title: 200992310030_R02C01 Sample558


title: 3999078077_R04C01 Sample590

status: Public on Apr 07 2021

type: genomic

city: Exeter

first: Jonathan

last: Mill

address: RILD Building, RD&E Hospital

department: Medical School

country: United Kingdom

institute: University of Exeter

hyb_protocol: Samples were processed according to the Illumina Infinium HumanMethylation450K BeadChip (Illumina) protocol.

scan_protocol: Samples were assessed using the Illumina Infinium HumanMethylation450K BeadChip (Illumina) using a Illumina iScan System (Illumina).

data_processing: Data was imported using the R package methylumi methylumIDAT function. Data was then pre-processed in the R package wateRmelon using the pfilter and dasen functions.

label: hapten-labeled dideoxynucleotides

molecule: genomic DNA

organism: Homo sapiens

source_name: Whole Blood

label_protocol: 500 ng DNA from each sample was sodium bisulfite-treated using the EZ-96 DNA Methylation-Gol Kit (Zymo Research) according to the manufacturer’s standard protocol.

extract_protocol: DNA was extracted using a phenol/chloroform method

tag: status

value: FEP

tag: gender

value: M

tag: ageatbloodcollection


title: 3999078077_R03C02 Sample589

value: CON


title: 200992310027_R06C01 Sample555

hyb_protocol: Samples were processed according to the Illumina Infinium HumanMethylationEPIC BeadChip (Illumina) protocol.

scan_protocol: Samples were assessed using the Illumina Infinium HumanMethylationEPIC BeadChip (Illumina) using a Illumina iScan System (Illumina).

tag: phenotype

value: Control

tag: Sex

value: Female

tag: age


title: 3999078077_R02C01 Sample586

value: SCZ


title: 200992310027_R04C01 Sample554


title: 200992310027_R01C01 Sample552

value: Case


title: 3999078077_R03C01 Sample588


title: 200992310027_R02C01 Sample553

value: Male


title: 3999078077_R01C01 Sample584


title: 3999078077_R01C02 Sample585


title: 3999078077_R02C02 Sample587


title: 200992310025_R08C01 Sample551


title: 200992310025_R07C01 Sample550


title: 3999078076_R06C02 Sample583


title: 200992310025_R06C01 Sample549


title: 3999078078_R01C01 Sample594


title: 200992310025_R05C01 Sample548


title: 200992310025_R04C01 Sample547


title: 3999078076_R05C02 Sample581


title: 3999078076_R06C01 Sample582


title: 200992310027_R07C01 Sample556


title: 3999078076_R05C01 Sample580


title: 200992310017_R08C01 Sample544


title: 200992310017_R07C01 Sample543


title: 3999078076_R04C02 Sample579

value: F


title: 3999078076_R04C01 Sample578


title: 3999078076_R03C02 Sample577


title: 3999078076_R02C02 Sample575


title: 200992310025_R01C01 Sample545


title: 3999078076_R03C01 Sample576


title: 200992310017_R06C01 Sample542


title: 200992310030_R04C01 Sample560


title: 3999078076_R01C02 Sample573


title: 200992310017_R04C01 Sample540


title: 200992310017_R05C01 Sample541


title: 200992310017_R02C01 Sample538


title: 3999078069_R06C01 Sample571


title: 3999078069_R06C02 Sample572


title: 3999078076_R02C01 Sample574


title: 3999078069_R05C02 Sample570


title: 200992310025_R03C01 Sample546


title: 200992310017_R01C01 Sample537


title: 3999078069_R05C01 Sample569


title: 200992310015_R08C01 Sample536


title: 200992310015_R07C01 Sample535


title: 3999078069_R04C02 Sample568


title: 3999078069_R04C01 Sample567


title: 200992310015_R04C01 Sample533


title: 200992310015_R05C01 Sample534


title: 3999078069_R03C01 Sample565


title: 3999078069_R03C02 Sample566


title: 200992310015_R02C01 Sample531


title: 200992310015_R03C01 Sample532


title: 3999078069_R02C01 Sample564


title: 3999078069_R01C01 Sample562


title: 3999078069_R01C02 Sample563


title: 3999078067_R06C01 Sample561


title: 200992310014_R06C01 Sample528


title: 200992310015_R01C01 Sample530


title: 200992310017_R03C01 Sample539


title: 200992310014_R04C01 Sample526


title: 200992310014_R07C01 Sample529


title: 200992310014_R03C01 Sample525


title: 3999078067_R04C02 Sample558


title: 200992310014_R05C01 Sample527


title: 3999078067_R05C01 Sample559


title: 3999078067_R05C02 Sample560


title: 3999078067_R04C01 Sample557


title: 200992310014_R02C01 Sample524


title: 3999078067_R03C01 Sample556


title: 200992290048_R08C01 Sample522


title: 3999078067_R02C02 Sample555


title: 3999078067_R02C01 Sample554


title: 200992290048_R05C01 Sample521


title: 200992290048_R03C01 Sample519


title: 3999078067_R01C02 Sample553


title: 3999078067_R01C01 Sample552


title: 200992290048_R02C01 Sample518


title: 3999078032_R06C02 Sample551


title: 200992290048_R01C01 Sample517


title: 3999078032_R05C02 Sample549


title: 200992290047_R06C01 Sample515


title: 200992290047_R07C01 Sample516


title: 200992290047_R04C01 Sample513


title: 3999078032_R04C02 Sample547


title: 200992290047_R02C01 Sample511


title: 3999078032_R02C01 Sample544


title: 200992290047_R03C01 Sample512


title: 3999078032_R01C02 Sample543


title: 3999078027_R06C02 Sample542


title: 200992290043_R08C01 Sample509


title: 200992310014_R01C01 Sample523


title: 200992290043_R07C01 Sample508


title: 3999078032_R03C01 Sample546


title: 3999078027_R06C01 Sample541


title: 200992290048_R04C01 Sample520


title: 200992290043_R06C01 Sample507


title: 3999078027_R05C02 Sample540


title: 200992290043_R05C01 Sample506


title: 3999078032_R02C02 Sample545


title: 3999078027_R05C01 Sample539


title: 200992290043_R03C01 Sample504


title: 3999078027_R04C01 Sample537


title: 200992290043_R02C01 Sample503


title: 3999078032_R05C01 Sample548


title: 200992290047_R05C01 Sample514


title: 3999078032_R06C01 Sample550


title: 3999078027_R03C02 Sample536


title: 200992290047_R01C01 Sample510


title: 3999078027_R03C01 Sample535


title: 3999078027_R02C02 Sample534


title: 200992290038_R08C01 Sample501


title: 200992290038_R07C01 Sample500


title: 3999078027_R02C01 Sample533


title: 200992290038_R06C01 Sample499


title: 3999078027_R04C02 Sample538


title: 200992290038_R04C01 Sample498


title: 3999078027_R01C01 Sample531


title: 200992290038_R03C01 Sample497


title: 200992290038_R02C01 Sample496


title: 3999002103_R06C02 Sample530


title: 3999002103_R06C01 Sample529


title: 3999078027_R01C02 Sample532


title: 200992290057_R08C01 Sample495


title: 3999002103_R05C01 Sample527


title: 200992290057_R07C01 Sample494


title: 200992290043_R04C01 Sample505


title: 200992290057_R06C01 Sample493


title: 3999002103_R05C02 Sample528


title: 3999002103_R04C02 Sample526


title: 200992290057_R05C01 Sample492


title: 3999002103_R04C01 Sample525


title: 200992290043_R01C01 Sample502


title: 3999002103_R03C01 Sample523


title: 200992290057_R03C01 Sample490


title: 3999002103_R03C02 Sample524


title: 200992290057_R01C01 Sample489


title: 200992290057_R04C01 Sample491


title: 3999002103_R02C02 Sample522


title: 200992290055_R06C01 Sample487


title: 3999002103_R01C01 Sample520


title: 200992290055_R08C01 Sample488


title: 3999002095_R06C02 Sample519


title: 3999002095_R05C02 Sample517


title: 200992290055_R05C01 Sample486


title: 200992290055_R04C01 Sample485


title: 200992290055_R02C01 Sample483


title: 200992290055_R03C01 Sample484


title: 200992290054_R08C01 Sample481


title: 3999002095_R06C01 Sample518


title: 200992290055_R01C01 Sample482


title: 3999002095_R04C01 Sample514


title: 200992290054_R07C01 Sample480


title: 3999002095_R03C02 Sample513


title: 200992290054_R05C01 Sample479


title: 3999002095_R03C01 Sample512


title: 200992290054_R04C01 Sample478


title: 3999002095_R02C02 Sample511


title: 200992290054_R03C01 Sample477


title: 3999002095_R02C01 Sample510


title: 3999002095_R01C02 Sample509


title: 3999002095_R01C01 Sample508


title: 200992290054_R01C01 Sample475


title: 200992290039_R08C01 Sample474


title: 3999002103_R01C02 Sample521


title: 200992290054_R02C01 Sample476


title: 3999002075_R06C02 Sample507


title: 200992290039_R07C01 Sample473


title: 200992290039_R06C01 Sample472


title: 200992290039_R04C01 Sample470


title: 3999002095_R05C01 Sample516


title: 200992290039_R02C01 Sample469


title: 200992290039_R05C01 Sample471


title: 3999002075_R06C01 Sample506


title: 3999002095_R04C02 Sample515


title: 3999002075_R03C02 Sample501


title: 3999002075_R04C01 Sample502


title: 3999002075_R05C01 Sample504


title: 3999002075_R03C01 Sample500


title: 200992290037_R08C01 Sample467


title: 200992290037_R06C01 Sample465


title: 200992290037_R07C01 Sample466


title: 200992290037_R05C01 Sample464


title: 3999002075_R01C02 Sample497


title: 3999002075_R01C01 Sample496


title: 200992290037_R04C01 Sample463


title: 3999002034_R06C01 Sample494


title: 3999002075_R05C02 Sample505


title: 200992290037_R03C01 Sample462


title: 3999002034_R05C02 Sample493


title: 3999002075_R04C02 Sample503


title: 3999002034_R05C01 Sample492


title: 3999002034_R04C02 Sample491


title: 200992290032_R07C01 Sample458


title: 3999002034_R06C02 Sample495


title: 200992290032_R08C01 Sample459


title: 200992290032_R06C01 Sample457


title: 200992290032_R05C01 Sample456


title: 3999002034_R03C02 Sample489


title: 200992290037_R01C01 Sample460


title: 3999002034_R03C01 Sample488


title: 200992290039_R01C01 Sample468


title: 3999002075_R02C02 Sample499


title: 3999002034_R02C02 Sample487


title: 3999002075_R02C01 Sample498


title: 3999002034_R02C01 Sample486


title: 200992290028_R07C01 Sample452


title: 3999002034_R01C02 Sample485


title: 200992290028_R06C01 Sample451


title: 200992290032_R03C01 Sample455


title: 3999002021_R06C02 Sample484


title: 200992290037_R02C01 Sample461


title: 200992290028_R05C01 Sample450


title: 3999002021_R06C01 Sample483


title: 200992290028_R03C01 Sample448


title: 3999002021_R05C01 Sample481


title: 3999002021_R05C02 Sample482


title: 200992290028_R01C01 Sample447


title: 200992290028_R04C01 Sample449


title: 3999002034_R04C01 Sample490


title: 200992290024_R08C01 Sample446


title: 3999002021_R04C02 Sample480


title: 3999002021_R03C02 Sample478


title: 3999002021_R02C02 Sample476


title: 200992290024_R04C01 Sample443


title: 3999002021_R03C01 Sample477


title: 3999002021_R04C01 Sample479


title: 200992290024_R07C01 Sample445


title: 200992290028_R08C01 Sample453


title: 200992290024_R02C01 Sample441


title: 200992290024_R03C01 Sample442


title: 3999002021_R01C02 Sample474


title: 3999002021_R01C01 Sample473


title: 3999002008_R06C02 Sample472


title: 3999002021_R02C01 Sample475


title: 3999002008_R06C01 Sample471


title: 3999002008_R05C02 Sample470


title: 200992290023_R06C01 Sample437


title: 200992290023_R07C01 Sample438


title: 3999002008_R05C01 Sample469


title: 3999002008_R04C02 Sample468


title: 200992290023_R04C01 Sample435


title: 200992290024_R05C01 Sample444


title: 3999002008_R04C01 Sample467


title: 200992290023_R01C01 Sample432


title: 200992290023_R02C01 Sample433


title: 200992290022_R06C01 Sample429


title: 3999002008_R03C01 Sample465


title: 200992290022_R07C01 Sample430


title: 200992290022_R08C01 Sample431


title: 3999002008_R02C02 Sample464


title: 200992290023_R08C01 Sample439


title: 3999002008_R01C02 Sample463


title: 200992290022_R05C01 Sample428


title: 3998998154_R06C01 Sample461


title: 200992290024_R01C01 Sample440


title: 3998998154_R06C02 Sample462


title: 200992290023_R03C01 Sample434


title: 200992290022_R04C01 Sample427


title: 3998998154_R04C02 Sample460


title: 200992290023_R05C01 Sample436


title: 200992290022_R03C01 Sample426


title: 3999002008_R03C02 Sample466


title: 200992290032_R01C01 Sample454


title: 3998998154_R03C02 Sample458


title: 200992290020_R08C01 Sample424


title: 3998998154_R03C01 Sample457


title: 200992290020_R07C01 Sample423


title: 3998998154_R02C02 Sample456


title: 200992290020_R05C01 Sample421


title: 200992290020_R06C01 Sample422


title: 3998998154_R02C01 Sample455


title: MTZ-SIS3-1

type: SRA

city: Wuhan

first: Ruilin

last: Zhang

address: 185 Donghu Road

country: China

institute: Wuhan University

description: Zebrafish

library_source: transcriptomic

data_processing:
Illumina Casava 1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to GRCz10.86 whole genome using Hisat2 v2.0.5.
HTSeq (v0.6.1) estimated gene expression levels from the pair-end clean data.
Genome_build: GRCz10.86
Supplementary_files_format_and_content: *.anno.fpkm.txt: Tab-delimited text files include FPKM values for each sample.

molecule: total RNA

organism: Danio rerio

source_name: Heart

growth_protocol: Zebrafish were raised and maintained under standard conditions.

extract_protocol:
Hearts were removed from zebrafish, and RNA was harvested using Trizol reagent. The total RNA of injured hearts and SIS3-treated injured hearts were 2.17μg and 1.95μg, respectively.
RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: Tg(vmhc:mCherry-NTR) larvae were treated with 5 mM MTZ (metronidazole, Sigma) in E3 water at 72 hpf for four hours. After washing, the larvae were then incubated in 2 μM Smad3 phosphorylation inhibitor (SIS3, Selleck) or 0.2% DMSO (dimethyl sulfoxide, Fisher Scientific) as control from 76 to 124 hpf.

tag: genotype/variation

tag: tissue

value: Heart

tag: condition

value: Injured

tag: treatment

value: 5dpf (2dpt)


title: 3998998154_R01C01 Sample454


title: C-SIS3-1

description: Zebrafish

value: Uninjured


title: MTZ-DMSO-1

description: Zebrafish

value: DMSO


title: 200992290020_R04C01 Sample420


title: ZWT097 DKO CAR 3

type: RNA

city: Memphis

first: Hongbo

last: Chi

state: TN

address: 262 Danny Thomas Place

department: Immunology

country: USA

institute: St Jude Children's Research Hospital

hyb_protocol: Six micrograms of biotinylated cDNA was fragmented and then hybridized for 16 hr at 45C on an Affymetrix GeneChip. Following hybridization, GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

data_processing: Probe signals were quantile normalized and summarized by the RMA algorithm using the Affymetrix Expression Console software v1.1

label: biotin

organism: Mus musculus

source_name: transferred CAR T cells sorted from spleens of B6 recipients

label_protocol: Total RNA (1 - 20 ng) were converted into biotinylated cDNA using the NuGEN WTA Pico v2 protocol and the NuGEN Encore Biotin module

growth_protocol: CD8+ CAR T cells were isolated by flow cytometric sorting of splenocytes based on reporters and congenical markers: Regnase-1 KO CAR (mCherry+Thy1.1+Thy1.2+) and Regnase-1 TCF-1 DKO (Ametrine+GFP+Thy1.1–Thy1.2+) 7 days after co-transfer

extract_protocol: Total RNA samples were prepared according to the prototol of RNeasy Micro kit from Qiagen,

treatment_protocol: Sorted cells were lysed with lysis buffer from RNeasy Micro kit from Qiagen.

tag: strain

value: CAR transgenic mice were bred on a B6 background and then to Thy1.1 and Rosa26-Cas9 knockin mice.

value: DKO CAR


title: 3998998154_R04C01 Sample459


title: ZWT098 DKO CAR 4


title: ZWT099 DKO CAR 5


title: ZWT095 DKO CAR 1


title: ZWT093 KO CAR 4

value: KO CAR


title: MN-Ctrl rep1

city: Beijing

first: Jie

address: Qing Hua Yuan

department: Basic Medical Sciences, School of Medicine

institute: Tsinghua University

data_processing:
Base-calling were carried out by Illumina Casava1.8 software.
Reads were trimmed with the trim_galore software with default parameter. Then, the reads were mapped to Sscrofa11.1 whole genome using hisat2 with parameter -p 16.
Then, we counted for each gene how many reads mapped to it using htseq-count version 0.11.1 with parameters -r pos -a 10 -t exon -s no -i gene_id -m union
Genome_build: Sscrofa11.1
Supplementary_files_format_and_content: tab-delimited text files include reads count number for each Sample

organism: Sus scrofa

source_name: mucosa

extract_protocol:
Total RNA was isolated from the fresh tissues with RNeasy Plus Mini Kit (Qiagen) according to manufacturer’s instructions and treated with RNase-free DNase.
RNA-seq libraries were prepared using Smart-seq2 as the manufacturer’s instructions and the cDNA were subject to Illumina TruSeq library preparation. The sequencing was performed by Hiseq X Ten (Illumina).

value: Guizhou minipig

value: 8 months

tag: cell type

value: Mucosa of neobladder from control group


title: 200992290022_R01C01 Sample425

value: Control


title: ZWT094 KO CAR 5


title: ZWT092 KO CAR 3


title: 3998998153_R06C01 Sample453

value: FEP


title: ZWT090 KO CAR 1


title: MN-Exp rep2

value: Mucosa of neobldder from experimental group


title: MN-Exp rep1


title: 200992290020_R03C01 Sample419

value: Female


title: MN-Ctrl rep2


title: 3998998153_R05C02 Sample452

value: SCZ

value: M


title: ZWT096 DKO CAR 2


title: C-DMSO-1

description: Zebrafish

value: Heart


title: 200992290020_R02C01 Sample418


title: NP rep2

value: Normal peritoneum


title: NP rep1


title: 200992290011_R08C01 Sample417

value: Case

value: Male


title: 3998998153_R05C01 Sample451

value: F


title: 3998998153_R04C02 Sample450


title: MNB rep1

value: Mucosa of normal bladder


title: 200992290011_R07C01 Sample416


title: 3998998153_R04C01 Sample449


title: ZWT091 KO CAR 2

value: CAR transgenic mice were bred on a B6 background and then to Thy1.1 and Rosa26-Cas9 knockin mice.


title: 200992290011_R05C01 Sample415


title: 200992290011_R04C01 Sample414


title: Verdial Vélez-Málaga A

city: JAEN

first: Jorge

middle: Antolín

last: Ramirez

state: --- Select a state ---

address: Campus Las Lagunillas s/n 23071

department: Experimental Biology

country: Spain

institute: University of Jaen

data_processing:
Base-calling: Illumina HiSeq 2500 sequencing software
Alignment: DNAStar (ArrayStar 15) Qseq software for RNA-Seq analyses
Generation of normalized abundance measurements: DNAStar (ArrayStar 15) Qseq software for RNA-Seq analyses
Genome_build: Oleur061 assembled genome from Olea europaea cv. Picual (PRJNA556567)
Supplementary_files_format_and_content: The attached processed data file is an excel spreadsheet with RPKM values of each gene in each cultivar, including A and B biological replicates.

organism: Olea europaea

source_name: root

growth_protocol: Plants were grown under field conditions at IFAPA Córdoba (Andalusia, Spain, mediterranean climate).

extract_protocol:
Spectrum Plant Total RNA kit (Sigma-Aldrich, St. Louis, MO) used according to the manufacturer’s instructions. A pool of the cDNA libraries was sequenced by paired-end sequencing (101 x 2) with an Illumina HiSeq 2000 sequencer. Two biological replicates per sample were sequenced, and each replicate was loaded twice on two different lanes in the flow cell.
poly(A)+ RNA was isolated on poly-T oligo-attached magnetic beads in order to get suitable mRNA templates to perform the reverse transcription. The cDNA was amplified through PCR obtaining double stranded cDNA libraries. The quality of those libraries was checked in a TapeStation 4200, with a high sensitivity bioassay (Agilent Technologies). Finally, cDNA libraries were sequenced by paired-end sequencing (100 x 2) on an Illumina HiSeq2500 sequencer, using the rapid mode and running 2 different lines in the flow cell as technical replicates for each sample.

treatment_protocol: Root tissues were washed with water and inmediatly frozen in liquid nitrogen.

tag: developmental stage

value: adult

tag: cultivar

value: Verdial Velez-Malaga

value: whole root tissue


title: Uslu A

value: Uslu


title: Uslu B


title: Temprano B

value: Temprano


title: 3998998153_R03C01 Sample447

value: FEP


title: 3998998153_R03C02 Sample448


title: Fishomi B

value: Fishomi


title: 200992290011_R03C01 Sample413

value: Control


title: Temprano A


title: 3998998153_R02C02 Sample446

value: CON


title: Fishomi A


title: 200992290011_R02C01 Sample412


title: 3998998153_R02C01 Sample445

value: M


title: 200992290011_R01C01 Sample411

value: Female


title: Piñonera A

value: Pinonera


title: Picual A

value: Picual


title: 3998998153_R01C02 Sample444


title: MNB rep2

value: Guizhou minipig

value: 8 months


title: Piñonera B


title: Verdial Vélez-Málaga B


title: 3998998153_R01C01 Sample443

value: F


title: 200863770116_R08C01 Sample410

value: Male


title: Picudo A

value: adult

value: Picudo


title: Picudo B

value: whole root tissue


title: 200863770116_R07C01 Sample409


title: Mazanillera de Sevilla B

value: Mazanillera de Sevilla


title: 200863770116_R04C01 Sample407

value: Case


title: Manzanillera de Huercal-Overa B

value: Manzanillera de Huercal-Overa


title: 200863770116_R06C01 Sample408


title: 3998998139_R06C02 Sample442

value: SCZ


title: 3998998139_R05C02 Sample440

value: FEP


title: Mazanillera de Sevilla A


title: Myrtolia A

value: Myrtolia


title: Myrtolia B


title: Morrut B

value: Morrut


title: Picual B


title: Majhol-1013 B


title: 200863770116_R02C01 Sample405


title: Manzanillera de Huercal-Overa A


title: 200863770116_R03C01 Sample406

value: Control


title: Majhol-1013 A


title: 200863770116_R01C01 Sample404


title: 200863770115_R08C01 Sample403


title: Majhol-152 B


title: Majhol-152 A


title: Menya B

value: Menya


title: Menya A


title: Lianolia Kerkyras  B

value: Lianolia Kerkyras


title: 200863770115_R07C01 Sample402


title: 3998998139_R06C01 Sample441


title: 3998998139_R04C01 Sample437

value: M


title: Lianolia Kerkyras  A


title: 3998998139_R05C01 Sample439


title: Mavreya B

value: Mavreya


title: 3998998139_R01C02 Sample434

value: CON


title: 200863770115_R05C01 Sample401

value: Male


title: 3998998139_R01C01 Sample433


title: 200863770115_R04C01 Sample400


title: 3998998139_R03C01 Sample436


title: Mastoidis B

value: adult

value: Mastoidis


title: 200863770115_R03C01 Sample399


title: 3998998139_R04C02 Sample438

value: F


title: Mastoidis A

value: whole root tissue


title: Mari B

value: Mari


title: Mavreya A


title: 200863770115_R02C01 Sample398

value: Case


title: Mari A


title: 3998998136_R06C02 Sample432


title: Maarri A

value: Maarri


title: 3998998136_R05C02 Sample431


title: Morrut A


title: 200863770115_R01C01 Sample397

value: Female


title: Llumeta B

value: Llumeta


title: 3998998136_R05C01 Sample430

value: FEP


title: Maarri B


title: 200863770113_R08C01 Sample396

value: Control


title: Leccino A

value: Leccino


title: Leccino B


title: 3998998136_R04C02 Sample429


title: Koroneiki B

value: Koroneiki


title: 200863770113_R06C01 Sample395


title: 3998998136_R04C01 Sample428

value: SCZ

value: M


title: Koroneiki A


title: Llumeta A


title: 3998998136_R02C02 Sample427


title: 200863770113_R03C01 Sample393


title: 3998998136_R02C01 Sample426


title: Kalamon B

value: Kalamon


title: 200863770113_R02C01 Sample392


title: Klon-14-182 B


title: Jabali B

value: Jabali


title: Klon-14-182 A

value: adult


title: Kalamon A


title: 3998998134_R06C01 Sample425


title: Grappolo B

value: Grappolo


title: 3998998134_R05C02 Sample424

value: CON

value: F


title: Frantoio B

value: Frantoio

value: whole root tissue


title: Forastera de Tortosa A

value: Forastera de Tortosa


title: 3998998134_R05C01 Sample423


title: 200863770112_R08C01 Sample390

value: Case

value: Female


title: 3998998134_R04C02 Sample422


title: 200863770112_R07C01 Sample389


title: 200863770113_R01C01 Sample391


title: Dokkar B

value: Dokkar


title: Forastera de Tortosa B


title: 200863770112_R06C01 Sample388


title: 3998998134_R04C01 Sample421


title: Dokkar A


title: 200863770113_R04C01 Sample394

value: Control


title: 200863770112_R05C01 Sample387


title: Chemlal B

value: Chemlal


title: Chemlal A


title: 3998998139_R02C02 Sample435


title: 200863770112_R03C01 Sample385

value: Male


title: 200863770112_R04C01 Sample386


title: Barri B

value: Barri


title: 3998998134_R03C01 Sample419

value: M


title: Grappolo A


title: Frantoio A


title: Jabali A


title: Barri A


title: Barnea B

value: Barnea


title: 200863770112_R02C01 Sample384


title: Arbequina B

value: Arbequina


title: 200863770112_R01C01 Sample383


title: 3998998134_R01C02 Sample417

value: FEP


title: 3998998134_R01C01 Sample416


title: 200863770098_R08C01 Sample382


title: Abou Salt Mohazam A

value: adult

value: Abou Salt Mohazam


title: Abou Kanani B

value: Abou Kanani


title: 200863770098_R07C01 Sample381


title: Abou Kanani A


title: Arbequina A


title: Abbadi Abou Gabra B

value: Abbadi Abou Gabra


title: 3998998134_R03C02 Sample420


title: Abou Salt Mohazam B

value: whole root tissue


title: 3998998114_R06C01 Sample414

value: CON


title: Barnea A


title: Abbadi Abou Gabra A


title: 3998998114_R05C02 Sample413

value: SCZ


title: 3998998134_R02C02 Sample418


title: 3998998114_R06C02 Sample415


title: 200863770098_R05C01 Sample380

value: Case


title: 200863770098_R03C01 Sample378

value: Female


title: 200863770098_R04C01 Sample379

value: Control


title: 3998998114_R04C02 Sample411

value: F


title: 3998998114_R05C01 Sample412


title: 200863770098_R02C01 Sample377

value: Male


title: 3998998114_R03C02 Sample410


title: 200863770098_R01C01 Sample376


title: 200889820120_R08C01 Sample375


title: 3998998114_R03C01 Sample409


title: 3998998114_R02C01 Sample407


title: 200889820120_R07C01 Sample374


title: NonCD7_Dim

city: Amsterdam

first: Manon

last: Wildenberg

address: Meibergdreef 9

department: Gastroenterology

country: Netherlands

institute: Amsterdam UMC

hyb_protocol: Fragmented cDNA was hybridized on human Clariom S HTassay platform following standard hybridisation protocol (Thermofisher)

scan_protocol: Gene Titan instrument

data_processing: Data were analysed using Affimetrix expression console, RMA as normalization method

label: Biotin

source_name: Mesentery, macrophage, CD11b Dim, NonIBD

label_protocol: Samples were labeled using 3′ IVT Pico Kit (Affymetrix) and RNA Amplification Kit (Nugene) according to manufacturer's protocols

extract_protocol: Bioline Isolate II RNA mini kit

treatment_protocol: Mesenteric resections specimes were digested using 1 mg/mL Collagenase D, 1 mg/mL soybean trypsin inhibitor and 50 ug/mL DNase I, grade II from bovine pancreas followed by mechanical dissociation using GentleMACS. Cells were isolated by flow cytometry.

value: macrophage

tag: cd11b population

value: Dim

tag: diagnosis

value: NonIBD


title: 200889820120_R06C01 Sample373


title: 3998998114_R02C02 Sample408


title: 3998998114_R01C02 Sample406


title: NonCD7_High

source_name: Mesentery, macrophage, CD11b High, NonIBD

value: High


title: 3998998114_R01C01 Sample405

value: M


title: NonCD5_High

source_name: Mesentery, macrophage, CD11b High, Ulcerative colitis

value: Ulcerative colitis


title: NonCD6_Dim


title: NonCD6_High


title: NonCD5_Dim

source_name: Mesentery, macrophage, CD11b Dim, Ulcerative colitis


title: CD4_High

source_name: Mesentery, macrophage, CD11b High, Crohn

value: Crohn's disease


title: NonCD4_Dim


title: CD5_High


title: 200889820120_R05C01 Sample372


title: 200889820120_R04C01 Sample371


title: CD5_Dim

source_name: Mesentery, macrophage, CD11b Dim, Crohn


title: CD4_Dim


title: CD3_High


title: NonCD3_Dim


title: NonCD4_High


title: 3998998093_R05C02 Sample404


title: 200889820120_R02C01 Sample370


title: 3998998093_R04C02 Sample403


title: 200889820119_R08C01 Sample369


title: CD2_High


title: NonCD2_Dim

source_name: Mesentery, macrophage, CD11b Dim, IBDU

value: IBDU


title: CD3_Dim


title: NonCD2_High

source_name: Mesentery, macrophage, CD11b High, IBDU


title: NonCD3_High


title: 200889820119_R07C01 Sample368


title: NonCD1_High


title: T403_S18

city: Atlanta

first: Steven

middle: Douglas

last: Knutson

state: GA

address: 1515 Dickey Drive

department: Chemistry

institute: Emory University

data_processing:
Trimmomatic v0.36 , java -Xmx8000m -jar /sw/eicc/Pkgs/Trimmomatic/0.36/trimmomatic-0.36.jar PE -phred33 -threads 30 $a"_R1_001.fastq.gz" $a"_R2_001.fastq.gz" trimmed_data/$a"_trimmo_R1.fastq.gz" trimmed_data/singletons/$a"_trimmo_R1_singletons.fastq.gz" trimmed_data/$a"_trimmo_R2.fastq.gz" trimmed_data/singletons/$a"_trimmo_R2_singletons.fastq.gz" HEADCROP:3
STAR v2.5.2 , --genomeDir $work_dir/index --readFilesIn $a"_L001_trimmo_R1.fastq.gz" $a"_L001_trimmo_R2.fastq.gz" --runThreadN 25 --readFilesCommand zcat --sjdbGTFfile $ref_annotation_dir/genes.gtf --outSAMtype BAM SortedByCoordinate --outFilterMatchNminOverLread 0.95 --outFileNamePrefix $work_dir/mapping/$a/
Samtools v1.3, samtools index $work_dir/mapping/$a/Aligned.sortedByCoord.out.bam
Picardtools v2.0.1, java -Xmx20g -jar /sw/eicc/Pkgs/picardtools/2.0.1/picard.jar MarkDuplicates  METRICS_FILE=$work_dir/mapping/$a/deleteme.metrics REMOVE_DUPLICATES=true ASSUME_SORTED=true VALIDATION_STRINGENCY=LENIENT INPUT=$work_dir/mapping/$a/Aligned.sortedByCoord.out.bam OUTPUT=$work_dir/mapping/$a/unique.bam
RNAEditingIndexer script: https://github.com/a2iEditing/RNAEditingIndexer
docker run -v /home/rarthur/projects/knutson/rnaeditingindexer/full_trimmed_data/bams:/data/bams:rw -v /home/rarthur/projects/knutson/rnaeditingindexer/full_trimmed_data/indexer_output:/data/output:rw eicc/rnaeditingindexer:2019 RNAEditingIndex -d /data/bams -f .bam -l /data/output/logs_dir -o /data/output/cmpileups -os /data/output/summary_dir --genome hg38 --stranded --paired_end
Genome_build: hg38, UCSC complete, downloaded Aug 2015

growth_protocol: HEK293T cells were grown and maintained  in T75 flasks with DMEM complete medium (10% FBS).

extract_protocol:
Total RNA isolated with Monarch Total RNA purification kit (NEB) followed by two rounds of oligo-dT purification.
SMARTer® Stranded Total RNA Sample Prep Kit - Low Input Mammalian 24 reactions, (Takara Bio); standard 8-bp i5 and i7 Illumina index barcodes and adapters were added to each library. Libraries were sequenced on the Illumina HiSeq 2500 following the manufacturer's protocols.

treatment_protocol: Transfection (lipofectamine 3000) with increasing amounts of ADAR1 plasmid (addgene # 117928)

tag: cell line

value: ADAR1 plasmid transfection (40 ug/T75)


title: T401_S16


title: 3998998093_R03C02 Sample401

tag: status

value: FEP


title: NonCD1_Dim


title: T402_S17


title: 3998998093_R04C01 Sample402

tag: gender


title: T103_S12

value: ADAR1 plasmid transfection (10 ug/T75)


title: 3998998093_R02C02 Sample399

value: SCZ

tag: ageatbloodcollection


title: T202_S14

value: ADAR1 plasmid transfection (20 ug/T75)


title: 200889820119_R06C01 Sample367

tag: phenotype

value: Case


title: T102_S11


title: T203_S15


title: 3998998093_R03C01 Sample400


title: CD1_High


title: T201_S13


title: 3998998093_R02C01 Sample398


title: T101_S10


title: T52_S8

value: ADAR1 plasmid transfection (5 ug/T75)


title: 200889820119_R03C01 Sample364

value: Control

tag: Sex


title: 3998998093_R01C02 Sample397


title: T51_S7


title: 3998998093_R01C01 Sample396

value: CON


title: WT1_S4


title: 200889820119_R02C01 Sample363

value: Male

tag: age


title: 200889820119_R05C01 Sample366


title: 200889820118_R08C01 Sample361


title: 3998998092_R06C02 Sample395


title: 200889820118_R07C01 Sample360

value: Female


title: 3998998092_R04C02 Sample393


title: 200889820118_R06C01 Sample359


title: WT3_S6


title: Sample42

city: Madison

first: Francisco

last: Peñagaricano

state: Wisconsin

address: 1675 Observatory Drive

department: Animal and Dairy Sciences

institute: University of Wisconsin-Madison

data_processing:
The quality of the sequencing reads was evaluated using FastQC software (version 0.11.7). Read trimming was performed using Trim Galore software (version 0.4.4).
Reads were mapped to the latest bovine reference genome (ARS-UCD1.2) using Hisat2 sofware (version 2.1.0).
The number of reads that mapped to each gene was obtained using the script htseq-count (mode intersection-nonempty).
Genome_build: Bovine genome assembly: (ARS-UCD1.2)
Supplementary_files_format_and_content: Tab-delimited text files including ensembl gene id and number of mapped reads

organism: Bos taurus

source_name: Endometrium

extract_protocol:
RNA extraction was performed using RNeasy Mini Kit (Qiagen, Valencia, CA). RNA concentration and quality were determined using Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA) and Qubit 2.0 Fluorometer (Thermo Fisher Scientific Inc, Waltham, MA). Bioanalyzer and Qubit RNA integrity numbers ranged between 5.6 and 8.7, and between 6.9 and 9.4, respectively.
All the RNA-sequencing procedures were performed by Novogene Bioinformatics Technology Co., Ltd (Beijing, China). Sequencing libraries were prepared using a Poly-A tail capture method and sequenced with NovaSeq 6000.

value: Endometrium

tag: breed

value: Angus x Brahman

tag: block

tag: pregnancy


title: Sample46

tag: tissue


title: Sample43


title: Sample45


title: Sample40


title: 200889820119_R01C01 Sample362


title: Sample36


title: WT2_S5

tag: treatment


title: Sample49


title: Sample35


title: T53_S9


title: 200889820118_R01C01 Sample356


title: Sample48


title: Sample34


title: 3998998092_R05C01 Sample394

value: M


title: Sample33


title: 3998998092_R02C01 Sample389


title: 3998998092_R03C01 Sample390


title: 3998998092_R01C02 Sample388


title: Sample31


title: Sample39


title: 200889820118_R05C01 Sample358


title: 3998998092_R01C01 Sample387

value: F


title: Sample37


title: Sample28


title: 3998998092_R03C02 Sample391


title: Sample29


title: 200889820079_R06C01 Sample353


title: 200889820118_R03C01 Sample357


title: 3998998088_R06C02 Sample386


title: Sample27


title: Sample26


title: 200889820079_R05C01 Sample352


title: 3998998088_R06C01 Sample385


title: 200889820079_R04C01 Sample351


title: Sample24


title: Sample23


title: 200889820079_R03C01 Sample350


title: 3998998088_R05C02 Sample384


title: Sample25


title: 3998998088_R05C01 Sample383


title: Sample22


title: Sample21


title: Sample20


title: Sample32


title: Sample18


title: 3998998088_R04C02 Sample382


title: 200889820079_R07C01 Sample354


title: Sample17


title: 200889820079_R01C01 Sample348


title: 200889820079_R02C01 Sample349


title: 200889820079_R08C01 Sample355


title: 200864580060_R08C01 Sample347


title: Sample30


title: 3998998088_R03C02 Sample380


title: Sample16


title: 200864580060_R07C01 Sample346


title: 3998998088_R03C01 Sample379


title: Sample13


title: Sample11


title: Sample12


title: 200889820119_R04C01 Sample365


title: Sample9


title: 3998998088_R02C02 Sample378


title: 3998998088_R02C01 Sample377


title: 200864580060_R06C01 Sample345


title: 200864580060_R05C01 Sample344


title: 200864580060_R04C01 Sample343


title: Sample8


title: Sample7


title: Sample6


title: Sample5


title: 3998998088_R01C02 Sample376


title: Sample3


title: Sample15


title: 3998998088_R04C01 Sample381


title: Sample4


title: Sample1


title: Sample2


title: 200864580035_R08C01 Sample341


title: 200864580060_R02C01 Sample342


title: Sample10


title: 200864580035_R05C01 Sample339


title: 3998998088_R01C01 Sample375


title: 3998998075_R06C02 Sample374


title: 200864580035_R06C01 Sample340


title: 3998998075_R06C01 Sample373


title: 200864580035_R04C01 Sample338


title: 3998998075_R05C02 Sample372


title: 3998998075_R05C01 Sample371


title: SOX15_cuttag rep3

city: Munster

first: Veeramohan

last: Veerapandian

state: North Rhine-Westphalia

address: Röntgenstr. 20

department: Department Tissue Morphogenesis

country: Germany

institute: Max Planck Institute for Molecular Biomedicine

library_source: genomic

data_processing:
fastqc
Read were aligned to hg38 using Bowtie2 (version 2.2.5) with the parameters --very-sensitive –end-to-end.
Bowtie2 SAM output files were converted to sorted BAM files using SAMtools. Multiple mapped reads were discarded.
Samtools was used to discard reads with mapping quality < 35
Peaks were called using MACS2 with options -g hs -f BAMPE --cutoff-analysis -B --call-summits
For each binding location, the read coverage for all libraries was calculated using the bedtools multicov function.
Genome_build: hg38
Supplementary_files_format_and_content: bigwig file were generated with genomeCoverageBed followed by bedGraphToBigWig.

source_name: Differentiating cells

growth_protocol: The Fy-hES-3 and all KO cell lines were cultured in feeder-free medium (CELLAPY, CA1001500,) on Matrigel (Corning, 354277). Cell media were changed daily and cells were passaged every 4 to 6 days using EDTA (CELLAPY, CA3001500). It was confirmed that the cells were not contaminated by mycoplasma with each passage.

extract_protocol:
The hESCs, 4i cells and EBs were washed once in PBS one time and dissociated into single cells with TrypLE Express enzyme or Trypsin. Then the dissociated cells were collected for next experiments.
In order to study the distribution of SOX15 in hPGCLC, we used NovoNGS ® CUT&Tag 2.0 High-Sensitivity Kit (N259-YH01, Novoprotein) to capture SOX15-binding sites. The experimental process was performed according to the manufacturer’s instructions. In brief, 1×105 day 4 SOX15-3×Flag-p2A-EGFP hPGCLC were prepared and immobilized on concanavalin A beads. Beads are incubated with a Flag primary antibody (F1804, Sigma), followed by incubation with a secondary antibody anti-Mouse IgG (ab6708, Abcam). Beads were washed and incubated with pA-Tn5. Tn5 was activated by addition of Mg2+ and incubated at 37°C for 1 h. Reactions were stopped by the addition of 10 µL 0.5M EDTA, 3 µL 10% SDS and 2.5 µL 20 mg/mL Proteinase K to each sample. DNA was extracted with phenol-chloroform and constructed CUT&Tag library according to the manufacturer’s instructions. Library was quantified by Equalbit dsDNA HS Assay Kit (Vazyme, EQ111-01) using Qubit™ 4 Fluorometer (Invitrogen, Q33226). Libraries were subjected to paired-end 150 bp sequencing on NovaSeq platform at Novogene.

treatment_protocol: hPGCLCs were generated from hESCs based on the protocol (Shino Mitsunag, 2017) with slight modifications. The hESCs on Matrigel were treated with TrypLETM Express enzyme to enable their dissociation into single cells. The 4i hESCs were induced by plating 7.0×104 hESCs per well of 12-well plate on mouse embryonic feeders (MEFs) in 4i medium containing KnockOut DMEM (ThermoFisher, 10829018), 20% Knockout Serum Replacement (ThermoFisher, 10828-028 or A3181501), 1% NEAA (ThermoFisher, 11140050), 1mM sodium pyruvate (ThermoFisher, 11360070), 1% Glutmax (ThermoFisher, 35050061), and 0.055mM 2-mercaptoethanol (ThermoFisher, 21985023), 20 ng/ml human LIF (Peprotech, 300-05-500), 8 ng/ml bFGF (SCI), 1 ng/ml TGF-β1 (Peprotech, 100-21), 3 mM CHIR99021 (TOCRIS, 4423), 1 mM PD0325901 (TOCRIS, 4192), 5 mM SB203580 (TOCRIS bioscience), and 5 mM SP600125 (TOCRIS). 10µM of a ROCK inhibitor (R&D, 1254/10) was used for 24 hr after the induction and then change the medium daily without ROCK inhibitor. After 4 days of induction, the cells were dissociated with TrypLE and plated into ultra-low cell attachment U-bottom 96-well plates (Corning, 7007) at a density of 3,500–4,000 cells/well in 100 µl hPGCLC medium. hPGCLC medium is composed of GMEM (ThermoFisher, 11710-035), 15% KSR, 1% NEAA, 1mM sodium pyruvate, 1% Glutmax, and 0.055mM 2-mercaptoethanol (all ThermoFisher), 300 ng/ml BMP4 (R&D Systems),100 ng/ml SCF (Peprotech, 300-07), 50 ng/ml EGF (R&D Systems), 100 ng/ml human LIF (Peprotech, 300-05-500) and 10 mM ROCK inhibitor. The medium was not changed until the EBs were used.

tag: cell type

value: Differentiating cells

tag: day of differentiation

tag: library strategy

value: ChIP-seq

tag: antibody

value: Flag

tag: assay kit details (vendor, catalog number, and lot# )

value: NovoNGS CUT&Tag 2.0 High-Sensitivity Kit (N259-YH01, Novoprotein)


title: 3998998075_R04C01 Sample370

value: FEP


title: SOX15_cuttag rep2


title: 200864580035_R03C01 Sample337


title: Sh2

city: China

first: Xiaoqin

last: Fan

state: Guangdong

address: Sungang West Road

department: Institute of Translational Medicine

institute: Shenzhen Second People's Hospital

description:
Gene expression data from stable transfect lentivirus YBX3 shRNA nasopharyngeal carcinoma cells
mRNA_Expression_ReadCount.txt

data_processing:
Illumina bcl2fastq 2.0 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence,  then mapped to hg38 whole genome using hisat2 v2.2.0.
Transcript abundance readcount values were obtained from gene-level count matrices were generated by Htseq v0.12.4, and FPKM values were generated by  StringTie v2.1.4.
Gene readcounts were normalized using geometric mean (GEO) in DESeq2 package and log2 transformed. Removal of unwanted variation (RUV) was used to remove batch effects.
Differential gene expression was performed on normalized gene counts use DESeq2.
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text file includes gene abundance(Readcounts and FPKM values) for each sample

source_name: nasopharyngeal carcinoma

growth_protocol: The mice were cultured at 37°C  in a humidified incubator with 5 % CO2

extract_protocol:
Total RNA was extracted from each cell sample using the Trizol method.
RNA-seq libraries were prepared using the NEBNext UltraTM RNA Library Preparation Kit for Illumina (NEB, USA) following manufacturer’s recommendations.

treatment_protocol: The 5-8F cells were plated onto 6 well plates and transfected with the YBX3-shRNAs or nontargeting control according to manufacturer‘s instruction of GenePharma.

value: nasopharyngeal carcinoma cells

value: stable transfect lentivirus YBX3 shRNA

tag: genotype

value: case


title: 200864580035_R02C01 Sample336


title: Sh3


title: Sh1


title: 3998998075_R03C02 Sample369

tag: status


title: NC3

description:
Gene expression data from stable transfect lentivirus non-tageting nasopharyngeal carcinoma cells.
mRNA_Expression_ReadCount.txt

value: stable transfect lentivirus non-tageting control

value: control


title: 3998998075_R02C01 Sample368

value: SCZ

tag: gender


title: 200864580008_R08C01 Sample334

value: Control


title: NC1


title: 3998998075_R01C02 Sample367

tag: ageatbloodcollection


title: D6SOX15-/-_clone3 rep2 (RNA-Seq)

data_processing:
fastqc
The human transcriptome index was generated by RSEM with bowtie 2 and then the raw reads were aligned to the transcriptome index
Per-gene read counts were calculated using RSEM GC normalized using EDAseq
Genes with mean read counts over all traits and replicates of less than 20 were discarded
DESeq2 for differential gene expression and WGCNA
Genome_build: hg38
Supplementary_files_format_and_content: text file

extract_protocol:
Total RNA was isolated with TRIzol
TruSeq Nano RNA sample prep kit (Illumina) was used for library constructions.

tag: day of reprogramming


title: D6SOX15-/-_clone3 rep1 (RNA-Seq)


title: D6SOX15-/- rep3 (RNA-Seq)


title: 3998998049_R06C02 Sample366


title: 200864580008_R07C01 Sample333

tag: phenotype

tag: Sex

value: Female


title: 200864580008_R06C01 Sample332

value: Case

tag: age


title: D6SOX15-/- rep1 (RNA-Seq)


title: D6SOX15-/- rep2 (RNA-Seq)


title: D4SOX15-/- rep3 (RNA-Seq)


title: SOX15_cuttag rep1


title: 3998998049_R06C01 Sample365


title: D4SOX15-/- rep2 (RNA-Seq)


title: 3998998049_R05C01 Sample363


title: 3998998049_R05C02 Sample364


title: 200864580008_R03C01 Sample330

value: Male


title: D2SOX15-/- rep3 (RNA-Seq)


title: D4SOX15-/- rep1 (RNA-Seq)


title: D2SOX15-/- rep2 (RNA-Seq)


title: NC2


title: 200864580008_R01C01 Sample329


title: D2SOX15-/- rep1 (RNA-Seq)


title: 200864580008_R05C01 Sample331


title: 3998998049_R04C01 Sample361

value: CON


title: hESC_SOX15-/- rep2 (RNA-Seq)

source_name: ESC primed

value: ESC primed

value: day -4


title: hESC_SOX15-/- rep3 (RNA-Seq)


title: hESC_SOX15-/- rep1 (RNA-Seq)


title: 200864580071_R07C01 Sample327

source_name: Whole Blood


title: D6N rep2 (RNA-Seq)

value: Differentiating cells

value: wt


title: D4N rep2 (RNA-Seq)


title: 3998998049_R03C02 Sample360

value: M


title: 200864580071_R05C01 Sample326


title: D4N rep1 (RNA-Seq)


title: D6N rep1 (RNA-Seq)


title: 3998998049_R03C01 Sample359


title: D2N rep1 (RNA-Seq)


title: 3998998049_R01C01 Sample358

value: FEP


title: 200864580071_R08C01 Sample328


title: 3998998049_R04C02 Sample362


title: 200864580071_R03C01 Sample324


title: D2N rep2 (RNA-Seq)


title: 200864580035_R01C01 Sample335


title: 3998998026_R06C02 Sample357


title: D4SP rep1 (RNA-Seq)


title: D4SP rep2 (RNA-Seq)


title: D6DP rep1 (RNA-Seq)


title: 3998998026_R05C02 Sample355


title: 200864580071_R02C01 Sample323


title: 3998998026_R05C01 Sample354


title: 200864580066_R08C01 Sample321


title: D4DP rep2 (RNA-Seq)


title: 3998998026_R06C01 Sample356


title: D4DP rep1 (RNA-Seq)


title: D2DP rep2 (RNA-Seq)


title: 200864580066_R07C01 Sample320


title: 3998998026_R04C02 Sample353

value: F


title: D1 rep2 (RNA-Seq)

source_name: ESC naïve

value: ESC naive


title: D2DP rep1 (RNA-Seq)


title: 200864580071_R01C01 Sample322


title: D1 rep1 (RNA-Seq)


title: 200864580066_R06C01 Sample319


title: D0 (4i) rep2 (RNA-Seq)


title: D0 (4i) rep1 (RNA-Seq)


title: 3998998026_R04C01 Sample352


title: hESC rep2 (RNA-Seq)


title: 200864580066_R05C01 Sample318


title: D6DP rep2 (RNA-Seq)


title: 3998998026_R03C02 Sample351


title: hESC rep1 (RNA-Seq)


title: 3998998026_R03C01 Sample350


title: 200864580071_R04C01 Sample325


title: D6SOX15-/- rep2

description:
SOX15KO.D6.comb.chrpeak_peaks.narrowPeak
SOX15KO.D6.comb.bw

extract_protocol:
TruePrep DNA Library Prep Kit V2 Illumina (Vazyme, TD501 & TD202)
The hESCs, 4i cells and EBs were washed once in PBS one time and dissociated into single cells with TrypLE Express enzyme or Trypsin. Then the dissociated cells were collected for next experiments.
ATAC-seq was performed by using TruePrep DNA Library Prep Kit V2 for Illumina (Vazyme, TD501&TD202) according to the manufacturer’s recommendations. The details of the operation are listed. Different stages of cells according to human primordial germ cells like cells in vitro induction system were collected in PBS(2%BSA) and spun at 500 g at 4°C for 10 min. The pellet was resuspended in 50 μl lysis buffer and incubated at 4 °C for 15 min and then spun at 500 g at 4°C for 5 min. The supernatants were removed by carefully pipetting away from the pellets. For the transposition reaction, 10 μl 5X TTBL buffer, 5μl TTE Mix V50 were combined and added to each pellet up to 50 μl. The samples were incubatedat 37°C for 30 min followed by immediate purification using Beckman Beads according to the manufacturer’s specification, except for the final elution volume, which was 24 μl. The PCR was set up in a 50 μl reaction volume using 24 μl of transposed DNA, 10 μl of 5x TAB, 5 μl PPM and 5 μl P5 and P7 primers TruePrepTM Index Kit V2 for Illumina® (Vazyme, TD202). PCR parameters were: 72 °C for 5 min, 98 °C for 30 s and 15 cycles of 98 °C for 10 s, 60 °C for 30 s and 72 °C for 30 s. The libraries were purified using a QIAGEN MinElute PCR purification kit (QIAGEN,Cat#28004) followed by Agencourt AMPure XP beads (Beckman Coulter, A63880) according to the manufacturer’s recommendations. Library fragments ranging from 200 to 700 bp were enriched and the final elution volume was 30 μl. Libraries were sequenced pair-end 150bp sequencing on an Illumina HiseqXten at Novogene in Beijing (http://www.novogene.com/tech/service/seq/product/).

tag: cell line


title: 200864580066_R04C01 Sample317


title: 200864580066_R02C01 Sample316


title: D6SOX15-/- rep1


title: D4SOX15-/- rep2

description:
SOX15KO.D4.comb.chrpeak_peaks.narrowPeak
SOX15KO.D4.comb.bw


title: D4SOX15-/- rep1


title: D2SOX15-/- rep2

description:
SOX15KO.D2.comb.chrpeak_peaks.narrowPeak
SOX15KO.D2.comb.bw


title: 3998998026_R02C02 Sample349


title: 200864580066_R01C01 Sample315


title: 200864580064_R08C01 Sample314


title: 3998998026_R01C02 Sample347


title: 3998998026_R02C01 Sample348


title: 3998998092_R04C01 Sample392


title: 3998998026_R01C01 Sample346


title: D4N rep1

description:
Day4.N.comb.chrpeak_peaks.narrowPeak
Day4.N.comb.bw


title: D6N rep2

description:
Day6.N.comb.chrpeak_peaks.narrowPeak
Day6.N.comb.bw


title: 200864580064_R07C01 Sample313


title: D2SOX15-/- rep1


title: D4N rep2


title: 200864580064_R06C01 Sample312


title: 3998998025_R06C02 Sample345


title: 200864580064_R04C01 Sample310


title: D4SP rep2

description:
Day4.SP.comb.chrpeak_peaks.narrowPeak
Day4.SP.comb.bw


title: 200864580064_R05C01 Sample311


title: D2N rep1

description:
Day2.N.comb.chrpeak_peaks.narrowPeak
Day2.N.comb.bw


title: D4DP rep1

description:
Day4.DP.comb.chrpeak_peaks.narrowPeak
Day4.DP.comb.bw


title: D4SP rep1


title: D4DP rep2


title: D6DP rep1

description:
Day6.DP.comb.chrpeak_peaks.narrowPeak
Day6.DP.comb.bw


title: D6DP rep2


title: 3998998025_R04C02 Sample341


title: 200864580064_R02C01 Sample308


title: 3998998025_R05C02 Sample343


title: 200864580064_R01C01 Sample307


title: D2DP rep2

description:
Day2.DP.comb.chrpeak_peaks.narrowPeak
Day2.DP.comb.bw


title: D6N rep1


title: 3998998025_R04C01 Sample340


title: 200864580063_R08C01 Sample306


title: D1 rep1

description:
Day1.comb.chrpeak_peaks.narrowPeak
Day1.comb.bw


title: 3998998025_R06C01 Sample344


title: D1 rep2


title: D0 (4i) rep2

description:
hES.4i.comb.chrpeak_peaks.narrowPeak
hES.4i.comb.bw


title: D0 (4i) rep1


title: 200864580063_R07C01 Sample305


title: 200864580064_R03C01 Sample309


title: hESC rep2

description:
hES.primed.comb.chrpeak_peaks.narrowPeak
hES.primed.comb.bw

value: day -3


title: 3998998025_R02C01 Sample338


title: 200864580063_R06C01 Sample304


title: hESC rep1


title: 3998998025_R05C01 Sample342


title: fve-8-sRNA-repeat1

city: college station

first: Di

last: Sun

state: TX

institute: TAMU

data_processing:
Sequenced reads were mapped to genome by tophat2 to generate bam files
bam files were sorted by samtools
sorted bam files were count by Htseq-count.
use edgeR to get normalized reads
Genome_build: TAIR_10
Supplementary_files_format_and_content: txt files containing normalized reads of all genes.

organism: Arabidopsis thaliana

source_name: whole seedlings

growth_protocol: seedlings were sterilized with 10% bleach for 20 min. After 4 times wash with water, seedlings were sown on MS medium and grow for 5-days under mid light condition.

extract_protocol:
RNA was harvested by Trizol reagent.
RNA-seq library was prepared with TruSeq Stranded Total RNA kit (Illumina) according to the manufacturer’s manual. sRNA-seq libarary was prepared according to D. Sun, Z. Ma, J. Zhu, X. Zhang, in Arabidopsis Protocols. (Springer, 2021), pp. 225-254..

treatment_protocol: no treatment

value: whole seedlings

tag: development stage

tag: ecotype

value: Ler


title: 10008538014_R06C02 Sample337

value: SCZ


title: fve-8-sRNA-repeat2

tag: tissue


title: 200864580063_R04C01 Sample303

value: Control


title: 10008538014_R06C01 Sample336


title: WT-sRNA-repeat1


title: D2DP rep1

tag: cell type


title: 10008538014_R05C02 Sample335


title: 200864580063_R03C01 Sample302


title: fve-8-RNA-repeat2


title: fve-8-RNA-repeat1


title: fve-8-RNA-repeat3


title: WT-RNA-repeat3


title: 200864580063_R02C01 Sample301

value: Female


title: 10008538014_R05C01 Sample334


title: 200864580063_R01C01 Sample300


title: 10008538014_R04C02 Sample333


title: WT-RNA-repeat2


title: WT-RNA-repeat1


title: 200864580061_R08C01 Sample299


title: P4_RNA_cKO_3

city: st. louis

first: Naveen

last: Reddy

state: MO

address: 660 S Euclid Ave

institute: Washington University In St. Louis

data_processing:
ChIP-seq reads were aligned to the mm10 and hg38 genome assemblies using Bowtie2
Data were filtered using a map quality score of >10
Peaks were called using MACS2 on each dataset. Bandwidth = 200; q-value 0.05
RNA-seq reads were aligned to mm10 genome assembly using RNA STAR 2.6
Genome_build: mm10, hg38
Supplementary_files_format_and_content: Text or excel workbooks containing raw read counts or CPM, histone enrichment, or fold change

source_name: Anterior Mouse Cerebellum

growth_protocol: Brain tissue was taken from CHD7 conditional knockout and control mice maintained under standard housing conditions.

extract_protocol:
RNA was extracted from the anterior cerebella of P4 mice using Trizol (Invitrogen) according to the manufacturer’s instructions. ChIP lysates clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.
Libraries were prepared according to Illumina's instructions.

value: Anterior Mouse Cerebellum

value: CHD7 cKO

value: pooled male and female

tag: strain

tag: chip antibody

value: None (RNA-seq)


title: P4_RNA_cKO_5


title: P4_RNA_cKO_4


title: 10008538014_R03C02 Sample332

value: CON


title: 3998998025_R02C02 Sample339


title: 200864580061_R06C01 Sample297

value: Male


title: P4_RNA_cKO_2


title: P4_RNA_cKO_1


title: 10008538014_R02C02 Sample331


title: 200864580061_R07C01 Sample298


title: WT-sRNA-repeat2


title: 10008538014_R01C02 Sample330


title: P4_RNA_Ctrl_5

value: CHD7 Ctrl


title: 10008538014_R01C01 Sample329


title: 200864580061_R05C01 Sample296

value: Case


title: P4_RNA_Ctrl_4


title: 200864580061_R03C01 Sample295


title: KO_KPC_cells_IL-6_rep2

city: Suita

first: Daisuke

last: Okuzaki

state: Osaka

address: Yamadaoka 3-1

department: Immunology Frontier Research Center

country: Japan

institute: Osaka univ.

description: KO KPC cells with IL-6 stimulation for 48 h

data_processing:
Sequencing was performed on an Illumina HiSeq 2500 platform in a 75-base single-end mode.
Illumina Casava1.8.2 software was used for base calling.
The sequenced reads were mapped to the mouse reference genome sequences (mm10) using TopHat version 2.0.13 in combination with Bowtie2 version 2.2.3 and SAMtools version 0.1.19.
The fragments per kilobase of exon per million mapped fragments (FPKMs) were calculated using Cufflinks version 2.2.1.
Genome_build: mm10
Supplementary_files_format_and_content: FPKM processed value in csv file

extract_protocol:
Total RNAs were extracted using RNeasy Mini kit (Qiagen) according to the  manufacturer’s instructions.
Library preparation was performed using a TruSeq stranded mRNA sample prep kit (Illumina, San Diego, CA) according to the manufacturer’s instructions.

value: KPC (LSL-KrasG12D/+; LSL-Trp53R172H/+; Pdx-1-Cre) cells

value: Arid5a gene-knockout (KO) KPC mice


title: WT_KPC_cells_IL-6_rep2

description: WT KPC cells with IL-6 stimulation for 48 h

value: KPC mice


title: KO_KPC_cells_IL-6_rep1

source_name: KO KPC cells with IL-6 stimulation for 48 h


title: WT_KPC_cells_IL-6_rep1

source_name: WT KPC cells with IL-6 stimulation for 48 h


title: 10007688014_R06C02 Sample328

value: M


title: P4_RNA_Ctrl_3


title: 10007688014_R06C01 Sample327

value: F


title: 200864580061_R02C01 Sample294


title: KO_KPC cells_rep2

description: KO KPC cells without IL-6 stimulation for 48 h


title: 200864580061_R01C01 Sample293


title: D2N rep2

value: Differentiating cells

tag: day of differentiation

value: wt

tag: antibody


title: 200864580045_R08C01 Sample292


title: 10007688014_R05C01 Sample325

value: SCZ


title: WT_KPC cells_rep1

description: WT KPC cells without IL-6 stimulation for 48 h


title: KO_KPC cells_rep1

source_name: KO KPC cells without IL-6 stimulation for 48 h


title: KO_MC38_cells_rep1

description: Arid5a gene-knockout (KO) MC38 cells

source_name: Arid5a gene-knockout (KO) MC38 cells

value: CRC mouse model MC38, in which derived tumors show increased infiltration of immunosuppressive cells, such as MDSCs, and excluding T cells (Mariathasan et al., 2018, Mosely et al., 2017)

value: Arid5a-deficient MC38 cells


title: 200864580045_R07C01 Sample291

value: Control

value: Female


title: WT_MC38_cells_rep2

description: WT MC38 cells

source_name: WT MC38 cells

value: MC38 cells


title: 10007688014_R04C02 Sample324

value: FEP


title: 10007688014_R05C02 Sample326


title: 200864580045_R04C01 Sample289

value: Male


title: KO_MC38_cells_rep2

description: Arid5a gene-knockout (KO) MC38 cells


title: 10007688014_R04C01 Sample323


title: WT_MC38_cells_rep1

description: WT MC38 cells


title: WT_KPC cells_rep2

source_name: WT KPC cells without IL-6 stimulation for 48 h


title: 200864580045_R03C01 Sample288


title: 200864580045_R06C01 Sample290


title: 10007688014_R03C02 Sample322

value: CON


title: 200864580045_R02C01 Sample287

value: Case


title: 10007688014_R02C01 Sample319


title: 10007688014_R02C02 Sample320


title: A [miRNA]

city: hefei

first: lu

last: zong

state: anhui

address: lujiang road

institute: Anhui Provincal Hospital

data_processing:
the Solexa CHASTITY quanlity filtered reads were harvested as Clean Reads. The adaptor sequences were trimmed and the adaptor-trimmed-reads (>= 15nt) were left.
miRDeep2 software was used to predict the novel miRNAs with these trimmed reads. Then, the trimmed reads were aligned to merged pre-miRNA databases (known pre-miRNA from miRBase v21 plus the newly predicted pre-miRNAs) using Novoalign software (v2.07.11) with at most one mismatch.
Reads (counts < 2) were discarded when calculating the miRNA expression. In order to characterize the isomiR variability, sequences that matched the miRNA precursors in the mature miRNAs region ±4 nt (no more than 1 mismatch) were accepted as mature miRNA isomiRs, which were grouped according to the 5-prime (5p) or 3-prime (3p) arm of the precursor hairpin. The numbers of mapped tags that were defined as the raw expression levels of that miRNA. To correct for the difference in tag counts between samples, the tag counts were scaled to TPM (the copy number of transcripts per million) based on the total number of tag aligned.
Choosing a different isomiR sequence for measuring miRNA expression can affect the ability to detect differential miRNA expression. We use the most abundant isomiR, the mature miRNA annotated in miRBase and all isoforms of miRNA(5p or 3p) to calculate the miRNAs expression.When comparing the differentially expressed miRNA profiles between two groups, fold change and p-value were calculated and used to identify significant differentially expressed miRNAs (Based on ALL_Isoform value). Differentially expressed miRNAs between two samples were filtered through Fold change (Based on ALL_Isoform value).
Genome_build: Hg19
Supplementary_files_format_and_content: tab-delimited text files include TagCount_ALL_Isoform for each Sample
Supplementary_files_format_and_content: Matrix table with TagCount_ALL_Isoform for every miRNA and every sample

source_name: thin endometrium

extract_protocol:
Total RNA of each sample was used to prepare the miRNA sequencing library.
size selection of ~135-155 bp PCR amplified fragments (corresponding to ~15-35 nt small RNAs).   The libraries were denatured as single-stranded DNA molecules, captured on Illumina flow cells, amplified in situ as clusters and finally sequenced for 50 cycles on Illumina NextSeq per the manufacturer's instructions.

value: thin endometrium


title: N [miRNA]

source_name: adjacent normal endometrium

value: adjacent normal endometrium


title: 10007688014_R01C02 Sample318


title: 11w_CT_Ex1

city: Kyoto

first: Yasuhiro

last: Takashima

address: 53 Kawahara-cho, Shogoin, Sakyo-ku

institute: Kyoto University

data_processing:
Basecalls were performed using bcl2fastq v2.17.1.14.
Low quality bases and adapters in sequenced reads were trimmed with cutadapt-1.16
The sequenced reads were mapped to the hg38 human reference genome using hisat2 (version 2.1.0) with the human GENCODE (version 30) annotation gtf file.
The uniquely mapped reads were summarized at gene level using HTSeq-count v0.11.2
Genome_build: hg38
Supplementary_files_format_and_content: The tab-delimited text file include counted values for each gene in each sample.

source_name: Cytotrophoblast at 11 gestational weeks_1

growth_protocol: Primed human PSCs were maintained on MEF under DMEM/F12 with 20% KSR, 1% NEAA, 4 ng/ml bFGF and 0.1 uM 2-ME. Naïve human PSCs were maintained on MEF with t2iLGo medium, which consists of N2B27 (Ndiff227) with 1 uM PD0325901, 1 uM CHIR99021, 10 ng/ml hLIF and 3 uM Go6983. For nTE(D1, D2, D3) induction, Naïve PSCs were seeded on Laminin-E8. The initial induction medium was composed Ndiff227, 2uM A83-01u, 2uM PD0325901, 10 ng/ml recombinant human BMP4. The following day, medium was changed to Ndiff277, 2uM A83-01, 2uM PD0325901, 1 ug/ml JAK inhibitor I (Merck). The medium was changed next day. nCT were induced by ACE medium (Ndiff227, 1uM A83-01, 2uM CHIR99021, and 50 ng/ml EGF) for 12 days. nCT can be maintained in ACE medium more than 30 passages. nST and nEVT were induced by 2uM forskolin, and , 7.5 uM A83-01/100 ng/ml NRG1. pBAP cells were induced in 10 ng/ml BMP4, 1uM A83-01, and 0.1uM PD173074. CT30 trophoblast stem cells were cultured in 0.5 uM A83-01, 2uM CHIR99021, 50ng/ml EGF, 1 μM SB431542 (Tocris), 0.8 uM VPA, 5 uM Y-27632 by Okae et al (2018 Cell stem Cell).

extract_protocol:
Total RNA was extracted using miRNeasy Mini Kit (QIAGEN)
To generate RNA-seq libraries, Truseq Stranded mRNA LT sample prep kit (Illumina) was used according to the supplier’s instruction.

value: Cytotrophoblast

tag: Stage

value: 11 gestational weeks


title: 200864580044_R06C01 Sample284

extract_protocol: DNA was extracted using a phenol/chloroform method


title: 9w_CT_Ex1

source_name: Cytotrophoblast at 9 gestational weeks_1

value: 9 gestational weeks


title: 10007688014_R01C01 Sample317

tag: status

value: M


title: 200864580044_R05C01 Sample283


title: 7w_CT_Ex2

source_name: Cytotrophoblast at 7 gestational weeks_2

value: 7 gestational weeks


title: 10006044018_R06C01 Sample316

tag: gender

value: F


title: 7w_CT_Ex1

source_name: Cytotrophoblast at 7 gestational weeks_1


title: Y-320 treated replicate 3 [Y1_3]

city: Vancouver

first: Stephane

last: Flibotte

state: BC

address: 2370-6270 University Blvd.

department: Faculty of Science

country: Canada

institute: University of British Columbia

data_processing:
For each sample, counts per transcript were obtained with kallisto version 0.46.1 using the human reference transcriptome GRCh38 downloaded from ensembl on February 22nd 2019.
Counts from various isoforns were then summed up with a perl script to obtain the number of counts for each gene and sample.
Genome_build: hg38
Supplementary_files_format_and_content: Matrix of counts for each gene and sample in a tab-delimited text file (see supplementary file kallisto_gene_counts.txt).

source_name: HDQ-P1_Y-320 treated

growth_protocol: HDQ-P1 cells were cultured in high glucose DMEM supplemented with 10% (vol/vol) fetal bovine serum (FBS) and 1% antibiotic-antimycotic (Gibco/Thermo Fisher Scientific).

extract_protocol:
RNA was extracted using RNeasy kit (Qiagen) following the manufacturer’s protocol. Total RNA quality and concentration was assessed using an Agilent 2100 Bioanalyzer (Agilent).
Libraries for RNA-seq were generated using the Illumina Neoprep System and sequenced using the Illumina Nextseq 500.

treatment_protocol: Three samples were treated with 1 µM Y-320 for 48 hours.

tag: treatment

value: 1 µM Y-320 for 48 hours


title: Y-320 treated replicate 2 [Y1_2]


title: 200864580044_R02C01 Sample281

data_processing: Data was imported using the R package methylumi methylumIDAT function. Data was then pre-processed in the R package wateRmelon using the pfilter and dasen functions.

source_name: Whole Blood


title: 200864580044_R03C01 Sample282


title: 10006044018_R05C01 Sample314

tag: ageatbloodcollection


title: Untreated replicate 3 [UnT_3]

value: untreated


title: 10007688014_R03C01 Sample321


title: Untreated replicate 2 [UnT_2]


title: 10006044018_R04C01 Sample313


title: 200864580044_R01C01 Sample280

tag: phenotype

value: Control


title: Untreated replicate 1 [UnT_1]


title: 200864580045_R01C01 Sample286

tag: Sex


title: 200864580044_R08C01 Sample285

value: Female

tag: age


title: 10006044018_R02C02 Sample311

value: SCZ


title: 10006044018_R02C01 Sample310


title: 200864580036_R04C01 Sample276


title: 10006044018_R01C02 Sample309


title: 10006044018_R01C01 Sample308

value: FEP


title: 200864580036_R02C01 Sample274

value: Male


title: 10006044018_R05C02 Sample315


title: Y-320 treated replicate 1 [Y1_1]

tag: cell line


title: pBAP_D2_Ex2

description:
19_P_D2_Ex2
processed data file: gene_counts.txt

data_processing:
Basecalls were performed using bcl2fastq v2.17.1.14.
Low quality bases and adapters in sequenced reads were trimmed with cutadapt-1.16.
The sequenced reads were mapped to the hg38 human reference genome using hisat2 (version 2.1.0) with the human GENCODE (version 30) annotation gtf file.
The uniquely mapped reads were summarized at gene level using HTSeq-count v0.11.2.
Genome_build: hg38
Supplementary_files_format_and_content: gene_counts.txt: The tab-delimited text file includes counted values for each gene in each sample.

source_name: pBAP_D2 from Primed H9 (hESCs)_2

extract_protocol:
Total RNA was extracted using miRNeasy Mini Kit (QIAGEN).
To generate RNA-seq libraries, TruSeq Stranded mRNA LT sample prep kit (Illumina) was used according to the supplier’s instruction.

value: H9 ESCs

value: BAP treatment day2

tag: analysis method

value: RNA-seq


title: pBAP_D2_Ex1

description:
19_P_D2_Ex1
processed data file: gene_counts.txt

source_name: pBAP_D2 from Primed H9 (hESCs)_1


title: 200864580036_R01C01 Sample273

value: Case


title: 200864580030_R08C01 Sample272


title: pBAP_D1_Ex2

description:
18_P_D1_Ex2
processed data file: gene_counts.txt

source_name: pBAP_D1 from Primed H9 (hESCs)_2

value: BAP treatment day1


title: pBAP_D1_Ex1

description:
18_P_D1_Ex1
processed data file: gene_counts.txt

source_name: pBAP_D1 from Primed H9 (hESCs)_1


title: 10006044017_R06C02 Sample307


title: 200864580036_R08C01 Sample279


title: 10006044017_R06C01 Sample306


title: 10006044017_R05C02 Sample305

value: CON


title: 200864580030_R07C01 Sample271


title: 200864580036_R06C01 Sample278


title: Primed_Ex2

description:
17_Primed_Ex2
processed data file: gene_counts.txt

source_name: Primed H9 (hESCs)_2

value: primed human PSCs


title: 10006044018_R03C02 Sample312


title: 200864580036_R05C01 Sample277


title: Primed_Ex1

description:
17_Primed_Ex1
processed data file: gene_counts.txt

source_name: Primed H9 (hESCs)_1


title: nEVT_Ex1

description:
16_N_EVT_Ex1
processed data file: gene_counts.txt

source_name: nEVT from Naïve H9_Ex1

value: A83_Neuregulin treatment


title: 10006044017_R04C02 Sample304


title: nEVT_Ex2

description:
16_N_EVT_Ex2
processed data file: gene_counts.txt

source_name: nEVT from Naïve H9_Ex2


title: 10006044017_R04C01 Sample303


title: pBAP_D3_Ex2

description:
20_P_D3_Ex2
processed data file: gene_counts.txt

source_name: pBAP_D3 from Primed H9 (hESCs)_2

value: BAP treatment day3


title: 200864580030_R06C01 Sample270


title: 200864580036_R03C01 Sample275


title: nST_Ex1

description:
14_N_ST_Ex1
processed data file: gene_counts.txt

source_name: nST from Naïve H9_Ex1

value: Forskolin treatment


title: pBAP_D3_Ex1

description:
20_P_D3_Ex1
processed data file: gene_counts.txt

source_name: pBAP_D3 from Primed H9 (hESCs)_1


title: 10006044017_R03C02 Sample302

value: M


title: CT30_Ex2

description:
10_CT30_Ex2
processed data file: gene_counts.txt

source_name: Placenta-derived trophoblast stem cellsCT30_Ex2

value: Okae et al. Cell Stem Cell 2018


title: DS41_muAs_huNeu-2 [RNA-seq]

city: Houston

first: Brittney

last: Lozzi

address: 1 Baylor Plaza

department: Cell & Gene Therapy

institute: Baylor College of Medicine

description:
DS41_muAs_huNeu-2
coculture_FPKM.csv

data_processing:
Quality control was performed on fastq files using fastQC and multiQC. Paired end reads were mapped to the mouse genome (mm10) using STAR (v2.5.0a). Co-cultured samples were aligned and filtered using Sargasso.
Reads Per Million (RPM) were calculated using GenomicAlignments (v1.16.0) and DESeq2 (v1.20.0) was used for read count normalization and differential gene expression for mES_astrocytes. Transcript abundance estimation (fpkm) values were determined using cufflinks for co-cultured samples.
Genome_build: mm10 (GRCm38), hg38 (GRCh38)
Supplementary_files_format_and_content: *.csv: Comma-separated text files include CPM and FPKM values from ES_astrocytes.

organism:
Homo sapiens
Mus musculus

source_name: mES_astrocyte with iNeuron

growth_protocol: The mES_astrocyte cultures were generated from mouse embryonic stem cells grown on feeder layers for 1-2 days, following which the cells were grown as neurospheres to induce formation of neural stem cells for 1 week. These were further differentiated in DMEM/F12 media supplemented with N2/B27 and growth factors EGF/FGF2 to generate astrocytes from 2-10 weeks. All RNA-Seq studies was performed from day7-day35 cultures.

extract_protocol:
Spheres were washed with PBS and frozen with Trizol. RNA was isolated using Trizol and chloroform and purified using the RNeasy Mini Kit (QIAGEN).
Illumina sequencing libraries were constructed from 300-500ng of total RNA using the TruSeq Stranded mRNA Library preparation kit (Illumina).

treatment_protocol: In triplicate, mES_astrocytes were treated with neuroactive chemicals for 30 minutes before harvesting for RNA isolation.

value: stem cell induced astrocyte and neuron

tag: time point

value: 35 days


title: 200864580030_R03C01 Sample267

city: Exeter

first: Jonathan

institute: University of Exeter


title: 10006044017_R03C01 Sample301


title: DS58_muAs_huNeu-1 [RNA-seq]

description:
DS58_muAs_huNeu-1
coculture_FPKM.csv


title: CT30_Ex1

description:
10_CT30_Ex1
processed data file: gene_counts.txt

source_name: Placenta-derived trophoblast stem cells_CT30_Ex1


title: iPS_nCT_P16_Ex2

description:
09_N_iPS_CT_P16_Ex2
processed data file: gene_counts.txt

source_name: nCT_P15 from 409B2 iPSC (hESCs)_2

value: 409B2 iPSCs

value: ACE treatment


title: 10006044017_R02C02 Sample300


title: 200864580030_R02C01 Sample266

value: Control

value: Male


title: 10006044017_R02C01 Sample299

value: SCZ

value: F


title: 200864580030_R01C01 Sample265

value: Female


title: nTE_D3

data_processing:
The 10X Genomics Cell Ranger pipeline (version 5.0.1) was used to perform sample demultiplexing, alignment to the hg38 human reference genome (refdata-gex-GRCh38-2020-A, 10x Genomics), barcode/UMI processing, and gene counting for each cell.
Genome_build: hg38
Supplementary_files_format_and_content: tsv files contain lists of genes and barcodes for each sample, mtx files count gene UMI couns for each sample

source_name: nTE_D3 from Naïve H9 (hESCs)

growth_protocol: To induce nTE_D2 and _D3, naïve pluripotent stem cells were seeded on Laminin511-E8 and cultured in Ndiff227, 2uM A83-01, 2uM PD0325901, 10 ng/ml recombinant human BMP4. Medium was changed to Ndiff277, 2uM A83-01, 2uM PD0325901, 1 ug/ml JAK inhibitor I (Merck) on day 1. TACSTD2 positive cells were collected on day 2 and day 3. TACSTD2 and ENPEP double positive cells were sorted on day 3 and recultured in ACE medium (Ndiff227, 1uM A83-01, 2uM CHIR99021, and 50 ng/ml EGF). Recultured cells were collected on day 5 and day 10.

extract_protocol:
Cultured cells were dissociated with Accutase. Single cells were collected using a BD FACSAria II (BD Biosciences). nTE_D2 and nTE_D3 samples were purified with TACSTD2 antibody. For scRNAseq, single cell suspensions of all samples were resuspended in PBS-1% BSA at 1000cells/μL and barcoded with a 10x Chromium Controller (10x Genomics).
Sequencing libraries were constructed with reagents from a Chromium Single Cell 3' Reagent Kits v3.1 (10x Genomics). Sequencing was performed with Illumina HiSeq 4000.

value: H9 ESCs

value: ABPJ treatment

value: 3 days


title: nCT_D5

source_name: nCT_D5 from Naïve H9 (hESCs)

value: 5 days


title: nCT_D10

source_name: nCT_D10 from Naïve H9 (hESCs)

value: 10 days


title: iPS_nCT_P16_Ex1

description:
09_N_iPS_CT_P16_Ex1
processed data file: gene_counts.txt

source_name: nCT_P15 from 409B2 iPSC (hESCs)_1

value: RNA-seq


title: nST_Ex2

description:
14_N_ST_Ex2
processed data file: gene_counts.txt

source_name: nST from Naïve H9_Ex2

value: Forskolin treatment


title: cR_nCT_P15_Ex2

description:
08_N_cR_CT_P15_Ex2
processed data file: gene_counts.txt

source_name: cR_nCT_P15 from Naïve H9 (hESCs)_2


title: cR_nCT_P15_Ex1

description:
08_N_cR_CT_P15_Ex1
processed data file: gene_counts.txt

source_name: cR_nCT_P15 from Naïve H9 (hESCs)_1


title: nTE_D2

source_name: nTE_D2 from Naïve H9 (hESCs)

value: 2 days


title: 200864580025_R08C01 Sample264

source_name: Whole Blood


title: 10006044016_R06C02 Sample297

value: FEP


title: nCT_P15_Ex2

description:
07_N_CT_P15_Ex2
processed data file: gene_counts.txt

source_name: nCT_P15 from Naïve H9 (hESCs)_2


title: T98G_HSP90_inhib_replicate_6

city: Munich

first: Kristian

last: Unger

address: Marchioninistr. 15

department: Department of radiation oncology

institute: LMU University Hospital

data_processing:
Trimming of adapter sequences using BBDUK k=13 ktrim=r useshortkmers=t mink=5 qtrim=r trimq=10 minlength=20.
Alignment of sequences using STAR against GRCh38.93 --runThreadN 8 --outFilterType BySJout --outFilterMultimapNmax 20 --alignSJoverhangMin 8 --alignSJDBoverhangMin 1 --outFilterMismatchNmax 999 --readFilesCommand zcat --outFilterMismatchNoverLmax 0.1 --alignIntronMin 20 --alignIntronMax 1000000 --alignMatesGapMax 1000000 --outSAMattributes NH HI NM MD --outSAMtype BAM SortedByCoordinate --outFileNamePrefix
Counting of reads at gene level using htseq -m intersection-nonempty -s yes -f bam -r pos using Homo_sapiens.GRCh38.93.gtf
Genome_build: hg38 (GRCh38)
Supplementary_files_format_and_content: *.htseqcount.txt: HTSeq raw counts files.

source_name: glioblastoma

growth_protocol: LN229 and T98G cells were cultivated in Dulbecco’s Modified Eagle medium (DMEM), supplemented with 10% heat-inactivated fetal calf serum, 100 U/ml penicillin, and 0.1 mg/ml streptomycin (all from ThermoScientific, Schwerte, Germany) at 37°C and 7.5% CO2.

extract_protocol:
Upon stimulation, RNA was extracted by using the NucleoSpin RNA II extraction kit (Macherey & Nagel, Dueren, Germany).
RNA libraries were prepared for sequencing using the Lexogen Quantseq 3`-RNAseq library preparation kit according to the manufacturer's protocol.

treatment_protocol: Cells were treated with 10 nM of the HSP90 inhibitor NW457 or the vehicle control for 24 h.

value: Glioblastoma cell line

value: HSP90 inhibitor


title: 10006044016_R06C01 Sample296

last: Mill

address: RILD Building, RD&E Hospital


title: T98G_HSP90_inhib_replicate_5


title: 200864580030_R04C01 Sample268


title: nCT_P15_Ex1

description:
07_N_CT_P15_Ex1
processed data file: gene_counts.txt

source_name: nCT_P15 from Naïve H9 (hESCs)_1

value: ACE treatment


title: T98G_HSP90_inhib_replicate_3


title: 10006044016_R05C01 Sample294

value: CON


title: nCT_P10_Ex2

description:
06_N_CT_P10_Ex2
processed data file: gene_counts.txt

source_name: nCT_P10 from Naïve H9 (hESCs)_2


title: 200864580025_R06C01 Sample262

value: Control


title: 10006044016_R05C02 Sample295

value: M


title: 200864580025_R02C01 Sample260


title: 10006044017_R01C02 Sample298

value: SCZ


title: 200864580025_R01C01 Sample259

value: Case

value: Male


title: 10006044016_R04C02 Sample293

value: F


title: 10006044016_R04C01 Sample292


title: T98G_HSP90_inhib_replicate_1


title: 200864580002_R08C01 Sample258

value: Female


title: nCT_P3_Ex2

description:
05_N_CT_P3_Ex2
processed data file: gene_counts.txt

source_name: nCT_P3 from Naïve H9 (hESCs)_2

value: H9 ESCs


title: nCT_P10_Ex1

description:
06_N_CT_P10_Ex1
processed data file: gene_counts.txt

source_name: nCT_P10 from Naïve H9 (hESCs)_1


title: 10006044016_R03C02 Sample291


title: T98G_control_replicate_6

value: Untreated


title: 200864580025_R07C01 Sample263


title: 200864580002_R07C01 Sample257


title: 10006044016_R03C01 Sample290


title: nTE_D3_Ex2

description:
04_N_D3_Ex2
processed data file: gene_counts.txt

source_name: nTE_D3 from Naïve H9 (hESCs)_2

value: ABPJ treatment for 3 day

value: RNA-seq


title: T98G_control_replicate_5


title: T98G_control_replicate_4


title: 200864580002_R05C01 Sample256


title: nTE_D3_Ex1

description:
04_N_D3_Ex1
processed data file: gene_counts.txt

source_name: nTE_D3 from Naïve H9 (hESCs)_1


title: 10006044016_R02C02 Sample289


title: 200864580002_R03C01 Sample255


title: T98G_control_replicate_3


title: T98G_HSP90_inhib_replicate_2


title: 200864580002_R02C01 Sample254


title: 10006044016_R01C02 Sample287


title: nTE_D2_Ex1

description:
03_N_D2_Ex1
processed data file: gene_counts.txt

source_name: nTE_D2 from Naïve H9 (hESCs)_1

value: ABPJ treatment for 2 day


title: T98G_control_replicate_2


title: nTE_D2_Ex2

description:
03_N_D2_Ex2
processed data file: gene_counts.txt

source_name: nTE_D2 from Naïve H9 (hESCs)_2


title: T98G_control_replicate_1


title: 10006044016_R01C01 Sample286

value: FEP


title: 200864580001_R08C01 Sample252


title: LN229_HSP90_inhib_replicate_6

value: Glioblastoma cell line


title: 200864580002_R01C01 Sample253


title: nTE_D1_Ex1

description:
02_N_D1_Ex1
processed data file: gene_counts.txt

source_name: nTE_D1 from Naïve H9 (hESCs)_1

value: ABPJ treatment for 1 day


title: 10005839173_R06C02 Sample285


title: Naive_Ex2

description:
01_Naive_Ex2
processed data file: gene_counts.txt

source_name: Naïve H9 (hESCs)_2

value: Naive human PSCs


title: LN229_HSP90_inhib_replicate_5

value: HSP90 inhibitor


title: LN229_HSP90_inhib_replicate_4


title: 200864580001_R06C01 Sample250


title: Naive_Ex1

description:
01_Naive_Ex1
processed data file: gene_counts.txt

source_name: Naïve H9 (hESCs)_1


title: 10005839173_R05C02 Sample284


title: 200864580001_R04C01 Sample249

value: Control


title: 10005839173_R05C01 Sample283

value: M


title: 10006044016_R02C01 Sample288

value: SCZ


title: LN229_HSP90_inhib_replicate_3


title: 200864580025_R05C01 Sample261


title: 10005839173_R04C01 Sample282

value: CON


title: LN229_HSP90_inhib_replicate_2


title: 200864580001_R03C01 Sample248

value: Case

value: Male


title: 10005839173_R03C02 Sample281


title: WAT, Obese T2D, SNS_001_S1

city: Trieste

first: Silvano

last: Piazza

address: localita' Padriciano 99

country: Italy

institute: ICGEB

description:
White adipose tissue from a subject in Obese T2D condition
N25_SNS_001_S1

data_processing:
Basecalls performed using CASAVA (Illumina Inc.)
Transcript quantification was conducted with STAR (v2.5.3a)  (assigned to a gene using using the STAR function “quantMode GeneCounts”) mapped to the human genome version GRCh38 and with reference annotation.
Read counts generated by STAR were analysed by using DESeq2 package (Love, 2014) for detecting genes that were differentially expressed. An adjusted p-value cut off of 0.05 was decided as threshold for detection of DEGs.
Genome_build: human genome version GRCh38 and with reference annotation.
Supplementary_files_format_and_content: tab-delimited text files include COUNTS values for each Sample

source_name: White adipose tissue

extract_protocol:
Total RNA was obtained from adipose tissue biopsies by the guanidinium–thiocyanate extraction method. Quality of RNA was evaluated using Tapestation 2200 (Agilent).
Library preparation was performed using TruSeq Stranded Total RNA Sample Preparation Kit with Ribo-Zero Gold (Illumina), with an input amount of RNA between 156 - 650ng. The TruSeq Stranded Total RNA Sample Preparation Guide (15031048 Rev. E) was followed with the following modifications; 13 PCR cycles (650ng of input RNA) or 14 PCR cycles (with input RNA lower than 650ng).
RNA-Seq on a NextSeq500 instrument (Illumina) with Nextseq500 Kit High Output V2 reagent (Illumina), read length 2*75, and loading concentration 1,45pM.

tag: tissue

value: White adipose tissue

tag: condition

value: Obese T2D


title: WAT, Obese T2D, RTL_029_S23

description:
White adipose tissue from a subject in Obese T2D condition
N24_RTL_029_S23


title: nTE_D1_Ex2

description:
02_N_D1_Ex2
processed data file: gene_counts.txt

source_name: nTE_D1 from Naïve H9 (hESCs)_2

value: H9 ESCs


title: nCT_P3_Ex1

description:
05_N_CT_P3_Ex1
processed data file: gene_counts.txt

source_name: nCT_P3 from Naïve H9 (hESCs)_1

value: ACE treatment


title: 200864580001_R02C01 Sample247

source_name: Whole Blood


title: 10005839173_R03C01 Sample280


title: LN229_control_replicate_5

tag: cell type

value: Untreated


title: LN229_HSP90_inhib_replicate_1


title: 10005839173_R02C02 Sample279

value: F


title: 200864580001_R01C01 Sample246

value: Female


title: WAT, Obese NGT, OFJ_015_S16

description:
White adipose tissue from a subject in Obese NGT condition
N22_OFJ_015_S16

value: Obese NGT


title: 200863770119_R08C01 Sample245


title: 200863770119_R06C01 Sample244


title: LN229_control_replicate_3

value: Glioblastoma cell line


title: 10005839173_R01C02 Sample278


title: WAT, Obese NGT, MTZ_012_S15

description:
White adipose tissue from a subject in Obese NGT condition
N20_MTZ_012_S15


title: 10005839173_R01C01 Sample277

value: FEP


title: 200863770119_R05C01 Sample243


title: LN229_control_replicate_2


title: 10005839172_R06C02 Sample276


title: WAT, Lean, MLS_027_S13

description:
White adipose tissue from a subject in Lean condition
N19_MLS_027_S13

value: Lean


title: 200863770119_R04C01 Sample242


title: WAT, Obese NGT, MES_018_S17

description:
White adipose tissue from a subject in Obese NGT condition
N18_MES_018_S17


title: 10005839172_R06C01 Sample275


title: LN229_control_replicate_1


title: WAT, Obese NGT, LSD_030_S21

description:
White adipose tissue from a subject in Obese NGT condition
N17_LSD_030_S21


title: 2012_P1_POOR [RNA-seq]

city: New York

first: Nicholas

last: Brady

state: NY

address: 1188 York Ave

department: Pathology and Laboratory Medicine

institute: Weill Cornell Medicine

data_processing:
Quality control of raw sequencing reads was performed using FastQC
Low-quality reads were removed using Trimmomatic with a sliding window of 4bp and quality threshold of 20
Reads passing QC were aligned to mm10 using STAR
BAM file creation, sorting, and indexing were performed using SAMtools
Transcript abundances in FPKM were caluculated using Cufflinks
Genome_build: mm10
Supplementary_files_format_and_content: Transcript abundances in FPKM calculated using Cufflinks in comma-separated values (CSV) format

source_name: Mouse tumor

extract_protocol:
RNA extraction from GEM prostate tumors was performed using the Maxwell 16 LEV simplyRNA Tissue Kit (Promega, AS1280). Regions of the cryopreserved tumor samples that were identified by a blinded pathologist were excised with a biopsy punch and processed as described.
Libraries were generated using the TruSeq RNA Library Prep Kit [Non-stranded, polyA+] (Illumina) following the manufacturer's recommended protocol.

tag: genotype

value: PbCre/+; Pten f/f; NMYC/+; Rb1 f/f

value: 24 weeks

value: Mouse tumor

value: Castrated

tag: pathology

value: Poorly Differentiated


title: 200863770119_R02C01 Sample240

value: Control


title: 200863770119_R03C01 Sample241

value: Male


title: WAT, Lean, PVF_011_S24

description:
White adipose tissue from a subject in Lean condition
N23_PVF_011_S24

value: White adipose tissue

value: M


title: LN229_control_replicate_4

source_name: glioblastoma


title: 10005839172_R05C02 Sample274

value: SCZ


title: 1968_P1_SQ [RNA-seq]

value: 21 weeks

value: Squamous


title: 200863770119_R01C01 Sample239

value: Case

value: Female


title: WAT, Obese T2D, OEM_007_S5

description:
White adipose tissue from a subject in Obese T2D condition
N21_OEM_007_S5

value: Obese T2D


title: WAT, Lean, KNS_017_S10

description:
White adipose tissue from a subject in Lean condition
N15_KNS_017_S10

value: F


title: WAT, Obese T2D, LAS_003_S3

description:
White adipose tissue from a subject in Obese T2D condition
N16_LAS_003_S3


title: 10005839172_R04C02 Sample272

value: FEP


title: 10005839172_R05C01 Sample273

value: CON


title: 200864580001_R07C01 Sample251


title: 2012_P1_OST_POOR [RNA-seq]

value: PbCre/+; Pten f/f; NMYC/+; Rb1 f/f

value: 24 weeks

value: Osteoid/Poorly Differentiated


title: 10005839172_R04C01 Sample271


title: 200864580030_R05C01 Sample269


title: 200863770118_R07C01 Sample237


title: 200863770118_R08C01 Sample238


title: WAT, Obese NGT, JPS_033_S22

description:
White adipose tissue from a subject in Obese NGT condition
N14_JPS_033_S22

value: Obese NGT


title: WAT, Obese T2D, JNJ_009_S6

description:
White adipose tissue from a subject in Obese T2D condition
N13_JNJ_009_S6


title: 2211_P3_POOR [RNA-seq]

value: PbCre/+; Pten f/+; NMYC/NMYC; Rb1 f/f

value: 19 weeks

value: Mouse tumor

value: Intact

value: Poorly Differentiated


title: 10005839172_R03C01 Sample269

value: M


title: 10005839172_R03C02 Sample270


title: 2211_P1_NEPC [RNA-seq]

value: Neuroendocrine


title: 200863770118_R05C01 Sample235

value: Case

value: Male


title: 2418-2_P4_SQ [RNA-seq]

value: PbCre/+; Pten f/f; NMYC/NMYC; Rb1 f/f

value: 13 weeks

value: Squamous


title: WAT, Lean, IRO_032_S14

description:
White adipose tissue from a subject in Lean condition
N12_IRO_032_S14

value: White adipose tissue

value: Lean

value: F


title: 2012_P1_SQ [RNA-seq]

value: PbCre/+; Pten f/f; NMYC/+; Rb1 f/f

value: 24 weeks

value: Castrated


title: 10005839172_R02C01 Sample268

value: CON


title: 2418-2_P2_POOR_NE [RNA-seq]

value: Mouse tumor

value: Poorly Differentiated/Neuroendocrine


title: 10005839172_R01C02 Sample267

value: FEP


title: WAT, Obese T2D, GLO_004_S4

description:
White adipose tissue from a subject in Obese T2D condition
N10_GLO_004_S4

value: Obese T2D


title: 200863770118_R03C01 Sample234

value: Control


title: WAT, Lean, HSQ_006_S8

description:
White adipose tissue from a subject in Lean condition
N11_HSQ_006_S8

value: M


title: 10005839172_R01C01 Sample266

value: SCZ


title: 2418-2_P1_POOR [RNA-seq]

value: PbCre/+; Pten f/f; NMYC/NMYC; Rb1 f/f

value: Intact

value: Poorly Differentiated


title: 200863770118_R02C01 Sample233

value: Case

value: Male


title: 200863770118_R01C01 Sample232


title: WAT, Lean, EAO_022_S12

description:
White adipose tissue from a subject in Lean condition
N9_EAO_022_S12

value: White adipose tissue

value: Lean

value: F


title: 2266-2_P1_CONV [RNA-seq]

value: 12 weeks

value: Conventional


title: 10005839164_R06C02 Sample265


title: WAT, Obese T2D, CAJ_002_S2

description:
White adipose tissue from a subject in Obese T2D condition
N8_CAJ_002_S2


title: 2266-2_P1_POOR [RNA-seq]

value: Mouse tumor


title: 200863770111_R08C01 Sample231

value: Female


title: 10005839164_R06C01 Sample264

value: CON


title: WAT, Lean, BHN_016_S9

description:
White adipose tissue from a subject in Lean condition
N7_BHN_016_S9


title: 2404_P1_CONV [RNA-seq]

value: PbCre/+; Pten f/f; NMYC/NMYC; Rb1 +/+

value: 8 weeks


title: 200863770118_R06C01 Sample236


title: 10005839164_R05C01 Sample263

value: FEP

value: M


title: 200863770111_R06C01 Sample229


title: 2128_P1_CONV [RNA-seq]

value: 16 weeks


title: 10005839164_R04C02 Sample262

value: SCZ


title: 1845_P1_CONV [RNA-seq]

value: PbCre/+; Pten f/f; NMYC/+; Rb1 f/+

value: Intact


title: 10005839164_R04C01 Sample261


title: WAT, Lean, AEP_021_S11

description:
White adipose tissue from a subject in Lean condition
N5_AEP_021_S11


title: WAT, Lean, AEA_031_S25

description:
White adipose tissue from a subject in Lean condition
N4_AEA_031_S25


title: 10005839164_R03C02 Sample260


title: 200863770111_R02C01 Sample226

value: Case

value: Male


title: WAT, Obese NGT, AAN_023_S19

description:
White adipose tissue from a subject in Obese NGT condition
N3_AAN_023_S19

value: White adipose tissue

value: Obese NGT


title: 1803_P1_SQ [RNA-seq]

value: PbCre/+; Pten f/f; NMYC/NMYC ; Rb1 f/f

value: Squamous


title: 1806_P1_CONV [RNA-seq]

value: Mouse tumor

value: Conventional


title: 200863770111_R03C01 Sample227

value: Control


title: 10005839164_R03C01 Sample259


title: 1803_P1_POOR [RNA-seq]

value: Poorly Differentiated


title: 10005839164_R02C02 Sample258


title: 200863770111_R01C01 Sample225


title: WAT, Obese NGT, AAB_024_S20

description:
White adipose tissue from a subject in Obese NGT condition
N1_AAB_024_S20

value: F


title: 200863770100_R08C01 Sample224


title: 10005839164_R02C01 Sample257


title: 1803_P1_MOD [RNA-seq]

value: Moderately Differentiated


title: WAT, Obese T2D, AIK_026_S7

description:
White adipose tissue from a subject in Obese T2D condition
N6_AIK_026_S7

value: Obese T2D


title: 200863770111_R07C01 Sample230


title: 200863770100_R07C01 Sample223


title: 1715_P2_SQ_CONV [RNA-seq]

value: PbCre/+ ; Pten f/f; NMYC/+; Rb1 f/+

value: 17 weeks

value: Squamous/Convetional


title: TT_72h_rep1

city: Göttingen

first: Jinmi

last: Choi

address: Am Fassberg 11

department: Molecular Biology

institute: Max Planck Institute for Biophysical Chemistry

description: 4sU-labeled RNA

data_processing:
Library strategy: TT-seq (Schwalb et al., 2016)
Sequencing data preprocessing. Paired-end reads with additional 6 base reads of barcodes were obtained for each of the samples. Reads from TT-seq/RNA-seq or ChIP-seq/ATAC-seq were demultiplexed and mapped with STAR 2.3.0 (Dobin et al., 2013) or Bowtie2.2.5/Bowtie1.0.0 (Langmead and Salzberg, 2012), respectively, to the hg20/hg38 (GRCh38) genome assembly (Human Genome Reference Consortium). For ATAC-seq, chromosome M was removed. Samtools (Li et al., 2009) was used to quality filter SAM files, whereby alignments with MAPQ smaller than 7 (-q 7) were skipped and only proper pairs (-f99, -f147, -f83, -f 163) were selected. Further data processing was carried out using the R/Bioconductor environment.
For ChIP-seq , we used the 'callpeak' function of MACS2.1.1 (Zhang et al., 2008) with ‘--BAMPE’ options. To catalogue all the C/EBPα, BRD4 or H3K4me1 binding sites over all the time points, we merged and reduced all peaks, and removed those falling +/- 4Mb of centromeric heterochromatin regions. Duplicates were removed. To obtain the enriched signal (count matrix), read count within the merged peaks were normalized by library size followed by a normalization with counts in corresponding input.
For ATAC-seq, reads were aligned to GRCh38 genome assembly without mitochondrial chromosome (ChrM) using Bowtie1.0.0 (Langmead et al., 2009). Bigwig files were generated by Deeptools 2.3.4 .
For TT-seq, we used a spike-in (RNAs) as described in (Schwalb et al., 2016) to allow antisense bias determination (ratio of spurious reads originating from the opposite strand introduced by the RT reactions) in TT-seq signal. Read counts for all spike-ins necessary to that end were calculated using HTSeq (Anders et al., 2015).
For Total RNA-seq, reads were aligned to GRCh38 genome assembly with STAR2.4.2 ((Dobin et al., 2013).
Genome_build: hg20/hg38 (GRCh38) genome assembly (Human Genome Reference Consortium http://hgdownload.soe.ucsc.edu/downloads.html#human)
Supplementary_files_format_and_content: BRD4allPeaks_reduced.txt:Merged BRD4 peaks from all the time points.; BRD4mat.txt: BRD4 count table for genomic coordinates in BRD4allPeaks_reduced.txt, normalized with size factors and input
Supplementary_files_format_and_content: CEBPallPeaks_reduced.txt:Merged CEBPa peaks from all the time points; CEBPmat.txt: CEBP coverage normalized to size factors and input on the genomic coordinates in CEBPallPeaks_reduced.txt
Supplementary_files_format_and_content: H3K4me1allpeaks_reduced.txt:Merged H3K4me1 peaks from all the time points; H3K4me1mat.txt: H3K4me1 coverage normalized to size factors and input on the genomic coordinates in H3K4me1allPeaks_reduced.txt
Supplementary_files_format_and_content: The bigwig files of ATAC-seq were generated by deepTools2.3.4 (Ramirez et al., 2016) using --normalizeSizefactors1X options.
Supplementary_files_format_and_content: Strand specific bigwig files of TT-seq and RNA-seq were generated by deepTools2.3.4 (Ramirez et al., 2016) using --normalizeSizefactors1X --filterRNAstrand options.

source_name: BLaER

extract_protocol:
ChIP-seq: At each time point, 3x10^7 cells were harvested and fixed with 1% of formaldehyde for 8 minutes (Thermo Scientific, 28908). Formaldehyde was quenched with 0.2M glycine for 5 min. Chromatin was sheared to 200-500 bp in size using the Covaris S220 ultrasonicator (16min for C/EBPα and BRD4, 18min for H3K4me1). A fraction of the resulting chromatin was used as input control. Sheared chromatin (50ug for C/EBPα and BRD4, 30ul for H3K4me1) was incubated with 5 ug of antibodies - anti-C/EBPα (Santa Cruz, sc-61), anti-H3K4me1 (abcam, ab8895), anti-BRD4 (Bethyl Laboratories, A301–985A100)- bound to protein-A beads (Life Technologies, 9999-01). Samples were incubated at 65ºC overnight to reverse the crosslinks, followed by RNase and proteinase K treatments.
ATAC-seq: ATAC-seq was performed as described (Buenrostro et al., 2013). Briefly, 5 x 10^4 cells were harvested and treated with Nextera Tn5 Transposase (Illumina, FC-121-1030) for 45 min at 37°C.
Total RNA-seq: Total RNA was extracted from the cells labelled with 0.5mM 4-thiouridine (4sU, Carbosynth, 13957-31-8) for 5 min. RNA prepared using QIAzol according to the manufacturer’s instructions was fragmented to 1500 – 5000 bp in size using Covaris S220 Ultrasonicator before the library preparation.
At each time point, 1-2.2 x 10^8 cells were labeled with 0.5mM 4-thiouridine (4sU, Carbosynth, 13957-31-8) for 5 min and harvested by centrifuging at 500g for 2 min. Harvested pellets were lysed with QIAzol (Qiagen, 79306). Following addition of 5ng of spike-in mix per 1 x 10^8 cells, total RNA was purified using QIAzol (Qiagen, 79306) according to the manufacturer’s instructions. Total RNA (300ug) was fragmented to 1500 – 5000 bp in size using Covaris S220 Ultrasonicator. Newly synthesized RNAs were purified as described (Schwalb et al., 2016) with the following modifications. After streptavidin pull down, the resulting RNA was purified with RNeasy Micro Kit (Qiagen, 74004), together with DNase treatment (Qiagen, 79254).
ChIP-seq: NEB Ultra DNA Library kit (NEB, E7370S) ; ATAC-seq:Nextera Tn5 Transposase ((Illumina, FC-121-1030)) 1x NEBNext High-Fidelity 2x PCR Master Mix (NEB, M0541S) ; Total RNA-seq and TT-seq Ovation Universal RNA-seq System (Nugen, 0343)

value: RCH-ACV stably expressing estrogen inducible C/EBPa

value: Beta-estradiol (100nM) treatment 24h + 5 min 4sU labeling


title: 200863770111_R05C01 Sample228

value: Female


title: 1715_P2_POOR [RNA-seq]

value: Intact


title: 10005839164_R01C01 Sample255

value: CON

value: M


title: 10005839164_R01C02 Sample256

value: FEP


title: 200863770100_R06C01 Sample222

value: Case

value: Male


title: TT_72h_rep2

description: 4sU-labeled RNA

value: Ovation Universal RNA-seq System (Nugen, 0343)

value: Beta-estradiol (100nM) treatment 24h+ 5 min 4sU labeling


title: TT_36h_rep2

description: 4sU-labeled RNA

value: Beta-estradiol (100nM) treatment 12h + 5 min 4sU labeling


title: 200863770100_R05C01 Sample221


title: 1640_P3_MOD_POOR [RNA-seq]

value: 32 weeks

value: Mouse tumor

value: Moderate/Poorly Differentiated


title: 200863770100_R04C01 Sample220


title: 10005839158_R06C02 Sample254

value: SCZ

value: F


title: WAT, Obese NGT, AAM_019_S18

description:
White adipose tissue from a subject in Obese NGT condition
N2_AAM_019_S18

value: White adipose tissue

value: Obese NGT


title: 200863770100_R03C01 Sample219

value: Control


title: 1640_P1_CONV [RNA-seq]

value: PbCre/+ ; Pten f/f; NMYC/+; Rb1 f/+

value: Intact

value: Conventional


title: 1560_P3_POOR [RNA-seq]

value: Poorly Differentiated


title: 10005839158_R05C02 Sample252

value: FEP


title: TT_30h_rep1

description: 4sU-labeled RNA

value: RCH-ACV stably expressing estrogen inducible C/EBPa

value: Beta-estradiol (100nM) treatment 0h + 5 min 4sU labeling


title: 10005839158_R04C02 Sample251

value: M


title: 200863770100_R01C01 Sample217

value: Female