kyoto

address: 465, Kajii-cho, Kawaramachi-Hirokoji, Kamigyo-ku

country: Japan

institute: Department of Pediatrics, Graduate School of Medical Science, Kyoto Prefectural University of Medicine

hyb_protocol: Following fragmentation, 15 ug of cRNA was hybridized for 16 hr at 45 ̊C on GeneChip Human Genome U133 Plus 2.0 Array. GeneChip array was washed and stained in the GeneChip Fluidics Station 450 (Thermo Fisher Scientific).

scan_protocol: GeneChip array was scanned using GeneChip Scanner 3000 7G.

data_processing: Single Array Analysis was calculated by Microarray Suite version 5.0 (MAS5.0) with Thermo Fisher Scientific default setting and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 500.

source_name: Mouse Nup98::Nsd1-transduced 32D cells

label_protocol: Biotinylated cRNA was synthesized by GeneChip 3' IVT PLUS Reagent Kit(Thermo Fisher Scientific) from 100 ng total RNA according to the manufacturer's instructions. Biotinylated cRNA yield was checked with the NanoDrop ND-2000 Spectrophotometer.

extract_protocol: Ethanol precipitation of total RNA was performed using an RNeasy Mini Kit according to the manufacturer's instructions.

value: IL-3 dependent cells from Friend leukemia virus-infected mouse bone marrow.


title: miRNA_C48Gs1


title: MCF7_B_1

value: B

value: High dose (BPA) of 250 nM


title: MCF7_E_5

value: E

value: Mid dose (BPAF, BPAP, BPB, BPF, BPS and BPZ) at 50 nM


title: 135_asfv

status: Public on Oct 24 2022

city: Cerdanyola del Vallès (Bellaterra)

first: Jordi

last: Argilaguet

state: Spain

address: Campus de la Universitat Autònoma de Barcelona, Edifici CReSA s/n

department: CReSA

institute: IRTA

data_processing:
Mappings using STAR/2.5.3a against Sscrofa11.1
Gene quantification was performed with RSEM/1.3.0
Annotation Ensembl release 100
Genome_build: Sscrofa11.1
Supplementary_files_format_and_content: COUNTS_genes_RODRIGUEZFER_01.tsv (raw counts)

organism: Sus scrofa

source_name: PBMC

extract_protocol:
Trizol + RNeasy Mini Kit Qiagen
Kapa Stranded mRNA

value: PBMC

tag: status

tag: Sex

value: M

value: asfv


title: MCF10A_C_1

value: C

value: Mid dose (BPA) of 50 nM


title: 142_rpmi

value: rpmi


title: 135_rpmi


title: scRNA-seq_mBCC_DMSO

city: Stanford

first: Anthony

last: Oro

state: CA

address: 269 Campus Drvie

department: Dermatology

institute: Stanford University

description: single cell RNA-seq

data_processing:
scRNA data was processed using the 10x Genomics CellRanger pipeline
Seurat was used to call cluster and generate UMAPs
Monocle was used to perform pseudotime analysis
Genome_build: mm10
Supplementary_files_format_and_content: count matrix

source_name: mouse BCC

growth_protocol: Ptch1+/-;p53f/f;K14CreER mice were induced to form tumors (Whitson et al., 2018; PMID: 29400712)

extract_protocol:
Tumors were dissociated by first mincing into pieces smaller than 1 mm in diameter and then incubated in 40 mL of a 0.5% collagenase solution (Gibco; 25200056) for 1hrs with rotation at 37°C . 5 mL of 0.25% Trypsin was then added and incubated for an additional 15min with rotation at 37°C . Cells were then FACS sorted for live cells, and then processed using the 10X Genomics Next GEM scRNA-Seq solution.
Library construction followed the 10X Genomics Next GEM scRNA-Seq pipeline.

treatment_protocol: No additional treatment for Sample 1/mBCC sample. For Sample 2/mBCC_DMSO and Sample 3/mBCC_VISMO, primary Ptch1+/-;p53f/f;K14CreER tumor cells were transplanted into NodScid host, which then formed tumors. Once tumors were formed, mice were either treated with Vismodegib (100 mg/kg) or DMSO control for 2 weeks and then harvested.

value: Mouse tumor from Ptch1+/-;p53f/f;K14CreER model


title: 130_asfv

value: vaccinated


title: 121_asfv


title: 121_rpmi


title: 130_rpmi


title: 113_asfv


title: 32D_MSCVpuro_2

source_name: Mouse mock-transduced 32D cells


title: 32D_MSCVpuro_1


title: 142_asfv


title: 113_rpmi


title: 134_asfv


title: 32D_MSCVpuro_3


title: miRNA_C48Gs2

value: gill tissues

value: wild-type


title: 133_asfv


title: 133_rpmi


title: 32D_Nup98Nsd1_2


title: 134_rpmi


title: 129_asfv


title: scRNA-seq_mBCC_VISMO

description: single cell RNA-seq


title: 129_rpmi


title: SA-11018-20 LN SUBMAN #12 BA71DCD2

data_processing:
Cellrager 5.0.1 count against Sscrofa11.1+KP055815
Genome_build: Sscrofa 11.1 + KP055815
Supplementary_files_format_and_content: Hdf5 (Feature-Barcode Matrix)

source_name: Cell suspension

extract_protocol:
10XChromium-Seq
10X Chromium 3' RNA-seq

value: submandibular lymph node cells


title: SA-11018-20 LN SUBMAN #3 BA71DCD2

value: control


title: AP_S3_4

city: Aurora

first: Subbiah

last: Pugazhenthi

state: CO

address: 1700 N Wheeling St

department: Endocrinology

institute: RMRVA & Anschutz Campus - Sch of Med - Endocrinology

description: APP/PS1/Sirt3-/- 3

data_processing:
Sequence reads were trimmed for adaptor sequence/low-quality sequence
clean reads were obtained and mapped to the mouse genome assembly (GRCm38/mm10), using TopHat software
gene expression levels were calculated, using the reads per kilo bases per million reads (RPKM) method
sample_readcount(compare): the readcount values of each sample after normalized.
differential gene expression analysis was performed using DESeq2 package
Assembly: mm10
Supplementary files format and content: Excel file includes FPKM values for each Sample

source_name: Brain cortex

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen). 2 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were preapred using  NEBNextULtra RNA Library Prep Kit from Illumina following manufacturer's protocols.

value: Brain cortex

value: human APP and a mutant human presenilin 1 , and Sirt3 Knock out

value: Female

tag: age

value: 8 months old


title: AP_S3_2

description: APP/PS1/Sirt3-/- 2


title: AP_S3_1

description: APP/PS1/Sirt3-/- 1


title: S3_4

description: Sirt3-/- 3

value: Sirt3 knock out


title: S3_1

description: Sirt3-/- 1


title: AP_4

description: APP/PS1 3

value: human APP and a mutant human presenilin 1


title: S3_2

description: Sirt3-/- 2


title: 32D_Nup98Nsd1_1

value: IL-3 dependent cells from Friend leukemia virus-infected mouse bone marrow.


title: AP_2

description: APP/PS1 2


title: WT_4

description: wild type 3

value: WT


title: AP_1

description: APP/PS1 1


title: WT_2

description: wild type 2


title: WT_1

description: wild type 1


title: Pilote_Gen3G-Plasma-T1-PubM2828

city: Chicoutimi

first: Luigi

last: Bouchard

state: Quebec

address: 305 rue Saint-Vallier, Pavillon des Augustines

department: Biochimie et génomique fonctionnelle

country: Canada

institute: Université de Sherbrooke

data_processing:
The extra-cellular RNA processing toolkit (exceRpt) pipeline version 4.6.3 (PMID : 30956140) was used to process miRNA sequencing data from fastq files.
Low quality reads (Phred score < 20 for more than  80% of the read) and adapters sequences were removed with FASTX-Toolkit. High quality sequences were mapped to the human genome (GRCh37) and miRBase version 21 using STAR. As rRNA contamination was almost inexistant in our samples (average of 1.04±0.90% of total mapped reads based on metrics from STAR), the mapping step to the rRNA was removed to speed tup the process.
Read count extraction was performed using the Rscript provided for processing exceRpt output for multiple sample (PMID : 30956140).
Samples with < 500k miRNAs reads and samples with >25M miRNAs reads were considered outliers and removed from the downstream analysis (differential analysis using DESeq2 package).
DESeq2 function collapseReplicates was used to combined technical replicates in the analysis for data that were extracted and sequenced twice. Technical replicate have the same ID and fastq files contains either "pilote" or "projet". Technical replicate are identified in the technical replicates column (N = 12 originally, 9 gave consent for genetic data sharing)
Assembly: GRCh37
Supplementary files format and content: tab-seperated value files include raw read counts (non-normalized) for each Sample
Supplementary files format and content: Gen3G_Plasma_miRNA_v1_geo_rawcounts.txt

source_name: plasma

extract_protocol:
Total RNA was extracted using the mirVana PARIS kit and protocol (Thermo Fisher Scientific, catalogue # AM1556), in a randomized order, from either 500μl of plasma kept at −80 °C until extraction. Seventy-five μl of nuclease-free water was used to eluate total RNA which was then precipitated following the method described by Burgos et al. (PMID: 23525801). Briefly, 35 μl of cold (4°C) 7 M ammonium acetate solution (ThermoFisher Scientific, catalogue # 02002268) were added to 70μl of total RNA. This was followed by the addition of 420μl of chilled (−20°C) absolute ethanol (Commercial Alcohols, ON, Canada; catalogue # P006EAAN) and overnight precipitation at −20°C. The mix was then centrifuged at 16 000g at 4°C for 30 min. RNA pellets were then washed twice with 200 μl of cold 80% ethanol followed by centrifugation at 16 000g at 4°C for 5min. It was then dried for 30min at room temperature and 5μl of nuclease-free water was added. The total volume was used for library preparation.
Samples were randomized before library preparation. An adapted version of the Truseq Small RNA Sample Prep kit (Illumina, BC, Canada; catalogue # RS-200- 0012) protocol from Burgos et al. (PMID: 23525801) was used to manage low concentrated miRNA samples. In this protocol, half of the standard volumes were used for ligation (3′ and 5′ ends) of RNA sample (5μl), reverse transcription, barcoding (index 1-20: one index per sample) and PCR amplification (15 cycles) to preserve the ratio between RNA amount (which is lower in plasma samples) and the reagents. Purification and size-selection (145-160bp) of the libraries were done by migration on a Novex polyacrylamide TBE Gel, 6% (ThermoFisher Scientific, catalogue # EC6265BOX) followed by elution in 300 μl of nuclease-free water and overnight incubation at 500 RPM at room temperature on an incubating microplate shaker (VWR, ON, Canada, catalogue #12620-930). The libraries were then precipitated according to the manufacturer's instructions (including incubation of the precipitation mix at −80°C for 30min) and were resus- pended in 25 μl of 10 mM Tris-HCI pH 8.5 buffer. The Agilent 2100 Bioanalyzer and Agilent High Sensitivity DNA Kit (Agilent, Mississauga, ON, Can- ada; catalog # 5067-4626) or the Kapa Illumina GA with Revised Primers-SYBR Fast Universal kit (Kapa Biosystems) and a LabChip GX (PerkinElmer, catalog# CLS760672) instrument were used to assess the quality of each library (i.e., concentration, library length and primer dimers absence). Library sequencing, including quality control and sample pooling, was performed at the McGill University and Génome Québec Innovation Centre (Québec, Canada). Librairies were quantified by qPCR and pooled equimolarly (HiSeq 2500: 7pM final molarity; 12 libraries with different indexes per lane; HiSeq 4000: 10pM final molarity; 20 libraries with dif- ferent indexes per lane), before being denatured and clustered on single-read Illumina flow cells (catalog # GD-401-3001 and catalog GD-410-1001) according to the manufacturer’s standard protocol. The libraries were then sequenced on Illumina HiSeq 2500 or HiSeq 4000 sequencing platforms for 50 cycles, with 7 cycles indexing read. Twelve samples were extracted twice and sequenced on both platforms to confirm standardization and platform comparability.

value: plasma

value: female

tag: pregnancy status_1

value: Normal


title: Pilote_Gen3G-Plasma-T1-PubM2849


title: Pilote_Gen3G-Plasma-T1-PubM2803


title: Pilote_Gen3G-Plasma-T1-PubM2819


title: Pilote_Gen3G-Plasma-T1-PubM2784


title: Pilote_Gen3G-Plasma-T1-PubM2765

tag: replicate

value: technical replicate


title: Pilote_Gen3G-Plasma-T1-PubM2634

value: Gestational diabetes mellitus


title: Pilote_Gen3G-Plasma-T1-PubM2793


title: Pilote_Gen3G-Plasma-T1-PubM2622

tag: pregnancy status_2

value: Other pregnancy complications


title: Pilote_Gen3G-Plasma-T1-PubM2856


title: Pilote_Gen3G-Plasma-T1-PubM2656


title: Pilote_Gen3G-Plasma-T1-PubM2628


title: Pilote_Gen3G-Plasma-T1-PubM2636


title: Pilote_Gen3G-Plasma-T1-PubM2549


title: Pilote_Gen3G-Plasma-T1-PubM2543


title: Pilote_Gen3G-Plasma-T1-PubM2515


title: Pilote_Gen3G-Plasma-T1-PubM2386


title: Pilote_Gen3G-Plasma-T1-PubM2439


title: Pilote_Gen3G-Plasma-T1-PubM2468


title: Pilote_Gen3G-Plasma-T1-PubM2430


title: Pilote_Gen3G-Plasma-T1-PubM2447


title: Pilote_Gen3G-Plasma-T1-PubM2470


title: Pilote_Gen3G-Plasma-T1-PubM2361


title: Pilote_Gen3G-Plasma-T1-PubM2345


title: Pilote_Gen3G-Plasma-T1-PubM2480


title: Pilote_Gen3G-Plasma-T1-PubM2600


title: Pilote_Gen3G-Plasma-T1-PubM2337


title: Pilote_Gen3G-Plasma-T1-PubM2577


title: Pilote_Gen3G-Plasma-T1-PubM2284


title: Pilote_Gen3G-Plasma-T1-PubM2331


title: Pilote_Gen3G-Plasma-T1-PubM2197


title: Pilote_Gen3G-Plasma-T1-PubM2169


title: Pilote_Gen3G-Plasma-T1-PubM2276


title: Pilote_Gen3G-Plasma-T1-PubM2268


title: Pilote_Gen3G-Plasma-T1-PubM2119


title: Pilote_Gen3G-Plasma-T1-PubM2114


title: Pilote_Gen3G-Plasma-T1-PubM2157


title: Pilote_Gen3G-Plasma-T1-PubM2153


title: Pilote_Gen3G-Plasma-T1-PubM2232


title: Pilote_Gen3G-Plasma-T1-PubM2495


title: Pilote_Gen3G-Plasma-T1-PubM2464


title: Pilote_Gen3G-Plasma-T1-PubM2080


title: Pilote_Gen3G-Plasma-T1-PubM2039


title: Pilote_Gen3G-Plasma-T1-PubM2025


title: Pilote_Gen3G-Plasma-T1-PubM2028


title: CG2: siRNA-CTR-2 + Chi3l1 incubation

city: Bronx

first: Jorge

middle: Eduardo

last: Fajardo

state: NY

address: 1300 Morris Park Avenue

department: Systems and Computational Biology

institute: Albert Einstein College of Medicine

data_processing:
FASTQ files of sequencing reads for each sample provided by GENEWIZ were aligned to the GRCh38/hg38 human reference genome provided by UC Santa Cruz’s Genome Browser Gateway (https://hgdownload.soe.ucsc.edu/downloads.html) using HISAT2 (http://daehwankimlab.github.io/hisat2/manual/).  Reads with a mapping quality of 30 or better were retained for analysis.
DEBrowser ws used to perform differential gene expression analysis

source_name: Patient derived glioma stem cells

growth_protocol: The IRB of Rhode Island Hospital has approved the collection of patient-derived glioblastoma multiforme (GBM) tissue. All collections were performed with patient consent and in completely de-identified manner. Primary hGSC spheres were cultured from human glioma samples as previously described (Galli et al., 2004) All hGCs used in this study were authenticated by ATCC using short tandem repeat (STR) analysis. All human primary cells used were between passages 5 and 30. GSCs were cultured either as spheres or as attached on fibronectin-coated plates (10ug/ml, Millipore Sigma) in a medium of 1X Neurobasal Medium (Fisher Scientific), B27 serum-free supplement, minus Vitamin A (Fisher Scientific), 100X Glutamax (Fisher Scientific), 1mg/ml Heparin (STEMCELL Technologies), 20 ng/ml epidermal growth factor (Peprotech), 20ng/ml basic-fibroblast growth factor (Peprotech), and 1% Antibiotic-Antimycotic (Fisher Scientific).

extract_protocol:
72 hours post-transfection, RNA was isolated using Rneasy mini kit with DNAse digestion on column (Qiagen)
Preparation of libraries and next-generation RNA-sequencing were performed by GENEWIZ

treatment_protocol: GSCs were treated for a week with Chi3l1 (500ng/ml). Cells were transfected with X2 (Mirus Bio) lipid and 100nM siMAZ (Dharmacon) or non targeted siCTR (Dharmacon) in complete media without heparin. 24 hours post-transfection, media was replaced with heparin containing media. 72 hours post-transfection, RNA was isolated using Rneasy mini kit with DNAse digestion on column (Qiagen).

value: brain

value: siRNA-CTR + Chi3l1 incubation

value: glioma stem cells


title: CG4: siRNA-MAZ-2 + Chi3l1 incubation

value: siRNA-MAZ + Chi3l1 incubation


title: CG1: siRNA-CTR-1 + Chi3l1 incubation


title: Glioma stem cells + CHI3L1 rep1

data_processing:
FASTQ files of sequencing reads for each sample provided by GENEWIZ were filtered, deduplicated, and aligned to the GRCh38/hg38 human reference genome provided by UC Santa Cruz’s Genome Browser Gateway (https://hgdownload.soe.ucsc.edu/downloads.html) using the paired-end alignment feature of the Bowtie2 (http://bowtie-bio.sourceforge.net/bowtie2/manual.shtml). All genomic comparisons and alignments were performed and made with reference to chromosomes 1-22 and chromosome X of the hg38 reference genome. The resultant BAM files from FASTQ alignment were sorted and indexed using the SAMtools program suite (https://github.com/samtools/samtools) for managing high-throughput sequencing data, specifically via the sort, view, and index functions in the toolkit. Duplicates reads were removed with the MarkDuplicates function of the package Picard Tools (https://broadinstitute.github.io/picard/). Finally, peak calling was performed on the BAM files to detect genomic sites with significantly enriched chromatin accessibility using the Genrich (https://github.com/jsh58/Genrich) peak-calling software. Briefly, a consensus peakset was derived for each treatment group by performing individual peak calling on each treatment representative and then merging the overlapping peak regions that meet the significance criteria when examined through the Fisher's combined probability test. Peak calling parameters specified in the terminal command included a false discovery rate (FDR) adjusted p-value significance threshold of 0.05 (-q 0.05), a minimum peak length of 200 bp (-l 200), and a designation for peak calling to occur in the optimized ATAC-Seq processing mode (-j). Two separate ./Genrich command calls on the set of control BAM files and the set of CHI3L1-treated BAM files, respectively, resulted in two narrowPeak files, one for each biological condition being interrogated.
ATAC-Seq data analyses in this investigation were performed in the R programming language, version 3.6.1 (https://www.R-project.org/). The processing of the narrowPeak files into a computationally manageable GRanges object was done using the readPeakFile function in the “ChIPSeeker” library. Biological annotation of the fragment reads was conducted through the annotatePeak function and with respect to annotated transcripts from the “TxDb.Hsapiens.UCSC.hg38.knownGene” database. Visualization of peak densities around biologically relevant transcription start sites (TSS) was accomplished using the plotAvgProf2 function.
To perform statistically meaningful comparisons between treatment groups in order to identify differentially accessible chromatin regions, a consensus peak set between the two groups had to first be determined. This was done by writing a modified script of the publicly available runConsensusRegions function in order to account for personal filtering and overlapping peak considerations. Sequence read counts of each peak range in the consensus peakset for each sample were calculated via the featureCounts function in the “Subread” package. The resulting counts matrix was then converted into a DESeq data set and normalized via Median-by-Ratio Normalization for differential chromatin accessibility analysis by DESeq2 (Love et al., 2014). Comparisons for differential peak enrichment and extracted results were made on the basis of treatment condition (CTRL vs. CHI3L1), and differentially accessible chromatin regions were defined as peak regions with a normalized count fold change greater than 1.5 and a p-value smaller than 0.05. To identify differentially accessible promoter regions, promoter sequences were first defined as the genomic ranges within 3000 bp upstream and downstream of a TSS in the hg38 reference genome. The differentially accessible regions that overlapped with the predefined promoter regions were queried and further labeled as differentially accessible promoter sites. Determining genes associated with differentially accessible chromatin regions was done through a many-to-many mapping algorithm implemented in the seq2gene function where a peak sequence range that overlaps within a predefined search radius of a promoter will then be functionally associated with the set of genes regulated by that promoter. The promoter in this case was set to be 1000 bp upstream and downstream of a TSS, and the flanking radius to search beyond the promoter was 3000 bp upstream and downstream. Genes were returned with their Entrez ID labels, which could then be converted into their respective HGNC gene symbol via the getSYMBOL function in Bioconductor.
The identification of enriched transcription binding motifs within promoter regions using hypergeometric enrichment calculations was performed using the HOMER motif analysis package, specifically the findMotifsGenome.pl program. The following parameters were used for the determination of enriched motifs: “hg38 -len 8,10,12 -mask -size given”, meaning motifs as defined by the hg38 genome with a length of 8, 10, or 12 bp were interrogated throughout the entire range of the peak region with repeat-masking to determine whether a given motif was overrepresented in the provided promoter region. Both de novo and known motif enrichment results were considered for further downstream analysis of transcription factor binding activity.
Determination of the specific fragment/tag densities at promoter regions was also made possible through HOMER via their makeTagDirectory.pl and annotatePeaks.pl programs. First, a tag directory from the previously mentioned BAM files and its unique narrowPeak file had to be constructed using the makeTagDirectory.pl function call. Next the annotatePeaks.pl function with the -hist parameter was executed to quantify the density of sequence reads within 1000 bp upstream and downstream of the center of the promoter peak.
Genome_build: GRCh38/hg38 human reference genome
Supplementary_files_format_and_content: .narrowPeak

source_name: Glioma stem cells + CHI3L1

extract_protocol:
ATAC-seq libraries were prepared according to the protocol established and optimized before (Ackermann et al., 2016; Buenrostro et al., 2013). Specifically, collected cell samples with low viability (<85%) were first treated with 200 U/ml DNase (Worthington) for 30 minutes at 37°C for 30 minutes, followed immediately by thorough washing to remove residual DNase.
Cell lysis was performed using 50 ul of cold lysis buffer composed of resuspension buffer, 0.1% NP-40, 0.1% Tween-20, and 0.01% Digitonin (Promega), and transposition of the resulting nuclei pellet from the lysate by Tn5 transposase was accomplished using the Nextera DNA Library Prep Kit (Illumina). DNA isolation from the transposition reaction was done using MinElute Reaction Cleanup Kit (Qiagen), and the library was generated from the isolated DNA through PCR amplification protocol. Purification of the library for optimal library preparation included removal of primer dimers and DNA fragments larger than 1000 base pairs (bp) through double-sided bead purification with Agencourt AMPure XP beads (Beckman Coulter). Sequencing of the final library was performed by GENEWIZ using the Illumina HiSeq 2500 system to ideally identify and record 150 bp paired-end fragment read occurrences in the resulting FASTQ file for each technical replicate.

value: Treated with 200 ng recCHI3L1


title: Pilote_Gen3G-Plasma-T1-PubM2130


title: Control glioma stem cells rep2

source_name: Control glioma stem cells

value: Untreated


title: Control glioma stem cells rep1


title: Projet_Gen3G-Plasma-V1-PubM2875


title: Projet_Gen3G-Plasma-V1-PubM2872


title: Projet_Gen3G-Plasma-V1-PubM2864


title: Projet_Gen3G-Plasma-V1-PubM2876


title: Projet_Gen3G-Plasma-V1-PubM2865


title: CG3: siRNA-MAZ-1 + Chi3l1 incubation


title: Projet_Gen3G-Plasma-V1-PubM2863


title: Pilote_Gen3G-Plasma-T1-PubM2012


title: P_C_B

city: San Francisco

first: Hanbing

last: Song

address: 513 Parnassus Ave.

institute: UCSF

data_processing:
Alignment and transcriptome profling via Kalliso
Assembly: hg19
Supplementary files format and content: .tsv file of gene-level read counts and tpm

source_name: Prostate epithelial cell line

extract_protocol:
Qiagen RNA extraction Kit (RNeasy)
This was performed by Novogene (https://en.novogene.com/services/research-services/transcriptome-sequencing/mrna-sequencing/?gclid=EAIaIQobChMInNezm_nx-gIVZgetBh1GEwnSEAAYASAAEgK57PD_BwE).

value: CIC KO

tag: disease

value: prostate

tag: cell line


title: Projet_Gen3G-Plasma-V1-PubM2861


title: P_EC_A

value: CIC-ERF codeletion


title: P_C_A


title: P_A


title: Projet_Gen3G-Plasma-V1-PubM2843


title: Projet_Gen3G-Plasma-V1-PubM2850


title: Projet_Gen3G-Plasma-V1-PubM2845


title: Projet_Gen3G-Plasma-V1-PubM2862


title: Projet_Gen3G-Plasma-V1-PubM2844


title: Glioma stem cells + CHI3L1 rep2

tag: treatment

value: Treated with 400 ng recCHI3L1


title: Projet_Gen3G-Plasma-V1-PubM2842


title: P_EC_B


title: P_E_B

value: ERF KD


title: Projet_Gen3G-Plasma-V1-PubM2871

value: plasma


title: P_E_A


title: P_B

value: WT


title: Projet_Gen3G-Plasma-V1-PubM2840

value: female

value: Normal


title: Projet_Gen3G-Plasma-V1-PubM2822


title: Projet_Gen3G-Plasma-V1-PubM2831


title: Projet_Gen3G-Plasma-V1-PubM2847


title: 140054

description: Gene expression data from nasal brushing of subject 140054.

value: Male

tag: smoking status

value: Former smoker

tag: fev1 % predicted

tag: cancer status

value: Cancer


title: Projet_Gen3G-Plasma-V1-PubM2827


title: Projet_Gen3G-Plasma-V1-PubM2811


title: Projet_Gen3G-Plasma-V1-PubM2818

value: Gestational diabetes mellitus


title: Projet_Gen3G-Plasma-V1-PubM2812


title: Projet_Gen3G-Plasma-V1-PubM2801


title: Projet_Gen3G-Plasma-V1-PubM2829


title: Projet_Gen3G-Plasma-V1-PubM2796


title: Projet_Gen3G-Plasma-V1-PubM2815


title: Projet_Gen3G-Plasma-V1-PubM2816


title: Projet_Gen3G-Plasma-V1-PubM2806

value: Other pregnancy complications


title: Projet_Gen3G-Plasma-V1-PubM2793

value: technical replicate


title: Projet_Gen3G-Plasma-V1-PubM2788


title: Projet_Gen3G-Plasma-V1-PubM2804


title: Projet_Gen3G-Plasma-V1-PubM2790


title: Projet_Gen3G-Plasma-V1-PubM2807


title: Projet_Gen3G-Plasma-V1-PubM2833


title: Projet_Gen3G-Plasma-V1-PubM2785


title: Projet_Gen3G-Plasma-V1-PubM2783


title: Projet_Gen3G-Plasma-V1-PubM2774


title: Projet_Gen3G-Plasma-V1-PubM2776


title: Projet_Gen3G-Plasma-V1-PubM2777


title: Projet_Gen3G-Plasma-V1-PubM2765


title: Projet_Gen3G-Plasma-V1-PubM2770


title: Projet_Gen3G-Plasma-V1-PubM2768


title: Projet_Gen3G-Plasma-V1-PubM2760


title: Projet_Gen3G-Plasma-V1-PubM2751


title: Projet_Gen3G-Plasma-V1-PubM2752


title: Projet_Gen3G-Plasma-V1-PubM2754


title: Projet_Gen3G-Plasma-V1-PubM2749


title: Projet_Gen3G-Plasma-V1-PubM2750


title: Projet_Gen3G-Plasma-V1-PubM2740


title: Projet_Gen3G-Plasma-V1-PubM2737


title: Projet_Gen3G-Plasma-V1-PubM2748


title: Projet_Gen3G-Plasma-V1-PubM2736


title: Projet_Gen3G-Plasma-V1-PubM2747


title: Projet_Gen3G-Plasma-V1-PubM2716


title: Projet_Gen3G-Plasma-V1-PubM2721


title: Projet_Gen3G-Plasma-V1-PubM2728


title: Projet_Gen3G-Plasma-V1-PubM2714


title: Projet_Gen3G-Plasma-V1-PubM2713


title: Projet_Gen3G-Plasma-V1-PubM2769


title: Projet_Gen3G-Plasma-V1-PubM2707


title: Projet_Gen3G-Plasma-V1-PubM2700


title: Projet_Gen3G-Plasma-V1-PubM2706


title: Projet_Gen3G-Plasma-V1-PubM2745


title: Projet_Gen3G-Plasma-V1-PubM2692


title: Projet_Gen3G-Plasma-V1-PubM2687


title: Projet_Gen3G-Plasma-V1-PubM2723


title: Projet_Gen3G-Plasma-V1-PubM2689


title: Projet_Gen3G-Plasma-V1-PubM2741


title: Projet_Gen3G-Plasma-V1-PubM2685


title: Projet_Gen3G-Plasma-V1-PubM2735


title: Projet_Gen3G-Plasma-V1-PubM2715


title: Projet_Gen3G-Plasma-V1-PubM2674


title: Projet_Gen3G-Plasma-V1-PubM2678


title: Projet_Gen3G-Plasma-V1-PubM2670


title: Projet_Gen3G-Plasma-V1-PubM2671


title: Projet_Gen3G-Plasma-V1-PubM2681


title: Projet_Gen3G-Plasma-V1-PubM2669


title: Projet_Gen3G-Plasma-V1-PubM2666


title: Projet_Gen3G-Plasma-V1-PubM2709


title: Projet_Gen3G-Plasma-V1-PubM2664


title: Projet_Gen3G-Plasma-V1-PubM2662


title: Projet_Gen3G-Plasma-V1-PubM2657


title: Projet_Gen3G-Plasma-V1-PubM2653


title: Projet_Gen3G-Plasma-V1-PubM2655


title: Projet_Gen3G-Plasma-V1-PubM2661


title: Projet_Gen3G-Plasma-V1-PubM2649


title: Projet_Gen3G-Plasma-V1-PubM2646


title: Projet_Gen3G-Plasma-V1-PubM2648


title: Projet_Gen3G-Plasma-V1-PubM2643


title: Projet_Gen3G-Plasma-V1-PubM2644


title: Projet_Gen3G-Plasma-V1-PubM2632


title: Projet_Gen3G-Plasma-V1-PubM2630


title: Projet_Gen3G-Plasma-V1-PubM2622


title: Projet_Gen3G-Plasma-V1-PubM2621


title: Projet_Gen3G-Plasma-V1-PubM2616


title: Projet_Gen3G-Plasma-V1-PubM2633


title: Projet_Gen3G-Plasma-V1-PubM2614


title: Projet_Gen3G-Plasma-V1-PubM2610


title: Projet_Gen3G-Plasma-V1-PubM2602


title: Projet_Gen3G-Plasma-V1-PubM2603


title: Projet_Gen3G-Plasma-V1-PubM2601


title: Projet_Gen3G-Plasma-V1-PubM2619


title: Projet_Gen3G-Plasma-V1-PubM2590


title: Projet_Gen3G-Plasma-V1-PubM2605


title: Projet_Gen3G-Plasma-V1-PubM2612


title: Projet_Gen3G-Plasma-V1-PubM2585


title: Projet_Gen3G-Plasma-V1-PubM2586


title: Projet_Gen3G-Plasma-V1-PubM2599


title: Projet_Gen3G-Plasma-V1-PubM2581


title: Projet_Gen3G-Plasma-V1-PubM2578


title: Projet_Gen3G-Plasma-V1-PubM2583


title: Projet_Gen3G-Plasma-V1-PubM2638


title: Projet_Gen3G-Plasma-V1-PubM2575


title: Projet_Gen3G-Plasma-V1-PubM2573


title: Projet_Gen3G-Plasma-V1-PubM2571


title: Projet_Gen3G-Plasma-V1-PubM2572


title: Projet_Gen3G-Plasma-V1-PubM2552


title: Projet_Gen3G-Plasma-V1-PubM2561


title: Projet_Gen3G-Plasma-V1-PubM2568


title: Projet_Gen3G-Plasma-V1-PubM2562


title: Projet_Gen3G-Plasma-V1-PubM2551


title: Projet_Gen3G-Plasma-V1-PubM2576


title: Projet_Gen3G-Plasma-V1-PubM2546


title: Projet_Gen3G-Plasma-V1-PubM2542


title: Projet_Gen3G-Plasma-V1-PubM2560


title: Projet_Gen3G-Plasma-V1-PubM2541


title: Projet_Gen3G-Plasma-V1-PubM2521


title: Projet_Gen3G-Plasma-V1-PubM2539


title: Projet_Gen3G-Plasma-V1-PubM2524


title: Projet_Gen3G-Plasma-V1-PubM2519


title: Projet_Gen3G-Plasma-V1-PubM2526


title: Projet_Gen3G-Plasma-V1-PubM2514


title: Projet_Gen3G-Plasma-V1-PubM2518


title: Projet_Gen3G-Plasma-V1-PubM2523


title: Projet_Gen3G-Plasma-V1-PubM2511


title: Projet_Gen3G-Plasma-V1-PubM2507


title: Projet_Gen3G-Plasma-V1-PubM2510


title: Projet_Gen3G-Plasma-V1-PubM2506


title: Projet_Gen3G-Plasma-V1-PubM2540


title: Projet_Gen3G-Plasma-V1-PubM2505


title: Projet_Gen3G-Plasma-V1-PubM2503


title: Projet_Gen3G-Plasma-V1-PubM2502


title: Projet_Gen3G-Plasma-V1-PubM2477


title: Projet_Gen3G-Plasma-V1-PubM2582


title: Projet_Gen3G-Plasma-V1-PubM2491


title: Projet_Gen3G-Plasma-V1-PubM2494


title: Projet_Gen3G-Plasma-V1-PubM2474


title: Projet_Gen3G-Plasma-V1-PubM2490


title: Projet_Gen3G-Plasma-V1-PubM2487


title: Projet_Gen3G-Plasma-V1-PubM2486


title: Projet_Gen3G-Plasma-V1-PubM2469


title: Projet_Gen3G-Plasma-V1-PubM2471


title: Projet_Gen3G-Plasma-V1-PubM2489


title: Projet_Gen3G-Plasma-V1-PubM2466


title: Projet_Gen3G-Plasma-V1-PubM2465


title: Projet_Gen3G-Plasma-V1-PubM2464


title: Projet_Gen3G-Plasma-V1-PubM2461


title: Projet_Gen3G-Plasma-V1-PubM2459


title: Projet_Gen3G-Plasma-V1-PubM2463


title: Projet_Gen3G-Plasma-V1-PubM2500


title: 25__37_S25

city: Münster

first: Marisol

last: Herrera-Rivero

state: NRW

address: Albert-Schweitzer-Campus 1

country: Germany

institute: University of Münster

description:
n.a.
22DLR

data_processing:
Data was automatically demultiplexed using the Illumina bcl2fastq2 Conversion Software v2.20
FastQ files underwent two rounds of quality control, pre-trimming and post-alignment, using FastQC v0.11.7
Removal of Illumina adapters and low-quality sequences was performed with Trimmomatic v0.38. Reads of length<15 bases, as well as leading and/or trailing bases with quality< 3 or no base call, and bases with average quality<15 in a 4-base sliding window were removed
Alignment was performed with HISAT2 v2.1.0 [29] using the mouse genome assembly mm10 (Mus musculus, GRCm38)
Mapped reads (primary alignments) were sorted by read name using SAMtools v1.8 and read counts were calculated with HTSeq v0.11.2
Assembly: mm10
Supplementary files format and content: Raw counts

molecule: polyA RNA

source_name: posterior amygdala

extract_protocol:
Total RNA was isolated using the RNeasy Micro Kit (Qiagen), followed by a DNase digestion step.
Library preparation was carried out upon mRNA enrichment with the NEBNext Single Cell/Low Input RNA Library Prep Kit for Illumina (New England BioLabs). Single read sequencing took place on a NextSeq 2000 System (Illumina), using the corresponding NextSeq 2000 P3 v3 chemistry, with a read length of 72 base pairs.

treatment_protocol: To test for an effect of genotype and environment on emotional cognitive bias in mice, we used a two-by-two full factorial design, where mice from both strains (C57BL/6J and B6D2F1N) were randomly assigned to either standard or enriched (with access to a playground 1h per day) housing conditions. Therefore, four experimental groups were included in the study. The environmental treatment commenced on the post-natal day (PND) 77 and continued until the end of the experiment. Emotional cognitive bias was assessed using an active choice (Go/Go-task) cognitive judgement bias (CJB) test. As the CJB test requires prior discrimination training, we began training the animals on PND 70. Training duration, though, was dependent on the learning speed of each mouse (37-90 days). Performing the CJB test itself took five days. Five mice that did not fulfil the learning criterion were excluded. Therefore, 19 mice that completed the CBJ test were sacrificed to dissect the anterior and posterior portions of the amygdala for transcriptome analyses

value: posterior amygdala

value: enriched environment


title: 29__21_S29

description:
n.a.
12CL


title: Projet_Gen3G-Plasma-V1-PubM2481


title: 16__17_S16

description:
n.a.
13BR


title: Projet_Gen3G-Plasma-V1-PubM2452


title: 23__13_S23

description:
n.a.
23BLR


title: Projet_Gen3G-Plasma-V1-PubM2449


title: Projet_Gen3G-Plasma-V1-PubM2448


title: Projet_Gen3G-Plasma-V1-PubM2446


title: Projet_Gen3G-Plasma-V1-PubM2440


title: Projet_Gen3G-Plasma-V1-PubM2434


title: Th17 cells, +IL1B, Replicate 2

city: Jena

first: Alberto

last: Garcia Lopez

state: Thuringia

address: Adolf-Reichwein-Straße 23

department: Microbiome Dynamics

institute: Leibniz Institute for Natural Product Research and Infection Biology Hans Knöll Institute

hyb_protocol: Affymetrix protocol.

scan_protocol: Arrays were scanned with an Affymetrix GeneChip Scanner 3000, using the GCOS software version 1.4 from Affymetrix.

data_processing: For quality control data were analyzed using the GeneChip Operating Software (GCOS, Affymetrix), version 1.4. Quality checks were performed according to the manufacturer's recommendations. Gene expression was quantified by RMA using affy R package.

label: Biotin

source_name: Th17 cells

label_protocol: Labeling and hybridization of total RNA to HG-U133_Plus_2  GeneChips was performed using the whole-transcriptome pico KIT from Affymetrix according to the manufacturer's instruction. Hybridization was performed in a Hybridization Oven 640, and chips were washed and stained in the Fluidics Station 400 (both Affymetrix).

extract_protocol: Total RNA was extracted using the RNeasy Micro Kit (Qiagen) according to the manufacturer’s instruction, including the recommended DNase digest. The purity and integrity of RNA were assessed for each sample using an Agilent 2100 Bioanalyzer with the RNA 6000 Nano LabChip and amount was checked with a NanoDrop ND-1000 spectrophotometer. Contaminating genomic DNA was removed by an on-column DNA digestion step (Qiagen).

tag: condition

tag: cell type


title: Th17 cells, +IL1B, Replicate 1


title: Th17 cells, -IL1B, Replicate 2


title: 34__8_S34

description:
optimist
21DL

tag: tissue

value: control environment


title: 13__29_S13

description:
optimist
22ALR


title: Projet_Gen3G-Plasma-V1-PubM2430


title: 11__31_S11

description:
optimist
23AR


title: Projet_Gen3G-Plasma-V1-PubM2454


title: Th17 cells, -IL1B, Replicate 3


title: 35__4_S35

description:
n.a.
11CR


title: Th17 cells, +IL1B, Replicate 3


title: Projet_Gen3G-Plasma-V1-PubM2426


title: Projet_Gen3G-Plasma-V1-PubM2423


title: 22__18_S22

description:
pessimist
12BL


title: 31__10_S31

description:
n.a.
13CR


title: 36__11_S36

description:
pessimist
11AL


title: Projet_Gen3G-Plasma-V1-PubM2421


title: 12__23_S12

description:
pessimist
11DL


title: Projet_Gen3G-Plasma-V1-PubM2424


title: Projet_Gen3G-Plasma-V1-PubM2418


title: 06__6_S6

description:
n.a.
12DL


title: 24__7_S24

description:
pessimist
21BL


title: 32__14_S32

description:
pessimist
21CL


title: 15__27_S15

description:
optimist
21AL


title: Projet_Gen3G-Plasma-V1-PubM2411


title: Projet_Gen3G-Plasma-V1-PubM2444


title: 09__35_S9

description:
n.a.
12AL


title: Th17 cells, -IL1B, Replicate 1


title: Projet_Gen3G-Plasma-V1-PubM2404


title: Projet_Gen3G-Plasma-V1-PubM2409


title: 07__33_S7

description:
n.a.
23DR


title: 03__36_S3

description:
n.a.
22DLR

source_name: anterior amygdala

value: anterior amygdala


title: Projet_Gen3G-Plasma-V1-PubM2399


title: Projet_Gen3G-Plasma-V1-PubM2401


title: 27__16_S27

description:
n.a.
13BR


title: 10__25_S10

description:
n.a.
13DR


title: Projet_Gen3G-Plasma-V1-PubM2396


title: Projet_Gen3G-Plasma-V1-PubM2391


title: 18__30_S18

description:
optimist
23AR


title: 02__12_S2

description:
n.a.
23BLR


title: 04__22_S4

description:
pessimist
11DL


title: Projet_Gen3G-Plasma-V1-PubM2383


title: Projet_Gen3G-Plasma-V1-PubM2388


title: 21__28_S21

description:
optimist
22ALR


title: Projet_Gen3G-Plasma-V1-PubM2389


title: 14__20_S14

description:
pessimist
12BL


title: Projet_Gen3G-Plasma-V1-PubM2387


title: 26__5_S26

description:
n.a.
12DL


title: Projet_Gen3G-Plasma-V1-PubM2382


title: 33__15_S33

description:
pessimist
21CL


title: Projet_Gen3G-Plasma-V1-PubM2381


title: 20__26_S20

description:
optimist
21AL


title: Projet_Gen3G-Plasma-V1-PubM2376


title: Projet_Gen3G-Plasma-V1-PubM2380


title: Projet_Gen3G-Plasma-V1-PubM2368


title: Projet_Gen3G-Plasma-V1-PubM2416


title: 17__34_S17

description:
n.a.
12AL


title: Projet_Gen3G-Plasma-V1-PubM2392


title: Projet_Gen3G-Plasma-V1-PubM2369


title: 37__2_S37

description:
pessimist
21BL


title: 05__24_S5

description:
n.a.
13DR


title: 19__32_S19

description:
n.a.
23DR


title: Projet_Gen3G-Plasma-V1-PubM2379


title: Projet_Gen3G-Plasma-V1-PubM2367


title: 30__1_S30

description:
optimist
21DL


title: 28__3_S28

description:
n.a.
11CR


title: PT91_F_27w6d [SU0091_15_11]

city: Sheffield

first: Khondoker

middle: Mehedi

last: Akram

state: South Yorkshire

address: Tree Root Walk

department: Oncology and Metabolism

institute: University of Sheffield

data_processing:
Sequencing data were demultiplexed by guppy v0.3.0, base calling software (ONT).
Reads quality assessment was done by pycoQC v2.5.2 tool. The average PHRED quality of reads were between 10-11. Any PHRED quality score that fell below 8 was not considered for subsequent data analysis.
The adaptors were trimmed using Porechop v0.2.3 (ONT).
The filtered reads were then mapped to the reference sequence of the human genome (hg38) using minimap2- 2.17-r941.
Differential gene expression analysis was conducted using the R packages (version 3.6.0) and Galaxy platform by limma and edgeR methods.
Assembly: hg38
Supplementary files format and content: Tab-delimited text files include normalised counts matrix files (output from edgeR and limma) that contain all features (genes) for all samples in a single file.
Supplementary files format and content: Tab-delimited text files contain DEGs with LogFC, average expression values and FDR or adj.P.Val

source_name: placenta

extract_protocol:
Total RNA was extracted from the villous tissue samples using RNeasy Plus Mini Kit (QIAgen, Cat No- 74134), following the manufacturer’s instruction. Briefly, 35 mg of frozen tissue was lysed in RLT Lysis buffer using a TissueLyser LT homogeniser (Qiagen, Cat No- 85600) for 10 min at 50 Hz. Genomic DNA was removed using a gDNA eliminator spin column. The quality and quantity of the yield RNA was checked using Nanodrop ND1000, Qubit RNA HS Assay Kit (ThermoFisher, Cat No- Q32852) and Agilent 6000 Nano kit (Agilent, Cat No- 5067-1511). All RNA samples were stored in -80 degree C prior to library preparation.
Sequencing libraries were prepared using the Oxford Nanopore Technologies (ONT) PCR-cDNA Barcoding Kit (Oxford Nanopore, Cat No- SQK-PCB109). 50 ng of total RNA from each sample was used for library preparation.

value: placenta

tag: tissue type

value: fresh villous tissue

value: Preterm

value: No treatment

tag: fetus

value: Female, 27 wks 6 days GA


title: PT92_M_29w5d [SU0092_16_12]

value: Male, 29 wks 5 days GA


title: Projet_Gen3G-Plasma-V1-PubM2362

value: plasma

value: female


title: Projet_Gen3G-Plasma-V1-PubM2393

value: Normal


title: PT71_M_36w5d [SU0071_13_9]

value: Male, 36 wks 5 days GA


title: T64_F_40w6d [SU0064_12_8]

value: Term

value: Female, 40 wks 6 days GA


title: Projet_Gen3G-Plasma-V1-PubM2363


title: T60_M_40w [SU0060_11_7]

value: Male, 40 wks GA


title: Projet_Gen3G-Plasma-V1-PubM2360


title: T89_F_41w [SU0089_14_10]

value: Female, 41 wks GA


title: Projet_Gen3G-Plasma-V1-PubM2350


title: T59_M_40w3d [SU0059_10_6]

value: Male, 40 wks 3 days GA


title: PT58_F_33w4d [SU0058_9_5]

value: Female, 33 wks 4 days GA


title: Projet_Gen3G-Plasma-V1-PubM2348


title: Projet_Gen3G-Plasma-V1-PubM2347


title: PT53_M_35w4d [SU0053_7_7]

value: Male, 35 wks 4 days GA


title: T54_F_41w [SU0054_8_8]

value: placenta


title: Projet_Gen3G-Plasma-V1-PubM2342


title: Projet_Gen3G-Plasma-V1-PubM2337

value: technical replicate


title: Projet_Gen3G-Plasma-V1-PubM2329


title: Projet_Gen3G-Plasma-V1-PubM2331

value: Gestational diabetes mellitus


title: PT47_M_36w3d [SU0047_5_5]

value: fresh villous tissue

value: Preterm

value: No treatment

value: Male, 36 wks 3 days GA


title: T44_M_38w1d [SU0044_3_3]

value: Male, 38 wks 1 days GA


title: Projet_Gen3G-Plasma-V1-PubM2333

value: plasma

value: female

value: Normal


title: T50_M_39w1d [SU0050_6_6]

value: Term

value: Male, 39 wks 1 day GA


title: Projet_Gen3G-Plasma-V1-PubM2365


title: Projet_Gen3G-Plasma-V1-PubM2327


title: suc-WT-29-2

first: Jacob

last: Gibson

address: 25 Shattuck St

institute: Harvard University

data_processing:
Quality control and adapter trimming was performed with bcl2fastq 2.20.0.445
Read mapping was performed with HISAT2 2.2.0
Read quantification was performed using Subread’s featureCounts functionality 2.0.1
Read counts loaded into R (4.0.2) and were normalized using edgeR’s Trimmed Mean of M values (TMM) algorithm.  Subsequent values were then converted to counts per million (cpm).
Differential expression analysis was performed using edgeR’s Quasi-Linear F-Test (qlfTest) functionality against treatment groups (v1.15.5)
Assembly: Vibrio cholerae N16961

organism: Vibrio cholerae

growth_protocol: Grown to midlog in LB then resuspended in defined medium supplemented with sucrose for 2 hours

extract_protocol:
Cell pelletes were dissolved in trizol and RNA was extracted with  Direct-zol RNA Miniprep kit (Zymo ZR2052) according to their instructions.
RNA-seq libraries were constructed and sequenced by the Microbial Genome Sequencing Center (Pittsburgh, PA).

tag: strain

tag: genotype

value: WT


title: T43_M_39w4d [SU0043_2_2]

value: Male, 39 wks 4 days GA


title: suc-WT-29-1


title: Projet_Gen3G-Plasma-V1-PubM2325

tag: Sex


title: suc-dPepA-273-3

value: delta-pepA


title: PT41_F_36w1d [SU0041_1_1]

value: Female, 36 wks 1 day GA


title: PT49_M_29w [SU0049_BC12_pt]

value: placenta

value: Male, 29 wks GA


title: suc-dPepA-273-1


title: suc-dCRPdPepA-277-3

value: delta-crp delta-pepA


title: suc-WT-29-3


title: suc-dPepA-273-2


title: Projet_Gen3G-Plasma-V1-PubM2322

tag: pregnancy status_1


title: Projet_Gen3G-Plasma-V1-PubM2324

value: Other pregnancy complications


title: suc-dCRPdPepA-277-1


title: suc-dCRPdPepA-277-2


title: PT46_M_24w [SU0046_BC11_pt]

value: fresh villous tissue

value: Preterm

value: Male, 24 wks GA


title: Projet_Gen3G-Plasma-V1-PubM2320


title: PT45_M_33w1d [SU0045_4_4]

value: No treatment

value: Male, 33 wks 1 day GA


title: PT36_F_33w1d [SU0036_BC08_pt]

value: Female, 33 wks 1 day GA


title: Projet_Gen3G-Plasma-V1-PubM2319

value: plasma

value: female

value: Normal


title: suc-dCRP-44-2

value: delta-crp


title: T42_M_37w3d [SU0042_BC10_tt]

value: Term

value: Male, 37 wks 3 days GA


title: suc-dCRP-44-1


title: T40_F_39w5d [SU0040_BC09_tt]

value: Female, 39 wks 5 days GA


title: Mock, rep1

data_processing:
Paired end reads were mapped to Vibrio cholerae N16961 reference genome using Bowtie2 (version 2.4.1). An in-silico size selection was performed to select reads that were 400 bp or shorter.
QuEST (version 2.424) was used to identify putative DNA binding sites defined as regions with >2-fold enrichment over background from an untagged mock sample (KDE: 45; region: 500; enrichment: 2; seed value: 1.125; extend value: 1.5; Peak shift when needed:100)
Assembly: Vibrio cholerae N16961
Supplementary files format and content: bigwig
Supplementary files format and content: tsv file with putative binding regions

extract_protocol:
Cells were fixed with 1% formaldehyde for 15 minutes and quenched with 500 mM glycine for 15 mintues. Cells were lysed and chromatin were sheared by sonication  (Sonic Dismembrator Model F60, Fisher Scientific). Proteins and bound DNA were purifed with Anti-V5 sepharose beads (A7345, Sigma).
Libraries were prepared using NEBNext Ultra DNA Library Prep Kit for Illumina (NEB, E7645S) according to manufactruers protocol. Libraries underwent 10 rounds of amplification without size selection.

value: WT

tag: chip antibody

value: V5 Tag antibody (GenScript, A01724)


title: Mock, rep2


title: PepA, rep3


title: PT34_F_35w [SU0034_BC07_pt]

value: placenta

value: Female, 35 wks GA


title: PepA, rep2


title: Projet_Gen3G-Plasma-V1-PubM2312

value: Other pregnancy complications


title: dPepA_CRP, rep3

value: delta-pepA, crp-V5


title: dPepA_CRP, rep2


title: T33_F_37w6d [SU0033_BC06_tt]

value: fresh villous tissue

value: Female, 37 wks 6 days GA


title: Projet_Gen3G-Plasma-V1-PubM2308


title: suc-dCRP-44-3


title: Projet_Gen3G-Plasma-V1-PubM2307


title: Mock, rep3


title: Projet_Gen3G-Plasma-V1-PubM2306


title: dCRP_PepA, rep1

value: delta-crp, pepA-V5


title: Projet_Gen3G-Plasma-V1-PubM2314


title: dCRP_PepA, rep2


title: T24_M_39w6d [SU0024_BC03_tt]

value: No treatment

value: Male, 39 wks 6 days GA


title: CRP, rep3


title: PepA, rep1


title: Projet_Gen3G-Plasma-V1-PubM2301

value: plasma

value: female


title: IVT_ZBED5

city: Chicago

first: Shun

last: Liu

state: IL

address: 929 E. 57th. Street

department: Chemistry

institute: University of Chicago

description: site specific m6A quantification

data_processing:
For site-specific m6A quantification by amplicon deep sequencing, raw next-generation sequencing data were merged by Pear v0.9.8. before mapping to the target sequences using bwa-mem2 v2.2.1. Mapped reads were sorted and indexed using samtools v1.14. Bases mapped to individual A sites were counted using pysamstats v1.1.1. A and G counts were extracted for individual A sites covered by R2 using re.finditer. Methylation levels are reported as apparent A fractions. For site-specific m6A quantification by eTAM-Sanger, the A and G fractions observed at all A sites were quantified by EditR. Methylation levels are reported as apparent A fractions.
Assembly: hg38
Supplementary files format and content: individual transcripts with site specific m6A quantificaton in the XLSX format

growth_protocol: HeLa cell line was grown in DMEM (Gibco, 11965092) media supplemented with 10% FBS (Gibco) and 1% 100× Pen/Strep (Gibco). All cells were cultured at 37°C under 5.0% CO2.

extract_protocol:
Purified HeLa poly A+ RNA (300 ng) was depleted of poly A tails, end-repaired, ligated to 3’ adapters and immobilized on Dynabeads MyOne Streptavidin C1 (Invitrogen) as described in eTAM-seq library preparation. The RNA was deaminated and reverse transcribed following the same protocol for NGS library construction. The beads were washed by resuspension in 0.1% PBST (v/v), 1x Binding/Wash buffer, and twice in 10 mM Tris HCl, pH 7.5, consecutively. cDNA was eluted by boiling the beads in DNase-free water (Invitrogen) and transferred into new tubes immediately. PCR amplification using transcript-specific primers was performed using the eluted cDNA. To demonstrate m6A quantification with limited input, the same protocol was applied to 50 ng, 5 ng, or 5 ng of HeLa total RNA. The resulting cDNA was split into two halves to amply ACTB and EIF2A fragments.
Both rounds of PCR were set up using EvaGreen qPCR Master Mix. 1st round PCR was carried out at a 20 uL scale with cDNA generated from different amounts of mRNA or total RNA, and 0.5 uM forward and reverse primers. Primers were designed to recognize sequences post deamination, leaving out 10-20 nt sequences surrounding the target m6A sites. PCR reactions were analyzed by agarose gel electrophoresis. 1 uL of PCR products were subjected to enzymatic cleanup (Exonuclease I and Shrimp Alkaline Phosphatase, New England BioLabs, M0293 and M0371) and Sanger sequencing. Gel purification was performed for PCR reactions that did not yield bright and single bands. 2nd round PCR was carried out at a 20 uL scale with 1 uL of the 1st round PCR reaction as template, 0.5 uM specified Illumina P7 and P5 index primer pairs. Barcoded PCR reactions were combined and gel purified using QIAquick Gel Extraction Kit (Qiagen, 28706) before being subjected to next-generation sequencing on an Illumina MiSeq Instrument.

value: HeLa

tag: library type

value: in vitro transcribed RNA


title: dCRP_PepA, rep3


title: CRP, rep1


title: T02_F_37w5d [SU0002_BC01_tt]

value: Term

value: Female, 37 wks 5 days GA


title: CRP, rep2


title: IVT_TPX2

description: site specific m6A quantification


title: T32_F_41w1d [SU0032_BC05_tt]

value: Female, 41 wks 1 day GA


title: Projet_Gen3G-Plasma-V1-PubM2300

value: Normal


title: dPepA_CRP, rep1

value: V5 Tag antibody (GenScript, A01724)


title: T35_F_38w2d [SU0035_12_tt]

value: placenta

value: Female, 38 wks 2 days GA


title: PT29_F_36w2d [SU0029_11_pt]

value: Preterm

value: Female, 36 wks 2 days GA


title: IVT_TPT1

description: site specific m6A quantification


title: Projet_Gen3G-Plasma-V1-PubM2298


title: Projet_Gen3G-Plasma-V1-PubM2294


title: PT30_F_36w3d [SU0030_BC04_pt]

value: fresh villous tissue

value: Female, 36 wks 3 days GA


title: IVT_OGT

description: site specific m6A quantification


title: IVT_MYC

description: site specific m6A quantification


title: PT26_M_24w4d [SU0026_10_pt]

value: No treatment

value: Male, 24 wks 4 days GA


title: Projet_Gen3G-Plasma-V1-PubM2292

value: plasma

value: Other pregnancy complications


title: Projet_Gen3G-Plasma-V1-PubM2302

value: female


title: PT25_M_33w3d [SU0025_9_pt]

value: Male, 33 wks 3 days GA


title: IVT_MALAT1

description: site specific m6A quantification

value: HeLa

value: in vitro transcribed RNA


title: Projet_Gen3G-Plasma-V1-PubM2288


title: IVT_EIF2A

description: site specific m6A quantification


title: T22_M_38w5d [SU0022_8_tt]

value: Term

value: Male, 38 wks 5 days GA


title: Projet_Gen3G-Plasma-V1-PubM2313

value: Normal


title: IVT_HDAC2

description: site specific m6A quantification


title: PT06_F_35w3d [SU0006_BC02_pt]

value: placenta

value: Female, 35 wks 3 days GA


title: PT21_M_34w5d [SU0021_7_pt]

value: Preterm

value: Male, 34 wks 5 days GA


title: IVT_CIAO1

description: site specific m6A quantification


title: IVT_SLC7A5

description: site specific m6A quantification


title: IVT_CLCN3

description: site specific m6A quantification


title: Projet_Gen3G-Plasma-V1-PubM2274


title: IVT_CAND1

description: site specific m6A quantification


title: IVT_ACTB

description: site specific m6A quantification


title: Projet_Gen3G-Plasma-V1-PubM2270


title: HeLa_ZBED5

description: site specific m6A quantification

value: in vivo transcribed RNA


title: Projet_Gen3G-Plasma-V1-PubM2268

value: Gestational diabetes mellitus

tag: replicate

value: technical replicate


title: HeLa_TPT1

description: site specific m6A quantification


title: IVT_ILF3

description: site specific m6A quantification


title: PT16_M_31w3d [SU0016_4_pt]

value: fresh villous tissue

value: No treatment

value: Male, 31 wks 3 days GA


title: IVT_HOXB7

description: site specific m6A quantification


title: T20_M_38w1d [SU0020_6_tt]

value: Male, 38 wks 1 day GA


title: HeLa_SLC7A5

description: site specific m6A quantification


title: HeLa_PPIB

description: site specific m6A quantification


title: Projet_Gen3G-Plasma-V1-PubM2267

value: plasma

value: female


title: PT14_M_29w4d [SU0014_3_pt]

value: Male, 29 wks 4 days GA


title: IVT_CXCR4

description: site specific m6A quantification

value: HeLa

value: in vitro transcribed RNA


title: Projet_Gen3G-Plasma-V1-PubM2286

value: Normal


title: HeLa_MYC

description: site specific m6A quantification


title: HeLa_OGT

description: site specific m6A quantification


title: Projet_Gen3G-Plasma-V1-PubM2262


title: T07_F_40w5d [SU0007_2_tt]

value: placenta

value: Term

value: Female, 40 wks 5 days GA


title: HeLa_JUNB

description: site specific m6A quantification


title: HeLa_MALAT1

description: site specific m6A quantification


title: HeLa_ILF3

description: site specific m6A quantification


title: T01_M_38w4d [SU0001_1_tt]

value: Male, 38 wks 4 days GA


title: Projet_Gen3G-Plasma-V1-PubM2261

tag: pregnancy status_2

value: Other pregnancy complications


title: HeLa_HOXB7

description: site specific m6A quantification

tag: treatment

value: in vivo transcribed RNA


title: HeLa_TPX2

description: site specific m6A quantification


title: unmethylated_E. coli tRNA_WTTadA

description: unmethylated_E. coli tRNA_WTTadA

data_processing:
For site-specific m6A quantification by amplicon deep sequencing, raw next-generation sequencing data were merged by Pear v0.9.8. before mapping to the target sequences using bwa-mem2 v2.2.1. Mapped reads were sorted and indexed using samtools v1.14. Bases mapped to individual A sites were counted using pysamstats v1.1.1. A and G counts were extracted for individual A sites covered by R2 using re.finditer. Methylation levels are reported as apparent A fractions. For site-specific m6A quantification by eTAM-Sanger, the A and G fractions observed at all A sites were quantified by EditR. Methylation levels are reported as apparent A fractions.
Assembly: NA
Supplementary files format and content: two synthetic RNA probes and one E. coli tRNA with site specific m6A quantificaton in the XLSX format

organism: Escherichia coli

source_name: unmethylated_E. coli tRNA_WTTadA

extract_protocol:
Double-stranded DNA templates carrying T7 promoter were prepared by primer extension with two single-stranded DNA oligos. Unmethylated and methylated E. coli tRNA (Arg2, CGT), RNA#1, and RNA#2 were synthesized by in vitro transcription using T7 RNA polymerase. ATP and N6-methyl-ATP (TriLink, N-1013) were supplied in the presence of UTP, CTP, and GTP to synthesize unmethylated and methylated RNA, respectively. RNA was purified by E.Z.N.A Micro RNA kits (Omega Bio-Tek, R7034) and quantified by NanoDrop One (Thermo Fisher Scientific). All reactions were carried out in deamination buffer (50 mM Tris, 25 mM KCl, 2.5 mM MgCl2, 2 mM dithiothreitol, and 10 % (v/v) glycerol; pH 7.5) in the presence of 10 U SUPERaseIn RNase Inhibitor (Thermo Fisher Scientific, AM2694). RNA was always preheated to 95oC for 3 min and immediately cooled down before use. To assay deaminase activity on the natural substrate E. coli tRNA, 200 ng RNA and 100 nM wild type TadA or TadA8.20 were incubated at 37oC for 1 h. For a typical deamination assay on RNA probes, 10 ng RNA was incubated with 10 uM TadA8.20 in 20 uL deamination buffer at 37°C for 3 h. All reactions were quenched by incubating at 95°C for 10 min. Temperature and pH were adjusted to identify the optimal condition for in vitro deamination.
Both rounds of PCR were set up using EvaGreen qPCR Master Mix. 1st round PCR was carried out at a 20 uL scale with cDNA generated from different amounts of mRNA or total RNA, and 0.5 uM forward and reverse primers. Primers were designed to recognize sequences post deamination, leaving out 10-20 nt sequences surrounding the target m6A sites. PCR reactions were analyzed by agarose gel electrophoresis. 1 uL of PCR products were subjected to enzymatic cleanup (Exonuclease I and Shrimp Alkaline Phosphatase, New England BioLabs, M0293 and M0371) and Sanger sequencing. Gel purification was performed for PCR reactions that did not yield bright and single bands. 2nd round PCR was carried out at a 20 uL scale with 1 uL of the 1st round PCR reaction as template, 0.5 uM specified Illumina P7 and P5 index primer pairs. Barcoded PCR reactions were combined and gel purified using QIAquick Gel Extraction Kit (Qiagen, 28706) before being subjected to next-generation sequencing on an Illumina MiSeq Instrument.

value: whole strain

value: WTTadA


title: unmethylated_E. coli tRNA_TadA8.20

description: unmethylated_E. coli tRNA_TadA8.20

source_name: unmethylated_E. coli tRNA_TadA8.20


title: T19_M_40w [SU0019_5_tt]

value: fresh villous tissue

value: No treatment

value: Male, 40 wks GA


title: HeLa_HDAC2

description: site specific m6A quantification


title: HeLa_H2AFX

description: site specific m6A quantification


title: Projet_Gen3G-Plasma-V1-PubM2257

value: plasma


title: HeLa_GRWD1

description: site specific m6A quantification


title: HeLa_EIF2A

description: site specific m6A quantification


title: HeLa_CXCR4

description: site specific m6A quantification


title: unmethylated_E. coli tRNA

description: unmethylated_E. coli tRNA

source_name: unmethylated_E. coli tRNA

value: no treatment


title: Projet_Gen3G-Plasma-V1-PubM2253

value: female


title: Projet_Gen3G-Plasma-V1-PubM2255


title: HeLa_CLCN3

description: site specific m6A quantification

value: HeLa


title: Projet_Gen3G-Plasma-V1-PubM2264


title: Projet_Gen3G-Plasma-V1-PubM2252


title: HeLa_CIAO1

description: site specific m6A quantification


title: methylated_E. coli tRNA_WTTadA

description: methylated_E. coli tRNA_WTTadA

source_name: methylated_E. coli tRNA_WTTadA

value: in vitro transcribed RNA


title: methylated_E. coli tRNA_TadA8.20

description: methylated_E. coli tRNA_TadA8.20

source_name: methylated_E. coli tRNA_TadA8.20


title: HeLa_CAND1

description: site specific m6A quantification


title: Projet_Gen3G-Plasma-V1-PubM2250


title: HeLa_ACTB

description: site specific m6A quantification


title: Projet_Gen3G-Plasma-V1-PubM2246

value: Normal


title: HeLa_ACTB_25 ng_total RNA

description: site specific m6A quantificaiton from limited total RNA

source_name: HeLa_ACTB_25 ng_total RNA


title: HeLa_ACTB_2.5 ng_total RNA

source_name: HeLa_ACTB_2.5 ng_total RNA


title: HeLa_EIF2A_0.25 ng_total RNA

source_name: HeLa_EIF2A_0.25 ng_total RNA


title: Projet_Gen3G-Plasma-V1-PubM2245

source_name: plasma

value: Gestational diabetes mellitus


title: methylated_E. coli tRNA

description: methylated_E. coli tRNA

source_name: methylated_E. coli tRNA


title: HeLa_ACTB_0.25 ng_total RNA

source_name: HeLa_ACTB_0.25 ng_total RNA


title: HeLa_EIF2A_2.5 ng_total RNA

source_name: HeLa_EIF2A_2.5 ng_total RNA


title: Projet_Gen3G-Plasma-V1-PubM2234


title: HeLa_EIF2A_100 fold dilution

description: site specific m6A quantificaiton for serial diluted sample

source_name: HeLa_EIF2A_100 fold dilution


title: HeLa_EIF2A_1000 fold dilution

source_name: HeLa_EIF2A_1000 fold dilution


title: Projet_Gen3G-Plasma-V1-PubM2236


title: HeLa_EIF2A_10 fold dilution

source_name: HeLa_EIF2A_10 fold dilution


title: HeLa_EIF2A_no dilution

source_name: HeLa_EIF2A_no dilution


title: Projet_Gen3G-Plasma-V1-PubM2231


title: HeLa_ACTB_1000 fold dilution

source_name: HeLa_ACTB_1000 fold dilution


title: Projet_Gen3G-Plasma-V1-PubM2229


title: HeLa_ACTB_10 fold dilution

source_name: HeLa_ACTB_10 fold dilution


title: HeLa_ACTB_100 fold dilution

source_name: HeLa_ACTB_100 fold dilution


title: HeLa_EIF2A_25 ng_total RNA

source_name: HeLa_EIF2A_25 ng_total RNA


title: HeLa_ACTB_no dilution

source_name: HeLa_ACTB_no dilution


title: Projet_Gen3G-Plasma-V1-PubM2227


title: unmethylated_RNA2#_TadA8.20

organism: synthetic construct


title: unmethylated_RNA2#


title: Projet_Gen3G-Plasma-V1-PubM2225


title: unmethylated_RNA1#_TadA8.20


title: unmethylated_RNA1#


title: Projet_Gen3G-Plasma-V1-PubM2224


title: methylated_RNA2#_TadA8.20


title: Projet_Gen3G-Plasma-V1-PubM2223


title: methylated_RNA2#


title: S9

city: Dublin

first: Eoin

last: Brennan

address: Belfield, Dublin 4

country: Ireland

institute: University College Dublin

description:
Doyle_et_al.Normalized_read_counts.xlsx
S9

data_processing:
Raw transcript reads were aligned to the human genome using Partek Flow Software
Reads were quantile normalized.
Genome_build: hg19
Supplementary_files_format_and_content: Excel files of normalized read counts for each sample.

source_name: Kidney

extract_protocol:
Kidney biopsy tissue was frozen at -80C in RNALater until processing. RNA extracted using E.Z.N.A.® Total RNA Kit I
BGI standard protocol

value: Kidney

tag: source

value: Percutaneous kidney biopsy

tag: age

tag: egfr

tag: % tubulointerstitial fibrosis on kidney biopsy

value: Female

tag: progressive ckd


title: S7

description:
Doyle_et_al.Normalized_read_counts.xlsx
S7

tag: tissue

value: Male


title: sAML8

city: St. Louis

first: Tim

last: Kong

state: MO

address: CSRB 8838

description: Patient sequencing

hyb_protocol: cDNA were then probed by GeneChipHuman Gene 2.0 ST Arrays (Affymatrix)

scan_protocol: GeneChips were scanned by the Genome Technology Access Center at  Washington University School of Medicine.

data_processing: Raw files were processed with the oligo package, quality controlled with AUC and RLE cut-offs, and normalized using the RMA-normalized log2-transformed algorithm.

source_name: sAML PBMC

label_protocol: mRNA was isolated, amplified, and converted to biotinylated sense-strand cDNA with WT Pico Reagent Kit.

extract_protocol: Cryopreserved cells were thawed, filtered, and stained with the following immunostaining panel for sorting: CD34, CD38, CD3, CD19, CD14, and CD16 antibodies, in addition to 7-AAD viability marker. 7AAD- lin- CD34+ cells were sorted and mRNA was isolated using the Qiagen RNeasy Mini Kit.

tag: disease

value: sAML


title: sAML4

institute: Washington University School of Medicine

description: Patient sequencing


title: Projet_Gen3G-Plasma-V1-PubM2219


title: sAML3

description: Patient sequencing


title: S6

description:
Doyle_et_al.Normalized_read_counts.xlsx
S6


title: sAML2

description: Patient sequencing


title: sAML7

description: Patient sequencing


title: MF34

description: Patient sequencing

source_name: MF PBMC

value: MF


title: sAML9

description: Patient sequencing


title: Projet_Gen3G-Plasma-V1-PubM2216


title: MF33

description: Patient sequencing


title: MF31

description: Patient sequencing


title: S5

description:
Doyle_et_al.Normalized_read_counts.xlsx
S5


title: MF32

description: Patient sequencing


title: Projet_Gen3G-Plasma-V1-PubM2212


title: methylated_RNA1#

tag: cell type


title: methylated_RNA1#_TadA8.20


title: PMC_RNAseq

city: Munich

first: Georgios

middle: T

last: Stathopoulos

state: Bayern

address: Max-Lebsche-Platz

department: Comprehensive Pneumology Center

institute: Helmholz Zentrum Munich

data_processing:
base calling was performed with Torrent suite
alignment was performed with TMAP
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using FeuturesCounts funtion from Subread software
The data were filtered, normalized and the differential gene expression was computed using the packages limma (https://bioconductor.org/packages/release/bioc/html/limma.html) and edgeR(https://bioconductor.org/packages/release/bioc/html/edgeR.html) on R
aligment for variant call was performed with STAR, TMAP and TopHAT2
the variant calling was performed with samtools 1.6,the file were also called for single nucleotide variation and indel with bcftools
the SNV impact was calculated with snpEff 4.3
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample; variant calling format for each cell line sample
Supplementary_files_format_and_content: PMC_RNAseq is missing from RPKM_normalized_RNAsig_gene_expression.txt on purpose because it was not used for the differential gene expression analysis, but only as post-filter for the variant calling files.

source_name: Primary lung mesothelial cell

growth_protocol: cells were cultured in minimum supplemented medium (DMEM+10% FBS + 1% PEN/STREP) for over 12 months or over 60 passages.Mouse wilt type primary epithilial cells(PLE) and mesothilial cells(PMC) were not cultured

extract_protocol:
Total RNA from the cells was extracted with the Trizol protocol followed by Qiagen RNeasy Mini Kit
Libraries were prepared according to Thermoscientific Ion Torrent specifications

tag: sample type

value: control sample from healthy mouse

tag: passages

tag: strain


title: Projet_Gen3G-Plasma-V1-PubM2211

source_name: plasma

tag: Sex

tag: pregnancy status_1


title: PLE2_RNAseq

source_name: Primary lung epithilial cell

value: BALB/cJ


title: S45

description:
Doyle_et_al.Normalized_read_counts.xlsx
S45


title: MF28

description: Patient sequencing


title: S44

description:
Doyle_et_al.Normalized_read_counts.xlsx
S44


title: S46

description:
Doyle_et_al.Normalized_read_counts.xlsx
S46


title: Projet_Gen3G-Plasma-V1-PubM2207


title: MF30

description: Patient sequencing


title: Projet_Gen3G-Plasma-V1-PubM2203

value: Other pregnancy complications


title: S43

description:
Doyle_et_al.Normalized_read_counts.xlsx
S43


title: CULA1_RNAseq

source_name: urathane induced lung adenocarcinoma cell line

value: cancinogen induced lung adenocarcinoma cell line

value: more than 60


title: FELA2_RNAseq

source_name: DEN induced lung adenocarcinoma cell line

value: carcinogen induced lung adenocarcinoma cell line

value: FVB/NJ


title: S36

description:
Doyle_et_al.Normalized_read_counts.xlsx
S36


title: Projet_Gen3G-Plasma-V1-PubM2202

value: plasma

value: female


title: BELA2_RNAseq


title: FELA1_RNAseq


title: Projet_Gen3G-Plasma-V1-PubM2191


title: MF21

description: Patient sequencing


title: S37

description:
Doyle_et_al.Normalized_read_counts.xlsx
S37


title: Projet_Gen3G-Plasma-V1-PubM2198

value: Normal


title: MF23

description: Patient sequencing


title: PLE1_RNAseq


title: S35

description:
Doyle_et_al.Normalized_read_counts.xlsx
S35


title: MF26

description: Patient sequencing


title: MF19

description: Patient sequencing


title: BELA1_RNAseq


title: Projet_Gen3G-Plasma-V1-PubM2210


title: S34

description:
Doyle_et_al.Normalized_read_counts.xlsx
S34


title: S32

description:
Doyle_et_al.Normalized_read_counts.xlsx
S32


title: MF9

description: Patient sequencing


title: BULA2_RNAseq


title: Projet_Gen3G-Plasma-V1-PubM2189


title: BULA1_RNAseq


title: MF10

description: Patient sequencing


title: MF2

description: Patient sequencing


title: FULA3_RNAseq


title: MF4

description: Patient sequencing


title: S29

description:
Doyle_et_al.Normalized_read_counts.xlsx
S29


title: S27

description:
Doyle_et_al.Normalized_read_counts.xlsx
S27


title: Projet_Gen3G-Plasma-V1-PubM2184


title: Projet_Gen3G-Plasma-V1-PubM2183


title: FULA2_RNAseq


title: N32

description: Patient sequencing

source_name: Patient NBM

value: NBM


title: Projet_Gen3G-Plasma-V1-PubM2180


title: Projet_Gen3G-Plasma-V1-PubM2190


title: S24

description:
Doyle_et_al.Normalized_read_counts.xlsx
S24

value: Kidney


title: N26

description: Patient sequencing


title: D42

description:
Doyle_et_al.Normalized_read_counts.xlsx
D42

value: Percutaneous kidney biopsy


title: FULA1_RNAseq


title: S26

description:
Doyle_et_al.Normalized_read_counts.xlsx
S26

value: Female


title: N18

description: Patient sequencing


title: Projet_Gen3G-Plasma-V1-PubM2179


title: Human Thyroid Organoid c-AMP day45_rep2

city: Bruxelles

first: Sabine

last: Costagliola

address: 808 route de lennik

department: IRIBHM

country: Belgium

institute: Université Libre de Bruxelles

data_processing:
Removal of low-quality bases and Illumina adapter sequences were performed using Trimmomatic software (Bolger et al. 2014) and sequence reads were aligned against the human reference genome using HiSat2 software (Kim, 2015). Raw reads were determined with HTSeq software (Anders et al 2015) using the Ensembl genome annotation GRCh38.p13.
Assembly: GRCh38
Supplementary files format and content: Comma-Separated File containing raw counts per sample. Samples correspond to columns of the matrix.

source_name: hESC-derived differentiated cells

extract_protocol:
Trypsin based dissociation followed by FACS sorting of NKX2-1/GFP+ alive cells
Ovarion Solo RNA-seq Systems (NuGen)

tag: cell line

tag: time point

value: day 45


title: N8

description: Patient sequencing


title: Projet_Gen3G-Plasma-V1-PubM2178


title: S23

description:
Doyle_et_al.Normalized_read_counts.xlsx
S23

value: Male


title: D46

description:
Doyle_et_al.Normalized_read_counts.xlsx
D46


title: S2

description:
Doyle_et_al.Normalized_read_counts.xlsx
S2


title: Human Thyroid Organoid c-AMP day45_rep1


title: N7

description: Patient sequencing


title: Projet_Gen3G-Plasma-V1-PubM2175


title: Human Thyroid Organoid c-AMP day38_rep2

value: day 38


title: Projet_Gen3G-Plasma-V1-PubM2174


title: S18

description:
Doyle_et_al.Normalized_read_counts.xlsx
S18


title: Human Thyroid Organoid c-AMP day38_rep1


title: D43

description:
Doyle_et_al.Normalized_read_counts.xlsx
D43


title: D18

description:
Doyle_et_al.Normalized_read_counts.xlsx
D18


title: Projet_Gen3G-Plasma-V1-PubM2173


title: Human Thyroid Organoid TSH SB day45_rep2

data_processing:
Removal of low-quality bases and Illumina adapter sequences were performed using Trimmomatic software (Bolger et al. 2014) and sequence reads were aligned against the human reference genome using HiSat2 software (Kim, 2015). Raw reads were determined with HTSeq software (Anders et al 2015) using the Ensembl genome annotation GRCh38.p13.
Genome_build: GRCh38
Supplementary_files_format_and_content: File containing raw counts per sample.


title: S13

description:
Doyle_et_al.Normalized_read_counts.xlsx
S13


title: D29

description:
Doyle_et_al.Normalized_read_counts.xlsx
D29


title: S11

description:
Doyle_et_al.Normalized_read_counts.xlsx
S11


title: Human Thyroid Organoid TSH DEX day38_rep2


title: Human Thyroid Organoid TSH SB day45_rep1


title: Projet_Gen3G-Plasma-V1-PubM2166


title: Projet_Gen3G-Plasma-V1-PubM2172


title: S1

description:
Doyle_et_al.Normalized_read_counts.xlsx
S1


title: D1

description:
Doyle_et_al.Normalized_read_counts.xlsx
D1


title: D47

description:
Doyle_et_al.Normalized_read_counts.xlsx
D47


title: Human Thyroid Organoid c-AMP day31_rep2


title: D44

description:
Doyle_et_al.Normalized_read_counts.xlsx
D44


title: D5

description:
Doyle_et_al.Normalized_read_counts.xlsx
D5


title: S14

description:
Doyle_et_al.Normalized_read_counts.xlsx
S14


title: Projet_Gen3G-Plasma-V1-PubM2167


title: Human Thyroid Organoid TSH DEX day38_rep1


title: D45

description:
Doyle_et_al.Normalized_read_counts.xlsx
D45


title: Human Thyroid Organoid c-AMP day31_rep1