title: spleen-tcr

status: Public on Jul 31 2020

type: SRA

city: Guangzhou

first: Jinyong

last: Wang

state: GuangDong

address: 190 Kai Yuan Avenue, Science Park, Guangzhou, China

country: China

institute: Guangzhou Institutes of Biomedicine and Health (GIBH)

library_source: transcriptomic

data_processing:
Bcl2fastq convert .bcl files into fastq files
Fastq files were aligned, assembled and exported in clonotypes table with MiXCR.
Genome_build: built-in library of reference germline V, D, J and C gene sequences for human and mouse based on corresponding loci from GenBank, employed by MiXCR
Supplementary_files_format_and_content: clonotype information

molecule: polyA RNA

organism: Mus musculus

source_name: T cells

growth_protocol: The process cells derived from ESC/iPSC.

extract_protocol:
RNA of TCR reportire extraction and reverse transcription into double-stranded DNA were prepared using SMARTer Mouse TCR a/b Profiling Kit (Clontech , 634402)
Libraries were prepared according to instruction of SMARTer Mouse TCR a/b Profiling Kit.

treatment_protocol: 15000 T cells were sorted from the spleen or thymus of recipient mice.

tag: strain

tag: tissue

value: Spleen

tag: cell type

value: T cells


title: thymus-tcr

value: Thymus


title: HD53D140035

type: RNA

city: San Sebastián

first: David

last: Otaegui

state: Guipuzcoa

address: Paseo Dr begiristain s/n

department: Neurosciences

country: Spain

institute: Biodonostia Research institute

hyb_protocol: not provided

scan_protocol: not provided

data_processing: BRB array Tool

label: biotin

molecule: total RNA

organism: Homo sapiens

source_name: Blood

label_protocol: not provided

extract_protocol: not provided

value: blood

tag: age

tag: condition

value: Frail


title: HD53D140021

value: Dep


title: HD53D140013

value: Robust


title: HD53D140050


title: HD53D140012


title: HD53D140044


title: HD53D140005


title: HD53D140039


title: HD53D140033


title: HD53D140016


title: HD53D140026


title: HD53D140037


title: HD53D140004


title: WT2

city: New York

first: Susan

last: Logan

state: NY

address: 450 East 29th St

department: Urology

country: USA

institute: NYU School of Medicine

data_processing:
Reads were trimmed using cutadapt1. Quality scores were assessed using FastQC
Reads were aligned to the Mus musculus genome build mm10 using STAR
Individual sample reads were quantified using HTseq4 and normalized via Relative Log Expression (RLE) using DESeq2 R library
Genome_build: mm10
Supplementary_files_format_and_content: Differential gene expression file

source_name: Primary Sertoli cells infected with empty plasmid

growth_protocol: Sertoli cells were isolated from WT and KO mice and grown into DMEM/F-12 media. Differential plating was done for 24hr to enrich for Sertoli cells.

extract_protocol:
RNA was isolated using RNeasy kit from Qiagen
RNA-Seq library were prepared using the Illumina TruSeq® Stranded mRNA LT kit (Cat #RS- RS-122-2101 or RS-122-2102), on a Beckman Biomek FX instrument, using 250 ng of total RNA as input, amplified by 12 cycles of PCR

treatment_protocol: Cells were infected twice for 24 hours each

tag: strain background

tag: genotype/variation

value: wild type

value: Primary Sertoli cells


title: KO3

source_name: Primary Sertoli cells from UXT KO animals infected with a viral construct containing CRE recombinase

value: UXT KO


title: WT3


title: HD53D140003


title: HD53D140015


title: HD53D140014


title: HD53D140007


title: HD53D140054


title: HD53D140011


title: MGIN_101; Renca-HA Atg12ko T21 C

city: Toronto

first: Jason

last: Moffat

state: ON

address: 686 Bay Street, Room 13.9705

department: Molecular Genetics

country: Canada

institute: University of Toronto

description:
gRNA amplicon
MGIN_101

library_source: genomic

data_processing:
Library strategy: CRISPRseq
FASTQ files were pre-processed to extract Cas9 guide sequence using a bespoke Perl script.
The Cas9 guide sequence was extracted from read1 files as the 20 bases preceeding 'CGGTGTTT'.
Trimmed FASTQ files were then aligned to the mTKO or mValidation FASTA file using bowtie v0.12.1 using the following command line parameters:   -p 16 -v 3 -l 18 --chunkmbs 256 -t <library_file> --un unmapped.fastq --al mapped.fastq -1 <trimmed_read1.fastq> aligned.sam
The number of reads aligning to each guide sequence was enumerated for each aligned .sam file, and alignment statistics were recorded.  Guide IDs and counts were written to individual count files.
All individual count files were merged along with library annotations in R.
Supplementary_files_format_and_content: tab-delimited read count matrix

molecule: genomic DNA

source_name: Renca cell line + haemagglutinin antigen + Atg12ko

growth_protocol: Cells were cultured in RPMI media supplemented with 10% FBS and 1% Penicillin/Streptomycin and serially passaged for ~18-35 days (propagated in biological triplicates)

extract_protocol:
Genomic DNA was extracted using the Wizard Genomic DNA Purification kit (Promega) according to manufacturer’s instructions
For each tumor sample, the gRNA cassette was amplified directly from genomic DNA using primers harboring Illumina TruSeq adaptors with i5 and i7 barcodes. The resulting sequencing libraries were pooled and gel-purified.

treatment_protocol: Cells were repeatedly exposed (2-3 times for ~12-48 hours) to IFNa [10ng/ml], TNFa [10ng/ml] or cytotoxic T-lymphocytes [variable effector to target ratios]

tag: treatment

value: T cell (drop-out)

tag: crispr library

value: mTKO

tag: time point


title: HD53D140009


title: MGIN_88; Renca-HA Fitm2ko T18 C

description:
gRNA amplicon
MGIN_88

source_name: Renca cell line + haemagglutinin antigen + Fitm2ko


title: MGIN_94; Renca-HA Atg12ko T21 B

description:
gRNA amplicon
MGIN_94

value: Control


title: MGIN_90; Renca-HA Atg12ko T15 A

description:
gRNA amplicon
MGIN_90


title: HD53D140010


title: HD53D140006


title: MGIN_84; Renca-HA Fitm2ko T18 B

description:
gRNA amplicon
MGIN_84


title: MGIN_86; Renca-HA Fitm2ko T18 A

description:
gRNA amplicon
MGIN_86


title: KO2


title: KO1


title: WT1


title: HD53D140018


title: HD53D140008


title: HD53D140002


title: MGIN_60; Renca Fitm2ko T19 A

description:
gRNA amplicon
MGIN_60

source_name: Renca cell line + Fitm2ko


title: MGIN_66; Renca Fitm2ko T20 A

description:
gRNA amplicon
MGIN_66

value: IFN-gamma


title: MGIN_62; Renca Fitm2ko T19 C

description:
gRNA amplicon
MGIN_62


title: MGIN_100; Renca-HA Atg12ko T21 B

description:
gRNA amplicon
MGIN_100


title: MGIN_95; Renca-HA Atg12ko T21 C

description:
gRNA amplicon
MGIN_95


title: MGIN_93; Renca-HA Atg12ko T21 A

description:
gRNA amplicon
MGIN_93


title: MGIN_98; Renca-HA Atg12ko T15 C

description:
gRNA amplicon
MGIN_98


title: MGIN_96; Renca-HA Atg12ko T15 A

description:
gRNA amplicon
MGIN_96


title: MGIN_92; Renca-HA Atg12ko T15 C

description:
gRNA amplicon
MGIN_92


title: MGIN_68; Renca Fitm2ko T20 C

description:
gRNA amplicon
MGIN_68


title: MGIN_65; Renca Fitm2ko T8 C

description:
gRNA amplicon
MGIN_65


title: MGIN_61; Renca Fitm2ko T19 B

description:
gRNA amplicon
MGIN_61


title: MGIN_99; Renca-HA Atg12ko T21 A

description:
gRNA amplicon
MGIN_99


title: MGIN_55; Renca Atg12ko T14 C

description:
gRNA amplicon
MGIN_55

source_name: Renca cell line + Atg12ko

value: TNF-alpha


title: MGIN_56; Renca Fitm2ko T0

description:
gRNA amplicon
MGIN_56


title: MGIN_63; Renca Fitm2ko T8 A

description:
gRNA amplicon
MGIN_63


title: MGIN_97; Renca-HA Atg12ko T15 B

description:
gRNA amplicon
MGIN_97


title: MGIN_89; Renca-HA Atg12ko T0

description:
gRNA amplicon
MGIN_89


title: MGIN_91; Renca-HA Atg12ko T15 B

description:
gRNA amplicon
MGIN_91


title: MGIN_83; Renca-HA Fitm2ko T18 A

description:
gRNA amplicon
MGIN_83


title: MGIN_82; Renca-HA Fitm2ko T0

description:
gRNA amplicon
MGIN_82


title: MGIN_67; Renca Fitm2ko T20 B

description:
gRNA amplicon
MGIN_67


title: MGIN_49; Renca Atg12ko T10 C

description:
gRNA amplicon
MGIN_49


title: MGIN_87; Renca-HA Fitm2ko T18 B

description:
gRNA amplicon
MGIN_87


title: MGIN_85; Renca-HA Fitm2ko T18 C

description:
gRNA amplicon
MGIN_85


title: MGIN_57; Renca Fitm2ko T10 A

description:
gRNA amplicon
MGIN_57


title: MGIN_59; Renca Fitm2ko T10 C

description:
gRNA amplicon
MGIN_59


title: MGIN_58; Renca Fitm2ko T10 B

description:
gRNA amplicon
MGIN_58


title: MGIN_54; Renca Atg12ko T14 B

description:
gRNA amplicon
MGIN_54


title: MUS_18_Renca-HA T22 C

data_processing:
Library strategy: CRISPR screen
FASTQ files were pre-processed to extract Cas9 guide sequence using a bespoke Perl script.
The Cas9 guide sequence was extracted from read1 files as the 20 bases preceeding 'CGGTGTTT'.
Trimmed FASTQ files were then aligned to the mTKO or mValidation FASTA file using bowtie v0.12.1 using the following command line parameters:   -p 16 -v 3 -l 18 --chunkmbs 256 -t <library_file> --un unmapped.fastq --al mapped.fastq -1 <trimmed_read1.fastq> aligned.sam
The number of reads aligning to each guide sequence was enumerated for each aligned .sam file, and alignment statistics were recorded.  Guide IDs and counts were written to individual count files.
All individual count files were merged along with library annotations in R.
Supplementary_files_format_and_content: tab-delimited read count matrix
mTKO_readCounts_4May20.txt: read count matrix
mVal_readCounts_4May20.txt: read count matrix
mTKO_library.txt: library annotation file
mVal_library.txt: library annotation file

source_name: Renca cell line + haemagglutinin antigen

tag: cell line

value: Renca

tag: sequenced molecule

value: gRNA amplicon


title: MUS_17_Renca-HA T22 B


title: MUS_19_Renca-HA T24 A


title: MUS_16_Renca-HA T22 A


title: MUS_20_Renca-HA T24 B


title: MGIN_64; Renca Fitm2ko T8 B

description:
gRNA amplicon
MGIN_64


title: MUS_153_Renca-HA T16 C


title: MGIN_53; Renca Atg12ko T14 A

description:
gRNA amplicon
MGIN_53


title: MGIN_46; Renca Atg12ko T9 C

description:
gRNA amplicon
MGIN_46


title: MGIN_52; Renca Atg12ko T14 C

description:
gRNA amplicon
MGIN_52


title: MUS_27_Renca-HA T15 C


title: MGIN_51; Renca Atg12ko T14 B

description:
gRNA amplicon
MGIN_51


title: MGIN_43; Renca Atg12ko T0

description:
gRNA amplicon
MGIN_43


title: MUS_15_Renca-HA T0


title: MUS_145_MC38-Ova T15 C

source_name: MC38 cell line + ovalbumin antigen


title: MGIN_47; Renca Atg12ko T10 A

description:
gRNA amplicon
MGIN_47


title: MGIN_48; Renca Atg12ko T10 B

description:
gRNA amplicon
MGIN_48


title: MUS_143_MC38-Ova T15 A


title: MGIN_44; Renca Atg12ko T9 A

description:
gRNA amplicon
MGIN_44


title: MUS_141_MC38-Ova T15 B


title: MUS_26_Renca-HA T15 B


title: MUS_81_MC38-Ova T12 B


title: MUS_80_MC38-Ova T12 A


title: MUS_76_MC38-Ova T12 C


title: MUS_21_Renca-HA T24 C


title: MUS_82_MC38-Ova T12 C


title: MUS_73_MC38-Ova T0


title: MGIN_50; Renca Atg12ko T14 A

description:
gRNA amplicon
MGIN_50


title: MUS_113_B16-Ova T17 B

source_name: B16 cell line + ovalbumin antigen


title: MUS_114_B16-Ova T17 C


title: MUS_104_B16-Ova T17 B


title: MUS_29_Renca-HA T16 B


title: MUS_28_Renca-HA T16 A


title: MUS_112_B16-Ova T17 A


title: MUS_111_B16-Ova T13 C


title: MUS_110_B16-Ova T13 B


title: MGIN_45; Renca Atg12ko T9 B

description:
gRNA amplicon
MGIN_45


title: MUS_144_MC38-Ova T15 B


title: MUS_142_MC38-Ova T15 C


title: MUS_140_MC38-Ova T15 A


title: MUS_46_4T1-HA T25 C

source_name: 4T1 cell line + haemagglutinin antigen


title: MUS_100_B16-Ova T13 A


title: MUS_45_4T1-HA T25 B


title: MUS_74_MC38-Ova T12 A


title: MUS_25_Renca-HA T15 A


title: MUS_75_MC38-Ova T12 B


title: MUS_39_4T1-HA T25 B


title: MUS_38_4T1-HA T25 A


title: MUS_103_B16-Ova T17 A


title: MUS_42_4T1-HA T13 B


title: MUS_41_4T1-HA T13 A


title: MUS_43_4T1-HA T13 C


title: MUS_51_CT26-HA T17 A

source_name: CT26 cell line + haemagglutinin antigen


title: MUS_99_B16-Ova T0


title: MUS_101_B16-Ova T13 B


title: MUS_52_CT26-HA T17 B


title: MUS_40_4T1-HA T25 C


title: MUS_59_CT26-HA T16 C


title: MUS_58_CT26-HA T16 B


title: MUS_105_B16-Ova T17 C


title: MUS_36_4T1-HA T14 B


title: MUS_55_CT26-HA T12 B


title: MUS_35_4T1-HA T14 A


title: MUS_44_4T1-HA T25 A


title: MUS_50_CT26-HA T11 C


title: MUS_47_CT26-HA T0


title: MUS_48_CT26-HA T11 A


title: MUS_53_CT26-HA T17 C


title: MUS_109_B16-Ova T13 A


title: MUS_34_4T1-HA T0


title: MUS_71_EMT6-HA T15 B

source_name: EMT6 cell line + haemagglutinin antigen


title: MUS_102_B16-Ova T13 C


title: MUS_56_CT26-HA T12 C


title: MUS_54_CT26-HA T12 A


title: MUS_67_EMT6-HA T10 A


title: MUS_37_4T1-HA T14 C


title: MUS_68_EMT6-HA T10 B


title: MUS_64_EMT6-HA T19 A


title: MUS_49_CT26-HA T11 B


title: MUS_62_EMT6-HA T11 B


title: WT6W

city: Jerusalem

first: Oren

last: Parnas

address: Faculty of Medicine, Ein-Kerem medical center

department: Immunology

country: Israel

institute: Hebrew University

data_processing:
The Illumina bcl2fastq (v1.8.3) was used to convert Illumina base call files (bcl) to FASTQ files. Alignment of FASTQs to the mm10/hg19 reference was done by Cell Ranger  (v3.0, 10X Genomics). mm10/hg19 reference downloaded from 10x (v1.2.0, 10X Genomics) and a tdTomato sequence gene was added to mm10. Library constriction was performed according to standard  3’ 10x genomics kit and sequence using illumine Hi-Seq and Next-seq machine.
First analysis of the data was done using R package Seurat(v2.3.4). Raw transcript counts gene-cell matrices were filtered to remove cells with: (i) fewer than 200 transcripts, (ii) total UMI counts lower then 1000,(iii) cells with more than 5% or 10% mitochondrial genes for 10x chemistry v2 or v3, respectively. In addition, genes that expressed in less than 3 cells were removed. The gene-cell matrices were then normalized such that the number of UMIs in each cell was divided by the total UMI counts, multiplied by 10,000 and log transformed. Data was scaled using ScaleData Function from Seurat to remove unwanted sources of variation, so that cell-cycle heterogeneity or UMI counts does not contribute to PCA or downstream analysis.
Genome_build: mm10 and added tdTomato gene
Genome_build: hg19
Supplementary_files_format_and_content: All processed data merged are tab-delimited csv file from raw data of the Seurat object@raw.data and can be distinguish by barcode name.
Supplementary_files_format_and_content: rows are genes, columns are cell barcodes and the values are normalized and log transformed

source_name: Pancreas cells

extract_protocol:
The pancreas was removed and washed and the acinar cells were isolated using 10mg collagenase P and 0.2mg trypsin inhibitor live cells were isolated by using MACS dead cells removal kit (Miltenyi Biotech #130-090-101) with MACS MS columns. The stomach was removed and the cells isolated first with dissociation buffer containing 2mg collagenase P and then with dissociation buffer containing 5 mg Dispase II (Roche #D4693) at 37C.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: genotype

tag: pti

value: 6 weeks

value: Pancreas cells


title: WT9M

value: 9 months


title: PRT17

value: 17 days


title: MUS_72_EMT6-HA T15 C


title: MUS_70_EMT6-HA T15 A


title: MUS_57_CT26-HA T16 A


title: MUS_69_EMT6-HA T10 C


title: MUS_65_EMT6-HA T19 B


title: MUS_63_EMT6-HA T11 C


title: MUS_60_EMT6-HA T0


title: MUS_61_EMT6-HA T11 A


title: Adult_whole_DTAmut_d1

city: Minato-ku

first: Hideto

last: Koso

state: Tokyo

address: 4-6-1 Shirokanedai

country: Japan

institute: Institute of Medical Science, The University of Tokyo

data_processing:
CASAVA-1.8.2 (for d5 samples) and bcl2fastq-1.8.4 (for d1 samples) used for basecalling with default parameters
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to the mouse mm9 reference genome assembly with the option (--coverage-search --max-multihits 50).
FPKM (Fragments Per Kilobase of transcript per Million mapped reads) with Cufflinks ver. 2.1.1 with the default option.
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample.

source_name: Retina

extract_protocol:
RNA was harvested retinas using Sepazol reagent. The RNA-seq library was constructed using the mRNA-seq sample preparation kit (Illumina).
RNA libraries were prepared for sequencing using standard Illumina protocols.

value: C57BL/6；129 mixed

value: ~8 weeks of age

value: Msi1-CreERT2/+; R26R-DTA/+

value: retina

value: day 1 post-injury


title: Adult_whole_DTAwt_d1


title: MUS_66_EMT6-HA T19 C


title: BxPC3 Luc 3

city: Moscow

first: Sergey

last: Nikulin

address: 7, Vavilova st.

department: Faculty of Biology and Biotechnology

country: Russia

institute: HSE University

description: BxPC3 control cells

hyb_protocol: Hybridization was carried out with GeneChip™ Hybridization, Wash, and Stain Kit (Thermo Fisher Scientific) according to the manufacturer's recommendations.

scan_protocol: Gene-Chip Scanner 3000 7G system (Affymetrix).

data_processing:
CEL-files were jointly processed in Transcriptome Analysis Console 4.0.0.25 (Thermo Fisher Scientific, USA) with summation method Gene + Exon - SST-RMA (Analysis Version 1) and empirical Bayes method.
HTA-2_0.r3.pgf
HTA-2_0.r3.Psrs.mps

source_name: BxPC3 Luc

label_protocol: Labelling was carried out with GeneChip™ WT PLUS Reagent Kit (Thermo Fisher Scientific) according to the manufacturer's recommendations using 500 ng total RNA as starting material.

growth_protocol: Mice were injected subcutaneously between the scapula with 1 x 10^6 cells. Animals were sacrificed when primary tumors exceeded 1,5 cm^3 or ulcerated the mouse skin.

extract_protocol: RNA was extracted from frozen tumor samples using the miRNeasy Mini Kit (Qiagen) as recommended by the manufacturer.

treatment_protocol: not applicable

tag: origin

value: Xenograft

tag: knockdown itgav

value: no


title: Woman 6

city: LYON

first: Jerome

last: Lamartine

address: 7 passage du Vercors

country: France

institute: Université Lyon I

description: RNA from a four millimeters punch skin biopsies

hyb_protocol: Fragmentation of cDNA (5.5 µg) and hybridization was performed following Affymetrix protocols

scan_protocol: The arrays were read with a confocal laser (GeneChip Scanner 3000 7G, Affymetrix)

data_processing: CEL files were generated using the Affymetrix GeneChip Command Console (AGCC) software 3.0. The obtained data were normalized with Affymetrix Expression Console software v1.3.1 using the RMA statistical algorithm.

source_name: Full skin (neck, close to ear)

label_protocol: RNA (100 ng) was reverse-transcribed, pre-amplified and labeled with the GeneChip WT PLUS reagent kit

growth_protocol: No growth, total skin

extract_protocol: After temporary storage of skin biopsies in RNAlater® at 4°C, RNAs were rapidly extracted using mirVana® isolation kit  according to the manufacturer’s instructions

treatment_protocol: No treatment

tag: real age


title: PaCa 5061 ITGAV kd 3

description: PaCa 5061 cells with knockdown of ITGAV gene

source_name: PaCa 5061 ITGAV kd

value: yes

value: PaCa 5061


title: BxPC3 ITGAV kd 3

description: BxPC3 cells with knockdown of ITGAV gene

source_name: BxPC3 ITGAV kd


title: Woman 8


title: Woman 10


title: BxPC3 ITGAV kd 1


title: PaCa 5061 Luc 2

description: PaCa 5061 control cells

source_name: PaCa 5061 Luc


title: BxPC3 ITGAV kd 2


title: Woman 4


title: PaCa 5061 ITGAV kd 1


title: Woman 3


title: Woman 12


title: PaCa 5061 ITGAV kd 2


title: Woman 11


title: Woman 9


title: BxPC3 Luc 2

description: BxPC3 control cells


title: Woman 7


title: RsPhoto_RppH_Plus_Rep3

city: Madison

first: Kevin

middle: S

last: Myers

state: WI

address: 5127 WEI, 1552 University Ave

department: Great Lakes Bioenergy Research Center

institute: University of Wisconsin - Madison

description: Rhodobacter sphaeroides Transcription Start Site sequencing sample grown under photosynthetic conditions (1% CO2 and 99% O2). RppH Plus. Biological repliate 3

data_processing:
The resulting FASTQ files are split using the index barcode sequences to separate the sequences for the RppH- and RppH+ samples using fastx_barcode_splitter.pl version 0.0.13.2 (www.hannonlab.cshl.edu/fastx_toolkit).
The sequences are then trimmed to remove any remaining adapter-derived bases using Trimmomatic version 0.3 (HEADCROP of 6, MINLEN of 25) (19).
The trimmed sequence reads are aligned to the R. sphaeroides genome (GCF_000012905.2, Assembly ASM1290v2) using Bowtie2 version 2.3.5.1 (20), allowing for one mismatch. The aligned Bowtie2 file is then further processed with Picard tools version 2.10.0 (https://broadinstitute.github.io/picard/) and samtools (21).
The bedtools version 2.27.0 genomeCov command (https://bedtools.readthedocs.io/en/latest/) is used to map genomic locations that corresponds to the position of the first base in each aligned read, which is defined as the transcription start site. A pseudocount of 1 was added to all TSS read values to prevent dividing by zero and edgeR version 3.10 (22) was used to identify locations with a statistically significant increase in read abundance in the RppH+ strain compared to the RppH- strain.
Locations with a significant increase in read count in the RppH+ sample (FDR ≤ 0.05) were retained and TSSs were associated with genes downstream within 350 bp of the translation start site.
Genome_build: GCF_000012905.2, Assembly ASM1290v2
Supplementary_files_format_and_content: Bedtools GenomeCov mapped read value to each location in the genome; TSS locations

organism: Cereibacter sphaeroides 2.4.1

growth_protocol: Three replicates of R. sphaeroides 2.4.1 cultures were inoculated from an overnight culture into Sistrom’s minimal medium (14) and grown at 30°C. Aerobic cultures were grown in roux bottles and sparged with 1% CO2, 30% O2, and 69% N2 while anaerobic cultures were sparged with 5% CO2 and 95% N2 while exposed to an incandescent light with an intensity of ~10 W/m2 as previously described (15). Aerobic cultures were grown until mid-log phase (OD600 of ~0.3-0.4) and anaerobic cultures were collected at an OD600 of ~0.7-0.9 to achieve similar cell densities between the two growth conditions.

extract_protocol:
RNA was isolated using a hot phenol method
The isolated RNA was split into two equal groups and one group was treated with the enzyme RppH (17) (NEB, M0356S) at 37°C for 2 hours to remove the outer two phosphate groups from the 5ʹ end of the non-processed RNA species (RppH+ sample). The other group is untreated (no incubation with RppH) and thus the non-processed RNA species retain a tri-phosphate at the 5ʹ end of these molecules (RppH- sample). Both groups are treated with NaIO4 for 1.5 hours at 4°C in the dark to inactivate the 3ʹ end of the RNA transcripts and reduce the production of side products during the subsequent ligation of amplification primers (18). The sequencing adapter with desired index barcode sequence is ligated to the 5ʹ end of RNA species with a single phosphate group (Table 1). Note that RNA species with tri-phosphate groups at the 5ʹ end of the RNA are not substrates for ligation and thus will form a product with this sequencing adapter. The ligated RNA is purified using SPRI beads (Beckman, B23317), eluted in water, and quantitated using a NanoDrop 2000. Both the RppH+ and RppH- samples are subjected to rRNA depletion using the RiboZero kit (Epicentre, MRZB12424) following standard protocols and then reverse transcribed using a random primer attached to the second Illumina sequencing adapter (Table 1) following manufacturer’s recommendations. PCR is used to amplify cDNA species in both the RppH- and RppH+ samples that contain both Illumina sequencing adapters using a KAPA Hi-Fi PCR-read mix (KAPA Biosystems KK2601) following manufacturer’s protocol. The PCR products are cleaned using SPRI beads twice and resuspended in a final volume of 20 µL. The TSS-seq library is quantified using a 2100 Bioanalyzer (Agilent) and identifying fragments ~130 bp.
The samples were sequenced on an Illumina HiSeq 2500

value: RppH+

tag: growth condition

value: photosynthetic

tag: growth phase

value: exponential


title: BxPC3 Luc 1

description: BxPC3 control cells


title: PaCa 5061 Luc 3

description: PaCa 5061 control cells


title: Woman 5


title: Woman 2


title: RsPhoto_RppH_Minus_Rep1

description: Rhodobacter sphaeroides Transcription Start Site sequencing sample grown under photosynthetic conditions (1% CO2 and 99% O2). RppH Minus. Biological repliate 1

value: RppH-


title: PaCa 5061 Luc 1

description: PaCa 5061 control cells


title: RsPhoto_RppH_Minus_Rep3

description: Rhodobacter sphaeroides Transcription Start Site sequencing sample grown under photosynthetic conditions (1% CO2 and 99% O2). RppH Minus. Biological repliate 3


title: RsPhoto_RppH_Minus_Rep2

description: Rhodobacter sphaeroides Transcription Start Site sequencing sample grown under photosynthetic conditions (1% CO2 and 99% O2). RppH Minus. Biological repliate 2


title: RsPhoto_RppH_Plus_Rep2

description: Rhodobacter sphaeroides Transcription Start Site sequencing sample grown under photosynthetic conditions (1% CO2 and 99% O2). RppH Plus. Biological repliate 2


title: RsAero_RppH_Minus_Rep3

description: Rhodobacter sphaeroides Transcription Start Site sequencing sample grown under aerobic conditions (1% CO2, 30% O2, and 69% N2). RppH Minus. Biological repliate 3

value: aerobic


title: RsAero_RppH_Minus_Rep1

description: Rhodobacter sphaeroides Transcription Start Site sequencing sample grown under aerobic conditions (1% CO2, 30% O2, and 69% N2). RppH Minus. Biological repliate 1


title: RsAero_RppH_Minus_Rep2

description: Rhodobacter sphaeroides Transcription Start Site sequencing sample grown under aerobic conditions (1% CO2, 30% O2, and 69% N2). RppH Minus. Biological repliate 2


title: RsAero_RppH_Plus_Rep1

description: Rhodobacter sphaeroides Transcription Start Site sequencing sample grown under aerobic conditions (1% CO2, 30% O2, and 69% N2). RppH Plus. Biological repliate 1


title: RsPhoto_RppH_Plus_Rep1

description: Rhodobacter sphaeroides Transcription Start Site sequencing sample grown under photosynthetic conditions (1% CO2 and 99% O2). RppH Plus. Biological repliate 1


title: iHEC-sc89

data_processing:
Bcl2fastq (verison 2.16.0.10) convert .bcl files into fastq files
Fastq files were aligned to mm10 genome.*.ht2 files to generate *.sam file by HISAT2 (version 2.1.0). And the used samtools (version 0.1.19) to convert and sort the sam file to bam file. StringTie (version 1.3.4) were used to calculated genes expression level in TPM.
Gene expression levels in TPM of different samples were normalized by Stringtie.
Genome_build: mm10
Supplementary_files_format_and_content: TPM table was a csv file

source_name: hematopoietic endothelia cells

growth_protocol: Expression of defined factors in ESC/iPSC led to the production of an hematopoietic cell type

extract_protocol:
The procedure of RNA extraction and reverse transcription into double-stranded DNA were prepared using Discover-sc WTA Kit V2(Vazyme, N711)
Libraries were prepared according to instruction of TruePrepTM  DNA Library Prep Kit V2 (Vazyme,TD503).

treatment_protocol: The single HCs were sorted for RNAseq analysis.

tag: cell type

value: hematopoietic endothelia cells

tag: strain


title: iHEC-sc83


title: RsAero_RppH_Plus_Rep3

description: Rhodobacter sphaeroides Transcription Start Site sequencing sample grown under aerobic conditions (1% CO2, 30% O2, and 69% N2). RppH Plus. Biological repliate 3


title: Woman 1


title: RsAero_RppH_Plus_Rep2

description: Rhodobacter sphaeroides Transcription Start Site sequencing sample grown under aerobic conditions (1% CO2, 30% O2, and 69% N2). RppH Plus. Biological repliate 2


title: iHEC-sc82


title: iHEC-sc80


title: iHEC-sc88


title: iHEC-sc76


title: iHEC-sc81


title: iHEC-sc85


title: iHEC-sc69


title: iHEC-sc75


title: iHEC-sc67


title: iHEC-sc66


title: iHEC-sc77


title: iHEC-sc72


title: iHEC-sc70


title: iHEC-sc78


title: iHEC-sc64


title: iHEC-sc79


title: iHEC-sc65


title: iHEC-sc61


title: iHEC-sc68


title: iHEC-sc60


title: iHEC-sc63


title: iHEC-sc59


title: iHEC-sc54


title: iHEC-sc58


title: iHEC-sc56


title: iHEC-sc52


title: iHEC-sc53


title: iHEC-sc50


title: iHEC-sc47


title: iHEC-sc45


title: iHEC-sc49


title: iHEC-sc46


title: iHEC-sc44


title: iHEC-sc41


title: iHEC-sc43


title: iHEC-sc39


title: iHEC-sc40


title: iHEC-sc37


title: iHEC-sc42


title: iHEC-sc38


title: iHEC-sc36


title: iHEC-sc33


title: iHEC-sc29


title: iHEC-sc30


title: iHEC-sc35


title: iHEC-sc31


title: iHEC-sc28


title: iHEC-sc27


title: iHEC-sc25


title: iHEC-sc24


title: iHEC-sc20


title: iHEC-sc19


title: iHEC-sc21


title: iHEC-sc23


title: iHEC-sc18


title: iHEC-sc22


title: iHEC-sc16


title: iHEC-sc15


title: iHEC-sc13


title: iHEC-sc12


title: iHEC-sc10


title: iHEC-sc11


title: iHEC-sc9


title: iHEC-sc8


title: iHEC-sc7


title: iHEC-sc32


title: iHEC-sc3


title: iHEC-sc5


title: iHEC-sc1


title: iHEC-sc4


title: iHEC-sc6


title: B16-OVA repl2

data_processing:
FASTQ files were first filtered using a bespoke Perl script to remove reads shorter than 36bp.
Filtered FASTQ files were aligned to Gencode M12 gene annotations and mm10 genome build using the STAR short-read aligner (v2.6.0a)
Read count files generated by STAR were merged with gene annotations in R
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text read counts

source_name: B16-OVA cell line

growth_protocol: Cells were cultured in RPMI media supplemented with 10% FBS and 1% Penicillin/Streptomycin for 48 hours

extract_protocol:
Trizol protocol
1000 ng per sample was processed using the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (New England Biolabs, E7760L) and included polyA-enrichment using NEBNext Poly(A) mRNA Magnetic Isolation Module (New England Biolabs, E7490L), fragmentation for 15 minutes at 94°C prior to first strand synthesis, and 8 cycles of amplification after adapter ligation.

treatment_protocol: No treatment was performed


title: MC38-OVA repl2

source_name: MC38-OVA cell line


title: CT26-HA repl2

source_name: CT26-HA cell line


title: CT26-HA repl1


title: EMT6-HA repl1

source_name: EMT6-HA cell line


title: 4T1-HA repl2

source_name: 4T1-HA cell line


title: EMT6-HA repl2


title: 4T1-HA repl1


title: MUS_159_Renca-HA T24 B

source_name: Renca cell line + haemagglutinin antigen

value: Renca

value: Control

value: mTKO-validation

value: gRNA amplicon


title: B16-OVA repl1


title: MUS_160_Renca-HA T24 C


title: MUS_163_Renca-HA T15 C

value: T cell (drop-out)


title: MUS_158_Renca-HA T24 A


title: MUS_162_Renca-HA T15 B


title: MUS_166_Renca-HA T22 C


title: MUS_165_Renca-HA T22 B


title: MUS_157_Renca-HA T15 C


title: MUS_172_4T1-HA T24 B

source_name: 4T1 cell line + haemagglutinin antigen


title: MUS_155_Renca-HA T15 A


title: MUS_173_4T1-HA T24 C


title: MUS_161_Renca-HA T15 A


title: MUS_156_Renca-HA T15 B


title: MUS_154_Renca-HA T0


title: MUS_179_4T1-HA T22 C


title: MC38-OVA repl1


title: MUS_174_4T1-HA T15 A


title: MUS_176_4T1-HA T15 C


title: MUS_168_4T1-HA T15 A


title: MUS_186_CT26-HA T24 C

source_name: CT26 cell line + haemagglutinin antigen


title: MUS_178_4T1-HA T22 B


title: MUS_171_4T1-HA T24 A


title: MUS_184_CT26-HA T24 A


title: MUS_192_CT26-HA T22 C


title: MUS_177_4T1-HA T22 A


title: MUS_189_CT26-HA T15 C


title: MUS_175_4T1-HA T15 B


title: MUS_183_CT26-HA T15 C


title: MUS_187_CT26-HA T15 A


title: MUS_182_CT26-HA T15 B


title: MUS_170_4T1-HA T15 C


title: MUS_180_CT26-HA T0


title: MUS_181_CT26-HA T15 A


title: MUS_169_4T1-HA T15 B


title: MUS_164_Renca-HA T22 A


title: MUS_167_4T1-HA T0


title: MUS_199_EMT6-HA T24 C

source_name: EMT6 cell line + haemagglutinin antigen


title: MUS_185_CT26-HA T24 B


title: MUS_205_EMT6-HA T22 C


title: MUS_203_EMT6-HA T22 A


title: MUS_190_CT26-HA T22 A


title: MUS_191_CT26-HA T22 B


title: MUS_188_CT26-HA T15 B


title: MUS_200_EMT6-HA T15 A


title: MUS_196_EMT6-HA T15 C


title: MUS_198_EMT6-HA T24 B


title: MUS_204_EMT6-HA T22 B


title: MUS_194_EMT6-HA T15 A


title: MUS_197_EMT6-HA T24 A


title: Human skeletal muscle at athlete subject 5

city: bunkyo-ku

first: saori

last: kakehi

address: 2-1-1 hongo

department: Graduated shool of medicine

institute: Juntendo University

description: Gene expression data from human skeletal muscle

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45℃ onGeneChip® Human Genome U133 Plus 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G2500A.

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100.

source_name: Vastus lateralis muscle at athlete subject

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

extract_protocol: Total RNA extraction was performed with Lipid tissue mini kit（Qiagen) according to the manufacturer's instructions.

tag: Sex

value: male

tag: tissue

value: Vastus lateralis muscle

tag: group

value: endurance-trained


title: Human skeletal muscle at control subject 3

source_name: Vastus lateralis muscle at control subject

value: control


title: Ependymoma_primary (1269-1)

city: Aurora

first: Andrew

middle: M

last: Donson

state: CO

department: Pediatrics

institute: CU Anschutz Medical Campus

hyb_protocol: Following fragmentation, 11.5 ug of cRNA were hybridized for 16 hr at 45C on GeneChips. GeneChips were washed and stained in the Affymetrix Fluidics Station 450

scan_protocol: GeneChips were scanned using the Affymetrix Gene Chip Scanner 7G.

data_processing: Microarray .CEL file data was background corrected and normalized using the gcRMA algorithm, resulting in log 2 expression values.

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol (Expression Analysis Technical Manual, 2001, Affymetrix).

extract_protocol:
[collection protocol] Tumor samples were snap frozen in liquid nitrogen or transferred to RNAlater immediately after surgical removal as part of patient care. All samples were collected with appropriate IRB approval (COM-IRB#95-500 and 09-0906 )
RNeasy (Qiagen) extraction of total RNA was performed according to the manufacturer's instructions.

value: brain tumor (ependymoma)

tag: tumor type

value: primary


title: MUS_202_EMT6-HA T15 C

tag: treatment

tag: crispr library


title: Human skeletal muscle at athlete subject 4


title: Human skeletal muscle at control subject 4


title: Human skeletal muscle at athlete subject 2


title: Human skeletal muscle at athlete subject 1


title: Human skeletal muscle at control subject 7


title: MUS_217_MC38-Ova T12 B

source_name: MC38 cell line + ovalbumin antigen

tag: cell line

tag: time point


title: Human skeletal muscle at athlete subject 3


title: Human skeletal muscle at control subject 2


title: Human skeletal muscle at control subject 6


title: MUS_216_MC38-Ova T12 A

tag: sequenced molecule


title: Human skeletal muscle at control subject 5


title: MUS_193_EMT6-HA T0


title: MUS_211_MC38-Ova T12 B


title: Human skeletal muscle at control subject 1


title: Ependymoma_primary (987-1)


title: Human skeletal muscle at control subject 8


title: MUS_215_MC38-Ova T11 C


title: Ependymoma_primary (965-1)


title: Ependymoma_recurrent (1101-2)

value: recurrent


title: MUS_208_MC38-Ova T11 B


title: MUS_218_MC38-Ova T12 C


title: Ependymoma_primary (943-1)


title: MUS_214_MC38-Ova T11 B


title: MUS_231_B16-Ova T15 C

source_name: B16 cell line + ovalbumin antigen


title: Ependymoma_recurrent (816-3)


title: MUS_230_B16-Ova T15 B


title: Ependymoma_primary (1067-1)


title: Ependymoma_primary (1101-1)


title: Ependymoma_primary (811-1)


title: MUS_223_B16-Ova T15 A


title: Ependymoma_recurrent (816-2)


title: Ependymoma_recurrent (930-2)


title: Ependymoma_primary (727-1)


title: MUS_212_MC38-Ova T12 C


title: Ependymoma_primary (930-1)


title: Ependymoma_primary (770-1)


title: Ependymoma_recurrent (723-2)


title: Ependymoma_primary (911-1)


title: MUS_227_B16-Ova T12 B


title: MUS_213_MC38-Ova T11 A


title: Ependymoma_primary (897-1)


title: Ependymoma_recurrent (897-2)


title: Ependymoma_primary (700-1)


title: MUS_201_EMT6-HA T15 B


title: MUS_210_MC38-Ova T12 A


title: MUS_207_MC38-Ova T11 A


title: MUS_221_B16-Ova T12 B


title: Ependymoma_primary (816-1)


title: Ependymoma_primary (483-1)


title: MUS_206_MC38-Ova T0


title: MUS_220_B16-Ova T12 A


title: MUS_222_B16-Ova T12 C


title: MUS_209_MC38-Ova T11 C


title: MUS_229_B16-Ova T15 A


title: MUS_225_B16-Ova T15 C


title: MUS_250_Renca T18 C

source_name: Renca cell line

value: TNF-alpha

value: mTKO


title: MUS_228_B16-Ova T12 C


title: Ependymoma_recurrent (811-4)


title: MUS_224_B16-Ova T15 B


title: Ependymoma_recurrent (483-2)


title: Ependymoma_primary (781-1)


title: Ependymoma_recurrent (811-2)


title: MUS_226_B16-Ova T12 A


title: MUS_243_Renca T18 B

value: IFN-gamma


title: Ependymoma_primary (723-1)


title: MUS_242_Renca T18 A


title: MUS_238_Renca T18 C


title: MUS_237_Renca T18 B


title: MUS_236_Renca T18 A


title: MUS_248_Renca T18 A


title: Ependymoma_primary (246-1)


title: MUS_219_B16-Ova T0


title: Ependymoma_primary (1239-1)


title: Ependymoma_recurrent (246-2)


title: Ependymoma_recurrent (364-2)


title: Ependymoma_primary (364-1)


title: Ependymoma_primary (392-1)


title: Ependymoma_recurrent (928-3)


title: Ependymoma_recurrent (928-2)


title: MUS_195_EMT6-HA T15 B


title: Ependymoma_primary (928-1)


title: MUS_249_Renca T18 B


title: Stomach

source_name: Stomach cells

tag: genotype

tag: pti

value: Stomach cells


title: MUS_232_Renca T0


title: MUS_234_Renca T12 B


title: Ependymoma_primary (839-1)


title: WT15M

source_name: Pancreas cells

value: 15 months

value: Pancreas cells


title: Ependymoma_primary (419-1)


title: Ependymoma_primary (821-1)


title: Ependymoma_primary (80-1)


title: Ependymoma_primary (110-1)


title: Ependymoma_recurrent (691-3)


title: Ependymoma_primary (1048-1)


title: MUS_246_Renca T12 B

value: Renca


title: MUS_247_Renca T12 C


title: MUS_240_Renca T12 B


title: MUS_245_Renca T12 A


title: MUS_244_Renca T18 C


title: MUS_241_Renca T12 C


title: Ependymoma_recurrent (691-2)


title: MUS_235_Renca T12 C

value: Control


title: MUS_239_Renca T12 A

value: gRNA amplicon


title: Ependymoma_primary (1010-1)


title: MUS_233_Renca T12 A


title: WT5M2

value: 5 months


title: WT6M tdtomato+ cells

value: 6 months


title: FI_3M

value: 3 months


title: F20_3M


title: WT5M1


title: Ependymoma_recurrent (839-2)


title: Ependymoma_primary (871-1)


title: Ependymoma_recurrent (821-2)


title: Ependymoma_primary (848-1)


title: A_24

city: Port Saint Lucie

first: Emily

last: Speranza

state: FL

address: 9801 SW Discovery Wy

department: Florida Research and Innovation Center

institute: Cleveland Clinic Lerner Research Institute

data_processing:
Files were demultiplexed and trimmed
Alignemnt to the mm10 genome done with the STAR aligner
Counts to the genes was done using FeatureCounts
Genome_build: mm10
Supplementary_files_format_and_content: text file with raw counts

source_name: ko LSEC_Mid

extract_protocol:
iCad5-MyD88(wt/wt) and iCad5-MyD88(fl/fl) mouse livers with cells were processed fresh and sorted to identify macrophages or the gradient of endothelial cells. Cells were sorted directly into Trizol on ice. Direct-zol RNA MiniPrep Plus columns were used to extract RNA
TruSeq Stranded mRNA (with TruSeq Dual CD Indexes)

value: iCad-MyD88 (fl/fl)

value: liver

value: Endothelium

tag: cd117 expression

value: Middle


title: Ependymoma_primary (758-1)

value: brain tumor (ependymoma)

value: primary


title: A_23

source_name: ko LSEC_Lo

value: Low


title: A_22

source_name: ko LSEC_Hi

value: Hi


title: Ependymoma_primary (691-1)


title: Ependymoma_primary (812-1)


title: Ependymoma_primary (859-1)


title: A_21

source_name: ko Mac

value: Macrophage


title: A_20

source_name: wt LSEC_Mid

value: iCad-MyD88 (wt/wt)


title: Ependymoma_primary (507-1)


title: A_19

source_name: wt LSEC_Lo


title: A_18

source_name: wt LSEC_Hi


title: Ependymoma_recurrent (459-2)

value: recurrent


title: Ependymoma_primary (492-1)


title: A_17

source_name: wt Mac


title: Ependymoma_recurrent (507-2)


title: A_16


title: Ependymoma_primary (459-1)


title: Ependymoma_recurrent (393-2)


title: A_15


title: Ependymoma_recurrent (321-2)


title: Ependymoma_primary (393-1)


title: Ependymoma_primary (321-1)


title: Ependymoma_recurrent (393-3)


title: A_14


title: A_13


title: A_12


title: Ependymoma_primary (319-1)


title: A_10


title: A_9


title: A_11


title: A_8


title: Ependymoma_recurrent (319-2)


title: Ependymoma_recurrent (195-4)


title: Ependymoma_primary (318-1)


title: A_7


title: A_6


title: Ependymoma_primary (64-1)


title: A_5


title: Ependymoma_primary (195-1)


title: Hela_PF14_4hrs_01

city: Abu Dhabi

first: Piergiorgio

last: Percipalle

state: Abu Dhabi

address: Saadiyat Campus, Abu Dhabi

department: Biology Department, Science Division

country: United Arab Emirates

institute: New York University Abu Dhabi

data_processing:
All the analysis was performed using the NYU Abu Dhabi High Performance Computational (HPC) cluster called “Dalma” running SLURM. All of the analysis, including quality trimming and subsequent analysis, was executed using the BioSAILs  workflow execution system. The raw reads were quality trimmed using Trimmomatic  version 0.36 to trim low quality bases, systematic base calling errors, as well sequencing adapter contamination, specifically, the parameters used were “trimmomatic_adapter.fa:2:30:10 TRAILING:3 LEADING:3 SLIDINGWINDOW:4:15MINLEN:36”. FastQC  was used to assess the quality of the sequenced reads pre/post quality trimming.
The quality trimmed RNAseq reads were aligned to the human GRCh38 genome using HISAT2  version 2.0.4. The resulting SAM alignment files for each sequenced sample were then converted to BAM format and sorted by coordinate using SAMtools  version 0.1.19. These alignment files were then processed using STRINGTIE  version 1.3.0 together with the corresponding GTF annotation file of the reference genome, to produce a GTF file per sample. The resulting GTF files were then combined using STRINGTIE –merge to produced a “merged” GTF file for all the samples, before running STRINGTIE again on a per sample basis (using the merged GTF file produced earlier). The BAM alignment files were also processed using HTseq-count  using the reference annotation file to produce raw counts for each sample. The raw counts were then analyzed using the online analysis portal NASQAR  in order to merge, normalize and identify differentially expressed genes.
Supplementary_files_format_and_content: tab-delimited text files include read counts for each sample

source_name: HeLa cells

growth_protocol: Full DMEM medium with 10%FBS and Pen/Strep

extract_protocol:
RNAzol was used to isolate total RNA
The RNA seq libraries were prepared with TruSeq RNA Library Prep kit v2 as per protocol instructions. Resulting libraries concentration, size distribution and quality were assessed on a Qubit fluorometer with a dsDNA high sensitivity kit and on an Agilent 2100 bioanalyzer using a DNA 7500 kit. Then libraries were normalized, pooled and quantified with a KAPA Library quantification kit for Illumina platforms on a ABI StepOnePlus qPCR machine, then loaded on a high output flow cell and single-end sequenced (100 bp) on an Illumina HiSeq 2500 next generation sequencer.

treatment_protocol: For peptide treatment, 5x105 cells were seeded in 6-well plates with 2ml of full-DMEM medium 24hrs before the treatment. Next day, medium was exchanged with pre-warmed DMEM medium supplemented with respective peptide and incubated for defined time. As a negative control were used HeLa cells with pre-warmed DMEM medium supplemented with 1xPBS. For the treatment, each peptide stock was mixed with full DMEM media to final concentration of 2 µM for each peptide.

value: HeLa

tag: agent

value: 4 hours


title: Hela_TP10_4hrs_02


title: Hela_mtCPP1_4hrs_01


title: Hela_TP10_4hrs_01


title: Hela_PF14_4hrs_02


title: Hela_mtCPP1_4hrs_02


title: Hela_Penet_4hrs_02

value: Penetratin


title: Ependymoma_recurrent (195-2)


title: A_3


title: A_2


title: Hela_untreated_02

value: untreated


title: Hela_Penet_1hrs_01

value: 1 hour


title: Hela_Penet_4hrs_01


title: Hela_untreated_01


title: SP_5

city: Worcester

first: Ricardo

middle: Tostes

last: Gazzinelli

state: Massachusetts

address: 364 Plantation Street

department: Medicine

institute: University of Massachusetts Medical School

data_processing:
Reads were trimmed with Trimmomatic and mapped to the Genome Reference Consortium Mouse Build 38 patch release 5 (GRCm38.p5) using STAR aligner
FPKM values were calculated with CUFFLINKS.
Differential analysis were done using CUFFLINKS
Genome_build: GRCm38.p5
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each sample.

source_name: Spleen

growth_protocol: Mice were fed ad libitum and kept on a regular light cycle with lights on from 7:00 am to 7:00 pm and lights off from 7:00 pm to 7:00 am

extract_protocol:
Total RNA was extracted using Qiagen RNeasy Mini Kit (QIAGEN, Cat #74104 ) and was cleaned and treated with DNase I (Qiagen Rnase-Free Dnase Set, Cat #79254).
Poly-A containing mRNA molecules were purified using poly-T oligo attached magnetic beads and fragmented using divalent cations. The RNA fragments were transcribed into cDNA using  II Reverse Transcriptase (Invitrogen), followed by second strand cDNA synthesis using DNA Polymerase I and RNase H. Finally, cDNA fragments then have the addition of a single 'A' base and subsequent ligation of the adapter. The products were then purified and enriched by PCR using paired-end primers (Illumina) for 15 cycles to create the final cDNA library.
RNA-seq libraries were prepared using the TruSeq Stranded mRNA Kit (Illumina) following the manufacturer’s instructions. Each sample was sequenced twice (lane1 and lane2).

treatment_protocol: MoDCs sorted from Spleen of C57BL/6 mice 5 days post infection with 10E5 P. berghei ANKA infected red blood

value: Spleen

value: Female

tag: age

value: 10 weeks

value: Wild Type

tag: infection

value: PbA-infected

value: MO-DC


title: SP_4

tag: cell type


title: ATACseq.HC2.D78.Rep3

city: Atlanta

last: Escayg

state: GA

address: 615 Michael Street

department: Human Genetics

institute: Emory University

data_processing:
ATAC-seq: Raw sequencing reads were trimmed for sequencing adapters utilizing the CutAdapt package in Python
RNA-seq: Raw sequencing reads were trimmed for sequencing adapters utilizing Trimmomatic v.0.38
ATAC-seq: Reads were mapped to the hg38 human reference genome using Bowtie2 v2.2.4
RNA-seq: Reads were mapped to the hg38 human reference genome using TopHat v2.1.1
ATAC-seq: MACS2 v.2.1.0 was used to call ATAC-seq peaks, and counts were normalized to reads per peak per million (rppm) using the equation: (total reads x 106)/(unique reads x fraction of reads in peaks)
RNA-seq: HTSeq v0.11.0 was used to determine gene counts from uniquely-mapped, paired reads.
ATAC-seq: edgeR was utilized to determine changes in chromatin accessibility between samples at D22, D50, and D78. Differentially accessible regions (DARs) of chromatin were defined by FDR < 0.05 and absolute fold change > 2.
RNA-seq: DESeq2 was utilized to normalize gene counts and determine changes in gene expression between cells at D22, D50, and D78. Genes were considered to have detectable expression if at least two samples within a given time point (D22, D50, or D78) exhibited a DESeq2-normalized expression value > 3. Differentially expressed genes (DEGs) were defined by FDR < 0.05 and absolute fold change > 2.
Genome_build: hg38
Supplementary_files_format_and_content: ATAC-seq: Bigwig files were generated using bedGraphToBigWig, scores represent reads per million (rpm). The supplementary tab-delimited text file includes rpm values for each sample across detected peaks.
Supplementary_files_format_and_content: RNA-seq: Tab-delimited text files include DESeq2 normalized expression values for each sample.

growth_protocol: The HC1 and HC2 human induced pluripotent stem cell (iPSC) lines were previously generated using skin biopsy samples from two healthy adult males (Wen et al. 2014, Nature). iPSCs (passage < 35) were cultured on irradiated mouse embryonic fibroblasts (MEFs) in human iPSC media consisting of DMEM/F12 (#11320082, Invitrogen) supplemented with 20% KnockOut Serum Replacement (#10828028, Invitrogen), 2 mM GlutaMAX (#35050079, Invitrogen), 100 μM non-essential amino acids (NEAA, #11140050, Invitrogen), 100 μM 2-mercaptoethanol (#21985023, Invitrogen), and 10 ng/mL human basic FGF (#100-18B, PeproTech, Rocky Hill, NJ, USA) as previously described (28). Media were changed daily and iPSC lines were passaged by incubation for 1 hr at 37°C in DMEM/F12 media with 1 mg/ml collagenase (#17018029, Invitrogen). For differentiation of iPSCs into cortical GABAergic interneurons (GINs), iPSC colonies were detached from the feeder layer with collagenase and resuspended in EB medium, comprised of FGF2-free human iPSC media supplemented with 2 μM dorsomorphin (#3093, Tocris Bioscience, Bristol, UK) and 2 μM A-83-01 (#2939, Tocris Bioscience). Cells were grown in non-treated polystyrene plates for 6 days, and media was changed daily. On day 7 (D7) of the differentiation protocol, floating embryoid bodies (EBs) were transferred to Matrigel-coated 6-well plates (#354432, Corning). Cells were first grown in NPC1 media, consisting of DMEM/F12 with 1× N-2 supplement (#17502001, Invitrogen), 1× NEAA, 2 μg/ml heparin (#H3149, MilliporeSigma), and 1 μg/ml of recombinant human SHH (#100-45, PeproTech). On D11, the NPC1 media was replaced with NPC2 medium, comprised of DMEM/F12 with 1× N-2 supplement, 1× NEAA, 2 μg/ml heparin, and 1.5 μM Purmorphamine (#4551, Tocris Bioscience). From D7-D22, the media was changed once every two days. On D22, neural rosettes were mechanically picked and transferred to low-attachment plates (#3471, Corning) in NPC2 media supplemented with 1× B-27 (#17504044, Invitrogen). For further differentiation, neural progenitor spheres were dissociated by incubation with Accutase (#A1110501, Invitrogen) for 10 min at 37°C, then resuspended in Neuron medium, comprised of Neurobasal medium (#21103049, Invitrogen) supplemented with 2 mM GlutaMAX, 1× B-27, 1 μM cAMP (#20-198, MilliporeSigma), 200 ng/mL L‐ascorbic acid (#A4403, MilliporeSigma), 10 ng/mL recombinant BDNF (#450-02, PeproTech), and 10 ng/mL recombinant GDNF (#450-10, PeproTech). For quantification of GIN subtypes, additional cells were passaged onto coverslips coated with 50 µg/ml poly-D-lysine (#P6407, MilliporeSigma) and 10 µg/ml laminin (#L2020, MilliporeSigma). Cells were continuously cultured in Neuron media from D22-D78, and half of the media was replaced weekly. At D22, D50, and D78, cells were dissociated with Accutase and gently pelleted by centrifugation at 1,500 rpm for 5 min. Cells were resuspended in 1 mL TRIzol reagent (#15596026, ThermoFisher) for RNA-seq and qRT-PCR, or 1× PBS for ATAC-seq library preparation.

extract_protocol:
Differentiated cells were gently pelleted in 1× PBS and resuspended in a 25 μL tagmentation reaction consisting of 1× TD Buffer (10 mM TAPS-NaOH pH 8.1, 5 mM MgCl2, 10% DMF), 2.5 μL Tn5 transposase, 0.1% TWEEN 20, and 0.02% Digitonin, then incubated for 1 hr at 37 °C. Tagmented nuclei were diluted two-fold and incubated for 30 min at 40°C in lysis buffer, comprised of 300 mM NaCl, 100 mM EDTA, 0.6% SDS, 1.6 μg proteinase K.
Transposed DNA was isolated by size selection using SPRI-beads and PCR-amplified using 2× KAPA HiFi HotStart ReadyMix (#7958927001, Roche) and Nextera Indexing Primers (#FC-131-2003, Illumina, San Diego, CA, USA). Following PCR amplification, the size-selection step was repeated to enrich for low molecular weight DNA. Sample quality was assessed on a 2100 Bioanalyzer (Agilent Technologies), and libraries were pooled at an equimolar ratio for sequencing on a HiSeq2500 system (Illumina) with 50 bp paired-end chemistry.

tag: subject/cell line id

value: healthy control (HC2)

value: male

value: iPSC-derived GABAergic interneurons

value: 78 days post-differentiation


title: Hela_Penet_1hrs_02


title: SP_2

treatment_protocol: Monocytes sorted from Spleen of non-infected C57BL/6 mice

tag: strain

tag: Sex

value: non-infected

value: monocyte


title: SP_3

tag: tissue


title: A_4

value: iCad-MyD88 (wt/wt)

value: liver

value: Endothelium

value: Middle


title: ATACseq.HC2.D78.Rep2


title: SP_1


title: ATACseq.HC2.D78.Rep1


title: ATACseq.HC2.D50.Rep3

value: 50 days post-differentiation


title: A_1

value: Macrophage


title: BM_5

source_name: Bone Marrow

treatment_protocol: Inflammatory monocytes sorted from Bone Marrow of C57BL/6 mice 5 days post infection with 10E5 P. berghei ANKA infected red blood

value: Bone Marrow

value: Female

value: inflammatory monocyte


title: BM_3

treatment_protocol: Monocytes sorted from Bone Marrow of non-infected C57BL/6 mice

value: 10 weeks

value: Wild Type


title: ATACseq.HC1.D78.Rep3

value: healthy control (HC1)


title: ATACseq.HC2.D22.Rep2

value: healthy control (HC2)

value: male

value: iPSC-derived neural progenitor cells

value: 22 days post-differentiation


title: ATACseq.HC1.D78.Rep1

value: iPSC-derived GABAergic interneurons

value: 78 days post-differentiation


title: ATACseq.HC1.D78.Rep2


title: ATACseq.HC2.D50.Rep1


title: CD8-rep3

data_processing:
Bcl2fastq convert .bcl files into fastq files
Fastq files were aligned to mm10 genome.*.ht2 files to generate *.sam file by HISAT2. And the used samtools to convert and sort the sam file to bam file. StringTie were used to calculated genes expression level in TPM.
Gene expression levels of different samples were normalized by Stringtie, and finally generated TPM table with R
Genome_build: mm10
Supplementary_files_format_and_content: TPM table was a csv file

source_name: T cells

treatment_protocol: 1000 T cells were sorted for RNAseq analysis.

value: B-NDG

value: Spleen

value: T cells

tag: cell subtype


title: BM_6

value: PbA-infected


title: SP_6

value: MO-DC


title: BM_2

value: Bone Marrow

value: non-infected

value: monocyte


title: CD8-rep2


title: ATACseq.HC2.D22.Rep1


title: BM_1

value: Female

value: 10 weeks


title: ATACseq.HC2.D50.Rep2

value: 50 days post-differentiation


title: ATACseq.HC1.D50.Rep2

value: healthy control (HC1)


title: BM_4

value: Wild Type

value: inflammatory monocyte


title: CD8-rep1


title: ATACseq.HC1.D50.Rep1

value: male


title: ATACseq.HC1.D22.Rep3

value: iPSC-derived neural progenitor cells

value: 22 days post-differentiation


title: CD4-rep2

value: B-NDG


title: CD4-rep3

value: Spleen


title: ATACseq.HC1.D22.Rep1


title: ATACseq.HC1.D22.Rep2


title: Human PDAC

source_name: Pancreas tumor cells

value: Pancreas tumor cells


title: CD4-rep1

value: T cells


title: ATACseq.HC1.D50.Rep3

value: iPSC-derived GABAergic interneurons


title: 12-0100b

city: Bethesda

first: Mehdi

last: Pirooznia

state: MD

address: 12 SOUTH DR

institute: National Institutes of Health

description:
batch 2
12-0100

data_processing:
Sequencing reads were trimmed for adapter contamination with Cutadapt
then aligned to human genome with HISAT2
read counts were produced by using featureCounts
Genome_build: GENCODE release 26

source_name: whole blood

extract_protocol:
Red cell lysis (Quality Biological ACK Lysing Buffer Cat.# 118-156-101) followed by Qiagen Rneasy Mini kit (#74104)
Agilent Tapestation for determination of concentration and RIN number
RNA libraries were generated with standard Illumina protocols for total RNA and quantitated on the Agilent TapeStation (for DNA).
Libraries were sequenced on the Illumina HiSeq 2500.

value: whole blood

tag: bedtime cortisol

tag: awakening cortisol

tag: emotional stress

tag: sex (0=females; 1=male)


title: 12-0098b

description:
batch 2
12-0098


title: 12-0095b

description:
batch 2
12-0095


title: 12-0096b

description:
batch 2
12-0096


title: 12-0097b

description:
batch 2
12-0097


title: 12-0094b

description:
batch 2
12-0094


title: shRREB1_rep3

first: Rob

last: Rottapel

address: 101 College Street, Room 12-704

department: Medical Biophysics

institute: University Health Network

data_processing:
Filtered FASTQ files were aligned to Gencode v25 gene annotations and hg38 genome build using the STAR short-read aligner (v2.4.2a)
Read count files generated by STAR were merged with gene annotations in R
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text read counts

source_name: Cell line HEK293T

growth_protocol: DMEM, 10% FBS

extract_protocol:
RNA was extracted using TRIzol™ Reagent (Invitrogen) according to the manufacturer's instructions.
Libraries were prepared using Illumina TruSeq Stranded Total RNA Sample Preparation Kit

tag: cell line

tag: shRNA

value: shRNA targeting RREB1


title: 12-0093b

description:
batch 2
12-0093


title: shRREB1_rep1


title: 12-0090b

description:
batch 2
12-0090


title: 12-0092b

description:
batch 2
12-0092


title: N3

city: hefei

first: Xiaolin

last: Wang

address: anhui,hefei,huangshan road 443

institute: USTC

data_processing:
For mRNA and lncRNA analyses, the expression levels were calculated using TopHat2 and Cufflinks followed by the annotation references of Refseq and Ensemble transcript databases with the genome release Homo sapiens, hg19. The differentially expressed mRNA and lncRNA were determined by DEseq2 with the corresponding cutoff (P value <0.001, RPKM ≥10, |log2(fold change)| ≥1 for mRNA and P value <0.05, RPKM ≥1, |log2(fold change)| ≥1 for lncRNA).
For circular RNA (circRNA) prediction, we identified the candidates with find_circ (Memczak et al., 2013) and the junction reads were calculated as Transcripts Per Kilobase Million (TPM).
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample ...

source_name: Glioma patient

extract_protocol:
The clinical samples were cut into small pieces and homogenized in TRizol reagent (Life Technologies) by homogenizer. Total RNA was extracted by using TRizol reagent according to the manufacturer’s instructions.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: normal tissue


title: N1


title: G2

value: tumor


title: G3


title: shRREB1_rep2


title: Con2

value: shRNA control


title: G1


title: Con3


title: 12-0088b

description:
batch 2
12-0088


title: Con1


title: 12-0089b

description:
batch 2
12-0089


title: RNAseq.HC1.D78.Rep3

extract_protocol:
Total RNA was isolated from TRIzol preparations of HC1-derived GINs following manufacturer guidelines (ThermoFisher).
2 μg total RNA per sample was used to create libraries with a Kapa Biosystems stranded RNA-seq kit with capture beads (#KK8421, Kapa Biosystems, Wilmington, MA, USA). Libraries were pooled at equimolar concentrations and sequenced on a NextSeq 500 system (Illumina, San Diego, CA, USA), using 75 bp paired-end chemistry.

value: 78 days post-differentiation


title: 12-0099b

description:
batch 2
12-0099


title: RNAseq.HC1.D78.Rep2

value: healthy control (HC1)


title: 12-0086b

description:
batch 2
12-0086


title: 12-0087b

description:
batch 2
12-0087


title: 12-115b

description:
batch 1
12-0115


title: 12-116b

description:
batch 1
12-0116


title: RNAseq.HC1.D78.Rep1


title: RNAseq.HC1.D50.Rep1

value: 50 days post-differentiation


title: 12-113b

description:
batch 1
12-0113


title: RNAseq.HC1.D22.Rep3


title: RNAseq.HC1.D50.Rep2


title: 12-112b

description:
batch 1
12-0112


title: RNAseq.HC1.D22.Rep1


title: RNAseq.HC1.D22.Rep2


title: N2


title: 12-111b

description:
batch 1
12-0111


title: 2_3 single_cell_mrna_seq

city: Groningen

first: Bart

last: Eggen

state: Groningen

address: Antonius Deusinglaan 1

department: Department of Biomedical Sciences

country: Netherlands

institute: UMCG Groningen

data_processing:
RNA-Seq
Reads without cell barcode or UMIs were removed and remaining raw reads were aligned to the human genome using HiSat2 (v.2.1.0) in single-end mode.
Genome_build: Homo.sapiens.GrCh38
Supplementary_files_format_and_content: A tab-delimited text file containing gene counts of ~84 single cells, resulting in 12 processed data files for each sample.
ATAC-seq
Raw reads were aligned to the human genome using bowtie2 (v.2.3.4.3) in paired-end mode.
Samtools (v.1.9) was used to remove duplicated reads (rmdup), filter reads that mapped to mitochondrial genome or blacklisted regions, and sort the reads.
Reads longer than 100 bp were removed, and reads were normalized and scaled to the effective genome size using reads per genomic content (RPGC) with deeptools (v.3.3.0).
Peak calling was performed using JetBrains SPAN peak analyzer (v.0.11.0.4882) with an FDR threshold of 1E-6 and a gap of 2.
Genome_build: Homo.sapiens.GrCh38
Supplementary_files_format_and_content: A tab-delimited text file containing called peaks per sample.

source_name: doubleneg

extract_protocol: Microglia were isolated by mechanical tissue dissociation and Percoll gradient centrifugation at 4°C followed by flow cytometry of single, viable (DAPI-, DRAQ5+), CD45+, CD11B+ cells. From two samples, the  CD45-, CD11B- population was collected as well. After cell lysis and barcoded poly-dT primer annealing, RNA was reverse-transcribed with a biotinylated barcoded template switching oligo (BC-TSO). Primer-dimers and small fragments were removed by exonuclease treatment. cDNA libraries were amplified and multiplexed. When cDNA libraries showed an average size of 1.5-2 kb, libraries were tagmented and indexed according to the Illumina Nextera XT DNA preparation kit (Illumina, FC-131-1024) with an input of 500 pg cDNA. Samples were sequence on an Ilumina NextSeq 500. using 75 bp paired-end reads. Read 1 comprises the poolbarcode and read 2 the cDNA.

tag: donor/fetus

tag: gestational week+day


title: 11_4 single_cell_mrna_seq


title: 64_1 single_cell_mrna_seq

source_name: microglia


title: 66_4 single_cell_mrna_seq


title: 61_2 single_cell_mrna_seq


title: 58_3 single_cell_mrna_seq


title: 12-0108b

description:
batch 1
12-0108


title: 12-0103b

description:
batch 1
12-0103


title: 12-0102b

description:
batch 1
12-0102


title: 12-0107b

description:
batch 1
12-0107


title: 12-0105b

description:
batch 1
12-0105


title: 12-110b

description:
batch 1
12-0110


title: 55_4 single_cell_mrna_seq


title: 12-0106b

description:
batch 1
12-0106


title: C9HPPANXX_7_TGACCA

description:
batch 2
12-0044


title: C9HPPANXX_6_AGTCAA

description:
batch 2
12-0083


title: C9HPPANXX_6_CAGATC

description:
batch 2
12-0080


title: C9HPPANXX_6_CTTGTA

description:
batch 2
12-0082


title: C9HPPANXX_7_CGATGT

description:
batch 2
12-0043


title: C9HPPANXX_5_TGACCA

description:
batch 2
12-0076


title: 50_2 single_cell_mrna_seq


title: 53_1 single_cell_mrna_seq


title: 2_2 single_cell_mrna_seq


title: 47_3 single_cell_mrna_seq


title: 66_3 single_cell_mrna_seq


title: 63_4 single_cell_mrna_seq


title: 11_3 single_cell_mrna_seq


title: C9HPPANXX_5_GCCAAT

description:
batch 2
12-0079


title: 61_1 single_cell_mrna_seq


title: 58_2 single_cell_mrna_seq


title: C9HPPANXX_4_ATGTCA

description:
batch 2
12-0068


title: C9HPPANXX_5_ACAGTG

description:
batch 2
12-0078


title: C9HPPANXX_3_CTTGTA

description:
batch 2
12-0064


title: 50_1 single_cell_mrna_seq


title: 55_3 single_cell_mrna_seq


title: 52_4 single_cell_mrna_seq


title: 47_2 single_cell_mrna_seq


title: C9HPPANXX_3_AGTTCC

description:
batch 2
12-0067


title: C9HPPANXX_4_CCGTCC

description:
batch 2
12-0069


title: C9HPPANXX_3_CAGATC

description:
batch 2
12-0063


title: 44_4 single_cell_mrna_seq


title: C9HPPANXX_5_CGATGT

description:
batch 2
12-0074


title: C9HPPANXX_3_AGTCAA

description:
batch 2
12-0066


title: 2_1 single_cell_mrna_seq


title: 63_3 single_cell_mrna_seq


title: C9HPPANXX_2_TGACCA

description:
batch 2
12-0060


title: C9HPPANXX_2_GCCAAT

description:
batch 2
12-0062


title: 66_2 single_cell_mrna_seq


title: C9HPPANXX_4_GTGAAA

description:
batch 2
12-0073


title: 60_4 single_cell_mrna_seq


title: C9HPPANXX_2_CGATGT

description:
batch 2
12-0058


title: 58_1 single_cell_mrna_seq


title: 55_2 single_cell_mrna_seq


title: C9HPPANXX_1_GTGAAA

description:
batch 2
12-0057


title: △Ioc3_2 [MNase-seq]

city: Smithville

first: Blaine

last: Bartholomew

address: 1808 Park Road 1C

department: Epigenetics and Molecular Carcinogenesis

institute: MD Anderson Cancer Center

description:
processed data file:
dIOC3_Merged_Nucleosome_Calls_MNase_seq

data_processing:
DNA libraries for Illumina paired-end sequencing of nucleosomal DNA was performed as described previously (Zentner et al., 2013). The samples were sequenced using high throughput paired-end sequencing with a Illumina HiSeq 2000 Illumina sequencer. Paired-end sequence reads were mapped to the sacCer3 reference genome using Bowtie 2.0 (Langmead and Salzberg, 2012). Reads that mapped to the repetitive rRNA locus (chrXII: 451275 -469084) were filtered out (Gossett and Lieb, 2012). Dyad density maps were obtained for the mapped reads by considering the center of the paired sequence reads after normalizing to the mean genome wide coverage. Stereotypic nucleosome positions were identified using a greedy algorithm as described for Gene Track (Albert et al., 2008). These nucleosome calls include the nucleosome dyad position, standard deviation of the dyad and nucleosome occupancy values.
Genome_build: SacCer3
Supplementary_files_format_and_content: Excel file containing nucleosome calls

organism: Saccharomyces cerevisiae

growth_protocol: Yeast strains were grown in YPD to an OD 600 of approximately 0.7-0.9 in three independent biological replicates.

extract_protocol:
Strains with IOC3-FLAG and ioc3ΔcHLB-FLAG were grown as three biological replicates at 30˚C in YPD to an OD600 of 0.8. Samples were incubated with 1% formaldehyde for 20 min and quenched with glycine (125 mM final) for 5 min (Henikoff, 2015 ). Cells were harvested and converted to spheroplasts using 2 mg/ml zymolase (United Biologicals). Spheroplasts were digested with micrococcal nuclease (NEB M0247S) until ~70% of chromatin was converted into mononucleosomes. Samples were incubated overnight at 65°C with proteinase K (80 g/l, Roche 03115879001) and RNase A (30 g/l, Thermo Scientific EN 0531), and nucleosomal DNA isolated by phenol:chloroform extraction. DNA was analyzed on a 1.5% agarose gel with mononucleosomal DNA excised and purified using a Qiaquick gel extraction kit (Qiagen 28706).
Libraries were prepared using standard Illumina protocols

tag: strain background

tag: genotype/variation

tag: epitop tag

value: FLAG


title: Ioc3△cHLB_2 [MNase-seq]

description:
processed data file:
dcHLB_Merged_Nucleosome_Calls_MNase_seq


title: Ioc3△cHLB_3 [MNase-seq]


title: △Ioc3_3 [MNase-seq]


title: WT ISW1a_1 [MNase-seq]

description:
processed data file:
WT_ISW1a_Merged_Nucleosome_Calls_for_dcHLB_comparison_MNase_seq
WT_ISW1a_Merged_Nucleosome_Calls_for_dIoc3_comparison_MNase_seq

source_name: WT ISW1a

value: WT ISW1a


title: Ioc3△cHLB_1 [MNase-seq]


title: △Ioc3_1 [MNase-seq]


title: WT ISW1a_2 [MNase-seq]


title: C9HPPANXX_2_ACAGTG

description:
batch 2
12-0061

tag: age


title: 52_3 single_cell_mrna_seq


title: C9HPPANXX_1_GTCCGC

description:
batch 2
12-0056


title: 49_4 single_cell_mrna_seq


title: C9HPPANXX_1_CCGTCC

description:
batch 2
12-0055


title: 47_1 single_cell_mrna_seq


title: WT ISW1a_3 [MNase-seq]


title: MCF7 Control, rep2

city: Cheras

first: norlaily

last: mohd ali

state: Selangor

address: Universiti Tunku Abdul Rahman, Jln Sg Long

department: Faculty of Medicine and Health Sciences

country: Malaysia

institute: Universiti Tunku Abdul Rahman

description:
MCF_P_A4_miRNA-4_0_
miRNAs

hyb_protocol: Following ligation, 21.5ul of biotin-labeled sample were hybridized for 16 hours at 48C on GeneChip miRNA 4.0 arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the GeneChip Scanner 3000 7G.

data_processing: The raw CEL files were processed using the Affymetrix Expression Console Software (build 1.3.1) with microRNA arrays-RNA + DABG-Human only normalization to produce CHP files for each of the 6 samples. The six CHP files were then imported into the Affymetrix Transcriptome Analysis Console (TAC) 3.0 (build 3.0.0.466) using the Gene Level Differential Analysis option. Three conditions were created using TAC. One-way between-subject ANOVA (unpaired) were used as the algorithm options, and the default filter criteria was fold change >2 and <-2. The ANOVA p-value was set at <0.05.

source_name: Estrogen-dependent human breast adenocarcinoma

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 1 ug total RNA (FlashTaq Biotin HSR RNA Labeling kit, Affymetrix, 2013).

growth_protocol: The control and DK2-treated MCF-7 cells were cultured in tissue culture-treated flasks. Both are maintained in 5% CO2 humidified incubator.

extract_protocol: Total RNA with retention of small RNAs from the cells were extracted using miRNeasy kit according to the manufacturer's instructions.

treatment_protocol: MCF-7 was treated with 8.2 μM of DK2 at several time points.

tag: culture type

value: Monolayer

tag: treatment

value: Control


title: C9HPPANXX_1_ATGTCA

description:
batch 2
12-0053


title: MCF7 Control, rep1

description:
MCF7_P_A3_miRNA-4_0_
miRNAs


title: 44_3 single_cell_mrna_seq


title: C9HRBANXX_8_CTTGTA

description:
batch 1
12-0050


title: C9HRBANXX_8_CAGATC

description:
batch 1
12-0048


title: C9HRBANXX_8_AGTTCC

description:
batch 1
12-0052


title: MCF7 Control, rep3

description:
MCF_P_A4_miRNA-4_0_2
miRNAs


title: MCF7-DK2 Treated, rep2

description:
MCF_DK2 2_(miRNA-4_0)
miRNAs


title: MCF7-DK2 Treated, rep1

description:
MCF_DK2 1_(miRNA-4_0)
miRNAs


title: MCF7-DK2 Treated, rep3

description:
MCF_DK2 3_(miRNA-4_0)
miRNAs


title: 41_4 single_cell_mrna_seq


title: 66_1 single_cell_mrna_seq


title: 17_7C_gel

city: yufu

first: Ruofei

last: Zhu

institute: Oita University

hyb_protocol: cRNA was hybridized to a 60K 60-mer oligomicroarray (SurePrint G3 Human Gene Expression Microarray 8x60K v2 ; Agilent Technologies) according to the manufacturer's instructions.

scan_protocol: The hybridized microarray slides were scanned using an Agilent scanner. The relative hybridization intensities and background hybridization values were calculated using Feature Extraction Software version 9.5.1.1 (Agilent Technologies).

data_processing: The scanned images were analyzed with Feature Extraction Software 9.5.1.1 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities.  The raw signal intensities and flags for each probe were calculated from the hybridization intensities and spot information according to the procedures recommended by Agilent Technologies using the Flag criteria in the GeneSpring Software. In addition, the raw signal intensities of all samples were normalized by the quantile algorithm with the Bioconductor.

source_name: ovarian endometriotic cysts stromal cell,3rdG,3D floating culture.

label_protocol: cRNA was amplified and labelled using a Low input Quick Amp Labelling Kit (Agilent Technologies).

extract_protocol: The total RNA was isolated from cells using RNeasy Mini kit according to the manufacturer's instructions.

tag: growth

value: 3D floating gel culture

tag: gender

value: female

value: Endometrium

tag: cell type

value: Endometriotic cyst stromal cells


title: 17_4C_gel

tag: tissue


title: 17_1C_gel_2


title: 60_3 single_cell_mrna_seq


title: 17_5C_gel


title: C9HRBANXX_7_TGACCA

description:
batch 1
12-0045

tag: bedtime cortisol

tag: awakening cortisol


title: C9HRBANXX_7_CGATGT

description:
batch 1
12-0042

tag: emotional stress

tag: sex (0=females; 1=male)


title: Moffat_78_Renca_sgFitm2_IFNgTx_replA

city: Toronto

first: Jason

last: Moffat

address: 686 Bay Street, Room 13.9705

institute: University of Toronto

source_name: Renca

extract_protocol:
RNA was extracted from cultured cells using the RNeasy Plus Mini Kit (QIAGEN) according to manufacturer’s protocol. Briefly, cells were lysed on ice in RTL plus buffer (QIAGEN) and passed through QIAshredder columns. Supernatant was then transferred to RNeasy spin columns and an on-column DNase treatment was performed using the RNase-free DNase set (QIAGEN).
1000 ng per sample was processed using the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (New England Biolabs, E7760L) and included polyA-enrichment using NEBNext Poly(A) mRNA Magnetic Isolation Module (New England Biolabs, E7490L), fragmentation for 15 minutes at 94°C prior to first strand synthesis, and 8 cycles of amplification after adapter ligation.

value: IFNg (10ng/mL for 48h)

tag: cell line

value: Renca


title: 57_4 single_cell_mrna_seq

tag: donor/fetus


title: 63_2 single_cell_mrna_seq

tag: gestational week+day


title: 52_2 single_cell_mrna_seq


title: 55_1 single_cell_mrna_seq


title: Moffat_77_Renca_sgFitm2_IFNgTx_replB


title: Moffat_75_Renca_sgFitm2_ControlTx_replC

value: control


title: C9HRBANXX_8_AGTCAA

description:
batch 1
12-0051

value: whole blood


title: C9HRBANXX_7_ACAGTG

description:
batch 1
12-0046


title: 17_7C

source_name: ovarian endometriotic cysts stromal cell,3rdG,2D culture

value: 2D culture


title: Moffat_76_Renca_sgFitm2_IFNgTx_replC


title: 17_5C_5


title: 14_40E_dienogest

source_name: Eutopic endometrial stromal cell,3rdG,3D floating gel culture.

value: Eutopic endometrial stromal cells


title: 17_4C_3


title: Moffat_73_Renca_sgFitm2_ControlTx_replA


title: 14_37E_dienogest


title: 17_1C_2


title: 14_40E_control

source_name: Eutopic endometrial stromal cell,3rdG, 2D culture


title: 49_3 single_cell_mrna_seq


title: 14_45E_dienogest


title: C9HRBANXX_6_GTGAAA

description:
batch 1
12-0041


title: 14_45E_control


title: 14_38E_dienogest


title: Moffat_72_Renca_sgAtg12_TNFTx_replC

value: TNF (10ng/mL for 24hr)


title: 14_38E_control


title: Moffat_74_Renca_sgFitm2_ControlTx_replB


title: Moffat_70_Renca_sgAtg12_TNFTx_replA


title: Moffat_69_Renca_sgAtg12_IFNgTx_replC


title: C9HRBANXX_6_CCGTCC

description:
batch 1
12-0039


title: Moffat_68_Renca_sgAtg12_IFNgTx_replB


title: C9HRBANXX_6_ATGTCA

description:
batch 1
12-0037


title: Moffat_67_Renca_sgAtg12_IFNgTx_replA


title: Moffat_66_Renca_sgAtg12_Control48hTx_replC

value: control 48h


title: 41_3 single_cell_mrna_seq


title: 44_2 single_cell_mrna_seq


title: Moffat_65_Renca_sgAtg12_Control48hTx_replB


title: C9HRBANXX_6_GTCCGC

description:
batch 1
12-0040


title: C9HRBANXX_5_CTTGTA

description:
batch 1
12-0033


title: C9HRBANXX_5_CAGATC

description:
batch 1
12-0032


title: Moffat_71_Renca_sgAtg12_TNFTx_replB


title: 63_1 single_cell_mrna_seq


title: 46_4 single_cell_mrna_seq


title: C9HRBANXX_5_AGTTCC

description:
batch 1
12-0036


title: Moffat_63_Renca_sgAtg12_Control24hTx_replC

value: control 24h


title: Moffat_62_Renca_sgAtg12_Control24hTx_replB


title: Moffat_64_Renca_sgAtg12_Control48hTx_replA


title: 57_3 single_cell_mrna_seq


title: C9HRBANXX_5_AGTCAA

description:
batch 1
12-0034


title: Moffat_59_Renca_WT_TNFTx_replB

value: WT


title: 54_4 single_cell_mrna_seq


title: Moffat_60_Renca_WT_TNFTx_replC


title: 14_37E_control


title: Moffat_61_Renca_sgAtg12_Control24hTx_replA


title: C9HRBANXX_4_TGACCA

description:
batch 1
12-0029


title: 52_1 single_cell_mrna_seq


title: Moffat_54_Renca_WT_Control48hTx_replC


title: C9HRBANXX_4_CGATGT

description:
batch 1
12-0028


title: Moffat_53_Renca_WT_Control48hTx_replB


title: Moffat_56_Renca_WT_IFNgTx_replB


title: 60_2 single_cell_mrna_seq


title: Moffat_52_Renca_WT_Control48hTx_replA


title: C9HRBANXX_3_GTGAAA

description:
batch 1
12-0027


title: Moffat_50_Renca_WT_Control24hTx_replB


title: 44_1 single_cell_mrna_seq


title: Moffat_51_Renca_WT_Control24hTx_replC


title: Moffat_49_Renca_WT_Control24hTx_replA


title: Moffat_48_Renca-HA-Cas9_sgFitm2-1_IFNgTx_replC

value: Renca-HA


title: Moffat_58_Renca_WT_TNFTx_replA


title: Moffat_47_Renca-HA-Cas9_sgFitm2-1_IFNgTx_replB


title: Moffat_57_Renca_WT_IFNgTx_replC


title: Moffat_46_Renca-HA-Cas9_sgFitm2-1_IFNgTx_replA


title: C9HRBANXX_3_CCGTCC

description:
batch 1
12-0024


title: 60_1 single_cell_mrna_seq


title: 35_4 single_cell_mrna_seq


title: C9HRBANXX_4_GCCAAT

description:
batch 1
12-0031


title: Moffat_45_Renca-HA-Cas9_sgFitm2-1_ControlTx_replC


title: Moffat_55_Renca_WT_IFNgTx_replA


title: 46_3 single_cell_mrna_seq


title: C9HRBANXX_3_ATGTCA

description:
batch 1
12-0023


title: Moffat_44_Renca-HA-Cas9_sgFitm2-1_ControlTx_replB


title: 57_2 single_cell_mrna_seq


title: C9HRBANXX_4_ACAGTG

description:
batch 1
12-0030


title: C9HRBANXX_2_CTTGTA

description:
batch 1
12-0016


title: Moffat_43_Renca-HA-Cas9_sgFitm2-1_ControlTx_replA


title: Moffat_42_Renca-HA-Cas9_sgIntergenic_IFNgTx_replC

value: sgIntergenic


title: Moffat_41_Renca-HA-Cas9_sgIntergenic_IFNgTx_replB


title: 54_3 single_cell_mrna_seq


title: 49_2 single_cell_mrna_seq


title: C9HRBANXX_2_AGTTCC

description:
batch 1
12-0019


title: 41_2 single_cell_mrna_seq


title: Moffat_39_Renca-HA-Cas9_sgIntergenic_ControlTx_replC


title: 51_4 single_cell_mrna_seq


title: Moffat_40_Renca-HA-Cas9_sgIntergenic_IFNgTx_replA


title: C9HRBANXX_3_GTCCGC

description:
batch 1
12-0025


title: Moffat_37_Renca-HA-Cas9_sgIntergenic_ControlTx_replA


title: C9HRBANXX_2_AGTCAA

description:
batch 1
12-0017


title: 49_1 single_cell_mrna_seq


title: Moffat_38_Renca-HA-Cas9_sgIntergenic_ControlTx_replB


title: C9HRBANXX_1_TGACCA

description:
batch 1
12-0004


title: Moffat_35_B16F10-Ova-Cas9_sgFitm2-1_IFNgTx_replB


title: 46_2 single_cell_mrna_seq


title: Moffat_33_B16F10-Ova-Cas9_sgFitm2-1_ControlTx_replC


title: C9HRBANXX_1_GCCAAT

description:
batch 1
12-0010


title: 43_4 single_cell_mrna_seq


title: Moffat_32_B16F10-Ova-Cas9_sgFitm2-1_ControlTx_replB


title: C9HRBANXX_1_CGATGT

description:
batch 1
12-0003


title: 6_4 single_cell_mrna_seq


title: Moffat_27_B16F10-Ova-Cas9_sgIntergenic_ControlTx_replC


title: Moffat_30_B16F10-Ova-Cas9_sgIntergenic_IFNgTx_replC

value: IFNg (1ong/mL for 48h)


title: C9HRBANXX_1_ACAGTG

description:
batch 1
12-0009


title: Moffat_34_B16F10-Ova-Cas9_sgFitm2-1_IFNgTx_replA


title: Moffat_28_B16F10-Ova-Cas9_sgIntergenic_IFNgTx_replA


title: Moffat_31_B16F10-Ova-Cas9_sgFitm2-1_ControlTx_replA


title: 41_1 single_cell_mrna_seq


title: 35_3 single_cell_mrna_seq


title: Moffat_36_B16F10-Ova-Cas9_sgFitm2-1_IFNgTx_replC


title: Classical CD14+/CD16- monocytes, asthmatic subject 10 - HDL

data_processing:
quality controls of paired-end reads were assessed using FastQC tools
Adapter sequences and low-quality bases were trimmed using Cutadapt Alignment was performed by using HISAT2
Uniquely mapped paired-end reads were used for subsequent FeatureCounts for gene level abundance estimation
Limma-voom was employed for DEA
Genome_build: GRCh38
Supplementary_files_format_and_content: count matrix, raw count, tab delimited

source_name: Human Peripheral Blood

extract_protocol:
Total RNA was isolated from CD45+/CD14+/CD16-classical monocytes from asthmatic subjects using the Direct-Zol™ RNA MiniPrep kit (#R2052; Zymo Research, Irvine, CA).
Sequencing libraries were constructed from 100 ng to 500 ng of total RNA with the TruSeq Stranded Total RNA Library Prep kit (#20020596; Illumina, San Diego, CA) and the Ribo-Zero™ rRNA Removal (#MRZH11124; Illumina, San Diego, CA) kit. Fragment sizes of the RNAseq libraries were verified using a 2100 Bioanalyzer (#G2939BA; Agilent Technologies, Santa Clara, CA) and concentrations were quantified using a Qubit 3 Fluorometer (#Q33226; ThermoFisher Scientific, Waltham, MA).
Rigorous quality controls of paired-end reads were assessed using FastQC (Babraham Bioinformatics, Cambridge, UK). If required, adapter sequences and low-quality bases were trimmed using cutadapt software. Reads were aligned to the reference genome using HISAT2 v2.1.0 (Johns Hopkins University Center for Computational Biology, Baltimore, MD). Only uniquely mapped paired-end reads were used for subsequent analyses. featureCounts (WEHI Bioinformatics, Parkville, Melbourne, Victoria, Australia) was used for gene level abundance estimation using GENCODE Comprehensive gene annotations v25. Principal component analysis (PCA) was used to assess outlier samples. Genes were kept in the analysis if they had Counts Per Million (CPM) >1 in at least half the samples. Differential expression analysis comparing monocytes that were treated with normal HDL versus normal HDL enriched with recombinant human SAA1 at the gene levels of summarization were then carried out using open-source Limma R package (Bioconductor).  Limma-voom was employed to implement a gene-wise linear modelling which processes the read counts into log2 counts per million (logCPM) with associated precision weights. The logCPM values were normalized between samples using trimmed mean of M-values (TMM). Adjustment for multiple testing was performed by reporting the false discovery rate (FDR) q-values for each feature. Features with q-value <5% were regarded as genome-wide significant. R statistical software environment with the GAGE Bioconductor packages was used to carry out analyses on pre-defined gene ontology (GO) gene sets by conducting two sample t-tests on the log-based fold changes of target gene set and control sets. The GO categories included were Biological Process (BP), Cellular Component (CC), and Molecular Function (MF). FDR q-values were estimated to correct the p-values for the multiple testing issue.

treatment_protocol: CD45+/CD14+/CD16- classical monocytes were isolated from the blood of asthmatic subjects by negative selection using the RosetteSep Human Monocyte Enrichment Cocktail (#15068, StemCell Technologies), followed by flow sorting.  Purified CD45+/CD14+/CD16- classical monocytes were cultured for 24 h in RPMI 1640 media + 2% fetal bovine serum with normal HDL (4 ucg/ml) that had or had not been enriched with recombinant human SAA1 (2 ucg).

tag: individual

tag: condition

value: asthma

value: HDL

value: Peripheral Blood

value: Classical CD14+/CD16- monocyte


title: Moffat_25_B16F10-Ova-Cas9_sgIntergenic_ControlTx_replA


title: Moffat_24_Renca-HA-Cas9_sgATG12-1_IFNgTx_replC

value: IFNg (10ng/mL for 48h)


title: Classical CD14+/CD16- monocytes, asthmatic subject 10 - HDL+SAA1


title: Moffat_26_B16F10-Ova-Cas9_sgIntergenic_ControlTx_replB


title: Moffat_22_Renca-HA-Cas9_sgATG12-1_IFNgTx_replA


title: 57_1 single_cell_mrna_seq


title: Classical CD14+/CD16- monocytes, asthmatic subject 9 - HDL+SAA1


title: 54_2 single_cell_mrna_seq


title: Classical CD14+/CD16- monocytes, asthmatic subject 9 - HDL


title: Moffat_23_Renca-HA-Cas9_sgATG12-1_IFNgTx_replB


title: Moffat_21_Renca-HA-Cas9_sgATG12-1_ControlTx_replC


title: Classical CD14+/CD16- monocytes, asthmatic subject 8 - HDL+SAA1


title: 51_3 single_cell_mrna_seq


title: Moffat_20_Renca-HA-Cas9_sgATG12-1_ControlTx_replB


title: Moffat_18_Renca-HA-Cas9_sgIntergenic_IFNgTx_replC


title: 48_4 single_cell_mrna_seq


title: Classical CD14+/CD16- monocytes, asthmatic subject 8 - HDL


title: Moffat_16_Renca-HA-Cas9_sgIntergenic_IFNgTx_replA


title: 46_1 single_cell_mrna_seq


title: Moffat_17_Renca-HA-Cas9_sgIntergenic_IFNgTx_replB


title: Classical CD14+/CD16- monocytes, asthmatic subject 7 - HDL+SAA1


title: Moffat_15_Renca-HA-Cas9_sgIntergenic_ControlTx_replC


title: 43-3 single_cell_mrna_seq


title: Moffat_14_Renca-HA-Cas9_sgIntergenic_ControlTx_replB


title: 40-4 single_cell_mrna_seq


title: Moffat_13_Renca-HA-Cas9_sgIntergenic_ControlTx_replA


title: Classical CD14+/CD16- monocytes, asthmatic subject 6 - HDL+SAA1


title: Moffat_11_MC38-Ova-Cas9MC38-Ova-Cas9_sgATG12-1_IFNgTx_replB


title: Moffat_12_MC38-Ova-Cas9MC38-Ova-Cas9_sgATG12-1_IFNgTx_replC


title: Moffat_10_MC38-Ova-Cas9MC38-Ova-Cas9_sgATG12-1_IFNgTx_replA


title: 35-2 single_cell_mrna_seq


title: Classical CD14+/CD16- monocytes, asthmatic subject 7 - HDL


title: Moffat_08_MC38-Ova-Cas9_sgATG12-1_ControlTx_replB


title: Classical CD14+/CD16- monocytes, asthmatic subject 5 - HDL+SAA1


title: Moffat_19_Renca-HA-Cas9_sgATG12-1_ControlTx_replA


title: Moffat_07_MC38-Ova-Cas9_sgATG12-1_ControlTx_replA


title: Classical CD14+/CD16- monocytes, asthmatic subject 6 - HDL


title: Moffat_09_MC38-Ova-Cas9_sgATG12-1_ControlTx_replC


title: 32-3 single_cell_mrna_seq


title: Moffat_06_MC38-Ova-Cas9_sgIntergenic_IFNgTx_replC


title: Moffat_05_MC38-Ova-Cas9_sgIntergenic_IFNgTx_replB


title: Classical CD14+/CD16- monocytes, asthmatic subject 5 - HDL


title: Moffat_04_MC38-Ova-Cas9_sgIntergenic_IFNgTx_replA


title: Classical CD14+/CD16- monocytes, asthmatic subject 4 - HDL+SAA1


title: Moffat_29_B16F10-Ova-Cas9_sgIntergenic_IFNgTx_replB


title: 38-1 single_cell_mrna_seq


title: Moffat_03_MC38-Ova-Cas9_sgIntergenic_ControlTx_replC


title: Moffat_02_MC38-Ova-Cas9_sgIntergenic_ControlTx_replB


title: Classical CD14+/CD16- monocytes, asthmatic subject 4 - HDL


title: 54-1 single_cell_mrna_seq


title: Renca-HA repl2

source_name: Renca-HA cell line

extract_protocol:
Trizol protocol
1000 ng per sample was processed using the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (New England Biolabs, E7760L) and included polyA-enrichment using NEBNext Poly(A) mRNA Magnetic Isolation Module (New England Biolabs, E7490L), fragmentation for 15 minutes at 94°C prior to first strand synthesis, and 8 cycles of amplification after adapter ligation.


title: 51-2 single_cell_mrna_seq


title: Classical CD14+/CD16- monocytes, asthmatic subject 3 - HDL+SAA1


title: 45-4 single_cell_mrna_seq


title: 48-3 single_cell_mrna_seq


title: Classical CD14+/CD16- monocytes, asthmatic subject 2 - HDL+SAA1


title: Classical CD14+/CD16- monocytes, asthmatic subject 2 - HDL


title: Classical CD14+/CD16- monocytes, asthmatic subject 3 - HDL


title: 43_2 single_cell_mrna_seq


title: 29-4 single_cell_mrna_seq


title: 18mo-10ppm-female-rep2.WGBS

city: RTP

first: Janine

last: Santos

state: NC

address: 111 TW Alexander drive

department: GISBL

institute: NIEHS

description: WGBS

data_processing:
For consistency and quality reasons, only read1 was used in WGBS analysis. Reads were filtered to retain only those with average base quality score >20. Adapter trimming was performed with Cutadapt v1.2 (parameters -a AGATCGGAAGAG -O 5 -q 0 -f fastq); only reads at least 30nt after trimming were retained.
Filtered and trimmed WGBS reads were mapped to the mm10 reference genome via Bismark v0.18.1 at default parameters using Bowtie2 v2.3.0. Reads not mapped as full-length queries were re-submitted after clipping at the 3' end in an attempt to salvage additional alignments.
Mapped hits were deduplicated within libraries. Additional post-mapping processing included discarding reads with 3 or more methylated cytosines in non-CpG context and clipping alignments to remove regions with positional methylation bias as determined by the tool bismark_methylation_extractor. Mapped hits from multiple libraries of the same animal were aggregated after all quality filters and clipping were applied.
RNA-seq reads were filtered to retain only those with average base quality score >20. Read pairs were mapped to the mm10 reference genome via TopHat with the following parameters: --b2-sensitive --library-type fr-unstranded -g 1 --mate-inner-dist -40 --mate-std-dev 50. Resulting hits were coordinate-sorted and deduplicated with Picard tool suite v1.96.
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: Counts of methylated and unmethylated counts at CpG sites in tab-delimited text format (WGBS); percent methylation at CpG sites in bigWig format (WGBS).
Supplementary_files_format_and_content: RPKM per gene per sample in tab-delimited text format (RNAseq).

source_name: mouse liver

extract_protocol:
Livers were surgically retrieved, frozen in dry ice, and stored at -80°C. Pelleted minced tissue was homogenized further with sterile disposable pestles using a hand-held motor (Kimble) in the presence of 1 mL of Trizol reagent (Invitrogen) and fractionated according to the manufacturer's instructions to obtain total RNA, genomic DNA, and protein fractions.
WGBS libraries were constructed from starting 1ug genomic DNA and 50ng phage lambda, sheared via BioRuptor, subjected to bisulfite conversion (EZ DNA methylation kit; Zymo research), ligated and amplified with methylated adapters (TruSeq RNA v2; Illumina) and low-input DNA ligation chemistry (HyperPrep; KAPA Biosystems).
RNAseq libraries were constructed starting with poly-A-selected RNA from 1 µg of DNaseI-treated total RNA input using a magnetic poly-dT bead hybridization capture (Illumina), eluted in 10µL of nuclease-free H2O, transferred as magnetically isolated supernatant to RNase-free wells of a 96-well reaction plate, and used directly for rRNA-free library assembly using a KAPA Stranded RNA-Seq with RiboErase commercial kit (KAPA Biosystems).

treatment_protocol: Rotenone was administered through the diet at 10 ppm for 8 weeks; control diet did not contain rotenone.

value: liver

tag: Sex

value: female

value: 18 months

tag: dam treatment

value: 10ppm rotenone


title: 18mo-0ppm-female-rep1.WGBS

description: WGBS

tag: age

value: control


title: 18mo-0ppm-female-rep3.WGBS

description: WGBS


title: 12mo-10ppm-female-rep3.WGBS

description: WGBS

value: 12 months


title: 12mo-10ppm-female-rep2.WGBS

description: WGBS


title: 37_4 single_cell_mrna_seq


title: 18mo-10ppm-female-rep3.WGBS

description: WGBS


title: 12mo-10ppm-female-rep1.WGBS

description: WGBS


title: Renca-HA repl1

data_processing:
FASTQ files were first filtered using a bespoke Perl script to remove reads shorter than 36bp.
Filtered FASTQ files were aligned to Gencode M12 gene annotations and mm10 genome build using the STAR short-read aligner (v2.6.0a)
Read count files generated by STAR were merged with gene annotations in R
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text read counts


title: 12mo-0ppm-female-rep3.WGBS

description: WGBS


title: Classical CD14+/CD16- monocytes, asthmatic subject 1 - HDL

tag: treatment


title: 12mo-0ppm-female-rep2.WGBS

description: WGBS


title: Fetal_Rep3_H3K27Ac (chip-seq)

city: Cleveland

first: Xiaoxiao

last: Liu

state: Ohio

address: 10900 Euclid Ave

department: Genetics and Genomes Sciences

institute: Case Western Reserve University

data_processing:
ChIP-seq data were mapped to human reference genome hg19 using Bowtie. The first 36 bases of each read were used for mapping. We only use non-redundant reads to eliminate possible duplicates from biased PCR amplification.
Genome_build: hg19
Supplementary_files_format_and_content: For each Chip-Seq replicate, processed results are provided in the bed file.

source_name: Fetal anterior temporal cortex

extract_protocol:
For ChIP-seq, nuclei were extracted and chromatins were fragmented by sonication. The TF/histone-DNA complexes were isolated by antibody.
All ChIP-seq libraries were generated following a ChIPmentation protocol with Nextera adapters.

tag: developmental stage

value: Adult

value: brain (adult anterior temporal cortex)

tag: chip antibody

value: H3k27Ac (Abcam, ab4729)


title: 35_1 single_cell_mrna_seq


title: Classical CD14+/CD16- monocytes, asthmatic subject 1 - HDL+SAA1

tag: cell type


title: Fetal_Rep2_H3K4me3 (chip-seq)

tag: tissue

value: H3K4me3 (Abcam, ab8580)


title: 12mo-0ppm-female-rep1.WGBS

description: WGBS


title: 18mo-0ppm-female-rep2.WGBS

description: WGBS


title: 29_3 single_cell_mrna_seq


title: Fetal_Rep2_CTCF (chip-seq)

value: CTCF (Abcam, ab70303)


title: 18mo-10ppm-female-rep1.WGBS

description: WGBS


title: 32_2 single_cell_mrna_seq


title: 26_4 single_cell_mrna_seq


title: 6mo-10ppm-female-rep1.WGBS

description: WGBS

value: 6 months


title: 6mo-10ppm-female-rep2.WGBS

description: WGBS


title: 6mo-0ppm-female-rep3.WGBS

description: WGBS


title: Fetal_Rep1_H3K27Ac (chip-seq)


title: D22-10ppm-female-rep4.WGBS

description: WGBS


title: 6mo-0ppm-female-rep4.WGBS

description: WGBS


title: 51_1 single_cell_mrna_seq


title: D22-0ppm-female-rep1.WGBS

description: WGBS


title: 18mo-10ppm-female-rep2.RNAseq

description:
PolyA RNA
processed data file: RNAseq_RPKM_matrix.txt


title: 48_2 single_cell_mrna_seq


title: 18mo-10ppm-female-rep1.RNAseq


title: 18mo-0ppm-female-rep3.RNAseq


title: Fetal_Rep1_CTCF (chip-seq)


title: 18mo-0ppm-female-rep2.RNAseq


title: 18mo-0ppm-female-rep1.RNAseq


title: Adult_Rep3_H3K27Ac (chip-seq)

source_name: Adult anterior temporal cortex


title: 43_1 single_cell_mrna_seq


title: 12mo-10ppm-female-rep3.RNAseq


title: 18mo-10ppm-female-rep3.RNAseq


title: Adult_Rep3_H3K4me3 (chip-seq)


title: 12mo-10ppm-female-rep2.RNAseq


title: Fetal_Rep1_H3K4me3 (chip-seq)


title: 11_2 single_cell_mrna_seq


title: Adult_Rep3_CTCF (chip-seq)


title: 34_4 single_cell_mrna_seq


title: Adult_Rep1_H3K27Ac (chip-seq)


title: Moffat_01_MC38-Ova-Cas9_sgIntergenic_ControlTx_replA

value: sgIntergenic


title: 6mo-10ppm-female-rep5.RNAseq


title: 12mo-0ppm-female-rep1.RNAseq


title: 32_1 single_cell_mrna_seq


title: 37_3 single_cell_mrna_seq


title: 12mo-0ppm-female-rep2.RNAseq


title: 12mo-10ppm-female-rep1.RNAseq


title: 12mo-0ppm-female-rep3.RNAseq


title: 40_3 single_cell_mrna_seq


title: Adult_Rep1_CTCF (chip-seq)


title: 6mo-10ppm-female-rep2.RNAseq


title: Adult_Rep1_H3K4me3 (chip-seq)


title: 6mo-10ppm-female-rep1.RNAseq


title: 45_3 single_cell_mrna_seq


title: 6mo-0ppm-female-rep4.RNAseq


title: 29_2 single_cell_mrna_seq


title: 6mo-0ppm-female-rep3.RNAseq


title: 6mo-0ppm-female-rep2.RNAseq


title: D22-10ppm-female-rep4.RNAseq


title: 26_3 single_cell_mrna_seq


title: D22-10ppm-female-rep2.RNAseq


title: ME50 (eHi-C)

data_processing:
ChIP-seq data were mapped to human reference genome hg19 using Bowtie. The first 36 bases of each read were used for mapping. We only use non-redundant reads to eliminate possible duplicates from biased PCR amplification.
The paired-end easy Hi-C reads were mapped to hg19 using BOWTIE. Because nearly all the mappable reads start with HindIII sequence AGCTT, we trimmed the first 5 bases from every read, took the next 36 bases, and added the 6-base sequence AAGCTT to the 5’ of every read before mapping using the whole 42 bases.
For eHi-C library, the only type of invalid cis- pairs are self-circles with two ends within the same HindIII fragment facing each other. We excluded those pairs from further analysis.
We next split all these reads into three classes based on their strand orientations (“same-strand”, “inward”, or “outward”), and generated the resulting lists of fragment pairs (with Hi-C read counts) from each class of reads.
Genome_build: hg19
Supplementary_files_format_and_content: For each Chip-Seq replicate, processed results are provided in the bed file.
Supplementary_files_format_and_content: For eHi-C, processed results are provided in the frag_loop.txt files. Each has 4 columns: frag1_location, frag1_strand, frag2_location, and frag2_strand

extract_protocol:
For Hi-C, nuclei were extraced after fixing using a cell lysis buffer. For ChIP-seq, nuclei were extracted and chromatins were fragmented by sonication. The TF/histone-DNA complexes were isolated by antibody.
All Hi-C libraries were constructed following illumina insctructions accompanying Truseq sample preparation kit.  Random indexes were introduced for eHi-C libraries to remove PCR duplication. Generally, PCR amplification was done with 7-9 cycles. All ChIP-seq libraries were generated following a ChIPmentation protocol with Nextera adapters.

value: brain (anterior temporal cortex)

tag: restriction enzyme

value: HindIII and DpnII


title: D22-10ppm-female-rep1.RNAseq


title: ME49 (eHi-C)


title: 23_4 single_cell_mrna_seq


title: D22-0ppm-female-rep3.RNAseq


title: ME51 (eHi-C)


title: 48_1 single_cell_mrna_seq


title: D22-0ppm-female-rep2.RNAseq


title: D22-0ppm-female-rep1.RNAseq


title: 34_3 single_cell_mrna_seq


title: 45_2 single_cell_mrna_seq


title: 42_4 single_cell_mrna_seq


title: 37_2 single_cell_mrna_seq


title: ME47 (eHi-C)

value: Fetal


title: ME45 (eHi-C)


title: 11_1 single_cell_mrna_seq


title: Fetal_Rep2_H3K27Ac (chip-seq)


title: Adult_Rep2_H3K27Ac (chip-seq)


title: ME46 (eHi-C)


title: Fetal_Rep3_CTCF (chip-seq)


title: D21_49

city: Guangzhou

first: Jinyong

address: 190 Kai Yuan Avenue, Science Park, Guangzhou, China

institute: Guangzhou Institutes of Biomedicine and Health (GIBH)

data_processing:
Bcl2fastq (verison 2.16.0.10) convert .bcl files into fastq files
Fastq files were aligned to mm10 genome.*.ht2 files to generate *.sam file by HISAT2 (version 2.1.0). And the used samtools (version 0.1.19) to convert and sort the sam file to bam file. StringTie (version 1.3.4) were used to calculated genes expression level in TPM.
Gene expression levels in TPM of different samples were normalized by Stringtie.
Genome_build: mm10
Supplementary_files_format_and_content: TPM table was a csv file

source_name: Day10 induced hematopoietic progenitor cells

growth_protocol: Expression of defined factors Hoxa9 and Runx1 in ESC/iPSC led to the production of an hematopoietic cell type

extract_protocol:
The procedure of RNA extraction and reverse transcription into double-stranded DNA were prepared using Discover-sc WTA Kit V2(Vazyme, N711)
Libraries were prepared according to instruction of TruePrepTM  DNA Library Prep Kit V2 (Vazyme,TD503).

treatment_protocol: The single iHECs and iHPCs were sorted for RNAseq analysis.

tag: strain


title: D21_56

value: Day10 induced hematopoietic progenitor cells


title: D21_55


title: D21_51


title: D21_54


title: D21_52


title: D21_45


title: 29_1 single_cell_mrna_seq


title: D21_48


title: Adult_Rep2_H3K4me3 (chip-seq)


title: D21_47


title: D21_46


title: 26_2 single_cell_mrna_seq


title: Fetal_Rep3_H3K4me3 (chip-seq)


title: Adult_Rep2_CTCF (chip-seq)


title: D21_50


title: 31_4 single_cell_mrna_seq


title: D21_53


title: D21_44


title: D21_43


title: D21_41


title: 20_4 single_cell_mrna_seq


title: D21_39


title: 23_3 single_cell_mrna_seq


title: D21_40