title: GD3

city: Nanjing

first: Chunmei

last: Ma

address: 101 Longmian road,Nanjing

institute: Nanjing medical university

data_processing:
Basecalls performed using BGISEQ-500
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to GRCm38.p6 whole genome using bowtie v2.2.5 with parameters -q --phred64 --sensitive --dpad 0 --gbar 99999999 --mp 1,1 --np 1 --score-min L,0,-0.1 -p 16 -k 200
Data were filtered using SOAPnuke version v1.5.2 with parameters -l 15 -q 0.2 -n 0.05
Genome_build: GRCm38.p6
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample

source_name: CD45+CD11b+F4/80+ macrophages

growth_protocol: Macrophages isolated from colons of WT and Gsdmd-/- mice by FACS sorting.

extract_protocol:
RNA isolation were performed on a BGISEQ-500 (Beijing Genomic Institution, BGI)
RNA libraries were prepared for sequencing using standard BGISEQ-500 protocols

treatment_protocol: WT and Gsdmd-/- mice were treated with DSS to induce colitis mice model

tag: genotype/variation

value: Gsdmd-/-

value: colon

value: 10 weeks


title: w1118_Female_1hr_2

status: Public on Jul 06 2020

type: SRA

city: Detroit

first: Ekta

middle: J

last: Shah

state: Michigan

address: 275 E.  Hancock

country: USA

institute: Wayne State University

library_source: transcriptomic

data_processing:
After de-multiplexing with Illumina’s CASAVA 1.8.2 software, the 50 bp reads were aligned to the Drosophila genome (Build dm3) with STAR_2.4 and tabulated for each gene region.
Differential gene expression analysis was used to compare transcriptome changes between conditions using edgeR v.3.22.3 and transcripts were defined  as significantly differentially expressed at absolute Log2 fold change >1, FDR <0.05
Genome_build: Dm3
Supplementary_files_format_and_content: Differential gene expression and counts data.xlsx

molecule: total RNA

organism: Drosophila melanogaster

source_name: Brain

extract_protocol:
Direct-zolä RNA MicroPrep kit
QuantSeq 3' mRNA-Seq Library Prep Kit FWD (low-input protocol and 15 ng RNA input)

tag: strain

tag: Sex

value: Female

tag: treatment

value: traumatic brain injury

tag: time point


title: Col00Sh3

city: Amherst

first: Jeeyon

last: Jeong

state: MA

address: 25 East Drive

department: Biology

institute: Amherst College

data_processing:
Illumina Casava1.8 software used for basecalling.
Raw reads were filgered to remove reads containing adapters or reads of low quality, then mapped to Arabidopsis TAIR10 reference genome using TopHat2 (TMR>70%; MMR<10%)
RPKM (Reads Per Kilo bases per Million reads) method (Mortazavi et al 2008)
Genome_build: TAIR10
Supplementary_files_format_and_content: RPKM

organism: Arabidopsis thaliana

source_name: Shoot

growth_protocol: Germinated and grown for 12 days on B5, followed by 3 days on iron sufficient (+Fe) or iron deficient (-Fe) media; 16/8 light/dark cycle at 22°C

extract_protocol:
Total RNA was extracted from fresh Arabidopsis root tissue using Plant RNA Isolation Kit (Agilent) per manufacturer's instructions.
RNA libraries were prepared for sequencing using TruSeq Stranded mRNA Library Prep Kit

treatment_protocol: Grown for 3 days on iron sufficient (+Fe) or iron deficient (-Fe) media

tag: genotype

value: wild type

tag: tissue

value: root

value: iron deficient


title: 6_D492M_KD_MEG3

city: Reykjavik

first: Zuzana

last: Budkova

address: Vatnsmyrarvegi 14

department: BioMedical Center, School of Health Sciences

country: Iceland

institute: University of Iceland

description: CRISPRi pLenti-dCas9-KRAB-mCherry

data_processing:
Illumina
STAR version 2.6.1
htseq-count
DESeq2
Genome_build: Ensembl primary assembly, version GRCh38
Supplementary_files_format_and_content: tab-delimited text files include htseq-count values for each Sample

organism: Homo sapiens

source_name: Breast epithelial cell line D492M

growth_protocol: D492M was cultured in H14 medium (DMEM:F12 supplemented with 50 IU/ml penicillin, 50 ug/ml streptomycin, 250 ng/ml insulin, 10 ug/ml transferrin, 2.6 ng/ml sodium selenite, 0.1 nM estradiol, 0.5 ug/ml hydrocortisone, 5 ug/ml prolactin and 10 ng/ml EGF), in flasks coated with collagen I. Media was changed three times a week.

extract_protocol:
RNA was extracted using a Tri-Reagent standard protocol
Libraries were prepared according to Illumina's instructions

tag: passages

tag: cell type

value: Breast epithelial cell line (D492) mesenchymal derivative (D492M)

value: MEG3 knockdown


title: GD2

country: China

organism: Mus musculus

tag: age


title: w1118_Female_1hr_1


title: 9_D492M_KD_MGE3

description: CRISPRi pLenti-dCas9-KRAB-mCherry


title: Col00Sh2


title: 4_D492M_KD_ctrl

description: CRISPRi pLenti-dCas9-KRAB-mCherry

value: control


title: GD1


title: w1118_Female_Ctrl_3


title: 3_D492M_KD_ctrl

description: CRISPRi pLenti-dCas9-KRAB-mCherry


title: 2_D492M_KD_ctrl

description: CRISPRi pLenti-dCas9-KRAB-mCherry


title: WT3


title: WT2


title: Col50Sh 3

value: iron sufficient


title: clf50Sh1

value: clf


title: w1118_Female_Ctrl_2


title: Col50Sh 2


title: Col50Sh 1


title: 1_D492M_KD_ctrl

description: CRISPRi pLenti-dCas9-KRAB-mCherry


title: WT1


title: Col00Sh1


title: N2_0

status: Public on Jul 05 2020

city: Seoul

first: Sung Noh

last: Hong

address: 81 Irwon-Ro, Gangnam-gu

department: Gastroenterolgy

country: South Korea

institute: Samsung Medical Center

data_processing:
The raw gene expression matrix from the CellRanger pipeline was filtered, normalized using the Seurat v3.1.4, and filtered according to >200 genes, <6000 genes, and <30% of mitochondrial gene expression in UMI counts. From the filtered cells, the gene expression matrices were normalized to the total UMI counts per cell and transformed to the natural log scale. To merge independent samples, ‘FindIntegrationAnchors’ and ‘IntegrateData’ were used in Seurat and batch effects were corrected. The number of principal components estimated using ‘RunPCA’ followed by ‘ElbowPlot’. Dimensionality reduction was implemented using ‘RunUMAP’.
Genome_build: CGCh38
Supplementary_files_format_and_content: raw_feature_bc_matrix

source_name: TNF free control intestinal organoid

growth_protocol: The epithelium was isolated by endoscopic biopsy samples with 10 mM ethylenediaminetetraacetic acid (EDTA) and 1 mM dithiothreitol (DTT) in PBS for 30 min at 4 °C on a rocker at 50 rpm. The supernatant containing villi and debris was decanted and discarded. To release the large amounts of intestinal crypts, the mucosal surface of biopsy samples were gently scraped using glass coverslips under a dissecting microscope. The detached crypts were suspended in PBS and were broken down using pipetting with bended pipette tip. The fraction was centrifuged at 200× g for 2 min at 4 °C, and the pellet was suspended in basic medium. Isolated crypts were pelleted with three quick spins, resuspended in Matrigel, and plated in 48-well culture plates. After incubating at 37 °C for 15 min, 250 μl maintenance media (50% Wnt3a conditioned medium + 50% 2× basic medium supplemented with 50 ng/ml recombinant human epidermal growth factor (EGF), 100 ng/ml recombinant human noggin, 500 ng/ml recombinant human R-spondin 1, 10 mM nicotinamide, 10 μM p160ROCK inhibitor (Y27632), 10 μM p38 MAP kinase inhibitor (SB202190), and 10 nM PGE2) was added. GSK3 inhibitor (CHIR99021; 2.5 μM) was included in the medium for the first 2 days. The medium was changed every 2 days and organoids were passaged 1:2 at day 7 after crypt plating. For passaging, the organoids and Matrigel were mechanically disrupted using a P1000 pipette and further mechanical dissociation was achieved using a P200 pipette. The dissociated organoids were washed with 10 ml basal culture medium and centrifuged at 200× g for 30 s at 4 °C. The supernatant was discarded, the pellet was resuspended in 2 ml of cell dissociation enzyme, and then incubated for 5 min at 37 °C in a water bath. The solution was gently mixed using a P200 pipette and centrifuged at 500× g for 5 min at 4 °C. The supernatant was discarded and the cell pellet was resuspended in Matrigel using pre-chilled pipet tips. The crypt suspension (50 μl) was plated in Matrigel in each well of the pre-warmed 48-well culture plate. The plate was incubated at 37 °C in a 5% CO2 atmosphere for 20 min to allow complete polymerization of Matrigel prior to the addition of 250 μl maintenance media. The entire medium was changed every 2 days and organoids were passaged 1:2 every week. After 4–6 passages, most organoids in the maintenance medium were uniform spheroids and able to passage stably for a long time. To recapitulate the organ physiological parameters, spheroids were cultured in differentiation medium, which was the maintenance medium without Wnt3A conditional medium, SB202190, nicotinamide, and PGE2. The entire medium was changed every 2 days and enteroids were cultured for 8 days after passage. And then, total RNA was extracted from intestinal organoids using the RNeasy Mini Kit according to the manufacturer’s instructions.

extract_protocol:
For library construction, total RNA is extracted from a sample. After performing quality control (QC), qualified samples
10x Chromium libraries were prepared according to the manufacturer’s protocol (10x Genomics) targeting 10,000 cells. Following the manufacturer’s instructions, barcoded sequencing libraries were generated using Chromium Single Cell 3’ Reagent kit v3 and sequenced on HiSeqXten. Sequencing data were aligned to a human genome reference (CGCh38) and processed using CellRanger 3.1.0 pipeline (10X Genomics).

treatment_protocol: Organoids were cultured in the maintenance medium for 2 days to obtain a stable number of organoids before inducing organoid differentiation. On day 2, the maintenance medium for organoids was replaced with the TNFɑ (30ng/mL) -containing enteroid medium. Control and Crohn’s organoids—cultured for the long-term (passage ≥ 6)—were treated with 30 ng/ml TNFɑ every 24 hours until harvest.

tag: disease

tag: status

value: TNF-treated

value: small intestine


title: 93_0

source_name: TNF free Crohn's intestinal organoid

value: Crohn's disease

value: TNF-free


title: N2_30

source_name: TNF (30ng/mL) treated control intestinal organoid

value: TNF (30ng/mL)-treated


title: 93_30

source_name: TNF (30ng/mL) treated Crohn's intestinal organoid


title: w1118_Female_Ctrl_1


title: ExVivo_pDC_ldcSSc_3

type: RNA

city: Verona

first: Marzia

last: Rossato

address: Strada Le Grazie 15

department: Biotechnology

country: Italy

institute: University of Verona

hyb_protocol: Standard Illumina BeadChip hybridization protocol

scan_protocol: Standard Illumina BeadChip scanning protocol

data_processing: Data normalization was performed using Genome Studio (Illumina) and filtering using GenePattern (Broad Institute)

source_name: Peripheral Blood

label_protocol: Samples were prepared and labelled according to the protocol for the Illumina MicroRNA Expression Profiling Assay (Catalog # MI-501-1001, Part # 11317302 Rev. A)

extract_protocol: RNA was extracted with Trizol reagent, followed by clean-up and DNase I treatment with QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser.

treatment_protocol: pDCs were isolated by positive selection from peripheral blood mononuclear cells using immunomagnetic labelling using the BDCA-4/Neuropilin-1 MicroBead kit (Miltenyi Biotec). The purity of isolated pDCs (>90%) was assessed by FACS after staining with anti-BDCA4 and CD123.

value: BDCA-4+ pDC

tag: gender

value: female

value: 47 years


title: ExVivo_pDC_edcSSc_2

value: 50 years


title: ExVivo_pDC_ldcSSc_5

value: 53 years


title: ExVivo_pDC_ldcSSc_7

value: 36 years


title: ExVivo_pDC_edcSSc_1

value: 45 years


title: ExVivo_pDC_edcSSc_4

value: 52 years


title: ExVivo_pDC_ldcSSc_4

value: 66 years


title: ExVivo_pDC_edcSSc_3

value: 65 years


title: D_pseudoobscura

city: Leuven

first: Stein

last: Aerts

address: Herestraat 49

department: Center for Human Genetics

country: Belgium

institute: KULeuven

data_processing:
Sequenced reads were trimmed for adaptor sequence, then mapped to their respective genomes using tophat2 v 2.0.3 (default parameters)
HT-Seq count (option -str=no) was used to count the number of reads falling within each species exonic regions.
RPKM values were calculated for each sample independetly .
Ensembl GeneTreess 2013 was used to obtain orthology relationships across Drosophila species
Normalization across one-to-one orthologous regions was performed using the upper-quantile methodology.
Genome_build: D.melanogaster 5.46; D.persimilis 1.3; D.pseudoobscura 2.30; D.simulans 1.4; D.yakuba 1.3
Supplementary_files_format_and_content: tab-delimited text files include htseq counts for each sample and normalized values for one-to-one orthologs across the Drosophila species under study.

organism: Drosophila pseudoobscura

source_name: Johnston's Organ

growth_protocol: All flies were raised at 25˚C on standards fly food

extract_protocol:
RNA was extracted with the RNAqueous micro kit (Ambion)
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Johnston's Organ

value: Adult

tag: reference genome annotation

value: D.pseudoobscura 2.30


title: ExVivo_pDC_edcSSc_5

value: 55 years


title: Mm-RNaseP-DMSO-InCell

city: Ann Arbor

first: Chase

middle: Andrew

last: Weidmann

state: MI

address: 1150 W. Medical Center Drive

department: Biological Chemistry

institute: University of Michigan

description:
Mm_RNaseP_ncRNAs.fa
Mm-RNaseP-InCell-SHAPE-MaP.txt
Mm-RNaseP-deltaSHAPE.txt

data_processing:
Library strategy: SHAPE-MaP
For XIST/Xist, nextera reads were trimmed (TrimGalore) an additional 14 nt on each side to accommodate RT primer.
Adduct locations identified by Shapemapper2 software
Correlated mutation events were identified using ringmapper software on shapemapper outputs (.mut files)
In-cell perturbations in SHAPE reactivity were calculated using deltaSHAPE software
RNA structure models were generated from SHAPE data using SuperFold software
RNP-MaP analysis was generated with in-house software from shapemapper outputs

molecule: nuclear RNA

source_name: Mouse SM33 embryonic stem cells

growth_protocol: Adherent mammalian cells used in chemical probing experiments, either SM33 or HEK293 cells, were grown to 80-90% confluency in either 6-well plates (for targeted priming) or 10-cm dishes (for RNA antisense pulldown). HEK293 cells were cultured in DMEM with 10% FBS. SM33 cells were cultured in embryonic stem cell media [DMEM high glucose with sodium pyruvate, 15 % FBS, 0.1 mM non-essential amino acids (Gibco), 2 mM L-glutamine, 0.1 mM β-mercaptoethanol,1000 U/mL leukemia inhibitory factor (ESGRO, Millipore Sigma)]. Cultures were grown with 100 U/mL penicillin and 100 µg/mL streptomycin. To induce expression of the Xist RNA, SM33 cells were supplemented with 2 µg/mL doxycycline 16 hours before treatment. For all experiments when performing biological replicates, chemical probing and sequencing library preparation were performed on distinct populations of cells on different days.

extract_protocol:
library prep: TruSeq
Trizol

value: DMSO

tag: treatment type

value: In-Cell

tag: enrichment

value: gene-specific amplification

tag: target

value: RNase P

tag: rt priming

value: gene-specific


title: Mm-RNaseP-DMSO-CellFree

description:
Mm_RNaseP_ncRNAs.fa
Mm-RNaseP-CellFree-SHAPE-MaP.txt
Mm-RNaseP-deltaSHAPE.txt

extract_protocol:
library prep: TruSeq
nuclear fractionation, proteinase K lysis, buffer exchange (treatment), PCA extraction

value: Extracted


title: ExVivo_pDC_HC_7

value: BDCA-4+ pDC

value: female


title: ExVivo_pDC_ldcSSc_1

value: 47 years


title: ExVivo_pDC_HC_6

value: 48 years


title: ExVivo_pDC_ldcSSc_6


title: ExVivo_pDC_HC_2


title: ExVivo_pDC_HC_3

value: 46 years


title: ExVivo_pDC_HC_4

value: 32 years


title: ExVivo_pDC_HC_5

value: male


title: ExVivo_pDC_HC_1


title: Mm-RNaseP-25mM5NIA-InCell

value: 25mM 5NIA


title: Mm-RNaseP-25mM5NIA-CellFree


title: Mm-Rmrp-DMSO-InCell

description:
Mm_Rmrp_ncRNA.fa
Mm-Rmrp-InCell-SHAPE-MaP.txt
Mm-Rmrp-deltaSHAPE.txt

value: Rmrp


title: ExVivo_pDC_ldcSSc_2

value: 39 years


title: Mm-Rmrp-DMSO-CellFree

description:
Mm_Rmrp_ncRNA.fa
Mm-Rmrp-CellFree-SHAPE-MaP.txt
Mm-Rmrp-deltaSHAPE.txt


title: Mm-Rmrp-25mM5NIA-CellFree


title: Mm-U1-10mMSDA

description:
Mm_U1s_snRNA.fa
MmU1BG_shapemapper_output.txt

data_processing:
Library strategy: RNP-MaP
For XIST/Xist, nextera reads were trimmed (TrimGalore) an additional 14 nt on each side to accommodate RT primer.
Adduct locations identified by Shapemapper2 software
Correlated mutation events were identified using ringmapper software on shapemapper outputs (.mut files)
In-cell perturbations in SHAPE reactivity were calculated using deltaSHAPE software
RNA structure models were generated from SHAPE data using SuperFold software
RNP-MaP analysis was generated with in-house software from shapemapper outputs

extract_protocol:
library prep: TruSeq
nuclear fractionation, proteinase K lysis, PCA extraction

value: 10mM SDA only

value: U1 snRNA


title: Mm-U1-3JUV

value: 3JUV only

value: In-Cell


title: Mm-U1-3JUV-10mMSDA-Extracted

value: 3JUV and 10mM SDA

value: gene-specific amplification


title: Mm-U1-3JUV-10mMSDA-InCell

value: gene-specific


title: Mm-Rmrp-2JUV-10mMSDA

description:
Mm_Rmrp_ncRNA.fa
MmRmrpUVGradient_shapemapper_output.txt

value: 2JUV and 10mM SDA


title: Mm-Rmrp-3JUV-D


title: Mm-Rmrp-3JUV-10mMSDA-D


title: Mm-RNaseP-3JUV

description:
Mm_RNaseP_ncRNAs.fa
MmRNasePBG_shapemapper_output.txt

value: RNase P


title: Mm-Rmrp-3JUV-1mMSDA

description:
Mm_Rmrp_ncRNA.fa
MmRmrpSDAGradient_shapemapper_output.txt

value: 3JUV and 1mM SDA


title: Mm-RNaseP-10mMSDA


title: Mm-RNaseP-NT

value: No Treatment


title: Mm-Rmrp-3JUV-5mMSDA

value: 3JUV and 5mM SDA


title: Mm-RNaseP-3JUV-10mMSDA-InCell


title: Mm-Rmrp-1JUV-10mMSDA

value: 1JUV and 10mM SDA


title: Mm-Rmrp-3JUV-2mMSDA

value: 3JUV and 2mM SDA


title: Mm-Rmrp-3JUV-10mMSDA-B

description:
Mm_Rmrp_ncRNA.fa
MmRmrpBG2_shapemapper_output.txt


title: Mm-Rmrp-3JUV-B

description:
Mm_Rmrp_ncRNA.fa
MmRmrpBG2_shapemapper_output.txt
MmRmrpSDAGradient_shapemapper_output.txt


title: Mm-Rmrp-3JUV-10mMSDA-C


title: Mm-Rmrp-3JUV-10mMPreQuenchSDA

value: 3JUV and 10mM SDA (quenched)


title: Mm-Rmrp-NT

description:
Mm_Rmrp_ncRNA.fa
MmRmrpBG_shapemapper_output.txt

value: Rmrp


title: Mm-Rmrp-3JUV-10mMDAEtOH

value: 3JUV and 10mM DA-EtOH


title: Mm-Rmrp-3JUV-10mMSDA-InCell


title: Mm-Rmrp-3JUV-A


title: Mm-U1-NT


title: Mm-Rmrp-3JUV-10mMSDA-Extracted

value: Extracted


title: Mm-RNaseP-3JUV-10mMSDA-Extracted


title: Mm-Rmrp-10mMSDA

value: 10mM SDA only


title: 17_2

city: Riga

first: Monta

last: Brīvība

address: Ratsupites 1

country: Latvia

institute: Latvian Biomedical Research and Study Centre

description: Ion Torrent, Ion Proton System

data_processing:
The reads were trimmed with Trimmomatic 0.36 using window size 5 and quality threshold 10.
Sequencing reads were mapped against human reference genome GRCh38 release 90 and read counts were calculated with STAR 2.5.3a.
Genome_build: GRCh38
Supplementary_files_format_and_content: Text file containing RNA-Seq read counts per gene for all samples claculated with STAR 2.5.3a.

source_name: Venous blood sample

extract_protocol:
Total RNA isolation was performed with Tempus™ Spin RNA Isolation Kit (Thermo Fisher Scientific), according to the manufacturer's instructions.
Ribosomal RNA depletion was done with Low Input RiboMinus™ Eukaryote System v2 (Thermo Fisher Scientific, USA) by processing 500ng of total RNA from each sample. For cDNA library preparation we used Ion Total RNA-Seq Kit v2 (Thermo Fisher Scientific, USA), sequencing was done on Ion Proton™ System and Ion PI™ Chip (Thermo Fisher Scientific, USA), following the manufacturer’s instructions.

treatment_protocol: Venous blood samples were collected in Tempus™ Blood RNA Tubes (ThermoFisher Scientific), containing Stabilizing Reagent.

tag: patient diagnosis

value: type 2 diabetes mellitus

value: blood

tag: time point of blood collcetion regarding metformin intervention

value: after three months long metformin course


title: 16_2

description: Ion Torrent, Ion Proton System


title: 16_1

description: Ion Torrent, Ion Proton System

value: before administration of metformin


title: 17_1

description: Ion Torrent, Ion Proton System


title: 13_2

description: Ion Torrent, Ion Proton System


title: UT_127

city: Memphis

first: Khyobeni

last: Mozhui

state: TN

address: 66 N. Pauline Street, #631

department: Preventive Medicine

institute: University of Tennessee Health Science Center

description: MBD-protein captured; the processed files are in logRPKM

library_source: genomic

data_processing:
FASTQ files were first inspected with the FastQC tool (v.0.11.8) (https://www.bioinformatics.babraham.ac.uk/projects/fastqc/) and all files passed the initial quality checks.
Alignment was then done to the mouse reference genome (mm10/GRCm38) using the Bowtie2 aligner (v.2.3.4.3) (Langmead and Salzberg, 2012), and alignment quality was evaluated with SAMtools (v.1.9) (Li et al., 2009), and SAMstat v.1.5.1 (Lassmann et al., 2011).
Potential PCR duplicates and reads with mapping quality of less than 10 were filtered out, and sorted Bam files were created. Then provided bam files are sorted
The sorted Bam files were then analyzed using the MEDIPS R package (Chavez et al., 2010). Sequenced reads were counted for every 150 bp non-overlapping window with normalization to the local CpG density (i.e., coupling factor CF). This process was done according to the following MEDIPS parameters: ws =150, extend = 150, uniq = 1, shift=0. The read counts generated on the MEDIPS package were loaded to the EdgeR R package (Robinson et al., 2010). First, bins with no CpGs (CF = 0) and mean read counts ≤ 1 were excluded, resulting in 4,286,826 bins. The Y chromosome was also excluded, and only reads with more than 1 count per million in 2 or more libraries were retained using the EdgeR R package (Robinson et al., 2010). This resulted in 368300 CpG regions, and logRPKM values for these are provided.
Genome_build: mm10/GRCm38
Supplementary_files_format_and_content: csv file; contains columns with index, bin name, chromosome (chr), start, end,  CF (CouplingFactor or CpG density), CpG%, GC%, VariantCount (number of sequence variants in the 150 bp bin), followed by methylation data as logRPKM for 70 samples.

molecule: genomic DNA

source_name: Liver

extract_protocol:
DNA from liver tissue was extracted using Qiagen DNeasy Blood & Tissue Kit (http://www.qiagen.com); methylated-CpG enrichment done using MethylMiner DNA enrichment kit (https://www.thermofisher.com) according to the manufacturer’s standard protocol
Library construction and sequencing were carried out at Novogene (https://en.novogene.com). Sequencing was done at approximately 50 million reads per sample (150 bp paired-end) on Illumina HiSeq 4000 platform

tag: strain

tag: age in days

tag: Sex

value: F

tag: diet

value: standard chow

value: liver


title: 15_1

description: Ion Torrent, Ion Proton System

tag: tissue


title: UT_178


title: 13_1

description: Ion Torrent, Ion Proton System


title: 14_2

description: Ion Torrent, Ion Proton System


title: 12_1

description: Ion Torrent, Ion Proton System


title: 11_1

description: Ion Torrent, Ion Proton System


title: 10_2

description: Ion Torrent, Ion Proton System


title: 12_2

description: Ion Torrent, Ion Proton System


title: 15_2

description: Ion Torrent, Ion Proton System


title: 10_1

description: Ion Torrent, Ion Proton System


title: 9_1

description: Ion Torrent, Ion Proton System


title: 9_2

description: Ion Torrent, Ion Proton System


title: 8_2

description: Ion Torrent, Ion Proton System


title: 7_1

description: Ion Torrent, Ion Proton System


title: 6_2

description: Ion Torrent, Ion Proton System


title: 7_2

description: Ion Torrent, Ion Proton System


title: 5_2

description: Ion Torrent, Ion Proton System


title: 6_1

description: Ion Torrent, Ion Proton System


title: Replicate3_8

city: Cambridge

first: Felix

last: Krueger

address: Granta Park

department: Bioinformatics

country: United Kingdom

institute: Altos Labs

description:
RNA (see 10X Genomics 3' scRNAseq V2 library preparation protocol)
Transduction replicate 3, 10X lane 8

data_processing:
All 10X scRNA-seq data was processed with the default CellRanger v2.1 pipeline (Zheng et al. 2017) for mapping to the mm10 mouse genome assembly. Gene counts were further analysed with scanpy (Wolf et al. 2018). To keep only high-quality cells, we filtered out cells with less than 4,000 UMI counts and/or less than 1,600 detected genes, cells with more than 20000 UMI counts and/or more than 5,000 genes, and cells with more than 5% of UMI reads coming from mitochondrial genes. After this filtering, we kept 109,061 cells from replicate 1, 118,646 cells from replicate 2 and 107,591 cells from replicate 3. Next, we assigned sgRNA expression to every cell using the amplicon sgRNA libraries and we kept only cells assigned to a unique sgRNA: 71,047 cells in replicate 1, 71,188 cells in replicate 2 and 61,729 cells in replicate 3, which summed up 203,964 cells in total across replicates. A gene was considered for downstream analysis if it was detected (UMI count >0) in at least in 10 out of the 203,964 cells that passed filtering. The final dataset after quality control consisted of 20,690 genes. The number of UMIs for every cell was adjusted by library size dividing by the total number of UMIs per cell, log-transformed, and scaled with the factor of 10,000.
Using the amplicon sgRNA libraries, the potential sgRNA sequence (nucleotides 24-43 of the read) was compared to the collection of designed guides. By taking only exact matches to the white list of sgRNAs, the majority of 475 sgRNA sequences were recovered (470-474, variable from one library to another) and 16% of reads on average (15.3%-16.8% for different libraries) were left unassigned to a sgRNA. To correct for sequencing mistakes, we allowed a minimum edit distance (Levenshtein distance – 4 edits) between any two sequences of the designed sgRNAs as well as the CROP-sgRNA-MS2 vector sequence surrounding the potential sgRNA in the read. For the reads left unassigned to a sgRNA at this stage, if there was a sgRNA sequence within Levenshtein distance of 1 or 2 and if the upstream 23 nucleotides and downstream 23 nucleotides matched the CROP-sgRNA-MS2 vector sequence with up to 4 edits each, the respective sgRNA was assigned to the read. After this correction procedure, approximately 2% of reads were left unassigned. Cell barcodes detected in the amplicon libraries were then matched with barcodes detected in the regular 10X scRNA-seq libraries. Out of the 317,847 cells that passed quality control across the three transduction replicates in the regular 10X libraries, 249,767 cell barcodes were captured in the amplicon sgRNA libraries (85,993 in replicate 1, 86,671 in replicate 2 and 77,103 in replicate 3). A sgRNA was assigned to a cell if more than 90% of all the amplicon reads containing the sgRNA had the same cell barcode, with standard error of binomial proportion of less than 10%.
Genome_build: mm10
Supplementary_files_format_and_content: Barcodes detected, genes detected and matrix files are provided for each sample

source_name: Embryonic stem cells

growth_protocol: Mouse embryonic stem cells (mESCs) were grown under serum/LIF conditions: DMEM (Gibco, 11995-040), 15% fetal bovine serum, 1 U/ml penicillin - 1 mg/ml streptomycin (Gibco, 15140-122), 0.1 mM nonessential amino acids (Gibco, 11140-050), 4 mM GlutaMAX (Gibco, 35050-061), 50 mM β-mercaptoethanol (Gibco, 31350-010), and 103 U/ml LIF (Stem Cell Institute, Cambridge), and cultured at 37 ̊C in 5% CO2 on gelatinized tissue-culture plates. The media was refreshed every day and the cells passaged every other day with Trypsin EDTA (Thermo Fisher Scientific, 25200056).

extract_protocol:
See 10X Genomics V2 Single Cell 3′ Solution kit user guide
For 10X libraries, see 10X Genomics V2 Single Cell 3′ Solution kit user guide. Amplicon sgRNA libraries were performed on full length 10X cDNA samples as previously described (Hill et al. 2018); briefly, 10 ng of full length 10X cDNA were used as starting material and each round of PCR amplification with the primers described in (Hill et al. 2018) was monitored by KAPA SYBR to avoid overcycling.
Each 10X library was sequenced on an Illumina HiSeq4000 lane with 26 cycles for read 1, 98 cycles for read 2 and 8 cycles i7 sample index. The 24 amplicon libraries were multiplexed and sequenced across two lanes of an Illumina Hiseq2500 Rapid Run, with 27 cycles for read 1, 267 cycles for read 2 and 8 cycles for i7 sample index.

treatment_protocol: The lentiviral library of 475 sgRNAs cloned into the CROP-sgRNA-MS2 backbone was transduced in triplicates into SAM mESCs by direct supplementation of the concentrated lentivirus into the medium for 24 hours. The transductions were done at <0.1 multiplicity-of-infection (MOI) into 5 million SAM ESCs, achieving a representation >1000 cells / sgRNA, considering that <10% of the cells were transduced. Two days after transduction, mCherry expression was analysed by flow-cytometry on BD LSR Fortessa and selection with 1 ug/ul puromycin started afterwards. Cells were selected and passaged for 8 days after addition of puromycin before harvesting for 10X single-cell RNA-sequencing library preparation.

value: 129/Ola ES-E14


title: 5_1

description: Ion Torrent, Ion Proton System


title: 14_1

description: Ion Torrent, Ion Proton System


title: 4_2

description: Ion Torrent, Ion Proton System


title: 11_2

description: Ion Torrent, Ion Proton System


title: 8_1

description: Ion Torrent, Ion Proton System


title: 2_1

description: Ion Torrent, Ion Proton System


title: 3_1

description: Ion Torrent, Ion Proton System


title: 1_1

description: Ion Torrent, Ion Proton System


title: 3_2

description: Ion Torrent, Ion Proton System


title: 2_2

description: Ion Torrent, Ion Proton System


title: 1_2

description: Ion Torrent, Ion Proton System


title: Replicate3_7

description:
RNA (see 10X Genomics 3' scRNAseq V2 library preparation protocol)
Transduction replicate 3, 10X lane 7


title: Replicate3_6

description:
RNA (see 10X Genomics 3' scRNAseq V2 library preparation protocol)
Transduction replicate 3, 10X lane 6


title: adipocyte HFD mRNA rep 3

city: Boston

first: NORC

last: Boston

address: 3 Blackfan Circle, CLS0733

institute: Beth Israel Deaconess Medical Center

data_processing:
RNA-seq:
RNA-seq data were aligned to the mm10 mouse genome using HISAT2 (Kim et al., 2015).
Duplicates and low quality reads were removed by Picard (http://picard.sourceforge.net)
Reads were assigned to transcripts, normalized and quantified using featureCounts (Liao et al., 2014) and EdgeR (Robinson et al., 2010).
Low expressed genes (log2 CPM≥2) were filtered out, and differentially expressed genes were defined at log2 fold-change (FC) ≥0.5 and log2 false discovery rate (FDR)≤0.05
Gene ontology analysis was performed using Metascape. Morpheus (https://software. broadinstitute.org/morpheus/) was used to visualize heatmaps.
ChIP-seq:
ChIP-seq data were aligned to the mm10 mouse genome using Bowtie2 (Langmead and Salzberg, 2012).
Duplicates and low quality reads were removed by Picard (http://picard.sourceforge.net)
Reads were processed using samtools (Li et al., 2009)
Peaks were called by MACS2 (Zhang et al., 2008), and low peaks (4<fold higher coverage than whole cell extract (WCE)) were removed.
Reads were assigned to peaks, normalized and quantified using featureCounts and EdgeR. We used the cutoffs of log2CPM≥2, log2FC≥1, FDR≤0.05 for H3K27ac ChIP-seq and log2CPM≥6, log2FC≥1, FDR≤0.25 for PPARg ChIP-seq.
For ChIP-seq track visualization, reads were processed to the BigWig file format using bedtools (Quinlan and Hall, 2010) and bedGraphToBigWig (Kent et al., 2010).
Processed Bigwig files were viewed in WashU Epigenome Browser (Zhou and Wang, 2012).
ChIP-seq peak heatmaps and distribution plots were generated with the normalized BigWig files within 10kb genomic regions surrounding peaks by using deepTools2 (Ramirez et al., 2016).
Intersecting peaks were determined using bedtools, and peaks were assigned to genes using HOMER (Heinz et al., 2010), and GO analysis was performed by Metascape.
Motif enrichment analysis was conducted using FIMO from the MEME package (Grant et al., 2011) with the JASPAR database (Mathelier et al., 2014)
Genome_build: mm10
Supplementary_files_format_and_content: read counts with batch normalization; bigwig

molecule: polyA RNA

source_name: adipocyte HFD mRNA

growth_protocol: Mice were maintained on a standard chow diet (8664 Harlan Teklad, 6.4% w/w fat) under a regular 12h light/12h dark cycle at constant temperature (23°C).

extract_protocol:
RNA-seq: TRAP was performed as previously described (Roh et al., Cell Rep 2017). Adipose tissues were homogenized and processed to immunoprecipitation using anti-GFP antibody. Immunoprecipitates were washed and subjected to RNA extraction using Qiagen Micro RNeasy kit according to the manufacturer’s instructions. Isolated RNA was quantified by Qubit, and RNA integrity was analyzed by Agilent Bioanalyzer.
ChIP-seq: Tissues were dounce homogenized, and cross-linked nuclei were isolated and sorted by BD FACS Aria II using mCherry fluorescence. Sorted nuclei were sheared by Covaris E220 and used for ChIP for overnight. Immunoprecipitates were washed and subjected to elution and reverse crosslinking. DNA was then extracted by AMPure XP beads according to the manufacturer’s manual.
RNA-seq: TRAP-isolated RNA (≤100ng) was treated with the Ribo-Zero rRNA removal kit (Epicentre) to deplete ribosomal RNA and converted into double stranded cDNA using NEBNext mRNA Second Strand Synthesis Module. cDNA was subsequently tagmented and amplified for 12 cycles by using Nextera XT DNA Library Preparation Kit. Sequencing libraries were analyzed Qubit and Agilent Bioanalyzer, pooled at a final concentration of 12pM, and sequenced on a HiSeq2500.
ChIP-seq: Sequencing libraries were constructed using the “on-bead” preparation method as previously described (Roh et al., Cell Rep, 2017). ChIP-isolated DNA was subjected to end repair/phosphorylation using the End-It DNA End-Repair Kit (Epicentre), A-tailing using the Klenow Fragment and index adaptor ligation using Quick Ligase (NEB). AMPure XP beads were left in all the reactions to allow isolation of DNA using PEG (Polyethylene Glycol 8000)/NaCl solution, thus minimizing loss between reactions. After ligation, DNA was eluted and amplified by PCR for 14-16 cycles using the PfuUltra II Hotstart PCR Master Mix. DNA sized between 250 and 600bp was selected by gel electrophoresis and extraction using E-Gel EX Agarose Gels (Invitrogen) and MinElute Gel Extraction kits (Qiagen). Libraries were analyzed using the Qubit and Agilent Bioanalyzer, pooled at a final concentration of 12pM and sequenced on a HiSeq2500 or NextSeq 500500 system.

treatment_protocol: Mice were fed chow or HFD for 10 weeks.

tag: strain background

tag: treatment

value: HFD for 10 weeks

value: epididymal WAT

tag: molecule subtype

value: translating mRNA


title: adipocyte HFD mRNA rep 1


title: adipocyte HFD mRNA rep 2


title: Replicate3_4

description:
RNA (see 10X Genomics 3' scRNAseq V2 library preparation protocol)
Transduction replicate 3, 10X lane 4


title: Replicate2_6

description:
RNA (see 10X Genomics 3' scRNAseq V2 library preparation protocol)
Transduction replicate 2, 10X lane 6


title: Replicate2_8

description:
RNA (see 10X Genomics 3' scRNAseq V2 library preparation protocol)
Transduction replicate 2, 10X lane 8


title: Replicate3_1

description:
RNA (see 10X Genomics 3' scRNAseq V2 library preparation protocol)
Transduction replicate 3, 10X lane 1


title: Replicate3_3

description:
RNA (see 10X Genomics 3' scRNAseq V2 library preparation protocol)
Transduction replicate 3, 10X lane 3


title: adipocyte chow mRNA rep 2

source_name: adipocyte chow mRNA

value: chow for 10 weeks


title: 4_1

description: Ion Torrent, Ion Proton System


title: Replicate3_2

description:
RNA (see 10X Genomics 3' scRNAseq V2 library preparation protocol)
Transduction replicate 3, 10X lane 2


title: Replicate2_7

description:
RNA (see 10X Genomics 3' scRNAseq V2 library preparation protocol)
Transduction replicate 2, 10X lane 7


title: adipocyte chow mRNA rep 3


title: adipocyte chow mRNA rep 1


title: Replicate2_5

description:
RNA (see 10X Genomics 3' scRNAseq V2 library preparation protocol)
Transduction replicate 2, 10X lane 5


title: Replicate2_2

description:
RNA (see 10X Genomics 3' scRNAseq V2 library preparation protocol)
Transduction replicate 2, 10X lane 2


title: Replicate2_3

description:
RNA (see 10X Genomics 3' scRNAseq V2 library preparation protocol)
Transduction replicate 2, 10X lane 3


title: Replicate3_5

description:
RNA (see 10X Genomics 3' scRNAseq V2 library preparation protocol)
Transduction replicate 3, 10X lane 5


title: LDLR KO + REGN1500 (ANGPTL3 mAb) rep3

city: Tarrytown

first: Rene

middle: Christian

last: Adam

state: New York

address: 777 Old Saw Mill River Road

institute: Regeneron Pharmaceuticals

description: liver.ANGPTL3 mAb_3

data_processing:
Illumina bcl2fastq v2.17 used to convert BCL to fastq
Reads were decoded based on their barcodes. Read quality was evaluated using FastQC.
Reads were mapped to the reference genome (mouse: GRCm38) using using ArrayStudio® software (OmicSoft®, Cary, NC) allowing two mismatches.
Genome_build: GRCm38
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each sample

extract_protocol:
Livers were removed and stored in RNAlater. RNA was then harvested using MagMAX-96 for Microarrays Total RNA Isolation kit (Ambion). Genomic DNA was removed using MagMAXTurboDNase buffer and TURBO DNase from the MagMAX kit listed above. mRNA was purified from total RNA using Dynabeads mRNA Purification kit (Invitrogen).
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Mice were treated once weekly for 3 weeks with 25mg/kg control mAb or ANGPTL3 mAb. Livers were harvested 6 days after the last mAb treatment.

tag: antibody

value: 75% C57BL/6NTac 25% 129S6/SvEvTac

tag: genotype

value: LDLR KO


title: LDLR KO + REGN1500 (ANGPTL3 mAb) rep5

description: liver.ANGPTL3 mAb_5


title: LDLR KO + REGN1500 (ANGPTL3 mAb) rep2

description: liver.ANGPTL3 mAb_2


title: Replicate1_8

description:
RNA (see 10X Genomics 3' scRNAseq V2 library preparation protocol)
Transduction replicate 1, 10X lane 8


title: Replicate2_1

description:
RNA (see 10X Genomics 3' scRNAseq V2 library preparation protocol)
Transduction replicate 2, 10X lane 1


title: Replicate1_7

description:
RNA (see 10X Genomics 3' scRNAseq V2 library preparation protocol)
Transduction replicate 1, 10X lane 7


title: Replicate1_6

description:
RNA (see 10X Genomics 3' scRNAseq V2 library preparation protocol)
Transduction replicate 1, 10X lane 6


title: Replicate1_5

description:
RNA (see 10X Genomics 3' scRNAseq V2 library preparation protocol)
Transduction replicate 1, 10X lane 5


title: LDLR KO + REGN1945 (Control mAb) rep6

description: liver_ctrl mAb_6


title: LDLR KO + REGN1945 (Control mAb) rep5

description: liver_ctrl mAb_5


title: Replicate2_4

description:
RNA (see 10X Genomics 3' scRNAseq V2 library preparation protocol)
Transduction replicate 2, 10X lane 4


title: Replicate1_4

description:
RNA (see 10X Genomics 3' scRNAseq V2 library preparation protocol)
Transduction replicate 1, 10X lane 4


title: LDLR KO + REGN1945 (Control mAb) rep3

description: liver_ctrl mAb_3


title: LDLR KO + REGN1945 (Control mAb) rep4

description: liver_ctrl mAb_4


title: Replicate1_3

description:
RNA (see 10X Genomics 3' scRNAseq V2 library preparation protocol)
Transduction replicate 1, 10X lane 3


title: amplicon_sgRNA_3

description:
RNA (see 10X Genomics 3' scRNAseq V2 library preparation protocol)
Amplicon sgRNA library for 10X cDNA sample 3_1 to 3_8


title: LDLR KO + REGN1945 (Control mAb) rep2

description: liver_ctrl mAb_2


title: Replicate1_1

description:
RNA (see 10X Genomics 3' scRNAseq V2 library preparation protocol)
Transduction replicate 1, 10X lane 1


title: LDLR KO + REGN1945 (Control mAb) rep1

description: liver_ctrl mAb_1


title: E14_mESCs

description: RNA (see 10X Genomics 3' scRNAseq V2 library preparation protocol)

data_processing:
10X scRNA-seq data was processed with the default CellRanger v2.1 pipeline (Zheng et al. 2017) for mapping to the mm10 mouse genome assembly. Gene counts were further analysed with scanpy (Wolf et al. 2018). For quality control, cells with less than 15,000 UMI counts and/or less than 4,000 detected genes, cells with more than 40,000 UMI counts and/or more than 6,500 detected genes, and cells with more than 5% of UMI reads coming from mitochondrial genes were discarded. After this quality control, 1,138 E14 ESCs, 687 SAM ESCs transduced with the non-targeting control 461, 1227 SAM ESCs transduced with the MERVL LTR sgRNAs 459 and 460 and 899 SAM ESCs transduced with the Zscan4 sgRNAs 457 and 458 were kept. A gene was considered for downstream analysis if it was detected (UMI count >0) in at least in 10 cells that passed filtering across the dataset. The final dataset consisted of 16,498 genes across 3,951 cells. For gene expression quantification, the number of UMIs for every cell was adjusted by library size dividing by the total number of UMIs per cell, log-transformed, and scaled with the factor of 10,000
Genome_build: mm10
Supplementary_files_format_and_content: Barcodes detected, genes detected and matrix files are provided for each sample

extract_protocol:
See 10X Genomics V2 Single Cell 3′ Solution kit user guide
See 10X Genomics V2 Single Cell 3′ Solution kit user guide
Each 10X library was sequenced on an Illumina HiSeq4000 lane with 75 cycles for read 1, 75 cycles for read 2 and 8 cycles i7 sample index.

treatment_protocol: Individual sgRNAs were transduced into SAM ESCs by direct supplementation of concentrated lentivirus into the medium for 24 hours. 48 hours after transduction, 1 ug/ul puromycin was added to the medium for selection of transduced cells. Cells were selected and passaged for 8 days after addition of puromycin before single-cell RNA-sequencing library preparation.

tag: cell type

value: E14 mESCs


title: Non_targeting_sgRNA_controls

value: SAM mESCs (E14 + stable integration of dCas9-VP64 and MS2-p65-HSF1) transduced with a non targeting sgRNA control

tag: transduction


title: amplicon_sgRNA_1

description:
RNA (see 10X Genomics 3' scRNAseq V2 library preparation protocol)
Amplicon sgRNA library for 10X cDNA samples 1_1 to 1_8


title: Smarca5_sgRNA_353_replicate_C

description: CRISPRa of Smarca5

data_processing:
Raw FastQ data were trimmed with Trim Galore (v0.6.1, default parameters) and mapped to the mouse mm10 genome assembly using HISAT2 v2.0.5, as guided by known splice sites taken from Ensembl v68. Hits were filtered to remove mappings with MAPQ scores <20. Data were quantitated at mRNA level using the RNA-seq quantitation pipeline in SeqMonk software (www.bioinformatics.babraham.ac.uk/projects/seqmonk/) with strand specific quantification using mRNA probes. Quantified data are reported in log2 reads per million.
Genome_build: mm10/GRCm38
Supplementary_files_format_and_content: Quantified data for each sample are reported in log2 reads per million.

extract_protocol:
RNA was isolated using RNeasy Mini kit (Qiagen, 74104) and treated with DNaseI (Thermo Fisher Scientific, EN0521) following manufacturer’s instructions.
Opposite strand-specific polyA RNA libraries were made using 1 μg DNase-treated RNA using the Sanger Institute Illumina bespoke pipeline.
50 bp single-end, Illumina HiSeq4000

treatment_protocol: For CRISPRa, individual lentiviral transductions were performed into SAM mESCs with the specified sgRNA targeting the promoter of the gene of interest, by direct supplementation of lentivirus into the cells for 24 hours; 48 hours after transduction, cells were selected with 1ug/ul puromycin for sgRNA expression and RNA was harvested 8 days later. For cDNA overexpression, GFP fusion constructs with the gene of interest were transfected into E14 mESCs using Lipofectamine 2000 Reagent Opti-MEM (GIBCO, 31985) (Thermo Fisher Scientific, 11668019), following manufacturer’s instructions; cells were grown for 48 hours before GFP+ FACS sorting on BD Influx High-Speed Cell Sorter and RNA extraction.

value: SAM mESCs (E14 + stable integration of dCas9-VP64 and MS2-p65-HSF1)


title: amplicon_sgRNA_2

description:
RNA (see 10X Genomics 3' scRNAseq V2 library preparation protocol)
Amplicon sgRNA library for 10X cDNA sample 2_1 to 2_8


title: MERVL_LTR_sgRNAs

value: SAM mESCs (E14 + stable integration of dCas9-VP64 and MS2-p65-HSF1) transduced with MERVL LTR sgRNAs


title: LDLR KO + REGN1500 (ANGPTL3 mAb) rep1

description: liver.ANGPTL3 mAb_1


title: LDLR KO + REGN1500 (ANGPTL3 mAb) rep4

description: liver.ANGPTL3 mAb_4


title: Zscan4_sgRNA

value: SAM mESCs (E14 + stable integration of dCas9-VP64 and MS2-p65-HSF1) transduced with sgRNAs targeting the promoters of the Zscan4 gene cluster


title: Smarca5_sgRNA_353_replicate_B

description: CRISPRa of Smarca5


title: Smarca5_sgRNA_353_replicate_A

description: CRISPRa of Smarca5


title: SAM_rep2

data_processing:
Raw FastQ data were trimmed with Trim Galore (v0.6.1, default parameters) and mapped to the mouse mm10/GRCm38 genome assembly using HISAT2 v2.0.5, as guided by known splice sites taken from Ensembl v68. Hits were filtered to remove mappings with MAPQ scores <20. Data were quantitated at mRNA level using the RNA-seq quantitation pipeline in SeqMonk software (www.bioinformatics.babraham.ac.uk/projects/seqmonk/) with strand specific quantification using mRNA probes. Quantified data are reported in log2 reads per million.
Genome_build: mm10/GRCm38
Supplementary_files_format_and_content: Quantified data for each sample are reported in log2 reads per million.

extract_protocol:
RNA was isolated using RNeasy Mini kit (Qiagen, 74104) and treated with DNaseI (Thermo Fisher Scientific, EN0521) following manufacturer’s instructions.
Opposite strand-specific total RNA libraries (ribozero) were made using 1 μg DNase-treated RNA using the Sanger Institute Illumina bespoke pipeline.
100 bp paired-end, Illumina HiSeq 2500 Rapid Run.

treatment_protocol: SAM mouse embryonic stem cells (ESCs) were generated by lentiviral transduction of lenti dCas9-VP64_Blast (Addgene 61425) and lenti MS2-p65-HSF1_Hygro (Addgene 61426) into E14 mouse ESCs, followed by antibiotic selection and manual subcloning. Clones were checked by genomic PCR and one clone was used for consecutive experiments.

tag: exogenous integrations

value: 129/Ola ES-E14 + stable integration of dCas9-VP64 and MS2-p65-HSF2


title: SAM_rep1

value: 129/Ola ES-E14 + stable integration of dCas9-VP64 and MS2-p65-HSF1


title: Smarca5-GFP+_replicate_C

description: cDNA overexpression of Smarca5


title: E14_rep3


title: E14_rep2


title: Smarca5-GFP+_replicate_A

description: cDNA overexpression of Smarca5


title: Smarca5-GFP+_replicate_B

description: cDNA overexpression of Smarca5


title: E14_rep1


title: Patz1_sgRNA_103_replicate_B

description: CRISPRa of Patz1


title: Patz1_sgRNA_103_replicate_C

description: CRISPRa of Patz1


title: ChIPseq-PolII

city: Shenzhen

first: Zhijun

last: Han

state: Guangdong

address: No 1088,xueyuan Rd., Nanshan District

institute: Southern University of Science and Technology

data_processing:
Basecalls performed using CASAVA version 1.4
We downloaded the file containing mouse indels and SNPs information (about 21 million SNPs) (mgp.v5.merged.indels.dbSNP142.normed.vcf) from Mouse Genomes Project (ftp://ftp-mouse.sanger.ac.uk) and examined the SNPs between C57BL/6J and CAST/EiJ using SNPsplit toolkit. Next, we built the mm10 Bowtie2 index with all SNP positions being masked by the ambiguity base ’N’. All reads from B6 and Cast Hi-C libraries were mapped to this N-masked reference using Bowtie2 (with parameter --very-sensitive -L 30 --score-min L,-0.6,-0.2 --end-to-end). For retrieving the high confident SNPs, we re-called the genotype for each SNP locus in B6 and Cast Hi-C libraries using samtools mpileup with reads MAPQ >= 30. The called SNPs showing identical states with that downloaded from house mouse genome project were selected for further analyses. In total, we obtained 13 million high confident SNPs for distinguishing Cast haploid reads and B6 haploid reads in hybrid mice.
The paired-end reads from Hi-C, also known as paired-end tags (PETs), were mapped to N-masked mm10 reference with bowtie2 separately. Both ends of the PETs with MAPQ >= 30 were kept. The PETs with the same start and the same end were treated as redundant PETs, among which only one PET was kept for further analysis. Intra-chromosomal PETs within 10Kb were as self-ligations and were filtered out. The interaction matrix was constructed at different scales, with different bin sizes from 20Kb to 100Kb. The matrix were normalized using iterative correction algorithm ICE. A|B compartments were calculated as described in Lieberman-Aiden et al. PETs from hybrid mice Hi-C library were split into haploid using SNPsplit using highly confident SNPs, and the downstream processing was similar to normal Hi-C samples.
ChIP-seq reads were mapped and filtered similarly to Hi-C reads. Peaks were called using macs2. Haploid ChIP-seq data sets were generated the same as Hi-C. For comparison of the differences of histone modifications and TF bindings between Fb6 and Fcast, we counted the allele-specific reads located in the peaks using bedtools intersect, the significances of the difference were calculated by DESeq. ChIP-seq reads were extended to 150bp and normalized by sample size, then converted to bedGraph for visualization.
RNA-seq reads were mapped to N-masked mm10 reference by TopHat2, reads with MAPQ >= 30 were kept for measuring gene expression level. The batch effect of replicates was adjusted by ComBat from R package sva, and differentially expressed genes were identified by DESeq2 with FDR < 0.05 and fold change > 1.8. Allele-specific reads were grouped by SNPsplit, whereas allele-specific gene expression was counted and quantified as normal.
Genome_build: mm10
Supplementary_files_format_and_content: TAB-delimited text files for filtered Hi-C PETs in format of 'chr1 site1 genotype1 chr2 site2 genotype2', where genotype 'G1' stands for B6, 'G2' stands for Cast, 'UA' is unassigned, '.' is unparsed. TAB-delimited text files contain raw reads count for each gene (RNA-seq samples) or for each peak (ChIP-seq samples, first column is peak ID, second column is Fb6 count, third column is Fcast count). BigWig files for processed ChIP-seq signal. BroadPeak files for called ChIP-seq peaks.

source_name: Naive CD4+ T cells

growth_protocol: All the mice, including B6, Cast and hybrid mice, were between 6 and 8 weeks at the time of experimentation.

extract_protocol:
Splenic and lymph node CD4+ T cells from all mice were prepared by MACS purification with CD4 microbeads (Miltenyi Biotec), and the purity was usually 90%–95%. Naive T cells were obtained by surface staining with anti-CD4, anti-CD62L, anti-CD44, and anti-CD25. The CD4+ CD62L+ CD44CD25 population was isolated by flow-cytometry cell sorting with a Mo-Flo cell sorter (Dako, Carpinteria, CA).
The three enzyme Hi-C (3e Hi-C) was performed according to our previous studies. About 1,000,000 CD4+ naïve cells were stained with Biotin anti-CD45.2 antibody, bound to biotin binder (Dynabeads Biotin Binder, Cat#11047, Invitrogen) and cross-linked with 1% formaldehyde for 10 mins. Biotin binders were blocked by 0.5mM biotin solution. Cells were lysed and subsequently digested with 20 Units CviQ I (NEB), and 20 Units CviA II (NEB) at 25 C for 20 minutes, then 20 Units Bfa I (NEB) at 37 C for 20 minutes. The reaction was stopped by washing the cells twice with 600 mL wash buffer (10mM NaCl, 1mM EDTA, 0.1% triton-100). DNA ends were marked by biotin-14-dATP with Klenow (large) for 1hr at 37 C. Blunt-end DNA fragments were ligated with T4 DNA Ligase overnight at 16 C. DNA was then reverse cross-linked and purified by phenol/chloroform extraction. Biotin was removed from unligated DNA-ends by T4 DNA polymerase for 2hrs at 12 C. DNA was purified by phenol/chloroform and sheared to 300-500 bp by sonication followed by DNA-end repair and addition of ‘‘A’’. Biotin labeled DNA was pull-downed by streptavidin beads followed by Illumina adaptor ligation and PCR amplification. DNA fragments of 300 to 700 bp were isolated 2% agarose gel and sequenced by paired-end sequencing on Illumina Hiseq 2500. ChIP-Seq experiments were performed as described previously. In brief, five millions of CD4 Naïve T cells were fixed for 10 min with 1% formadehyde in complete medium, sonicated and chromatin immunoprecipitation was performed with antibodies against CTCF (07-729, Millipore), RNA Polymerase II (ab5408, Abcam), H3K4me3 (ab8580, Abcam) and H3K4me2 (ab32356, Abcam). The DNA was then ligated with the ‘‘Y’’-shaped Illumina adaptor and amplified for 18 cycles using indexing primers as described. PCR products between 160-300bp were isolated on 2% E-gel for sequencing on Illumina Hiseq2500. Total RNA was purified with an miRNeasy micro kit (217084; Qiagen) and a DNase set (79254; Qiagen) for the option of on-column digestion with DNase. 10 ng purified total RNA was used for amplification of cDNA with the Ovation RNA-Seq System V2 (7102-08; NuGEN Technologies). 200 ng cDNA was sonicated in a Diagenode Bioruptor (level M, for a total of 30 min of 20s on and 20s off) to size range of 100–400bp. Indexed libraries were prepared with a Multiplexing Sample Preparation Oligonucleotide Kit (1005709; Illumina) and an End-It DNA End-repair Kit (ER81050; Epcentre) according to the user’s manual (Epcentre) and sample preparation guide (Illumina).

value: B6 x Cast

tag: age

value: 6-29 weeks

value: Naive CD4+ T cells


title: ChIPseq-CTCF

value: 6-28 weeks


title: ChIPseq-H3K4me3

value: 6-26 weeks


title: ChIPseq-H3K4me2

value: 6-25 weeks


title: Non_targeting_462_replicate_B

description: Non targeting sgRNA control for CRISPRa

value: 129/Ola ES-E14


title: Patz1-GFP+_replicate_C

description: cDNA overexpression of Patz1


title: Patz1-GFP+_replicate_B

description: cDNA overexpression of Patz1


title: RNAseq-Cast-rep2

value: CAST/EiJ

value: 6-23 weeks


title: Non_targeting_462_replicate_C

description: Non targeting sgRNA control for CRISPRa


title: Non_targeting_461_replicate_C

description: Non targeting sgRNA control for CRISPRa


title: RNAseq-Cast-rep1

value: 6-22 weeks


title: RNAseq-Hybrid-rep2

value: 6-20 weeks


title: Patz1-GFP+_replicate_A

description: cDNA overexpression of Patz1

value: E14 mESCs


title: RNAseq-Hybrid-rep3

value: 6-21 weeks


title: RNAseq-Hybrid-rep1

value: 6-19 weeks


title: Non_targeting_461_replicate_A

description: Non targeting sgRNA control for CRISPRa

value: SAM mESCs (E14 + stable integration of dCas9-VP64 and MS2-p65-HSF1)


title: Non_targeting_461_replicate_B

description: Non targeting sgRNA control for CRISPRa


title: GFP+_replicate_C

description: cDNA overexpression of GFP (control)


title: RNAseq-B6-rep2

value: 6-17 weeks


title: Patz1_sgRNA_103_replicate_A

description: CRISPRa of Patz1


title: RNAseq-B6-rep3

value: 6-18 weeks


title: GFP+_replicate_A

description: cDNA overexpression of GFP (control)


title: Dppa2_sgRNA_323_replicate_C

description: CRISPRa of Dppa2


title: RNAseq-B6-rep1

value: 6-16 weeks


title: RNAseq-Cast-rep3

value: 6-24 weeks


title: Dppa2_sgRNA_323_replicate_B

description: CRISPRa of Dppa2


title: HiC-Cast-rep1

value: 6-14 weeks

value: Naive CD4+ T cells


title: HiC-Hybrid-rep2

value: B6 x Cast

value: 6-13 weeks


title: Non_targeting_462_replicate_A

description: Non targeting sgRNA control for CRISPRa

value: 129/Ola ES-E14


title: HiC-Cast-rep2

value: CAST/EiJ

value: 6-15 weeks


title: Dppa2_sgRNA_323_replicate_A

description: CRISPRa of Dppa2


title: HiC-Hybrid-rep1

value: 6-12 weeks


title: Carhsp1_sgRNA_287_replicate_C

description: CRISPRa of Carhsp1


title: Dppa2-GFP+_replicate_C

description: cDNA overexpression of Dppa2


title: Dppa2-GFP+_replicate_B

description: cDNA overexpression of Dppa2


title: HiC-B6-rep3

value: 6-10 weeks


title: Dppa2-GFP+_replicate_A

description: cDNA overexpression of Dppa2

value: E14 mESCs


title: Carhsp1_sgRNA_287_replicate_A

description: CRISPRa of Carhsp1


title: Carhsp1_sgRNA_287_replicate_B

description: CRISPRa of Carhsp1


title: HiC-B6-rep1

value: 6-8 weeks


title: HiC-B6-rep2

value: 6-9 weeks


title: GFP+_replicate_B

description: cDNA overexpression of GFP (control)


title: miR-203 tKI iPSCs (induced with dox) clon2

city: Madrid

first: Maria

last: Salazar

state: Comunidad de Madrid

address: C/ Melchor Fernández Almagro, 3

department: Molecular Oncology

country: Spain

institute: CNIO

description:
MSRV9
iPS generated by in vitro reprogramming from mouse embryonic cells (MEFs) that were obtained from our animal model ColA1_miR203; Rosa26rtTA. Once the iPs were stablished, cells were treated with DOX, in order to transiently over-express miR-203.
Strand-specific RNA-seq (dUTP)

data_processing:
RNA-seq processing:
RNA-seq data was analysed with the nextpresso pipeline (http://bioinfo.cnio.es/nextpresso/) as follows:
Reads are quality-checked with FastQC, and aligned to the mouse genome (GRCm38/mm10) with TopHat-2.0.10 (using Bowtie 1.0.0 and Samtools 0.1.19), allowing 2 mismatches and 20 multihits
Transcripts quantification and differential expression are calculated with Cufflinks 2.2.1, using the Mus musculus GRCm38/mm10 transcript annotations from the UCSC Genome Browser
Genome_build: GRCm38/mm10
Supplementary_files_format_and_content: FPKM values calculated with Cuffnorm

source_name: miR-203 tKI iPSC

growth_protocol: iPS cells were grown over feeders, and cultured in DMEM supplemented with 20% KSR and Gentamycin.

extract_protocol:
miRVana RNA isolation Kit form Thermo Fisher Scientific
1 µg of total RNA  was extracted. Sample RNA Integrity Numbers were in the range 9.1 to 10 when assayed on an Agilent 2100 Bioanalyzer. PolyA+ fraction was purified and randomly fragmented, converted to double stranded cDNA and processed through subsequent enzymatic treatments of end-repair, dA-tailing, and ligation to adapters as in Illumina's "TruSeq Stranded mRNA Sample Preparation Part # 15031047 Rev. D" kit (this kit incorporates dUTP during 2nd strand cDNA synthesis, which implies that only the cDNA strand generated during 1st strand synthesis is eventually sequenced). Adapter-ligated library was completed by PCR with Illumina PE primers (8 cycles). The resulting purified cDNA library was applied to an Illumina flow cell for cluster generation and sequenced on an Illumina HiSeq2500 by following manufacturer's protocols.

treatment_protocol: For samples MSRV1-4, the indicated siRNAs were transfected using the manufacturer´s protocol (Dharmacon) and samples were colected 1 week later. For samples MSRV7-10, miR-203 tKI iPSCs were treated with Doxycycline during 5 days, in order to induce the expression of miR-203 transiently. DOX withdrawal was prolongued during 2 weeks.

value: iPSC

value: ColA1_miR203 (KI/KI); Rosa26rtTA (KI/KI)

value: DOX during 5 days


title: Mm-Rmrp-25mM5NIA-InCell

description:
Mm_Rmrp_ncRNA.fa
Mm-Rmrp-InCell-SHAPE-MaP.txt
Mm-Rmrp-deltaSHAPE.txt

value: 25mM 5NIA

tag: treatment type

value: In-Cell

tag: enrichment

value: gene-specific amplification

tag: target

value: Rmrp

tag: rt priming

value: gene-specific


title: Carhsp1-GFP+_replicate_C

description: cDNA overexpression of Carhsp1

tag: strain


title: Carhsp1-GFP+_replicate_B

description: cDNA overexpression of Carhsp1


title: miR-203 KI iPSCs (not induced) clon1

description:
MSRV8
iPS generated by in vitro reprogramming from mouse embryonic cells (MEFs) that were obtained from our animal model ColA1_miR203; Rosa26rtTA. Once the iPs were stablished, cells were treated with DOX, in order to transiently over-express miR-203.
Strand-specific RNA-seq (dUTP)

value: vehicle


title: WT iPSCs si Dnmt3a and Dnmt3b

description:
MSRV4
iPS generated by in vitro reprogramming from mouse embryonic cells (MEFs) that were obtained from WT mice.
Strand-specific RNA-seq (dUTP)

source_name: WT iPSCs

value: WT iPSC

value: WT IPSCs were transfected with siRNA Dnmt3a and siRNA Dnmt3b


title: Carhsp1-GFP+_replicate_A

description: cDNA overexpression of Carhsp1

value: 129/Ola ES-E14


title: WT iPSCs si Dnmt3b

description:
MSRV3
iPS generated by in vitro reprogramming from mouse embryonic cells (MEFs) that were obtained from WT mice.
Strand-specific RNA-seq (dUTP)

value: WT IPSCs were transfected with siRNA Dnmt3b


title: Sub1.8d.2r

city: Riverside

first: Maureen

last: Hummel

state: California

address: 900 University Avenue

department: Botany and Plant Sciences

institute: University of California

data_processing:
Processing of RNA-seq data was performed using the package systemPipeR
Alignment to IRGSP-1.0.30 Ensembl Plants Oryza sativa Nipponbare genome with added SUB1A-1 gene with bowtie2/2.2.5 and tophat/2.0.14
Aligned reads were counted against the Oryza_sativa.IRGSP-1.0.30 genome release 30 (Ensembl) with added SUB1A-1 gene as separate Chromosome using the summarizeOverlaps function in union mode
Genome_build: Oryza_sativa.IRGSP-1.0.30

organism: Oryza sativa

source_name: Oryza sativa coleoptile 8-days-old

extract_protocol: poly(A)+ selected; library construction method based on Wang et al., 2011  PloS one 6: e26426

tag: cultivar

value: Indica

value: 8 days old

value: coleoptile


title: Sub1.4d.2r

source_name: Oryza sativa coleoptile 4-days-old

value: 4 days old


title: C9HMNANXX_6_160502_BGU--016_Mouse_CAGATC_R_160502_SHANAI_LIB_M001

data_processing:
Alignment to genome using bwa-meth 0.10 with default parameters
Merging of bam files using picard 1.91. Merged samples are {9, 10}, {11, 12}, {13, 14}, {15, 16}, {17, 18}, {19, 20}, {21, 22}, {23, 24}
Methylation calling and tabulation using bwa-meth 0.10 tabulate module with parameter '--map-q 60'
Genome_build: mm10
Supplementary_files_format_and_content: Tab-separated value file (.tsv) containing tabulated counts for methylated and total reads per CpG site.

source_name: Mouse cell line

growth_protocol: iPS cells were grown over feeders, and cultured in DMEM supplemented with 20% KSR and Gentamycin, using standard methods. For Ebs formation, standard "hanging-drop" protocols were used.

extract_protocol:
DNA samples were extracted using the QIAamp DNA KIT, from QUIAGEN. For bisulphite conversion, the details are explained below.
DNA samples were prepared for whole genome bisulphite sequencing using the TrueMethyl® Whole Genome Kit (CEGX®) according to the manufacturer’s instructions. Briefly, 200 ng of genomic DNA was sheared to 800 bp using M220 Focused-ultrasonicator™(Covaris®). Then the fragmented DNA was denatured and oxidised by a chemical oxidant to convert 5-hydroxymethyl cytosine to 5-formylcytosine (5fC). The purpose of the oxidation was to ensure that we purely captured the information for 5’ methyl cytosine methylation and not an indistinguishable pattern combination of 5’methyl cytosine and 5’hydroxymethyl cytosine. Following oxidation, the DNA was subjected to bisulphite conversion for the deamination of cytosines and 5fC to uracils. Bisulphite converted DNA was desulfonated and purified to then proceed to library preparation. In this “post-bisulfite conversion” library preparation method, the fragmented single stranded bisulfite converted DNA was adapted with sequencing adaptors at the 3’end followed by an extension step and finally ligation of adaptors at the 5’ end of the molecules. Finally, the libraries were indexed and amplified. The PCR was performed for 10 cycles followed by bead-based purification. An additional purification and size selection step using Agencourt AMPure XP beads (Beckman Coulter, Cat: A63881) was performed to remove adaptor dimers. The purified library was eluted in a final volume of 14 ml pure water. Quality of the library obtained was checked using the DNA High sensitivity chip on the Agilent Bioanalyzer. The library was quantified using Qubit and KAPA Biosystems Library quantification kit (#KK4824) according to manufacturer’s instructions. A total of 12pMol of multiplexed libraries were sequenced on a 125 bp paired-end (PE) format (Illumina HiSeq2500).

treatment_protocol: During 5 days, the cells were treated with Doxycycline, in order to induce the expression of miR-203 transiently. DOX withdrawal was then established and prolongued until day 32.

value: Ebs from iPs miR-203 KI-N9 + DOX


title: HiC-B6-rep4

value: 6-11 weeks

value: Naive CD4+ T cells


title: WT iPSCs siDnmt3a

description:
MSRV2
iPS generated by in vitro reprogramming from mouse embryonic cells (MEFs) that were obtained from WT mice.
Strand-specific RNA-seq (dUTP)

value: WT IPSCs were transfected with siRNA Dnmt3a


title: miR-203 KI iPSCs (not induced) clon2

description:
MSRV10
iPS generated by in vitro reprogramming from mouse embryonic cells (MEFs) that were obtained from our animal model ColA1_miR203; Rosa26rtTA. Once the iPs were stablished, cells were treated with DOX, in order to transiently over-express miR-203.
Strand-specific RNA-seq (dUTP)

value: iPSC

value: ColA1_miR203 (KI/KI); Rosa26rtTA (KI/KI)


title: C9HMNANXX_5_160502_BGU--013_Mouse_CAGATC_R_160502_SHANAI_LIB_M001


title: Sub1.2d.3r

source_name: Oryza sativa embryo 2-days-old

value: 2 days old

value: embryo


title: Sub1.4d.1r


title: H2Y35ADXY_1_160202_BDI--002_Mouse_ATGTCA_R_160201_WENQU_M002

value: Ebs from iPs miR-203 KI-N5 + DOX


title: H2Y35ADXY_2_160202_BDI--002_Mouse_ATGTCA_R_160201_WENQU_M002


title: miR-203 tKI iPSCs (induced with dox) clon1

description:
MSRV7
iPS generated by in vitro reprogramming from mouse embryonic cells (MEFs) that were obtained from our animal model ColA1_miR203; Rosa26rtTA. Once the iPs were stablished, cells were treated with DOX, in order to transiently over-express miR-203.
Strand-specific RNA-seq (dUTP)

value: DOX during 5 days


title: C9HMNANXX_3_160502_BGU--008_Mouse_GATCAG_R_160502_SHANAI_LIB_M001

value: iPs miR-203 KI-N9 long after DOX


title: C9HMNANXX_4_160502_BGU--011_Mouse_GATCAG_R_160502_SHANAI_LIB_M001


title: Sub1.14d.3r

source_name: Oryza sativa coleoptile 14-days-old

value: 14 days old


title: H2Y35ADXY_2_160202_BDI--001_Mouse_GCCAAT_R_160201_WENQU_M002

value: iPs miR-203 KI-N5 long after DOX


title: Sub1.14d.2r

value: Indica


title: Day7-3

city: Harbin

first: Baoguang

last: Liu

state: Heilongjiang Province

address: No.51 Hexing Road

department: forestry

institute: Northest forestry university

data_processing:
Nine libraries with different index numbers were pooled by mixing equal quantities of DNA from each library and applied as one lane for HiSeq 2000 sequencing
100 bp average read lengths were obtained after removing the library sequence index sequences from each read, reads were mapped to the reference P. trichocarpa genome release V3.0 (Phytozome V10.0, http://www.phytozome.com) using the program “TOPHAT”.
Genome_build: P. trichocarpa
Supplementary_files_format_and_content: xlsx file with phytozome Populus trichocarpa gene model name (version 3) and the read counts

organism: Populus trichocarpa

source_name: Stem differentiating xylem

growth_protocol: P. trichocarpa  trees were grown in ½ Mircle-Gro Soil (Scotts Miracle-Gro products, Maysville, OH, USA) and ½ Metro-Mix 200 (Sun Gro, Bellevue, WA, USA) in the green house for 6 monthes (16 h light/8 h dark cycle with supplemental light of ~ 300 µE m-2 s-1) before tissue harvested for characterzation.

extract_protocol:
SDX was lightly scraped (0.2–0.5 mm in depth) using a razor blade from the upper (TW region) of the bent stems, as well as from corresponding locations on the controls (non-bent trees). SDX tissues were immediately frozen in liquid nitrogen for RNA isolation. Total RNA from P. trichocarpa was isolated using the Qiagen RNeasy Mini kit (Invitrogen) for RNA-seq
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: P. trichocarpa trees (6 months old) were used to induce TW formation by mechanical bending of the stem to an angle of 90°. For transcriptomic analysis, stem differentiating xylem (SDX) tissues were collected 3-days and 7-days after bending.

value: Stem differentiating xylem

tag: days after bending treatment

value: 7 day


title: H2Y35ADXY_1_160202_BDI--001_Mouse_GCCAAT_R_160201_WENQU_M002


title: Day7-2

tag: tissue


title: Sub1.8d.3r

value: 8 days old

value: coleoptile


title: C9HMNANXX_4_160502_BGU--010_Mouse_ACTTGA_R_160502_SHANAI_LIB_M001

value: iPs miR-203 KI-N9 short after DOX


title: WT iPSCs siC

description:
MSRV1
iPS generated by in vitro reprogramming from mouse embryonic cells (MEFs) that were obtained from WT mice.
Strand-specific RNA-seq (dUTP)

value: WT iPSC

value: WT IPSCs were transfected with siRNA Control


title: Day7-1


title: Sub1.14d.1r


title: Sub1.4d.3r

value: 4 days old


title: C9HMNANXX_3_160502_BGU--007_Mouse_ACTTGA_R_160502_SHANAI_LIB_M001


title: IR64.8d.3r


title: IR64.8d.2r


title: Day3-1

value: 3 day


title: Sub1.2d.2r

value: 2 days old


title: C9HMNANXX_6_160502_BGU--017_Mouse_GTGAAA_R_160502_SHANAI_LIB_M001

value: iPs miR-203 KI-N5 short after DOX


title: IR64.8d.1r


title: Day0-3

value: 0 day


title: Sub1.2d.1r

value: embryo


title: Day0-2


title: C9HMNANXX_5_160502_BGU--014_Mouse_GTGAAA_R_160502_SHANAI_LIB_M001


title: Day0-1


title: IR64.4d.3r


title: Hs-XISTE-3JUV-InVitro

description:
HsXIST-Eplus.fa
Hs-XISTE-RNP-MaP-InVitro-shapemapper-output.txt

molecule: other

source_name: Reconstituted solution

extract_protocol:
library prep: Nextera XT
proteinase K lysis, SPRI bead purification

value: 3JUV Only

value: In Solution

value: XIST E Region

value: random (9-mer)


title: C9HMNANXX_4_160502_BGU--009_Mouse_TTAGGC_R_160502_SHANAI_LIB_M001

value: iPs miR-203 KI-N9 (t=0)


title: Day3-3

value: Stem differentiating xylem


title: IR64.4d.2r

value: Indica


title: Hs-XISTE-3JUV-2mMSDA-100nMTIA1-InVitro

value: 3JUV-2mM SDA-100nM TIA1


title: Hs-XISTE-3JUV-2mMSDA-500nMTIA1-InVitro

value: 3JUV-2mM SDA-500nM TIA1


title: IR64.4d.1r

value: coleoptile


title: Hs-XISTE-3JUV-2mMSDA-500nMPTBP1-InVitro

value: 3JUV-2mM SDA-500nM PTBP1


title: C9HMNANXX_3_160502_BGU--006_Mouse_TTAGGC_R_160502_SHANAI_LIB_M001


title: Hs-XISTE-3JUV-2mMSDA-1uMTIA1-InVitro

value: 3JUV-2mM SDA-1uM TIA1


title: H2Y35ADXY_2_160202_BDI--000_Mouse_ACAGTG_R_160201_WENQU_M002

value: iPs miR-203 KI-N5 (t=0)


title: H2Y35ADXY_1_160202_BDI--000_Mouse_ACAGTG_R_160201_WENQU_M002


title: Hs-XISTE-3JUV-2mMSDA-100nMPTBP1-InVitro

value: 3JUV-2mM SDA-100nM PTBP1


title: Day3-2

value: 3 day


title: IR64.2d.3r

value: 2 days old


title: Hs-XISTE-3JUV-2mMSDA-500nMMATR3-InVitro

value: 3JUV-2mM SDA-500nM MATR3


title: IR64.2d.2r

value: embryo


title: C9HMNANXX_2_160502_BGU--005_Mouse_CTTGTA_R_160502_SHANAI_LIB_M001

value: Ebs from iPs WT (10 days of differentiation)


title: Hs-XISTE-3JUV-2mMSDA-1uMMATR3-InVitro

value: 3JUV-2mM SDA-1uM MATR3

value: In Solution

value: XIST E Region


title: Hs-XISTE-3JUV-2mMSDA-100nMMATR3-InVitro

value: 3JUV-2mM SDA-100nM MATR3

value: random (9-mer)


title: Hs-XISTE-3JUV-2mMSDA-1uMBSA-InVitro

value: 3JUV-2mM SDA-1uM BSA


title: C9HMNANXX_1_160502_BGU--002_Mouse_CTTGTA_R_160502_SHANAI_LIB_M001


title: Hs-XISTE-3JUV-2mMSDA-InVitro

value: 3JUV-2mM SDA


title: IR64.2d.1r

value: Indica


title: Hs-RMRP-3JUV-C

description:
Hs_RMRP_ncRNA.fa
Hs-RMRP-RNPMaP-shapemapper-output.txt

source_name: Human HEK293 cells

value: 3JUV only

value: In-Cell

value: gene-specific amplification

value: RMRP

value: gene-specific


title: C9HMNANXX_2_160502_BGU--004_Mouse_GAGTGG_R_160502_SHANAI_LIB_M001

value: iPs WT long after DOX


title: IR64.14d.3r

value: 14 days old

value: coleoptile


title: Hs-RMRP-2mMPhotoLys

description:
Hs_RMRP_ncRNA.fa
Hs-RMRP-PhotoLysineMaP-shapemapper-output.txt

value: 2mM photo-lysine


title: C9HMNANXX_1_160502_BGU--001_Mouse_GAGTGG_R_160502_SHANAI_LIB_M001


title: IR64.14d.2r


title: Hs-RMRP-3JUV-10mMSDA-C

value: 3JUV and 10mM SDA


title: Hs-XISTE-3JUV-2mMSDA-1uMPTBP1-InVitro

value: 3JUV-2mM SDA-1uM PTBP1

value: In Solution


title: HEK293-cytoplasmRNA-3JUV-Rep2

description:
Hs_28S-18S_rRNA_4V6X.fa
Hs-18S-RNPMaP-Rep2-shapemapper-output.txt
Hs-28S-RNPMaP-Rep2-shapemapper-output.txt

molecule: cytoplasmic RNA

extract_protocol:
library prep: Nextera XT
cytoplasmic fractionation, proteinase K lysis, PCA extraction

value: ribosomal RNA


title: HEK293-cytoplasmRNA-3JUV-Rep1

description:
Hs_28S-18S_rRNA_4V6X.fa
Hs-18S-RNPMaP-Rep1-shapemapper-output.txt
Hs-28S-RNPMaP-Rep1-shapemapper-output.txt

value: random (9-mer)


title: IR64.14d.1r


title: HEK293-cytoplasmRNA-3JUV-10mMSDA-Rep2


title: C9HMNANXX_6_160502_BGU--015_Mouse_CGATGT_R_160502_SHANAI_LIB_M001

value: iPs WT short after DOX


title: AG1Sub1.8d.2r

value: 8 days old


title: Hs-RMRP-10JUV-2mMPhotoLys

value: 10JUV and 2mM photo-lysine


title: AG1Sub1.8d.3r

value: Indica


title: C9HMNANXX_5_160502_BGU--012_Mouse_CGATGT_R_160502_SHANAI_LIB_M001


title: C9HMNANXX_2_160502_BGU--003_Mouse_ATCACG_R_160502_SHANAI_LIB_M001

value: iPs WT t=0


title: HEK293-cytoplasmRNA-3JUV-10mMSDA-Rep1

value: In-Cell


title: Hs-RNaseP-3JUV-Rep1

description:
Hs_RPPH1_ncRNA.fa
Hs-RNaseP-RNPMaP-Rep1-shapemapper-output.txt
Hs-RNaseP-RNPMaP-Rep1-ringmapper-output.txt

value: 3JUV only

value: gene-specific amplification

value: RNase P RNA


title: Hs-RNaseP-3JUV-10mMSDA-Rep1

value: gene-specific


title: C9HMNANXX_1_160502_BGU--000_Mouse_ATCACG_R_160502_SHANAI_LIB_M001


title: Hs-RNaseP-3JUV-Rep2

description:
Hs_RPPH1_ncRNA.fa
Hs-RNaseP-RNPMaP-Rep2-shapemapper-output.txt
Hs-RNaseP-RNPMaP-Rep2-ringmapper-output.txt


title: AG1Sub1.4d.2r

value: 4 days old

value: coleoptile


title: Hs-RMRP-3JUV-Rep2

description:
Hs_RMRP_ncRNA.fa
Hs-RMRP-RNPMaP-Rep2-shapemapper-output.txt
Hs-RMRP-RNPMaP-Rep2-ringmapper-output.txt

value: RMRP


title: AG1Sub1.4d.1r


title: Hs-RMRP-3JUV-Rep1

description:
Hs_RMRP_ncRNA.fa
Hs-RMRP-RNPMaP-Rep1-shapemapper-output.txt
Hs-RMRP-RNPMaP-Rep1-ringmapper-output.txt


title: Hs-RMRP-3JUV-10mMSDA-Rep2

value: 3JUV and 10mM SDA


title: Hs-RMRP-3JUV-10mMSDA-Rep1


title: Hs-U1-3JUV-Rep1

description:
Hs_U1snRNAs.fa
Hs-U1-RNPMaP-Rep1-shapemapper-output.txt
Hs-U1-RNPMaP-Rep1-ringmapper-output.txt

value: U1 snRNA


title: KIXDEB

description:
Strand-specific RNA-seq (dUTP)
ALLsamples.genes.fpkm_table.xls

data_processing:
RNA-seq processing:
RNA-seq data was analysed with the nextpresso pipeline as follows:
Reads are quality-checked with FastQC, and aligned to the mouse genome (GRCm38/mm10) with TopHat-2.0.10 (using Bowtie 1.0.0 and Samtools 0.1.19), allowing 2 mismatches and 5 multihits
Transcripts quantification and differential expression are calculated with Cufflinks 2.2.1, using the Mus musculus GRCm38/mm10 transcript annotations from the UCSC Genome Browser
Genome_build: GRCm38/mm10
Supplementary_files_format_and_content: FPKM values calculated with Cufflinks

source_name: Embryoid bodies derived from miR-203 tKI iPSCs

growth_protocol: iPS cells were grown over feeders, and cultured in DMEM supplemented with 20% KSR and Gentamycin. For Ebs formation, standard "hanging-drop" protocols were used.

extract_protocol:
miRVana RNA isolation Kit form Thermo Fisher Scientific
1 µg of total RNA  was extracted. Sample RNA Integrity Numbers were in the range 9.2 to 10 when assayed on an Agilent 2100 Bioanalyzer. PolyA+ fraction was purified and randomly fragmented, converted to double stranded cDNA and processed through subsequent enzymatic treatments of end-repair, dA-tailing, and ligation to adapters as in Illumina's "TruSeq Stranded mRNA Sample Preparation Part # 15031047 Rev. D" kit (this kit incorporates dUTP during 2nd strand cDNA synthesis, which implies that only the cDNA strand generated during 1st strand synthesis is eventually sequenced). Adapter-ligated library was completed by PCR with Illumina PE primers (8 cycles). The resulting purified cDNA library was applied to an Illumina flow cell for cluster generation and sequenced on an Illumina HiSeq2500 by following manufacturer's protocols.

treatment_protocol: During 5-7 days, the cells were treated with Doxycycline, in order to induce the expression of miR-203 transiently. DOX withdrawal was prolongued until day 32.

value: Embryoid bodies generated from the above-described iPSCs.

value: DOX during 5-7 days

value: ColA1_miR203; Rosa26rtTA


title: AG1Sub1.2d.2r

value: 2 days old

value: embryo


title: AG1Sub1.2d.3r

value: Indica


title: Hs-U1-3JUV-10mMSDA-Rep2

description:
Hs_U1snRNAs.fa
Hs-U1-RNPMaP-Rep2-shapemapper-output.txt
Hs-U1-RNPMaP-Rep2-ringmapper-output.txt

extract_protocol:
library prep: TruSeq
nuclear fractionation, proteinase K lysis, PCA extraction


title: AG1Sub1.8d.1r

value: 8 days old


title: Hs-RNaseP-3JUV-10mMSDA-Rep2

value: In-Cell


title: Hs-U1-3JUV-10mMSDA-Rep1


title: AG1Sub1.14d.3r

value: 14 days old


title: KIVEB


title: KIXV10

description:
iPS generated by in vitro reprogramming from mouse embryonic cells (MEFs) that were obtained from our animal model ColA1_miR203; Rosa26rtTA. Once the iPs were stablished, cells were treated with DOX, in order to transiently over-express miR-203.
Strand-specific RNA-seq (dUTP)
ALLsamples.genes.fpkm_table.xls

value: iPS


title: KIXD10


title: AG1Sub1.14d.2r


title: KIDEB


title: KIXVEB


title: AG1.8d.3r


title: AG1Sub1.14d.1r


title: KIV10


title: KID10


title: Hs-U1-3JUV-Rep2

value: 3JUV only

value: gene-specific amplification


title: AG1.8d.2r


title: KIXD4


title: TERAT_WT (II)

description: teratomas derived from WT IPSC

data_processing:
RNA-seq data was analyzed with the nextpresso pipeline as follows:
Reads are quality-checked with FastQC, and aligned to the mouse genome (GRCm38/mm10) with TopHat-2.0.10 (using Bowtie 1.0.0 and Samtools 0.1.19), allowing 2 mismatches and 5 multihits
Transcripts quantification and differential expression are calculated with Cufflinks 2.2.1, using the Mus musculus GRCm38/mm10 transcript annotations from the UCSC Genome Browser
Genome_build: GRCm38/mm10
Supplementary_files_format_and_content: FPKM values calculated with Cufflinks

source_name: teratomas derived from iPs cells

growth_protocol:
teratomas derived from iPS cells, that were generated by in vitro reprogramming using MEFs derived from WT mice.
iPS cells were grown over feeders, and cultured in DMEM supplemented with 20% KSR and Gentamycin. For teratomas generation, IPSCs (3 to 5 million cells) were injected in the flank of immuno-suppressed mice.

extract_protocol:
miRVana RNA isolation Kit form Thermo Fisher Scientific
0.8 µg of total RNA sample (0.5 µg for sample iPS_KI_C1) was extracted from the cells. RNA Integrity Numbers were in the range 7.-10.0 when assayed on an Agilent 2100 Bioanalyzer. PolyA+ fraction was purified and randomly fragmented, converted to double stranded cDNA and processed through subsequent enzymatic treatments of end-repair, dA-tailing, and ligation to adapters as in Illumina's "TruSeq Stranded mRNA Sample Preparation Part # 15031047 Rev. D" kit (this kit incorporates dUTP during 2nd strand cDNA synthesis, which implies that only the cDNA strand generated during 1st strand synthesis is eventually sequenced). Adapter-ligated library was completed by PCR with Illumina PE primers (8-11 cycles). The resulting purified cDNA library was applied to an Illumina flow cell for cluster generation and sequenced on an Illumina HiSeq2000 sequencer by following manufacturer's protocols.
Strand-specific RNA-Seq (dUTP)

treatment_protocol: During 5-7 days, the cells were treated with Doxycycline, in order to induce the expression of miR-203 transiently, only in the case of miR-203 cKI cells.

tag: genotype/variation

value: teratoma


title: TERAT_KI_2 (II)

description: teratomas derived from miR-203 KI IPSC

growth_protocol:
teratomas derived from iPS cells, that were generated by in vitro reprogramming using MEFs derived from our animal model ColA1_miR203; Rosa26rtTA.
iPS cells were grown over feeders, and cultured in DMEM supplemented with 20% KSR and Gentamycin. For teratomas generation, IPSCs (3 to 5 million cells) were injected in the flank of immuno-suppressed mice.


title: AG1.8d.1r

value: coleoptile


title: KIXV4

tag: treatment


title: iPS_WT_C6 (II)

description: WT IPSC

source_name: iPs cells

growth_protocol:
iPS generated by in vitro reprogramming from mouse embryonic cells (MEFs) that were obtained from WT mice.
iPS cells were grown over feeders, and cultured in DMEM supplemented with 20% KSR and Gentamycin. For teratomas generation, IPSCs (3 to 5 million cells) were injected in the flank of immuno-suppressed mice.

value: IPSC


title: TERAT_KI_1 (II)

description: teratomas derived from miR-203 KI IPSC


title: KIV4


title: AG1.4d.3r

value: 4 days old


title: iPS_WT_C1 (II)

description: WT IPSC


title: iPS_KO_C4 (II)

description: miR-203 KO IPSC

growth_protocol:
iPS generated by in vitro reprogramming from mouse embryonic cells (MEFs) that were obtained from our animal model miR203_KO.
iPS cells were grown over feeders, and cultured in DMEM supplemented with 20% KSR and Gentamycin. For teratomas generation, IPSCs (3 to 5 million cells) were injected in the flank of immuno-suppressed mice.


title: AG1.4d.2r


title: iPS_KO_C3 (II)

description: miR-203 KO IPSC


title: AG1.4d.1r


title: 04_MDA-EMPTYplasmid

city: lille

first: frédéric

last: leprêtre

address: Boulevard du Pr Leclercq

department: CHU of Lille, CBP

country: France

institute: Lille University

description: MDA-MB-231-KO-PDL1 +EMPTY plasmid

hyb_protocol: Agilent-039494 SurePrint G3 Human GE v2 8x60K Microarray 039381 (Feature Number version) were scanned on an Agilent G2505B scanner.

scan_protocol: Images were quantified using Agilent Feature Extraction Software (version V.10.7.3.1).

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

source_name: MDA-EMPTY

label_protocol: manufacturer's instructions

growth_protocol: MEM alpha, 10% FCS, 1% NEAA, 1% NaPyr and 1% Pen/Strep, 37°C, 5% CO2

extract_protocol: Total RNA extracted using manufacturer's instructions

treatment_protocol: MDA-MB-231 breast cancer cells knock-out for PD-L1 encoding gene were transfected with an EMPTY (control) plasmid or with a cDNA-PDL1-expressing plasmid to generate the MDA-EMPTY cells and the MDA-PDL11 cells respectively

value: mammary gland/breast; derived from metastatic site:pleural effusion


title: 07_MDA-PD-L1plasmid

description: MDA-MB-231-KO-PDL1 +PDL1 plasmid


title: 05_MDA-PD-L1plasmid

description: MDA-MB-231-KO-PDL1 +PDL1 plasmid


title: KIXV1


title: iPS_KI_C2 (II)

description: miR-203 KI IPSC

growth_protocol:
iPS generated by in vitro reprogramming from mouse embryonic cells (MEFs) that were obtained from our animal model ColA1_miR203; Rosa26rtTA. Once the iPs were established, cells were treated with DOX, in order to transiently over-express miR-203.
iPS cells were grown over feeders, and cultured in DMEM supplemented with 20% KSR and Gentamycin. For teratomas generation, IPSCs (3 to 5 million cells) were injected in the flank of immuno-suppressed mice.


title: 01_MDA-EMPTYplasmid

description: MDA-MB-231-KO-PDL1 +EMPTY plasmid


title: 02_MDA-EMPTYplasmid

description: MDA-MB-231-KO-PDL1 +EMPTY plasmid


title: 03_MDA-EMPTYplasmid

description: MDA-MB-231-KO-PDL1 +EMPTY plasmid


title: 08_MDA-PD-L1plasmid

description: MDA-MB-231-KO-PDL1 +PDL1 plasmid


title: AG1.2d.3r


title: 06_MDA-PD-L1plasmid

description: MDA-MB-231-KO-PDL1 +PDL1 plasmid


title: KID4


title: KI_N9 (I)

description: miR-203 KI IPSC

data_processing:
RNA-seq data was analysed with the nextpresso pipeline as follows:
Reads are quality-checked with FastQC, and aligned to the mouse genome (GRCm38/mm10) with TopHat-2.0.10 (using Bowtie 1.0.0 and Samtools 0.1.19), allowing 2 mismatches and 5 multihits
Transcripts quantification and differential expression are calculated with Cufflinks 2.2.1, using the Mus musculus GRCm38/mm10 transcript annotations from the UCSC Genome Browser
Genome_build: GRCm38/mm10
Supplementary_files_format_and_content: FPKM values calculated with Cufflinks

growth_protocol:
iPS generated by in vitro reprogramming from mouse embryonic cells (MEFs) that were obtained from our animal model ColA1_miR203; Rosa26rtTA.
ES cells were grown over feeders, in DMEM supplemented with 10% FCS and Gentamycin. iPS cells were grown also over feeders, and cultured in DMEM supplemented with 20% KSR and Gentamycin.

extract_protocol:
miRVana RNA isolation kit from Thermo Fisher Scientific
1 µg of total RNA sample was extracted from the cells. Sample RNA Integrity Numbers were in the range 9-10 when assayed on an Agilent 2100 Bioanalyzer. PolyA+ fraction was purified and randomly fragmented, converted to double stranded cDNA and processed through subsequent enzymatic treatments of end-repair, dA-tailing, and ligation to adapters as in Illumina's "TruSeq Stranded mRNA Sample Preparation Part # 15031047 Rev. D" kit (this kit incorporates dUTP during 2nd strand cDNA synthesis, which implies that only the cDNA strand generated during 1st strand synthesis is eventually sequenced). Adapter-ligated library was completed by PCR with Illumina PE primers (8 cycles). The resulting purified cDNA library was applied to an Illumina flow cell for cluster generation and sequenced on an Illumina HiSeq2000 by following manufacturer's protocols.
Strand-specific RNA-Seq (dUTP)


title: iPS_KI_C1 (II)

description: miR-203 KI IPSC

growth_protocol:
iPS generated by in vitro reprogramming from mouse embryonic cells (MEFs) that were obtained from our animal model ColA1_miR203;Rosa26rtTA. Once the iPs were established, cells were treated with DOX, in order to transiently over-express miR-203.
iPS cells were grown over feeders, and cultured in DMEM supplemented with 20% KSR and Gentamycin. For teratomas generation, IPSCs (3 to 5 million cells) were injected in the flank of immuno-suppressed mice.


title: TERAT_KO (II)

description: teratomas derived from miR-203 KO IPSC

growth_protocol:
teratomas derived from iPS cells, that were generated by in vitro reprogramming using MEFs derived from our animal model miR203_KO; Rosa26rtTA.
iPS cells were grown over feeders, and cultured in DMEM supplemented with 20% KSR and Gentamycin. For teratomas generation, IPSCs (3 to 5 million cells) were injected in the flank of immuno-suppressed mice.


title: KIV1


title: KID1


title: AG1.2d.2r


title: KI_DOX_C4 (I)

description: miR-203 KI IPSC

growth_protocol:
iPS generated by in vitro reprogramming from mouse embryonic cells (MEFs) that were obtained from our animal model ColA1_miR203; Rosa26rtTA. Once the iPs were established, cells were treated with DOX, in order to transiently over-express miR-203.
ES cells were grown over feeders, in DMEM supplemented with 10% FCS and Gentamycin. iPS cells were grown also over feeders, and cultured in DMEM supplemented with 20% KSR and Gentamycin.


title: KI_N5 (I)

description: miR-203 KI IPSC


title: KI_DOX_C2 (I)

description: miR-203 KI IPSC


title: AG1.2d.1r


title: Hs-XIST-DMSO-IC-2

description:
HsXIST_ncRNA.fa
Hs-XIST-InCell-SHAPE-MaP-Rep2.txt
Hs-XIST-InCell-SHAPE-MaP-Rep2-SuperFold.ct

data_processing:
Library strategy: SHAPE-MaP
For XIST/Xist, nextera reads were trimmed (TrimGalore) an additional 14 nt on each side to accommodate RT primer.
Adduct locations identified by Shapemapper2 software
Correlated mutation events were identified using ringmapper software on shapemapper outputs (.mut files)
In-cell perturbations in SHAPE reactivity were calculated using deltaSHAPE software
RNA structure models were generated from SHAPE data using SuperFold software
RNP-MaP analysis was generated with in-house software from shapemapper outputs

growth_protocol: Adherent mammalian cells used in chemical probing experiments, either SM33 or HEK293 cells, were grown to 80-90% confluency in either 6-well plates (for targeted priming) or 10-cm dishes (for RNA antisense pulldown). HEK293 cells were cultured in DMEM with 10% FBS. SM33 cells were cultured in embryonic stem cell media [DMEM high glucose with sodium pyruvate, 15 % FBS, 0.1 mM non-essential amino acids (Gibco), 2 mM L-glutamine, 0.1 mM β-mercaptoethanol,1000 U/mL leukemia inhibitory factor (ESGRO, Millipore Sigma)]. Cultures were grown with 100 U/mL penicillin and 100 µg/mL streptomycin. To induce expression of the Xist RNA, SM33 cells were supplemented with 2 µg/mL doxycycline 16 hours before treatment. For all experiments when performing biological replicates, chemical probing and sequencing library preparation were performed on distinct populations of cells on different days.

extract_protocol:
library prep: Nextera XT
Trizol

value: DMSO

value: RNA antisense pulldown

value: XIST lncRNA

value: random (9-mer)


title: AG1.14d.3r


title: KI_N5_DOX (I)

description: miR-203 KI IPSC

value: ColA1_miR203; Rosa26rtTA

value: DOX during 5-7 days


title: KI_DOX_C3 (I)

description: miR-203 KI IPSC


title: KI_N9_DOX (I)

description: miR-203 KI IPSC


title: KIXD1


title: iPS_WT_MIMICS_3P5P (I)

description: WT IPSC

growth_protocol:
iPS generated by in vitro reprogramming from mouse embryonic cells (MEFs) that were obtained from WT mice. Cells then were transfected transiently with miR203 mimics.
ES cells were grown over feeders, in DMEM supplemented with 10% FCS and Gentamycin. iPS cells were grown also over feeders, and cultured in DMEM supplemented with 20% KSR and Gentamycin.

value: transfection with miR203 3p/5p mimics


title: AG1.14d.2r

value: Indica


title: KI_DOX_C1 (I)

description: miR-203 KI IPSC


title: Hs-XIST-DMSO-IC-1

description:
HsXIST_ncRNA.fa
Hs-XIST-InCell-SHAPE-MaP-Rep1.txt
Hs-XIST-InCell-SHAPE-MaP-Rep1-SuperFold.ct

value: In-Cell


title: AG1.14d.1r

value: 14 days old


title: iPS_WT_C3 (I)

description: WT IPSC

growth_protocol:
iPS generated by in vitro reprogramming from mouse embryonic cells (MEFs) that were obtained from WT mice.
ES cells were grown over feeders, in DMEM supplemented with 10% FCS and Gentamycin. iPS cells were grown also over feeders, and cultured in DMEM supplemented with 20% KSR and Gentamycin.


title: iPS_WT_C2 (I)

description: WT IPSC


title: Hs-XIST-DMSO-CF-2

description:
HsXIST_ncRNA.fa
Hs-XIST-CellFree-SHAPE-MaP-Rep2.txt
Hs-XIST-CellFree-SHAPE-MaP-Rep2-SuperFold.ct

extract_protocol:
library prep: Nextera XT
nuclear fractionation, proteinase K lysis, buffer exchange (treatment), PCA extraction

value: Extracted


title: ES_WT_C3 (I)

description: WT ESC

source_name: ES cells

growth_protocol:
standard WT ES cells obtained from C57/black6 mice
ES cells were grown over feeders, in DMEM supplemented with 10% FCS and Gentamycin. iPS cells were grown also over feeders, and cultured in DMEM supplemented with 20% KSR and Gentamycin.

value: ESC


title: iPS_WT_C1 (I)

description: WT IPSC


title: Hs-XIST-DMSO-CF-1

description:
HsXIST_ncRNA.fa
Hs-XIST-CellFree-SHAPE-MaP-Rep1.txt
Hs-XIST-CellFree-SHAPE-MaP-Rep1-SuperFold.ct


title: ES_WT_C2 (I)

description: WT ESC


title: ES_WT_C1 (I)

description: WT ESC


title: Hs-XIST-5NIA-IC-2

value: 25mM 5NIA


title: D_yakuba

data_processing:
Sequenced reads were trimmed for adaptor sequence, then mapped to their respective genomes using tophat2 v 2.0.3 (default parameters)
HT-Seq count (option -str=no) was used to count the number of reads falling within each species exonic regions.
RPKM values were calculated for each sample independetly .
Ensembl GeneTreess 2013 was used to obtain orthology relationships across Drosophila species
Normalization across one-to-one orthologous regions was performed using the upper-quantile methodology.
Genome_build: D.melanogaster 5.46; D.persimilis 1.3; D.pseudoobscura 2.30; D.simulans 1.4; D.yakuba 1.3
Supplementary_files_format_and_content: tab-delimited text files include htseq counts for each sample and normalized values for one-to-one orthologs across the Drosophila species under study.

organism: Drosophila yakuba

source_name: Johnston's Organ

growth_protocol: All flies were raised at 25˚C on standards fly food

extract_protocol:
RNA was extracted with the RNAqueous micro kit (Ambion)
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Johnston's Organ

value: Adult

tag: reference genome annotation

value: D.yakuba 1.3


title: Hs-XIST-5NIA-IC-1


title: Hs-XIST-5NIA-CF-1


title: Staphylococcus aureus-C03215_C13396-low

city: Oxford

first: Craig

last: MacLean

address: 11a Mansfield Road

institute: University of Oxford

data_processing:
Transcript quantification from the raw reads was performed using Salmon v0.11.3, mapping to BX571856.1, using the inbuilt fragment GC bias correction and automatic detection of library type.
The BX571856.1 reference transcriptome was indexed using Salmon, which removed sequence-identical duplicate transcripts and used a kmer length of 31bp.
The DESeq2 library in R was used to estimate gene counts and perform differential expression analysis in bioconductor, with the requirement of at least 1 read mapping to each gene for every strain.
Genome_build: BX571856.1
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

organism: Staphylococcus aureus

source_name: Staphylcoccus aureus colony

growth_protocol: The strains were grown for 16 h overnight in MH2 broth at 37 °C at 225 rpm, diluted 1:20 in a fresh pre-warmed MH2 and incubated for an additional 1 h and 20 min until they reached a density of 0.160-0.170 OD595 (including blank). Ciprofloxacin was added to achieve a final concentration of 1 mg/l.

extract_protocol:
The cells in RNA-protect solution were thawed, centrifuged for 10 min at 5000 rpm and separated from the supernatant. Next, the cells were mixed with 100 µl of enzymatic digest buffer (30 mM Tris-HCl, 1 mM EDTA, 2 mg/ml protease K (Thermo Fisher), 3.25 mg/ml lysozyme (Sigma-Aldrich, 62970) and 0.15 mg/ml lysostaphin (Sigma-Aldrich, L7386)), re-suspended by pipetting and incubated for 10 min at room temperature with shaking. 350 µl of RTL buffer (containing 2-mercaptoethanol (Sigma-Aldrich, M3148)) was added and RNA extraction was performed using RNeasy Mini Kit (Qiagen), following the manufacturer’s protocol and including the optional step of DNase I on-column digestion. Elution was performed twice using the same volume of 50 µl of RNase-free water. RNA concentration was determined using the QuantiFluor RNA System (Promega).
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: After 1.5 h exposure to ciprofloxacin, treatment was stopped by spinning cells for 10 min at 7000 rpm, decanting supernatant and re-suspending the cells in 200 µl of PBS. Finally, 500 µl of RNA-protect Bacteria Reagent (Qiagen) was added and the cells were equilibrated at room temperature for 5 min and then frozen at -80 °C.

tag: evolvability

value: low

tag: multilocus sequence type


title: Staphylococcus aureus-C13331_C13244-low


title: Staphylococcus aureus-C12782_C12807-low


title: Staphylococcus aureus-C01186_C13179-low


title: HsXIST-UV

description:
HsXIST_ncRNA.fa
Hs-XIST-RNPMaP-shapemapper-output.txt
Hs-XIST-RNPMaP-ringmapper-output.txt

data_processing:
Library strategy: RNP-MaP
For XIST/Xist, nextera reads were trimmed (TrimGalore) an additional 14 nt on each side to accommodate RT primer.
Adduct locations identified by Shapemapper2 software
Correlated mutation events were identified using ringmapper software on shapemapper outputs (.mut files)
In-cell perturbations in SHAPE reactivity were calculated using deltaSHAPE software
RNA structure models were generated from SHAPE data using SuperFold software
RNP-MaP analysis was generated with in-house software from shapemapper outputs

extract_protocol:
library prep: Nextera XT
nuclear fractionation, proteinase K lysis, PCA extraction

value: 3JUV only


title: Staphylococcus aureus-C03206_C01268-low


title: Staphylococcus aureus-C03299_C12783-low


title: Staphylococcus aureus-C03184_C03224-low


title: Staphylococcus aureus-C03353_C03415-low