title: PTH-pretreated, non-loaded, replicate 5,cortical bone,L [808]

value: L


title: Pt29_Benign

status: Public on Jan 31 2024

type: SRA

city: Baltimore

first: Angelo

last: De Marzo

state: Maryland

address: 1550 Orleans Street, CRB II RM 138

country: USA

institute: Johns Hopkins University School of Medicine

library_source: transcriptomic

data_processing:
Trim galore v0.6.3 was used to trim the reads.
Bwa v0.7.7 (mem) was used to align to the hg19 and hg38 human genome builds.
Piccard-tools v1.119 & GATK v3.6.0 were used to create a recalibrated bam file.
Assembly: hg19 and hg38 human genome builds
Supplementary files format and content: Posterior mean estimate transcripts per million (pmeTPM) for each sample
Supplementary files format and content: Expected count for each sample

molecule: total RNA

organism: Homo sapiens

source_name: Prostate

extract_protocol:
Tissue digestion and DNA/RNA extraction was performed using Allprep DNA/RNA Kits following the manufacturer’s recommendations (Qiagen, 802804)
Libraries were constructed according to the protocol provided in the Illumina Nano TruSeq Library prep guide. Assessment of the yield and size distribution of the amplified library was performed on the Agilent 2100 Bioanalyzer using the High Sensitivity Chip. Libraries were then pooled at equal molar concentrations for sequencing. Sequencing was performed using Illumina HiSeqX and NovaSeq6000 with Paired End 150 bp x 150 bp read configuration.

tag: tissue

value: Prostate


title: Pt30_Benign


title: microglia_bhb_lps_3

city: California

first: Natalia

middle: Faraj

last: Murad

state: CA

address: 500 Parnassus Ave

department: HemOnc

institute: University of California, San Francisco

data_processing:
Adapters removal and QC with trimmomatic (standard options)
Mapping to the genome GRch38 ensembl with STAR aligner
Count matrix generated with RSEM
Assembly: GRch38
Supplementary files format and content: Tab delimited text file with raw counts

source_name: brain

extract_protocol:
RNA was isolated using the Quick-RNA MicroPrep Kit (Zymo Research) according to the manufacturer’s protocol.
The library was prepared with the KAPA RNA HyperPrep Kit (Roche) and sequenced on a HiSeq 4000 (Illumina).

value: brain

tag: cell line

value: primary

tag: cell type

value: microglia

tag: treatment


title: Br_26_KD_12

description: brain keto diet 26 months

data_processing:
Data trimmed with trimmomatic, mapped to the reference genome with STAR and count matrix generated with RSEM.
Assembly: GRCm38
Supplementary files format and content: Normalized counts in a tab delimited file.

organism: Mus musculus

extract_protocol:
For in vivo sequencing, RNA was isolated using the Direct-zol RNA MiniPrep kit (Zymo Research) following the manufacturer’s protocol.
RNA integrity and concentrations were assessed using an Agilent Bioanalyzer. The library was prepared using the KAPA RNA HyperPrep Kit (Roche) and QIAseq FastSelect RNA Removal Kit (QIAGEN)

tag: genotype

value: keto diet - 26 months


title: Pt29_Cancer


title: PTH-pretreated, non-loaded, replicate 5,cancellous bone,L [807]

city: Ithaca

first: Marjolein

last: van der Meulen

state: NY

address: Weill Hall

department: BME

institute: Cornell University

data_processing:
Computational was performed in a Unix environment
12bp were trimmed from 5’ end of sequenc reads using fastx_trimmer
Sequence reads were trimmed using trimmomatic(v0.39)
Trimmed sequences were mapped to mm10 using STAR
Each sample contained over 1 million of uniquely mapped reads to the mouse genome. Genes with less than 3 counts per million were not included for analysis.
Assembly: mm10
Supplementary files format and content: normalizedcounts.xls file includes normalized value from edgeR for each sample

source_name: cancellous bone

extract_protocol:
RNA was extracted using Rneasy kit (Qiagen). 20uL of total RNA was used for construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using Truseq (Illumina) – 3’ RNAseq Kit following maufacturer’s protocols

value: cancellous bone

tag: limb

tag: age

value: 26 wks


title: microglia_bhb_lps_1


title: microglia_bhb_lps_2


title: Br_26_CD_6

description: brain control diet 26 months

value: control diet - 26 months


title: Br_26_CD_5

description: brain control diet 26 months


title: PTH-pretreated, non-loaded, replicate 9,cancellous bone,L [863]


title: microglia_lps_3

value: lps


title: Pt28_Benign


title: microglia_lps_2


title: PTH-pretreated, non-loaded, rep4,cancellous bone,Right [800]

value: Right


title: Br_26_CD_4

description: brain control diet 26 months


title: microglia_lps_1


title: Br_26_CD_3

description: brain control diet 26 months


title: Br_26_CD_7

description: brain control diet 26 months


title: Br_26_CD_2

description: brain control diet 26 months


title: PTH-pretreated, non-loaded, rep3,cancellous bone,L [793]


title: Pt27_Benign


title: microglia_bhb_3

value: bhb


title: PTH-pretreated, non-loaded, rep2,cortical bone,Right [787]

source_name: cortical bone

value: cortical bone


title: Br_26_CD_1

description: brain control diet 26 months


title: PTH-pretreated, non-loaded, rep4,cortical bone,Right [801]


title: microglia_bhb_2


title: Pt28_Cancer


title: Pt26_Benign


title: Br_12_KD_17

description: brain keto diet 12 months

value: keto diet - 12 months


title: microglia_bhb_1


title: Pt26_Cancer


title: PTH-pretreated, non-loaded, rep2,cancellous bone,Right [786]


title: Br_12_KD_14

description: brain keto diet 12 months


title: Pt25_Benign


title: microglia_control_3

value: control


title: PTH-pretreated, non-loaded, rep3,cortical bone,L [794]


title: Pt27_Cancer


title: neurons_control_3

value: neurons


title: PTH-pretreated, non-loaded, rep1,cortical bone,Right [815]


title: Pt25_Cancer


title: Pt24_Cancer


title: vehicle, non-loaded, rep7,cortical bone,L [724]


title: microglia_control_1


title: Br_12_KD_02

description: brain keto diet 12 months


title: astro_bhb_lps_3

value: astrocytes


title: vehicle, non-loaded, rep6,cortical bone,Right [717]


title: Br_12_KD_05

description: brain keto diet 12 months


title: vehicle, non-loaded, rep7,cancellous bone,L [723]

value: L


title: Pt23_Benign

value: Prostate


title: Pt40_Benign


title: astro_bhb_lps_2

value: brain


title: Br_12_KD_08

description: brain keto diet 12 months


title: Pt24_Benign


title: astro_bhb_lps_1

value: primary


title: Pt23_Cancer


title: Br_12_KD_11

description: brain keto diet 12 months


title: Pt22_Benign


title: Br_12_CD_16

description: brain control diet 12 months

value: control diet - 12 months


title: vehicle, non-loaded, rep6,cancellous bone,Right [716]


title: Br_12_CD_13

description: brain control diet 12 months


title: PTH-pretreated, non-loaded, rep1,cancellous bone,L [835]


title: microglia_control_2

value: microglia


title: astro_lps_2


title: vehicle, non-loaded, rep5,cancellous bone,L [709]

value: cancellous bone


title: vehicle, non-loaded, rep4,cortical bone,L [696]

value: 26 wks


title: Br_12_CD_7

description: brain control diet 12 months


title: astro_lps_1


title: Br_12_CD_4

description: brain control diet 12 months


title: vehicle, non-loaded, rep4,cancellous bone,L [695]


title: astro_bhb_3


title: Br_12_KD_10

description: brain keto diet 12 months


title: Pt21_Cancer


title: vehicle, non-loaded, rep3,cortical bone,Right [689]


title: Br_12_CD_1

description: brain control diet 12 months


title: Pt20_Benign


title: astro_bhb_2


title: vehicle, non-loaded, rep3,cancellous bone,Right [688]


title: vehicle, non-loaded, rep5,cortical bone,L [710]


title: Pt20_Cancer


title: vehicle, non-loaded, rep2,cortical bone,L [682]


title: GEX_CD27_KO

city: GOSSELIES

first: Abdulkader

last: AZOUZ

address: Rue Adrienne Bolland, 8

country: Belgium

institute: Université Libre de Bruxelles

description: 10x Genomics

library_source: transcriptomic single cell

data_processing:
Cell Ranger (10x Genomics) functions mkfastq and count were used to align to the mm10 genome and demultiplex the sequencing data and generate gene-barcode matrices.
Assembly: mm10
Supplementary files format and content: Cell ranger output files

source_name: Stromal vascular fractions of VAT

extract_protocol:
Stromal vascular fractions of VAT of 10 WT or CD27-/- mice were pooled and TCRb+ CD4+ cells were subsequently FACS-sorted
Cells were loaded on the Chromium Controller (10x Genomics) and Single-cell RNA-seq libraries were prepared using the Chromium Single Cell 3ʹ v2 Reagent Kit (10x Genomics) according to manufacturer’s protocol.

value: Stromal vascular fractions of VAT

value: TCRb+ CD4+


title: astro_bhb_1


title: vehicle, non-loaded, rep2,cancellous bone,L [681]


title: Pt19_Benign


title: Pt21_Benign


title: astro_lps_3

value: lps


title: Pt19_Cancer


title: Pt22_Cancer


title: Pt18_Cancer


title: astro_control_2


title: vehicle, non-loaded, rep1,cancellous bone,Right [674]

value: Right


title: astro_control_1


title: PTH-pretreated, vehicle, 2wks of daily loading, rep4,cortical bone,L [668]

value: cortical bone

value: 28 wks


title: GEX_WT

description: 10x Genomics


title: Pt18_Benign


title: astro_control_3

value: control


title: Pt17_Benign


title: RNA-seq: Persisting epimutations PGCLC BPS 1uM rep 2

city: San Antonio

first: Jake

middle: Dean

last: Lehle

state: TX

address: 16631 Vance Jackson Rd APT#1220

department: NDRB

institute: The University of Texas at San Antonio

data_processing:
The quality of the fastq reads was checked using FastQC. Reads were aligned to the mm10 mouse reference genome using the Rsubreads package to produce read counts. These were then used for differential gene expression analysis using the edgeR package. Briefly, gene counts were normalized using the trimmed mean of M-value normalization (TMM) method before determining counts per million (CPM) values. For a gene to be classified as showing differential gene expression between BPS-treated and EtOH vehicle-only control samples, a threshold of both a Benjamini-Hochberg adjusted p-value ≤ 0.05 and a false discovery rate (FDR) ≤ 0.05 had to be met.
Assembly: mm10
Supplementary files format and content: CPM

molecule: polyA RNA

source_name: PGCLC

growth_protocol: See the publication for a full description of specific growth protocols for each cell types included in the study.

extract_protocol:
Total RNA was extracted from cells using Trizol and contaminating genomic DNA was removed by RQ1 DNase (M6101) treatment according to the manufacturer’s instructions (Promega Corporation, WI USA).
Strand-specific RNA-seq libraries were prepared with the NEBNext® Ultra™ II Directional RNA Library Prep Kit for Illumina® sequencing (E7760S) according to the manufacturer’s protocol (New England Biolabs, MA USA).

treatment_protocol: For all cell types except PGCLCs, 1 μM BPS was added to media gassed with 5% CO2, 5% O2, and balanced N2 and then injected into sealed T-25 cell culture flasks and left to incubate for 24 hours. The media was gassed to ensure enrichment to 5% CO2, which is normally regulated by the cell incubator, limiting the potential for the pH to change in the media during this exposure period due to the absorption of CO2 by incubating cells. Following 24 hours of exposure, media containing BPS was removed and cells were washed and allowed to recover in fresh untreated media (without BPS or EtOH) for 24 hours prior to harvesting. PGCLCs were not suitable for this exposure paradigm as EpiLCs undergo differentiation to PGCLCs in cell aggregates formed in low-adherence round-bottom 96 well plates and cannot be maintained in T-25 sealed flasks. Therefore, diluted BPS was added to PGCLC media and added to cells in round-bottom 96 well plates to incubate for 24 hours prior to a shortened wash and “chase” period of 8 hours prior to cell sorting.

value: PGCLC

value: BPS 1uM


title: RNA-seq: Persisting epimutations PGCLC BPS 1uM rep 3


title: PTH-pretreated, vehicle, 2wks of daily loading, rep2,cancellous bone,L [653]

value: L


title: Pt17_Cancer

value: Prostate


title: RNA-seq: Persisting epimutations PGCLC con rep 2

value: Control


title: vehicle, non-loaded, rep1,cortical bone,Right [675]


title: RNA-seq: Persisting epimutations PGCLC con rep 1


title: RNA-seq: Persisting epimutations PGCLC BPS 1uM rep 1


title: Pt16_Cancer


title: Pt16_Benign


title: PTH-pretreated, vehicle, 2wks of daily loading, rep3,cortical bone,L [640]


title: PTH-pretreated, vehicle, 2wks of daily loading, rep7,cancellous bone,Right [646]


title: HPa092619-C

city: Rochester

first: Madhusudan

last: Grover

state: MN

address: 200 First St SW

institute: Mayo Clinic

data_processing:
Sequencing analysis was performed using cellranger v3.1
Quality control was performed by excluding cells with low gene counts and high mitochondrial content
Assembly: hg38
Supplementary files format and content: Cellranger outputs including feature matrices

source_name: Gastric Muscle

extract_protocol:
The tissue dissociation was performed using Multi Tissue Dissociation kit 1 (Miltenyi Biotec, 130-110-201) as per manufacturer’s instructions with slight modifications.
Single Cell 3' v3 from 10X Genomics
(sequencing protocol)  Libraries were sequenced at 60,000 fragment reads per cell following Illumina’s standard protocol using the Illumina cBot and HiSeq 3000/4000 PE Cluster Kit. The flow cells were sequenced as 100 X 2 paired end reads on an Illumina HiSeq 4000 using HiSeq 3000/4000 sequencing kit and HCS v3.3.52 collection software. Base-calling was performed using Illumina’s RTA version 2.7.3.

value: Gastric Muscle

value: CD45+ cells

tag: disease state

value: Idiopathic gastroparesis


title: TAb_10102019-A


title: TAa082819


title: TMA_072419


title: TAa092519-A


title: TBa_062619


title: RNA-seq: Persisting epimutations iPSC BPS 1uM rep 1

source_name: iPSC

value: iPSC


title: RNA-seq: Persisting epimutations iPSC BPS 1uM rep 3


title: PTH-pretreated, vehicle, 2wks of daily loading, rep1,cancellous bone,L [639]

value: cancellous bone


title: Pt15_Cancer


title: HPa100319-B


title: Pt14_Cancer


title: CD45_plus__19-018


title: Pt14_Benign


title: PTH-pretreated, vehicle, 2wks of daily loading, rep7,cortical bone,Right [647]


title: PTH-pretreated, vehicle, 2wks of daily loading, rep6,cortical bone,Right [633]


title: PTH-pretreated, vehicle, 2wks of daily loading, rep6,cancellous bone,Right [632]


title: CD45_plus__19-014


title: RNA-seq: Persisting epimutations iPSC con rep 3


title: CD45_plus__19-013


title: RNA-seq: Persisting epimutations iPSC BPS 1uM rep 2


title: Pt13_Cancer


title: RNA-seq: Persisting epimutations iPSC con rep 1


title: RNA-seq: PGCLC BPS 1uM rep 3


title: PTH-pretreated, vehicle, 2wks of daily loading, rep5,cancellous bone,Right [618]


title: RNA-seq: Persisting epimutations iPSC con rep 2


title: PTH-pretreated, vehicle, 2wks of daily loading, rep5,cortical bone,Right [619]


title: Pt13_Benign


title: PTH-pretreated, vehicle, 2wks of daily loading, rep2,cortical bone,L [612]


title: RNA-seq: PGCLC BPS 1uM rep 2


title: Pt12_Benign


title: PTH-pretreated, vehicle, 2wks of daily loading, rep4,cortical bone,Right [605]


title: Pt12_Cancer


title: RNA-seq: PGCLC con rep 3


title: RNA-seq: PGCLC BPS 1uM rep 1


title: CD45_plus__19-006


title: Pt11_Benign


title: PTH-pretreated, vehicle, 2wks of daily loading, rep4,cancellous bone,Right [604]


title: CD45_plus__19-010


title: RNA-seq: PGCLC con rep 2


title: vehicle, vehicle, 1wk of daily loading, rep6,cortical bone,Right [45]

value: 27 wks


title: 19-026_09272019


title: Pt11_Cancer


title: RNA-seq: PGCLC con rep 1


title: Pt10_Cancer


title: vehicle, vehicle, 1wk of daily loading, rep5,cortical bone,Right [17]


title: Pt10_Benign


title: RNA-seq: Granulosa BPS 1uM rep 3

source_name: Granulosa Cells

value: Granulosa Cells


title: RNA-seq: Granulosa BPS 1uM rep 2


title: Pt9_Benign


title: Pt15_Benign


title: RNA-seq: Granulosa BPS 1uM rep 1


title: 19-022_08292019


title: CD45_plus__022219


title: Pt9_Cancer


title: 19-023_09042019


title: vehicle, vehicle, 1wk of daily loading, rep7,cortical bone,Right [73]


title: PTH-pretreated, ALN-treated, 2wks of daily loading, rep7,lymph node,L [C24]

source_name: lymph node

value: lymph node


title: PTH-pretreated, ALN-treated, 2wks of daily loading, rep7,lymph node,Right [C23]

value: Right


title: 19-024_09112019_CD45


title: Pt8_Benign


title: 19-021a_082119


title: RNA-seq: Granulosa con rep 2


title: T21 Differentiated Neuroectoderm, Day 17, RNA, Replicate 3

city: Madison

first: Anita

last: Bhattacharyya

state: Wisconsin

address: 1500 Highland Ave

department: Waisman Center

institute: University of Wisconsin - Madison

data_processing:
Trimmomatic v0.36:  Remove Illumina adapter contamination
STAR v2.5.3a:  Align to genome and extract gene counts
DEseq2 v1.20.0:  Differential gene expression
Assembly: hg19
Supplementary files format and content: tab:  Raw gene counts for each sample (generated using STAR --quantMode GeneCounts)

source_name: iPSCs derived differentiated neuroectoderm

growth_protocol: iPSCs were maintained on mouse embryonic fibroblasts (MEFs) feeder plates and differentiated to definitive neuroectoderm following previously published studies (Chambers et al., 2009, Zhang et al., 2001, Pankratz et al., 2007).

extract_protocol:
RNA was harvested using Direct-zol RNA Micro Prep Kit from Zymo Research
RNA libraries were prepared using the Illumina TruSeq Stranded RNA Sample Prep Kit on 500 ng of total RNA

value: iPSCs

value: Isogenic Trisomy 21

tag: time

value: day 17


title: PTH-pretreated, ALN-treated, 2wks of daily loading, rep6,lymph node,L [C22]

value: 28 wks


title: Pt8_Cancer


title: 19-025a_09122019


title: Pt7_Cancer


title: T21 Differentiated Neuroectoderm, Day 17, RNA, Replicate 2

value: iPSCs derived differentiated neuroectoderm


title: RNA-seq: Granulosa con rep 1


title: RNA-seq: Sertoli BPS 1uM rep 3

source_name: Sertoli Cells

value: Sertoli Cells

value: BPS 1uM


title: Pt7_Benign

value: Prostate


title: PTH-pretreated, ALN-treated, 2wks of daily loading, rep8,lymph node,L [C26]

value: L


title: PTH-pretreated, ALN-treated, 2wks of daily loading, rep8,lymph node,Right [C25]


title: PTH-pretreated, ALN-treated, 2wks of daily loading, rep5,lymph node,L [C20]


title: RNA-seq: Sertoli BPS 1uM rep 2


title: RNA-seq: Granulosa con rep 3

value: Control


title: T21 Early Neuroectoderm, Day 10, RNA, Replicate 3

source_name: iPSCs derived early neuroectoderm

value: iPSCs derived early neuroectoderm

value: day 10


title: PTH-pretreated, ALN-treated, 2wks of daily loading, rep5,lymph node,Right [C19]


title: Pt6_Cancer


title: CD45_plus__19-011

value: Gastric Muscle

value: CD45+ cells


title: Pt6_Benign


title: RNA-seq: Sertoli BPS 1uM rep 1


title: PTH-pretreated, ALN-treated, 2wks of daily loading, rep4,lymph node,L [C18]


title: Pt5_Cancer


title: RNA-seq: Sertoli con rep 3


title: T21 Early Neuroectoderm, Day 10, RNA, Replicate 1


title: RNA-seq: Sertoli con rep 2


title: T21 EB, Day 6, RNA, Replicate 3

source_name: iPSCs derived embryoid bodies

value: iPSCs derived embryoid bodies

value: day 6


title: PTH-pretreated, ALN-treated, 2wks of daily loading, rep4,lymph node,Right [C17]

value: lymph node

value: Right


title: RNA-seq: Sertoli con rep 1


title: PTH-pretreated, ALN-treated, 2wks of daily loading, rep6,lymph node,Right [C21]


title: Pt4_Benign


title: Pt5_Benign


title: T21 EB, Day 6, RNA, Replicate 2

value: iPSCs

value: Isogenic Trisomy 21


title: PTH-pretreated, ALN-treated, 2wks of daily loading, rep3,lymph node,Right [C15]

value: 28 wks


title: RNA-seq: Persisting epimutations PGCLC con rep 3

value: PGCLC


title: T21 Differentiated Neuroectoderm, Day 17, RNA, Replicate 1

value: iPSCs derived differentiated neuroectoderm

value: day 17


title: Pt4_Cancer

value: Prostate


title: T21 Early Neuroectoderm, Day 10, RNA, Replicate 2


title: T21 EB, Day 6, RNA, Replicate 1


title: PTH-pretreated, ALN-treated, 2wks of daily loading, rep2,lymph node,Right [C13]


title: RNA-seq: Prelim iPSC BPS 100uM rep 1

value: iPSC

value: BPS 100uM


title: Pt3_Cancer


title: PTH-pretreated, ALN-treated, 2wks of daily loading, rep2,lymph node,L [C14]

value: L


title: Control Differentiated Neuroectoderm, Day 17, RNA, Replicate 3

value: Isogenic Euploid Control


title: PTH-pretreated, ALN-treated, 2wks of daily loading, rep1,lymph node,L [C12]


title: Control Differentiated Neuroectoderm, Day 17, RNA, Replicate 1


title: RNA-seq: Prelim iPSC BPS 50uM rep 3

value: BPS 50uM


title: Pt3_Benign


title: RNA-seq: Prelim iPSC BPS 100uM rep 3


title: PTH-pretreated, ALN-treated, 2wks of daily loading, rep3,lymph node,L [C16]


title: RNA-seq: Prelim iPSC BPS 50uM rep 2


title: Control Early Neuroectoderm, Day 10, RNA, Replicate 3

value: iPSCs derived early neuroectoderm

value: day 10


title: Pt2_Benign


title: Pt2_Cancer


title: RNA-seq: Prelim iPSC BPS 50uM rep 1


title: Control Early Neuroectoderm, Day 10, RNA, Replicate 2


title: RNA-seq: Prelim iPSC BPS 100uM rep 2


title: PTH-pretreated, ALN-treated, 2wks of daily loading, rep1,lymph node,Right [C11]


title: vehicle, ALN-treated, 2wks of daily loading, rep8,lymph node,L [C10]


title: vehicle, ALN-treated, 2wks of daily loading, rep8,lymph node,Right [C09]


title: Control Early Neuroectoderm, Day 10, RNA, Replicate 1


title: Pt1_Benign


title: RNA-seq: Prelim iPSC BPS 1uM rep 3

value: BPS 1uM


title: Pt1_Cancer


title: Control Differentiated Neuroectoderm, Day 17, RNA, Replicate 2


title: vehicle, ALN-treated, 2wks of daily loading, rep7,lymph node,L [C08]

value: lymph node


title: RNA-seq: Prelim iPSC BPS 1uM rep 2


title: Control EB, Day 6, RNA, Replicate 3

value: iPSCs derived embryoid bodies

value: day 6


title: GES-1_TGFβ_2

city: Shiyan

first: Qin

last: Shanshan

address: Renmin Road 30, Maojian District

country: China

institute: Institute of Basic Medical Sciences, School of Basic Medical Sciences, Hubei University of Medicine

data_processing:
Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts. In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data. At the same time, Q20, Q30 and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality.
Reads were mapped to human genome assembly GRCh38 (ftp://ftp.ensembl.org/pub/release-89/fasta/homo_sapiens/dna/Homo_sapiens.GRCh38.dna.toplevel.fa.gz) using HISAT2 with default parameters.
HTSeq v0.13.5 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene. GTF file:ftp://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_human/release_29/gencode.v29.annotation.gtf.gz.
Assembly: GRCh38
Supplementary files format and content: FileincludeCount and FPKM valuesforeachsample

growth_protocol: The human normal gastric cell line GES-1 was purchased from the Shanghai Cell Bank of Chinese Academy of Sciences (Shanghai, China). The two gastric cancer cell lines were cultured in DMEM medium containing 10% fetal bovine serum (FBS), 100 U/mL penicillin, 100 U/mL streptomycin and 0.03% glutamine at 37 oC in 5% CO2.

extract_protocol:
After 48 hours, remove the medium and directly add 800μL Trizol into the 6-well plate to harvest samples. Total RNA was extracted using Trizol reagent (Invitrogen, USA) according to the manufacturer’s instructions. The RNA purity and concentration was checked using the NanoPhotometer spectrophotometer (IMPLEN, CA, USA).
A total amount of 1.5 µg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext Ultra RNA Library Prep Kit for Illumina (NEB, USA) following manufacturer's recommendations and index codes were added to attribute sequences to each sample.

treatment_protocol: The GC cells were seeded into 6-well plates and grown overnight. The next day, when the cell plating density reached 20%-30%, GC cells were treated with 10 ng/mL rhTGF-beta. At 48 h post-transfection, cells were harvested for RNA sequencing.

value: GC cell

value: 10 ng/mL rhTGFβ


title: GES-1_TGFβ_1


title: Control EB, Day 6, RNA, Replicate 1

value: iPSCs


title: RNA-seq: Prelim iPSC con rep 1

value: Control


title: RNA-seq: Prelim iPSC con rep 3


title: vehicle, ALN-treated, 2wks of daily loading, rep6,lymph node,L [C06]

value: 28 wks


title: vehicle, ALN-treated, 2wks of daily loading, rep6,lymph node,Right [C05]

value: Right


title: vehicle, ALN-treated, 2wks of daily loading, rep7,lymph node,Right [C07]


title: GES-1_NC_2

value: PBS


title: P05

city: Beijing

first: Yongjie

last: Liu

address: No. 1 West Beichen Road, Chaoyang District

institute: Institute of Genetics and Developmental Biology

data_processing:
All 10× Genomics scRNA-seq gene expression raw sequencing data were processed using CellRanger software v.6.0.0
The gene-cell unique molecular identifier (UMI) matrix was analyzed with R software and the Seurat package (version 4.3.0)
The cells in each sample were also filtered for less than 50% mitochondrial reads
All genes that were not detected in ≥3 cells were discarded
Cells with fewer than 200 genes or greater than 5000 total genes were also removed
Assembly: GRCh38
Supplementary files format and content: gene-cell unique molecular identifier (UMI) matrix

source_name: polyps from Peutz-Jeghers syndrome

extract_protocol:
For the preparation of single-cell suspensions from human tissues, both normal colonic tissues and colonic polyps were processed using the same protocol. Briefly, following surgical resection, tissues were immediately placed in RPMI 1640 medium  supplemented with 5% fetal bovine serum (FBS) and transported on ice to the laboratory. The tissues were minced on ice into pieces <1 mm3 and transferred to 10 ml Hanks’ solution containing 1 mg/ml collagenase IV, 1 mg/ml hyaluronidase (Sigma‒Aldrich, St. Louis, MO, USA) and 0.5 mg/ml DNase Ⅰ supplemented with 5% FBS for 30 min at 37 °C. Next, 10 ml ice-cold RPMI 1640 medium with 5% FBS was added. Following centrifugation using a swing-out rotor at 400 × g and 4 °C for 5 min, the supernatant was decanted and discarded, and the cell pellet was resuspended in 2 ml of red blood cell lysis buffer. Following a 5-min incubation at room temperature, the samples were centrifuged (500×g, 4 °C, 5 min). The samples were then resuspended in 1 ml PBS containing 0.04% BSA and filtered through 70-μm cell strainers. The prepared cells were then counted and assessed for viability with Trypan blue using a blood cell counting chamber. The cells were then resuspended at a concentration of 1–1.5 × 106 cells/ml with a final viability of > 80% for scRNA-seq.
Single-cell suspensions were loaded as approximately 10,000 cells per chip position within 15 min of completion of cell suspension preparation using Chromium Single-Cell 3´ reagent kits v3.1. Libraries were prepared using 10X Genomics library kits and sequenced on an Illumina NovaSeq 6000 to generate 150-bp paired-end reads according to the manufacturer’s instructions

value: polyps from Peutz-Jeghers syndrome


title: RNA-seq: Prelim iPSC BPS 1uM rep 1

value: iPSC


title: RNA-seq: Prelim iPSC con rep 2


title: GES-1_NC_1


title: A431 cells, IAA (500 μM) 3, 24 hours

city: Cardiff

first: Van Dien

last: Nguyen

address: Heath Park

department: School of Medicine

country: United Kingdom

institute: Cardiff University

data_processing:
Sequencing reads of all samples were first quality controlled using FastQC v0.11.8 (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/), followed by a trimming process using trimmomatic v0.38 (PMID: 24695404) to obtain high-quality reads
Qualified reads were then mapped to GRCh38 with STAR v2.7.0e
subsequently went through an indexing process with samtools v1.10
Finally, the aligned files were used for generating gene counts by featureCounts programme under subread v2.0.0
ll the mapping process was done on the Hawk high performance computing system based at Cardiff University (https://portal.supercomputing.wales/index.php/about-hawk/).
Assembly: GRCh38
Supplementary files format and content: rpkm normalised counts
Supplementary files format and content: rpkm.all.csv

source_name: A431 cells

extract_protocol:
RNA samples were extracted using NucleoSpin RNA Mini kit (MACHEREY-NAGEL 740955)
Library was prepared using NEB Ultra II directional RNA library prep kit (NEB E7760)
Samples were sequenced using an Illumina HiSeq 4000 with 75 bp paired-end reads

value: A431 cells

value: Wild type

value: IAA (500 uM)


title: A431 cells, IAA (500 μM) 1, 24 hours


title: Control EB, Day 6, RNA, Replicate 2

value: Isogenic Euploid Control


title: vehicle, ALN-treated, 2wks of daily loading, rep5,lymph node,L [C04]

value: L


title: P04

description: gene-cell unique molecular identifier (UMI) matrix


title: EM-seq: Persisting epimutations PGCLC BPS 1uM rep 2

library_source: genomic

data_processing:
EM-seq data was processed using the comprehensive wg-blimp v10.0.0 software pipeline. In brief, reads were trimmed prior to initiating the wg-blimp pipeline using Trim Galore. Sequenced reads were aligned to the mm10 genome using gemBS. The BAM files from alignment underwent a series of QC tests including read quality scoring by FastQC, overall and per-chromosome read coverage calculation, GC content, duplication rate, clipping profiles by Qualimap, and deduplication by the Picard toolkit. Methylation calling was performed by MethylDackel and statistically significant DMC/DMR calling was performed by the metilene and BSmooth algorithms. Metilene uses a binary segmentation algorithm combined with a two-dimensional statistical test that allows the detection of DMCs/DMRs in large methylation experiments with multiple groups of samples. Finally, potential regulatory regions were identified through the use of MethylSeekR. Results from the pipeline were displayed in the wg-blimp interactive results web browser that was built using the R Shiny local browser hosting framework.
Assembly: mm10
Supplementary files format and content: bedGraph
Library strategy: EM-seq

molecule: genomic DNA

extract_protocol:
Genomic DNA was extracted from cells and smaller fragmented DNA (≤ 10 kb) and contaminating RNA were removed by cleaning the genomic DNA on a genomic DNA clean and concentratorTM-10 column (D4011), according to the manufacturer’s instructions (Zymo Research, CA USA). DNA concentration was determined using a Qubit (Q32850) and genomic DNA (100 ng) was sheered using a Bioruptor® and the size of the sheered DNA was determined using a TapeStation 4200 according to the manufacturer’s instructions in the UTSA Genomics Core (Diagenode Inc, NJ USA & Agilent Technologies, Inc CA USA).
Large size (470-520 bp) EM-seq libraries were prepared with the NEBNext® Enzymatic Methyl-seq kit (E7120S) according to the manufacturer’s protocol (New England Biolabs, MA USA). Briefly, this process consisted of A-tailing, adaptor ligation, DNA oxidation by TET2 initiated by the addition of Fe (II), strand denaturization with formamide, deamination by APOBEC3A, polymerase chain reaction amplification, and bead selection to generate the final libraries. Distinct index adaptors were used for multiplexing samples across multiple sequencing lanes.

value: PGCLC

value: BPS 1uM


title: EM-seq: Persisting epimutations PGCLC BPS 1uM rep 3


title: vehicle, ALN-treated, 2wks of daily loading, rep5,lymph node,Right [C03]

value: lymph node


title: A431 cells, cvxIAA (5 μM) 3, 24 hours

value: cvxIAA (5 uM)


title: vehicle, ALN-treated, 2wks of daily loading, rep4,lymph node,Right [C01]


title: P03


title: A431 cells, IAA (500 μM) 2, 24 hours


title: EM-seq: Persisting epimutations PGCLC BPS 1uM rep 1


title: A431 cells, cvxIAA (5 μM) 2, 24 hours


title: P02


title: vehicle, ALN-treated, 2wks of daily loading, rep3,lymph node,L [B99]


title: EM-seq: Persisting epimutations PGCLC con rep 3


title: vehicle, ALN-treated, 2wks of daily loading, rep4,lymph node,L [C02]


title: A431 cells, cvxIAA (5 μM) 1, 24 hours


title: P01


title: J02

source_name: polyps from juvenile polyposis syndromes


title: vehicle, ALN-treated, 2wks of daily loading, rep2,lymph node,L [B97]


title: EM-seq: Persisting epimutations PGCLC con rep 2


title: A431 cells, Pico_cvxIAA (0.5 μM) 2, 24 hours

value: pico_cvxIAA (0.5 uM)


title: J01

value: polyps from juvenile polyposis syndromes


title: S11

source_name: polyps from solitary juvenile polyps

value: polyps from solitary juvenile polyps


title: A431 cells, Pico_cvxIAA (0.5 μM) 1, 24 hours


title: vehicle, ALN-treated, 2wks of daily loading, rep3,lymph node,Right [B98]

value: 28 wks


title: vehicle, ALN-treated, 2wks of daily loading, rep1,lymph node,L [B95]


title: vehicle, ALN-treated, 2wks of daily loading, rep2,lymph node,Right [B96]

value: Right


title: EM-seq: Persisting epimutations iPSC BPS 1uM rep 2


title: EM-seq: Persisting epimutations PGCLC con rep 1

value: Control


title: PTH-pretreated, non-loaded, replicate 16,lymph node,L [890]

value: 26 wks


title: EM-seq: Persisting epimutations iPSC BPS 1uM rep 1

value: iPSC


title: A431 cells, Pico_cvxIAA (0.5 μM) 3, 24 hours

value: A431 cells


title: A431 cells, control 3, 24 hours

value: Wild type

value: DMSO


title: S10


title: vehicle, ALN-treated, 2wks of daily loading, rep1,lymph node,Right [B94]


title: EM-seq: Persisting epimutations iPSC BPS 1uM rep 3


title: EM-seq: Persisting epimutations iPSC con rep 3


title: S08


title: PTH-pretreated, non-loaded, replicate 15,lymph node,Right [883]


title: A431 cells, control 1, 24 hours


title: EM-seq: Persisting epimutations iPSC con rep 2


title: LP_TE9_1

city: La Jolla

first: Heidi

last: Cook-Andersen

state: California

address: 2880 Torrey Pines Scenic Drive, Rm 4811

department: Department of Reproductive Medicine

institute: University of California, San Diego

data_processing:
Adapter sequences were trimmed via cutadapt (v1.10)
Mapping to the genome was conducted via STAR (2.5.2a) and annotated using the Ensembl GRCh38 genome.
Samtools was used to process sam files, and to sort and remove PRC duplicates of bam files
Counts for each gene were quantified using the Subread package FeatureCounts using the gene level quantification in paired-end mode (release 1.5.2)
Count data was normalized to TPM using the Bioconductor package edgeR
Genome_build: GRCh38
Supplementary_files_format_and_content: Tab delimited txt file includes raw counts and normalized TPM reads for each sample

source_name: human blastocyst

growth_protocol: blastocysts were derived from ICSI-fertilized oocytes and cultured under standard conditions in the IVF Clinic (7%CO2/5%O2 in G1 media (from Day 0 to 3) and in G2 media (from Day 3 to 5-6) (Vitrolife) covered in mineral oil). Trophectoderm biopsies (3-5 cells) were collected for preimplantation genetic screening (PGS) before freezing by vitrification on day 5 or 6. PGS analysis was performed via either array comparative genomic hybridization (array CGH) or via next generation sequencing (NGS) by outside commercial laboratories. Prior to analysis, embryos were thawed according to standard protocols and cultured in G-PGD media (Vitrolife) for approximately 12 additional hours, at which time a final stage and morphological grade were assigned before laser dissection and freezing for analysis. Vitrification and thawing were conducted using the Cryotop method (Kitazato). An experienced embryologist used laser dissection to separate the mural TE (mTE) from the ICM compartment. The mTE and ICM samples were individually washed in TE Wash Buffer (1mg/ml bovine serum albumin in 1XPBS), transferred to individual 0.2ml PCR tubes, and frozen immediately in liquid nitrogen.

extract_protocol:
RNA isolation and cDNA synthesis were carried out using the SMARTer® Ultra® Low Input RNA Kit for Sequencing – v4 (Clontech, Cat.no. 634888).
Libraries were generated from the resulting cDNA (0.2ng/ul per sample) using the Nextera XT DNA library preparation kit (Illumina, Cat.no. FC-131-1024)
Indexed sequence libraries were pooled for multiplexing, normalized by MiSeq read number, and paired-end sequencing was performed on a HiSeq 4000.

treatment_protocol: No treatment

tag: phenotype

value: LP (Low-Potential)

value: Trophectoderm (TE)


title: S07


title: PTH-pretreated, non-loaded, replicate 14,lymph node,L [876]

value: L


title: A431 cells, control 2, 24 hours


title: S09


title: EM-seq: Persisting epimutations iPSC con rep 1


title: PTH-pretreated, non-loaded, replicate 13,lymph node,Right [869]


title: LP_TE17_2


title: PTH-pretreated, non-loaded, replicate 12,lymph node,L [862]


title: LP_TE4_2


title: S04


title: S05


title: PTH-pretreated, non-loaded, replicate 11,lymph node,Right [855]


title: LP_TE11_1


title: LP_TE12_1


title: S03


title: PTH-pretreated, non-loaded, replicate 9,lymph node,Right [841]


title: S02


title: LP_TE13_1


title: PTH-pretreated, non-loaded, rep8,lymph node,L [834]


title: M biol rep 1

city: Princeton

first: Celeste

middle: M

last: Nelson

state: NJ

address: 25 William Street

institute: Princeton Univerisity

description:
DESeq2_result_file.tabular.txt
Normalized_counts_file.tabular.txt
rLog-Normalized_counts_file.tabular.txt
VST-Normalized_counts.tabular.txt

data_processing:
Galaxy
HISAT2 was used to align paired-ends and align to Mouse Dec. 2011 (GRCm38/mm19) (mm10).
featureCounts was used to measure gene expression for each sample.
DESeq2 was used for determining normalized counts and differentially expressed features.
Normalized counts were used to determine Z-score for specific genes.
Assembly: GRC m38/mm10 (mm10)
Supplementary files format and content: featureCounts files contain counts of gene expression for each gene (tabular)
Supplementary files format and content: DESeq2 result file (tabular)
Supplementary files format and content: Normalized counts from DESeq2 (tabular)
Supplementary files format and content: rLog normalized counts from DESeq2 (tabular)
Supplementary files format and content: VST normalized counts from DESeq2 (tabular)

growth_protocol: The parental and clonal populations were maintained in RPMI-1640 medium (Hyclone) supplemented with 10% fetal bovine serum (heat-inactivated, Atlanta Biologicals) and 1% gentamicin (Gibco) in humidified atmosphere with 5% CO2 at 37C. Clonal populations were also maintained with 250 µm/mL G418 antibiotic in the medium, but this was removed for culture before the collection of RNA.

extract_protocol:
RNA was collected using an RNeasy Mini Kit (Qiagen) following the manufacturer’s instructions after 72 hours in culture and when the cells had reached ~80% confluency.
RNA-Seq Directional Library Prep on Apollo 324 Robot
NovaSeq SP 100 nucleotide Flowcell v1.5

treatment_protocol: For the generation of the E1, E2, A, and M populations, the parental population was transfected with the purified pNLS-iRFP670 plasmid DNA. The E1, E2, A, and M populations are a result of the isolation of single cells and the generation of clonal populations.

value: mammary carcinoma

value: iRFP670 expressing

tag: population

value: M


title: A biol rep 2

value: A


title: M biol rep 3


title: M biol rep 2


title: LP_TE10_2


title: S01


title: A biol rep 1


title: S06


title: LP_TE10_1


title: PTH-pretreated, non-loaded, rep7,lymph node,Right [827]

value: lymph node


title: N01

source_name: Normal colonic tissue

value: Normal colonic tissue


title: N02


title: A biol rep 3


title: E2 biol rep 2


title: E2 biol rep 3


title: grna library 12, scRNA-seq

city: Durham

first: Charles

middle: A

last: Gersbach

state: North Carolina

address: 101 science drive rm 2323

institute: Duke University

description: 10X Genomics 3' GEX v3.1

data_processing:
All data processing steps were performed using CellRanger v6.0.1 and the human reference genome (‘refdata-gex-GRCh38-2020-A’) was downloaded from 10X Genomics’ software downloads webpage. Fastq files for each flow cell lane and sequencing run were generated from .bcl files using the cellranger mkfastq pipeline. The corresponding fastq files for each sample were then merged. The merged fastqs were then processed using the cellranger count pipeline with the number of expected cells specified (--expect-cells = 15000). The gene expression libraries were then aggregated using the cellranger aggr pipeline. The gRNA libraries were aligned to a custom bowtie index containing all protospacer sequences included in the pooled gRNA library and the UMI counts corresponding to each gRNA-cell pair were obtained.
Assembly: hg38
Supplementary files format and content: Tar files with MatrixMarket, cellular barcodes and features trio of compressed files (matrix.mtx.gz, barcodes.tsv.gz and features.tsv.gz) per GEX and gRNA 10x lane. Aggregated files with counts across all lanes are also provided as supplementary files

source_name: HFF

growth_protocol: Primary human neonatal fibroblasts (HFF cells) were acquired from ATCC (CRL-2097) and cultured in DMEM with 10% FBS, 1% AntiAnti, and 1% NEAA (Sigma) on tissue culture plastic. All work was performed within 30 doublings from the initial passage of the vial.

extract_protocol: Cells were washed 3x with PBS and then resuspended to a final concentration of 1000 cells/uL. Approximately 20,000 cells were loaded onto each channel of a 10X Genomics’ 3’ Gene Expression (GEX) v3.1 assay chip. Downstream processing was performed according to the manufacturer’s protocol. To recover the protospacer sequences (gRNA libraries), a tri-nested PCR was performed separately for each GEX library using 10% of the purified cDNA as input to reaction 1 as previously described [PMID: 30612741]. Briefly, 4ng cDNA was input into a 50 uL reaction with KAPA HiFi and PCR primers prLRB470 and prLRB471. The reaction was amplified for 12 cycles and then purified using 25 uL of AMPure XP DNA beads and eluted in 25 uL H20. 1 uL of the purified sample was input into reaction 2 using PCR primers prLRB472 and prLRB473. The reaction was amplified for 14 cycles and purified as described above. 1 uL of the purified sample was input into reaction 3 using PCR primers prLRB473 and prLRB289-302, amplifying each sample with a unique i7 sequencing index. The reaction was amplified for 7 cycles, purified using 25 uL of AMPure XP DNA beads (Beckman Coulter #A63881), and eluted in 25 uL Buffer EB (Qiagen #19086). Quality control of final libraries was performed prior to sequencing using the Agilent 2200 TapeStation with High Sensitivity DNA 5000 reagents, Qubit High Sensitivity dsDNA reagents, and KAPA Library Quantification Kit for Illumina platforms.

treatment_protocol: To perform screening, 775k HFF cells stably expressing dCas9-KRAB were transduced at 0.33MOI with the CROP-seq lentivirus to maintain a coverage of at least 150 cells/gRNA. Following 20 hours, viral media was removed and replaced with regular growth media, and 48 hours post-transduction the cells selected with puromycin (1.5 ug/mL) for 4 days. Following puromycin selection, HFF cells were maintained until day 8, at which point cells were trypsinized and 150k cells were moved on to 10X library prep.

value: HFF

value: Human foreskin fibroblasts

value: gRNA library


title: PTH-pretreated, non-loaded, rep5,lymph node,Right [813]

value: Right

value: 26 wks


title: HP_TE7_2

value: HP (High-Potential)


title: E2 biol rep 1


title: PTH-pretreated, non-loaded, replicate 10,lymph node,L [848]


title: PTH-pretreated, non-loaded, rep6,lymph node,L [820]


title: PTH-pretreated, non-loaded, rep4,lymph node,L [806]


title: E1 biol rep 3


title: HP_TE15_2


title: PTH-pretreated, non-loaded, rep3,lymph node,Right [799]


title: HP_TE13_2


title: grna library 10, scRNA-seq

description: 10X Genomics 3' GEX v3.1


title: HP_TE12_2


title: HP_TE1_1


title: E1 biol rep 2


title: PTH-pretreated, non-loaded, rep2,lymph node,L [792]


title: grna library 8, scRNA-seq

description: 10X Genomics 3' GEX v3.1


title: grna library 9, scRNA-seq

description: 10X Genomics 3' GEX v3.1


title: E1 biol rep 1


title: parental biol rep 3

value: WT

value: parental


title: PTH-pretreated, non-loaded, rep1,lymph node,Right [785]


title: grna library 7, scRNA-seq

description: 10X Genomics 3' GEX v3.1


title: grna library 11, scRNA-seq

description: 10X Genomics 3' GEX v3.1


title: HP_TE14_2


title: parental biol rep 2


title: vehicle, non-loaded, rep15,lymph node,Right [771]


title: LP_ICM4_2

value: LP (Low-Potential)

value: Inner Cell Mass (ICM)


title: grna library 5, scRNA-seq

description: 10X Genomics 3' GEX v3.1


title: LP_ICM13_1


title: grna library 4, scRNA-seq

description: 10X Genomics 3' GEX v3.1


title: LP_ICM12_1


title: grna library 6, scRNA-seq

description: 10X Genomics 3' GEX v3.1


title: AA, baseline, scRNAseq

city: Oklahoma City

first: Huiping

last: Shi

state: Oklahoma

address: 825 NE 13th St

institute: Oklahoma Medical Research Foundation

description: 10x Genomics

data_processing:
Cell Ranger software was used for read alignment, feature-barcode matrix generation, and cell clustering
Assembly: mm39
Supplementary files format and content: Tab-separated value files and matrix files

source_name: Liver

extract_protocol:
Mouse liver was perfused and digested in situ. Liver cells were passed through 40 μm cell strainers, followed by low-speed centrifugation to enrich non-parenchymal cells. Dead cells were removed using Ficoll solution. FACS sorting was used to enrich macrophage populations and sort live single cells.
The Chromium Next GEM 3' Kit v3.1 (Cat#1000268, 10x Genomics) was used to capture the single cell poly-adenylated mRNA according to the 10x Genomics 3' protocol. Sequencing libraries were prepared using the 10x Genomics Library Construction Kit (Cat#1000190) with the Dual Index Kit TT Set A (Cat#1000215).

value: Liver

value: A/A

value: Baseline


title: parental biol rep 1

value: mammary carcinoma


title: SS, baseline, scRNAseq

description: 10x Genomics

value: S/S


title: vehicle, non-loaded, rep13,lymph node,Right [757]

value: lymph node


title: SS, TNF, scRNAseq

description: 10x Genomics

value: 500 ng TNF


title: vehicle, non-loaded, rep11,lymph node,Right [743]


title: grna library 2, scRNA-seq

description: 10X Genomics 3' GEX v3.1

value: HFF


title: LP_ICM17_2


title: LP_ICM11_1


title: LP_ICM10_2


title: vehicle, non-loaded, rep12,lymph node,L [750]

value: L


title: vehicle, non-loaded, rep16,lymph node,L [778]


title: AA, TNF, scRNAseq

description: 10x Genomics


title: vehicle, non-loaded, rep10,lymph node,L [736]


title: LP_ICM9_1


title: LP_ICM10_1


title: vehicle, non-loaded, rep14,lymph node,L [764]


title: GEX library 12, scRNA-seq

description: 10X Genomics 3' GEX v3.1

value: Human foreskin fibroblasts

value: gRNA library


title: vehicle, non-loaded, rep9,lymph node,Right [729]

value: Right

value: 26 wks


title: Liver, male, 2B6, 10 PFOS, sample 159 [M_159_2B6_10]

city: Central

first: Lanie

last: Williams

state: SOUTH CAROLINA

address: 1980 West Main Street, Unit 67

department: Biological Sciences

institute: Clemson University

description:
M2B6_10_3
Raw_Counts_Male_Cyp2bnull_hCYP2B6_PFOS.xlsx
M2B6_10_vs_M2B6_0.xlsx
M2B6_10_vs_M2B6_1.xlsx
M2B6_10_vs_MN_10.xlsx
F2B6_10_vs_M2B6_10.xlsx

data_processing:
Quality checks of raw reads were performed using FASTQC (Andews, 2010).
Adaptor and low quality reads were trimmed with Trim Galore (https://www.bioinformatics.babraham.ac.uk/projects/trim_galore/).
Reads were aligned to the reference renome with RSEM (Haas, 2013).
Mapped reads were counted with featureCounts (Liao, 2014).
Differential expression analysis was performed in edgeR.
Assembly: GRCm39
Supplementary files format and content: Two Excel files for raw counts in males and females named - Raw_Counts_Female_Cyp2bnull_hCYP2B6_PFOS and Raw_Counts_Male_Cyp2bnull_hCYP2B6_PFOS
Supplementary files format and content: Excel files for each comparison of differential expression after processing in EdgeR. File name describes the comparison performed. F2B6 - female hCYP2B6; FN - female Cyp2b-null; M2B6 - male hCYP2B6; MN - male Cyp2b-null. Numbers indicate PFOS treatment - 0, 1, or 10 corresponds to 0, 1, or 10 mg/kg/day PFOS.

growth_protocol: Ten to twelve week old mice were kept in a controlled facility with a 12h:12h light:dark cycle at 24 degrees Celsius and fed a normal diet of 18% kcal fat for 21 days.

extract_protocol:
RNA extractions were performed on 20 mg of liver tissue previously stored at -80C. RNA was extracted with TRIzol (Life Technology, Carlsbad, CA USA) and chloroform. Quality was checked via Nanodrop (Thermo Fisher Scientific, Walkham, MA USA) to ensure both A260/280 and A260/230 values were about 2.0.
Library construction was performed by Novogene (Sacramento, CA USA) using messenger RNA purified from total RNA. Quality was checked with Qubit (Thermo Fisher Scientific, Walkham, MA USA).

treatment_protocol: PFOS (0, 1 or 10 mg/kg/day) was dissolved in water and 0.5% Tween 20 and administered via oral gavage.

value: 10 mg/kg/day PFOS

tag: Sex

value: Male


title: grna library 3, scRNA-seq

description: 10X Genomics 3' GEX v3.1


title: HP_ICM7_2

value: HP (High-Potential)


title: GEX library 11, scRNA-seq

description: 10X Genomics 3' GEX v3.1


title: HP_ICM15_2

value: Inner Cell Mass (ICM)


title: vehicle, non-loaded, rep7,lymph node,Right [715]


title: Liver, male, 2B6, 10 PFOS, sample 149 [M_149_2B6_10]

description:
M2B6_10_1
Raw_Counts_Male_Cyp2bnull_hCYP2B6_PFOS.xlsx
M2B6_10_vs_M2B6_0.xlsx
M2B6_10_vs_M2B6_1.xlsx
M2B6_10_vs_MN_10.xlsx
F2B6_10_vs_M2B6_10.xlsx

value: Liver


title: Liver, male, 2B6, 10 PFOS, sample 154 [M_154_2B6_10]

description:
M2B6_10_2
Raw_Counts_Male_Cyp2bnull_hCYP2B6_PFOS.xlsx
M2B6_10_vs_M2B6_0.xlsx
M2B6_10_vs_M2B6_1.xlsx
M2B6_10_vs_MN_10.xlsx
F2B6_10_vs_M2B6_10.xlsx


title: grna library 1, scRNA-seq

description: 10X Genomics 3' GEX v3.1


title: HP_ICM13_2


title: GEX library 9, scRNA-seq

description: 10X Genomics 3' GEX v3.1


title: GEX library 10, scRNA-seq

description: 10X Genomics 3' GEX v3.1


title: vehicle, non-loaded, rep6,lymph node,L [708]


title: Liver, male, null, 10 PFOS, sample 207 [M_207_N_10]

description:
MN_10_3
Raw_Counts_Male_Cyp2bnull_hCYP2B6_PFOS.xlsx
MN_10_vs_MN_0.xlsx
MN_10_vs_MN_1.xlsx
M2B6_10_vs_MN_10.xlsx
FN_10_vs_MN 10.xlsx


title: Liver, male, 2B6, 10 PFOS, sample 160 [M_160_2B6_10]

description:
M2B6_10_4
Raw_Counts_Male_Cyp2bnull_hCYP2B6_PFOS.xlsx
M2B6_10_vs_M2B6_0.xlsx
M2B6_10_vs_M2B6_1.xlsx
M2B6_10_vs_MN_10.xlsx
F2B6_10_vs_M2B6_10.xlsx


title: GEX library 8, scRNA-seq

description: 10X Genomics 3' GEX v3.1


title: vehicle, non-loaded, rep4,lymph node,L [694]


title: HP_ICM12_2


title: HP_ICM1_1


title: vehicle, non-loaded, rep8,lymph node,L [722]


title: Mature Osteoclast biol rep 3

city: Philadelphia

first: Chao

last: Song

state: Pennsylvania

address: 4141 Spruce St., Room 308

institute: Children's Hospital of Philadelphia

data_processing:
Raw sequence data (.bcl files) generated from the sequencer were converted into fastq files and de-multiplexed using Illumina's bcl2fastq 2.17 software
After investigating the quality of the raw data, sequence reads were trimmed to remove possible adapter sequences and nucleotides with poor quality using Trimmomatic v.0.36
The trimmed reads were mapped to the reference genome available on ENSEMBL using the STAR aligner v.2.5.2b
After extraction of gene hit counts, the gene hit counts table was used for downstream differential expression analysis.
Assembly: mm10
Supplementary files format and content: tab-delimited text files include TPM values for each Sample

source_name: Mature Osteoclast

growth_protocol: BMM were cultured with customized αMEM supplemented with 10% fetal bovine serum (FBS) (Atlanta Biologicals) together with 10% CMG14-12 cell culture supernatant.

extract_protocol:
Total RNA was extracted with RNeasy kits (Qiagen, USA) before being subjected to high-throughput RNA sequencing (Genewiz, USA).
The RNA sequencing libraries were prepared using the NEBNext Ultra II RNA Library Prep Kit for Illumina following manufacturer’s instructions (New England Biolabs, USA)

treatment_protocol: For osteoclast differentiation assays, BMM were cultured with customized αMEM containing 10% FBS, 1/50 CMG14-12 supernatant and 75 ng/ml recombinant RANKL for 4 days.

value: Mature Osteoclast

value: WT

value: Osteoclastogenic differentiation for 4 days


title: HP_ICM14_2


title: vehicle, non-loaded, rep3,lymph node,Right [687]


title: Liver, male, null, 10 PFOS, sample 201 [M_201_N_10]

description:
MN_10_2
Raw_Counts_Male_Cyp2bnull_hCYP2B6_PFOS.xlsx
MN_10_vs_MN_0.xlsx
MN_10_vs_MN_1.xlsx
M2B6_10_vs_MN_10.xlsx
FN_10_vs_MN 10.xlsx


title: Liver, male, null, 10 PFOS, sample 199 [M_199_N_10]

description:
MN_10_1
Raw_Counts_Male_Cyp2bnull_hCYP2B6_PFOS.xlsx
MN_10_vs_MN_0.xlsx
MN_10_vs_MN_1.xlsx
M2B6_10_vs_MN_10.xlsx
FN_10_vs_MN 10.xlsx


title: Liver, male, null, 10 PFOS, sample 208 [M_208_N_10]

description:
MN_10_4
Raw_Counts_Male_Cyp2bnull_hCYP2B6_PFOS.xlsx
MN_10_vs_MN_0.xlsx
MN_10_vs_MN_1.xlsx
M2B6_10_vs_MN_10.xlsx
FN_10_vs_MN 10.xlsx


title: Mature Osteoclast biol rep 2


title: Mature Osteoclast biol rep 1


title: vehicle, non-loaded, rep2,lymph node,L [680]


title: Liver, male, 2B6, 1 PFOS, sample 141 [M_141_2B6_1]

description:
M2B6_1_3
Raw_Counts_Male_Cyp2bnull_hCYP2B6_PFOS.xlsx
M2B6_1_vs_M2B6_0.xlsx
M2B6_10_vs_M2B6_1.xlsx
M2B6_1_vs_MN_1.xlsx
F2B6_1_vs_M2B6_1.xlsx

value: 1 mg/kg/day PFOS


title: vehicle, non-loaded, rep5,lymph node,Right [701]

value: lymph node


title: GEX library 4, scRNA-seq

description: 10X Genomics 3' GEX v3.1


title: GEX library 6, scRNA-seq

description: 10X Genomics 3' GEX v3.1


title: GEX library 5, scRNA-seq

description: 10X Genomics 3' GEX v3.1


title: GEX library 7, scRNA-seq

description: 10X Genomics 3' GEX v3.1


title: GEX library 3, scRNA-seq

description: 10X Genomics 3' GEX v3.1


title: PTH-pretreated, ALN-treated, 2wks of daily loading, rep8,cartilage,Right [B93]

source_name: cartilage

value: cartilage

value: 28 wks


title: PTH-pretreated, ALN-treated, 2wks of daily loading, rep8,cartilage,L [B92]

value: L


title: Liver, male, 2B6, 1 PFOS, sample 136 [M_136_2B6_1]

description:
M2B6_1_2
Raw_Counts_Male_Cyp2bnull_hCYP2B6_PFOS.xlsx
M2B6_1_vs_M2B6_0.xlsx
M2B6_10_vs_M2B6_1.xlsx
M2B6_1_vs_MN_1.xlsx
F2B6_1_vs_M2B6_1.xlsx


title: Liver, male, 2B6, 1 PFOS, sample 133 [M_133_2B6_1]

description:
M2B6_1_1
Raw_Counts_Male_Cyp2bnull_hCYP2B6_PFOS.xlsx
M2B6_1_vs_M2B6_0.xlsx
M2B6_10_vs_M2B6_1.xlsx
M2B6_1_vs_MN_1.xlsx
F2B6_1_vs_M2B6_1.xlsx


title: BMM biol rep 2

source_name: BMM

value: BMM

value: No treatment


title: Liver, male, 2B6, 1 PFOS, sample 143 [M_143_2B6_1]

description:
M2B6_1_4
Raw_Counts_Male_Cyp2bnull_hCYP2B6_PFOS.xlsx
M2B6_1_vs_M2B6_0.xlsx
M2B6_10_vs_M2B6_1.xlsx
M2B6_1_vs_MN_1.xlsx
F2B6_1_vs_M2B6_1.xlsx


title: GEX library 1, scRNA-seq

description: 10X Genomics 3' GEX v3.1

value: HFF

value: Human foreskin fibroblasts

value: gRNA library


title: GEX library 2, scRNA-seq

description: 10X Genomics 3' GEX v3.1


title: BMM biol rep 3


title: BMM biol rep 1


title: PTH-pretreated, ALN-treated, 2wks of daily loading, rep7,cartilage,Right [B91]

value: Right


title: Patient with R22W mutation in TFRC

city: Adelaide

first: Nick

last: Warnock

state: South Australia

address: UniSA Bradley Building, North Terrace

department: Centre for Cancer Biology

country: Australia

institute: SA Pathology

data_processing:
Adapters were trimmed using cutadapt version 4.1 and the following parameters: -a CTGTCTCTTATACACATCT -A CTGTCTCTTATACACATCT --minimum-length=18 --error-rate 0.2 --overlap=5
Reads were aligned to the hg38 reference genome using STAR version 2.7.7a, producing gene counts for each sample
Assembly: GCA_000001405.15_GRCh38_no_alt_analysis_set.fna.gz using RefSeq annotations
Supplementary files format and content: <library_name>.hg38.ReadsPerGene.out.tab: tab-separated gene counts file for each sample
Supplementary files format and content: gene_counts.tsv: tab-separated file containing strand-specific gene counts for all samples

source_name: PBMCs

extract_protocol:
Total RNA was extracted from the peripheral blood mononuclear cells (PBMCs) of the patient and healthy controls using Blood RNA purification kit (Macherey-Nagel).
RNA libraries were prepared using an Illumina Stranded mRNA Prep kit according to the manufacturer's protocols

value: PBMCs


title: Liver, male, null, 1 PFOS, sample 195 [M_195_N_1]

description:
MN_1_3
Raw_Counts_Male_Cyp2bnull_hCYP2B6_PFOS.xlsx
MN_1_vs_MN_0.xlsx
MN_10_vs_MN_1.xlsx
M2B6_1_vs_MN_1.xlsx
FN_1_vs_MN_1.xlsx

value: Male


title: vehicle, non-loaded, rep1,lymph node,Right [673]

source_name: lymph node

value: 26 wks


title: PTH-pretreated, ALN-treated, 2wks of daily loading, rep6,cartilage,Right [B89]


title: Liver, male, null, 1 PFOS, sample 184 [M_184_N_1]

description:
MN_1_2
Raw_Counts_Male_Cyp2bnull_hCYP2B6_PFOS.xlsx
MN_1_vs_MN_0.xlsx
MN_10_vs_MN_1.xlsx
M2B6_1_vs_MN_1.xlsx
FN_1_vs_MN_1.xlsx

value: Liver


title: PTH-pretreated, ALN-treated, 2wks of daily loading, rep7,cartilage,L [B90]


title: replicate2, ASCs_NWAT

city: Changsha

first: Limin

last: Xie

state: Hunan

address: No.139，Renmin Road Central Changsha, Hunan, China

institute: The second xiangya hospital of central south university

data_processing:
The Cell Ranger software was obtained from 10× Genomics website.  Alignment, filtering, barcode counting, and UMI counting were performed with cell ranger count module on the raw sequencing data to generate a gene-barcode matrix for subsequent analysis.
The output of Cell Ranger filtered gene expression matrix were analyzed by R software with the Seurat package.
Before the downstream analysis, a step-by-step quality-filtering process was used to remove low-quality nuclei. First, mitochondrial reads were filtered on the threshold of 15%, the UMIs were filtered on the threshold of 1000, detected features were filtered on the threshold of 300, and the ratio of the number of UMIs to features was filtered with a threshold of 2.5. Second, outlier detection was performed using PCA calculated from quality metrics in Scater38. Third, genes expressed in fewer than ten nuclei were removed. Fourth, the nuclei were clustered using Seurat39, and clusters with fewer UMIs low features, or high doublet scores40 were removed iteratively.
After removal of low-quality cells, the gene expression matrices were normalized by the NormalizeData function in Seurat.
Assembly: GRCm38.p6
Supplementary files format and content: tab-delimited text file includes raw counts for each sample
Supplementary files format and content: tab-delimited text file includes FPKM values for each sample

source_name: Perirenal white adipose tissue

extract_protocol:
The mulitiple white adipose tissues were obtained, then cut into small pieces (~1mm) and digested with 1 mg/ml Type II collagenase (Sigma-Aldrich, MO) and 1% bovine serum albumin (Gibco, CA) at 37°C for 45 min with constant rocking. The cell mixture was filtered through a 70 μm filter into a single-cell suspension, followed by centrifugation at 500 g for 5 min, and stromal vascular cells were treated with a red cell lysis buffer. Appropriate cell suspensions were then hybridized with fluorescent dye-conjugated antibodies against the following mouse antigens.
RNA libraries for RNA-seq were prepared following manufacture's protocols.

value: Perirenal white adipose tissue

value: male

value: adipose-derived stem cells

tag: diet

value: chow diet

tag: strain

value: C57BL/6J wild type


title: replicate1, ASCs_NWAT


title: PTH-pretreated, ALN-treated, 2wks of daily loading, rep6,cartilage,L [B88]

data_processing:
Computational was performed in a Unix environment
12bp were trimmed from 5’ end of sequenc reads using fastx_trimmer
Sequence reads were trimmed using trimmomatic(v0.39)
Trimmed sequences were mapped to mm10 using STAR
Each sample contained over 1 million of uniquely mapped reads to the mouse genome. Genes with less than 3 counts per million were not included for analysis.
Assembly: mm10
Supplementary files format and content: normalizedcounts.xls file includes normalized value from edgeR for each sample

extract_protocol:
RNA was extracted using Rneasy kit (Qiagen). 20uL of total RNA was used for construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using Truseq (Illumina) – 3’ RNAseq Kit following maufacturer’s protocols

value: cartilage

value: 28 wks


title: PTH-pretreated, ALN-treated, 2wks of daily loading, rep5,cartilage,Right [B87]


title: replicate2, ASCs_MWAT

source_name: Mesenteric white adipose tissue

value: Mesenteric white adipose tissue


title: Liver, male, null, 1 PFOS, sample 181 [M_181_N_1]

description:
MN_1_1
Raw_Counts_Male_Cyp2bnull_hCYP2B6_PFOS.xlsx
MN_1_vs_MN_0.xlsx
MN_10_vs_MN_1.xlsx
M2B6_1_vs_MN_1.xlsx
FN_1_vs_MN_1.xlsx

value: 1 mg/kg/day PFOS


title: Liver, male, 2B6, 0 PFOS, sample 120 [M_120_2B6_0]

description:
M2B6_0_4
Raw_Counts_Male_Cyp2bnull_hCYP2B6_PFOS.xlsx
M2B6_10_vs_M2B6_0.xlsx
M2B6_1_vs_M2B6_0.xlsx
M2B6_0_vs_MN_0.xlsx
F2B6_0_vs_M2B6_0.xlsx

value: 0 mg/kg/day PFOS


title: replicate1, ASCs_MWAT


title: Liver, male, 2B6, 0 PFOS, sample 118 [M_118_2B6_0]

description:
M2B6_0_3
Raw_Counts_Male_Cyp2bnull_hCYP2B6_PFOS.xlsx
M2B6_10_vs_M2B6_0.xlsx
M2B6_1_vs_M2B6_0.xlsx
M2B6_0_vs_MN_0.xlsx
F2B6_0_vs_M2B6_0.xlsx


title: PTH-pretreated, ALN-treated, 2wks of daily loading, rep5,cartilage,L [B86]

value: L


title: PBMCs of CAD patients for the input group

city: Nanjing

first: Enzhi

last: Jia

state: Jiangsu

address: Guangzhou Road 300

institute: The First Affiliated Hospital of Nanjing Medical University

description: case-input

data_processing:
Paired-end reads were harvested from Illumina Novaseq 6000 sequencer, and were quality controlled by FastQC. After 3’ adaptor-trimming and low quality reads removing by cutadapt software (v1.9.3), clean reads were obtained.
Clean reads were mapped to the human reference genome (UCSC hg38) via HISAT2 software (v 2.2.0).
Assembly: hg38
Supplementary files format and content: all.id.txt: Tab-delimited text file includes raw counts for each sample.
Library strategy: ChIRP-RNA-seq

source_name: Blood

extract_protocol:
RNA bound to BTBD7_hsa_circ_0000563 was harvested using ChIRP kit (Gzscbio, China).
RNA library was constructed using NEBNext® Ultra™ RNA Library Prep Kit for Illumina® (NEB, USA) according to the manufacturer’s instructions.

value: Blood

tag: diagnosis

value: Coronary artery disease

tag: sample type

value: Input


title: Liver, male, null, 1 PFOS, sample 196 [M_196_N_1]

description:
MN_1_4
Raw_Counts_Male_Cyp2bnull_hCYP2B6_PFOS.xlsx
MN_1_vs_MN_0.xlsx
MN_10_vs_MN_1.xlsx
M2B6_1_vs_MN_1.xlsx
FN_1_vs_MN_1.xlsx

value: Male


title: PTH-pretreated, ALN-treated, 2wks of daily loading, rep4,cartilage,Right [B85]

city: Ithaca

first: Marjolein

last: van der Meulen

address: Weill Hall

institute: Cornell University

value: Right


title: 8032-S9_S9_L002

city: 5841 S Maryland Ave. MC3026

first: Eric

last: Thompson

state: IL

institute: The University of Chicago

description: D324 G207 24hr

data_processing:
Sample fastq file quality metrics were assessed via FastQC v0.11.9 and MultiQC v1.11. Paired-end reads were aligned to the GRCh38.p14 human reference genome via STAR v2.7.2b with default parameter settings. Post-alignment quality metrics were assessed via the log file output of STAR. Quantification and generation of the raw counts matrix were performed by featureCounts v1.6.3. The raw counts matrix was then normalized, and differential expression was calculated via DeSeq2 R package v1.36.0.
Assembly: GRCh38.p14
Supplementary files format and content: Single .csv file contains gene counts for all samples with each sample containing two entries; one for each sequencing lane (L001 and L002)

source_name: D324 medulloblastoma

growth_protocol: D283,D324, D556, D456: DMEM-12 plus 10% FNS, 1% NEAA, 1% glutamine; X21584: neurobasal medium plus FGF, EGF, B-27 supplement, L-glutamine, amphotericin, and gentamicin; D341: Improved MEM Zinc option.

extract_protocol:
The Sequencing and Genomic Technologies (SGT) Core Facility at Duke University performed RNA sequencing. The SGT Core Facility extracted total RNA from cell pellets using the RNeasy Plus Mini Kit from Qiagen (catalog #: 74134). mRNA was enriched from total RNA and reverse-transcribed into cDNA to build sequencing libraries using the KAPA mRNA HyperPrep Kit from Roche (KK8581).
Libraries were pooled to equimolar concentrations and sequenced on the NovaSeq 6000 S2 flow cell to produce 50 bp paired-end reads.

value: medulloblastoma cell line


title: PBMCs of CAD patients for the target group

description: case-target

value: PBMCs

value: Bound to BTBD7_hsa_circ_0000563


title: replicate1, ASCs_EWAT

source_name: Epididymal white adipose tissue

value: Epididymal white adipose tissue

value: male

value: adipose-derived stem cells


title: Liver, male, 2B6, 0 PFOS, sample 107 [M_107_2B6_0]

description:
M2B6_0_1
Raw_Counts_Male_Cyp2bnull_hCYP2B6_PFOS.xlsx
M2B6_10_vs_M2B6_0.xlsx
M2B6_1_vs_M2B6_0.xlsx
M2B6_0_vs_MN_0.xlsx
F2B6_0_vs_M2B6_0.xlsx

value: Liver


title: replicate2, ASCs_SWAT

source_name: Subcutaneous white adipose tissue

value: Subcutaneous white adipose tissue

value: chow diet

value: C57BL/6J wild type


title: replicate2, ASCs_EWAT


title: 8032-S9_S9_L001

description: D324 G207 24hr


title: Liver, male, 2B6, 0 PFOS, sample 109 [M_109_2B6_0]

description:
M2B6_0_2
Raw_Counts_Male_Cyp2bnull_hCYP2B6_PFOS.xlsx
M2B6_10_vs_M2B6_0.xlsx
M2B6_1_vs_M2B6_0.xlsx
M2B6_0_vs_MN_0.xlsx
F2B6_0_vs_M2B6_0.xlsx

value: 0 mg/kg/day PFOS


title: PTH-pretreated, ALN-treated, 2wks of daily loading, rep4,cartilage,L [B84]

value: cartilage

value: L

value: 28 wks


title: PTH-pretreated, ALN-treated, 2wks of daily loading, rep3,cartilage,Right [B83]


title: Liver, male, null, 0 PFOS, sample 179 [M_179_N_0]

description:
MN_0_4
Raw_Counts_Male_Cyp2bnull_hCYP2B6_PFOS.xlsx
MN_10_vs_MN_0.xlsx
MN_1_vs_MN_0.xlsx
M2B6_0_vs_MN_0.xlsx
FN_0_vs_MN_0.xlsx


title: 8032-S8_S8_L002

description: D324 G207 24hr


title: replicate1, ASCs_SWAT


title: PTH-pretreated, ALN-treated, 2wks of daily loading, rep3,cartilage,L [B82]


title: 8032-S8_S8_L001

description: D324 G207 24hr


title: Liver, male, null, 0 PFOS, sample 129 [M_129_N_0]

description:
MN_0_2
Raw_Counts_Male_Cyp2bnull_hCYP2B6_PFOS.xlsx
MN_10_vs_MN_0.xlsx
MN_1_vs_MN_0.xlsx
M2B6_0_vs_MN_0.xlsx
FN_0_vs_MN_0.xlsx


title: PTH-pretreated, ALN-treated, 2wks of daily loading, rep2,cartilage,Right [B81]


title: Liver, male, null, 0 PFOS, sample 167 [M_167_N_0]

description:
MN_0_3
Raw_Counts_Male_Cyp2bnull_hCYP2B6_PFOS.xlsx
MN_10_vs_MN_0.xlsx
MN_1_vs_MN_0.xlsx
M2B6_0_vs_MN_0.xlsx
FN_0_vs_MN_0.xlsx


title: PTH-pretreated, ALN-treated, 2wks of daily loading, rep2,cartilage,L [B80]


title: PTH-pretreated, ALN-treated, 2wks of daily loading, rep1,cartilage,Right [B79]


title: Liver, male, null, 0 PFOS, sample 126 [M_126_N_0]

description:
MN_0_1
Raw_Counts_Male_Cyp2bnull_hCYP2B6_PFOS.xlsx
MN_10_vs_MN_0.xlsx
MN_1_vs_MN_0.xlsx
M2B6_0_vs_MN_0.xlsx
FN_0_vs_MN_0.xlsx


title: 8032-S7_S7_L001

description: D324 G207 24hr


title: PTH-pretreated, ALN-treated, 2wks of daily loading, rep1,cartilage,L [B78]


title: 8032-S78_S78_L002

description: D283 PVSRIPO 24hr

source_name: D283 medulloblastoma

value: PVSRIPO


title: Liver, female, 2B6, 10 PFOS, sample 150 [F150_2B6_10]

description:
F2B6_10_3
Raw_Counts_Female_Cyp2bnull_hCYP2B6_PFOS.xlsx
F2B6_10_vs_F2B6_0.xlsx
F2B6_10_vs_F2B6_1.xlsx
F2B6_10_vs_FN_10.xlsx
F2B6_10_vs_M2B6_10.xlsx

value: 10 mg/kg/day PFOS

value: Female


title: Liver, female, 2B6, 10 PFOS, sample 152 [F152_2B6_10]

description:
F2B6_10_4
Raw_Counts_Female_Cyp2bnull_hCYP2B6_PFOS.xlsx
F2B6_10_vs_F2B6_0.xlsx
F2B6_10_vs_F2B6_1.xlsx
F2B6_10_vs_FN_10.xlsx
F2B6_10_vs_M2B6_10.xlsx


title: vehicle, ALN-treated, 2wks of daily loading, rep8,cartilage,Right [B77]

value: Right


title: Liver, female, 2B6, 10 PFOS, sample 144 [F144_2B6_10]

description:
F2B6_10_2
Raw_Counts_Female_Cyp2bnull_hCYP2B6_PFOS.xlsx
F2B6_10_vs_F2B6_0.xlsx
F2B6_10_vs_F2B6_1.xlsx
F2B6_10_vs_FN_10.xlsx
F2B6_10_vs_M2B6_10.xlsx


title: 8032-S78_S78_L001

description: D283 PVSRIPO 24hr

value: medulloblastoma cell line


title: Liver, female, 2B6, 10 PFOS, sample 142 [F142_2B6_10]

description:
F2B6_10_1
Raw_Counts_Female_Cyp2bnull_hCYP2B6_PFOS.xlsx
F2B6_10_vs_F2B6_0.xlsx
F2B6_10_vs_F2B6_1.xlsx
F2B6_10_vs_FN_10.xlsx
F2B6_10_vs_M2B6_10.xlsx


title: 8032-S77_S77_L002

description: D283 PVSRIPO 24hr


title: 8032-S77_S77_L001

description: D283 PVSRIPO 24hr


title: vehicle, ALN-treated, 2wks of daily loading, rep7,cartilage,Right [B75]


title: Liver, female, null, 10 PFOS, sample 156 [F156_N_10]

description:
FN_10_4
Raw_Counts_Female_Cyp2bnull_hCYP2B6_PFOS.xlsx
FN_10_vs_FN_0.xlsx
FN_10_vs_FN_1.xlsx
F2B6_10_vs_FN_10.xlsx
FN_10_vs_MN 10.xlsx


title: 8032-S76_S76_L002

description: D283 PVSRIPO 24hr


title: vehicle, ALN-treated, 2wks of daily loading, rep7,cartilage,L [B74]


title: 8032-S7_S7_L002

description: D324 G207 24hr


title: 8032-S76_S76_L001

description: D283 PVSRIPO 24hr


title: Liver, female, null, 10 PFOS, sample 137 [F137_N_10]

description:
FN_10_2
Raw_Counts_Female_Cyp2bnull_hCYP2B6_PFOS.xlsx
FN_10_vs_FN_0.xlsx
FN_10_vs_FN_1.xlsx
F2B6_10_vs_FN_10.xlsx
FN_10_vs_MN 10.xlsx


title: vehicle, ALN-treated, 2wks of daily loading, rep6,cartilage,Right [B73]


title: vehicle, ALN-treated, 2wks of daily loading, rep8,cartilage,L [B76]


title: Liver, female, null, 10 PFOS, sample 134 [F134_N_10]

description:
FN_10_1
Raw_Counts_Female_Cyp2bnull_hCYP2B6_PFOS.xlsx
FN_10_vs_FN_0.xlsx
FN_10_vs_FN_1.xlsx
F2B6_10_vs_FN_10.xlsx
FN_10_vs_MN 10.xlsx


title: vehicle, ALN-treated, 2wks of daily loading, rep6,cartilage,L [B72]


title: 8032-S75_S75_L001

description: D283 PVSRIPO 8hr


title: Col_2DG_1mM_24h_3

city: Kyoto

first: Akira

last: Mine

state: Kyoto

address: Kitashirakawaoiwake-cho

department: Graduate School of Agriculture

country: Japan

institute: Kyoto university

data_processing:
RNA-seq was performed on the HiseqX platform at Macrogen.
Reads were quality filtered by fastp (ver. 0.19.7) with the parameters -A -x -f 8 -q 30.
Arabidopsis genome indexes were generated by STAR (ver. 2.6.1b) using the the paremeters --runMode genomeGenerate --genomeDir /home/user/ngs/data1/At_genome_sjdbOverhang139/ --genomeFastaFiles Arabidopsis_thaliana.TAIR10.dna.toplevel.fa --sjdbGTFfile Arabidopsis_thaliana.TAIR10.34.gtf --sjdbOverhang 139 --runThreadN 8
Reads were mapped by STAR (ver. 2.6.1b) with the parameters --runMode alignReads --genomeDir /home/user/ngs/data1/At_genome_sjdbOverhang139/ --runThreadN 8 --outFilterScoreMinOverLread 0.3 --outFilterMatchNminOverLread 0.3, and transformed to a count per gene per library by featureCounts (ver. 1.6.0) with the parameters -s 1 -t exon -g gene_id -a /home/user/ngs/data1/At_genome/Arabidopsis_thaliana.TAIR10.34.gtf.
Supplementary_files_format_and_content: Tab-delimited text file including raw read counts per gene for each sample.

organism: Arabidopsis thaliana

source_name: Seven-day-old plants

growth_protocol: Arabidopsis plants were grown in a chamber at 22°C with a 16 h light period on 1/2 MS 25mM sucrose agar media.

extract_protocol:
Total RNAs were extracted using Sepazol-RNA I Super G (Nacalai tesque), followed by RQ1 RNase-Free DNase  (Promega) treatment.
Libraries were prepared from 500 ng of total RNA. BrAD-seq (Townsley et al., 2015) was used to to create strand specific 3-prime digital gene expression.

treatment_protocol: Six-day-old Arabidopsis plants were transferred into 1/2 liquid media with 25 mM sucrose (for flg22) or without sucrose (for 2-deoxy-d-glucose) for 1 day, and treated with 1μM flg22 or 1mM 2-deoxy-d-glucose

value: Col

tag: replicate


title: OE_LINC4

type: RNA

city: Barcelona

first: Júlia

last: Perera-Bel

address: Doctor Aiguader, 88

department: MARData-BU

country: Spain

institute: Hospital del Mar Research Institute

description: Gene expression data from in vitro differentiated adipocytes (lincRNA overexpression during 96h)

hyb_protocol: Sample was hybridized to Affymetrix Clariom S Human array using an Affymetrix GeneChip Hybridization Oven 645

scan_protocol: GeneChip was scanned using the Affymetrix Expression Wash, Stain and Scan User Manual (P/N 702731 Rev. 3) (Affymetrix Inc., Santa Clara, CA, USA) using Affymetrix GeneChip Scanner 3000 7G.

data_processing: The data were analyzed using the RMA algorithm and then LIMMA was applied to calculate significant differential expression between samples

label: Biotin

source_name: Cultures of in vitro differentiated primary subcutaneous human adipocytes

label_protocol: 100ng of total RNA from each sample was processed and labelled according to manual GeneChip WT PLUS Reagent kit (P/N 703174 Rev. 2, Affymetrix Inc., Santa Clara, CA, USA)

growth_protocol: To induce the adipogenic conversion of adipocyte progenitors, human preadipocytes (SP-F-1, Zen-Bio, Inc.) were led to grow as a monolayer in preadipocyte medium (PM-1) until reaching confluence, and then incubated with adipocyte differentiation medium (DM-2) for 7 days. This media is composed of DMEM / Ham’s F-12 (1:1), HEPES, FBS, biotin, pantothenate, insulin, dexamethasone, IBMX, PPARγ agonist, penicillin, streptomycin and amphotericin B. Thereafter, differentiating adipocytes were maintained in adipocyte maintenance medium (AM-1) for 7 additional days (DM-2 without dexamethasone, IBMX and PPARγ agonists). During this process, the shape of preadipocytes evolves from the flattened form to rounded cells containing abundant lipid droplets, and are thus considered differentiated, mature adipocytes (~12th day and thereafter).

extract_protocol: Total RNA was purified from human adipose tissue and cells using RNeasy Mini Kit (QIAgen, 74104). Fat samples (~150 µg) and cell monolayers were homogenized in 0.6 mL of QIAzol® Lysis Reagent (QIAgen, 79306).

treatment_protocol: Differentiated fat cells were transfected 1:3 with either our construct or an empty plasmid control using the FuGENE® HD Transfection Reagent (Promega)

tag: tissue

value: in vitro differentiated adipocytes

tag: condition

value: LINC


title: Col_Suc_25mM_24h_3


title: OE_LINC2

value: Cultures of in vitro differentiated primary subcutaneous human adipocytes


title: 8032-S74_S74_L002

description: D283 PVSRIPO 8hr

tag: cell type

tag: cell line


title: Col_Suc_0mM_24h_3

tag: genotype

tag: treatment


title: Liver, female, null, 10 PFOS, sample 138 [F138_N_10]

description:
FN_10_3
Raw_Counts_Female_Cyp2bnull_hCYP2B6_PFOS.xlsx
FN_10_vs_FN_0.xlsx
FN_10_vs_FN_1.xlsx
F2B6_10_vs_FN_10.xlsx
FN_10_vs_MN 10.xlsx

value: Liver


title: OE_LINC5


title: 8032-S74_S74_L001

description: D283 PVSRIPO 8hr


title: Liver, female, 2B6, 1 PFOS, sample 128 [F128_2B6_1]

description:
F2B6_1_3
Raw_Counts_Female_Cyp2bnull_hCYP2B6_PFOS.xlsx
F2B6_1_vs_F2B6_0.xlsx
F2B6_10_vs_F2B6_1.xlsx
F2B6_1_vs_FN_1.xlsx
F2B6_1_vs_M2B6_1.xlsx

value: 1 mg/kg/day PFOS


title: OE_LINC1


title: Liver, female, 2B6, 1 PFOS, sample 125 [F125_2B6_1]

description:
F2B6_1_2
Raw_Counts_Female_Cyp2bnull_hCYP2B6_PFOS.xlsx
F2B6_1_vs_F2B6_0.xlsx
F2B6_10_vs_F2B6_1.xlsx
F2B6_1_vs_FN_1.xlsx
F2B6_1_vs_M2B6_1.xlsx


title: CONTROL4

description: Gene expression data from in vitro differentiated adipocytes (non-targeting control)

value: Control


title: vehicle, ALN-treated, 2wks of daily loading, rep5,cartilage,L [B70]

tag: limb

tag: age


title: vehicle, ALN-treated, 2wks of daily loading, rep4,cartilage,Right [B69]


title: CONTROL6


title: Col_Suc_25mM_24h_2

tag: time


title: 8032-S75_S75_L002

description: D283 PVSRIPO 8hr


title: vehicle, ALN-treated, 2wks of daily loading, rep5,cartilage,Right [B71]


title: vehicle, ALN-treated, 2wks of daily loading, rep4,cartilage,L [B68]


title: Liver, female, 2B6, 1 PFOS, sample 121 [F121_2B6_1]

description:
F2B6_1_1
Raw_Counts_Female_Cyp2bnull_hCYP2B6_PFOS.xlsx
F2B6_1_vs_F2B6_0.xlsx
F2B6_10_vs_F2B6_1.xlsx
F2B6_1_vs_FN_1.xlsx
F2B6_1_vs_M2B6_1.xlsx


title: OE_LINC3


title: Liver, female, 2B6, 1 PFOS, sample 131 [F131_2B6_1]

description:
F2B6_1_4
Raw_Counts_Female_Cyp2bnull_hCYP2B6_PFOS.xlsx
F2B6_1_vs_F2B6_0.xlsx
F2B6_10_vs_F2B6_1.xlsx
F2B6_1_vs_FN_1.xlsx
F2B6_1_vs_M2B6_1.xlsx


title: CONTROL5


title: CONTROL1


title: Liver, female, null, 1 PFOS, sample 130 [F130_N_1]

description:
FN_1_4
Raw_Counts_Female_Cyp2bnull_hCYP2B6_PFOS.xlsx
FN_1_vs_FN_0.xlsx
FN_10_vs_FN_1.xlsx
F2B6_1_vs_FN_1.xlsx
FN_1_vs_MN_1.xlsx


title: 8032-S73_S73_L001

description: D283 PVSRIPO 8hr


title: Col_Suc_0mM_24h_2


title: 8032-S72_S72_L002

description: D341 PVSRIPO 24hr

source_name: D341 medulloblastoma


title: Liver, female, null, 1 PFOS, sample 123 [F123_N_1]

description:
FN_1_3
Raw_Counts_Female_Cyp2bnull_hCYP2B6_PFOS.xlsx
FN_1_vs_FN_0.xlsx
FN_10_vs_FN_1.xlsx
F2B6_1_vs_FN_1.xlsx
FN_1_vs_MN_1.xlsx


title: vehicle, ALN-treated, 2wks of daily loading, rep3,cartilage,L [B66]


title: 8032-S72_S72_L001

description: D341 PVSRIPO 24hr


title: Col_Suc_25mM_24h_1


title: vehicle, ALN-treated, 2wks of daily loading, rep2,cartilage,Right [B65]


title: Liver, female, null, 1 PFOS, sample 117 [F117_N_1]

description:
FN_1_2
Raw_Counts_Female_Cyp2bnull_hCYP2B6_PFOS.xlsx
FN_1_vs_FN_0.xlsx
FN_10_vs_FN_1.xlsx
F2B6_1_vs_FN_1.xlsx
FN_1_vs_MN_1.xlsx


title: Col_2DG_1mM_24h_1


title: CONTROL3


title: 8032-S71_S71_L002

description: D341 PVSRIPO 24hr


title: vehicle, ALN-treated, 2wks of daily loading, rep2,cartilage,L [B64]


title: 8032-S73_S73_L002

description: D283 PVSRIPO 8hr


title: Liver, female, null, 1 PFOS, sample 116 [F116_N_1]

description:
FN_1_1
Raw_Counts_Female_Cyp2bnull_hCYP2B6_PFOS.xlsx
FN_1_vs_FN_0.xlsx
FN_10_vs_FN_1.xlsx
F2B6_1_vs_FN_1.xlsx
FN_1_vs_MN_1.xlsx


title: 8032-S71_S71_L001

description: D341 PVSRIPO 24hr


title: vehicle, ALN-treated, 2wks of daily loading, rep1,cartilage,Right [B63]


title: Liver, female, 2B6, 0 PFOS, sample 112 [F112_2B6_0]

description:
F2B6_0_4
Raw_Counts_Female_Cyp2bnull_hCYP2B6_PFOS.xlsx
F2B6_10_vs_F2B6_0.xlsx
F2B6_1_vs_F2B6_0.xlsx
FN_0_vs_F2B6_0.xlsx
F2B6_0_vs_M2B6_0.xlsx


title: 8032-S70_S70_L002

description: D341 PVSRIPO 24hr


title: vehicle, ALN-treated, 2wks of daily loading, rep3,cartilage,Right [B67]


title: fls2_flg22_10h_3


title: Col_Suc_0mM_24h_1


title: stp1/4/13_flg22_10h_3


title: 8032-S6_S6_L001

description: D324 G207 8hr


title: Liver, female, 2B6, 0 PFOS, sample 104 [F104_2B6_0]

description:
F2B6_0_2
Raw_Counts_Female_Cyp2bnull_hCYP2B6_PFOS.xlsx
F2B6_10_vs_F2B6_0.xlsx
F2B6_1_vs_F2B6_0.xlsx
FN_0_vs_F2B6_0.xlsx
F2B6_0_vs_M2B6_0.xlsx


title: PTH-pretreated, ALN-treated, 2wks of daily loading, rep8,cortical bone,Right [B27]

source_name: cortical bone

value: cortical bone


title: 8032-S70_S70_L001

description: D341 PVSRIPO 24hr


title: Col_flg22_10h_3


title: Liver, female, 2B6, 0 PFOS, sample 110 [F110_2B6_0]

description:
F2B6_0_3
Raw_Counts_Female_Cyp2bnull_hCYP2B6_PFOS.xlsx
F2B6_10_vs_F2B6_0.xlsx
F2B6_1_vs_F2B6_0.xlsx
FN_0_vs_F2B6_0.xlsx
F2B6_0_vs_M2B6_0.xlsx

source_name: Liver

value: 0 mg/kg/day PFOS


title: 8032-S69_S69_L002

description: D341 PVSRIPO 8hr


title: Col_2DG_1mM_24h_2


title: Liver, female, 2B6, 0 PFOS, sample 101 [F101_2B6_0]

description:
F2B6_0_1
Raw_Counts_Female_Cyp2bnull_hCYP2B6_PFOS.xlsx
F2B6_10_vs_F2B6_0.xlsx
F2B6_1_vs_F2B6_0.xlsx
FN_0_vs_F2B6_0.xlsx
F2B6_0_vs_M2B6_0.xlsx


title: PTH-pretreated, ALN-treated, 2wks of daily loading, rep8,cortical bone,L [B23]


title: 8032-S6_S6_L002

description: D324 G207 8hr


title: PTH-pretreated, ALN-treated, 2wks of daily loading, rep8,cancellous bone,Right [B26]

source_name: cancellous bone

value: cancellous bone


title: stp1/4/13_flg22_10h_2


title: Liver, female, null, 0 PFOS, sample 114 [F114_N_0]

description:
FN_0_4
Raw_Counts_Female_Cyp2bnull_hCYP2B6_PFOS.xlsx
FN_10_vs_FN_0.xlsx
FN_1_vs_FN_0.xlsx
FN_0_vs_F2B6_0.xlsx
FN_0_vs_MN_0.xlsx


title: PTH-pretreated, ALN-treated, 2wks of daily loading, rep8,cancellous bone,L [B22]

value: L


title: 8032-S69_S69_L001

description: D341 PVSRIPO 8hr


title: Liver, female, null, 0 PFOS, sample 113 [F113_N_0]

description:
FN_0_3
Raw_Counts_Female_Cyp2bnull_hCYP2B6_PFOS.xlsx
FN_10_vs_FN_0.xlsx
FN_1_vs_FN_0.xlsx
FN_0_vs_F2B6_0.xlsx
FN_0_vs_MN_0.xlsx


title: vehicle, ALN-treated, 2wks of daily loading, rep1,cartilage,L [B62]

source_name: cartilage

value: cartilage

value: 28 wks


title: Col_flg22_10h_2


title: PTH-pretreated, ALN-treated, 2wks of daily loading, rep7,cortical bone,Right [B19]


title: Liver, female, null, 0 PFOS, sample 108 [F108_N_0]

description:
FN_0_2
Raw_Counts_Female_Cyp2bnull_hCYP2B6_PFOS.xlsx
FN_10_vs_FN_0.xlsx
FN_1_vs_FN_0.xlsx
FN_0_vs_F2B6_0.xlsx
FN_0_vs_MN_0.xlsx


title: fls2_flg22_10h_1


title: 8032-S68_S68_L002

description: D341 PVSRIPO 8hr

value: PVSRIPO


title: Liver, female, null, 0 PFOS, sample 100 [F100_N_0]

description:
FN_0_1
Raw_Counts_Female_Cyp2bnull_hCYP2B6_PFOS.xlsx
FN_10_vs_FN_0.xlsx
FN_1_vs_FN_0.xlsx
FN_0_vs_F2B6_0.xlsx
FN_0_vs_MN_0.xlsx

value: Female


title: stp1/4/13_flg22_10h_1


title: Col_flg22_10h_1


title: 8032-S68_S68_L001

description: D341 PVSRIPO 8hr


title: PTH-pretreated, ALN-treated, 2wks of daily loading, rep7,cortical bone,L [B15]


title: 8032-S67_S67_L002

description: D341 PVSRIPO 8hr


title: 5HT_4

city: New York

first: Katherine

last: Sanidad

address: 413 E69th St

institute: Weill Cornell Medicine

data_processing:
Annotation, mapping and counting of the resulted reads were analyzed by SALMON with default parameters
LEfSe followed by multiple hypotheses correction using signal-to-noise rate and false discovery rate analyses was used to discover genes with differential abundance. Differences at LEfSe p < 0.05  and FDR < 0.05 were considered significant.
Assembly: GRCm38
Supplementary files format and content: xlsx containing Salmon output (TPM and fold change calculations)

source_name: Small intestine

extract_protocol:
Total RNA from whole SI tissue was isolated using the Qiagen RNeasy® Mini Kit (Qiagen 74104)
Libraries were prepared for sequencing using the NEB Ultra II Directional RNA Library Prep kit with Poly A isolation module

treatment_protocol: GF WT neonatal mice were given 50 μL of 5-HT (12.5 μg/mL) or vehicle (PBS) at P8 and P9 via oral gavage. The mice were then sacrificed at P14 and SI tissue was harvested.

value: Small intestine

value: WT


title: 5HT_2


title: stp1/4/13_flg22_24h_3


title: 5HT_3


title: 8032-S67_S67_L001

description: D341 PVSRIPO 8hr

value: medulloblastoma cell line


title: PTH-pretreated, ALN-treated, 2wks of daily loading, rep6,cortical bone,Right [B11]

value: Right


title: 8032-S66_S66_L002

description: D556 PVSRIPO 24hr

source_name: D556 medulloblastoma


title: fls2_flg22_24h_3


title: 5HT_1


title: Col_flg22_24h_3

value: Col


title: 8032-S66_S66_L001

description: D556 PVSRIPO 24hr


title: PTH-pretreated, ALN-treated, 2wks of daily loading, rep6,cortical bone,L [B07]


title: PTH-pretreated, ALN-treated, 2wks of daily loading, rep6,cancellous bone,Right [B10]


title: PBS_4

value: PBS


title: 8032-S65_S65_L002

description: D556 PVSRIPO 24hr


title: PBS_3


title: PTH-pretreated, ALN-treated, 2wks of daily loading, rep6,cancellous bone,L [B06]


title: PTH-pretreated, ALN-treated, 2wks of daily loading, rep7,cancellous bone,Right [B18]


title: fls2_flg22_2h_3


title: stp1/4/13_flg22_2h_3


title: PTH-pretreated, ALN-treated, 2wks of daily loading, rep5,cortical bone,Right [B03]


title: 8032-S65_S65_L001

description: D556 PVSRIPO 24hr


title: PBS_2


title: Col_flg22_2h_3


title: 8032-S64_S64_L002

description: D556 PVSRIPO 24hr


title: PTH-pretreated, ALN-treated, 2wks of daily loading, rep5,cancellous bone,Right [B02]


title: fls2_flg22_24h_2


title: PBS_1


title: PTH-pretreated, ALN-treated, 2wks of daily loading, rep5,cancellous bone,L [A97]


title: 8032-S63_S63_L002

description: D556 PVSRIPO 8hr


title: fls2_flg22_2h_2


title: PTH-pretreated, ALN-treated, 2wks of daily loading, rep5,cortical bone,L [A98]


title: 8032-S64_S64_L001

description: D556 PVSRIPO 24hr


title: stp1/4/13_flg22_24h_2


title: 8032-S62_S62_L002

description: D556 PVSRIPO 8hr


title: GCI+FST+BLA

city: qingdao

first: xufeng

last: xu

address: No. 16 Jiangsu Road

institute: qingdao university

data_processing:
addgeneid.txt abundance files report read counts
Assembly: MM10
Supplementary files format and content: addgeneid.txt abundance files report read counts

molecule: nuclear RNA

source_name: brain

extract_protocol:
Seven days after GCI or sham operation, mice received forced swimming test, followed 30 min later by rapidly extracting the whole brains and placed on a precooled metal plate. Bilateral vmPFCs and BLAs were rapidly dissected according to anatomical landmarks.
Single cell sequencing was performed using the 10 X Genomics
Libraries were sequenced on the Illumina NovaSeq 6000 System at LC Bio Technology Co., Ltd. in Hangzhou, China.

value: brain

tag: tissue region

value: BLA

value: neuron

value: GCI+FST


title: GCI +FST +VMPFC, rep1

value: VMPFC

value: GCI +FST


title: PTH-pretreated, ALN-treated, 2wks of daily loading, rep4,cortical bone,Right [A94]

value: cortical bone


title: 8032-S63_S63_L001

description: D556 PVSRIPO 8hr


title: Col_flg22_24h_2


title: 8032-S62_S62_L001

description: D556 PVSRIPO 8hr


title: PTH-pretreated, ALN-treated, 2wks of daily loading, rep4,cancellous bone,Right [A93]

value: cancellous bone


title: SHAM + FST+ VMPFC, rep2

value: SHAM + FST


title: SHAM + FST+BLA


title: Col_flg22_2h_2


title: PTH-pretreated, ALN-treated, 2wks of daily loading, rep4,cortical bone,L [A90]

value: L

value: 28 wks


title: 8032-S61_S61_L002

description: D556 PVSRIPO 8hr

value: PVSRIPO


title: SHAM + FST+ VMPFC, rep1


title: stp1/4/13_flg22_2h_2


title: PTH-pretreated, ALN-treated, 2wks of daily loading, rep4,cancellous bone,L [A89]


title: fls2_flg22_24h_1


title: 8032-S61_S61_L001

description: D556 PVSRIPO 8hr


title: PTH-pretreated, ALN-treated, 2wks of daily loading, rep3,cortical bone,Right [A86]


title: stp1/4/13_flg22_24h_1


title: GCI +FST +VMPFC, rep2


title: RAW_NC_3

city: Dalian

first: Yanshuo

last: Han

address: No.2 Dagong Road

institute: Dalian University of Technology

data_processing:
Raw sequencing data was first filtered by fastp (version 0.23.4), low-quality reads were discarded and the reads contaminated with adaptor sequences were trimmed.(Parameters: ILLUMINACLIP:{adaptor.fa}:2:30:10  -phred33 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 HEADCROP:0 MINLEN:36 PE)
Clean Reads were further treated with in-house scripts to eliminate duplication bias introduced in library preparation and sequencing by Unique Molecular Identifier(UMI).
The de-duplicated consensus sequences were mapped to the GRCm38 using STAR software (version 2.5.3a) with default parameters.(Parameters: --outSAMtype BAM SortedByCoordinate)
Read count extraction and normalization were performed using featureCounts（Version 1.5.1）（parameter -T 10 -d 30 -D 1000 -C -s 1 -t {exon} -g {geneid} --primary -O -a {gff_annotation_file}）
Genes differentially expressed between groups were identified using the edgeR package (version 3.12.1).(Parameters: pvalue<0.05 |log2foldchang|>1)
Assembly: GRCm38
Supplementary files format and content: tab-delimited text file includes read count values for each Sample

growth_protocol: RAW264.7 macrophages were maintained in DMEM supplemented with 10% Fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37℃.

extract_protocol:
Total RNA was collected by TRIzol method. 2 μg total RNA was used for the construction of sequencing libraries.
RNA-seq libraries were prepared using KC-DigitalTM Stranded mRNA Library Prep Kit(Catalog NO. DR08502, Wuhan Seqhealth Co., Ltd. China) following manufacturer's instruction.

treatment_protocol: Then RAW264.7 macrophages were transfected with 50 nM concentration of Ep300_siRNA and nc_siRNA, respectively, using riboFECTTM CP transfection kit method (C10511-05, RiboBio) for 48 hours according to the instructions.

value: macrophages

value: WT


title: PTH-pretreated, ALN-treated, 2wks of daily loading, rep3,cancellous bone,Right [A85]

value: Right


title: RAW_NC_2


title: RAW_NC_1


title: PTH-pretreated, ALN-treated, 2wks of daily loading, rep3,cancellous bone,L [A81]


title: 8032-S5_S5_L002

description: D324 G207 8hr

value: medulloblastoma cell line


title: Col_flg22_24h_1

value: Col


title: stp1/4/13_flg22_2h_1


title: 8032-S5_S5_L001

description: D324 G207 8hr


title: PTH-pretreated, ALN-treated, 2wks of daily loading, rep3,cortical bone,L [A82]


title: fls2_flg22_2h_1


title: PTH-pretreated, ALN-treated, 2wks of daily loading, rep2,cortical bone,Right [A78]


title: 8032-S60_S60_L001

description: D324 PVSRIPO 24 hr


title: 8032-S59_S59_L002

description: D324 PVSRIPO 24 hr


title: 8032-S59_S59_L001

description: D324 PVSRIPO 24 hr


title: RAW_Ep300_2

value: Ep300 silenced


title: Col_flg22_2h_1


title: PTH-pretreated, ALN-treated, 2wks of daily loading, rep2,cancellous bone,Right [A77]


title: RAW_Ep300_1


title: JEL423_rep3

city: Riverside

first: Jason

last: Stajich

address: 900 Univeristy Avenue

department: Microbiology and Plant Pathology

institute: University of California, Riverside

data_processing:
Reads were aligned to reference genomes GCA_000149865.1 and  JAQIHF000000000 using Hisat2  v2.2.1
Raw read counts were generated with FeatureCounts from Rsubread (Liao, Smyth, and Shi 2019) and TPM values were calculated with edgeR (Robinson, McCarthy, and Smyth 2010)
Assembly: GCA_000149865.1 and  JAQIHF000000000
Supplementary files format and content: comma separated files containing transcript counts for each sample when aligning to the reference genome GCA_000149865.1
Supplementary files format and content: comma separated file containing transcript counts for each sample when aligning to the reference genome JAQIHF000000000

organism: Batrachochytrium dendrobatidis

source_name: fungi

growth_protocol: 5e5 zoospores from Bd strains CLFT044, CLFT061, CLFT067, CLFT071, CLFT085, and JEL423 were inoculated on 1% Tryptone agar and incubated at 18C for seven days.

extract_protocol:
RNA was extracted using TRIzol following manufacturer's protocols and incorporating a 12 hour isopropanol precipitation to increase yields.
mRNA library preparation (poly A enrichment) at Novogene

value: fungi

value: Bd-GPL


title: PTH-pretreated, ALN-treated, 2wks of daily loading, rep7,cancellous bone,L [B14]


title: JEL423_rep2


title: PTH-pretreated, ALN-treated, 2wks of daily loading, rep2,cortical bone,L [A74]


title: 8032-S58_S58_L002

description: D324 PVSRIPO 24 hr


title: pMacs, WT, M, Y, untreated, replicate 2

city: Atlanta

first: Karen

middle: N

last: McFarland

state: GA

address: 100 Woodruff Circle

department: Pharmacology

institute: Emory University

data_processing:
Reads were aligned to mouse genome GRCm39/v107 with STAR v2.7.9a
Gene counts were generated from bam files using Rsamtools v2.16.0 and the summarizeOverlaps function with the GenomicAlignments v1.36.0 package in R
Differential genes were analyzed with DESeq2 v1.40.2 in R using default settings.
Gene ontology enrichment analysis was performed with goseq v1.52.0 in R.
Assembly: GRCm39/v107
Supplementary files format and content: comma-separated text file includes FPKM values for each sample
Supplementary files format and content: comma-separated text file includes raw count values for each sample

source_name: primary peripheral macrophages

growth_protocol: Peritoneal macrophages were harvested from mice that had received a 1 ml intraperitoneal administration of 3% Brewer thioglycolate broth 72 hours prior collection. Mice also received Buprenorphine Sustained-Release every 48 hours for pain relief. Mice were sacrificed via cervical dislocation and abdomen sprayed with 70% Ethanol. The skin of the abdomen was split along the midline, taking care to avoid puncturing or cutting the abdominal cavity. 10 mL of cold RPMI media (Gibco; 11875119) was injected into the peritoneal cavity using a 27G needle. After gentle massaging of the peritoneal cavity, as much fluid was withdrawn as possible from the peritoneal cavity using a 25G needle and 10 mL syringe. Aspirated fluid was passed through a 70uM nylon filter onto 50mL falcon and pre-wet with 5mL of HBSS-/-. Filters were then washed twice with 5mL of HBSS-/- and then tubes spun at 400x g for 5 minutes at 4°C. Supernatant was aspirated and pellet resuspended in 3 mL pre-warmed growth media (RPMI, 10% FBS, 1% Pen-Strep). Cells were counted and viability recorded using trypan-blue exclusion on an automated cell-counter (Countess™; Thermo). Volume growth media was adjusted so that cells were plated at 5 x 105/mL in 6-, 24- or 96-well plates depending on the intended assay. Cells were incubated at 37°C, 5% CO2 for a minimum of 2-to-3 hours to allow macrophages to adhere. Wells were washed twice with sterile PBS to remove non-adherent cells and new, pre-warmed growth media added.

extract_protocol:
RNA from approximately 2-4 x 106 cells was isolated. RNeasy mini kit (Qiagen) was used according to manufacturer’s instructions. Briefly, 10 µL of β-mercaptoethanol was added to every 1 mL of RLT buffer. 350 µL was added to each well and cells homogenized manually with a mini cell scraper. Cell lysate was transferred to an RNAase free Eppendorf and an equal volume of 70% ethanol was added to each sample. Samples were loaded into supplier columns and centrifuged at 11,000 x g for 30 seconds and flow through discarded. 350 µL RW1 buffer was added to each column and centrifuged at 11,000 x g for 15 seconds and flow through discarded. RW1 buffer was added and columns centrifuged at 11,000 x g for 15 seconds. RPE buffer was added to columns, centrifuged for 11,000 x g for 30 seconds, repeated, and 30 µL RNase-free water was added and RNA was eluted. RNA concentration was quantified and 260/230 and 260/280 ratios recorded using a spectrophotometer. RIN values were assessed to ensure RNA integrity using Agilent RNA 6000 Nano Kit (Agilent) and Agilent 2100 Bioanalyzer
RNA was sent to the Interdisciplinary Center for Biotechnology Research (ICBR) core at the University of Florida, where library preparation was performed following the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina manual and 2x150bp paired-end sequencing completed on an Illumina NovaSeq 6000 (Illumina).

treatment_protocol: For cells requiring ex vivo stimulation, 100U of IFNγ (R&D) or vehicle (H2O) was added for 18 hours. For co-treatments, a final concentration of 40 nM Bafilomycin A1 (Sigma) and 100 nM PF360 (PF-06685360; MedChem) was used.

value: M

value: young

value: primary peripheral macrophages

value: wild-type

value: untreated


title: pMacs, WT, M, Y, untreated, replicate 3


title: 8032-S60_S60_L002

description: D324 PVSRIPO 24 hr


title: RAW_Ep300_3


title: PTH-pretreated, ALN-treated, 2wks of daily loading, rep2,cancellous bone,L [A73]

value: cancellous bone


title: 8032-S58_S58_L001

description: D324 PVSRIPO 24 hr


title: PTH-pretreated, ALN-treated, 2wks of daily loading, rep1,cortical bone,Right [A70]

value: cortical bone


title: pMacs, WT, M, Y, IFN-treated, replicate 5

value: interferon-gamma


title: CLFT085_rep3


title: 8032-S57_S57_L002

description: D324 PVSRIPO 8 hr

value: PVSRIPO


title: PTH-pretreated, ALN-treated, 2wks of daily loading, rep1,cancellous bone,Right [A69]

value: 28 wks


title: pMacs, WT, M, Y, untreated, replicate 1


title: pMacs, WT, M, Y, IFN-treated, replicate 4


title: 8032-S57_S57_L001

description: D324 PVSRIPO 8 hr


title: 8032-S56_S56_L002

description: D324 PVSRIPO 8 hr


title: CLFT085_rep2


title: CLFT085_rep1


title: PTH-pretreated, ALN-treated, 2wks of daily loading, rep1,cancellous bone,L [A65]

value: L


title: pMacs, WT, M, Y, IFN-treated, replicate 3


title: CLFT061_rep3

value: Bd-BRAZIL


title: 8032-S56_S56_L001

description: D324 PVSRIPO 8 hr

value: medulloblastoma cell line


title: CLFT061_rep2


title: JEL423_rep1


title: pMacs, WT, M, Y, IFN-treated, replicate 2


title: 8032-S55_S55_L002

description: D324 PVSRIPO 8 hr


title: vehicle, ALN-treated, 2wks of daily loading, rep8,cancellous bone,Right [A61]

value: Right


title: PTH-pretreated, ALN-treated, 2wks of daily loading, rep1,cortical bone,L [A66]


title: 8032-S55_S55_L001

description: D324 PVSRIPO 8 hr


title: vehicle, ALN-treated, 2wks of daily loading, rep8,cortical bone,Right [A62]


title: pMacs, WT, M, Y, IFN-treated, replicate 1


title: pMacs, WT, M, O, untreated, replicate 3

value: old


title: CLFT061_rep1

value: fungi


title: vehicle, ALN-treated, 2wks of daily loading, rep8,cortical bone,L [A58]


title: 8032-S54_S54_L002

description: X21584 G207 24hr

source_name: X21584 pediatric high grade glioma

value: pediatric high grade glioma cell line


title: CLFT044_rep2


title: 8032-S54_S54_L001

description: X21584 G207 24hr


title: CLFT044_rep1


title: 8032-S53_S53_L002

description: X21584 G207 24hr


title: 8032-S53_S53_L001

description: X21584 G207 24hr


title: pMacs, WT, M, O, IFN-treated, replicate 5

value: M


title: vehicle, ALN-treated, 2wks of daily loading, rep7,cortical bone,Right [A54]


title: pMacs, WT, M, O, IFN-treated, replicate 4


title: microorganism,mutant-coculture,24h,rep3

first: Yanan

last: Wang

state: Liaoning

address: Ganjingzi District

institute: Dalian Polytechnic University

data_processing:
clean data (clean reads) were obtained by removing  reads containing adapter, reads containing N base and low quality reads from  raw data.
Both building index of reference genome and aligning clean reads to reference genome were used Bowtie2-2.2.3.
Rockhopper was used to identify novel genes, operon, TSS, TTS and Cis_x0002_natural antisense transcripts.
Differential expression analysis of two  conditions/groups (two biological replicates per condition) was performed using  the DESeq R package
Gene Ontology (GO) enrichment analysis of differentially expressed genes was implemented by the GOseq R package and used KOBAS3 software to test the statistical enrichment of differential expression genes in KEGG pathways.
Assembly: 569
Supplementary files format and content: H. alvei H4WT and P. fluorescens ATCC13525
Supplementary files format and content: H. alvei H4ΔluxI and P. fluorescens ATCC13525

organism:
Pseudomonas fluorescens
Hafnia alvei

source_name: H. alvei H4 {delta}luxI +P. fluorescens ACTT13525

extract_protocol:
The RNA was harvested from H. alvei H4WT/ΔluxI and P. fluorescens ATCC13525
Total RNA was used as input material for the RNA sample preparations. For  prokaryotic samples, mRNA was purified from total RNA using probes to  remove rRNA.


title: pMacs, WT, M, O, untreated, replicate 1