title: RNAseq_ZT18a_mouse14

city: Mexico City

first: Mayra

last: Furlan-Magaril

state: Mexico City

address: Circuito exterior s/n

department: Molecular Genetics

country: Mexico

institute: IFC-UNAM

description:
ZT18 mouse 14, PoolA
RNAseq_ZT18_merge_norm_forward.bw
RNAseq_ZT18_merge_norm_reverse.bw

data_processing:
Raw sequencing data files for all samples were first processed with FastQC for general quality controls. Sequencing reads were mapped against the mouse genome (NCBIM37/mm9) using TopHat (D. Kim et al., 2013) with default parameters.
To create bigWig signal tracks for all time points we merged all biological replicates per time point using samtools (Li et al., 2009). Merged bam files per time point were processed with Deeptools bamCoverage to create strand-specific and RPKM normalized signal tracks suited for comparison.
Genome_build: Mus musculus mm9
Supplementary_files_format_and_content: big wig of the stranded reads

growth_protocol: Mice were under a 12 hours light 12 hours dark cycle. Fed ad libitum

extract_protocol:
Liver RNA was extracted using trizol reagent
Stranded Total RNA seq
Truseq stranded total RNA seq Ribo Zero Gold Illumina

tag: strain

value: liver

value: 8 week old

tag: Sex

value: male

tag: genotype

value: wilde type

tag: time point


title: RNAseq_ZT18b_mouse15

status: Public on May 04 2021

type: SRA

description:
ZT18 mouse 15, PoolB
RNAseq_ZT18_merge_norm_forward.bw
RNAseq_ZT18_merge_norm_reverse.bw

library_source: transcriptomic

molecule: total RNA

organism: Mus musculus

tag: tissue

tag: age


title: DNA_RAL04-D0

city: Atlanta

first: Rafick-Pierre

last: Sekaly

state: GA

address: 1750 Haygood Drive

department: Pathology

country: USA

institute: Emory University

description:
PathSeq
Uganda_Longitudinal_B1_PathSeq_TPM.xlsx

library_source: genomic

data_processing:
Library strategy: PathSeq metagenome
sorted cells/plasma: Raw sequencing reads were trimmed off adapter sequence contaminants using Trimmomatic v. 0.36
sorted cells/plasma: Mapped onto the Refseq Grch38 of the human genome using the STAR RNA-Seq aligner (version 2.5.3a)
sorted cells: Gene abundance was then estimated by counting using HTSeq (version 0.9.1)
sorted cells: Transcript counts were then normalized by TMM (Trimmed Mean of M-values by correcting for the library size
plasma: Unaligned paired-end reads were then assembled into contigs using Trinity
plasma: Trinity contigs were then aligned against HG38 again to further remove host-derived sequences with BLAST+. Trinity contigs that aligned to non-reference human sequences in the NCBI nucleotide database were also removed
plasma: Remaining contigs were then aligned against the NCBI nucleotide database and quantified with Salmon
plasma: Taxonomic information was assigned for each contig and transcripts per million (TPM) values were collapsed at the species level for each sample. TPM are normalized for sequencing read depth and length for each sample, allowing for a more accurate comparisons between proportion of reads mapping to the same gene in various samples
Genome_build: Human (Refseq Grch38) and Non-human (NCBI nucleotide database and quantified with Salmon)
Supplementary_files_format_and_content: xlsx data matrix files with normalized read counts (sorted cells; sample by transcript) or TPM (plasma; sample by species abundance)

molecule: genomic DNA

organism: human blood metagenome

source_name: Plasma

extract_protocol:
sorted cells: RNA was extracted from sorted cells lysed in RNAzol RT (MRC Inc., OH, USA), according to the manufacturer’s instructions. Briefly, 0.4 volume of sterile water was added to each lysate to allow aqueous and organic phase separation. Total RNA was then extracted from the aqueous phase by isopropanol precipitation. RNA pellets were washed with 70% ethanol and resuspended in sterile water. Extracted RNA was stored at -80°C until preparation of mRNA libraries. RNA yield and integrity were verified by microelectrophoresis using the High Sensitivity RNA ScreenTape Kit (Agilent) on the 2200 TapeStation system (Agilent).
plasma: Circulating total RNA and DNA were isolated from frozen plasma using RNAzolBD (MRC) according to the manufacturer’s recommendations.
sorted cells: mRNA libraries were constructed as described previously (Sandler et al., 2014) using the NEBNext Ultra RNA library preparation kit. Polyadenylated transcripts were purified with oligo-dT magnetic beads, fragmented, reverse transcribed using random hexamers and incorporated into barcoded cDNA libraries based on the Illumina TruSeq platform. Libraries were validated by microelectrophoresis on a 2100 Bioanalyzer system (Agilent), quantified with Kapa Library Quantification Kits (Roche), pooled and clustered on Illumina TruSeq v2 flow cells. Clustered flow cells were sequenced in 2x75 base paired-end runs on Illumina HiSeq 2000 and HiSeq 4000.
plasma: RNA fragmentation and reverse transcription using random hexamers, the obtained transcripts, as well as the isolated plasma DNA, were individually incorporated into barcoded cDNA libraries on the basis of the Illumina TruSeq platform. Libraries were validated by microelectrophoresis on a 2100 Bioanalyzer system (Agilent), quantified using Kapa Library Quantification Kits (Roche), pooled and clustered on Illumina patterned flow cells. Clustered flow cells were sequenced on an Illumina HiSeq 4000 in 75-base paired reads. To control for contamination, four water samples were processed along with plasma samples from nucleic acids extraction through sequencing.

value: Plasma

value: Uganda

tag: cd4 count

tag: cd8 count

value: cd8 t cell ratio:Data_in_Manuscript

value: Yes

value: No


title: DNA_QA17

description:
PathSeq
Uganda_QA_PathSeq_TPM.xlsx

value: cd8 t cell ratio:0.81

value: Post_ART_HIV_subject (~0-2yrs on ART)


title: RNAseq_ZT18a_mouse13

description:
ZT18 mouse 13, PoolA
RNAseq_ZT18_merge_norm_forward.bw
RNAseq_ZT18_merge_norm_reverse.bw


title: RNAseq_ZT12b_mouse12

description:
ZT12 mouse 12, PoolB
RNAseq_ZT12_merge_norm_forward.bw
RNAseq_ZT12_merge_norm_reverse.bw


title: DNA_QA15

description:
PathSeq
Uganda_QA_PathSeq_TPM.xlsx

value: cd8 t cell ratio:1.14


title: RNAseq_ZT18b_mouse16

description:
ZT18 mouse 16, PoolB
RNAseq_ZT18_merge_norm_forward.bw
RNAseq_ZT18_merge_norm_reverse.bw


title: RNA_C306L3I22

description:
RNASeq
Uganda_Longitudinal_Normalized_Corrected_expression_counts.xlsx

data_processing:
sorted cells/plasma: Raw sequencing reads were trimmed off adapter sequence contaminants using Trimmomatic v. 0.36
sorted cells/plasma: Mapped onto the Refseq Grch38 of the human genome using the STAR RNA-Seq aligner (version 2.5.3a)
sorted cells: Gene abundance was then estimated by counting using HTSeq (version 0.9.1)
sorted cells: Transcript counts were then normalized by TMM (Trimmed Mean of M-values by correcting for the library size
plasma: Unaligned paired-end reads were then assembled into contigs using Trinity
plasma: Trinity contigs were then aligned against HG38 again to further remove host-derived sequences with BLAST+. Trinity contigs that aligned to non-reference human sequences in the NCBI nucleotide database were also removed
plasma: Remaining contigs were then aligned against the NCBI nucleotide database and quantified with Salmon
plasma: Taxonomic information was assigned for each contig and transcripts per million (TPM) values were collapsed at the species level for each sample. TPM are normalized for sequencing read depth and length for each sample, allowing for a more accurate comparisons between proportion of reads mapping to the same gene in various samples
Genome_build: Human (Refseq Grch38) and Non-human (NCBI nucleotide database and quantified with Salmon)
Supplementary_files_format_and_content: xlsx data matrix files with normalized read counts (sorted cells; sample by transcript) or TPM (plasma; sample by species abundance)

organism: Homo sapiens

source_name: Sorted Monocytes

value: Sorted Monocytes


title: RNA_C306L3I19


title: DNA_QA13

description:
PathSeq
Uganda_QA_PathSeq_TPM.xlsx

value: cd8 t cell ratio:0.44


title: RNA_H5GYL3I9

source_name: Sorted mDC

value: Sorted mDC

value: Post_ART_HIV_subject (3months on ART)


title: DNA_QA10

description:
PathSeq
Uganda_QA_PathSeq_TPM.xlsx

value: cd8 t cell ratio:0.92

value: Healthy


title: DNA_QA11

description:
PathSeq
Uganda_QA_PathSeq_TPM.xlsx

value: cd8 t cell ratio:1.52


title: DNA_QA09

description:
PathSeq
Uganda_QA_PathSeq_TPM.xlsx

value: cd8 t cell ratio:1.75


title: RNAseq_ZT12a_mouse10

description:
ZT12 mouse 10, PoolA
RNAseq_ZT12_merge_norm_forward.bw
RNAseq_ZT12_merge_norm_reverse.bw

value: liver

value: 8 week old

value: male

value: wilde type


title: RNAseq_ZT12b_mouse11

description:
ZT12 mouse 11, PoolB
RNAseq_ZT12_merge_norm_forward.bw
RNAseq_ZT12_merge_norm_reverse.bw


title: DNA_QA14

description:
PathSeq
Uganda_QA_PathSeq_TPM.xlsx

value: Plasma

value: Uganda

value: cd8 t cell ratio:2.29

value: Yes


title: DNA_QA07

description:
PathSeq
Uganda_QA_PathSeq_TPM.xlsx

value: No

value: cd8 t cell ratio:1.31

value: Post_ART_HIV_subject (~0-2yrs on ART)


title: RNA_H5GYL3I8

value: Sorted mDC

value: cd8 t cell ratio:Data_in_Manuscript


title: RNAseq_ZT12a_mouse9

description:
ZT12 mouse 9, PoolA
RNAseq_ZT12_merge_norm_forward.bw
RNAseq_ZT12_merge_norm_reverse.bw


title: DNA_QA08

description:
PathSeq
Uganda_QA_PathSeq_TPM.xlsx

value: cd8 t cell ratio:0.24


title: RNA_H5GYL2I27

value: Post_ART_HIV_subject (3months on ART)


title: DNA_QA05

description:
PathSeq
Uganda_QA_PathSeq_TPM.xlsx

value: cd8 t cell ratio:1.55


title: RNA_H5GYL2I9


title: DNA_QA03

description:
PathSeq
Uganda_QA_PathSeq_TPM.xlsx

value: cd8 t cell ratio:0.65


title: RNA_H5GYL2I25


title: DNA_QA04

description:
PathSeq
Uganda_QA_PathSeq_TPM.xlsx

value: cd8 t cell ratio:2.15

value: Healthy


title: DNA_QA01

description:
PathSeq
Uganda_QA_PathSeq_TPM.xlsx

value: cd8 t cell ratio:1.27


title: RNAseq_ZT6b_mouse8

description:
ZT6 mouse 8, PoolB
RNAseq_ZT6_merge_norm_forward.bw
RNAseq_ZT6_merge_norm_reverse.bw

value: liver

value: 8 week old

value: male

value: wilde type


title: RNAseq_ZT6b_mouse7

description:
ZT6 mouse 7, PoolB
RNAseq_ZT6_merge_norm_forward.bw
RNAseq_ZT6_merge_norm_reverse.bw


title: DNA_QA02

description:
PathSeq
Uganda_QA_PathSeq_TPM.xlsx

value: Plasma

value: Uganda

value: cd8 t cell ratio:1.09

value: Yes


title: RNA_H5GYL2I23

value: Sorted mDC


title: DNA_049v09005987

description:
PathSeq
Cleveland_PathSeq_TPM.xlsx

value: No

value: USA:Cleveland, Ohio

value: Responder (>3yr on ART)


title: RNAseq_ZT6a_mouse6

description:
ZT6 mouse 6, PoolA
RNAseq_ZT6_merge_norm_forward.bw
RNAseq_ZT6_merge_norm_reverse.bw


title: DNA_049v09005969

description:
PathSeq
Cleveland_PathSeq_TPM.xlsx

value: Non_responder (>3yrs on ART)


title: RNA_H5GYL2I22

value: cd8 t cell ratio:Data_in_Manuscript

value: Post_ART_HIV_subject (3months on ART)


title: RNAseq_ZT6a_mouse5

description:
ZT6 mouse 5, PoolA
RNAseq_ZT6_merge_norm_forward.bw
RNAseq_ZT6_merge_norm_reverse.bw


title: RNA_H5GYL2I12


title: DNA_049v09005476

description:
PathSeq
Cleveland_PathSeq_TPM.xlsx


title: DNA_049v09005127

description:
PathSeq
Cleveland_PathSeq_TPM.xlsx


title: DNA_049v09005739

description:
PathSeq
Cleveland_PathSeq_TPM.xlsx


title: DNA_049v09005019

description:
PathSeq
Cleveland_PathSeq_TPM.xlsx


title: RNAseq_ZT0b_mouse4

description:
ZT0 mouse 4, PoolB
RNAseq_ZT0_merge_norm_forward.bw
RNAseq_ZT0_merge_norm_reverse.bw


title: RNAseq_ZT0b_mouse3

description:
ZT0 mouse 3, PoolB
RNAseq_ZT0_merge_norm_forward.bw
RNAseq_ZT0_merge_norm_reverse.bw


title: DNA_049v09004922

description:
PathSeq
Cleveland_PathSeq_TPM.xlsx


title: DNA_049v09004941

description:
PathSeq
Cleveland_PathSeq_TPM.xlsx


title: RNA_H5GYL2I11


title: RNA_H5GYL2I10


title: RNAseq_ZT0a_mouse2

description:
ZT0 mouse 2, PoolA
RNAseq_ZT0_merge_norm_forward.bw
RNAseq_ZT0_merge_norm_reverse.bw


title: DNA_049v09003712

description:
PathSeq
Cleveland_PathSeq_TPM.xlsx


title: RNA_DC_71

value: Post_ART_HIV_subject (24months on ART)


title: DNA_049v09003559

description:
PathSeq
Cleveland_PathSeq_TPM.xlsx


title: RNAseq_ZT0a_mouse1

description:
ZT0 mouse 1, PoolA
RNAseq_ZT0_merge_norm_forward.bw
RNAseq_ZT0_merge_norm_reverse.bw


title: RNA_DC_63


title: RNA_DC_55


title: DNA_049v09003551

description:
PathSeq
Cleveland_PathSeq_TPM.xlsx


title: DNA_049v09003555

description:
PathSeq
Cleveland_PathSeq_TPM.xlsx


title: HiC_ZT18_PoolC_lane5_NoIndex_L005

description:
ZT18 PoolC
Each Pool sample contained 2 livers from individual mouse
ZT18_ABC.hic

data_processing:
Hi-C sequenced reads were mapped to the mouse genome (mm9) using HiCUP (Wingett et al., 2015) with default parameters. Downstream processing was done using Juicer (Durand, et al., 2016) and data was visualized using Juicebox (Durand, Robinson, et al., 2016) . Hi-C heatmaps at different bin resolutions were created and normalized using Knight-Ruiz (KR) matrix balancing algorithm from Juicer.
Genome_build: Mus musculus mm9
Supplementary_files_format_and_content: Processing was done using Juicer (Durand, et al., 2016). Hi-C heatmaps at different bin resolutions were created and normalized using Knight-Ruiz (KR) matrix balancing algorithm from Juicer.

extract_protocol: HiC libraries were constructed using the Truseq Illumina system

treatment_protocol: In nucleus HiC was performed as described in Rubin, Barjas, Furlan-Magaril et al., 2017. https://doi.org/10.1038/ng.3935


title: DNA_049v09003500

description:
PathSeq
Cleveland_PathSeq_TPM.xlsx


title: HiC_ZT18_PoolB_lane3_NoIndex_L003

description:
ZT18 PoolB
Each Pool sample contained 2 livers from individual mouse
ZT18_ABC.hic


title: DNA_049v09002867

description:
PathSeq
Cleveland_PathSeq_TPM.xlsx


title: RNA_DC_47


title: DNA_049v09002833

description:
PathSeq
Cleveland_PathSeq_TPM.xlsx


title: HiC_ZT18_PoolA_rep2_lane4_NoIndex_L004

description:
ZT18 PoolA second sequencing lane
Each Pool sample contained 2 livers from individual mouse
ZT18_ABC.hic


title: DNA_049v09003832

description:
PathSeq
Cleveland_PathSeq_TPM.xlsx

value: cd8 t cell ratio:0.6


title: DNA_049v09002295

description:
PathSeq
Cleveland_PathSeq_TPM.xlsx


title: RNA_DC_39


title: HiC_ZT18_PoolA_lane4_NoIndex_L004

description:
ZT18 PoolA
Each Pool sample contained 2 livers from individual mouse
ZT18_ABC.hic

value: liver


title: DNA_049v09003655

description:
PathSeq
Cleveland_PathSeq_TPM.xlsx

value: cd8 t cell ratio:0.25


title: DNA_049v09002454

description:
PathSeq
Cleveland_PathSeq_TPM.xlsx


title: RNA_DC_31


title: DNA_049v09002049

description:
PathSeq
Cleveland_PathSeq_TPM.xlsx


title: DNA_049v09001995

description:
PathSeq
Cleveland_PathSeq_TPM.xlsx


title: DNA_049v09001920

description:
PathSeq
Cleveland_PathSeq_TPM.xlsx


title: DNA_049v09002210

description:
PathSeq
Cleveland_PathSeq_TPM.xlsx


title: DNA_049v09002100

description:
PathSeq
Cleveland_PathSeq_TPM.xlsx

value: cd8 t cell ratio:0.390625


title: DNA_049v09001901

description:
PathSeq
Cleveland_PathSeq_TPM.xlsx


title: HiC_ZT12_PoolB_lane2_NoIndex_L002

description:
ZT12 PoolB
Each Pool sample contained 2 livers from individual mouse
ZT12_ABC.hic

value: 8 week old

value: male

value: wilde type


title: HiC_ZT12_PoolC_lane8_NoIndex_L008

description:
ZT12 PoolC
Each Pool sample contained 2 livers from individual mouse
ZT12_ABC.hic


title: RNA_DC_15

description:
RNASeq
Uganda_Longitudinal_Normalized_Corrected_expression_counts.xlsx

value: Uganda


title: HiC_ZT12_PoolA_rep2_lane3_NoIndex_L003

description:
ZT12 PoolA second sequencing lane
Each Pool sample contained 2 livers from individual mouse
ZT12_ABC.hic


title: RNA_DC_7

value: Yes


title: RNA_DC_23

value: Sorted mDC


title: DNA_049v09001848

description:
PathSeq
Cleveland_PathSeq_TPM.xlsx

value: Plasma

value: No


title: RNA_mDC_RAL16_Mo12

value: Post_ART_HIV_subject (12months on ART)


title: DNA_049v09001894

description:
PathSeq
Cleveland_PathSeq_TPM.xlsx

value: USA:Cleveland, Ohio

value: Responder (>3yr on ART)


title: DNA_049v09001877

description:
PathSeq
Cleveland_PathSeq_TPM.xlsx

value: Non_responder (>3yrs on ART)


title: DNA_049v09001765

description:
PathSeq
Cleveland_PathSeq_TPM.xlsx


title: HiC_ZT6_PoolC_lane7_NoIndex_L007

description:
ZT6 PoolC
Each Pool sample contained 2 livers from individual mouse
ZT6_ABC.hic


title: DNA_049v09001761

description:
PathSeq
Cleveland_PathSeq_TPM.xlsx


title: DNA_049v09001681

description:
PathSeq
Cleveland_PathSeq_TPM.xlsx


title: RNA_mDC_RAL15_Mo12

value: cd8 t cell ratio:Data_in_Manuscript


title: DNA_049v09001654

description:
PathSeq
Cleveland_PathSeq_TPM.xlsx


title: RNA_mDC_RAL14_Mo12


title: DNA_049v09001619

description:
PathSeq
Cleveland_PathSeq_TPM.xlsx


title: HiC_ZT6_PoolB_lane1_NoIndex_L001

description:
ZT6 PoolB
Each Pool sample contained 2 livers from individual mouse
ZT6_ABC.hic


title: DNA_049v09001588

description:
PathSeq
Cleveland_PathSeq_TPM.xlsx


title: RNA_mDC_RAL13_Mo12


title: HiC_ZT12_PoolA_lane3_NoIndex_L003

description:
ZT12 PoolA
Each Pool sample contained 2 livers from individual mouse
ZT12_ABC.hic


title: HiC_ZT0_PoolC_lane6_NoIndex_L006

description:
ZT0 PoolC
Each Pool sample contained 2 livers from individual mouse
ZT0_ABC.hic


title: HiC_ZT6_PoolA_lane2_NoIndex_L002

description:
ZT6 PoolA
Each Pool sample contained 2 livers from individual mouse
ZT6_ABC.hic


title: RNA_mDC_RAL12_Mo12


title: Sample 7

city: Sevilla

first: Lorena

last: Buono

state: Sevilla

address: Carretera de Utrera km 1

country: Spain

institute: CABD

description: Chimera Oryzias latipes & Danio rerio

data_processing:
Each sample was mapped against the index genome built from both oryLat2 and danRer10 assembly using Hisat2 (Kim et al., 2015)
The aligned read SAM files were assembled into transcripts and their abundance was estimated by Cufflinks  v2.2.1(Trapnell et al., 2012)
Genome_build: oryLat2
Genome_build: danRer10
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample (Cufflinks output)

organism:
Danio rerio
Oryzias latipes

source_name: Total embryo

growth_protocol: Zebrafish embryos were raised in E3 medium at 28C, medaka and zebraka embryos were raised in ERM at 28C.

extract_protocol:
RNA was extracted according to the Trizol manufacture’s instructions.
poly A selection for the RNA from the NEBnext Poly A module

treatment_protocol: Blastomeres from zebrafish were transplanted into isochronic medaka blastulae.

tag: Stage

value: Embryo

value: Cab/AB


title: Sample 6

description: Chimera Oryzias latipes & Danio rerio


title: DNA_049v09001510

description:
PathSeq
Cleveland_PathSeq_TPM.xlsx


title: RNA_YD1417

description:
PathSeq
Montreal_PathSeq_TPM.xlsx

value: HD


title: HiC_ZT0_PoolB_lane8_NoIndex_L008

description:
ZT0 PoolB
Each Pool sample contained 2 livers from individual mouse
ZT0_ABC.hic

value: liver


title: RNA_mDC_RAL11_Mo12


title: DNA_049v09001514

description:
PathSeq
Cleveland_PathSeq_TPM.xlsx


title: HiC_ZT6_PoolA_rep2_lane2_NoIndex_L002

description:
ZT6 PoolA second sequencing lane
Each Pool sample contained 2 livers from individual mouse
ZT6_ABC.hic

value: 8 week old


title: RNA_VB115_2

description:
PathSeq
Montreal_PathSeq_TPM.xlsx


title: RNA_SV1296

description:
PathSeq
Montreal_PathSeq_TPM.xlsx


title: RNA_mDC_RAL08_Mo12


title: HiC_ZT0_PoolA_lane1_NoIndex_L001

description:
ZT0 PoolA
Each Pool sample contained 2 livers from individual mouse
ZT0_ABC.hic

value: male


title: 48H_DCA-240_Rep2

city: Paris

first: Monot

last: Marc

address: 25, rue du docteur roux

department: Genomes and Genetics

country: France

institute: Institut Pasteur

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence using AlienTrimmer_0.4.0. Only sequence with a minimum length of 30 were considered.
Sequenced were mapped to Clostridiaceae difficile 630 whole genome sequence complemented by the known ncRNA using bowtie v2
HtSeqCount was used for counting genes with default parameters
Statistical analyses were performed using R version 3 and Bioconductor packages.
The whole dataset was first normalized using the normalization function of DESeq2 and with default parameters.
The statistical test function of DESeq2 was then applied with the 9h BHISG value as a reference for reporting the expression data of 14, 24 and 48h BHISG with Deoxycholate at 120µM and 240µM.
Genome_build: Clostridioides difficile 630 (NC_009089.1) complemented by the known ncRNA (PMID: 23675309)
Supplementary_files_format_and_content: Genome annotation (Gene ID, Gene Name), Raw Counts and Normalized Counts (9H, 14H, 24H and 48H BHISG with and withoutDeoxycholate 120µM and 240µM), Normalized Counts , Statistics (FC, pvalue, Significant)

organism: Clostridioides difficile

source_name: Wild type strain 630

growth_protocol: Strains were grown aerobically in BHISG at 37°C for 9H, 14H, 24H and 48 H with 120µM, 240µM and without Deoxycholate

extract_protocol:
Total RNA was extracted using phenol, Trizol reagent and chloroform/isoamylalcohol.
RNA libraries were prepared for sequencing using standard Illumina protocols
Truseq stranded RNA seq kit

value: wild type

tag: treatment

value: BHISG DCA-240

tag: time


title: RNA_mDC_RAL07_Mo12

value: Uganda

value: Yes


title: RNA_mDC_RAL04_Mo12

value: Sorted mDC


title: 48H_DCA-240_Rep3


title: RNA_SM1408_2

description:
PathSeq
Montreal_PathSeq_TPM.xlsx

value: Plasma

value: No

value: Post_ART_HIV_subject (~0-2yrs on ART)


title: RNA_SV_1296_2

description:
PathSeq
Montreal_PathSeq_TPM.xlsx


title: 48H_DCA-120_Rep3

value: BHISG DCA-120


title: 48H_DCA-240_Rep1


title: RNA_mDC_RAL03_Mo12

value: Post_ART_HIV_subject (12months on ART)


title: CHiC_ZT18_PoolB_lane7_NoIndex_L007

description:
ZT18 PoolB
Each Pool sample contained 2 livers from individual mouse
ZT18All_step2_washU_text.txt

data_processing:
Library strategy: PChi-C
The sequenced reads were processed using HiCUP (Wingett et al., 2015).
The filtering and identification of significant interactions were performed with CHiCAGO (Cairns et al., 2016).
Genome_build: Mus musculus mm9
Supplementary_files_format_and_content: Processed data files contain significant interactions retrieved by the CHiCAGO pipeline (Cairns et al., 2016). The files contain the position of the HindIII fragments that contain promoters followed by the position of the HindIII fragments from the interaction partner. The last column displays the significance score from CHiCAGO.

extract_protocol:
Promoter Capture was performed as previously described (Schoenfelder et al., 2015; Schoenfelder et al., 2015). Briefly, Biotinylated 120-mer RNA baits were designed to target both ends of HindIII restriction fragments overlapping the Ensembl promoters of protein-coding and noncoding transcripts and UCEs as described in detail in Schoenfelder et al., 2015a. Promoter Capture was carried out using in nucleus Hi-C libraries derived from three biological replicates at ZT0 0, 6, 12, and 18 with the SureSelect target enrichment system and the biotinylated RNA bait library according to the manufacturer's instructions (Agilent Technologies). After library enrichment, a post-capture PCR amplification step was carried out using the PE PCR 1.0 and PE PCR 2.0 primers (Illumina) with 4-6 PCR amplification cycles as required. In nucleus Hi-C and CHi-C libraries were sequenced on the Illumina HiSeq 2000 platform.
Promoter Chi-C libraries were constructed using the Truseq Illumina system

value: wilde type


title: Sample 5

description: Chimera Oryzias latipes & Danio rerio

data_processing:
Each sample was mapped against the index genome built from both oryLat2 and danRer10 assembly using Hisat2 (Kim et al., 2015)
The aligned read SAM files were assembled into transcripts and their abundance was estimated by Cufflinks  v2.2.1(Trapnell et al., 2012)
Genome_build: danRer10
Genome_build: oryLat2
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample (Cufflinks output)

value: Embryo


title: RNA_mDC_RAL10_Mo12

value: cd8 t cell ratio:Data_in_Manuscript


title: HiC_ZT0_PoolA_rep2_lane1_NoIndex_L001

description:
ZT0 PoolA second sequencing lane
Each Pool sample contained 2 livers from individual mouse
ZT0_ABC.hic


title: RNA_DC_95


title: CHiC_ZT18_PoolA_rep2_lane2_NoIndex_L002

description:
ZT18 PoolA second sequencing lane
Each Pool sample contained 2 livers from individual mouse
ZT18All_step2_washU_text.txt


title: RNA_RD1214

description:
PathSeq
Montreal_PathSeq_TPM.xlsx

value: cd8 t cell ratio:0.21627907


title: 48H_DCA-120_Rep2


title: CHiC_ZT12_PoolC_lane3_NoIndex_L003

description:
ZT12 PoolC
Each Pool sample contained 2 livers from individual mouse
ZT12All_step2_washU_text.txt

value: liver


title: RNA_DC_87


title: RNA_OB1249

description:
PathSeq
Montreal_PathSeq_TPM.xlsx


title: CHiC_ZT18_PoolC_lane4_NoIndex_L004

description:
ZT18 PoolC
Each Pool sample contained 2 livers from individual mouse
ZT18All_step2_washU_text.txt

value: 8 week old


title: RNA_DC_79


title: 48H_DCA-120_Rep1


title: 48H_BHISG_Rep3

value: BHISG


title: RNA_NB1518

description:
PathSeq
Montreal_PathSeq_TPM.xlsx

value: cd8 t cell ratio:0.3109375


title: CHiC_ZT12_PoolB_lane6_NoIndex_L006

description:
ZT12 PoolB
Each Pool sample contained 2 livers from individual mouse
ZT12All_step2_washU_text.txt

value: male


title: RNA_OB1249_2

description:
PathSeq
Montreal_PathSeq_TPM.xlsx


title: 48H_BHISG_Rep2

value: wild type


title: 48H_BHISG_Rep1


title: RNA_H5GYL3I6

value: Uganda

value: Yes


title: CHiC_ZT12_PoolA_lane3_NoIndex_L003

description:
ZT12 PoolA
Each Pool sample contained 2 livers from individual mouse
ZT12All_step2_washU_text.txt


title: 24H_DCA-240_Rep3

value: BHISG DCA-240


title: RNA_KBC1196_3

description:
PathSeq
Montreal_PathSeq_TPM.xlsx

value: Plasma

value: No


title: RNA_H5GYL2I8

description:
RNASeq
Uganda_Longitudinal_Normalized_Corrected_expression_counts.xlsx

value: Sorted mDC


title: RNA_H5GYL3I7


title: 24H_DCA-240_Rep2


title: RNA_H5GYL2I7


title: RNA_NB1518_2

description:
PathSeq
Montreal_PathSeq_TPM.xlsx

value: cd8 t cell ratio:1.14953271

value: Post_ART_HIV_subject (~0-2yrs on ART)


title: RNA_JPR1150

description:
PathSeq
Montreal_PathSeq_TPM.xlsx


title: 24H_DCA-240_Rep1


title: CHiC_ZT6_PoolC_lane2_NoIndex_L002

description:
ZT6 PoolC
Each Pool sample contained 2 livers from individual mouse
ZT6All_step2_washU_text.txt

value: wilde type


title: CHiC_ZT18_PoolA_lane4_NoIndex_L004

description:
ZT18 PoolA
Each Pool sample contained 2 livers from individual mouse
ZT18All_step2_washU_text.txt


title: CHiC_ZT6_PoolB_lane5_NoIndex_L005

description:
ZT6 PoolB
Each Pool sample contained 2 livers from individual mouse
ZT6All_step2_washU_text.txt


title: RNA_H5GYL2I5

value: cd8 t cell ratio:Data_in_Manuscript


title: RNA_JL1235_3

description:
PathSeq
Montreal_PathSeq_TPM.xlsx


title: RNA_JL_1235

description:
PathSeq
Montreal_PathSeq_TPM.xlsx


title: 24H_DCA-120_Rep3

value: BHISG DCA-120


title: CHiC_ZT6_PoolA_rep2_lane8_NoIndex_L008

description:
ZT6 PoolA second sequencing lane
Each Pool sample contained 2 livers from individual mouse
ZT6All_step2_washU_text.txt

value: liver


title: 24H_DCA-120_Rep2


title: RNA_H5GYL2I6


title: CHiC_ZT6_PoolA_lane2_NoIndex_L002

description:
ZT6 PoolA
Each Pool sample contained 2 livers from individual mouse
ZT6All_step2_washU_text.txt

value: 8 week old


title: RNA_H5GYL2I21


title: RNA_GTJ1321

description:
PathSeq
Montreal_PathSeq_TPM.xlsx


title: CHiC_ZT0_PoolC_lane1_NoIndex_L001

description:
ZT0 PoolC
Each Pool sample contained 2 livers from individual mouse
ZT0All_step2_washU_text.txt


title: CHiC_ZT12_PoolA_rep2_lane1_NoIndex_L001

description:
ZT12 PoolA second sequencing lane
Each Pool sample contained 2 livers from individual mouse
ZT12All_step2_washU_text.txt


title: RNA_MIPAV1_06_015

description:
PathSeq
Montreal_PathSeq_TPM.xlsx


title: 24H_DCA-120_Rep1


title: RNA_H5GYL2I20


title: RNA_GL1587_3

description:
PathSeq
Montreal_PathSeq_TPM.xlsx


title: RNA_H5GYL2I2


title: RNA_GC1587_2

description:
PathSeq
Montreal_PathSeq_TPM.xlsx


title: RNA_H5GYL2I19


title: CHiC_ZT0_PoolA_rep2_lane7_NoIndex_L007

description:
ZT0 PoolA second sequencing lane
Each Pool sample contained 2 livers from individual mouse
ZT0All_step2_washU_text.txt


title: 24H_BHISG_Rep2

value: BHISG


title: 24H_BHISG_Rep1


title: CHiC_ZT0_PoolA_lane1_NoIndex_L001

description:
ZT0 PoolA
Each Pool sample contained 2 livers from individual mouse
ZT0All_step2_washU_text.txt


title: RNA_H5GYL2I18


title: ChIPseq_CTCF_ZT12_rep2

description:
ZT12 2nd biological replicate
ChIPseq_CTCF_ZT12_peaks_fimo_both_replicates.bed

data_processing:
Raw sequencing data files for all samples were first processed with FastQC for general quality controls. Sequencing reads were mapped against the mouse genome (NCBIM37/mm9) using Bowtie2 (Langmead and Salzberg, 2012) with default parameters for single and paired reads.
Mapped reads were filtered by map quality (-q 30) using samtools (samtools view). Bam files were sorted (samtools sort) and indexed (samtools index). Duplicates were removed with Pickard. Bam files were imported to deeTools v3.3.1 (Ram’rez et al., 2016) to create signal tracks with bamCoverage. Signal tracks for all data were visualized using IGV (Thorvaldsd—ttir et al., 2013).
Peak calling was performed using MACS2 callpeak function with default parameters (Zhang et al., 2008). Peak overlap analysis was performed using the Venn module of Intervene (Khan and Mathelier, 2017).
The MEME-ChIP tool (Ma et al., 2014) was used for motif analysis using the fasta sequences from peaks detected by MACS2 with default parameters.
Genome_build: Mus musculus mm9
Supplementary_files_format_and_content: Bed files with the genomic positions of the CTCF peaks detected from both replicates

extract_protocol:
For ChIP-seq, liver tissue for two biological replicates at ZT0 and ZT12 was dissected as processed as for Hi-C and then fixed in 1% formaldehyde for 5 minutes. Chromatin immunoprecipitation was performed as described (Rubin et al., 2017) using 10 _g of _-CTCF (Millipore, 07-729). DNA was purified using Zymo Research DNA purification columns.  Sequencing libraries were prepared with the NEBNext ChIP-seq library prep kit (NEB) according to manufacturer's instructions. DNA was purified using AMPure beads (Agencourt).
NEBnext library preparation protocol


title: 14H_DCA-240_Rep3


title: RNA_FM1317_2

description:
PathSeq
Montreal_PathSeq_TPM.xlsx

value: HD


title: RNA_EC1124EC

description:
PathSeq
Montreal_PathSeq_TPM.xlsx


title: RNA_EG1148_3

description:
PathSeq
Montreal_PathSeq_TPM.xlsx


title: RNA_DPL1241

description:
PathSeq
Montreal_PathSeq_TPM.xlsx


title: 518GAL3sh  rep3

city: Genève

first: Eliana

last: Marinari

address: Rue Michel-Servet 1

country: Switzerland

institute: UNIGE

data_processing:
The sequencing quality control was done with FastQC v.0.11.5.
sequences were aligned with STAR aligner v.2.5.3a
Picard tools for QC metrics
table counts were generated with HTSeq v0.6p1
The differential expression analysis was performed with the statistical analysis R/Bioconductor package edgeR v. 3.18.1
Genome_build: UCSC human hg38 reference
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample
Supplementary_files_format_and_content: txt file

source_name: GBM primary line

growth_protocol: GBM cell line cultured standard conditions

extract_protocol:
QIAGEN RNAeasy
RNA libraries were prepared for sequencing using standard Illumina protocols
SR100 – libraries TruSeqHT stranded – Illumina HiSeq 4000

treatment_protocol: sh GAL3 and shCtrl

tag: tumor

value: GBM

tag: sample

value: brain


title: 518GAL3sh  rep2


title: 14H_DCA-240_Rep1

value: wild type


title: ChIPseq_CTCF_ZT12_rep1

description:
ZT12 1st biological replicate
ChIPseq_CTCF_ZT12_peaks_fimo_both_replicates.bed

value: male


title: ChIPseq_CTCF_ZT0_rep1

description:
ZT0 1st biological replicate
ChIPseq_CTCF_ZT0_peaks_fimo_both_replicates.bed


title: ChIPseq_CTCF_ZT0_rep2

description:
ZT0 2nd biological replicate
ChIPseq_CTCF_ZT0_peaks_fimo_both_replicates.bed


title: RNA_CMG2049

description:
PathSeq
Montreal_PathSeq_TPM.xlsx


title: 24H_BHISG_Rep3


title: 518ctrl rep3


title: CHiC_ZT0_PoolB_lane4_NoIndex_L004

description:
ZT0 PoolB
Each Pool sample contained 2 livers from individual mouse
ZT0All_step2_washU_text.txt


title: 14H_DCA-120_Rep3


title: RNA_CMD1177

description:
PathSeq
Montreal_PathSeq_TPM.xlsx

value: Yes


title: 518ctrl rep2


title: RNA_CM1811

description:
PathSeq
Montreal_PathSeq_TPM.xlsx

value: Plasma


title: 518ctrl rep1


title: 14H_DCA-120_Rep1


title: RNA_CH1476_2

description:
PathSeq
Montreal_PathSeq_TPM.xlsx

value: No


title: 14H_DCA-240_Rep2

value: BHISG DCA-240


title: 518GAL3sh  rep1


title: IL-6 #1

city: Philadelphia

first: Yi

last: Fan

state: PA

address: 3400 Civic Center Blvd, SCTR 8-168

department: Radiation Oncology

institute: University of Pennsylvania

description: FPKM.txt

data_processing:
The sequences were aligned to the GRCm38 reference genome using RNA-Star (v2.4.2a; https://github.com/alexdobin/STAR).
The gene expression was normalized and calculated as FPKM (Fragments Per Kilobase Million) values by Cufflinks (v2.2.1) (http://cole-trapnell-lab.github.io/cufflinks/releases/v2.2.1/) with Gencode M5 gene annotations (https://www.gencodegenes.org/mouse/release_M5.html).
Genome_build: GRCm38
Supplementary_files_format_and_content: Tab-delimited text file that includes FPKM values for all samples.

source_name: Bone marrow-derived macrophages

growth_protocol: Freshly isolated femur and tibia from WT C57BL/6 mice were flushed with RPMI-1640 medium (Life Technologies). Cells were harvested and passed through a 40-μm strainer. Red cells were depleted with ACK lysis buffer (Thermo Fisher). BM cells were cultured in RPMI-1640 medium supplemented with 5% FBS (Life Technologies). Cells were incubated with 10 ng/ml mouse CSF-1 (Biolegend, 576404) for 3 days to induce macrophage differentiation.

extract_protocol:
Treated bone marrow-derived macrophages were lyzed in TRIzol (Thermo Fisher), and RNA was extracted according to the manufacturer’s instructions, followed by RNA purification using a RNeasy Plus Mini Kit (Qiagen).
DNA library was constructed with a TruSeq mRNA Stranded Kit (Illumina). The RNA from each step and library DNA quality were analyzed with RNA Nano assay chips, RNA Pico assay chips, and DNA Nano assay chips using a 2100 bioanalyer (Agilent). Library was subjected to next-generation sequencing analysis in a high-throughput sequencing center with a HiSeq2500 at the Children's Hospital of Philadelphia/Beijing Genomics Institute core facility (CHOP/BGI).

treatment_protocol: Bone marrow-derived macrophages were treated with 10ng/ml MCSF alone (control group) or MCSF plus 10ng/ml IL-4 (IL-5 group) or 1MCSF plus 00ng/ml IL-6 (IL-6 group) for 4 days.

tag: cell type

value: Bone marrow-derived macrophages

value: 10ng/ml MCSF + 100ng/ml IL-6


title: 14H_BHISG_Rep2


title: IL-6 #2

description: FPKM.txt


title: M24h3_M24h

city: Nanjing

first: Hongjian

last: Zhou

address: No.1 Wenyuan Road, Xianlin University Town, Nanjing

country: China

institute: Nanjing Normal University

data_processing:
For RNA-seq data, low-quality reads and adapters of the raw sequenced reads were removed by FastQC.
Trimmed reads were aligned to the D. melanogaster reference transcriptome build r6.08 (Bowtie 2.0.0, default settings)
TopHat (2.0.9) and Cufflinks (2.1.1) were then used to assemble transcripts
Genome_build: dm6
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

organism: Drosophila melanogaster

source_name: drosophila melanogaster

extract_protocol:
the total RNA were extracted from PBS treated w1118 flies control and M. luteus infected w1118 flies at 3, 12 and 24 h post-treatment (hpt) (3 replicates at each time-point, respectively) using Trizol reagent (Invitrogen, USA) following the manufacturer's procedure. The quantity and purity of total RNAs were checked using a Bioanalyzer 2100 and RNA 6000 Nano LabChip Kit (Agilent, CA, USA) with RIN value > 7.0.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: 24 hours after injection of M. luteus

tag: developmental stage

value: adult


title: M24h2_M24h


title: 14H_BHISG_Rep1


title: IL-4 #3

description: FPKM.txt

value: 10ng/ml MCSF + 10ng/ml IL-4


title: M24h1_M24h


title: RNA_AS1152

description:
PathSeq
Montreal_PathSeq_TPM.xlsx


title: IL-4 #1

description: FPKM.txt


title: 9H_DCA-240_Rep3


title: M12h3_M12h

value: 12 hours after injection of M. luteus


title: Control #3

description: FPKM.txt

value: 10ng/ml MCSF


title: 9H_DCA-240_Rep2


title: RNA_CBD1256

description:
PathSeq
Montreal_PathSeq_TPM.xlsx


title: 14H_DCA-120_Rep2

value: BHISG DCA-120


title: IL-6 #3

description: FPKM.txt


title: M12h2_M12h


title: Control #2

description: FPKM.txt


title: RNA_AM1408

description:
PathSeq
Montreal_PathSeq_TPM.xlsx


title: 9H_DCA-240_Rep1


title: 14H_BHISG_Rep3

value: BHISG


title: RNA_CH_1476

description:
PathSeq
Montreal_PathSeq_TPM.xlsx


title: M12h1_M12h


title: RNA_ABG1178A

description:
PathSeq
Montreal_PathSeq_TPM.xlsx


title: Control #1

description: FPKM.txt


title: IL-4 #2

description: FPKM.txt


title: 9H_DCA-120_Rep3


title: RNA_ABG_1178A_2

description:
PathSeq
Montreal_PathSeq_TPM.xlsx


title: M3h3_M3h

value: 3 hours after injection of M. luteus


title: 9H_DCA-120_Rep2


title: M3h2_M3h


title: 9H_DCA-120_Rep1


title: MB135-DUX4 + SkQ1 40nM 4d rep2

city: Villejuif

first: Anna

last: Schwager

state: Please Select

address: 114 Rue Edouard Vaillant

institute: Institut Gustave Roussy

data_processing:
Illumina Casava software used for basecalling.
Raw paired-end sequence reads were mapped to the human transcriptome using STAR (release 2.7.3a) in the 2-pass mode. Multiple-mapping reads were excluded (--outFilterMultimappedNmax 1).
Reads were assigned to genes via featureCounts (v 2.0.0), including fractions
Differential expression analysis was performed using DESeq2 R package (v 1.30.1)
Genome_build: Homo sapiens genome sequence GRCh38 with v99 gene annotations downloaded from Ensembl
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample
Supplementary_files_format_and_content: DESseq2 result tables with differentially expressed genes between different samples

source_name: cultured cells

growth_protocol: The cells were cultured at 37℃, 5% CO2 in the growth medium composed of 60% DMEM (Sigma Aldrich, D5796), 25% 199 Medium (Sigma Aldrich, M4530) and 15% FBS (Life technology, 10270) supplemented with 0.5ng/ml bFGF (Life technology, PHG0026), 0.2 ug/ml Dexamethasone, 100 units/mL penicillin and 100 µg/mL streptomycin (Thermo Fisher, 15140122).

extract_protocol:
The cells were lysed with trypsin and total RNA was extracted using Nucleospin RNA isolation kit (Macherey–Nagel, 740955) according to the manufacturer's protocol.
RNA-seq libraries were prepared using the Agilent SureSelect Automated Strand-Specific RNA Library Prep, with polyA selection. Prepared libraries were sequenced on an Illumina HiSeq2000.

treatment_protocol: The cells were treated with antioxidants (100 uM Tempol or 40 nM SkQ1) for 4 days prior to RNA extraction. Antioxidants were added once, directly to the growth medium.

tag: cell line

value: myoblasts

value: SkQ1 40nM 4d


title: MB135-DUX4 + SkQ1 40nM 4d rep1


title: RNA_RAL8-Mo9

description:
PathSeq
Uganda_Longitudinal_B2_PathSeq_TPM.xlsx

value: Uganda

value: cd8 t cell ratio:Data_in_Manuscript

value: Post_ART_HIV_subject (9months on ART)


title: RNA_AM1325

description:
PathSeq
Montreal_PathSeq_TPM.xlsx

value: Plasma

value: No

value: HD


title: 9H_BHISG_Rep3

value: wild type


title: RNA_106_106

description:
PathSeq
Montreal_PathSeq_TPM.xlsx

value: Yes


title: M3h1_M3h

value: adult


title: MB135-DUX4 + Tempol 100uM 4d rep2

value: Tempol 100uM 4d


title: RNA_RAL8-Mo12

value: Post_ART_HIV_subject (12months on ART)


title: MB135-DUX4 rep2

value: no


title: 9H_BHISG_Rep1


title: C24h3_C24h

value: 24 hours after injection of PBS


title: MB135-DUX4 + Tempol 100uM 4d rep1


title: C24h2_C24h


title: 9H_BHISG_Rep2

value: BHISG


title: RNA_RAL7-Mo9


title: RNA_RAL7-Mo12


title: C24h1_C24h


title: DRG sample collected on D14 with PBS injection, rep4

city: shenzhen

first: Mingzhu

last: Zhai

state: guangdong

address: shenzhen nanshan

institute: Southern university of science and technology

data_processing:
CASAVA version 1.4 software used for basecalling.
The "dirty" raw reads as reads which contain the sequence of adaptor, high content of unknown bases and low quality reads were  removed, then mapped to Rattus_norvegicus whole genome using bowtie2 with parameters for PE reads: -q --phred64 --sensitive --dpad 0 --gbar 99999999 --mp 1,1 --np 1 --score-min L,0,-0.1 -I 1 -X 1000 --no-mixed --no-discordant  -p 16 -k 200
Reads Per Kilobase of exon per Megabase of library size (RPKM) method was used in calculated expression level.
Supplementary_files_format_and_content: tab-delimited text files include reads count values for each Sample ...

organism: Rattus norvegicus

source_name: dorsal root ganglia

extract_protocol:
Dorsal root ganglia from TCI or Sham groups were flash frozen on dry ice, and RNA was harvested using Trizol reagent. RNA isolation was followed by chloroform extraction and isopropanol precipitation. The extracted RNA was approximately 1 μg for the construction of sequencing libraries.
RNA libraries were prepared for the sequencing using standard Illumina protocols

treatment_protocol:
Samples from TCI group were injected tumor cells into left tibia
Samples from sham group were injected PBS instead of tumor cells into left tibia

value: dorsal root ganglia

value: Day 14 after Sham operation


title: RNA_RAL4-Mo9


title: MB135 + SkQ1 40nM 4d rep2

value: myoblasts

value: SkQ1 40nM 4d


title: MB135-DUX4 rep1


title: C12h2_C12h

value: 12 hours after injection of PBS


title: DRG sample collected on D14 with PBS injection, rep3


title: RNA_RAL4-Mo12

value: Uganda

value: cd8 t cell ratio:Data_in_Manuscript


title: MB135 + SkQ1 40nM 4d rep1


title: DRG sample collected on D14 with PBS injection, rep2


title: C12h1_C12h


title: RNA_RAL3-Mo9

value: Plasma

value: Post_ART_HIV_subject (9months on ART)


title: MB135 + Tempol 100uM 4d rep2


title: DRG sample collected on D14 with PBS injection, rep1


title: C3h3_C3h

value: 3 hours after injection of PBS


title: MB135 + Tempol 100uM 4d rep1


title: RNA_RAL3-Mo12

value: Yes


title: C3h1_C3h

value: adult


title: DRG sample collected on D14 after TCI, rep3

value: Day 14 after TCI


title: RNA_RAL14-Mo12

value: Post_ART_HIV_subject (12months on ART)


title: DRG sample collected on D14 after TCI, rep2


title: MB135 rep2

value: no


title: MB135 rep1


title: C12h3_C12h


title: RNA_RAL13-Mo12


title: DRG sample collected on D14 after TCI, rep1


title: RNA_RAL12-Mo12_1


title: DRG sample collected on D7 after TCI, rep4

value: Day 7 after TCI


title: HeLa_siCSB_UV6h_r1

city: Ann Arbor

first: Mats

last: Ljungman

state: Michigan

address: NCRC, B520 Room 1346 2800 Plymouth Rd.

institute: University of Michigan

description: HeLa siERCC6 UV 6h recovery experiment 1

data_processing:
Library strategy: BruSeq
Illumina Casava v1.8.2 software used for basecalling.
Reads were mapped to the Human ribosomal DNA complete repeating unit (U13369.1) using Bowtie v.0.12.8 and parameters -n 3 -k 1 -m 1
Reads that did not map to the ribosomal DNA were mapped to the hg19 genome using TopHat v1.4.1 and parameters –min-isoform-fraction 0, --max-multihits 1, --no-closure-search, --no-coverage-search, --bowtie-n, --initial-read-mismatches 3
A coverage determination was then made for every base in the genome using Bedtools v.2.16.2 such that a base covered by one read was recorded as having a coverage of 1/read_length
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: hg19
Supplementary_files_format_and_content: The columns of the abundance measurement files indicate: (1) chromosome; (2) start; (3) end; (4) name; (5) score (placeholder); (6) strand; (7) gene span; (8) feature_type;  (9)  length (sum of feature lengths, e.g. introns and exons); (10) length (sum of feature lengths, e.g. introns and exons); (11) read count (sense strand); (12) density (RPK) – count/length; (13) RPKM - count/(length/1E3)/(mapped read count/1E6)

source_name: HeLa

growth_protocol: HeLa (American Type Culture Collection ATCC CCL-2, human cervical carcinoma, female) cells were grown at 37°C and 5% CO2 in Dulbecco’s modified Eagle’s medium (DMEM, Life Technologies) supplemented with 10% fetal bovine serum (EUROBIO), 100 U/ml penicillin and 100 microg/ml streptomycin (Life Technologies).

extract_protocol:
Cells were labeled with 2 mM Bromouridine (Sigma Aldrich) for 30 min, total RNA was isolated by using TRIzol reagent (Invitrogen), and Bru-labeled RNA was isolated from the total RNA by incubation with anti-BrdU antibodies (BD Biosciences) conjugated to magnetic beads (Dynabeads, Goat anti-Mouse IgG; Invitrogen) under gentle agitation at room temperature for 1 h. For more detail, see Paulsen et. al 2013 (Coordinated regulation of synthesis and stability of RNA during the acute TNF-induced proinflammatory response. Proc. Natl. Acad. Sci. U.S.A. 2013; 110:2240–2245)
cDNA libraries were made from the BrU-labeled RNA using the Illumina TruSeq library kit and sequenced using Illumina HiSeq sequencers at the University of Michigan DNA Sequencing Core with 52 bp single-end reads (on average 50 million reads per sample including 70% unique reads). Sequencing and read mapping (unique reads only) were carried out as described using the human genome reference assembly hg19/GRCh37 (Paulsen et al., 2014)

treatment_protocol: siRNA (siLUC control, siHIRA#1, siHIRA#2, siERCC6) purchased from Eurofins MWG Operon were transfected into cells using Lipofectamine RNAiMAX (Invitrogen) following manufacturer’s instructions. The final concentration of siRNA in the culture medium was 50 nM. Cells were harvested 72 h post-transfection. Nascent RNA sequencing from UV-irradiated cells was carried out as described (Andrade-Lima et al., 2015). HeLa cells exposed to 10 J/m2 UVC were allowed to recover 0, 2, 6, 24 h before incubation with 2 mM bromouridine (BrU) for 30 min at 37°C. Cells were exposed to global UVC irradiation at different time points post siRNA transfection (48 h, 66 h, 70 h or 72 h) to be subject to nascent RNA labeling with BrU all at the same time (72 h post siRNA). Non-irradiated cells were used as controls

value: HeLa

tag: transfection

value: UV

tag: bru labeling time

value: 0.5 hours

tag: time between end of bru labeling and rna extraction

value: 0 hours


title: RNA_RAL11-Mo12


title: DRG sample collected on D7 after TCI, rep3

value: dorsal root ganglia


title: HeLa_siCSB_UV2h_r1

description: HeLa siERCC6 UV 2h recovery experiment 1


title: HeLa_siCSB_UV0h_r1

description: HeLa siERCC6 UV 0h recovery experiment 1


title: RNA_RAL10-Mo12


title: DRG sample collected on D14 after TCI, rep4


title: RNA_RAL16-Mo12


title: DRG sample collected on D7 after TCI, rep1


title: HeLa_siCSB_UV24h_r1

description: HeLa siERCC6 UV 24h recovery experiment 1


title: RNA_181030_RAL15-Mo9


title: HeLa_siCSB_0h_r1

description: HeLa siERCC6 noUV experiment 1

value: no UV


title: C3h2_C3h

tag: strain


title: DRG sample collected on D1 after TCI, rep4

tag: time point

value: Day 1 after TCI


title: DRG sample collected on D1 after TCI, rep3

tag: tissue


title: HeLa_siLUC_UV24h_r3

description: HeLa siLUC UV 24h recovery experiment 3

value: siLUC


title: HeLa_siLUC_UV24h_r2

description: HeLa siLUC UV 24h recovery experiment 2


title: DRG sample collected on D1 after TCI, rep2


title: RNA_181030_RAL11-Mo9

value: Plasma

value: Uganda

value: cd8 t cell ratio:Data_in_Manuscript


title: RNA_181030_RAL12-Mo9

value: Yes

value: Post_ART_HIV_subject (9months on ART)


title: HeLa_siLUC_UV24h_r1

description: HeLa siLUC UV 24h recovery experiment 1


title: HeLa_siLUC_UV6h_r3

description: HeLa siLUC UV 6h recovery experiment 3


title: DRG sample collected on D1 after TCI, rep1


title: MDA-MB-231 replicate4

type: RNA

city: lille

first: frédéric

last: leprêtre

address: Boulevard du Pr Leclercq

department: CHU of Lille, CBP

institute: Lille University

description: CD43 expression consequences in MDA-MB-231 cells, replicate 4.

hyb_protocol: Hybridized to Agilent-026652 Whole Human Genome Microarray 4x44K.

scan_protocol: Agilent-026652 Whole Human Genome Microarray 4x44K were scanned on an Agilent G2505C scanner. Images were quantified using Agilent Feature Extraction Software (version V.10.7.3.1).

data_processing: Agilent Feature Extraction Software (v.10.7.3.1) was used for background subtraction and LOWESS normalization.

label_protocol: Manufacturer's instructions.

growth_protocol: MDA-MB-231 were grown as described by the American Type Culture Collection (Manassas, VA) with the addition of 0.6 mg/ml puromycin.

extract_protocol: Total RNA extracted using manufacturer's instructions.

treatment_protocol: MDA-MB-231 were stably transfected with the linearized plasmid pRFP-C-RS expressing shRNA with the ineffective target sequence   gcacuaccagaagcuaacucagauaguacu (OriGene Technologies, Inc., Rockville, MD). MDA-MB-231 were also stably transfected with four linearized pRFP-C-RS plasmids expressing shRNA targeting human CD43 mRNA at the coding strand sequences acaccgugacagguggaaccauaacaacg, acgcucaccacuuucuuuggcagacggaa, gagccaacaaccuaccaggaaguuuccau and uggcaacugacucucuggagaccuccacu (OriGene Technologies, Inc.).

tag: shRNA


title: RNA_181030_RAL10-Mo9

tag: cd4 count


title: MDA-MB-231 replicate2

description: CD43 expression consequences in MDA-MB-231 cells, replicate 2.


title: MDA-MB-231 replicate3

description: CD43 expression consequences in MDA-MB-231 cells, replicate 3.


title: MDA-MB-231 replicate1

description: CD43 expression consequences in MDA-MB-231 cells, replicate 1.


title: RNA_181030_RAL16-Mo9

tag: cd8 count


title: DRG sample collected on D7 after TCI, rep2


title: HeLa_siLUC_UV6h_r1

description: HeLa siLUC UV 6h recovery experiment 1


title: HeLa_siLUC_UV2h_r3

description: HeLa siLUC UV 2h recovery experiment 3


title: R442Q+i bla rep7

city: Beijing

first: Ting

last: WANG

address: Qinghuayuan Street

institute: Tsinghua University

description: mut+i bla7

data_processing:
Sequenced reads were trimmed for adaptor sequences, and masked for low-complexity or low-quality sequences, then mapped to mm10 genome using RSEM.
Fragments Per Kilobase per Million mapped reads (FPKM) of Refseq genes were caculated by RSEM.
Genome_build: mm10
Supplementary_files_format_and_content: Text files of gene names and FPKM values for each sample.

source_name: single embryo

growth_protocol: Zygotes  were cultured in KSOM at 37.5℃ in 5% CO2 incubator. To collect blastocysts, CHK1 WT and R442Q overexpression preimplantation embryos were cultured in KSOM containing 30nM Chk1 inhibitor at 37.5℃.

extract_protocol:
After removing the zona pellucida, zygotes, late 2-cell embryos and blastocysts were lysed in lysis buffer.
For RNA-seq, cDNA was generated using the SMART-seq2 protocol. Then cDNA was fragmented by Tn5 enzyme and subjected to Illumina Nextera library preparation. All libraries were sequenced on Illumina HiSeq X-10 according to the manufacturer's instruction.

treatment_protocol: Zygotes were injected with WT or R442Q mutant CHK1 mRNA, with or without the treatment of CHK1 inhibitor, then cultured  in 37℃ and 5% CO2 incubator.

value: blastocyst

tag: genotype

value: CHK1 R442Q mutant

value: Chk1 inhibitor


title: HeLa_siLUC_UV6h_r2

description: HeLa siLUC UV 6h recovery experiment 2

tag: treatment


title: R442Q+i bla rep6

description: mut+i bla6


title: RNA_RAL16-Mo4

description:
PathSeq
Uganda_Longitudinal_B1_PathSeq_TPM.xlsx

value: Post_ART_HIV_subject (4months on ART)


title: RNA_RAL16-Mo3

value: Post_ART_HIV_subject (3months on ART)


title: R442Q+i bla rep3

description: mut+i bla3


title: RNA_181030_RAL14-Mo9


title: R442Q+i bla rep4

description: mut+i bla4


title: HeLa_siLUC_UV2h_r2

description: HeLa siLUC UV 2h recovery experiment 2

value: HeLa

value: UV


title: RNA_RAL16-D0

value: No


title: R442Q+i bla rep5

description: mut+i bla5


title: HeLa_siLUC_UV2h_r1

description: HeLa siLUC UV 2h recovery experiment 1

value: 0.5 hours

value: 0 hours


title: RNA_RAL16-Mo24

value: Post_ART_HIV_subject (24months on ART)


title: HeLa_siLUC_UV0h_r2

description: HeLa siLUC UV 0h recovery experiment 2

value: siLUC


title: RNA_RAL15-Mo9

value: Plasma


title: R442Q+i bla rep1

description: mut+i bla1


title: R442Q+i bla rep2

description: mut+i bla2


title: WT+i bla rep7

description: wt+i bla7

value: WT


title: HeLa_siLUC_UV0h_r3

description: HeLa siLUC UV 0h recovery experiment 3


title: RNA_RAL15-Mo4

value: Uganda

value: cd8 t cell ratio:Data_in_Manuscript


title: RNA_RAL16-Mo9

value: Yes

value: Post_ART_HIV_subject (9months on ART)


title: HeLa_siLUC_UV0h_r1

description: HeLa siLUC UV 0h recovery experiment 1


title: WT+i bla rep6

description: wt+i bla6

value: blastocyst


title: RNA_RAL15-Mo24


title: HeLa_siLUC_0h_r3

description: HeLa siLUC noUV experiment 3

value: no UV


title: RNA_RAL15-Mo3


title: HeLa_siLUC_0h_r2

description: HeLa siLUC noUV experiment 2


title: WT+i bla rep5

description: wt+i bla5

value: Chk1 inhibitor


title: WT+i bla rep4

description: wt+i bla4


title: WT+i bla rep3

description: wt+i bla3


title: RNA_RAL15-D0


title: HeLa_siLUC_0h_r1

description: HeLa siLUC noUV experiment 1


title: RNA_RAL14-Mo9


title: HeLa_siHIRA_UV24h_r2

description: HeLa siHIRA#2 UV 24h recovery experiment 2


title: RNA_RAL14-Mo4

value: Post_ART_HIV_subject (4months on ART)


title: WT+i bla rep2

description: wt+i bla2


title: HeLa_siHIRA_UV24h_r1

description: HeLa siHIRA#1 UV 24h recovery experiment 1

value: HeLa


title: RNA_RAL14-Mo24


title: RNA_RAL14-Mo3

value: Post_ART_HIV_subject (3months on ART)


title: R442Q 2cell rep5

description: mut L2C-6

value: late 2-cell

value: CHK1 R442Q mutant


title: RNA_RAL14-D0

value: No


title: HeLa_siHIRA_UV6h_r2

description: HeLa siHIRA#2 UV 6h recovery experiment 2

value: UV

value: 0.5 hours

value: 0 hours


title: HeLa_siHIRA_UV6h_r1

description: HeLa siHIRA#1 UV 6h recovery experiment 1


title: R442Q 2cell rep4

description: mut L2C-5


title: HeLa_siHIRA_UV2h_r2

description: HeLa siHIRA#2 UV 2h recovery experiment 2


title: RNA_RAL13-Mo9

value: Plasma


title: R442Q 2cell rep3

description: mut L2C-3


title: R442Q 2cell rep2

description: mut L2C-2


title: HeLa_siHIRA_UV0h_r2

description: HeLa siHIRA#2 UV 0h recovery experiment 2


title: HeLa_siHIRA_UV0h_r1

description: HeLa siHIRA#1 UV 0h recovery experiment 1


title: RNA_RAL13-Mo3

value: Uganda


title: R442Q 2cell rep1

description: mut L2C-1


title: RNA_RAL13-Mo24

value: cd8 t cell ratio:Data_in_Manuscript

value: Post_ART_HIV_subject (24months on ART)


title: RNA_RAL13-D0

value: Yes


title: WT 2cell rep4

description: wt L2C-5

value: WT


title: HeLa_siHIRA_0h_r2

description: HeLa siHIRA#2 noUV experiment 2

value: no UV


title: HeLa_siHIRA_0h_r1

description: HeLa siHIRA#1 noUV experiment 1


title: WT 2cell rep2

description: wt L2C-2


title: LCL1-Input rep2

city: Shenzhen

first: Yonggang

last: Pei

state: GD

address: 1088 Xueyuan Avenue

department: School of Public Health and Emergency Management

institute: Southern University of Science and Technology

data_processing:
ChIP-Seq reads were mapped to the hg19 genome using Bowtie.
Peak calling, the annotations of enriched regions, motif discovery and pathway analysis were performed with HOMER (Hypergeometric Optimization of Motif EnRichment; http://homer.ucsd.edu/homer/).
Pathway analysis was also performed using HOMER.
The analyzed data were visualized using the R program (https://www.r-project.org/) and the Integrated Genome Browser.
Genome_build: hg19
Supplementary_files_format_and_content: bedGraph

source_name: lymphoblastoid cell line

growth_protocol: EBV-transformed immortalized LCL1 (lymphoblastoid cell line) cells were generated in our laboratory, which were grown in RPMI 1640 media (Hyclone, Logan, UT) supplemented with 5% fetal bovine serum (FBS), 25 U/ml penicillin, 50μg/ml streptomycin, and 2mM L-glutamine

extract_protocol:
30 million LCL1 cells were crosslinked with 1% formaldehyde and harvested for sonication. Then cell lysates including sheared genomic DNA were immunoprecipitated with the indicated antibody (anti-E2F1, anti-E2F6, anti-Rb, anti-HDAC1, and anti-HDAC2) or normal IgG to collect the DNA fragments that can bind with the interest proteins. The immune complexes were incubated with the salmon sperm DNA/protein A agarose slurry, and the collected DNAs were purified for further processes.
The DNA library was prepared with TruSeq ChIP Library Preparation Kit (IP-202-1012; Illumina, San Diego, CA). Then the purified DNAs were sequenced using the Illumina HiSeq platform by the Genome Technology Access Center (GTAC) at the Washington University in St. Louis.

value: EBV-transformed LCLs

tag: chip-seq antibody


title: WT 2cell rep3

description: wt L2C-4


title: RNA_RAL12-Mo9

data_processing:
Library strategy: PathSeq metagenome
sorted cells/plasma: Raw sequencing reads were trimmed off adapter sequence contaminants using Trimmomatic v. 0.36
sorted cells/plasma: Mapped onto the Refseq Grch38 of the human genome using the STAR RNA-Seq aligner (version 2.5.3a)
sorted cells: Gene abundance was then estimated by counting using HTSeq (version 0.9.1)
sorted cells: Transcript counts were then normalized by TMM (Trimmed Mean of M-values by correcting for the library size
plasma: Unaligned paired-end reads were then assembled into contigs using Trinity
plasma: Trinity contigs were then aligned against HG38 again to further remove host-derived sequences with BLAST+. Trinity contigs that aligned to non-reference human sequences in the NCBI nucleotide database were also removed
plasma: Remaining contigs were then aligned against the NCBI nucleotide database and quantified with Salmon
plasma: Taxonomic information was assigned for each contig and transcripts per million (TPM) values were collapsed at the species level for each sample. TPM are normalized for sequencing read depth and length for each sample, allowing for a more accurate comparisons between proportion of reads mapping to the same gene in various samples
Genome_build: Human (Refseq Grch38) and Non-human (NCBI nucleotide database and quantified with Salmon)
Supplementary_files_format_and_content: xlsx data matrix files with normalized read counts (sorted cells; sample by transcript) or TPM (plasma; sample by species abundance)

value: Post_ART_HIV_subject (9months on ART)


title: WT+i bla rep1

description: wt+i bla1

value: blastocyst

value: Chk1 inhibitor


title: LCL1-Input rep1


title: RNA_RAL12-Mo4

value: Post_ART_HIV_subject (4months on ART)


title: RNA_RAL12-Mo3

value: Post_ART_HIV_subject (3months on ART)


title: LCL1-Mo-IgG rep2

value: Mouse IgG (sc-2025; Santa Cruz)


title: WT 2cell rep1

description: wt L2C-1

value: late 2-cell


title: HeLa_siHIRA_UV2h_r1

description: HeLa siHIRA#1 UV 2h recovery experiment 1

value: HeLa

value: UV

value: 0.5 hours


title: R442Q zy rep6

description: mut zy-6

value: zygote

value: CHK1 R442Q mutant


title: RNA_RAL12-Mo24

value: Plasma

value: Uganda

value: cd8 t cell ratio:Data_in_Manuscript

value: Post_ART_HIV_subject (24months on ART)


title: LCL1-Mo-IgG rep1

value: EBV-transformed LCLs


title: R442Q zy rep5

description: mut zy-5


title: LCL1-Ra-IgG rep2

value: Rabbit IgG (sc-2027; Santa Cruz)


title: RNA_RAL13-Mo4

value: Yes


title: RNA_RAL12-D0

value: No


title: RNA_RAL11-Mo9

value: Post_ART_HIV_subject (9months on ART)


title: R442Q zy rep4

description: mut zy-4


title: R442Q zy rep3

description: mut zy-3


title: RNA_RAL11-Mo4

value: Post_ART_HIV_subject (4months on ART)


title: LCL1-Ra-IgG rep1


title: R442Q zy rep1

description: mut zy-1


title: LCL1-HDAC2 rep1

value: HDAC2 (ab7029; Abcam)


title: RNA_RAL11-Mo24


title: LCL1-HDAC1 rep1

value: HDAC1 (ab7028; Abcam)


title: RNA_RAL11-D0


title: LCL1-HDAC2 rep2


title: WT zy rep5

description: wt zy-6

value: WT


title: R442Q zy rep2

description: mut zy-2


title: RNA_RAL11-Mo3

value: Post_ART_HIV_subject (3months on ART)


title: WT zy rep4

description: wt zy-5


title: RNA_RAL10-Mo9


title: LCL1-HDAC1 rep2


title: LCL1-Rb rep2

value: Rb (G3-245; BD Pharmingen)


title: RNA_RAL10-Mo4


title: LCL1-Rb rep1


title: WT zy rep2

description: wt zy-3

value: zygote


title: WT zy rep3

description: wt zy-4


title: RNA_RAL10-Mo3


title: WT zy rep1

description: wt zy-2


title: LCL1-E2F1 rep2

value: E2F1 (sc-193X; Santa Cruz)


title: LCL1-E2F1 rep1


title: Meningioma Sample 7

city: Bethesda

first: Patrick

middle: J.

last: Cimino

state: MD

address: 10 Center Dr

department: NINDS

institute: National Institutes of Health

description: Meningioma Sample 7

data_processing:
Sequencing was performed using an Illumina HiSeq 2500 in Rapid Run mode and  employed a paired-end, 50 base read length (PE50) sequencing strategy.
RNA-seq reads were aligned to the UCSC hg19 assembly using star2 and counted for gene associations against the UCSC genes database with HTSeq
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include raw values for each Sample.

source_name: anaplastic meningioma

extract_protocol:
Total high-integrity RNA from anaplastic meningioma tissue was processed for RNA sequencing
Libraries were constructed using a stranded mRNA preparation kit and subsequently enriched for coding regions with in-solution hybridization capture (of entire exome)
Approximately 3 9 107 100-bp, paired-end reads per library were generated using Rapid Run v2 (Illumina) chemistry on a HiSeq 2500

tag: diagnosis

value: anaplastic meningioma

tag: tumor type

value: Secondary

value: brain

tag: radiation

value: yes


title: Meningioma Sample 5

description: Meningioma Sample 5


title: Meningioma Sample 6

description: Meningioma Sample 6


title: RNA_RAL10-Mo24

value: Plasma

value: Uganda

value: cd8 t cell ratio:Data_in_Manuscript

value: Post_ART_HIV_subject (24months on ART)


title: EKOiE_2i_Sox2_pEsrrb_mNr5a2_3

city: paris

first: Pablo

last: Navarro

address: 25 rue du Docteur Roux

data_processing:
RNA-seq: Stranded paired end RNA-seq reads were aligned to the mm10 genome using STAR and quantified by RSEMusing the RSEM-STAR pipeline, with additional options "--seed 1618 --calc-pme --calc-ci --estimate-rspd --forward-prob 0.0 --paired-end".
ChIP-seq: Paired reads were trimmed by aligning read pairs to discover regions of reverse complementarity surrounded by adapters. Alignment and trimming were performed with the BioSequences package for Julia 0.6 Reads were aligned with Bowtie2 to the mm10 genome, with options "-k 10". Reads were additionally filtered for those with a single discovered alignment (in Bowtie2 "k" mode this is mapping quality = 255) and an edit distance less than 4. Duplicate reads (those aligning with same left-right coordinate) were collapsed to one. BigWig files were generated from whole fragment piles and normalised to RPM.
Genome_build: mm10
Supplementary_files_format_and_content: RNA-seq: tab-delimited table with TPM for all genes
Supplementary_files_format_and_content: RNA-seq: tab-delimited table with estimated raw counts for all genes
Supplementary_files_format_and_content: ChIP-seq: bigwig files

source_name: embryonic stem cell

growth_protocol: ES cells were cultured on 0.1% gelatine (SIGMA, Cat# G1890-100G) in DMEM + GlutaMax-I (Gibco, Cat# 31966-021), 10% FCS (Gibco, Cat# 10270-098), 100 μM 2-mercaptoethanol (Gibco, Cat# 31350-010), 1× MEM non-essential amino acids (Gibco, Cat# 1140-035) and 10 ng×ml−1 recombinant LIF (MILTENYI BIOTEC, Cat# 130-099-895) (Referred to as FCS/LIF). Cells were passaged 1:10 every 2–3 days. For experiments in  2i/LIF, medium contained 1µM PD0325901 and 3 µM CHIR99021  (Axon Medchem Bv) - 0.5× DMEM/F12 (Gibco, Cat# 31331093), 0.5×Neurobasal (Gibco, Cat# 21103049), 0.5% N2 supplement 100× (Gibco, Cat# 17502048), 1% B27 supplement 50× (Gibco, Cat# 17504044), 10µg/mL Insulin (Sigma, Cat# I1882-100MG), 2 mM L-Glutamine (Invitrogen, Cat# 91139), 0.05% BSA (Sigma, Cat# A3311-10G), 100 μM 2-mercaptoethanol (Gibco, Cat# 31350-010), 10 ng/ml recombinant LIF (MILTENYI BIOTEC, Cat# 130-099-895) (Referred to as 2i/LIF). 2 days before RNA extraction or chromatin preparation, cell were washed in PBS and replated in the presence or absence of doxycycline (Sigma, Cat# I5148).

extract_protocol:
After trypsinisation, 10 million ES cells were crosslinked in 2 ml of freshly prepared PBS-DSG 2 mM at pH 7.0 (Sigma, Cat# 80424-5 mg) for 50 min at room temperature with occasional shaking. After pelleting and washing once in PBS, cells were incubated for 10 min in 2 ml PBS 1% formaldehyde (Thermo, Cat# 28908). Crosslinking was stopped with 0.125 mM glycine for 5 min at room temperature. Cells were pelleted and washed with ice-cold PBS. Cells were resuspended in 2 ml of swelling buffer (25 mM Hepes pH 7.95, 10 mM KCl, 10 mM EDTA) freshly supplemented with 1× protease inhibitor cocktail (PIC-Roche, Cat# 04 693 116 001) and 0.5% IGEPAL. After 30 min on ice, the suspension was passed 40 times in a dounce homogenizer. Cells were then centrifuged and resuspended in 300 μl of TSE150 (0.1% SDS, 1% Triton X-100, 2 mM EDTA, 20 mM Tris-HCl pH8, 150 mM NaCl) buffer, freshly supplemented with 1× PIC. Samples were sonicated in 1.5 ml tubes (Diagenode) using a Bioruptor Pico (Diagenode) for 7 cycles divided into 30 s ON–30 s OFF sub-cycles at maximum power, in circulating ice-cold water. After centrifugation (30 min, full speed, 4 °C), the supernatant was either used immediately for immunoprecipitation or stored at −80 °C until use, generally within the month. Five microliters were used to quantify the chromatin concentration and check DNA size (typically 200–350 bp). Chromatin from 107 cells was used for each ChIP-seq after pre-clearing it for 3 hours rotating on-wheel at 4 °C in 300 μl of TSE150 containing 50 μl of protein G Sepharose beads (Sigma, Cat# P3296-5 ML) 50% slurry, previously blocked with BSA (500 μg×ml−1; Roche, Cat#  5931665103) and yeast tRNA (1 μg×ml−1; Invitrogen, Cat# AM7119). Immunoprecipitations with anti-Esrrb mouse monoclonal (1µg per 2 million cells, Perseus Proteomics, Cat# H6-705-00), anti-Nanog rabbit polyclonal (0.6 μg per 2 million cells, Cosmobio, Cat#  REC-RCAB001P); anti-Oct4 rabbit polyclonal (1 μg per 2 million cells, Abcam Cat # ab19857); anti-Sox2 rabbit polyclonal (1 μl per 2 million cells – concentration not specified, Active Motif  Cat#  39844); anti-Flag mouse monoclonal (1 μg per 2 million cells Sigma Cat# F3165) antibodies, were performed overnight rotating on-wheel at 4 °C in 500 μl of TSE150. 20 μl were set apart for input DNA extraction and precipitation. 25 μl of blocked protein G beads 50% slurry was added for 4 h rotating on-wheel at 4 °C. Beads were pelleted and washed for 5 min rotating on-wheel at room temperature with 1 ml of buffer in the following order: 3 × TSE150, 1 × TSE500 (as TSE150 but 500 mM NaCl), 1× washing buffer (10 mM Tris-HCl pH8, 0.25M LiCl, 0.5% NP-40, 0.5% Na-deoxycholate, 1 mM EDTA), and 2 × TE (10 mM Tris-HCl pH8, 1 mM EDTA). Elution was performed in 100 μl of elution buffer (1% SDS, 10 mM EDTA, 50 mM Tris-HCl pH 8) for 15 min at 65 °C after vigorous vortexing. Eluates were collected after centrifugation and beads rinsed in 150 μl of TE-SDS1%. After centrifugation, the supernatant was pooled with the corresponding first eluate. For both immunoprecipitated and input chromatin, the crosslinking was reversed overnight at 65 °C, followed by proteinase K treatment, phenol/chloroform extraction and ethanol precipitation.
SPRI Bead preparation: 1 ml Sera-Mag™ Magnetic SpeedBeads™, carboxylated, 1 µm, 3 EDAC/PA5 (GE Healthcare Life Sciences, Cat# 65152105050250) were washed 3 times with a TE-Tween solution (10 mM Tris HCl pH 8, 1 mM EDTA, 0.05% Tween 20, pH 8.0) and resuspended in TE-Tween-20% PEG 8000 solution (10 mM Tris HCl pH 8, 1 mM EDTA, 0.05% Tween 20, pH 8.0).   End repair: Precipitated DNA was resuspended in 37.5µl of water and mixed with 2µl of 10mM dNTPs, 5µl of NEB T4 ligase buffer, 2.5µl of NEB T4 polymerase (Cat# M0203L), 0.5µl of NEB Klenow polymerase (Cat# M0210L) and 2.5µl of NEB T4 PNK (Cat# M0201L). Samples were incubated 30min at 20oC in a thermocycler. DNA was purified with SPRI beads: 90µl of SPRI bead suspension and 50µl isopropanol were added and samples transferred to a 96 well plate. After incubating for 5 min, the plate was put on a 96S Super Ring Magnet (Alpaqua, Cat# A001322), beads were allowed to separate completely, and the supernatant removed without disrupting the bead pellet. Beads were washed twice with 200µl of 70% Ethanol and the supernatant completely removed. DNA was eluted in 21µl of water.   A-Tailing: 20µl of sample were mixed with 2.5µl of NEB Buffer #2, 1µl of 5mM dATP, 1.5µl of NEB Klenow 3'-5' exo minus (Cat# M0212L), and incubated at 37oC for 30min in a thermocycler. DNA was purified with SPRI beads as before, but using a volume of 45µl of beads and 25µl isopropanol. DNA was elute in 20µl of water.   Adaptor ligation: 19µl of sample were mixed with 2.5µl of NEB T4 ligase buffer, 1.25µl of a 0.2µM solution of annealed adapters, and 2.5µl of NEB concentrated T4 ligase (Cat# M0202M) and incubated overnight at 16oC. DNA was purified with SPRI beads as before, but using a volume of 35µl of beads and no isopropanol, eluting in 20 µl of water. Adaptors were designed in house based on the structure of Illumina TruSeq™ indexed and forked adapters, modified to include extended indexes. 22.5µl each of 40µM ssDNA Barcoded and Universal adaptor solutions were mixed with 5µl of NEB buffer 2, and annealed in a thermocycler.   Barcoded adaptor:  5’P-GATCGGAAGAGCACACGTCTGAACTCCAGTCAC-Index -ATCTCGTATGCCGTCTTCTGCTTG.  5’P indicates the presence of a 5’phosphate group.   Universal adapter:   AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATC*T.   * indicates the presence of a phosphorothioate bond between the last C and T.  Library amplification: 19.5 µl of sample were mixed with 1µl of a 1:10 dilution of Quant-iT Picogreen dye (Invitrogen, Cat# P11496), 25µl of KAPA HiFi HotStart 2× master Mix (Kapa Bioscience Cat# KK2502), 1µl of 10µM PCR 1.0 and 1µl of PCR 2.0 primers (See below). The amplification mix was distributed in two wells of a LightCycler 384 plate (Roche, Cat# 4729749001) and on a LightCycler 480 II instrument (Roche, Cat# 05015243001) using the following program: 1’ at 98°C; N cycles: 10” at 98°C; 20” at 64°C; 45” at 72°C. The number of cycles N was determined on real time by monitoring the fluorescence such that the amplification was stopped during the exponential phase. Samples were removed from the plate and purified with 70 µl SPRI beads without isopropanol, and eluting in 40µl of water. 1µl was used to measure the DNA concentration with a Qubit 3 and the provided reagents (Invitrogen, Cat#Q33218). 1 ng of DNA was used to check fragment size with a D1000 High Sensitivity Screentape and appropriate reagents (Agilent, Cat# 5067-5584, Cat# 5067-5585) on an Agilent 2200 Tapestation.  Library sequencing: the libraries were sequenced (paired-end 150bp reads) by Novogene Co. Ltd.

tag: cell type

value: EKOiE

tag: culture

tag: ChIP

tag: antibody

value: Active Motif, 39844

tag: esrrb

value: p

value: m

tag: replicate


title: RNA_RAL10-D0

extract_protocol:
sorted cells: RNA was extracted from sorted cells lysed in RNAzol RT (MRC Inc., OH, USA), according to the manufacturer’s instructions. Briefly, 0.4 volume of sterile water was added to each lysate to allow aqueous and organic phase separation. Total RNA was then extracted from the aqueous phase by isopropanol precipitation. RNA pellets were washed with 70% ethanol and resuspended in sterile water. Extracted RNA was stored at -80°C until preparation of mRNA libraries. RNA yield and integrity were verified by microelectrophoresis using the High Sensitivity RNA ScreenTape Kit (Agilent) on the 2200 TapeStation system (Agilent).
plasma: Circulating total RNA and DNA were isolated from frozen plasma using RNAzolBD (MRC) according to the manufacturer’s recommendations.
sorted cells: mRNA libraries were constructed as described previously (Sandler et al., 2014) using the NEBNext Ultra RNA library preparation kit. Polyadenylated transcripts were purified with oligo-dT magnetic beads, fragmented, reverse transcribed using random hexamers and incorporated into barcoded cDNA libraries based on the Illumina TruSeq platform. Libraries were validated by microelectrophoresis on a 2100 Bioanalyzer system (Agilent), quantified with Kapa Library Quantification Kits (Roche), pooled and clustered on Illumina TruSeq v2 flow cells. Clustered flow cells were sequenced in 2x75 base paired-end runs on Illumina HiSeq 2000 and HiSeq 4000.
plasma: RNA fragmentation and reverse transcription using random hexamers, the obtained transcripts, as well as the isolated plasma DNA, were individually incorporated into barcoded cDNA libraries on the basis of the Illumina TruSeq platform. Libraries were validated by microelectrophoresis on a 2100 Bioanalyzer system (Agilent), quantified using Kapa Library Quantification Kits (Roche), pooled and clustered on Illumina patterned flow cells. Clustered flow cells were sequenced on an Illumina HiSeq 4000 in 75-base paired reads. To control for contamination, four water samples were processed along with plasma samples from nucleic acids extraction through sequencing.

value: Yes

value: No


title: LCL1-E2F6 rep2

value: EBV-transformed LCLs

value: E2F6 (sc-22823X; Santa Cruz)


title: Meningioma Sample 4

description: Meningioma Sample 4

value: Primary

value: no


title: RNA_RAL08-Mo9

value: Post_ART_HIV_subject (9months on ART)


title: LCL1-E2F6 rep1


title: EKOiE_2i_Sox2_mEsrrb_mNr5a2_3


title: RNA_RAL08-Mo4

value: Post_ART_HIV_subject (4months on ART)


title: Sample 4

organism: Danio rerio

tag: Stage

value: Embryo

tag: strain

value: AB


title: Meningioma Sample 8

description: Meningioma Sample 8

value: anaplastic meningioma

value: Secondary

tag: tissue

value: brain

value: yes


title: EKOiE_2i_Sox2_mEsrrb_pNr5a2_3

value: EKOiE

value: Active Motif, 39844


title: Meningioma Sample 3

description: Meningioma Sample 3


title: RNA_RAL08-Mo3

value: Plasma

value: Uganda

tag: cd4 count

value: cd8 t cell ratio:Data_in_Manuscript

value: Post_ART_HIV_subject (3months on ART)


title: EKOiE_2i_Oct4_pEsrrb_mNr5a2_3

value: Abcam, ab19857

value: p

value: m


title: Meningioma Sample 1

description: Meningioma Sample 1

value: Primary

value: no


title: Sample 3

value: Embryo


title: INPUT_rep2

city: Paris Cedex 05

first: Nicolas

last: Servant

address: 26 rue d'ulm

institute: Institut Curie

data_processing:
Raw fastq reads were aligned to the human reference genome (version hg19) using the BWA-mem algorithm (v0.7.5)
Reads with a mapping quality inferior to ten or marked as positional duplicates were removed
Peaks for ChIP experiments were detected using MACS2 (v.2.1.0), for each replicate independently, with relevant input reads as background, an FDR threshold of 0.05 and default parameters
Peaks were also called for cisplatin and Pt-ttpy g-H2AX IPs using the untreated condition reads as background
Bed files used in all the analyses were created by keeping the peaks present at the intersection between replicates
Genome_build: hg19
Supplementary_files_format_and_content: untr_peaks.narrowPeak: peaks called by MACS2 (gH2AX IP untreated cells vs INPUT)
Supplementary_files_format_and_content: cispt_untr_peaks.narrowPeak: peaks called by MACS2 (gH2AX IP in cisplatin-treated cells vs untreated cells IP)
Supplementary_files_format_and_content: ptttpy_untr_peaks.narrowPeak: peaks called by MACS2 (gH2AX IP in pt-ttpy-treated cells vs untreated cells IP)

source_name: A2780 cells

extract_protocol:
After stopping the fixation by glycine (0.125M) the cells are recovered by scraping, centrifuged and lysed with the lysis buffer (5mM PIPES pH8, 85mM KCl, 0.5% NP40, 1X inhibitor cocktail) using piston B (dounce homogenizer) 10 times in ice. The lysed cells are then aliquoted (approximately 2-4 million per tube) the nucleus was then lysed by the buffer (5mM Tris-HCl pH8, 10mM EDTA, 1% SDS, 1X inhibitor cocktail) and sonicated to obtain fragments of size 200-700bp. The sonicated chromatin was then incubated with ChIP Adembeads protein A / G (Sigma) which have already blocked for 15 minutes with 225 μl of “blocking buffer” and incubated with 1-3 μg of anti γH2AX antibody (anti -rabbit ab2893) in IP buffer (0.01% SDS, 1.1% triton X-100, 1.2mM EDTA, 16.7mM Tris-HCl pH8, 16.7mM NaCl) The beads were then washed with several washing buffers which contain increasing concentrations of NaCl, then the magnetic particles are suspended in 300 μl of elution buffer (0.1M NaHCO3, 1% SDS) and proteinase K. DNA was recovered and purified using phenol / chloroform , and its concentration assayed with Nano-drop and qubit.
DNA quality was assayed by Agilent 2100 expert high sensitivity DNA assay and the library prepared and high-throughput sequencing done on HiSeq2500 (Rapid Flow cell,50 bases Single Read, Illumina TruSeq Read)

treatment_protocol: The A2780 cells were treated with the IC80 doses of Pt-ttpy and cisplatin for 96 hours because under these conditions the two complexes induce 40-50% of damage to genomic DNA. At the end of the treatment, the cells were fixed with 4%.

tag: chip antibody

value: Untreated cells

tag: cell line


title: RNA_RAL07-Mo9

tag: cd8 count

value: Yes

value: Post_ART_HIV_subject (9months on ART)


title: EKOiE_2i_Oct4_mEsrrb_mNr5a2_3


title: YX3.917S

city: Johns Island

first: Jeanine

last: Morey

state: SC

address: 3419 Maybank Hwy, Ste B

department: Conservation Medicine

institute: National Marine Mammal Foundation

data_processing:
The Illumina BCL output files were converted to fastq-sanger file format and sequence quality triming was performed on CyVerse Discovery Environment with the HTProcess-prepare_directories-and-run_fastqc-0.1 and HTProcess_trimmomatic_0.33 apps.  The following Trimmomatic parameters were used: ILLUMINACLIP:TruSeq3-SE.fa 2:30:10; LEADING:10; TRAILING:10; SLIDINGWINDOW:4:20; HEADCROP:6; MINLEN:36.
Reads were mapped to the Tursiops truncatus genome, NIST Tru_tru v1 (GCF_001922835.1), on CyVerse Discovery Environment with the HTProcess_Tophat-2.1.1 app using Bowtie as the alignment engine.
Read counts as FPKM (fragments per kilobase of trnascript per million mapped reads) were generated on CyVerse Discovery Environment with the HTProcess_Cufflinks-2.2.1 app with the genome as a reference.
Genome_build: NIST Tur_tru v1
Supplementary_files_format_and_content: Processed data is supplied in a single file.  The first column, "locus", contains the id/location from the NIST Tur_tru v1 genome.  The remaining colums contain the FPKM values for each sample as generated by Cufflinks.

organism: Tursiops truncatus

source_name: skin

extract_protocol:
Total RNA was extracted using Qiagen Rneasy Lipid Tissue Mini kits with on-column Dnase digestion.
Libraries were constructed using a NEBNext ultra Directional RNA Library Prep kit for Illumina and indexed with the NEBNextMultiplex Oligos for Illumina

tag: Sex

value: Female

tag: location

value: Barataria Bay, LA

tag: sampling date

tag: fb field id


title: RNA_RAL07-Mo4

source_name: Plasma

value: Post_ART_HIV_subject (4months on ART)


title: YX1.917S


title: INPUT_rep1

tag: treatment


title: Pt-ttpy_rep2

value: IC80 dose of Pt-ttpy for 96 hours


title: EKOiE_2i_Oct4_pEsrrb_pNr5a2_3

tag: cell type

value: EKOiE

tag: culture


title: RNA_RAL07-Mo3

value: Plasma

value: Uganda


title: YR5.617S


title: EKOiE_2i_Oct4_mEsrrb_pNr5a2_3

tag: ChIP

tag: antibody


title: YX5.917S


title: Meningioma Sample 2

description: Meningioma Sample 2

tag: diagnosis

value: anaplastic meningioma

tag: tumor type

value: brain

tag: radiation


title: EKOiE_2i_Sox2_pEsrrb_pNr5a2_3

value: Active Motif, 39844

tag: esrrb

value: p

tag: replicate


title: YR3.617S


title: RNA_RAL07-Mo24

tag: tissue

tag: cd4 count

value: cd8 t cell ratio:Data_in_Manuscript

value: Post_ART_HIV_subject (24months on ART)


title: EKOiE_2i_Nanog_mEsrrb_mNr5a2_3

value: Nanog

value: Cosmobio, REC-RCAB001P

value: m


title: YR1.617S


title: CisPt_rep2

tag: chip antibody

value: IC80 dose of cisplatin for 96 hours

tag: cell line


title: RNA_RAL08-D0

tag: cd8 count

value: Yes

value: No


title: RNA_RAL04-Mo9

value: Post_ART_HIV_subject (9months on ART)


title: CisPt_rep1


title: EKOiE_2i_Nanog_pEsrrb_pNr5a2_3


title: Untreated_rep2

value: Untreated cells


title: YN9.617S

tag: Sex

value: Female

tag: location

value: Barataria Bay, LA

tag: sampling date


title: EKOiE_2i_Nanog_mEsrrb_pNr5a2_3

tag: cell type

value: EKOiE


title: YN5.617S

tag: fb field id


title: EKOiE_2i_Input_pEsrrb_mNr5a2_3

tag: culture

tag: ChIP

value: Input


title: EKOiE_2i_Nanog_pEsrrb_mNr5a2_3

tag: antibody


title: RNA_RAL04-Mo3

value: Plasma

value: Uganda

value: Post_ART_HIV_subject (3months on ART)


title: RNA_RAL04-Mo4

value: cd8 t cell ratio:Data_in_Manuscript

value: Post_ART_HIV_subject (4months on ART)


title: RNA_RAL04-Mo24

value: Post_ART_HIV_subject (24months on ART)


title: YN3.617S


title: EKOiE_2i_Input_mEsrrb_mNr5a2_3


title: YN1.617S


title: EKOiE_2i_Input_pEsrrb_pNr5a2_3

value: p


title: YK9.617S


title: SET1B_hypoxia_1

city: Cambridge

first: James

last: Nathan

address: Jeffrey Cheah Biomedical Centre

department: Medicine

country: United Kingdom

institute: University of Cambridge

data_processing:
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 Homo sapiens reference genome available on ENSEMBL using the STAR aligner v.2.5.2b, and BAM files generated.
Unique gene hit counts were calculated by using feature Counts from the Subread package v.1.5.2.
Using DESeq2, a comparison of gene expression between the groups of samples was performed. The Wald test was used to generate p-values and Log2 fold changes.
Genes with adjusted p-values < 0.05 and absolute log2 fold changes > 0.5  were called as differentially expressed genes for each comparison.
Genome_build: GRCh37 (hg19)
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

molecule: polyA RNA

source_name: Hela cells_SET1B_CRISPR

growth_protocol: Wildtype HeLa cells, SET1B KO or HIF1beta KO cells were grown on 15 cm dishes in complete DMEM media

extract_protocol:
Total RNA was extracted from HeLa cells using the RNeasy Plus minikit (QIAGEN)
Libraries were constructed according to Illumina protocols

treatment_protocol: Cells were incubated in  21% or 1 oxygen for 12 hr

value: HeLa

tag: genotype

value: SET1B KO

tag: ambient o2

tag: duration of hypoxia

value: 12 hours


title: SET1B_hypoxia_2


title: SET1B_2


title: RNA_RAL07-D0

city: Atlanta

first: Rafick-Pierre

last: Sekaly

address: 1750 Haygood Drive

value: Yes

value: No


title: EKOiE_2i_Input_mEsrrb_pNr5a2_3

tag: esrrb

value: m

tag: replicate


title: EKOiE_2i_Esrrb_pEsrrb_mNr5a2_3

value: Esrrb

value: Perseus Proteomics, H6-705-00


title: YK5.16S

value: Female

value: Barataria Bay, LA


title: SET1B_1


title: YK3.16S


title: RNA_RAL03-Mo4

tag: tissue

value: Plasma

tag: cd4 count


title: RNA_RAL03-Mo9

value: Uganda

value: Post_ART_HIV_subject (9months on ART)


title: HIF1b_hypoxia_2

source_name: Hela cells_HIF1b_CRISPR

tag: cell line

value: HIF1b KO

tag: chip antibody


title: EKOiE_2i_Esrrb_mEsrrb_mNr5a2_3

value: EKOiE


title: YK1.16S

tag: Sex


title: RNA_RAL03-Mo3

tag: cd8 count

value: cd8 t cell ratio:Data_in_Manuscript

value: Post_ART_HIV_subject (3months on ART)


title: YJ7.15S

tag: location

tag: sampling date


title: Untreated_rep1

tag: treatment

value: Untreated cells


title: RNA_RAL03-Mo24

value: Post_ART_HIV_subject (24months on ART)


title: EKOiE_2i_Esrrb_pEsrrb_pNr5a2_3

tag: cell type

tag: culture

value: p


title: RNA_RAL03-D0

value: Yes


title: YJ1.16S

tag: fb field id


title: HIF1b_2

value: HeLa

tag: genotype

value: 12 hours


title: RNA_RAL04-D0

value: No


title: RNA_QA37

description:
PathSeq
Uganda_QA_PathSeq_TPM.xlsx

value: cd8 t cell ratio:1.25


title: EKOiE_2i_Esrrb_mEsrrb_pNr5a2_3

tag: ChIP

value: Esrrb

tag: antibody

value: Perseus Proteomics, H6-705-00

value: m


title: HIF1b_1

tag: ambient o2

tag: duration of hypoxia


title: EKOiE_2i_Sox2_pEsrrb_mNr5a2_2

value: Active Motif, 39844

tag: esrrb

tag: replicate


title: YF4.917S

value: Male

value: Barataria Bay, LA


title: RNA_QA22

description:
PathSeq
Uganda_QA_PathSeq_TPM.xlsx

tag: tissue

value: Plasma

value: Uganda

tag: cd4 count

value: cd8 t cell ratio:0.67

value: Post_ART_HIV_subject (~0-2yrs on ART)


title: YF1.16S

tag: Sex

value: Female


title: EKOiE_2i_Sox2_pEsrrb_pNr5a2_2

value: EKOiE

value: p


title: Pt-ttpy_rep1

tag: chip antibody

value: IC80 dose of Pt-ttpy for 96 hours

tag: cell line


title: Control_Hypoxia_2

source_name: Hela cells_control_CRISPR

value: HeLa

value: control

value: 12 hours

value: wildtype


title: Control_Hypoxia_1


title: HIF1b_hypoxia_1

value: HIF1b KO


title: RNA_QA21

description:
PathSeq
Uganda_QA_PathSeq_TPM.xlsx

value: No

tag: cd8 count

value: cd8 t cell ratio:1.57

value: Healthy


title: YA9.16S

tag: location

value: Barataria Bay, LA

tag: sampling date


title: Control_2


title: YA7.16S


title: EKOiE_2i_Sox2_mEsrrb_pNr5a2_2

tag: cell type

tag: culture

value: Active Motif, 39844

value: m


title: EKOiE_2i_Oct4_pEsrrb_mNr5a2_2

value: Abcam, ab19857


title: Control_1

tag: genotype


title: YA4.917S

value: Male

tag: fb field id


title: RNA_QA18

description:
PathSeq
Uganda_QA_PathSeq_TPM.xlsx

value: Plasma

value: Uganda

value: cd8 t cell ratio:0.4

value: Yes

value: Post_ART_HIV_subject (~0-2yrs on ART)


title: RNA_QA19

description:
PathSeq
Uganda_QA_PathSeq_TPM.xlsx

value: cd8 t cell ratio:3.14


title: EKOiE_2i_Sox2_mEsrrb_mNr5a2_2

value: EKOiE

tag: ChIP

tag: antibody


title: YA3.917S

value: Female


title: YA6.917S


title: Control-Post-stimulation-rep1

first: Sebas

last: Chavez

address: Av. Manuel Siurot s/n

department: Instituto de Biomedicina de Sevilla

institute: Universidad de Sevilla

description: Serum starved for 48 hours (starting 24 hours after Control siRNA addition) and then serum was added and cells were recovered after 90 minutes.

data_processing:
Basecalls was performed by the Illumina HiSeq Control Software 2.2.58
Sequenced reads were  mapped to human genome GRCh38  whole genome using HISAT2  v0.12.2 with  default parameters.
exonix reads per gene  were cuantified using the featureCounts v1.5.2 with options -p -B  -O -t "exon" -g" "gene_id"  using as annotation the file Homo_sapiens.GRCh38.87.gtf form emsembl v.87
exonix reads per gene  were cuantified using the featureCounts v1.5.2 with options -p -B  -O -t "gene" -g" "gene_id"  using as annotation the file Homo_sapiens.GRCh38.87.gtf form emsembl v.87
gene expresion was estimated using Kallisto v. 0.43 against and index built on human genome  GRCh38.p7 using -b 100 option.
Genome_build: GRCh38.p7
Supplementary_files_format_and_content: count.exons, fragments per exon as counted by featuresCounts
Supplementary_files_format_and_content: count.genes fragments per exon as counted by featuresCounts
Supplementary_files_format_and_content: *.tpm, abundance files as stimated by kalisto in trascipts per million

source_name: HCT116 human colon carcinoma cells

growth_protocol: Human HCT166 cells were maintained in McCoy's 5A modified medium supplemented with 10 % foetal bovine serum, 60 mg/l penicillin, and 100 mg/l streptomycin.

extract_protocol:
Total RNA was extracted with RNAeasy mini kit (Qiagen), and treated with DNase previous to retrotranscription.
1 µg of DNase treated RNA was retrotranscribed by Super-Script III (Invitrogen) using random hexanucleotides as primers. Total RNA was depleted of 18S rRNA and then libraries were prepared.

treatment_protocol: For transfection of siRNA, Oligofectamine (Invitrogen) was used, following manufacturer´s instructuions. Sequences of the siRNAs are as follows: siControl (CGUACGCGGAAUACUUCGA); siPFDN2 (CAGCCUAGUGAUCGAUACA); siPFDN5 (AGAGAAGACAGCUGAGGAU).

tag: sirna

value: Control

tag: treatment

value: post-stimulation


title: Control-Post-stimulation-rep2


title: RNA_QA17

institute: Emory University

description:
PathSeq
Uganda_QA_PathSeq_TPM.xlsx

value: No

value: cd8 t cell ratio:0.81


title: EKOiE_2i_Oct4_mEsrrb_pNr5a2_2

tag: esrrb

value: p

tag: replicate


title: RNA_QA15

description:
PathSeq
Uganda_QA_PathSeq_TPM.xlsx

tag: tissue

tag: cd4 count

value: cd8 t cell ratio:1.14


title: EKOiE_2i_Oct4_mEsrrb_mNr5a2_2

value: m


title: Y99.917S

tag: Sex

value: Barataria Bay, LA


title: EKOiE_2i_Nanog_pEsrrb_mNr5a2_2

value: Nanog

value: Cosmobio, REC-RCAB001P


title: RNA_QA14

description:
PathSeq
Uganda_QA_PathSeq_TPM.xlsx

value: Plasma

value: Uganda

value: cd8 t cell ratio:2.29


title: RNA_QA20

description:
PathSeq
Uganda_QA_PathSeq_TPM.xlsx

value: cd8 t cell ratio:1.44

value: Healthy


title: Y98.617S

value: Male


title: PFDN5-Post-stimulation-rep1

description: Serum starved for 48 hours (starting 24 hours after PFDN5 siRNA addition) and then serum was added and cells were recovered after 90 minutes.

tag: cell line


title: PFDN2-Post-stimulation-rep2

description: Serum starved for 48 hours (starting 24 hours after PFDN2 siRNA addition) and then serum was added and cells were recovered after 90 minutes.


title: EKOiE_2i_Nanog_pEsrrb_pNr5a2_2

value: EKOiE


title: EKOiE_2i_Nanog_mEsrrb_mNr5a2_2


title: PFDN2-Post-stimulation-rep1


title: Y92.617S


title: EKOiE_2i_Oct4_pEsrrb_pNr5a2_2

value: Abcam, ab19857


title: RNA_QA13

description:
PathSeq
Uganda_QA_PathSeq_TPM.xlsx

tag: cd8 count

value: cd8 t cell ratio:0.44

value: Yes


title: Control-Pre-stimulation-rep2

description: Serum starved for 48 hours (starting 24 hours after Control siRNA addition).

value: Control

value: pre-stimulation


title: PFDN5-Post-stimulation-rep2

description: Serum starved for 48 hours (starting 24 hours after  PFDN5 siRNA addition) and then serum was added and cells were recovered after 90 minutes.

value: post-stimulation


title: Y53.16S

value: Female

tag: location


title: EKOiE_2i_Input_pEsrrb_mNr5a2_2

value: Input

value: p

value: m


title: YZ1.18B

data_processing:
The Illumina BCL output files were converted to fastq-sanger file format and sequence quality triming was performed on CyVerse Discovery Environment with the HTProcess-prepare_directories-and-run_fastqc-0.1 and HTProcess_trimmomatic_0.33 apps.  The following Trimmomatic parameters were used: ILLUMINACLIP:TruSeq3-SE.fa 2:30:10; LEADING:10; TRAILING:10; SLIDINGWINDOW:4:20; HEADCROP:6; MINLEN:36.
Reads were mapped to the Tursiops truncatus genome, NIST Tru_tru v1 (GCF_001922835.1), on CyVerse Discovery Environment with the HTProcess_Tophat-2.1.1 app using Bowtie as the alignment engine. Sequences annotated as hemoglobin were masked from alignment.
Read counts as FPKM (fragments per kilobase of trnascript per million mapped reads) were generated on CyVerse Discovery Environment with the HTProcess_Cufflinks-2.2.1 app with the genome as a reference. Sequences annotated as hemoglobin were masked from analysis.
Genome_build: NIST Tur_tru v1
Supplementary_files_format_and_content: Processed data is supplied in a single file.  The first column, "locus", contains the id/location from the NIST Tur_tru v1 genome.  The remaining colums contain the FPKM values for each sample as generated by Cufflinks.

source_name: blood

extract_protocol:
Whole blood RNA was extracted using a PAXgene Blood RNA Kit (Qiagen).
Libraries were constructed using a NEBNext ultra Directional RNA Library Prep kit for Illumina and indexed with the NEBNextMultiplex Oligos for Illumina

value: blood

value: Barataria Bay, LA

tag: sampling date


title: Control-Pre-stimulation-rep1


title: EKOiE_2i_Input_mEsrrb_mNr5a2_2

tag: cell type


title: YY9.18B


title: EKOiE_2i_Input_pEsrrb_pNr5a2_2

tag: culture


title: RNA_QA09

description:
PathSeq
Uganda_QA_PathSeq_TPM.xlsx

value: Plasma

value: No

value: Uganda

value: cd8 t cell ratio:1.75


title: PFDN5-Pre-stimulation-rep2

description: Serum starved for 48 hours (starting 24 hours after PFDN5 siRNA addition).


title: RNA_QA08

description:
PathSeq
Uganda_QA_PathSeq_TPM.xlsx

value: cd8 t cell ratio:0.24


title: RNA_QA07

description:
PathSeq
Uganda_QA_PathSeq_TPM.xlsx

value: cd8 t cell ratio:1.31

value: Post_ART_HIV_subject (~0-2yrs on ART)


title: PFDN5-Pre-stimulation-rep1


title: RNA_QA05

description:
PathSeq
Uganda_QA_PathSeq_TPM.xlsx

value: cd8 t cell ratio:1.55

value: Yes


title: YX9.18B


title: YY3.18B


title: Y94.617S

value: Male


title: EKOiE_2i_Input_mEsrrb_pNr5a2_2

value: EKOiE


title: PFDN2-Pre-stimulation-rep2

description: Serum starved for 48 hours (starting 24 hours after PFDN2 siRNA addition).

value: pre-stimulation


title: EKOiE_2i_Esrrb_pEsrrb_mNr5a2_2

value: Esrrb

value: Perseus Proteomics, H6-705-00


title: RNA_QA04

description:
PathSeq
Uganda_QA_PathSeq_TPM.xlsx

value: cd8 t cell ratio:2.15

value: Healthy


title: RNA_QA11

description:
PathSeq
Uganda_QA_PathSeq_TPM.xlsx

value: cd8 t cell ratio:1.52


title: EKOiE_2i_Nanog_mEsrrb_pNr5a2_2

value: Nanog

value: Cosmobio, REC-RCAB001P

value: m

value: p


title: EKOiE_2i_Esrrb_mEsrrb_mNr5a2_2


title: RNA_QA03

description:
PathSeq
Uganda_QA_PathSeq_TPM.xlsx

value: Plasma

value: No

value: Uganda

value: cd8 t cell ratio:0.65


title: B4 RNA-Seq normal control blood cells

city: Bologna

first: Allison

last: Piovesan

address: Via Belmeloro 8

department: Department of Experimental, Diagnostic and Specialty Medicine

country: Italy

institute: University of Bologna

description:
Normal control
B4_N

data_processing:
The CASAVA 1.8.2 version of the Illumina pipeline was used to processed raw data for both format conversion and de-multiplexing.
Raw sequencing data were processed with BBDuk (https://jgi.doe.gov/data-and-tools/bbtools/) in order to perform trimming and clipping. Bases with a quality score less than 25 were removed as well as reads shorten than 35 nucleotides. The quality of the reads, before and after trimming, was checked with the software FASTQC (https://www.bioinformatics.babraham.ac.uk/projects/fastqc/).
High-quality reads were mapped against the GRCh38 human reference genome, downloaded from Ensembl (Cunningham et al., 2019), with the software STAR (version 2.5.2b, https://github.com/alexdobin/STAR). Read summarisation was performed with featureCounts (http://subread.sourceforge.net/), only reads with a mapping quality higher than 30 were used for this scope.
The option -s 2 was used to indicate that the libraries are strand-specific. The resulting table was imported in R, and the package edgeR (https://bioconductor.org/packages/release/bioc/html/edgeR.html) was used to calculate fragments per kilobase million (FPKM) values.
Genome_build: GRCh38 (hg38)
Supplementary_files_format_and_content: Tab-delimited text files include FPKM values for each sample
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: Blood cells

extract_protocol:
Total RNA extraction was performed with the method of Chomczynski and Sacchi. One or if necessary two purification steps were performed using RNA Clean & Concentrator-5 Kit in order to remove possible genomic DNA contamination and to reach the minimum concentration of 50 ng/μL.
TruSeq Stranded Total RNA with Ribo-Zero Gold (Illumina, San Diego, CA) was used for library preparation following the manufacturer's instructions, starting with 200 ng of RNA as input.

treatment_protocol: Blood samples from T21 and normal control recruited donors were collected in ethylenediaminetetraacetic acid (EDTA)-coated blood collection tubes, kept at room temperature and treated within two hours from blood collection. Each sample was transferred into a new tube, and plasma fraction was isolated by centrifugation at 1200 g for 10 min, while 5 mL of denaturing solution was added to the remaining blood fraction including the red blood cells and all the buffy coat, and stored at -20°C until RNA extraction.

value: Blood cells (buffy coat and red blood cells)

tag: age (years)

tag: disease state


title: YX7.18B

value: blood

value: Female

value: Barataria Bay, LA

tag: fb field id


title: RNA_QA10

description:
PathSeq
Uganda_QA_PathSeq_TPM.xlsx

value: cd8 t cell ratio:0.92


title: EKOiE_2i_Esrrb_pEsrrb_pNr5a2_2

institute: Institut Pasteur

value: EKOiE

tag: ChIP

value: Esrrb

tag: antibody

value: Perseus Proteomics, H6-705-00


title: B3 RNA-Seq normal control blood cells

description:
Normal control
B3_N

value: Healthy


title: YX5.917B


title: YX3.917B


title: RNA_QA02

description:
PathSeq
Uganda_QA_PathSeq_TPM.xlsx

value: cd8 t cell ratio:1.09

value: Yes

value: Post_ART_HIV_subject (~0-2yrs on ART)


title: A4 RNA-Seq T21 blood cells

description:
Trisomy 21
A4_T21

value: Down syndrome


title: EKOiE_2i_Esrrb_mEsrrb_pNr5a2_2

value: m

value: p


title: A3 RNA-Seq T21 blood cells

description:
Trisomy 21
A3_T21


title: RNA_049v09005987

description:
PathSeq
Cleveland_PathSeq_TPM.xlsx

value: Plasma

value: No

value: USA:Cleveland, Ohio

value: Responder (>3yr on ART)


title: YV7.917B

value: blood

value: Female


title: EKOiE_2i_Sox2_mEsrrb_mNr5a2_1

value: Active Motif, 39844


title: B2 RNA-Seq normal control blood cells

description:
Normal control
B2_N

value: Blood cells (buffy coat and red blood cells)


title: RNA_049v09005969

description:
PathSeq
Cleveland_PathSeq_TPM.xlsx

value: Non_responder (>3yrs on ART)


title: EKOiE_2i_Sox2_pEsrrb_pNr5a2_1

value: EKOiE


title: PFDN2-Pre-stimulation-rep1

tag: sirna

tag: treatment

value: pre-stimulation


title: B1 RNA-Seq normal control blood cells

description:
Normal control
B1_N

value: Male

value: Healthy


title: RNA_049v09005739

description:
PathSeq
Cleveland_PathSeq_TPM.xlsx

value: Yes