title: -P/-N_6h_root_rep3

city: Tsukuba

first: Hinako

last: Takehisa

address: 2-1-2 Kannondai

country: Japan

institute: National Institute of Agrobiological Sciences (NIAS)

description: Gene expression of rice root at 6 h after both phosphorus and nitrogen deficiency treatments

hyb_protocol: 1,650 ng Cy3-labeled cRNA was fragmented and hybridized on a slide of rice 4x44K microarray RAP-DB (Agilent; G2519F#15241) at 65℃ for 17 hours. Hybridization and washing of the hybridized slide were performed according to the manufacture’s instruction.

scan_protocol: Slides were scanned on an Agilent G2505C DNA microarray scanner.

data_processing: The scanned images were analyzed with Feature Extraction Software 11.5.1.1 (Agilent) using default parameters to obtain background subtracted and spatially detrended processed signal intensities. The processed signal intensities were used for 75th percentile normalization and log2 transformation with R

organism: Oryza sativa Japonica Group

source_name: Phosphorus and nitrogen deficiencies, 6h, root, replicate3

label_protocol: One-color spike-mix was added to the total RNA prior to the labeling reaction and labeling was performed using a Quick Amp Labeling Kit, One-Color (Agilent Technologies) in the presence of cyanine-3 (Cy3)-CTP according to the modified manufacturer’s protocol. The cyanine-3-labeled cRNA was purified by RNeasy Mini Kit (Qiagen) and the cRNA yield was determined using the NanoDrop ND-1000 UV-VIS spectrophotomer (NanoDrop).

growth_protocol: Rice seeds were sterilized with 70% (v/v) ethanol solution and 1% (v/v) sodium hypochlorite solution, imbibed in distilled water in the dark at 28°C for 2 days, and transferred onto a nylon net floated in distilled water in a growth chamber (60% humidity; 14.5 h light period at 28°C and 9.5 h dark period at 23°C). After 3 days of germination, the seedlings were transferred in Yoshida nutrient solution (5-fold dilution, pH 5.5) and allowed to grow for another 4 days. The pH of the nutrient solution was adjusted using 1N NaOH and maintained using MES (buffer). The solution was renewed every 2 days.

extract_protocol: Total RNA was extracted from the each sample with a RNeasy Plant Mini kit (QIAGEN) according to the manufacturer’s protocol. The quantity and quality of the obtained RNAs were checked with Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA, USA).

treatment_protocol: The 7-day old seedlings were exposed to -P treatment (NaH2PO4・2H2O-free) for 5 days, and followed by -P/-N treatment (NaH2PO4・2H2O and NH4NO3-free) and  -P treatment (NaH2PO4・2H2O-free), respectively. Shoot and root samples were collected at 6 h after the treatments.

value: Nipponbare

tag: tissue

value: Root

tag: treatment

value: Phosphorus and nitrogen deficiencies

tag: time


title: BEAS2B: V600E_2

status: Public on Oct 06 2019

type: SRA

city: Clevleand

first: Mohamed

middle: E.

last: Abazeed

state: OH

department: Radiation Oncology/Translational Hematology Oncology Research

country: USA

institute: Cleveland Clinic

description: replicate 2

library_source: transcriptomic

data_processing:
Reads were aligned to a genome assembly using STAR and aligned reads were assigned.
Gene read counts were normalized within sample, averaged for replicates and log transformed.
Genome_build: hg19

molecule: total RNA

organism: Homo sapiens

growth_protocol: BEAS2B cells were grown in advanced DMEM-F12 media (ThermoFisher, MA) supplemented with 1% fetal bovine serum and 100 U/mL Penicillin, 100 g/mL of Streptomycin,  292 g/mL L-Glutamine and 1% HEPES. All cultures were maintained at 37o C in a humidified 5% CO2 atmosphere and tested to ensure absence of Mycoplasma.  Cultures were partitioned before >80% confluencey.

extract_protocol:
RNA was isolated using the Rneasy Plus Mini Kit.
Samples were checked using BioA and libraries were prepared using the TruSeq Stranded mRNA kit. Each library was quantified using Qubit and then pooled toether. Library pool was quantified using qPCR. Pool was then diluted to 4 nM and loaded on the HiSeq High Output Mode. Run was performed using a full flow cell (8 lanes) PE 100. 5% PhiX was spiked in to check run qaulity.

tag: cell line

tag: cell type

value: immortalized bronchial epitheial cells

tag: passages


title: S305_P06_LCP56

city: Bethesda

first: Xin

middle: Wei

last: Wang

state: MARYLAND

address: 37 Convent Drive

department: Laboratory of Human Carcinogenesis

institute: National Cancer Institute

description: Set 2 (Illumina HiSeq 4000)

data_processing: Basecalling performed by RTA version 2.4.11. Demultiplexing performed by Bcl2fastq version 2.17. Alignment, tagging, gene and transcript counting performed CellRanger version 2.2.0. Aggregation performed by CellRanger version 3.0.2. Genome_build: GRCh38. Supplementary_files_format_and_content: 1) cell barcodes (barcodes.tsv) 2) genes (genes.tsv), 3) count matrix (matrix.mtx), and 4) sample information (samples.txt).

source_name: Primary liver cancer single-cell

extract_protocol: Libraries were prepared according to 10x Genomics Single Cell 3′ v2 Reagent Kit user guide. Briefly, the samples were washed and re-suspended in PBS + 0.04% BSA. Sample viability was assessed and a final concentration of 1,200 cells/µl of sample was adjusted. The cDNAs was obtained after the GEM generation and barcoding, followed by GEM RT reaction and cleanup steps. Purified cDNA was amplified for 14 cycles before being cleaned up using SPRIselect beads (Beckman). Samples were then run on a Bioanalyzer (Agilent Technologies) to determine cDNA concentration. cDNA libraries were prepared as recommended by 10x Genomics V2 user guide with appropriate modifications to the PCR cycles based on the calculated cDNA concentration. For samples preparation on the 10x Genomics platform, the Chromium Single Cell 3′ Library and Gel Bead Kit v2 (PN-120237), Chromium Single Cell 3′ Chip kit v2 (PN-120236) and Chromium i7 Multiplex Kit (PN-120262) were used.

tag: cancer type

value: Intrahepatic cholangiocarcinoma

tag: cell number


title: -P 6h_root_rep3

type: RNA

description: Gene expression of rice root at 6 h after phosphorus deficiency treatment

source_name: Phosphorus deficiency, 6h, root, replicate3

tag: cultivar

value: Phosphorus deficiency


title: -P 6h_root_rep1

source_name: Phosphorus deficiency, 6h, root, replicate1


title: -P 6h_root_rep2

source_name: Phosphorus deficiency, 6h, root, replicate2


title: -P_6h_shoot_rep3

description: Gene expression of rice shoot at 6 h after phosphorus deficiency treatment

source_name: Phosphorus deficiency, 6h, shoot, replicate3

value: Shoot


title: -P/-N_6h_root_rep2

source_name: Phosphorus and nitrogen deficiencies, 6h, root, replicate2


title: Rhode Island Red-RIR40

status: Public on Oct 07 2019

type: genomic

city: Beijing

first: Changsheng

last: Nie

address: Yuanmingyuan road 2#

department: Animal Genetics and Breeding

country: China

institute: China Agricultural University

hyb_protocol: DNA was restriction digested, PCR amplified, fragmented, labeled and hybridized to each array according to the manufacturer's instructions.

scan_protocol: The Arrays were then washed using Affymetrix fluidics stations, and scanned using the Gene Chip Scanner 3000.

data_processing:
The array image was acquired using Affymetrix Operating Software (AxAS version 4.0.1).
Genotype Call (SNP call): A/T/C/G

label: biotin

molecule: genomic DNA

organism: Gallus gallus

source_name: Rhode Island Red

label_protocol: As per manufacturer (Affymetrix)

growth_protocol: chickens were grown according to standard conditions.

extract_protocol: Genomic DNA was extracted from peripheral blood using the Qiagen DNA Blood Mini Kit. DNA quality and quantity was assessed using a Nanodrop Spectrophotometer and agarose gel electrophoresis.

value: Blood


title: -P/-N_6h_shoot_rep1

description: Gene expression of rice shoot at 6 h after both phosphorus and nitrogen deficiency treatments

source_name: Phosphorus and nitrogen deficiencies, 6h, shoot, replicate1


title: BEAS2B: V600E_1

description: replicate 1


title: -P/-N_6h_shoot_rep2

source_name: Phosphorus and nitrogen deficiencies, 6h, shoot, replicate2


title: BEAS2B: V417F_1

description: replicate 1


title: -P/-N_6h_root_rep1

source_name: Phosphorus and nitrogen deficiencies, 6h, root, replicate1


title: E7-0-A-IP-K4M3_rep2

city: Shanghai City

first: Naihe

last: Jing

address: Yueyang Road 320

institute: shanghai institute of biochemistry and cell biology

description: processed data file: E7-0-A-K4M3.tagAlign.fc.signal.bw

library_source: genomic

data_processing:
Illumina CASAVA version 1.8 were used to the basecalling.
Sequencing adapters, low quality sequences and amplification primers were trimmed from the raw sequencing reads.
For RNA-seq data, trimmed clean reads were aligned to mouse reference genome (mm10) using TopHat (v2.0.9) with the default parameters
For the ChIP-seq data, the trimmed reads were mapped to the mouse genome (mm10 assembly) using BWA sligner (version 0.7.5a-r405) with the options "-I 15 -q 10 -t 4"
For the integrated HMM_state_15.enhancerRegion processed data, we show genome-wide 200bp tiles of ChromHMM results for enhancers. Only 4 types of enhancers identified by ChromHMM were annotated, 1 for bivalent, 2 for poised, 3 for active and 4 for double acylated enhancers. Other types were annotated as 0.
Genome_build: mm10
Supplementary_files_format_and_content: The bigwig files for RRBS data include the DNA methylation level of each single CpG site. The tagAlign files show the bed files for aligned reads. The "merge.dexseq_clean_refseq.gene.all.xls" file include the expression (FPKM) of all the RefSeq genes for eaach sample. The bigwig files for  ChIP-Seq show the genome wide coverge minus the input. The "HMM_state_15.enhancerRegion.kmeans.subKmeans.mergeAll.xls.gz" file includes the integrated analysis of all the sequenced epigenetic markers of this project.

organism: Mus musculus

source_name: mouse embryos

growth_protocol: Embryo were collected from pregnant mice at 6.5, 7.0 and 7.5 dpc; stem cells were cultured under regular condition.

extract_protocol:
RNA from embryo samples were extracted by 5M GuSCN (Invitrogen, # 20012-043), then RNA was precipitated by ethanol with the help of RNA carrier; genomic DNA from embryo samples were separated and extracted by modified microChIP or single cell based bisulfite seq.
Libraries of RNA samole were generated by using illumina Nextera XT DNA sample preparation kit; libraries of genomic DNA were construted by using NEBNext Ultra DNA Library Prep Kit for Illumina (NEB #7370L); libraries of single cell based bisulfite seq were constructed according to the protocol described in (H Guo et al,2015).

tag: antibody

tag: strain

value: ICR

tag: devlopmental stage

value: 7.0 dpc


title: -P/-N_6h_shoot_rep3

source_name: Phosphorus and nitrogen deficiencies, 6h, shoot, replicate3


title: BEAS2B: T599I_1

description: replicate 1


title: Arabidopsis leaf infected by 96-11-17M 72h rep 1

city: Daejeon

first: Seon-Kyu

last: Kim

address: 125 Gwahak-ro, Yuseong-gu, Daejeon 305-806, Korea

department: Personalized Genomic Medicine Research Center

country: South Korea

institute: Korea Research Institutue of Bioscience & Biotechnology

data_processing:
Base calling was performed by Illumina Genome Studio (V2010.1).
A reference genome sequence data of Arabidopsis thaliana was obtained from Illumina iGenome supporting site (assembly ID: TAIR10; http://support.illumina.com/sequencing/sequencing_software/igenome.html). Reference genome index was built by using bowtie2-build component of Bowtie2 (ver. 2.0, http://bowtie-bio.sourceforge.net/bowtie2) and SAMtools (ver. 0.1.18, http://samtools.sourceforge.net/).
Tophat2 was applied to tissue samples for mapping reads to reference genome. The fragments
per
kilobase
 of
transcript
 per
million
 fragments
mapped (FPKM) of each sample was estimated by Cufflinks software (V2.0.2).
Genome_build: TAIR10
Supplementary_files_format_and_content: tab-delimited text format with FPFM values

organism: Arabidopsis thaliana

source_name: Arabidopsis leaf

extract_protocol:
Total RNA was isolated by RNeasy Mini Kit (Qiagen, CA, USA), according to the manufacturer's protocol. The quality and integrity of the RNA were confirmed by agarose gel electrophoresis and ethidium bromide staining, followed by visual examination under ultraviolet light.
Sequencing library was prepared using TruSeq RNA Sample Preparation kit v2 (Illumina, CA, USA) according to the manufacturer’s protocols. Briefly, mRNA was purified from total RNA using poly-T oligo-attached magnetic beads, fragmented, and converted into cDNAs. Then, adapters were ligated and the fragments were amplified on a PCR.

tag: pathogen

value: Vibrio vulnificus

tag: pathogen strain

value: leaf

tag: infection time

tag: replication number


title: BEAS2B: T529A_2

description: replicate 2


title: BEAS2B: T529A_1

description: replicate 1


title: BEAS2B: T599I_2

description: replicate 2


title: -P_5d_root_rep3

description: Gene expression of rice root at 5 days after phosphorus deficiency treatment

data_processing: The scanned images were analyzed with Feature Extraction Software 10.5.1.1 (Agilent) using default parameters to obtain background subtracted and spatially detrended processed signal intensities. The processed signal intensities were used for 75th percentile normalization and log2 transformation with R

source_name: Phosphorus deficiency treatment, 5d, root, replicate3

treatment_protocol: The 7-day old seedlings were exposed to -P (NaH2PO4・2H2O-free) and control conditions, respectively. Root samples were collected at 5 d after the treatments.


title: Control_5d_root_rep3

description: Gene expression of rice root at 5 days after control treatment

source_name: Control treatment, 5d, root, replicate3

value: Control


title: Control_5d_root_rep2

source_name: Control treatment, 5d, root, replicate2


title: -P_6h_shoot_rep1

source_name: Phosphorus deficiency, 6h, shoot, replicate1


title: BEAS2B: S614P_1

description: replicate 1


title: BEAS2B: S605G_2

description: replicate 2


title: BEAS2B: S467L_2

description: replicate 2


title: -P_6h_shoot_rep2

source_name: Phosphorus deficiency, 6h, shoot, replicate2


title: -P_5d_root_rep2

source_name: Phosphorus deficiency treatment, 5d, root, replicate2


title: BEAS2B: S605G_1

description: replicate 1


title: -P_5d_root_rep1

source_name: Phosphorus deficiency treatment, 5d, root, replicate1


title: Control_5d_root_rep1

source_name: Control treatment, 5d, root, replicate1


title: BEAS2B: S467L_1

description: replicate 1


title: -N_6h_shoot_rep2

description: Gene expression of rice shoot at 6 h after nitrogen deficiency treatment

source_name: Nitrogen deficiency treatment, 6h, shoot, replicate2

treatment_protocol: The 7-day old seedlings were exposed to -N (NH4NO3-free) and control conditions. Shoot samples were collected at 6 h after the treatments.

value: Nitrogen deficiency


title: -N_6h_shoot_rep3

source_name: Nitrogen deficiency treatment, 6h, shoot, replicate3


title: Control_6h_shoot_rep3

description: Gene expression of rice shoot at 6 h after control treatment

source_name: Control treatment, 6h, shoot, replicate3


title: -N_6h_shoot_rep1

source_name: Nitrogen deficiency treatment, 6h, shoot, replicate1


title: BEAS2B: R682W_2

description: replicate 2


title: BEAS2B: S614P_2

description: replicate 2


title: BEAS2B: R682W_1

description: replicate 1


title: BEAS2B: R435S_2

description: replicate 2


title: BEAS2B: N581S_2

description: replicate 2


title: BEAS2B: R435S_1

description: replicate 1


title: K_4_5d_shoot_rep3

description: Gene expression of rice shoot at 5 days after potassium excess treatment (x4 of control conc.)

treatment_protocol: The 7-day old seedlings were exposed to N, P, and K excess treatments (x64, x16, and x4 of normal concentration) and control conditions, respectively. The amounts of NH4NO3 for N excess treatment, NaH2PO4・2H2O for P excess treatment, and K2SO4 for K excess treatment were changed to adjust the excess levels of each nutrient. Shoot samples were collected at 5 days after the treatments.

tag: nutrient

value: Potassium

value: Excess (x4)


title: Control_6h_shoot_rep1

source_name: Control treatment, 6h, shoot, replicate1

tag: tissue


title: Control_6h_shoot_rep2

source_name: Control treatment, 6h, shoot, replicate2

tag: treatment


title: K_4_5d_shoot_rep2


title: BEAS2B: N581S_1

description: replicate 1


title: K_16_5d_shoot_rep3

description: Gene expression of rice shoot at 5 days after potassium excess treatment (x16 of control conc.)

value: Excess (x16)


title: K_4_5d_shoot_rep1

value: Nipponbare


title: BEAS2B: L618W_2

description: replicate 2


title: BEAS2B: L618W_1

description: replicate 1


title: K_16_5d_shoot_rep2


title: BEAS2B: L613F_2

description: replicate 2


title: BEAS2B: L613F_1

description: replicate 1


title: K_16_5d_shoot_rep1


title: BEAS2B: L597V_2

description: replicate 2


title: K_64_5d_shoot_rep2

description: Gene expression of rice shoot at 5 days after potassium excess treatment (x64 of control conc.)

value: Excess (x64)


title: K_64_5d_shoot_rep3


title: BEAS2B: L597V_1

description: replicate 1


title: BEAS2B: L592M_2

description: replicate 2


title: BEAS2B: L592M_1

description: replicate 1


title: BEAS2B: L584F_2

description: replicate 2


title: BEAS2B: L584F_1

description: replicate 1


title: P_4_5d_shoot_rep1

description: Gene expression of rice shoot at 5 days after phosphorus excess treatment (x4 of control conc.)

value: Phosphorus


title: K_64_5d_shoot_rep1


title: BEAS2B: L505H_1

description: replicate 1

value: immortalized bronchial epitheial cells


title: P_16_5d_shoot_rep1

description: Gene expression of rice shoot at 5 days after phosphorus excess treatment (x16 of control conc.)


title: BEAS2B: L485S_2

description: replicate 2


title: BEAS2B: L485S_1

description: replicate 1


title: BEAS2B: L485_P490_Y_2

description: replicate 2


title: BEAS2B: L485_P490_Y_1

description: replicate 1


title: BEAS2B: K601N_2

description: replicate 2


title: P_16_5d_shoot_rep2


title: P_4_5d_shoot_rep2


title: BEAS2B: K601N_1

description: replicate 1


title: P_64_5d_shoot_rep3

description: Gene expression of rice shoot at 5 days after phosphorus excess treatment (x64 of control conc.)


title: P_4_5d_shoot_rep3


title: P_64_5d_shoot_rep2


title: BEAS2B: K483E_2

description: replicate 2


title: P_16_5d_shoot_rep3


title: P_64_5d_shoot_rep1


title: N_16_5d_shoot_rep3

description: Gene expression of rice shoot at 5 days after nitrogen excess treatment (x16 of control conc.)

value: Nitrogen


title: N_4_5d_shoot_rep1

description: Gene expression of rice shoot at 5 days after nitrogen excess treatment (x4 of control conc.)


title: N_4_5d_shoot_rep3


title: BEAS2B: K483E_1

description: replicate 1


title: BEAS2B: L505H_2

description: replicate 2


title: BEAS2B: I592V_2

description: replicate 2


title: Input

city: Shanghai

first: Shaorong

last: Gao

address: Siping Road NO.1239

institute: Tongji University

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, low quality and low complexity reads, then mapped to mm9 reference genome using bowtie2(v 2.2.3) command, reads that have map quality score less than 30 were removed from downstream analysis.
Peaks were called using masc2(v 2.1.0.20140616) with the parameters "macs2 callpeak –n Sample -g mm -B -q 0.05 --SPMR" relative to input samples.
Genome_build: mm9
Supplementary_files_format_and_content: Bigwig files are generated using macs2 pileup function and normalized to one million reads per sample using --SPMR option. Scores represent normalized tag counts per million reads.

source_name: Trophoblast stem cell

growth_protocol: Trophoblast stem cells were cultured in 70% FCM+F4H medium composed of 30% TS medium (RPMI1640 supplemented with 20% FBS, 1 mM sodium pyruvate, 100 µM β-mercaptoethanol, 2 mM L-glutamine), 70% FCM (feeder condition medium) and F4H (25 ng/ml fibroblast growth factor 4 (FGF4) and 1 µg/ml heparin).

extract_protocol:
~10^5 cells were resuspended in lysis buffer and chromatin was sonicated to 200-500 bp with Covaris M220 system. Then, the sonicated chromatin was immunoprecipitated with the antibodies. Antibodies used in ChIP assays were Esrrb, H3k4me1, H3k4me2, H3k4me3 and H3k27ac. ChIP DNA was reverse-crosslinked, eluted, and purified by phenol-chloroform-isoamyl alcohol extraction, followed by ethanol precipitation.
For sequencing, 10–100 ng DNA was used for library preparation following the New England Biolabs library preparation protocol.

treatment_protocol: Transfections were performed for 4-5 hours in Opti-MEM media supplemented with Fgf4 and heparin using 1% Lipofectamine 2000

value: TSCs

tag: genotype type

value: Esrrb overexpression

tag: chip antibody


title: BEAS2B: I592V_1

description: replicate 1

tag: cell line

tag: cell type


title: BEAS2B: H574Q_2

description: replicate 2

tag: passages


title: N_64_5d_shoot_rep1

description: Gene expression of rice shoot at 5 days after nitrogen excess treatment (x64 of control conc.)

value: Shoot


title: -P_24h_root_rep1

description: Gene expression of rice root at 24 h after phosphorus deficiency treatment

source_name: Phosphorus deficiency treatment, 24h, root, replicate1

treatment_protocol: The 7-day old seedlings were exposed to N (NH4NO3-free) , P (NaH2PO4・2H2O-free), and K (K2SO4-free) deficiency treatments and control condition, respectively. Root samples were collected at 6 and 24 hours after the treatments.

value: Root

value: Phosphorus deficiency

tag: time


title: BEAS2B: H574Q_1

description: replicate 1


title: N_64_5d_shoot_rep3

tag: cultivar


title: H3K27ac

value: anti-H3K27ac  (Abcam, Ab4729）


title: -P_24h_root_rep2

source_name: Phosphorus deficiency treatment, 24h, root, replicate2


title: -P_24h_root_rep3

source_name: Phosphorus deficiency treatment, 24h, root, replicate3


title: -K_24h_root_rep2

description: Gene expression of rice root at 24 h after potassium deficiency treatment

source_name: Potassium deficiency treatment, 24h, root, replicate2

value: Potassium deficiency


title: N_16_5d_shoot_rep1


title: -K_24h_root_rep1

source_name: Potassium deficiency treatment, 24h, root, replicate1


title: N_16_5d_shoot_rep2


title: N_4_5d_shoot_rep2


title: -K_24h_root_rep3

source_name: Potassium deficiency treatment, 24h, root, replicate3


title: N_64_5d_shoot_rep2


title: Control_24h_root_rep3

description: Gene expression of rice root at 24 h after control treatment

source_name: Control treatment, 24h, root, replicate3

value: Control


title: BEAS2B: I582M_1

description: replicate 1


title: H3k4me3_1

value: anti-H3K4me3  (Abcam, Ab8580）


title: H3k4me3_2


title: -N_24h_root_rep3

description: Gene expression of rice root at 24 h after nitrogen deficiency treatment

source_name: Nitrogen deficiency treatment, 24h, root, replicate3

value: Nitrogen deficiency


title: Esrrb

value: anti-Flag M2 (Sigma, F1804）


title: -N_24h_root_rep1

source_name: Nitrogen deficiency treatment, 24h, root, replicate1


title: H3k4me2

value: anti-H3K4me2  (Millipore, 07-449）


title: -N_24h_root_rep2

source_name: Nitrogen deficiency treatment, 24h, root, replicate2

value: Nipponbare


title: TSC_nobfgf_oeesrrb_2

description: forced expression of ectopic Esrrb in mouse trophoblast stem cell line, which is cultured in TSC medium without bFGF (Replicate 2)

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads were mapped to mm9 reference genome using tophat(v2.0.12) default commands.
Differentially expressed genes were identified by GFOLD (v 1.1.3) diff command, genes with absolute value of GFOLD less than 1 were excluded.
Genome_build: mm9
Supplementary_files_format_and_content: FPKM files of genes were generated using cufflinks(v1.2.0) default commands

growth_protocol: Esrrb plays an important role in maintaining self-renewal of trophoblast stem cells (TSCs) and reprogramming somatic cells to induced TSCs

extract_protocol:
Total RNA was isolated from cell pellets by Trizol reagent (Takara).
RNA-Seq library were generated using KAPA Strandard mRNA-Seq Kits according to the manufacturer’s recommendations. Briefly, the mRNA was enriched using oligo(dT) magnetic beads and sheared to create short fragments of approximately 300 bp. cDNA was synthesized using random hexamer primers and purified using 1.8X Agencourt AMPure XP beads (Beckman). Finally, the sequencing primers linked to the cDNA fragments (approximately 300 bp) were isolated by gel electrophoresis and enriched by PCR amplification to construct the library. The sequencing was performed at the Sequencing Center in National Institute of Biology, Beijing using the HiSeq 2500 system developed by Illumina. Paired-end 100-bp sequencing was applied.

treatment_protocol: Trophoblast stem cells (TSCs) are derived from the trophoectoderm of a blastocyst and can maintain self-renewal in vitro. Meanwhile, essential insights into the molecular mechanisms controlling placental developmental could be gained by using TSCs that can differentiate into the various placental trophoblast cell types in vitro. Esrrb is a transcription factor with pivotal roles in maintaining TSCs’ self-renewal, but the exact transcriptional networks that Esrrb involved in TSCs are largely unknown. In the present study, we elucidated the function of Esrrb during TSC self-renewal and differentiation. We demonstrate that precise levels of Essrb are critical for TSCs stemness maintenance and normal trophoblast differentiation, as Esrrb depletion results in down-regulation of the key TSC-specific transcription factors, consequently causing TSCs differentiation and forced expression of Esrrb can partially block TSCs differentiation in the absence of FGF4. This function of Esrrb is exerted by directly binding and activating a core set of TSC-specific target genes including Cdx2, Eomes, Sox2, Fgfr4 and BMP4. Furthermore, we investigate the role of Esrrb in reprogramming of mouse embryonic fibroblasts (MEFs) to induced TSCs (iTSCs). We show that Esrrb can facilitate the conversion of iTSCs from MEFs. Moreover, Esrrb can substitute for Eomes during this conversion process. Our findings provide a better understanding of the molecular mechanism of Esrrb in maintaining TSCs self-renewal and iTSCs reprogramming.

tag: genotype

value: forced expression of ectopic Esrrb

tag: culture condition

value: TSC medium without bFGF


title: BEAS2B: H574N_2

description: replicate 2

value: immortalized bronchial epitheial cells


title: Control_24h_root_rep2

source_name: Control treatment, 24h, root, replicate2


title: BEAS2B: I582M_2

description: replicate 2


title: H3k4me1

value: anti-H3K4me1  (Abcam, Ab8896）


title: BEAS2B: H574N_1

description: replicate 1


title: BEAS2B: V417F_2

description: replicate 2


title: TSC_nobfgf_oeesrrb_1

description: forced expression of ectopic Esrrb in mouse trophoblast stem cell line, which is cultured in TSC medium without bFGF (Replicate 1)

value: TSCs


title: BEAS2B: GFP_1

description: replicate 1


title: TSC_nobfgf_2

description: mouse trophoblast stem cell line cultured in TSC medium without bFGF (Replicate 2)


title: BEAS2B: GFP_2

description: replicate 2


title: -K_6h_root_rep3

description: Gene expression of rice root at 6 h after potassium deficiency treatment

source_name: Potassium deficiency treatment, 6h, root, replicate3


title: -K_6h_root_rep1

source_name: Potassium deficiency treatment, 6h, root, replicate1


title: BEAS2B: G469S_2

description: replicate 2


title: BEAS2B: G469S_1

description: replicate 1


title: Control_24h_root_rep1

source_name: Control treatment, 24h, root, replicate1


title: -P_6h_root_rep2

description: Gene expression of rice root at 6 h after phosphorus deficiency treatment

source_name: Phosphorus deficiency treatment, 6h, root, replicate2


title: -N_6h_root_rep2

description: Gene expression of rice root at 6 h after nitrogen deficiency treatment

source_name: Nitrogen deficiency treatment, 6h, root, replicate2


title: -K_6h_root_rep2

source_name: Potassium deficiency treatment, 6h, root, replicate2


title: -P_6h_root_rep3

source_name: Phosphorus deficiency treatment, 6h, root, replicate3


title: -N_6h_root_rep3

source_name: Nitrogen deficiency treatment, 6h, root, replicate3


title: -P_6h_root_rep1

source_name: Phosphorus deficiency treatment, 6h, root, replicate1


title: TSC_nobfgf_1

description: mouse trophoblast stem cell line cultured in TSC medium without bFGF (Replicate 1)

source_name: Trophoblast stem cell


title: Control_6h_root_rep1

description: Gene expression of rice root at 6 h after control treatment

source_name: Control treatment, 6h, root, replicate1


title: -N_6h_root_rep1

source_name: Nitrogen deficiency treatment, 6h, root, replicate1


title: BEAS2B: G469A_2

description: replicate 2


title: TSC_2

description: mouse trophoblast stem cell line cultured in standard TSC medium (Replicate 2)

value: standard TSC medium


title: Control_6h_root_rep2

source_name: Control treatment, 6h, root, replicate2


title: S19_P11_LCP39

description: Set 1 (Illumina NextSeq 500)

data_processing:
Basecalling performed by RTA version 1.12.4.2.
Demultiplexing performed by Bcl2fastq version 2.17.
Alignment, tagging, gene and transcript counting performed CellRanger version1.0.1.
Aggregation performed by CellRanger version 2.0.2.
Genome_build: GRCh38
Supplementary_files_format_and_content: 1) cell barcodes (barcodes.tsv) 2) genes (genes.tsv), 3) count matrix (matrix.mtx), and 4) sample information (samples.txt)

source_name: Primary liver cancer single-cell

tag: cancer type

value: Intrahepatic cholangiocarcinoma

tag: cell number


title: Control_6h_root_rep3

source_name: Control treatment, 6h, root, replicate3

value: Root


title: BEAS2B: G469A_1

description: replicate 1


title: LeafBlade_-K_69DAT_12:00_2013

description: Gene expression of rice leaf at 69 days after transplanting in potassium deficient paddy field

source_name: Leaf blade, potassium deficient condition, 69 days after transplanting, 12:00, 2013

growth_protocol: Rice seeds were sown in germination boxes, and after approximately 30 days the seedlings were transplanted into a paddy field with nitrogen, phosphorus, and potassium deficient conditions, respectively. Rice plants were cultivated in Tsukuba, Japan, during the cropping season (from late May to late September) in 2013.

treatment_protocol: We applied 55 kg/ha N, P2O5, and K2O to the control paddy field, 55 kg/ha P2O5 and K2O to the nitrogen deficient field, 55 kg/ha N and K2O to the phosphorus deficient field, and 55 kg/ha N and P2O5 to the potassium deficient field as basal fertilizer. Sampling of leaf blades for transcriptome profiling was carried out at 1-week intervals.

value: Leaf blade

tag: condition

value: Potassium deficient condition

tag: growth/development stage

value: 69 days after transplanting

tag: field

value: Paddy field


title: TSC_1

description: mouse trophoblast stem cell line cultured in standard TSC medium (Replicate 1)


title: LeafBlade_-K_55DAT_12:00_2013

description: Gene expression of rice leaf at 55 days after transplanting in potassium deficient paddy field

source_name: Leaf blade, potassium deficient condition, 55 days after transplanting, 12:00, 2013

value: 55 days after transplanting


title: BEAS2B: G466V_1

description: replicate 1


title: LeafBlade_-K_62DAT_12:00_2013

description: Gene expression of rice leaf at 62 days after transplanting in potassium deficient paddy field

source_name: Leaf blade, potassium deficient condition, 62 days after transplanting, 12:00, 2013

value: 62 days after transplanting


title: S15_P09_LCP38

description: Set 1 (Illumina NextSeq 500)

value: Hepatocellular carcinoma


title: LeafBlade_-K_34DAT_12:00_2013

description: Gene expression of rice leaf at 34 days after transplanting in potassium deficient paddy field

source_name: Leaf blade, potassium deficient condition, 34 days after transplanting, 12:00, 2013

value: 34 days after transplanting


title: S21_P13_LCP37

description: Set 1 (Illumina NextSeq 500)


title: LeafBlade_-K_41DAT_12:00_2013

description: Gene expression of rice leaf at 41 days after transplanting in potassium deficient paddy field

source_name: Leaf blade, potassium deficient condition, 41 days after transplanting, 12:00, 2013

value: Nipponbare

value: 41 days after transplanting


title: S20_P12_LCP35

description: Set 1 (Illumina NextSeq 500)


title: BEAS2B: G466V_2

description: replicate 2


title: BEAS2B: E586K_1

description: replicate 1


title: BEAS2B: E586K_2

description: replicate 2


title: S12_P07_LCP30

description: Set 1 (Illumina NextSeq 500)


title: S07_P02_LCP28

description: Set 1 (Illumina NextSeq 500)


title: BEAS2B: E375D_2

description: replicate 2


title: BEAS2B: F595L_2

description: replicate 2


title: BEAS2B: F595L_1

description: replicate 1


title: LeafBlade_-P_69DAT_12:00_2013

description: Gene expression of rice leaf at 69 days after transplanting in phosphorus deficient paddy field

source_name: Leaf blade, phosphorus deficient condition, 69 days after transplanting, 12:00, 2013

value: Phosphorus deficient condition


title: LeafBlade_-K_20DAT_12:00_2013

description: Gene expression of rice leaf at 20 days after transplanting in potassium deficient paddy field

source_name: Leaf blade, potassium deficient condition, 20 days after transplanting, 12:00, 2013

value: 20 days after transplanting


title: LeafBlade_-P_62DAT_12:00_2013

description: Gene expression of rice leaf at 62 days after transplanting in phosphorus deficient paddy field

source_name: Leaf blade, phosphorus deficient condition, 62 days after transplanting, 12:00, 2013


title: BEAS2B: E375D_1

description: replicate 1

value: immortalized bronchial epitheial cells


title: LeafBlade_-K_27DAT_12:00_2013

description: Gene expression of rice leaf at 27 days after transplanting in potassium deficient paddy field

source_name: Leaf blade, potassium deficient condition, 27 days after transplanting, 12:00, 2013

value: 27 days after transplanting


title: LeafBlade_-P_55DAT_12:00_2013

description: Gene expression of rice leaf at 55 days after transplanting in phosphorus deficient paddy field

source_name: Leaf blade, phosphorus deficient condition, 55 days after transplanting, 12:00, 2013


title: LeafBlade_-K_13DAT_12:00_2013

description: Gene expression of rice leaf at 13 days after transplanting in potassium deficient paddy field

source_name: Leaf blade, potassium deficient condition, 13 days after transplanting, 12:00, 2013

value: 13 days after transplanting


title: S09_P04_LCP25

description: Set 1 (Illumina NextSeq 500)

value: Intrahepatic cholangiocarcinoma


title: LeafBlade_-P_34DAT_12:00_2013

description: Gene expression of rice leaf at 34 days after transplanting in phosphorus deficient paddy field

source_name: Leaf blade, phosphorus deficient condition, 34 days after transplanting, 12:00, 2013


title: LeafBlade_-P_41DAT_12:00_2013

description: Gene expression of rice leaf at 41 days after transplanting in phosphorus deficient paddy field

source_name: Leaf blade, phosphorus deficient condition, 41 days after transplanting, 12:00, 2013


title: LeafBlade_-P_27DAT_12:00_2013

description: Gene expression of rice leaf at 27 days after transplanting in phosphorus deficient paddy field

source_name: Leaf blade, phosphorus deficient condition, 27 days after transplanting, 12:00, 2013


title: LeafBlade_-P_20DAT_12:00_2013

description: Gene expression of rice leaf at 20 days after transplanting in phosphorus deficient paddy field

source_name: Leaf blade, phosphorus deficient condition, 20 days after transplanting, 12:00, 2013


title: BEAS2B: D594H_1

description: replicate 1


title: LeafBlade_-N_69DAT_12:00_2013

description: Gene expression of rice leaf at 69 days after transplanting in nitrogen deficient paddy field

source_name: Leaf blade, nitrogen deficient condition, 69 days after transplanting, 12:00, 2013

value: Nitrogen deficient condition


title: LeafBlade_-P_48DAT_12:00_2013

description: Gene expression of rice leaf at 48 days after transplanting in phosphorus deficient paddy field

source_name: Leaf blade, phosphorus deficient condition, 48 days after transplanting, 12:00, 2013

value: Leaf blade

value: 48 days after transplanting


title: S10_P05_LCP23

description: Set 1 (Illumina NextSeq 500)

source_name: Primary liver cancer single-cell


title: LeafBlade_-N_62DAT_12:00_2013

description: Gene expression of rice leaf at 62 days after transplanting in nitrogen deficient paddy field

source_name: Leaf blade, nitrogen deficient condition, 62 days after transplanting, 12:00, 2013


title: LeafBlade_-N_55DAT_12:00_2013

description: Gene expression of rice leaf at 55 days after transplanting in nitrogen deficient paddy field

source_name: Leaf blade, nitrogen deficient condition, 55 days after transplanting, 12:00, 2013


title: LeafBlade_-P_13DAT_12:00_2013

description: Gene expression of rice leaf at 13 days after transplanting in phosphorus deficient paddy field

source_name: Leaf blade, phosphorus deficient condition, 13 days after transplanting, 12:00, 2013


title: LeafBlade_-N_48DAT_12:00_2013

description: Gene expression of rice leaf at 48 days after transplanting in nitrogen deficient paddy field

source_name: Leaf blade, nitrogen deficient condition, 48 days after transplanting, 12:00, 2013


title: LeafBlade_-N_41DAT_12:00_2013

description: Gene expression of rice leaf at 41 days after transplanting in nitrogen deficient paddy field

source_name: Leaf blade, nitrogen deficient condition, 41 days after transplanting, 12:00, 2013


title: S11_P06_LCP29

description: Set 1 (Illumina NextSeq 500)


title: S08_P03_LCP26

description: Set 1 (Illumina NextSeq 500)


title: BEAS2B: D594H_2

description: replicate 2


title: S02_P01_LCP21

description: Set 1 (Illumina NextSeq 500)


title: S16_P10_LCP18

description: Set 1 (Illumina NextSeq 500)


title: BEAS2B: Braf_WT_1

description: replicate 1


title: LeafBlade_-N_34DAT_12:00_2013

description: Gene expression of rice leaf at 34 days after transplanting in nitrogen deficient paddy field

source_name: Leaf blade, nitrogen deficient condition, 34 days after transplanting, 12:00, 2013


title: BEAS2B: A762E_2

description: replicate 2


title: C.alb-specific memory CD4 T cells

city: Marseille

first: Pierre

last: Milpied

address: Parc Scientifique de Luminy, case 906

country: France

institute: Centre d'Immunologie de Marseille-Luminy (CIML)

description: Fresh PBMCs (10-20x10e6 cells, final concentration 10x10e6 cells/ml) were stimulated for 3h at 37°C with 0.6 nmol/ml PepTivator Candida albicans MP65 (pool of 15 amino acids length peptides with 11 amino acid overlap, Miltenyi Biotec) in RPMI + 5% human serum in the presence of 1 µg/ml anti-CD40 (HB14, Miltenyi Biotec). After stimulation, PBMCs were labeled with PE-conjugated anti-CD154 (5C8, Miltenyi Biotec) and enriched with anti-PE magnetic beads (Miltenyi Biotec). After enrichment, cells were stained with PerCP-Cy5.5 anti-CD4 (RPA-T4, Biolegend), AlexaFluor700 anti-CD3 (SK7, Biolegend) and APC-Cy7 anti-CD45RA (HI100, Biolegend), and antigen-specific T cells were gated as CD3+CD4+CD45RA-CD154+ single live cells for single-cell sorting.

data_processing:
Library strategy: FB5P-seq
Fastq files were obtained from the sequencing facility (running Illumina NextSeq550 with HighOutput75cycles) after demultiplexing with bcl2fastq.
To generate single-cell UMI count matrices, we used Drop-seq-tools v1.12 running STAR v2.5.3a and HTSeq v0.9.1.
Quality control was performed on each dataset (Tonsil 1, Tonsil 2, T cells) independently to remove poor quality cells. Cells with less than 250 genes detected were removed. We further excluded cells with values below 3 median absolute deviations (MADs) from the median for UMI counts, for the number of genes detected, or for ERCC accuracy, and cells with values above 3 MADs from the median for ERCC transcript percentage.
Genome_build: GRCh38 with additional artificial chromosome for 92 ERCC spike-in genes.
Supplementary_files_format_and_content: csv files containing gene UMI counts (data file).
Supplementary_files_format_and_content: xlsx files containing additional cell-specific metadata (QC values, index sorting parameters, BCR or TCR parameters) for each filtered cell identified by a UniqueCellID.

molecule: polyA RNA

source_name: peripheral blood

extract_protocol:
Single cells were FACS sorted into ice-cold 96-well PCR plates (Thermofisher) containing 2 µl lysis mix per well. The lysis mix contained 0.5 µl 0.4% (v/v) Triton X-100 (Sigma-Aldrich), 0.05 µl 40 U/µl RnaseOUT (Thermofisher), 0.08 µl 25 mM dNTP mix (Thermofisher), 0.5 µl 10 µM (dT)30_Smarter primer (Table S3), 0.05 µl 0.5 pg/µl External RNA Controls Consortium (ERCC) spike-ins mix (Thermofisher), and 0.82 µl PCR-grade H20 (Qiagen). Immediately after cell sorting, each plate was covered with adhesive film (Thermofisher), briefly spun down in a benchtop plate centrifuge, and frozen on dry ice. Plates containing single cells in lysis mix were stored at -80°C and shipped on dry ice (only T cells) until further processing. The plate containing single cells in lysis mix was thawed on ice, briefly spun down in a benchtop plate centrifuge, and incubated in a thermal cycler for 3 minutes at 72°C (lid temperature 72°C). Immediately after, the plate was placed back on ice and 3 µl RT mastermix was added to each well. The RT mastermix contained 0.25 µl 200 U/µl SuperScript II (Thermofisher), 0.25 µl 40 U/µl RnaseOUT (Thermofisher), and 2.5 µl 2x RT mastermix. The 2x RT mastermix contained 1 µl 5x SuperScript II buffer (Thermofisher), 0.25 µl 100 mM DTT (Thermofisher), 1 µl 5 M betaine (Sigma-Aldrich), 0.03 µl 1 M MgCl2 (Sigma-Aldrich), 0.125 µl 100 µM well-specific template switching oligonucleotide TSO_BCx_UMI5_TATA (Table S3 and Table S4), and 0.095 µl PCR-grade H2O (Qiagen). Reverse transcription was performed in a thermal cycler (lid temperature 70°C) by 90 min at 42°C, followed by 10 cycles of 2 min at 50°C and 2 min at 42°C, then 15 min at 70°C. Plates with single-cell cDNA were stored at -20°C until further processing. For cDNA amplification, 7.5 µl LD-PCR mastermix were added to each well. The LD-PCR mastermix contained 6.25 µl 2x KAPA HiFi HotStart ReadyMix (Roche Diagnostics), 0.125 µl 20:µM PCR_Satija forward primer (Table S3), 0.125 µl 20 µM SmarterR reverse primer8 (Table S3), and 1 µl PCR-grade H2O (Qiagen). The amplification was performed in a thermal cycler (lid temperature 98°C) by 3 min at 98°C, followed by 22 cycles of 15 sec at 98°C, 20 sec at 67°C, 6 min at 72°C, then a final elongation for 5 min at 72°C. Plates with amplified single-cell cDNA were stored at -20°C until further processing.
For library preparation, 5 µl amplified cDNA from each well of a 96-well plate were pooled and completed to 500 µl with PCR-grade H2O (Qiagen). Two rounds of 0.6X solid-phase reversible immobilization beads (AmpureXP, Beckman, or CleanNGS, Proteigene) cleaning were used to purify 100 µl pooled cDNA with final elution in 15 µl PCR-grade H2O (Qiagen). After quantification with Qubit dsDNA HS assay (Thermofisher), 800 pg purified cDNA pool were processed with the Nextera XT DNA sample Preparation kit (Illumina), according to the manufacturer’s instructions with modifications to enrich 5’-ends of tagmented cDNA during library PCR. After tagmentation and neutralization, 25 µl tagmented cDNA was amplified with 15 µl Nextera PCR Mastermix, 5 µl Nextera i5 primer (S5xx, Illumina), and 5 µl of a custom i7 primer mix (0.5 µM i7_BCx + 10 µM i7_primer, Table S3). The amplification was performed in a thermal cycler (lid temperature 72°C) by 3 min at 72°C, 30 sec at 95°C, followed by 12 cycles of 10 sec at 95°C, 30 sec at 55°C, 30 sec at 72°C, then a final elongation for 5 min at 72°C. The resulting library was purified with 0.8X solid-phase reversible immobilization beads (AmpureXP, Beckman, or CleanNGS, Proteigene).
Libraries generated from multiple 96-well plates of single cells and carrying distinct i7 barcodes were pooled for sequencing on an Illumina NextSeq550 platform, with High Output 75 cycles flow cells, targeting 5x10e5 reads per cell in paired-end single-index mode with the following primers (Table S3) and cycles: Read1 (Read1_SP, 67 cycles), Read i7 (i7_SP, 8 cycles), Read2 (Read2_SP, 16 cycles).

value: Candida albicans specific memory CD4 T cells


title: BEAS2B: Braf_WT_2

description: replicate 2


title: BEAS2B: A598V_2

description: replicate 2


title: Tonsil 2 B cells

description: Frozen live cell suspensions were thawed at 37°C in RPMI + 10% FCS, then washed and resuspended in FACS buffer (PBS + 5% FCS + 2 mM EDTA) at a concentration of 10e8 cells/ml for staining. Cells were first incubated with 2% normal mouse serum and Fc-Block (BD Biosciences) for 10 min on ice. Then cells were incubated with a mix of fluorophore-conjugated antibodies (Table S2) for 30 min on ice. Cells were washed in PBS, then incubated with the Live/Dead Fixable Aqua Dead Cell Stain (Thermofisher) for 10 min on ice. After a final wash in FACS buffer, cells were resuspended in FACS buffer at a concentration of 10e7 cells/ml for cell sorting on a 4-laser BD FACS Influx (BD Biosciences). Mem B cells were gated as CD3-CD14-IgD-CD20+CD10-CD38loCD27+SSClo single live cells. GC B cells were gated as CD3-CD14-IgD-CD20+CD10+CD38+ single live cells. PB/PC cells were gated as CD3-CD14-IgD-CD38hiCD27+SSChi single live cells.

source_name: tonsil

value: Memory (Mem) B cells, germinal center (GC) B cells, Plasmablasts/Plasma cells (PB/PC)


title: BEAS2B: A598V_1

description: replicate 1


title: Tonsil 1 B cells


title: LeafBlade_Control_69DAT_12:00_2013

description: Gene expression of rice leaf at 69 days after transplanting in control paddy field

source_name: Leaf blade, control condition, 69 days after transplanting, 12:00, 2013

value: Control

value: 69 days after transplanting

value: Paddy field


title: BEAS2B: A762E_1

description: replicate 1


title: LeafBlade_-N_20DAT_12:00_2013

description: Gene expression of rice leaf at 20 days after transplanting in nitrogen deficient paddy field

source_name: Leaf blade, nitrogen deficient condition, 20 days after transplanting, 12:00, 2013


title: Gommerman_13v2_PPless-29

status: Public on Oct 05 2019

city: Toronto

first: Jennifer

last: Gommerman

state: Ontario

address: 1 King's College Circle, MSB 7310

department: Immunology

country: Canada

institute: University of Toronto

data_processing:
Sequenced reads were trimmed for adaptor sequence
Sequenced reads were mapped to the mouse whole genome (assembly mm10) using TopHat2 version 2.1.0 in its default setting
The reads mapping to multiple genomic regions were removed from subsequent analysis. The mapped reads were quantified against the refseq annotation using HTSeq-count version 0.7.2 in its default setting.
The read counts were normalized using a negative binomial model using Bioconductor package DESeq2 version 1.14.1. The differential expression analysis was performed using DESeq2. Plots using RNA-seq data were generated in R version 3.3.2.
Genome_build: mm10
Supplementary_files_format_and_content: plain text file for read count

source_name: MLN stromal cells

extract_protocol:
At day 8 post-RV infection, MLN from adult mice were dissected into small pieces and digested with Collagenase P, Dispase and DNase I. The single cells were stained with APC-eFluor 780 dump antibodies (CD45.2, Ter-119, EpCAM), FITC dump antibody (B220), and antibodies against PDPN (PE) and CD31 (eF450) in the presence of Fc block. The live CD45-/Ter-119-/EpCAM-/CD19-/CD31- stromal cells were sorted out on an Influx sorter.
RNA libraries were prepared for sequencing using Illumina Ultra-low Input cDNA library preparation kit

treatment_protocol: To inhibit LTbR signalling in utero, pregnant WT dams were injected with 200µg LTbR-Ig or control antibodies at day 14.5 and 17.5 of pregnancy via tail vein injections.

tag: strain

tag: bm chimeras

value: WT mice (E14/E17 LTbR-Ig)

tag: timepoint

value: day 8 post-rotavirus infection


title: Gommerman_14v2_PPless-46


title: LeafBlade_Control_62DAT_12:00_2013

description: Gene expression of rice leaf at 62 days after transplanting in control paddy field

source_name: Leaf blade, control condition, 62 days after transplanting, 12:00, 2013

value: Nipponbare

tag: tissue

value: 62 days after transplanting


title: LeafBlade_-N_13DAT_12:00_2013

description: Gene expression of rice leaf at 13 days after transplanting in nitrogen deficient paddy field

source_name: Leaf blade, nitrogen deficient condition, 13 days after transplanting, 12:00, 2013


title: LeafBlade_-N_27DAT_12:00_2013

description: Gene expression of rice leaf at 27 days after transplanting in nitrogen deficient paddy field

source_name: Leaf blade, nitrogen deficient condition, 27 days after transplanting, 12:00, 2013


title: LeafBlade_Control_55DAT_12:00_2013

description: Gene expression of rice leaf at 55 days after transplanting in control paddy field

source_name: Leaf blade, control condition, 55 days after transplanting, 12:00, 2013

value: 55 days after transplanting


title: LeafBlade_Control_48DAT_12:00_2013

description: Gene expression of rice leaf at 48 days after transplanting in control paddy field

source_name: Leaf blade, control condition, 48 days after transplanting, 12:00, 2013


title: LeafBlade_Control_41DAT_12:00_2013

description: Gene expression of rice leaf at 41 days after transplanting in control paddy field

source_name: Leaf blade, control condition, 41 days after transplanting, 12:00, 2013

value: 41 days after transplanting


title: Gommerman_11_WT-41

value: WT mice (E14/E17 control Ig)


title: LeafBlade_Control_27DAT_12:00_2013

description: Gene expression of rice leaf at 27 days after transplanting in control paddy field

source_name: Leaf blade, control condition, 27 days after transplanting, 12:00, 2013

value: 27 days after transplanting


title: LeafBlade_Control_13DAT_12:00_2013

description: Gene expression of rice leaf at 13 days after transplanting in control paddy field

source_name: Leaf blade, control condition, 13 days after transplanting, 12:00, 2013

value: 13 days after transplanting


title: LeafBlade_Control_20DAT_12:00_2013

description: Gene expression of rice leaf at 20 days after transplanting in control paddy field

source_name: Leaf blade, control condition, 20 days after transplanting, 12:00, 2013

value: 20 days after transplanting


title: LeafBlade_Control_34DAT_12:00_2013

description: Gene expression of rice leaf at 34 days after transplanting in control paddy field

source_name: Leaf blade, control condition, 34 days after transplanting, 12:00, 2013

value: Leaf blade

value: 34 days after transplanting


title: Gommerman_10v2_WT-22


title: Gommerman_07_WT-1


title: Gommerman_08_WT-2


title: Gommerman_6_B220high-WT-3

source_name: MLN B cells

extract_protocol:
At the day 8 post-rotavirus infection, the draining MLN were harvested from Blimp-1 YFP ->WT chimeric mice and ground between glass slides, followed by filtration with a 70-µm cell strainer. The single cells were stained with antibodies against mouse CD45.2 (APC-eFluor780), B220 (BV605) and APC-dump antibodies (CD3, CD11c and F4/80) in the presence of Fc block. The live CD45+/CD3-/CD11c-/F4/80-/B220low/YFPhigh (labeled as “B220low” in the sample names) or live CD45+/CD3-/CD11c-/F4/80-/B220high/YFPhigh (labeled as “B220high”) cells were sorted out on an Influx sorter.
RNA libraries were prepared for sequencing using Illumina Ultra-low Input cDNA library preparation kit

value: Blimp-1 YFP->WT mice


title: Gommerman_5_B220high-WT-2


title: Gommerman_3_B220low-WT-3


title: Gommerman_4_B220high-WT-1


title: Gommerman_2_B220low-WT-2


title: Gommerman_1_B220low-WT-1


title: ChIP-seq_estrogen_2h

city: Bergen

first: Tomasz

last: Stokowy

address: Nygardsgaten 5

department: IT Division

country: Norway

institute: University of Bergen

description: estrogen treated for 2hours (10nM)

data_processing:
Quality control of reads was performed with FastQC software
Reads were mapped to the human genome (hg19) with Bowtie2.0.4
Peak detection was carried with the MACS program (detected peaks are given in bed files)
HSF1 target sites were annotated to genomic regions using HOMER software (annotated binding sites are given in text file)
Peak intersections and their genomic coordinates were found using Bedtools software
The significance of differences between control untreated cells and cells subjected to estrogen and hyperthermia was estimated using MACS software; the FDR=0.05 level was selected as the significance threshold.
Genome_build: hg19
Supplementary_files_format_and_content: bed - detected peaks, can be open in text editors/Excel; txt - annotated binding sites, can be opened in text editors/Excel.

source_name: estrogen treated for 2hours (10nM)

growth_protocol: The wild-type MCF7 cells were purchased from ATCC (HTB-22) and used as a primary model. Cells were grown in DMEM/F12 medium supplemented with 10% fetal bovine serum and antibiotic-antimycotic cocktail (penicillin, streptomycin, amphotericin) at 37 °C in a humidified 5% CO2 atmosphere.

extract_protocol:
At the appointed experimental points culture medium was removed and fixation was performed using 1% formaldehyde in PBS for 12 min at RT with rotating. Formaldehyde fixation was quenched by glycine (125 mM final concentration) and then nuclei were isolated using buffers and protocol from iDeal ChIP-seq Kit for Transcription Factors (Diagenode). Chromatin of nuclei re-suspended in 200 µl was sheared using Bioruptor® PLUS combined with the Bioruptor® Water cooler & Single Cycle Valve (at HIGH power setting) with 20 cycles of 30 sec shearing followed by 30 sec of standby; chromatin fragments with approximate length 100-600 bp were obtained. Chromatin immunoprecipitation was carried out using the iDeal ChIP-seq Kit for Transcription Factors (Diagenode) with 30μg of chromatin and 3µl/sample of anti-HSF1 polyclonal antibody (ADI-SPA-901, Enzo) or without antibody (mock-IP), according to the manufacturer protocol.
Immunoprecipitated DNA fragments from six ChIP replicates was pooled. ChIP samples and input DNA were sequenced using the HiSeq 1500 system with TruSeq workflow (Illumina)

treatment_protocol: Cells were seeded on 10cm2 culture plates. Next day the medium was replaced into phenol-free DMEM/F12 medium supplemented with 5% dextran-activated charcoal-stripped FBS and 48 hours later cells were subjected to hyperthermia at 43°C for 15 minutes or 17β-estradiol was added to final concentration of 10nM for indicated time (1h and 2h).

tag: tumor

value: adenocarcinoma

tag: Sex

value: female

tag: age

value: 69 years

tag: tissue/cells

value: breast

tag: chip antibody

value: HSF1 polyclonal antibody (Enzo, ADI-SPA-901)


title: ChIP-seq_estrogen_1h

description: estrogen treated for 1hour (10nM)

source_name: estrogen treated for 1hour (10nM)

tag: cell line


title: ChIP-seq_control

description: untreated control

source_name: untreated control


title: ChIP-seq_hyperthermia_15min

description: subjected to hyperthermia (43°C) for 15minutes


title: RNA-seq_control

description:
untreated control cells
NG.7926_wt_k_lib80492_4027_8_1

data_processing:
alignment of reads to reference genome using hisat 2.0.5
feature counting using featureCounts
normalization using DESeq2
Genome_build: hg19
Supplementary_files_format_and_content: tab separated text counts file with samples in columns and genes in rows
Supplementary_files_format_and_content: tab separated text normalized expression file with samples in columns and genes in rows

source_name: untreated control cells

extract_protocol:
Total RNA from 10^6 cells was isolated using the Direct-ZolTM RNA MiniPrep Kit (Zymo Research) and digested with DNase I (Worthington Biochemical Corporation, NY, USA)
RNA libraries were prepared for sequencing according to the standard Illumina protocols

treatment_protocol: Cells were seeded on culture plates. Next day the medium was replaced into phenol-free DMEM/F12 medium supplemented with 5% dextran-activated charcoal-stripped FBS and 48 hours later 17β-estradiol was added to final concentration of 100nM for 4hour or cells were subjected to hyperthermia (43°C) for 1hour with 2hours of recovery.


title: RNA-seq_hyperthermia_2h

description:
cells subjected to hyperhermia (43°C) for 1hour & 2hours of recovery
NG.7926_wt_hs_lib80493_4027_1_1


title: RNA-seq_estrogen_4h

description:
cells treated with estrogen (100nM) for 4hours
NG.7926_wt_e2_lib80494_4027_8_1


title: dKO male 6M

city: Seoul

first: Ji Hoon

address: Kwanakro 1

institute: Seoul national University, Seoul, Korea

data_processing:
RNA-seq reads were aligned to the mm10 genome assembly using Tophat2 (v2.0.9).
bedtools was used to get read counts for genes (bedtools multicov -split -D).
read counts were obtained for each sample for RNA-seq data.
The reads were normalized (based on Generalized Linear Models ) using EdgeR.
Genome_build: mm10
Supplementary_files_format_and_content: Read counts

source_name: muscle stem cell

growth_protocol: All mouse lines were backcrossed onto a C57BL/6 background and were housed and handled according to the guidelines of the Institutional Animal Care and Use Committee (IACUC) at Seoul National University.

extract_protocol:
Limb muscles were mechanically dissected and dissociated in Dulbecco’s modified Eagle’s medium (DMEM) containing 10% horse serum (Hyclone, Logan, UT, USA), collagenase II (800 units/mL; Worthington, Lakewood, NJ, USA), and dispase (1.1 units/mL; StemCell Technologies, Vancouver, BC, Canada) at 37°C for 60 min. Digested suspensions were subsequently triturated and washed with DMEM to harvest mononuclear cells. Mononuclear cells were stained with Sca1-FITC (clone D7; BioLegend, San Diego, CA, USA), CD31-APC (clone MEC 13.3; BD Biosciences, Franklin Lakes, NJ, USA), CD45-APC (clone 30-F11; BD Biosciences), and Vcam1-Biotin (clone 429; BD Biosciences). Streptavidin-PE/Cy7 (BioLegend) was used as a secondary reagent. Stained cells were analysed and Lin–Vcam+Sca1– SCs were isolated using a FACS Aria III cell sorter (BD Biosciences). Total RNA was extracted from freshly isolated MuSCs using a TRIzol Reagent (Life Technologies, Carlsbad, CA, USA)
RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: To delete the genes, 3-months-old mice were orally administered with Tamoxifen (20 mg/mL in corn oil, Sigma) for 5 consecutive days.

tag: cell type

value: Freshly isolated MuSCs

tag: passages

tag: genotype

value: dKO


title: pMV261_stat_rep3

city: Moscow

first: Artem

last: Grigorov

address: Ulitsa Miklukho-Maklaya, 16/10

department: Genomics and Postgenomic Technologies

country: Russia

institute: Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry

data_processing:
Sequenced reads were mapped to M.tuberculosis H37Rv genome using bowtie2 v2.3.4.3 with parameters -p 4 --local
Read counting was performed using FeatureCounts
Genome_build: Al123456.3
Supplementary_files_format_and_content: comma-delimited text files includes raw counts for each sample

organism: Mycobacterium tuberculosis

source_name: bacterial culture

growth_protocol: M. tuberculosis H37Rv, pMV and OVER M. tuberculosis strains were initially grown from frozen stocks for 10 days in Sauton medium containing (per liter): 0.5 g KH2PO4, 1.4 g MgSO4×7H2O, 4 g L-asparagine, 60 ml glycerol, 0.05 g ferric ammonium citrate, 2 g sodium citrate, 0.1 ml 1% ZnSO4, pH 7.0 (adjusted with 1M NaOH), and supplemented with ADC growth supplement  [1], 0.05% Tween 80 and 50 µg/ml kanamycin (Sigma-Aldrich, St Louis, MO, USA) at 37°C with agitation (200 rpm). The starter cultures were inoculated into fresh medium (the same composition) and incubated until the stationary phase.

extract_protocol:
Bacterial cultures were grown up to the stationary phase,  rapidly cooled on ice, centrifuged, and total RNA was isolated by phenol-chloroform extraction after cell disruption with Bead Beater. After isolation, RNA was treated with Turbo DNase (Life Technologies, Carlsbad, CA, USA) to remove traces of genomic DNA, and purified with the RNeasy mini kit (Qiagen, Venlo, Netherlands).
RNA samples were depleted of 16S and 23S rRNA using RiboMinus Transcriptome Isolation Kit, Bacteria (ThermoFisher). Sequencing libraries were generated using the resulting ribosomal transcript-depleted RNA and NEBNext Ultra II Directional RNA Library Prep Kit (NEB) according to the manufacturers’ protocol.

tag: genotype/variation

value: pMV

tag: phase

value: Stationary

tag: experiment

value: overexpression


title: pMV261_stat_rep1


title: WT spindle rep2

city: Montreal

first: Eric

last: Lecuyer

state: Quebec

address: 110 Pine Ave W

department: RNA biology

institute: IRCM

data_processing:
Read quality was assessed using FastQC. No trimming was deemed necessary.
Read alignment was executed using TopHat on the Human GRCh37 genomes from Ensembl
The GTF annotation file used during the alignment and for counting the number of reads aligned to each feature was also downloaded from Ensembl (release 75). Read count was obtained with featureCounts
Normalized count values (FPKM) and differential expression was computed with DESeq2
Gene biotypes and additional information were obtained via the biomaRt R library.
Genome_build: Human GRCh37 genomes from Ensembl
Supplementary_files_format_and_content: FPKM_count

source_name: HCT116 cell line

growth_protocol: Colorectal HCT116 cells and STAU1-KO CRISPR-derived clones were cultured in McCoy's medium with 10% fetal bovine serum, 20 mM glutamine and 1% penicillin–streptomycin (Wisent) in a humidified atmosphere of 5% CO2 at 37°C.

extract_protocol:
Cells were diluted in lysis buffer (80 mM Pipes, pH 6.8, 1 mM MgCl2, and 1 mM EGTA) with 30% glycerol and 0.1% Triton X-100 and centrifuged over a 10-ml cushion of 60% glycerol for 10 min at 17,000 g. The microtubule pellet was dissolved in hypotonic buffer and centrifuged again to obtain purified mitotic spindle preparations. RNA was extracted using TRIZOL Reagent. TURBO DNA-free™ Kit was used to eliminate DNA contamination and RNA was purified with RNeasy mini kit.
RNAseq libraries were prepared using TruSeq stranded total RNA sample preparation kit (Illumina).
rRNA-depleted stranded RNA-seq

treatment_protocol: Cells were synchronized in late G2 with RO-3306 for 16h, released and incubated in the presence of taxol (100 μM) for 15 min. Mitotic cells were collected by shake-off.

value: Wilt type

value: Tumor cell line


title: STAU1-KO input rep2

source_name: STAU1-KO HCT116 cell line


title: STAU1-KO spindle rep1


title: STAU1-KO spindle rep2


title: WT male 6M

value: WT


title: ChIP-seq_Input_sample

description: input sample (mix of all treatments)

source_name: input sample (mix of all treatments)


title: pMV261_stat_rep2


title: STAU1-KO input rep1


title: WT spindle rep1


title: LeafBlade_-K_48DAT_12:00_2013

description: Gene expression of rice leaf at 48 days after transplanting in potassium deficient paddy field

source_name: Leaf blade, potassium deficient condition, 48 days after transplanting, 12:00, 2013

tag: cultivar

value: Nipponbare

tag: condition

value: Potassium deficient condition

tag: growth/development stage

value: 48 days after transplanting

tag: time

tag: field

value: Paddy field


title: MTS1338_over_stat_rep2

tag: strain

value: OVER


title: MTS1338_over_stat_rep1


title: RH2ET1SS03

city: MEXICO

first: ROSAURA

last: HERNANDEZ RIVAS

state: MEXICO

address: AV. IPN 2508

department: BIOMEDICINA MOLECULAR

country: Mexico

institute: CINVESTAV

data_processing:
A total of 34,897,385 and 46,698,915 paired-end RNA-seq reads for the RH2ET1SS01 and RH2ET1SS03 respectively, (corresponding to two biological replicates of cysts treatment with ethanol) and 33,531,808 and 36,965,892 paired-end RNA-seq reads for the RH2ET1SS02 and RH2ET1SS04 respectively (corresponding two biological replicates of cysts treatment with 200 nM of Trichostatin A) were adapter and quality trimmed using Trimmomatic version 0.36.5
The high-quality reads were aligned to the Entamoeba invadens reference genome (E. invadens IP1 genome) by TopHat2 v2.0.11. Only uniquely mapped reads were counted for further analysis. The transcriptome assemblies in FPKM and differential expression were executed with Cufflinks v2.2.1. For each RNA sample two technical replicates were merged.
We used a false discovery rate of ≤0.05 and the absolute value of log2 ratio ≥1.5 as the threshold to evaluate the significance of gene expression difference.
Genome_build: AmoebaDB 40
Supplementary_files_format_and_content: tabular text files include pval, qval and b values

organism: Entamoeba invadens

source_name: cysts

growth_protocol: Axenic cultures of E. invadens strain IP-1 trophozoites were maintained in LYI-S-2 medium supplement with 10% bovine serum and 2.5% Diamond vitamin mixture at 26 °C .

extract_protocol:
Total RNA extraction was carried out using the TRIZOL method
The integrity of the total RNA samples for the preparation of the RNA-seq libraries was determined by Automated Capillary Electrophoresis using the Bioanalyzer 2100 system (Agilent Technologies, Inc., Santa Clara, CA) and the Agilent RNA 6000 Nano chip, the values of RIN obtained for the samples were >8. The mRNA was enriched by magnetic beads. The construction of the RNA-seq libraries was performed using the TruSeq RNA Library Prep Kit v2 (Illumina, Inc., San Diego, CA).  Subsequently, the RNA was fragmented in a range of 100-400 pb. Both ends of the double-stranded cDNA were repaired to subsequently bind the specific Illumina adapters, using T4 DNA polymerase and T4 DNA ligase, respectively. Finally, each library was amplified by PCR with specific oligonucleotides for the P5 and P7 adapters of Illumina and thus increase the number of molecules for the massive sequencing. Each library was analyzed by Automated Capillary Electrophoresis (Bioanalyzer 2100, Agilent Technologies, Inc., Santa Clara, CA) using the DNA High Sensitivity chip. Finally, the libraries were quantified using the Qubit® fluorometer with the Qubit ds DNA HS Assay kit (Invitrogen). The libraries were clonally amplified in the Flowcell and sequenced with the NextSeq 500 platform of the Illumina brand (Illumina, Inc., San Diego, CA) and with the NextSeq 500/550 Mid Output kit v2 (150 cycles) with a run configuration Paired-End 2X150 indexed and following the protocol described by the manufacturer.

treatment_protocol: To induce encystation, trophozoites were harvested in the late logarithmic phase and the cells were transferred to screw cap glass tubes with LG encystation medium (TYI medium diluted to 47% without glucose) plus 5% bovine serum at a final concentration of 5x105/ml. TSA was added at a concentration of 200 nM and absolute ethanol was used as control. The cells were incubated for 24 h and after this time the cells were collected.

tag: treatment

value: cysts treatment with absolute ethanol during 24 h


title: RH2ET1SS04

value: cysts treatment with 200 nM of Trichostatin A during 24 h


title: RH2ET1SS01


title: RH2ET1SS02


title: WT input rep2


title: PC-3_20

city: Shenzhen

first: zhang

last: xiantong

address: Xinan Road

institute: Southern Medical University Shenzhen Hospital

data_processing:
Sequenced reads were trimmed for adaptor sequence, HISAT2 was used for alignment
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using featureCounts
Genome_build: Human genome build 75

source_name: prostate

growth_protocol: HepG2 cells were cultured in DMEM medium, and PC-3 in F12K medium. All cultured media were supplement with 10% fetal bovine serum, 100 units/ml penicillin sodium and 100 μg/ml streptomycin. Cultures were maintained in a 5% CO2 humidified atmosphere at 37°C.

extract_protocol:
Total RNA was extracted using RNeasy kit (Qiagen) and RNA concentration was quantified. The quality of total RNA was analyzed using Agilent 2100.
Sequencing libraries construction and paired-end deep sequencing were performed by Novogene (Tianjin, China) using Illumina PE150 system according to the manufacturers.

treatment_protocol: HepG2 and PC-3 cells were treated with or without CuC for 24 hours

value: cucurbitacin C

value: a bone metastasis of a grade IV prostatic adenocarcinoma cell

tag: tissue

value: prostate

tag: age

value: 62 years adult


title: MTS1338_over_stat_rep3


title: PC-3_C


title: HepG2_40

source_name: liver

value: hepatocellular carcinoma cell

value: liver

value: 15 years adolescent


title: PANC-1 cells, A2055, UP3

city: Wuhan

first: Pan

last: Shutao

state: State...

address: Wuhan, Hubei Province, China

institute: Tongji Hospital

description: Biological replicate 3 of 3. Stable LINC01111-upregulated transfected pancreatic cancer cells, harvested after several passages.

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Drosophila Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G3000.

data_processing: RMA normalization

source_name: Pancreatic cancer cells

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

growth_protocol: PANC-1 cell line were cultured in Dulbecco's Modified Eagle's Medium supplemented with 10% FBS. All cell lines were cultured in a humidified incubator containing 5% CO2 at 37°C.

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions.

treatment_protocol: We used a lentiviral system to establish stable LINC01111-upregulated (LINC01111-UP) PC cell line, and the qRT-PCR results confirmed the functioning system.

value: Pancreatic cancer cell line PANC-1


title: HepG2_20


title: WT input rep1

value: Wilt type

value: Tumor cell line


title: Sample 16_Ampicillin treated 6 weeks old replicate 5

status: Public on Oct 04 2019

city: Kingston

first: David

last: Lillicrap

state: ON

address: 88 Stuart Street

department: Pathology and Molecular Medicine

institute: Queen's University

data_processing:
Bacterial microbiome data were preprocessed using the QIIME 2 (Quantitative Insights Into Microbial Ecology, version 2019.4) pipeline.23 Raw paired-end data were manually imported into QIIME 2 using PairedEndFastqManifestPhred33 format for Illumina 2.0
Paired-end data were merged using q2-vsearch plugin (via vsearch join-pairs ).
Quality filtering and trimming of sequence reads was performed via the quality-filter q-score-joined function using default settings.
Sequences were denoised and chimeras were removed using the Deblur plugin25 (via denoise-16S, p-trim-length set at 233).
Open reference OTU picking and taxonomy assignment was performed against Greengenes 13_826 at 99% identity.
The taxonomy classification was performed using the Naive Bayes classifier (via fit-classifier-naive-bayes for training and classify-sklearn for application).
The phylogenetic diversity metrics were generated using the align-to-tree-mafft-fasttree pipeline from the q2-phylogeny plugin.
Finally, the alpha- and beta-diversity analysis was performed using q2‐diversity plugin [multiple citations: https://github.com/qiime2/q2-diversity/blob/master/q2_diversity/citations.bib]. Microbiome visualizations were made with MicrobiomeAnalyst.29
Genome_build: Greengeenes 13_826 at 99% identity

organism: mouse gut metagenome

source_name: Ampicillin treated 6 weeks old

growth_protocol: Mice were housed in sterile conditions in individually ventilated cages (Techniplast IsoCageP - Bioexclusion System positive pressure rack)

extract_protocol:
Mice were euthanized, the cecum dissected and contents collected under sterile conditions Cecal contents at 6 weeks of age and at study endpoint. Samples were immediately frozen and stored at -80oC until analysis. DNA from 50 mg of cecal contents was isolated from each mouse using DNeasy PowerSoil Kit (Qiagen).
DNA sequencing was performed by the Centre for the Analysis of Genome Evolution and Function (Toronto). The V4 hypervariable region of the 16s rRNA gene was amplified using a universal forward sequencing primer and a uniquely barcoded reverse sequencing primer to allow for multiplexing.22 All amplification reactions were done in triplicate, checked on a 1% agarose TBE gel and then pooled. The final library was purified using 0.8X magnetic Ampure XP beads, selecting for the bacterial V4 amplified band. The purified library was quantified and loaded on to the Illumina MiSeq for sequencing, according to manufacturer’s instructions (Illumina, San Diego, CA). Sequencing was performed using the V2 (150bp x 2) chemistry.

treatment_protocol: Ampicillin 12 hourly gastric gavage of 0.5mg (50mg/kg) for 7 days

value: C57BL6 Exon 16 KO Hemophilia A

value: 6 weeks old

tag: treatment group

value: Ampicillin treated

tag: molecule subtype

value: Cecal contents total DNA


title: Sample 20_Control Endpoint replicate 4

source_name: Control Endpoint

value: Endpoint

value: Control


title: Sample 17_Control Endpoint replicate 1


title: Sample 21_Ampicillin treated Endpoint replicate 1

source_name: Ampicillin treated Endpoint


title: Sample 22_Ampicillin treated Endpoint replicate 2


title: Sample 18_Control Endpoint replicate 2


title: Sample 24_Ampicillin treated Endpoint replicate 4


title: Sample 15_Ampicillin treated 6 weeks old replicate 4


title: Sample 23_Ampicillin treated Endpoint replicate 3


title: Sample 14_Ampicillin treated 6 weeks old replicate 3


title: Sample 13_Ampicillin treated 6 weeks old replicate 2


title: Sample 12_Ampicillin treated 6 weeks old replicate 1


title: Sample 6_Control 6 weeks old replicate 2

source_name: Control 6 weeks old


title: Sample 7_Control 6 weeks old replicate 3


title: Sample 8_Control 6 weeks old replicate 4


title: Sample 5_Control 6 weeks old replicate 1


title: D12 P

city: Tokyo

first: Norikazu

last: Saiki

address: 1-5-45 Yushima, Bunkyo-ku

department: Institute of Research

institute: Tokyo Medical and Dental University

data_processing:
Illumina OLB 1.9.4 software used for basecalling and bcl conversion/demultiplexing/fastq creation.
Transcripts Per Million (TPM) were quantified using kallisto v0.44.0
Supplementary_files_format_and_content: tab-delimited text files include TPM values for each Sample.

source_name: Boundary organoid

growth_protocol: colonies of hiPSCs were isolated in Accutase and 150,000 cells/mL were plated on Matrigel coated tissue culture plate. Medium was changed to RPMI 1640 medium containing 100 ng/mL Activin A and 50 ng/mL bone morphogenetic protein 4  at Day 1, 100 ng/mL Activin A and 0.2 % fetal calf serum at Day 2 and 100 ng/mL Activin A and 2% FCS at Day 3. For Day 4-7, cells were cultured in gut growth medium (Advanced DMEM/F12 with 15 mM HEPES, 2 mM L-glutamine, penicillin-streptomycin, B27 and N2) supplemented with 200 ng/mL noggin, 500 ng/ml fibroblast growth factor 4 and 2 µM CHIR99021 for anterior gut cell induction and supplemented with 500 ng/ml FGF 4 and 3 µM CHIR99021 for posterior gut cell induction. Cultures for cell differentiation were maintained at 37°C in an atmosphere of 5% CO2 / 95% air and the medium was replaced every day.   On Day 7, anterior or posterior gut cells were dissociated to single cells by incubation with TrypLE Express at 37°C. Cells were centrifuged at 1000 rpm for 3 minutes and, after removing supernatant, the pellet was re-suspended in gut growth medium containing 10 uM of Y-27632 dihydrochloride. The anterior or posterior gut cell suspensions were plated on 96 well round bottom ultra-low attachment plate at density of 10,000 cells/well and incubated at 37°C for 24 hours to form spheroid. On Day 8, generated single anterior spheroid and posterior spheroid were mixed on 96 well round bottom ultra-low attachment plate in gut growth medium for 24 hours to form fused boundary spheroids (A-P spheroids). On Day9, A-P spheroids were embedded in Matrigel drop and were cultured in gut growth medium to generate multi-organ organoids.

extract_protocol:
RNA was isolated using the RNeasy mini kit (Qiagen, Hilden, Germany).
Sample preparation for RNA sequencing was performed using SMART-seq v4 Ultra Low Input RNA Kit for Sequencing (Clontech Laboratories) according manufacture’s user manual.

tag: cell type

value: iPSC derived boundary organoid

tag: region

value: Posterior part of micro-dissected organoid

tag: culture period

value: day12 from undifferentiated iPSC


title: PANC-1 cells, A2051, NC2

description: Biological replicate 2 of 3. Control pancreatic cancer cells, untreated, harvested after several passages.

tag: cell line

tag: genotype

value: control


title: PANC-1 cells, A2054, UP2

description: Biological replicate 2 of 3. Stable LINC01111-upregulated transfected pancreatic cancer cells, harvested after several passages.


title: PANC-1 cells, A2052, NC3

description: Biological replicate 3 of 3. Control pancreatic cancer cells, untreated, harvested after several passages.


title: PANC-1 cells, A2053, UP1

description: Biological replicate 1 of 3. Stable LINC01111-upregulated transfected pancreatic cancer cells, harvested after several passages.


title: Sample 19_Control Endpoint replicate 3


title: D12 B

value: Boundary part  of micro-dissected organoid


title: Gommerman_09_PPless-5

source_name: MLN stromal cells

tag: bm chimeras

value: WT mice (E14/E17 LTbR-Ig)

tag: timepoint

value: day 8 post-rotavirus infection


title: D9 B

value: day9 from undifferentiated iPSC


title: D9 A

value: Anterior part  of micro-dissected organoid


title: D9 P


title: D12 A


title: D8 A

value: day8 from undifferentiated iPSC


title: D8 P


title: Fresh_3_E2

city: Salt Lake CIty

first: Jason

last: Gertz

state: UT

address: 2000 Circle of Hope

department: Oncological Sciences

institute: University of Utah

data_processing:
Library strategy: FFPEcap-seq
Reads were aligned to the hg19 build of the human genome using Bowtie V 1.1.2 and the following arguments: bowtie -S --chunkmbs 512 -m 1 -t --best -q -l 32 -e 80 -n 2. Reads were also aligned to a refSeq reference using Bowtie V 1.1.2 and the following arguments: bowtie -S -n 2 -a -m 10 -S --chunkmbs 512.
Unique Molecular Index and additional sequences were trimmed off of the 5' end of the read.  Indexes were added to the read name and reads with the same position and index were collapsed into a single read.
Genome aligned reads mapping to hg19 UCSC knownGene gene models were counted using featureCounts from the SubRead package. Normalized counts were generated using DESeq2.
Genome_build: hg19, refSeq
Supplementary_files_format_and_content: bw files contain reads mapped to the hg19 human genome build or a refseq reference. Reads have been collapsed, which removes duplicate molecules that contained identical unique molecular indexes and mapped to identical locations.
Supplementary_files_format_and_content: Tab file contains a matrix of normalized gene counts for matched FFPE derived RNA and freshly derived RNA FFPEcap-seq, and standard RNA-seq from GSE109892.

source_name: Ishikawa

growth_protocol: Ishikawa cells (Sigma Aldrich), were maintained at 37°C with 5% CO2 in RPMI-1640 media containing 10% fetal bovine serum, 50 U/mL penicillin, and 50 mg/mL streptomycin.

extract_protocol:
Fresh RNA was extracted with the Quick-RNA Miniprep kit.  For FFPE RNA, four 20 μm scrolls were collected from these samples and RNA was extracted using the RNeasy FFPE kit (Qiagen).
A detailed FFPEcap-seq protocol can be found in the supplemental protocol. RNA concentration was measured using a Qubit 2.0 with the RNA high sensitivity or RNA broad range assay (ThermoFisher), depending on the concentration.  Enzyme pre-treatment was performed using 1 μL (1 unit) Terminator Nuclease (Lucigen), 2 μL T4 Polynucleotide Kinase (New England Biolabs), 2 μL 10x Terminator Buffer A, 2 μL 10 mM ATP, 1 μL SUPERase In (ThermoFisher), input RNA, and water in a 20 μL reaction. Samples were incubated for 45 minutes at 30°C before being cleaned up with the RNA Clean and Concentration kit (Zymo Research). RNA was eluted using 6 μL of water, with 5 μL being collected after centrifugation. 1 μL of eluted RNA was used for quantification with the Qubit 2.0 RNA high sensitivity kit (ThermoFisher). For enzymatic treatment controls, the above procedure was followed except Terminator and T4 Polynucleotide Kinase were replaced with water. When polyphosphatase was tested, 1 μL (20 units) RNA 5’ polyphosphatase (Lucigen) was included in the reaction.  To begin the modified nanoCAGE library preparation, trehalose-sorbitol solution was made by adding 5 mL of a saturated trehalose solution (Sigma) to 10 mL of 1.28 g/mL sorbitol solution (Sigma). 1 g of celex 100 (Sigma) was added to the solution and vortexed vigorously and allowed to sit for 3 hours at room temperature.  The tube was then centrifuged for 10 minutes at 600xg and the supernatant was aliquoted and stored at -30°C.  Oligo master mix was made by combining 8 μL of Trehalose-Sorbitol solution with 1 μL 1 mM Template switching oligo, and 1 μL 100 μM reverse transcriptase oligo (see Table S1 for all oligo sequences).  All oligonucleotides were ordered from Integrated DNA technologies.  1 μL of the oligo master mix was combined with the remaining 4 μL of RNA and incubated at 65°C for 10 minutes, then immediately moved to ice for 2 minutes. The template switching reaction contained 1 μL Prime Script Reverse Transcriptase (Takara), 2 μL 5x Prime Script buffer, 1.5 μL 5M Betaine, 0.5 μL 200 mM DTT, and 0.625 μL 10 mM dNTP mixture. The template switching reaction mixture was combined with the RNA oligo mixture and heated to 22°C for 10 minutes, 40°C for 30 minutes, and then 75°C for 15 minutes.  The sample was then cleaned up using Ampure XP beads (Beckman Coulter) with a ratio of 1.5:1 of bead volume to sample volume.  The cDNA was eluted in 40 μL water. For second strand synthesis, 7.5 μL purified cDNA was added to 25 μL Phusion HF master mix (New England Biolabs), with 2.5 μL 10 μM 2nd strand forward primer, 2.5 μL of 10 μM 2nd strand reverse primer, and 12.5 μL of water. The reaction was heated at 95°C for 1 minute, followed by 24 cycles of 95°C for 15 seconds, 65°C for 10 seconds, and 68°C for 2 minutes.  This reaction was purified using Ampure XP beads (Beckman Coulter) with a 0.8:1 ratio of bead volume to sample volume and eluted in 30 μL water. The final library was created by taking 40 ng of purified double stranded cDNA and mixing it with 25 μL 2x Phusion HF master mix (New England Biolabs), 1.25 μL 10 μM library forward primer, 1.25 μL 10 μM library reverse primer (containing a sample index), and water to a total volume of 50 μL. Samples were heated to 95°C for 1 minute, followed by 2 cycles of 95°C for 15 seconds, 55°C for 10 seconds, and 68°C for 2 minutes, then followed by 8 cycles of 95°C for 15 seconds, 65°C for 10 seconds, and 68°C for 2 minutes. This reaction was purified using Ampure XP beads (Beckman Coulter) with a 0.8:1 ratio of bead volume to sample volume and eluted in 30 μL water.

treatment_protocol: Cells were transferred to hormone depleted media five days prior to RNA harvest in order to match previously performed RNA-seq experiments. Hormone depleted media consisted of phenol red-free RPMI-1640, 10% charcoal-dextran treated fetal bovine serum (Sigma Aldrich), 50 U/mL penicillin, and 50 mg/mL streptomycin.

tag: experiment group

value: Fresh and FFPE matched treatment analysis

value: Fresh


title: Fresh_Mock_Treatment_3_E2

value: Fresh Mock


title: Fresh_2

value: Fresh DMSO


title: FFPE_Mock_Treatment_3

value: FFPE Mock


title: FFPE_3

value: FFPE


title: PANC-1 cells, A2050, NC1

description: Biological replicate 1 of 3. Control pancreatic cancer cells, untreated, harvested after several passages.

value: Pancreatic cancer cell line PANC-1


title: FFPE_4


title: Fresh_Mock_Treatment_4


title: Fresh_1_DMSO


title: Fresh_4


title: FFPE_Mock_Treatment_2

value: FFPE Mock Treatment


title: Fresh_Mock_Treatment_2


title: FFPE_1


title: Fresh_Mock_Treatment_1_DMSO


title: FFPE_2


title: i18cs_1

description: Internal 18 Carbon Spacer 1

value: Concatemer blocking, protocol improvement

value: Internal 18 Carbon Spacer


title: i18cs_3mM_Mn

description: Internal 18 Carbon Spacer, 3mM Manganese


title: FFPE_Mock_Treatment_1


title: i18cs_3

description: Internal 18 Carbon Spacer 3


title: FFPE_Mock_Treatment_4


title: i18cs_2

description: Internal 18 Carbon Spacer 2


title: Iso_6mM_Mn

description: Iso 6mM  Manganese

value: Iso 6mM Manganese


title: Iso_1mM_Mn

description: Iso 1mM  Manganese

value: Iso 1mM Manganese


title: Iso_3mM_Mn

description: Iso 3mM  Manganese

value: Iso 3mM Manganese


title: Iso_4

description: Iso 4

value: Iso


title: Iso_Terminator

description: Iso Terminator

value: Iso Terminator


title: Iso_Terminator_1mM_Mn

description: Iso Terminator  1mM Manganese

value: Iso Terminator 1mM Manganese


title: Iso_Terminator_PNK_1mM_Mn

description: Iso Terminator PNK 1 mM Manganese

value: Iso Terminator PNK 1 mM Manganese


title: Iso_2

description: Iso 2


title: Iso_Mock_Treatment

description: Iso Mock Enzyme Treatment

value: Iso Mock Enzyme


title: Iso_3

description: Iso 3


title: Iso_No_Treatment

description: Iso No Treatmentment

value: Iso No


title: Iso_No_Treatment_1mM_Mn

description: Iso No Treatmentment 1 mM Manganese

value: Iso No Treatmentment 1 mM Manganese


title: Iso_Mock_Treatment_1mM_Mn

description: Iso  Mock Enzyme Treatment 1mM Manganese

value: Iso Mock Enzyme Treatment 1mM Manganese


title: Iso_1

description: Iso 1


title: Fresh_XRN_PNK

description: Fresh XRN PNK

value: Pretreatment initial analysis

value: Fresh XRN PNK


title: Fresh_Terminator_PNK

description: Fresh Terminator PNK

value: Fresh Terminator PNK


title: Fresh_No_Treatment_2

description: Fresh No Treatment 2

value: Fresh No Treatment


title: Fresh_Terminator_PNK_PP

description: Fresh Terminator PNK PP

value: Fresh Terminator PNK PP


title: Fresh_XRN_PNK_PP

description: Fresh XRN PNK PP

value: Fresh XRN PNK PP


title: Fresh_dilution_6.25ng

description: Fresh dilution 6.25ng

value: Input requirements

value: Fresh dilution 6.25ng


title: Fresh_No_Treatment

description: Fresh No Treatment


title: Fresh_dilution_400ng

description: Fresh dilution 400ng

value: Fresh dilution 400ng


title: Gommerman_12_PPless-27

value: WT mice (E14/E17 LTbR-Ig)

value: day 8 post-rotavirus infection


title: Fresh_dilution_25ng

description: Fresh dilution 25ng

value: Fresh dilution 25ng


title: RNA_Subject23_birth

city: Adelaide

first: Feargal

middle: J

last: Ryan

state: Adelaide

address: North Terrace

country: Australia

institute: SAHMRI

data_processing:
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to GRCh38 whole genome with hisat v2.1.0 with default parameters
Alignments to genes were counted with Feature Counts and Ensembl 93 annotation.
Differential expression analysis and normalization was conducted with EdgeR
Genome_build: GRCh38
Supplementary_files_format_and_content: FeatureCounts output raw reads counts

source_name: No_BPD_DHA_peripheral blood

extract_protocol:
RNA was extraction from blood and DNA eliminated with RiboPure kit.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: disease

tag: gender

value: Female

value: Postnatal day 1

value: DHA

value: Peripheral blood


title: RNA_Subject24_birth


title: FFPE_dilution_200ng

description: FFPE dilution 200ng

value: FFPE dilution 200ng


title: FFPE_dilution_400ng

description: FFPE dilution 400ng

value: FFPE dilution 400ng


title: FFPE_dilution_25ng

description: FFPE dilution 25ng

value: FFPE dilution 25ng


title: FFPE_dilution_100ng

description: FFPE dilution 100ng

value: FFPE dilution 100ng


title: FFPE_dilution_50ng

description: FFPE dilution 50ng

value: FFPE dilution 50ng


title: Fresh_dilution_100ng

description: Fresh dilution 100ng

value: Fresh dilution 100ng


title: Fresh_dilution_50ng

description: Fresh dilution 50ng

value: Fresh dilution 50ng


title: RNA_Subject21_birth

source_name: BPD_Control_peripheral blood

value: BPD

value: Male

value: Control


title: RNA_Subject28_birth


title: RNA_Subject37_birth

source_name: BPD_DHA_peripheral blood


title: Fresh_dilution_200ng

description: Fresh dilution 200ng

value: Input requirements

value: Fresh dilution 200ng


title: RNA_Subject23

value: Postmenstrual age 36 weeks


title: RNA_Subject39_birth


title: RNA_Subject50_birth


title: RNA_Subject5_birth

value: Female


title: Fresh_Mock_Treatment

description: Fresh Mock Enzyme Treatment

value: Pretreatment initial analysis

value: Fresh Mock Enzyme


title: RNA_Subject22_birth

value: Postnatal day 1

value: DHA

value: Peripheral blood


title: RNA_Subject15

source_name: No_BPD_Control_peripheral blood


title: RNA_Subject17


title: RNA_Subject12


title: Fresh_dilution_12.5ng

description: Fresh dilution 12.5ng

value: Fresh dilution 12.5ng


title: RNA_Subject50


title: RNA_Subject4


title: RNA_Subject48


title: RNA_Subject8


title: RNA_Subject42


title: RNA_Subject38_birth


title: RNA_Subject39


title: WT_TG_3_DropSeq

city: Bethesda

first: Minh

middle: Q

last: Nguyen

address: 9000, Rockville Pike

institute: NIDCR/NIH

description:
wildtype TG
D0-Drop.csv

data_processing:
bcl2fastq (v2.17) was used for basecalling
Sequence reads were processed using the Drop-seq cookbook (v 1.12) from the McCarroll lab (http://mccarrolllab.com/dropseq/) for Drop-seq libraries.  Sequence reads from 10x libraries were processed using Cell Ranger 2.1.0 from 10x Genomics (https://www.10xgenomics.com/)
Reads were aligned using STAR (v 2.5.3a) to a pre-mRNA mm10 genome.
Seurat package (v2 and v3) was used for downstream data analysis in R as described by the Satija lab (http://satijalab.org/seurat/)
Genome_build: mm10
Supplementary_files_format_and_content: csv files with cell barcodes and corresponding gene expression counts; only nuclei meeting minimum threshold of transcripts are included for analysis

source_name: trigeminal nuclei

extract_protocol:
Trigeminal ganglia were harvested and incubated in RNAlater (ThermoFisher) at 4oC overnight.  Tissues were then transferred and stored at -80oC until use.  Tissues were homogenized using a glass dounce homogenizer on ice.  Neuronal nuclei were isolated using rabbit anti-NeuN antibody (Abcam) followed by anti-rabbit IgG microbeads (Miltenyi Biotec) and LS column (Miltenyi Biotec).
Libraries construction were performed either with the Drop-seq protocol from the McCarroll lab (for Drop-seq runs) or with method from 10x Genomics for 10x Chromium runs.

value: > 6 wks

tag: genotype/variation

value: wildtype


title: RNA_Subject25


title: RNA_Subject32


title: RNA_Subject37


title: RNA_Subject5


title: RNA_Subject21


title: RNA_Subject29


title: RNA_Subject18


title: RNA_Subject22


title: RNA_Subject28


title: RNA_Subject16


title: WT_TG_2_DropSeq

description:
wildtype TG
D0-Drop.csv

tag: strain


title: RNA_Subject24

tag: treatment


title: WT_TG_1_DropSeq

description:
wildtype TG
D0-Drop.csv


title: KO-DN_rep2

city: Columbus

first: Patrick

middle: Leonard

last: Collins

address: 770 BRT,  460 W 12th Ave

department: Microbial Infection and Immunity

institute: Ohio State University

description:
Rep2
DNA - accessability. Illumina FC-121-1030
genomic DNA

data_processing:
ChIP-seq reads were aligned ot the mm9 genome assemply using NovaAlign with the following options:-r None -l 30 -e 100 -i 230 140
duplicates were removed using Picard markDuplicates
peaks were called using MACS2 findpeaks --broad
Bigwigs for visulazation were created using bedGraphToBigWig
Genome_build: mm19

source_name: NKp46- CCR6- ILC3

extract_protocol: ATAC-seq were processed as per manufacturers instructions (Illumina FC-121-1030)


title: WT-CCR6_rep2

source_name: NKp46- CCR6+ ILC3

value: Nr1d1 WT


title: KO-CCR6_rep2


title: Granuloma_macrophages_Balb/c_control_2

city: Münster

first: Niels-Arne

last: Münck

address: Roentgenstraße 21

department: Insitute of Immunology

country: Germany

institute: University of Münster

description: Primary murine macrophages isolated from phagocyte traps

hyb_protocol: GeneChips were washed and stained in an Affymetrix Fluidics Station 450

scan_protocol: Scanning was performed on a GeneChip Scanner 3000 7G

data_processing: Data was normalised using the MAS5 algorithm in Affymetrix MicroArray Suite

label: Biotin

source_name: Macrophages isolated from poly-acryl amide phagocyte traps

label_protocol: Labeling was done using a 3'IVT kit according to the manufacturers instructions.

growth_protocol: Phagocytes where isolated from phagocyte traps according to the protocol published in Model for Generation of Large Numbers of Primary, Inflammatory Skin-Derived Neutrophils, and Macrophages by John et al., 2013 in Methods in molecular biology, DOI: 10.1007/978-1-62703-227-8_27

extract_protocol: Total RNA extraction was performed using a Quiagen RNeasy micro kit.

treatment_protocol: Macrophages where isolated from the primary phagocyte mixture by adherence overnight and either infected with 5x MOI of metacyclical Leishmania major or left untreated as uninfected controls for 4h a 37°C

value: BALB/c

value: macrophages

tag: infection status

value: control


title: Granuloma_macrophages_C57_infected_ 3

value: infected


title: Granuloma_macrophages_C57_infected_ 2


title: Granuloma_macrophages_Balb/c_control_3


title: KO-CCR6_rep1

description:
Rep1
DNA - accessability. Illumina FC-121-1030
genomic DNA


title: WT-CCR6_rep1


title: KO-DN_rep1


title: Granuloma_macrophages_Balb/c_infected_ 3


title: Granuloma_macrophages_C57_control_ 3


title: Granuloma_macrophages_Balb/c_infected_ 1


title: Granuloma_macrophages_C57_control_ 1


title: Granuloma_macrophages_C57_control_ 2


title: WT-DN_rep2


title: mESC_RNAseq rep2

city: New York

first: Priscillia

last: Lhoumaud

state: NY

address: 550 first avenue Smilow 307

department: Pathology

institute: NYU Langone Health

description: RNAseq in WT mESC replicate 2 of 2

data_processing:
Reads were trimmed using trim-galore/0.4.4
Reads were aligned to the mm10 assembly of mouse genome using bowtie2 for ChIP-seq and ATAC-seq, and using Bismark/0.18.1 (bowtie2) for M-ChIP and M-ATAC to account for bisulfite conversion.
Reads with quality < 30 and duplicates were removed using Samtools/1.3
Peaks were called using PeakDeck
Bigwigs were generated from bam files with RPKM (Reads Per Kilobase per Megabase) normalization using Deeptools
reads counts were obtained using Htseq in genes for RNAseq or peaks for ChIP-seq
Genome_build: mm10
Supplementary_files_format_and_content: bigwigs and peak files were generated from bam files for data visualization. Methylation was extracted using bismark as coverage (.cov) and bedgraph files. Tsv files correspond to subsampling of methylation from coverage files inside peak regions.

source_name: emrbyonic stem cells

growth_protocol: KH2 embryonic stem cells (ESCs) were cultured on irradiated feeder cells in KO-DMEM (Invitrogen) supplemented with L-glutamine, penicillin/streptomycin, nonessential amino acids, β-mercaptoethanol, 1,000 U/mL LIF, and 15% FBS (ESC medium). To remove feeder cells from ESCs, cells were trypsin digested and pre-plated in ESC medium for 30 mins. Supernatant containing ESCs was used for further experiments.

extract_protocol:
Total RNA was extracted using the RNeasy Mini Kit from Qiagen (Cat. No. 74104) in accordance with the prescribed protocol provided with the kit.
For ATAC-seq (converted or not) nuclei were prepared from 50,000 cells for each transposition reaction. For ChIP-seq (converted or not), Lysates were clarified from sonicated nuclei and KLF4-bound chromatin was isolated with KLF4 antibody.
For ATAC-seq and ChIP-seq, sequencing libraries were constructed using the Illumina Nextera DNA Sample prep kit. For bisulfite converted samples, a transposome was assembled with methylated adaptors for transposition reaction. RNA libraries were prepared for sequencing using standard Illumina protocols.

value: emrbyonic stem cells

value: WT


title: WT-DN_rep1


title: Granuloma_macrophages_Balb/c_control_ 1


title: Granuloma_macrophages_C57_infected_ 1


title: mESC_RNAseq rep1

description: RNAseq in WT mESC replicate 1 of 2


title: AD_Hippocampus_rep2

city: NANJING

first: XIAOLEI

last: ZHU

state: JIANGSU

address: 321 ZHONGSHAN ROAD

department: Neurology

institute: Nanjing Drum Tower Hospital

hyb_protocol: Each sample was resuspended in 17ml nuclease free water. A master hybridization master mix was made consisting of diluted Hyb Spike-In controls, Agilent 10X blocking agent and Agilent Hi-RPM hybridization buffer. Aliquots of the master mix were added to each resuspended sample to a final volume of 45ml. The hybridization mix was incubated for 5 min at 1000C and then transferred to an ice/water bath to be incubated for 5 min. The samples were then briefly centrifuged to collect any condensation from the tube caps. The entire amount for each sample was dispensed into the center of a gasket well of an Agilent Mouse miRNA Release 21.0, 8x60K microarray slide (8 samples/slide). Once all samples were applied to the gasket slide, the chamber cover was clamped in place. The assembled slide cassette was placed into the hybridization oven and hybridized for 20 hrs at 550C at 20 rpm.

scan_protocol: The array was scanned using Agilent Scan Control vA.8.5.1 with the AgilentG3_miRNA protocol at a resolution of 5mm.

data_processing: miRNAs with Absent calls across all samples were filtered out. Quantile normalization was used to normalize the remaining miRNAs.

source_name: brain

label_protocol: Total RNA (100ng) from each sample (3 samples/group) was labeled using the Agilent miRNA Complete Labeling and Hybridization kit.

growth_protocol: All mice were raised in Pathogen-free room and the room was maintained at a constant temperature of 23±1℃ with a 12 h light/dark cycle. Food and water were available ad libitum in the home cages.

extract_protocol: The hippocampus were isolated and homogenized using a Tissue homogenizer, and the RNA was extracted and purified using RNeasy Mini Kit.

treatment_protocol: Mice were deeply anesthetized with pentobarbital sodium and then hippocampus were rapidly dissected from the fresh brains.

tag: Sex

value: male

tag: age


title: WT_Hippocampus_rep2

value: wild type


title: WT_Hippocampus_rep1


title: WT_Hippocampus_rep3


title: AD_Hippocampus_rep3