title: ATAC KO1

extract_protocol:
Nextera DNA library prep kit
Livers were collected after 6 hour refeeding and processed for either total RNA extraction for RNA-seq, or nuclei extraction for ChIP and ATAC-seq.
Libraries were prepared by the genome sequencing facility following manufacturers instructions for either the Kapa Biosystems or Nextera library prep kits.


title: ATAC R2

status: Public on Jan 02 2020

type: SRA

city: Berkeley

first: Jose

middle: A

last: Viscarra

state: Ca

address: 220 Morgan Hall

department: NST

country: USA

institute: UC Berkeley

library_source: genomic

data_processing:
Base-calling was performed by CASAVA bcl2fastq2 v2.2.
Adapters were trimmed using cutadapt-1.2.1.
For ChIP and ATAC-seq, reads were aligned to mm10 genome assembly using BWA - 0.7.17, peak-calling was performed by MACS2-2.1.1
For RNA-seq, reads were aligned to mm10 genome assembly using HISAT2 - 2.1.0, transcript counts were generated using Quantify to annotation model (Partek E/M), differential expression was determined by DESeq2-3.5.
Genome_build: mm10
Supplementary_files_format_and_content: bed files were generated by MACS2 and contain summits.
Supplementary_files_format_and_content: transcript count file contains the normalized abundance measurements, gene list file contains list of differentially expressed genes

molecule: genomic DNA

organism: Mus musculus

source_name: liver

growth_protocol: Wild-type or JMJD1C-LKO mice were maintained on chow diet for 6-8 weeks.

treatment_protocol: Mice were fasted overnight then refed high carbohydrate diet for 6 hours.

tag: tissue

value: liver

tag: strain

tag: chip antibody

tag: genotype

value: wildtype


title: CF5 OD1 replicate2

city: Aglantzia

first: Vasilis

middle: J

last: Promponas

state: Nicosia

address: 1 Panepistimiou Avenue

department: Department of Biological Sciences

country: Cyprus

institute: University of Cyprus

description:
CF5
YAbR9_OD1_CF5_3.bam

library_source: transcriptomic

data_processing:
Initial analysis, sample/barcode assignment, and genome mapping was performed on the Ion Proton server. Initial attempts to map reads on the genomes of origin gave poor results with respect to the number of unassigned RNAseq reads (not shown). Instead, we mapped all reads to the annotated P. aeruginosa PA14 genome as a reference (GCF_000014625.1_ASM1462v1_genomic.gff). Reads per gene were counted using featureCounts (Liao et al, 2014) and those corresponding to rRNA genes were in silico depleted to avoid skewing the statistics of independent samples prior to processing with DESeq2 (Love et al, 2014) for the detection of differentially expressed genes.
Pathway enrichment analysis: Relevant gene lists were uploaded to BioCyc SmartTables. Pathway enrichment was performed using the respective BioCyc functionality using the Fischer exact test and the Parent-Child Intersection method that has been shown to be robust against false positives (Grossmann et al., 2007). Multiple testing correction was performed with the Benjamini-Hochberg procedure. Reported adjusted p-values were considered significant when padj<0.05.
Cluster analysis of patterns of differential gene expression: Cluster analysis and visualization of patterns of up-/down-regulation for 78 select metabolic genes of P. aeruginosa PA14 was performed with ClustViz (Metsalu and Vilo, 2015) on a matrix where up-/down-regulation of each gene was represented with +1/-1, respectively.  Zero values were used to denote the absence of significant differential expression.
Genome_build: P. aeruginosa PA14 genome as a reference (GCF_000014625.1_ASM1462v1_genomic.gff)
Aligned RNAseq reads are provided in bam format and contain aligned reads against the P. aeruginosa PA14 genome (GCF_000014625.1_ASM1462v1_genomic.gff).
Supplementary_files_format_and_content: Differential gene expression analysis results were produced using deseq2 and are are provided in tab separated files.

molecule: total RNA

organism: Pseudomonas aeruginosa

source_name: Bacterial cell pellet

growth_protocol: Bacterial RNA was isolated from LB cultures grown at OD600nm 1 and 3

extract_protocol:
For bacteria RNA extraction we used the QIAzol lysis reagent and protocol (Qiagen).
The quantity of the bacterial RNA samples was measured on a NanoDrop ND1000 system and their quality analyzed on the Agilent 2100 Bioanalyzer system with the Agilent RNA 6000 Nano kit protocol (Agilent Technologies), according to manufacturer’s instructions. Bacterial RNA samples with RNA Integrity Number (RIN) > 7 were chosen for mRNA enrichment. The MICROBExpress™ Bacterial mRNA Enrichment Kit protocol (ThermoFisher Scientific) was performed on 5 – 10μg of bacterial RNA, according to the manufacturer’s instructions. The quality and quantity of enriched mRNA were measured using the NanoDrop and the Bioanalyzer systems. After the assessment of the enriched bacterial mRNAs, libraries were prepared using the Ion Total RNA-Seq Kit v2 protocol and reagents (ThermoFisher Scientific) according to the manufacturer’s instructions. The enriched mRNAs were fragmented, reverse transcribed and amplified after the addition of a specific (~10bp) barcode to each sample. The quantity and quality of the prepared libraries were assessed on a Bioanalyzer using the DNA High Sensitivity Kit, according to the manufacturer’s instructions. All libraries were diluted to 1nM and subsequently pooled together in pools of eight. 40pM of pooled libraries were further processed for templating and enrichment, and loaded onto the Ion Proton PI™ V2 chips (ThermoFisher Scientific). The procedure was performed on the Ion Chef™ System using the Ion PI™ IC200 Chef kit, protocol and reagents (ThermoFisher Scientific), according to the manufacturer's instructions.

tag: lb grown stage

value: Optical Density (OD) at 600nm = 1

tag: replicate number

value: OD1 replicate2


title: ATAC KO2

value: JMJD1C liver-specific knockout


title: CF5 OD3 replicate2

description:
CF5
YAbR27_OD3_CF5_.bam

value: Optical Density (OD) at 600nm = 3

value: OD3 replicate2


title: CF5 OD1 replicate1

description:
CF5
YAbR8_OD1_CF5_2.bam

value: OD1 replicate1


title: C3719 OD3 replicate1

description:
C3719
YAbR22_OD3_C3719_1.bam

value: OD3 replicate1


title: HGADFN003 iPSC replicate 1

type: RNA

city: Ottawa

first: Theodore

last: Perkins

state: ON

address: 501 Smyth Rd.

department: Cellular and Molecular Medicine

country: Canada

institute: Ottawa Hospital Research Institute

hyb_protocol: Affymetrix protocol

scan_protocol: An Affymetrix Gene Chip Scanner 3000 7G was used to scan the probe arrays.

data_processing: The data were analyzed using the R oligo package to generate RMA expression values

label: biotin

organism: Homo sapiens

source_name: HGADFN003 iPSC replicate 1

label_protocol: 300ng of total RNA was labeled and hybridized to GeneChip Human Gene 2.0 ST arrays (Affymetrix) according to the manufacturer’s protocol and scanned on a GeneChip Scanner 3000 7G (Affymetrix).

growth_protocol: Fibroblasts were cultured in DMEM media supplemented with 15% fetal bovine serum and 2mM L-glutamine. H9 hESCs and iPSCs were maintained on Matrigel in E8 medium (DMEM/F12 supplemented with L-ascorbic acid, sodium selenite, bFGF, TGF-β1, sodium bicarbonate, holo-transferrin, and gentamycin).

extract_protocol: Total RNA was isolated from cell pellets using the Nucleospin® RNA kit (Machery-Nagel) according to the manufacturer’s instructions.  Integrity and quantity of the isolated RNA was measured using the Bioanalyzer RNA 6000 nanochip (Agilent).

tag: Sex

value: Male

tag: cell line

tag: condition

value: HGPS

tag: cell type

value: iPSC


title: B136-33 OD3 replicate2

description:
B136-33
YAbR21_OD3_B133_3.bam


title: B136-33 OD3 replicate1

description:
B136-33
YAbR20r_OD3_B133_2.bam


title: ATAC R1


title: ATAC F1


title: ATAC F2


title: B136-33 OD1 replicate2

description:
B136-33
YAbR3_OD1_B133_3.bam


title: Input R1

extract_protocol:
Kapa Biosystems library prep kit
Livers were collected after 6 hour refeeding and processed for either total RNA extraction for RNA-seq, or nuclei extraction for ChIP and ATAC-seq.
Libraries were prepared by the genome sequencing facility following manufacturers instructions for either the Kapa Biosystems or Nextera library prep kits.


title: B136-33 OD1 replicate1

description:
B136-33
YAbR1_OD1_B133_1.bam


title: MTB-1 OD3 replicate2

description:
MTB-1
YAbR30_OD3_MTB_3.bam


title: Input F2


title: CF5 OD3 replicate1

description:
CF5
YAbR25_OD3_CF5_1.bam


title: MTB-1 OD3 replicate1

description:
MTB-1
YAbR28r_OD3_MTB_1.bam


title: Input R2


title: ChIP R1

value: Histone H3 dimethyl K9 (ab176882)


title: MTB-1 OD1 replicate2

description:
MTB-1
YAbR11_OD1_MTB_2.bam


title: ChIP F1


title: ChIP F2


title: MTB-1 OD1 replicate1

description:
MTB-1
YAbR10_OD1_MTB_1.bam


title: PA14 OD3 replicate2

description:
PA14
YAbR33_OD3_PA14_3.bam


title: PA14 OD3 replicate1

description:
PA14
YAbR32_OD3_PA14_2.bam


title: PA14 OD1 replicate1

description:
PA14
YAbR13_OD1_PA14_.bam


title: ChIP R2


title: MousePFC-H3K79me2-10pg-2

city: Blacksburg

first: Chang

last: Lu

state: VA

address: 235 Goodwin Hall, 635 Prices Fork Road, Virginia Tech

department: Chemical Engineering

institute: Virginia Tech

description: Library Preparation data. Name format: Sample Type-Histone (if applicable)-DNA amount-replicate number

data_processing:
Raw reads were trimmed with TrimGalore 0.4.1
Trimmed reads were aligned using bowtie 1.1.2
Reads were extended to 250bp
Sample was normalized and input subtracted
Sample was converted to BigWig format
Genome_build: hg19, mm9
Supplementary_files_format_and_content: Normalized ChIP-seq signal in BigWig format

source_name: CD1 mouse

growth_protocol: GM12878 cells were cultured in RPMI 1640 medium (11875-093, Gibco) plus 15% fetal bovine serum (26140-079, Gibco) and 100 U/ml penicillin-streptomycin (15140-122, Gibco) at 37 ℃ in a humidified incubator with 5% CO2. Cells were sub-cultured every 2-3 days to maintain them in exponential growth phase. Mouse brain samples require sorting of neuronal and glial nuclei using fluorescence-activated cell sorter (FACS).

extract_protocol:
GM12878 protocol: Sample containing 106 cells was used as the starting material and centrifuged at 1,600 g for 5 min and washed twice with 1 ml cold PBS. Cells were crosslinked by adding 1 ml freshly made 1% formaldehyde and incubating at room temperature for 5 min on a shaker. Crosslinking was promptly terminated by adding 50 µl of 2.5 M glycine and shaking for 5 min. The pellet was resuspended in 130 μl Covaris buffer (10 mM Tris-HCl, pH 8.1, 1 mM EDTA, 0.1% SDS and 1× protease inhibitor cocktail) and sonicated using the following conditions. Using Covaris M 220 (Covaris), the sample was sheared at 4 oC with 75 W peak incident power, 5% duty factor, and 200 cycles per burst for 12 min. The sheared sample was centrifuged in a 4 oC centrifuge at 14,000g for 10 min, and the supernatant was transferred to a new tube. Sheared chromatin was diluted with IP buffer (20 mM Tris-HCl, pH 8.0, 140 mM NaCl, 1 mM EDTA, 0.5 mM EGTA, 0.1% (w/v) sodium deoxycholate, 0.1% SDS, 1% (v/v) Triton X-100, with 1% freshly added PMSF and PIC) and diluted to appropriate concentrations. Mouse protocol: we also use cell lysis followed by micrococcal nuclease (MNase) digestion for chromatin fragmentation without crosslinking (that is, native ChIP-seq).
Library preparation was performed using the Swift Bio S2 library preparation kit (Swift Biosciences) using 40 μl of purified DNA for bulk assays or 2 ul purified DNA on the library preparation microfluidic platform. 2.5 μl of the low EDTA TE buffer in the 50 μl amplification cycle reaction mix was replaced with 2.5 μl of 20x EvaGreen, and amplification was terminated after samples saw an >3000 RFU increase (BioRad CFX Connect). Amplified DNA was then eluted into 7 μl low EDTA TE buffer where 2 μl could be used for qPCR analysis for preliminary quality control analysis, Kappa DNA quantification, and Tapestation fragment size analysis and the other 5 μl for library pooling. Libraries were pooled at 10 nM for sequencing by Illumina HiSeq 4000 with single-end 50 nt read.

value: Mouse Brain

tag: antibody

value: H3K79me2 Active Motif 39924


title: MousePFC-H3K4me3-Manual

value: H3K4me3 Millipore 07-473


title: MousePFC-H3K79me2-10pg-1


title: PA14 OD1 replicate2

description:
PA14
YAbR14_OD1_PA14_.bam


title: RNA-Seq of Zeugodacus cucurbitae male 9 [M9_4]

city: Beibei

first: Dong

last: Wei

state: Chongqing

address: Tiansheng

country: China

institute: Southwest University

data_processing:
Illumina CASAVA1.7 software used for base calling
The quality of the raw data was evaluated by fastx_toolkit_0.0.14 for the low-complexity or low-quality sequence
Raw reads were quanlity controled by SeqPrep and Sickle software
Clean reads were aligned to the reference genome using HISAT2 2.1.0
Gene expression analysis was conducted based on the sequenced reads using RNA-Seq with the Expectation-Maximization (RSEM, v1.3.1) method
Genome_build: https://www.ncbi.nlm.nih.gov/assembly/GCF_000806345.1/
Supplementary_files_format_and_content: tpm

organism: Zeugodacus cucurbitae

source_name: male 9-d-old

growth_protocol: Z. cucurbitae were reared at 26 – 27ºC with 70% relative humidity and a photoperiod of 14:10 h light: dark.

extract_protocol:
Total RNA was extracted using TRIZol reagent
RNA libraries were prepared for sequencing using standard Illumina protocols

value: whole body

tag: developmental stage

value: Late male adult

tag: replicate

value: Biological replicate 4


title: MousePFC-H3K36me3-10pg-2

value: H3K36me3 Active Motif 61101


title: RNA-Seq of Zeugodacus cucurbitae male 9 [M9_2]

value: Biological replicate 2


title: BJ1 iPSC replicate 3

source_name: BJ1 iPSC replicate 3

value: Normal


title: RNA-Seq of Zeugodacus cucurbitae male 9 [M9_3]

value: Biological replicate 3


title: RNA-Seq of Zeugodacus cucurbitae male 9 [M9_1]

value: Biological replicate 1


title: MousePFC-H3K36me3-10pg-1


title: MousePFC-H3K9me3-10pg-2

value: H3K9me3 Abcam ab8898


title: Input F1

value: liver

value: wildtype


title: MousePFC-H3K9me3-10pg-1


title: RNA-Seq of Zeugodacus cucurbitae male 5 [M5_2]

source_name: male 5-d-old

value: Middle male adult


title: RNA-Seq of Zeugodacus cucurbitae male 5 [M5_4]


title: HGADFN167 Fibroblast early passage replicate 2

value: Male

value: HGPS

value: Fibroblast


title: MousePFC-H3K4me3-10pg-2

value: Mouse Brain


title: MousePFC-H3K4me3-10pg-1

value: H3K4me3 Millipore 07-473


title: RNA-Seq of Zeugodacus cucurbitae male 5 [M5_3]

value: whole body


title: GM12878-10pg-Manual-2

source_name: GM12878 cell line


title: GM12878-10pg-2


title: GM12878-10pg-1


title: GM12878-50pg-2


title: RNA-Seq of Zeugodacus cucurbitae male 1 [M1_1]

source_name: male 1-d-old

value: Early male adult


title: RNA-Seq of Zeugodacus cucurbitae male 1 [M1_2]


title: RNA-Seq of Zeugodacus cucurbitae male 5 [M5_1]


title: GM12878-50pg-1


title: RNA-Seq of Zeugodacus cucurbitae female 9 [F9_3]

source_name: female 9-d-old

value: Late female adult


title: RNA-Seq of Zeugodacus cucurbitae female 9 [F9_2]


title: GM12878-100pg-2


title: GM12878-100pg-1


title: RNA-Seq of Zeugodacus cucurbitae female 9 [F9_1]


title: RNA-Seq of Zeugodacus cucurbitae female 5 [F5_4]

source_name: female 5-d-old

value: Middle female adult

value: Biological replicate 4


title: GM12878-200pg-2


title: GM12878-10pg-Manual-1


title: RNA-Seq of Zeugodacus cucurbitae male 1 [M1_3]


title: GM12878-200pg-1


title: RNA-Seq of Zeugodacus cucurbitae female 5 [F5_3]


title: CNBP-KO_CHX 3

city: Wuerzburg

first: Sanjay

middle: Kumar

last: Gupta

state: Bavaria

address: Biozentrum, Am Hubland

department: Dept of Biochemistry

country: Germany

institute: University of Wuerzburg

data_processing:
Illumina high-seq 2500 platform was used for sequencing
The reads were aligned to the hg19 genome using TopHat
Genome_build: hg19

source_name: HEK293 cells

growth_protocol: HEK293 cells were grown and routinely passaged in DMEM with 10% FCS and 1% pen/strip.

extract_protocol:
The riboseq library was generated using NEB ultradirectional library preparation kit as per manufacturers protocol.
Ribosome profiling

value: CRISPR-cas9 mediated CNBP knockout

tag: treatment

value: Cyclohexamide treated


title: RNA-Seq of Zeugodacus cucurbitae female 5 [F5_2]

value: Biological replicate 2


title: RNA-Seq of Zeugodacus cucurbitae female 1 [F1_3]

source_name: female 1-d-old

value: Early female adult

value: Biological replicate 3


title: RNA-Seq of Zeugodacus cucurbitae male 1 [M1_4]


title: RNA-Seq of Zeugodacus cucurbitae female 5 [F5_1]

value: Biological replicate 1


title: RNA-Seq of Zeugodacus cucurbitae pupa 9 [P9_4]

source_name: pupa 9-d-old

value: Late pupa


title: RNA-Seq of Zeugodacus cucurbitae pupa 9 [P9_3]


title: RNA-Seq of Zeugodacus cucurbitae female 1 [F1_2]


title: RNA-Seq of Zeugodacus cucurbitae female 1 [F1_4]


title: RNA-Seq of Zeugodacus cucurbitae female 1 [F1_1]


title: Wildtype_CHX 3


title: CNBP-KO_CHX 1


title: CNBP-KO_HRN_CHX

value: Harringtonine-Chyclohexamide treated


title: RNA-Seq of Zeugodacus cucurbitae pupa 9 [P9_1]


title: Wildtype_HRN_CHX 3


title: Wildtype_CHX 4


title: Wildtype_HRN_CHX 2


title: CNBP Knockout 3

data_processing:
Illumina high-seq 2500 platform was used for sequencing
The reads were aligned to the hg19 genome using TopHat
Transcripts were assembled using Cufflinks
Cuffdiff and CummeRbund was further used to find the differentially expressed genes and transcripts and to plot their abundance
Genome_build: hg19

extract_protocol: The RNA library was generated using NEB ultradirectional library preparation kit as per manufacturers protocol.


title: RNA-Seq of Zeugodacus cucurbitae pupa 5 [P5_3]

source_name: pupa 5-d-old

value: Middle pupa


title: RNA-Seq of Zeugodacus cucurbitae pupa 5 [P5_2]


title: RNA-Seq of Zeugodacus cucurbitae pupa 5 [P5_1]


title: Wildtype_CHX 5


title: Wildtype_CHX 2


title: CNBP Knockout 1


title: RNA-Seq of Zeugodacus cucurbitae pupa 9 [P9_2]


title: Wildtype_CHX 1


title: RNA-Seq of Zeugodacus cucurbitae pupa 1 [P1_4]

source_name: pupa 1-d-old

value: Early pupa


title: Wildtype 3


title: RNA-Seq of Zeugodacus cucurbitae pupa 5 [P5_4]


title: RNA-Seq of Zeugodacus cucurbitae pupa 1 [P1_3]


title: Wildtype 2


title: Wildtype 1


title: RNA-Seq of Zeugodacus cucurbitae pupa 1 [P1_2]


title: RNA-Seq of Zeugodacus cucurbitae pupa 1 [P1_1]


title: Normal Input replicate 2

data_processing:
Illumina Used for basecalling
Alignment of ChIP-seq to the human genome (hg19) data was performed using bowtie 1.1.0 with the following parameters: "-l 32 --strata --best -y --chunkmbs 3072 -n 2 -m 1".  Duplicate reads were removed using the rmdup function of samtools.
regions of enriched reads for H3K27me3 were determined using diffReps with "block" (10k window) option, comparing HGPS replicate sets with Normal replicate setss with matching input contorls
regions of enriched reads for H3K4me3 were determined using Pepr with comparing HGPS replicate sets with Normal replicaste sets for H3K4me3 and matching input controls and parameters --diff --peaktype=sharp --remove_artefacts
Genome_build: hg19
Supplementary_files_format_and_content: diffReps, peaks

source_name: Normal BJ1

growth_protocol: iPSC clones were grown and maintained on matrigel in E8 media (DMEM/F12 supplemented with L-ascorbic acid, sodium selenite, bFGF, TGF-β1, sodium bicarbonate, holo-transferrin, and gentamycin) before harvesting.

extract_protocol:
Nuclei pellets were resuspended in Covaris with 2mL of lysis buffer 3 (10mM Tris-HCl pH 8, 100mM NaCl, 1mM EDTA, 0.5mM EGTA, 0.1% Na-Deoxycholate, 0.5% Na-Laurylsarcosine) and sheared using a Covaris S2 sonicator (20% duty cycle, intensity 5, 200 cycles/burst) for 9 minutes per sample.  300ug of chromatin was used for each sample.
Before addition of antibodies, an aliquot of each sample was reserved for input control.  After reverse cross-linking and cleanup, approximately 20ng of each sample was prepared for sequencing using the ChIP-seq sample rep kit (Illumina) according to the manufacturer’s instructions.

tag: patient id

value: Normal

value: Input


title: RNA-Seq of Zeugodacus cucurbitae larva 3 [L7_3]

source_name: larva 3rd instar

value: whole body

value: 3rd instar larva


title: RNA-Seq of Zeugodacus cucurbitae larva 3 [L7_4]


title: High-dose [H 4]

city: Guangzhou

first: Jiaxing

last: Chen

state: Guangdong

address: Xingang Road No. 135, Haizhu District, Guangzhou

institute: Sun Yat-Sen University

description: Test

data_processing:
For the normalization it uses housekeeping gene:β-actin.
Target gene signals normalized to housekeeping genes; 2^-deltaCt, where deltaCt = (Ct_Target − Ct_HKG)].
Using excel to perform all deltadeltaCt based fold-change calculations from the threshold cycle data.

label: SYBR Green

organism: Epinephelus coioides

source_name: Gonadal tissues

label_protocol: PCR assays were performed using the ReverTra Ace qPCR RT Kit (TOYOBO, Osaka, Japan) in accordance with the manufacturer’s instructions.Real-time PCR was performed on a Roche Light Cycler 480 real-time PCR System using SYBR Green Real-time PCR Master Mix (Roche, Germany) according to the manufacturer's protocol. The real-time PCR conditions were as follows: denaturation at 95 °C for 5 min, followed by 40 cycles at 95 °C for 15 s, 56 °C for 20 s, and 72 °C for 20 s.

extract_protocol: Total RNA was extracted from the tissue samples using TRIzol reagent (Invitrogen, Carlsbad, CA, USA) .

tag: dose

value: 50 mg/kg body weight

tag: group

value: High-dose


title: CNBP Knockout 2


title: CNBP-KO_CHX 2


title: RNA-Seq of Zeugodacus cucurbitae larva 3 [L7_2]

tag: tissue


title: High-dose [H 3]

description: Test


title: HGPS Input replicate 2

source_name: HGPS AG01972

value: HGPS


title: HGPS Input replicate 1


title: RNA-Seq of Zeugodacus cucurbitae larva 2 [L3_4]

source_name: larva 2nd instar

value: 2nd instar larva

value: Biological replicate 4


title: Normal H3K27me3 replicate 2


title: High-dose [H 1]

description: Test


title: Medium-dose [M 4]

description: Test

value: 10 mg/kg body weight

value: Medium-dose


title: RNA-Seq of Zeugodacus cucurbitae female 9 [F9_4]

value: Late female adult


title: Normal H3K27me3 replicate 1


title: High-dose [H 2]

description: Test


title: Medium-dose [M 3]

description: Test


title: Normal Input replicate 1


title: RNA-Seq of Zeugodacus cucurbitae larva 2 [L3_2]

value: Biological replicate 2


title: HGPS H3K27me3 replicate 2


title: RNA-Seq of Zeugodacus cucurbitae larva 2 [L3_3]

value: Biological replicate 3


title: HGPS H3K27me3 replicate 1


title: Medium-dose [M 2]

description: Test


title: RNA-Seq of Zeugodacus cucurbitae larva 2 [L3_1]

value: Biological replicate 1


title: Medium-dose [M 1]

description: Test


title: Normal H3K4me3 replicate 2


title: RNA-Seq of Zeugodacus cucurbitae larva 1 [L1_3]

source_name: larva 1st instar

value: 1st instar larva


title: RNA-Seq of Zeugodacus cucurbitae larva 3 [L7_1]


title: HGPS H3K4me3 replicate 2


title: HGPS H3K4me3 replicate 1


title: RNA-Seq of Zeugodacus cucurbitae larva 1 [L1_2]


title: RNA-Seq of Zeugodacus cucurbitae larva 1 [L1_1]


title: Low-dose [L 3]

description: Test

value: 2 mg/kg body weight

value: Low-dose


title: RNA-Seq of Zeugodacus cucurbitae egg [E_4]

source_name: egg

value: Egg


title: Low-dose [L 1]

description: Test


title: Low-dose [L 2]

description: Test


title: Normal IgG replicate 1

value: Normal

value: IgG


title: Low-dose [L 4]

description: Test


title: Normal IgG replicate 2


title: Control [C 4]

description: Control

value: 0 mg/kg body weight

value: Control


title: HGPS IgG replicate 2

value: HGPS


title: RNA-Seq of Zeugodacus cucurbitae egg [E_3]

value: whole body


title: RNA-Seq of Zeugodacus cucurbitae larva 1 [L1_4]

value: Biological replicate 4


title: Control [C 2]

description: Control


title: Wildtype_HRN_CHX 1

value: Harringtonine-Chyclohexamide treated


title: Control [C 3]

description: Control


title: RNA-Seq of Zeugodacus cucurbitae egg [E_2]


title: HGPS IgG replicate 1


title: CAPH2 ChIP control induced rep2

status: Public on Jan 01 2020

city: Munich

first: Tamas

last: Schauer

address: Feodor-Lynen-Straße 21

department: Institute of Epigenetics and Stem Cells

institute: Helmholtz Zentrum München

data_processing:
ChIP-seq 50 bp single-end reads were aligned to the reference (Drosophila melangaster dm6) using bowtie2 (version 2.2.9).
Reads were processed using the Homer software package (Heinz et al., 2010). Bedgraph coverages were generated and normalized to the total number of reads and to the corresponding input using the makeUCSCfile command.
Genome_build: Drosophila melangaster dm6
Supplementary_files_format_and_content: Bedgraph format. Normalized coverage (ChIP/Input).

organism: Drosophila melanogaster

source_name: whole cell

extract_protocol:
ChiP is prefromed exactly as described in Gerland et al, 2017. Shortly, the cells were crosslinked in 1% FA for 5 min at room temperature and frozen. Chromatin from 50 million cells was sheared in TE/0.1%SDS, the buffer was adjusted to RIPA and after preclearing the sheared extract and taking 1/10 as an input, IP was done overnight. Beads were washed, after which RNA/protein digestion and decrosslinking was performed. DNA was purified using AMPure XP beads.
Libraries were prepared from 1 ng DNA with Microplex Diagenode kit, according to manufacture's instructions, without size selection.

value: L2-4 Flag-HA-HMR/pMT Hygro+Myc-LHR/pMT Hygro

value: control induced

tag: ChIP

value: CAPH2 (Hartl et al, 2008)


title: RNA-Seq of Zeugodacus cucurbitae egg [E_1]


title: HMR ChIP GST RNAi rep2

value: GST RNAi

value: HMR (Thomae et al, 2013)


title: CAPH2 ChIP HMR+LHR induced rep2

value: HMR+LHR induced


title: CAPH2 ChIP HMR+LHR induced rep1


title: HMR ChIP dCenpC RNAi rep1

value: dCenpC RNAi


title: HMR ChIP GST RNAi rep1


title: Control [C 1]

description: Control


title: Normal H3K4me3 replicate 1


title: Input HMR+LHR induced rep2

value: input


title: HMR ChIP dCenpC RNAi rep2


title: CAPH2 ChIP control induced rep1


title: Input control induced rep2


title: Input HMR+LHR induced rep1


title: Input GST RNAi rep1


title: Input GST RNAi rep2


title: Input dCenpC RNAi rep2


title: Input control induced rep1


title: Preimmune Chip-seq

city: Moscow

first: Natalia

last: Klimenko

address: 34/5 Vavilova Street

country: Russia

institute: Institute of Gene Biology (IGB) of the Russian Academy of Sciences

data_processing:
Read adapters and poly-A tails were removed using cutadapt software. Trimming of low-quality tails was performed using sickle in single-end mode, reads with the length less than 20 bp after trimming were discarded.
The remaining reads were aligned to build version dm6 of the Drosophila melanogaster genome using Bowtie (with enabling options --best, --strata, --tryhard). Only reads that aligned exactly one time were passed to further analysis. After alignment read duplicates were removed using Picard MarkDuplicates function.
Peaks overlapping with blacklist regions were discarded (blacklist regions were previously converted from dm3 to dm6 genome built version (https://sites.google.com/site/anshulkundaje/projects/blacklists)).
Peak calling was performed using MACS version 2 against preimmune control with suppression of model building and assigning reads extension length to 200.
For samples with one biological replicate (dCTCF) peaks with p value less than 0.00001 were selected. For samples with two replicates (ZAF1) peaks with p value less than 0.1 were passed to IDR pipeline to access reproducibility of chip-seq replicates. As far as Rescue Ratio (RR) and Self-consistency Ratio (SR) passed recommended thresholds (RR and SR were less than 2) two merged replicates was chosen for further analysis (ZAF1_repl1 + ZAF1_repl2) with idr p value threshold 0.05.
Genome_build: dm6 (Release 6 plus ISO1 MT)
Supplementary_files_format_and_content: Processed data was obtained by MACS2 and includes: bedGraph (bedgraph) read pileups and extended bed (narrowPeak) peak calls regions.

source_name: whole organism

growth_protocol: Wild-type Drosophila melanogaster (Oregon R) flies were grown in population cages at 25 degrees. Embryos were collected for 12 hours. The collected embryos were dechorionated using 50% bleach and fixed in 10 ml cross-linking solution (50 mM HEPES pH 8.0, 1 mM EDTA, 0.5 mM EGTA, 100 mM NaCl, 1.8% formaldehyde, pH 8.0) with 30ml n-heptane on a shaker table at RT for 15 minutes. The reaction was terminated with 125 mM glycine, 0.1% Triton X-100 in PBS. After washing out the fix, the embryos were blotted dry and frozen in liquid nitrogen. A small number of embryos from each collection were set aside for staging.

extract_protocol:
Chromatin for input (0.5 ug of DNA) was brought to RIPA conditions (140mM NaCl / 10mM Tris-HCl pH8,0 / 1mM EDTA / 1% TritonX100 / 0,1% SDS / 0,1% sodium deoxycholate, 1mM PMSF) was diluted in TE with 0.5% SDS, treated with RNase A for 30 min and protease K overnight, incubated at 65 degrees for 6 hours and phenol chloroform extracted. Sepharose was resuspended in TE with 0.5% SDS, treated with RNase A for 30 min and protease K overnight, incubated at 65 degrees for 6 hours and phenol chloroform extracted.
Libraries were prepared according to manufacturer's recommendations with small modifications. In short, 1-10ng of purified, RNase treated, and reverse cross-linked genomic DNA was end-repaired and terminal adenosine residues were added using the NEBNext reagents. Custom-made indexed adapters were ligated, after which the material was size selected at ~200-600 bp with Ampure XP beads (Beckman Coulter). PCR amplification was performed using PE1.0 and PE2.0 primers (custom-made) for 12 cycles for Input samples and 14 to 15 cycles for IP-ed samples using the Q5 Hot Start HiFi PCR Master Mix (NEB). The PCR-amplified library was purified using Ampure XP beads and its quality was assessed on a Bioanalyzer 2100 system (Agilent). The libraries were sequenced on a HiSeq 2000 (Illumina) in single end mode.

treatment_protocol: Approximately 1g of Drosophila embryos were resuspended in 15ml ice-cold 0.1% Triton X-100 in PBS with protease inhibitors (PIs) and dounced 20x with loose pestle on ice, followed by centrifugation at 400g for 1min at 4 degrees. The supernatant was transferred to a fresh tube and centrifuged at 1100g for 10min at 4 degrees. The pellet was resuspended in 15ml ice-cold Cell lysis buffer with PIs (5 mM HEPES pH 8.0, 85 mM KCl, 0.5% NP40) and dounced 20x with tight pestle. Two equal aliquots were transferred into 15ml falcon tubes and centrifuged at 2000g for 4min at 4 degrees. The pellets consisting of nuclei were resuspended in 1ml of ice-cold Nuclear Lysis Buffer with PIs (50 mM HEPES pH 8.0, 10 mM EDTA, 0.5% N-laurylsarcosine) and incubated for 20min at RT. 1ml ice-cold Nuclear Lysis Buffer with PIs was added to each tube and sonicated using the bioruptor. Chromatin was then transferred to 1.5 ml-eppendorf tubes and centrifuged at 14000 rpm for 10 min at 4 degrs. Finally, supernatants were pooled, aliquoted and frozen in liquid nitrogen. Chromatin (50 ug of DNA) was brought to RIPA conditions (140mM NaCl / 10mM Tris-HCl pH8,0 / 1mM EDTA / 1% TritonX100 / 0,1% SDS / 0,1% sodium deoxycholate, 1mM PMSF) and incubated with anti-ZAF1, anti-dCTCF antibodies and rat IgG at 4 degrees on a rotary shaker overnight. The antibody/antigen complexes were precipitated with 40 ul protein G sepharose at 4 degrees for 3 hrs and washed 1x with RIPA buffer, 3x with RIPA buffer with 500 mM NaCl.

tag: strain

value: Oregon-R

value: WT

value: Embryonic

value: Whole body

tag: chip antibody

value: rat IgG


title: ZAF1_repl2

tag: genotype

value: rat anti-ZAF1 (aa 105-225)


title: dCTCF

value: rat anti-dCTCF (aa 612-818)


title: Input dCenpC RNAi rep1


title: AB7237

city: Rehovot

first: Ido

last: Amit

address: 234 Herzl st.

department: Immunology

country: Israel

institute: Weizmann Institute of Science

data_processing:
bcl2fastq/2.15.0.4
Sequences with RMT of low quality (defined as RMT with minimum Phred score of less than 27) were filtered out.
Pool-barcode and well-barcode-RMT were extracted from the first and second end of the read (respectively) and concatenated to the fastq header, delimited by a underscore i.e. POOL_BARCODE_WELL_BARCODE_RMT while "NNNNNN" was used as a place holders if plate barcode was not used.
Reads were separated by POOL_BARCODE_WELL_BARCODE header data, allowing 1 sequencing error. This process created a single fastq file for each source well.
paired-end (read2 used to read cell and molecule barcodes only)
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include mRNA molecule count values for each Sample
Supplementary_files_format_and_content: Meta data file associating each single cell with its amplification batch and index sorting readouts

molecule: polyA RNA

source_name: C57BL/6 Ifnar KO

growth_protocol: All mice were maintained under specific pathogen-free conditions

extract_protocol:
Murine thymi were treated with enzymes cocktail (Collagenase, Dispase and Dnase) at 37C. Cells were separated by Percoll gradient density centrifugation, filtered and stained with Flow cytometry antibodies.
Murin small intestines were flushed with PBS, treated with EDTA, Dispase and Dnase, filtered and stained with Flow cytometry antibodies.
3' end mRNA libraries were prepared for sequencing using MARS-seq (Jaitin et al, Science 2014)

treatment_protocol:
Mice were infected in the footpad with either rVSV or rLCMV viruses. Draining popliteal lymph nodes (LN) were extracted. LN were processed and dendritic cells were single-cell sorted for single-cell RNA-seq
Mice were sacrified by CO2

tag: organ

value: Lymph node

tag: selection marker

value: Ifnar KO

tag: infection

value: LCMV

tag: infection duration

value: 8 hours

tag: age

value: 9 weeks


title: AB7236


title: ZAF1_repl1


title: AB7235

value: wildtype


title: Wild type replicate 3

city: London

first: Eugene

last: Schuster

address: 123 Old Brompton Road

department: Breast Cancer Research

country: United Kingdom

institute: Institute of Cancer Research

data_processing:
Fastq files aligned to genome with tophat-2.0.11.OSX_x86_64
htseq-count used to count sequence reads per gene
DESeq2 used to calculate differential expression analysis
Genome_build: BDGP5.70
Supplementary_files_format_and_content: htseq raw transcript counts and DESeq2 output to identify significantly differentiall expressed genes between dominate negative p110 mutant samples and wild type p110 samples

source_name: fat body

growth_protocol: Flies stocks were maintained  at 25°C on a 12 h Light : 12 h Dark cycle at 60% humidity  using standard sugar/yeast/agar (SYA) media

extract_protocol:
Fat bodies were dissected on ice, and total RNA was extracted using Trizol reagent followed by further purification with Qiagen RNeasy easy kit.
Illumina TruSeq mRNA library prep. Input amount was 1 ug and we used 10 PCR cycles

tag: gender

value: female

value: adult (7-10 day old)

tag: transgene

value: FB-GAL4 only

tag: stock

value: white Dahomey (Wolbachia positive

value: fat body


title: Wild type replicate 2

tag: developmental stage


title: AB7234


title: AB7233


title: AB7232

value: VSV


title: Dominate negative mutant replicate 3

value: FB-Dp110DN expression

value: dominate negative mutation in p110


title: Dominate negative mutant replicate 2


title: Dominate negative mutant replicate 1


title: Wild type replicate 1


title: AB7229


title: AB7230


title: AB7227


title: AB7228


title: AB7225

value: 48 hours


title: AB7224


title: AB7226


title: AB7222


title: AB7221


title: AB7231


title: Sall1-CreER:Ribotag_MG_Sort+aHA_IP_9

first: Louise

last: Chappell-Maor

address: 234 Hertzl Street

department: Immunology Department

data_processing:
Illumina bcl2fastq software used for basecalling.
Sample barcodes were used from read 2. Barcode is of size 7 followed by UMI of size 8
alignment: hisat 0.1.5  with deafult parameters
filter PCR amplification bias using alignment break site and UMI barcode (size 8).
create tag directory using makeTagDirectory from HOMER tools (http://homer.salk.edu/homer/ngs/)
HOMER, quantifying RNA expression in genes: analyzeRepeats.pl rna mm9 -d <List of tag dir> -count exons -condenseGenes -strand + -raw
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files include mRNA molecule count values for each Sample
Paired-end (read2 used to read sample barcodes and UMI only)

source_name: Brain

growth_protocol: Mice were maintained on a 12 hour light/dark cycle, with food and water provided ad libitum, and maintained under specific pathogen-free (SPF) conditions.

extract_protocol:
microglia isolation: Mice were anesthetized with Pental (1:2 in PBS) and were perfused with PBS. Brains were dissected, crudely chopped and incubated for 20 min at 37°C in a 1 ml HBSS solution containing 2% BSA, 1 mg/ml Collagenase D (Sigma) and 50µg/ml DNase1 (Sigma). In the middle of incubation homogenates were pipetted for further dissociation. Next, the homogenates were filtered through a 150μm mesh, washed with cold FACS buffer (2% FCS, 1mM EDTA in PBS-/-) and centrifuged at 2200 RPM, at 4°C, for 5 min. For the enrichment of microglia, the cell pellet was re-suspended with 3ml of 40% percoll solution and centrifuged at 2200 RPM, no acceleration and breaks, at RT for 15 min. Next, the cell pellet was resuspended, passed through 80µm mesh, washed with 5ml FACS buffer and centrifuged at 1400 RPM at 4°C for 5 min, followed by antibody (Ab) labeling and flow cytometry analysis.
immunoprecipitation: Mice were anesthetized with Pental (1:2 in PBS) and were perfused with PBS. Samples were homogenized on ice in ice-cold homogenization buffer (50 mM Tris, pH 7.4, 100 mM KCl, 12 mM MgCl2, 1% NP-40, 1 mM DTT, 1:100 protease inhibitor (Sigma), 200 units/ml RNasin (Promega) and 0.1 mg/ml cycloheximide (Sigma) in RNase free DDW) 10% w/v with a Dounce homogenizer (Sigma) until the suspension was homogeneous. To remove cell debris, 1 ml of the homogenate was transferred to an Eppendorf tube and was centrifuged at 10,000g and 4°C for 10 min. Supernatants were transferred to a fresh Eppendorf tube on ice, then 10μl was removed for 'input' analysis and 10µg of anti-HA antibody (H9658, Sigma) or 10µg of mouse monoclonal IgG1 antibody (Sigma, Cat# PP100) was added to the supernatant, *followed by 4 h of incubation with slow rotation in a cold room at 4 °C. Meanwhile, Dynabeads Protein G (Thermo Fisher Scientific), 100 μl per sample, were equilibrated to homogenization buffer by washing three times. At the end of 4 h of incubation with antibody, beads were added to each sample, followed by incubation overnight in cold room at 4 °C. After not more than 12 h, samples were washed three times with high-salt buffer (50 mM Tris, 300 mM KCl, 12 mM MgCl2, 1% NP-40, 1 mM DTT, 1:200 protease inhibitor, 100 units/ml RNasin and 0.1 mg/ml cycloheximide in RNase free DDW), 5 min per wash in a cold room on a rotator. At the end of the washes, beads were magnetized and excess buffer was removed, 100µl Lysis Buffer  was added to the beads (Ambion Life Technologies). For Sort+aHA IP samples (RiboTag IP after sorting), 30,000 microglial cells were sorted directly into 100µl Lysis Buffer (Ambion Life Technologies) containing 10µg of anti-HA antibody (H9658, Sigma) or 10µg of mouse monoclonal IgG1 antibody (Sigma, Cat# PP100), the rest of IP was continued as above from *.
PolyA-tailed mRNA was captured using the Dynabeads mRNA DIRECT kit (Ambion Life Technologies) according to manufacturer’s guidelines. RNA-seq libraries were constructed used a derivation of MARS-seq as described in Jaitin et al. (2014) adapted for bulk cell populations.

treatment_protocol: All mice were treated with Tamoxifen as follows: 5mg of tamoxifen (Sigma, diluted in corn oil) were administered to mice by gavage 4 times every other day at the age of 4-6 weeks.

value: Microglia FACS sorted from brain tissue

tag: immunoprecipiation antibody

value: anti-HA (Sigma H9658)


title: Sall1-CreER:Ribotag_MG_Sort+aHA_IP_7


title: Sall1-CreER:Ribotag_MG_Sort+aHA_IP_21


title: AB7223

value: Lymph node


title: Sall1-CreER:Ribotag_MG_Sort+aHA_IP_17


title: Sall1-CreER:Ribotag_MG_Sort_9


title: Sall1-CreER:Ribotag_MG_Sort_7


title: Sall1-CreER:Ribotag_MG_Sort_21


title: Sall1-CreER:Ribotag_MG_Sort_17


title: FT254 wt FTM vs. FT254 wt OCM

city: Berlin

first: Hans-Joachim

last: Mollenkopf

address: Charitéplatz 1

institute: Max-Planck-Institute for Infection Biology

description:
polarity(-)
252665226359_1_3

hyb_protocol: Whole human genome 4x44k microarrays were done according to the supplier’s protocol (Agilent Technologies).

scan_protocol: Scanning of microarrays was performed with 5 µm resolution and extended range (XDR)  using a DNA microarray laser scanner (Agilent Technologies)

data_processing: Raw microarray image data were analyzed with the Image Analysis / Feature Extraction software G2567AA (Version A.11.5.1.1, Agilent). The extracted MAGE-ML files were analyzed with the Rosetta Resolver Biosoftware (Rosetta Biosoftware). Intra-array data were normalized with the GE2_1105_Oct12 extraction protocol and interarray normalization was done by the mean of trimmed positive non-flagged/non-control reporters.

source_name: FT254 wt FTM

label_protocol: RNA labeling was performed with the Quick-Amp Labeling Kit  (Agilent Technologies) according supplier's instructions.

growth_protocol: Epithelial progenitor isolation from fallopian tube samples was done as previously described (Nat Commun. 2015 Dec 8;6:8989. doi: 10.1038/ncomms9989.) Organoids were cultured according to the following protocol: In brief, to initiate organoid growth approximately 30.000 cells, obtained from 2D culture, were seed per 50µL MatrigelTM and overlaid with a with growth factor cocktail stimulating different paracrine pathways (see treatment protocol). Medium was changed every 3-4 days and organoids were expanded every 2-3 weeks at a rate of 1:2 to 1:3. To do so, organoids were released from MatrigelTM, washed, taken up in pre-warmed TrypLETM and incubated for 7-10 min at 37°C for enzymatic digestion. Subsequently, organoids were vortexed, washed and pelleted. Finally, the shredded organoids were resuspended in fresh MatrigelTM and seeded into pre-warmed cell culture plates before FTM was added to the organoids. The medium was changed twice per week and the organoids kept in a humidified incubator with 37°C and 5% CO2.

extract_protocol: Total RNA was isolated according the manufacturer´s protocol.

treatment_protocol: To obtain stable knockdowns of PTEN and Rb, shRNA sequences targeting specific regions within the respective mRNAs, were cloned into the lentiviral vector pLVTHM (Addgene#12247) carrying either mCherry or GFP as a selection marker. The retroviral vector with the shRNA against p53 und puromycin selection marker was provided by Alexander Loewer. Replication deficient retro- and lentiviral particles were produced by transient transfection of 293T cells using FuGENE® 6 reagent (Promega). Lentiviral plasmids: psPAX2 (packaging plasmid; Addgene#12260), pMD2.G (VSV-G envelope plasmid; Addgene#12259), pLVTHM-GFP (Addgene#12247), pLVTHM-GFP/mCherry-Luci (shRNA against Luciferase as control vector; target sequence (5’-3’): AACTTACGCTGAGTACTTCGA), pLVTHM-mCherry-PTEN (pLVTHM-mCherry with shRNA against PTEN; target sequence (5’-3’): AGGCGCTATGTGTATTATTAT), pLVTHM-GFP-Rb (pLVTHM-GFP with shRNA against Rb; target sequence (5’-3’): GGTTGTAATGGCCACATATAG). Retroviral plasmids (retroviral plasmids were a gift by Alexander Loewer and are described in Brummelkamp, Bernards et al. 2002): retroviral packaging plasmid, retroviral envelope plasmid, pSUPER.retro (Empty vector, Addgene#3926), pSUPER.retro.p53 (pSUPER.retro with shRNA against p53; target sequence (5’-3’): GACTCCAGTGGTAATCTAC). To genetically modify primary FT epithelial cells, they were treated with retro-and lentiviruses in 2D culture. Either p53 single or p53/PTEN/Rb triple knockdown cells were generated. Freshly isolated FECs of an early passage (p0/p1) were transduced with 1x concentrated virus diluted in ADF supplemented with 12 mM HEPES, 1% GlutaMAXTM, 10ng/µL hEGF and 5µg/µL Polybrene. The cells were incubated for 12-18h with the viral suspension. When the cultures reached 80-90% confluence the cells were split and sequentially transduced and expanded until they reached max. passage 3. To retrieve successfully transduced cells carrying a fluorescent selection marker, FACS was performed. Collected cells were centrifuged directly after FACS and seeded in 3D culture with around 1.5 x 105 cells/ 50µL Matrigel. Cells transduced with the retroviral vector were selected by adding 0.5 µg/mL puromycin (Gibco) for 10 days to the respective cell culture. Organoids derived from genetically modified Fallopian tube epithelial cells were grown in MatrigelTM in either standard FT 3D medium (FTM): ADF, 25% conditioned Wnt3A medium and 25 % conditioned RSPO1 medium, supplemented with 12 mM HEPES, 1% GlutaMAXTM, 2% B27, 1% N2, 10 ng/µL human EGF, 100 ng/mL human noggin, 100 ng/mL human FGF-10, 1 mM nicotinamide, 9 µM ROCK inhibitor (Y-27632) and 0.5 µM TGF-β RI Kinase Inhibitor IV (SB431542). or in ovarian cancer optimized medium (OCM): ADF supplemented with 12 mM HEPES, 1% GlutaMAXTM, 2% B27, 1% N2, 10 ng/µL human EGF, 1 mM nicotinamide, 9 µM ROCK inhibitor (Y-27632), 0.5 µM TGF-β RI Kinase Inhibitor IV (SB431542) and 10ng/µL human BMP2. RNA was isolated from organoid cultures in passage 2 after seeding in Matrigel and start of differential treatment with the different media. In case it is not further indicated which medium was applied, the cells were cultivated in the standard FT 3D medium.

tag: donor id

value: human donor 254

value: fallopian tube

tag: culture type

value: fallopian organoid medium

tag: genotype/variation

value: wild type

source_name: FT254 wt OCM

value: ovarian cancer medium


title: FT254 sh FTM vs. FT254 sh OCM

description:
polarity(-)
252665226359_1_2

source_name: FT254 sh FTM

tag: tissue

value: triple sh RNA

source_name: FT254 sh OCM


title: FT253 sh OCM vs. FT253 sh FTM

description:
polarity(+)
252665226358_1_2

source_name: FT253 sh OCM

value: human donor 253

source_name: FT253 sh FTM


title: FT254 wt FTM vs. FT254 sh FTM

description:
polarity(-)
252665226359_1_4


title: FT253 sh OCM vs. FT253 wt OCM

description:
polarity(+)
252665226358_1_1

source_name: FT253 wt OCM


title: FT253 wt OCM vs. FT253 wt FTM

description:
polarity(+)
252665226358_1_3

source_name: FT253 wt FTM


title: FT254 wt OCM vs. FT254 sh OCM

description:
polarity(-)
252665226359_1_1


title: FT199 P53 vs. FT199 wt

description:
polarity(-)
252665219458_1_4

value: human donor 199

source_name: FT199 wt


title: FT253 sh FTM vs. FT253 wt FTM

description:
polarity(+)
252665226358_1_4


title: Sall1-CreER:Ribotag_IgG_IP_9

tag: strain

value: Homgenate from brain tissue

value: IgG1 isotype control (Merck PP100)


title: FT199 wt vs. FT199 P53

description:
polarity(+)
252665219458_1_3


title: FT199 wt vs. FT199 ev

description:
polarity(+)
252665219457_1_3

source_name: FT199 ev

value: empty vector


title: FT199 ev vs. FT199 wt

description:
polarity(-)
252665219457_1_4


title: FT199 P53 vs. FT199 ev

description:
polarity(-)
252665219458_1_2


title: KO rep2

city: Richmond

first: Mikhail

last: Dozmorov

address: 830 E Main St

department: Biostatistics

institute: Virginia Commonwealth University

data_processing:
Sequencing adapters were removed using Trimmomatic v.0.33 (Bolger et al., 2014). Quality control at each processing step was performed using the FastQC tool v0.11.2 (quality base calls, CG content distribution, duplicate levels, complexity level)  (Andrews, 2010).
The Mouse GRCm38/mm10 reference genome was obtained from the UCSC Genome Browser Gateway (http://hgdownload.soe.ucsc.edu/goldenPath/mm10/bigZips/chromFa.tar.gz), and the corresponding gene annotation file was obtained from Ensemble (ftp://ftp.ensembl.org/pub/release-83/gtf/mus_musculus/Mus_musculus.GRCm38.83.gtf.gz) on 02/20/2016. Only autosomes, mitochondrial and sex chromosomes were used.
Reads were aligned using the subread v.1.6.2 aligner (Liao et al., 2013).
Genome_build: mm10
Supplementary_files_format_and_content: txt.  Gene counts were obtained for each sample based on the last hg38 version of Ensembl transcriptome (v.87) using the featureCounts v.1.2.6 software (Liao et al., 2014).

source_name: mouse embryo cells

growth_protocol: Cells were cultured in DMEM supplemented with 10% FBS and pen/strep, sodium pyruvate, and non-essential amino acids.

extract_protocol:
Media was removed from cells and  washed two times with PBS. RNA was isolated using the RNAeasy Minikit (Qiagen).
After library Bioanalyzer QC analysis and quantification, individually indexed and compatible libraries were proportionally pooled and sequenced using the HiSeq 1000  sequencer (Illumina, San Diego, CA) with the sequencing setting of single read 1x51 bp, and about 25 million pass filter reads per sample were generated.

tag: cell type

value: Mouse Embryo, 14 days

tag: passage

value: passage 16

value: SphK2 null


title: FT192 P53 vs. FT192 wt

description:
polarity(-)
252665219457_1_2

value: human donor 192

source_name: FT192 wt


title: Sall1-CreER:Ribotag_IgG_IP_17

tag: genotype

tag: organ


title: Sall1-CreER:Ribotag_IgG_IP_21


title: Sall1-CreER:Ribotag_aHA_IP_9

value: anti-HA (Sigma H9658)


title: WT rep3


title: WT rep2


title: WT rep1


title: Sall1-CreER:Ribotag_aHA_IP_17


title: Cx3cr1-CreER:Ribotag_MG_Sort+aHA_IP_4

value: Microglia FACS sorted from brain tissue


title: Sall1-CreER:Ribotag_aHA_IP_21


title: FT192 P53 vs. FT192 ev

description:
polarity(-)
252665219456_1_4

source_name: FT192 ev


title: P16_B_S2

city: Nice

first: Dmitry

last: Bulavin

address: 28 Av Valomdrose

country: France

institute: IRCAN

data_processing:
Quality control  Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts. In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data. At the same time, Q20, Q30 and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality.
Reads mapping to the reference genome Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using Bowtie v2.2.3 and single-end clean reads were aligned to the reference genome using TopHat v2.0.12. We selected TopHat as the mapping tool for that TopHat can generate a database of splice junctions based on the gene model annotation file and thus a better mapping result than other non-splice mapping tools.
Quantification of gene expression level HTSeq v0.6.1 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene. FPKM, expected number of Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced, considers the effect of sequencing depth and gene length for the reads count at the same time, and is currently the most commonly used method for estimating gene expression levels (Trapnell, Cole, et al., 2010). For unigene DGE, we use RSEM to count the reads numbers mapped to each unigene.
Differential expression analysis Differential expression analysis of two conditions/groups (two biological replicates per condition) was performed using the DESeq R package (1.18.0). DESeq provide statistical routines for determining differential expression in digital gene expression data using a model based on the negative binomial distribution. The resulting P-values were adjusted using the Benjamini and Hochberg’s approach for controlling the false discovery rate. Genes with an adjusted P-value < 0.05 found by DESeq were assigned as differentially expressed. Prior to differential gene expression analysis, for each sequenced library, the read counts were adjusted by edgeR program package through one scaling normalized factor. Differential expression analysis of two conditions was performed using the DEGSeq R package (1.20.0). The P values were adjusted using the Benjamini & Hochberg method. Corrected P-value of 0.005 and log2 (fold change) of 1 were set as the threshold for significantly differential expression.

source_name: liver

growth_protocol: The minced liver was digested during 45-60min in 10 ml DMEM with 100 mg/ml Collagenase A and 10 mg/ml DNAseI. After inactivation enzymes with equal amount DMEM/10%FBS cells were strained through 70mm nylon mesh and washed several times with PBS/2%FBS. After the final wash ≈ 2X108 cells were re-suspended in 270 ml PBS/2%FBS and incubated on ice for 20 min with 30 ml CD31 MicroBeads (Miltenyi Biotec #130-097-418) and washed with PBS/2%FBS/2mM EDTA. CD31+ cells were separated on MACS LS Columns (Miltenyi Biotec #130-042-401) according the manufacturer recommendations. The separated cells were cultured in Endothelial Cell Growth Medium 2 (PromoCell #C-22111) at 370C/5%CO2.

extract_protocol:
Total RNA was extracted from cells stabilized in RNAprotect buffer according to the “Purification of total RNA from animal and human cells” protocol of the RNeasy Plus Micro Kit (QIAGEN, Hilden, Germany). In brief, cells were stored and shipped in RNAprotect buffer at 2-8 °C. After pelleting, the RNAprotect buffer was replaced by RLT Plus and the samples were homogenized by vortexing for 30 sec. Genomic DNA contamination was removed using gDNA Eliminator spin columns. Next one volume of 70 % ethanol was added and the samples were applied to RNeasy MinElute spin columns followed by several wash steps. Finally total RNA was eluted in 12 μl of nuclease free water. Purity and integrity of the RNA was assessed on the Agilent 2100 Bioanalyzer with the RNA 6000 Pico LabChip reagent set (Agilent, Palo Alto, CA, USA).
A total amount of 1 μg RNA per sample was used as input material for the RNA sample preparations. Sequencing manufacturer’s recommendations and index codes were added to attribute sequences to each sample. Briefly, mRNA was purified from total RNA using poly-T oligo-attached magnetic beads. Fragmentation was carried out using divalent cations under elevated temperature in NEBNext First Strand Synthesis Reaction Buffer (5X). First Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and RNase H. Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. After adenylation of 3’ ends of DNA fragments, NEBNext Adaptor with hairpin loop structure were ligated to prepare for hybridization. In order to select cDNA fragments of preferentially 150~200 bp in length, the library fragments were purified with AMPure XP system (Beckman Coulter, Beverly, USA). Then 3 μl USER Enzyme (NEB, USA) was used with size-selected, adaptor-ligated cDNA at 37 °C for 15 min followed by 5 min at 95 °C before PCR. Then PCR was performed with Phusion High-Fidelity DNA polymerase, Universal PCR primers and Index (X) Primer. At last, PCR products were purified (AMPure XP system) and library quality was assessed on the Agilent Bioanalyzer 2100 system.
The clustering of the index-coded samples was performed on a cBot Cluster Generation System using SR Cluster Kit cBot-HS (Illumina) according to the manufacturer’s instructions. After cluster generation, the library preparations were sequenced on an Illumina platform and 50 bp/100 bp single-end reads were generated.

value: CD31-positive cells

value: 1 year old

tag: cells sorted


title: FT192 wt vs. FT192 P53

description:
polarity(+)
252665219457_1_1

value: fallopian tube

value: fallopian organoid medium


title: FT199 ev vs. FT199 P53

description:
polarity(+)
252665219458_1_1


title: KO rep3


title: FT192 ev vs. FT192 P53

description:
polarity(+)
252665219456_1_3


title: KO rep1


title: Cx3cr1-CreER:Ribotag_MG_Sort+aHA_IP_3


title: Neg_F_S6


title: FT192 wt vs. FT192 ev

description:
polarity(+)
252665219456_1_1

value: wild type


title: Sall1-CreER:Ribotag_aHA_IP_7


title: FT192 ev vs. FT192 wt

description:
polarity(-)
252665219456_1_2


title: P16_C_S3


title: Cx3cr1-CreER:Ribotag_MG_Sort_3


title: Neg_D_S4


title: Neg_E_S5


title: Cx3cr1-CreER:Ribotag_MG_Sort+aHA_IP_1


title: Cx3cr1-CreER:Ribotag_MG_Sort_2


title: control rep3

first: Bernd

middle: Henrik

last: Northoff

address: Marchioninistr. 15

department: Institute of Laboratory Medicine

institute: Ludwig-Maximilians-University Munich

description: control

data_processing:
Illumina Casava v1.8.2 and bcf2fastq v1.8.4 were used for basecalling and generating fastq files.
Sequenced reads were trimmed for adaptor sequence and filtered for low-quality sequences.
Preprocessed reads were mapped to mm10 whole genome using segemehl v0.2.0 with parameters -S -A 90.
Mapped reads were counted using featureCounts v1.5.1according to mm10 RefSeq annotation.
Genome_build: mm10
Supplementary_files_format_and_content: Tab-delimited text files include raw counts for each sample.

source_name: Cortex

growth_protocol: Male C57BL/6J mice received Metronidazol, Neomycin, Ampicillin and Vancomycin with 5% sucrose in drinking water.

extract_protocol:
Total RNA was isolated from snap-frozen cortex using RNeasy Mini Kit (Qiagen).
Library preparation was performed using the Ovation Human FFPE RNA-Seq Library Systems (Nugen).

treatment_protocol: Mice were treated with SCFA or salt-matched control in drinking water ad libitum for 4 weeks starting at age of 6 - 8 weeks.

value: cortex


title: Cx3cr1-CreER:Ribotag_MG_Sort_1


title: control rep1

description: control


title: Sall1-CreER:Ribotag_IgG_IP_7


title: P16_A_S1


title: Cx3cr1-CreER:Ribotag_MG_Sort_4


title: Cx3cr1-CreER:Ribotag_IgG_IP_4


title: Cx3cr1-CreER:Ribotag_IgG_IP_2


title: SCFA treatment rep2

description: SCFA treatment


title: Cx3cr1-CreER:Ribotag_IgG_IP_3


title: SCFA treatment rep1

description: SCFA treatment


title: control rep2

description: control


title: Cx3cr1-CreER:Ribotag_aHA_IP_4


title: Cx3cr1-CreER:Ribotag_IgG_IP_1


title: Cx3cr1-CreER:Ribotag_aHA_IP_3


title: Cx3cr1-CreER:Ribotag_aHA_IP_2


title: Cx3cr1-CreER:Ribotag_aHA_IP_1


title: SCFA treatment rep3

description: SCFA treatment


title: MPs_ileum_day_4_23.11.14_A

first: Steffen

last: Jung

address: 234 Herzl Street

department: Department of Immunology

description: Single read (read2 used to read sample barcodes and UMI only)

data_processing:
Illumina bcl2fastq software used for basecalling.
Sample barcodes were extracted from read 2 and concatenated to the fastq header of read 1. Barcode is of size 7 followed by UMI of size 8
For example: the UMI GTACTGGT will appear in the following format: @NB501465:106:HFFKNBGX2:1:11101:5035:1075:AGGCTAAGTACTGGT:A6/A/E//EE////E:0
alignment: hisat 0.1.6  with deafult parameters
filter PCR amplification bias using alignment break site and UMI barcode (size 8) located in fastq header.
create tag directory using makeTagDirectory from HOMER tools (http://homer.salk.edu/homer/ngs/)
HOMER, quantifying RNA expression in genes: analyzeRepeats.pl rna mm9 -d <tagDir> -count exons -condenseGenes -strand + -raw
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files include mRNA molecule count values for each Sample

source_name: Ileum

extract_protocol:
Femurs and tibias of donor mice were removed and BM was flushed with cold PBS. BM was washed with cold PBS twice and filtered by 100 μm filter. Cells were suspended with PBS and loaded on equal amount of Ficoll (GE healthcare). Tubes were centrifuged 920 g in room temperature for 20 minutes without breaks and Buffy coats were collected and washed with cold PBS. CD11c-DTR > wt]. Cells were stained and sorted according to the following markers: CD117- CD11b+ CD115+ Ly6C+ GFPint.
Intestines were removed and fecal content flushed out with PBS; tubes were opened longitudinally and cut into 0.5 cm sections. Pieces were placed in 5ml / sample (up to 300gr of tissue) of Hanks' Balanced Salt Solution (HBSS) with 10% heat-inactivated FCS/FBS, 2.5mM EDTA and 1mM DL-Dithiothreitol ((DTT), Sigma-Aldrich Cat# D9779 ) and incubated on a 37oC shaker at 300rpm for 30 minutes to remove mucus and epithelial cells. Following incubation, samples were vortexed for 10 seconds and filtered through a crude cell strainer. Pieces that did not pass the strainer were collected and transferred to 5ml/sample of PBS +/+ with 5% heat-inactivated FCS/FBS, 1 mg/ml Collagenase VIII (Sigma-Aldrich Cat# C2139 ) and 0.1 mg/ml DNase I (Roche Cat# 10104159001 ). Tissue was incubated in a 37oC shaker at 300 rpm for 40 minutes (colon) or 20 minutes (ileum) in the solution. After incubation, samples were vortexed for 30 seconds until tissue was dissolved, then filtered through a crude cell strainer. The strainer was washed with PBS -/- and centrifuged in 4oC, 375G for 6 minutes. Cells were stained and subjected to FACS analysis or sorting.
Cells were sorted into 100 µl of lysis/binding buffer (Life Technologies) and stored at 80 °C. mRNA was captured using Dynabeads oligo(dT) (Life Technologies) according to manufacturer’s guidelines. A derivation of MARS-seq 21 was used  to prepare libraries for RNA-seq, as detailed in Shemer et al. 45. RNA-seq libraries were sequenced using the Illumina NextSeq 500. Raw reads were mapped to the genome (NCBI37/mm9) using hisat (version 0.1.6). Only reads with unique mapping were considered for further analysis. Gene expression levels were calculated and normalized using the HOMER software package (analyzeRepeats.pl rna mm9 -d<tagDir>-count exons -condenseGenes -strand + -raw). Gene expression matrix was clustered using k-means algorithm (MATLAB function kmeans) with correlation as the distance metric. PCA was performed by MATLAB function pca. Gene ontology was performed by DAVID (https://david.ncifcrf.gov). Data on molecules and pathways was partly obtained by Ingenuity Pathway Analysis (IPA), Ingenuity Target Explorer, Qiagen and Metascape Pathway analysis 23.

treatment_protocol: BM chimeras were treated with 18 ng / gram bodyweight Diphtheria toxin (DTx) (Sigma-Aldrich, Cat # D0564) for 2 consecutive days before transfer. At the day of transfer mice were injected with 106 BM monocytes IV. At days 1, 3, 5, 7 and 9 after transfer mice were injected with 9 ng / gr bodyweight DTx.

value: Ileum

tag: isolation

value: Cell sorting

tag: selection marker

tag: dt treatment

value: DT injections, every other day

tag: treatment

value: 9-18 ng DT/gr bodyweight


title: 231 shALDH1A3 #2

city: Toon

first: Daisuke

last: Yamashita

address: Shitsukawa

department: Neurosurgery

country: Japan

institute: Ehime University Graduate School of Medicine

description: sh&siRNA-treated MBA-231 cell individual gene FPKM values.xlsx

data_processing:
bcl2fastq version 1.8.4 software from Illumina to create the Fastq files
Raw FASTQ files were trimmed with TrimGalore! version 0.6.2 with parameters --paired --trim1
Trimmed FASTQ files were aligned with STAR version 2.5.4b with parameters --outReadsUnmapped Fastx --outSAMtype BAM SortedByCoordinate --outSAMattributes All
Transcript abundances were calculated with Cufflinks version 2.2.1 with parameters --library-type fr-firststrand -G -L
Differential expression was calculated with Cuffdiff using default parameters
Genome_build: Gencode GRCm38 p4 Release M11
Supplementary_files_format_and_content: tab delimited Excel files containing FPKM values for each sample and gene

source_name: Breast cancer cells

extract_protocol:
Total RNA was extracted from cells using the TRIzol Plus RNA Purification System (Invitrogen).
RNA integrity was checked by Agilent Bioanalyzer 2100, only samples with clean rRNA peaks were used.  Libraries for RNA-seq were prepared according to KAPA Stranded RNA-Seq Kit with RiboErase (KAPA Biosystems, Wilmington, MA) system. Final library quality and quantity were analyzed by Agilent Bioanalyzer 2100 and Life Technologies Qubit3.0 Fluorometer, respectively. 150 bp Paired-end sequencing was performed on Illumina HiSeq 4000 (Illumnia Inc., San Diego, CA).  RNA integrity was checked by Agilent Bioanalyzer 2100, only samples with clean rRNA peaks were used.  Libraries for RNA-seq were prepared according to KAPA Stranded RNA-Seq Kit with RiboErase (KAPA Biosystems, Wilmington, MA) system. Final library quality and quantity were analyzed by Agilent Bioanalyzer 2100 and Life Technologies Qubit3.0 Fluorometer, respectively. 150 bp Paired-end sequencing was performed on Illumina HiSeq 4000 (Illumnia Inc., San Diego, CA).  RNA integrity was checked by Agilent Bioanalyzer 2100, only samples with clean rRNA peaks were used.  Libraries for RNA-seq were prepared according to KAPA Stranded RNA-Seq Kit with RiboErase (KAPA Biosystems, Wilmington, MA) system. Final library quality and quantity were analyzed by Agilent Bioanalyzer 2100 and Life Technologies Qubit3.0 Fluorometer, respectively. 150 bp Paired-end sequencing was performed on Illumina HiSeq 4000 (Illumnia Inc., San Diego, CA).  RNA integrity was checked by Agilent Bioanalyzer 2100, only samples with clean rRNA peaks were used.  Libraries for RNA-seq were prepared according to KAPA Stranded RNA-Seq Kit with RiboErase (KAPA Biosystems, Wilmington, MA) system. Final library quality and quantity were analyzed by Agilent Bioanalyzer 2100 and Life Technologies Qubit3.0 Fluorometer, respectively. 150 bp Paired-end sequencing was performed on Illumina HiSeq 4000 (Illumnia Inc., San Diego, CA).

tag: group

value: Knockdown


title: BB_Monocyte_transfer_to_CX3CR1dtr_mice_gfp_only_4.M

source_name: Colon

value: Colon


title: BB_Monocyte_transfer_to_CX3CR1dtr_mice_gfp_only_2.M


title: BB_Monocyte_transfer_to_CX3CR1dtr_mice_gfp_only_5.M


title: BB_Monocyte_transfer_to_CX3CR1dtr_mice_gfp_only_1.M


title: BB_Monocyte_transfer_to_CX3CR1dtr_mice_gfp_only_3.M


title: 231 siALDH1A3


title: BB_Monocyte_transfer_to_CX3CR1dtr_mice_gfp_only_6.M


title: mono_CX_P_-_22.10.14

source_name: Blood

value: Blood

value: no treatment


title: 231 siNT

value: NT


title: 231 shALDH1A3 #1


title: 231 shNT #2


title: 231 shNT #1


title: MPs_ileum_2_day_8_8.1.15


title: 231-BoM

description: BC cell individual gene FPKM values.xlsx

value: Bone meta


title: MPs_ileum_2_day_8_27.11.14


title: MPs_ileum_2_day_12_1.12.14


title: 231-LM

value: Lung meta


title: MPs_ileum_1_day_8_8.1.14


title: MDA-231 #2

value: Control


title: MPs_ileum_1_day_8_27.11.14


title: 231-BM

value: Brain meta


title: MDA-231 #1


title: MPs_colon_day_12_12.1.15


title: MPs_colon_2_day_8_8.1.15


title: Infected_Donor4_BDQ2

city: Paris

first: Alexandre

last: Giraud-Gatineau

address: 25-28 rue du docteur roux

department: Microbiology

institute: Institut Pasteur

data_processing:
STAR v2.5.0b was used to map RNA-seq reads to the hg38 reference genome and quantify  gene expression (option--quantMode GeneCounts) by counting the fragments overlapping the Ensembl genes (GRCh38 v. 83).
Genome_build: hg38
Supplementary_files_format_and_content: The raw counts were generated using STAR v2.5.0b for GRCh38 Ensembl genes

source_name: Blood mononuclear cells

growth_protocol: Blood mononuclear cells were isolated by Ficoll-Paque centrifugation (GE Healthcare Life Sciences). CD14+ monocytes were isolated by positive selection using CD14 microbeads (Miltenyi Biotec) and allowed to differentiate into Mφs in the presence of granulocyte-macrophage colony-stimulating factor (GM-CSF) (20 ng/mL; R&D Systems) over a six-day period. RPMI medium + GM-CSF was added to the cell cultures every two days.

extract_protocol:
Total RNA from macrophages was extracted using QIAzol reagent (Life Technologies) and purified over RNeasy columns (Qiagen). The quality of all samples was assessed with an Agilent 2100 bioanalyzer (Agilent Technologies) to verify RNA integrity. Only samples with a good RNA yield and no RNA degradation (ratio of 28S to 18S, > 1.7; RNA integrity number > 9) were used for further experiments.
cDNA libraries were prepared with the Illumina TruSeq RNA Sample Preparation Kit v2 and were sequenced on an llumina HiSeq 2500

treatment_protocol: Macrophages from 4 donors were left untreated (control) or treated with 0.5 (BDQ1) or 5 (BDQ2) µg/mL bedaquiline for 18 h. Concerning infected cells, M. tuberculosis H37Rv was grown from a frozen stock to mid-log phase in 7H9 medium (Becton Dickinson), supplemented with albumin-dextrose-catalase (ADC, Difco). Before infection, bacteria were washed three times and re-suspended in 1 ml PBS. Clumps were dissociated by 30 passages through a needle and then allowed to sediment for 5 min. The density of bacteria in the supernatant was verified by measuring the OD600 and aliquot volumes defined to allow one bacterium-per two cell infections. Cells were infected in 6-well plates with each well containing 1.3 × 106 cells in 3 ml medium containing GM-CSF (R&D Systems). After 2 h of incubation at 37°C, infected cells were washed three times in PBS to remove extracellular bacteria and incubated in fresh medium. After 18h, macrophage from 4 donnors were treated with 0.5 (BDQ1) or 5 (BDQ2) µg/mL bedaquiline for 18 h. After incubation, the cell transcriptome was analyzed by mRNA sequencing.

tag: donor

value: human monocyte-derived macrophages

tag: infection status

value: infected

tag: bacterial strain

tag: treatment status

value: BDQ 5 microg/mL


title: MPs_colon_2_day_12_1.12.14


title: Cx3cr1-CreER:Ribotag_MG_Sort+aHA_IP_2

source_name: Brain

value: Microglia FACS sorted from brain tissue

tag: immunoprecipiation antibody

value: anti-HA (Sigma H9658)


title: MPs_ileum_day_12_12.1.15

value: Ileum

value: Cell sorting


title: Infected_Donor4_BDQ1

value: BDQ 0.5 microg/mL


title: Infected_Donor4_DMSO

value: DMSO


title: MP_ileum_HC_d12_3.11.14

value: DT injections, every other day

value: 9-18 ng DT/gr bodyweight


title: MPs_colon_1_day_8_8.1.15

value: Colon


title: MPs_colon_1_day_8_27.11.14


title: Uninfected_Donor4_DMSO

value: uninfected


title: Uninfected_Donor4_BDQ2


title: Infected_Donor4_Untreated

value: Untreated


title: Infected_Donor3_BDQ2


title: MP_3_ileum_SC_26.10.14_d4


title: Uninfected_Donor4_Untreated


title: MPS_ileum_day_4_23.11.14_B


title: Infected_Donor3_DMSO


title: Infected_Donor3_BDQ1


title: MPS_colon_2_day_4_23.11.14


title: Infected_Donor3_Untreated


title: MPS_colon_1_day_4_4.1.15


title: MPS_colon_1_day_4_23.11.14


title: Ileum_MPS_1_day_12_1.12.14


title: Uninfected_Donor3_BDQ1


title: Colon_SC_d8_30.10.14_MP


title: Uninfected_Donor3_DMSO


title: Uninfected_Donor3_Untreated


title: MPs_colon_1_day_12_1.12.14


title: CX_P_-_monocytes_19.11.14

value: Blood

value: no treatment


title: MP_colon_HC_d12_3.11.14


title: Uninfected_Donor4_BDQ1


title: CX_P_-_monocytes_31.12.14


title: MP_d4_ileum_4_26.10.14


title: Infected_Donor2_BDQ2


title: Infected_Donor2_BDQ1


title: Infected_Donor2_Untreated


title: Infected_Donor2_DMSO


title: F0-Trained3 miRNA seq

city: Atlanta

first: Brian

middle: George

last: Dias

state: GA

address: 954 Gatewood Rd NE

department: Psychiatry and Behavioral Sciences

institute: Emory University

data_processing:
Alignment was performed to mmu:miRbase20
The differential expression analysis was done by Exiqon using the EdgeR statistical software package (Bioconductor, http://www.bioconductor.org/) . Differential expression analysis investigates the relative change in expression (i.e. counts) between different samples. For normalization we use the trimmed mean of M-values method based on log-fold and absolute gene wise changes in expression levels between samples (TMM normalization).
Genome_build: mmu:miRbase20

source_name: sperm

extract_protocol:
Qiagen miRNeasy kit
Library was constructed by Exiqon using Illumina protocols, sequencing was performed on a NextSeq500 instrument, average of 20million reads/sample were generated, 50nt single-end reads were generated

tag: age

value: 2-month old adult

tag: tissue

value: sperm


title: F0-Trained1 miRNA seq

tag: strain


title: F0-Trained2 miRNA seq


title: Uninfected_Donor3_BDQ2

tag: cell type

value: human monocyte-derived macrophages


title: Uninfected_Donor2_BDQ2

value: BDQ 5 microg/mL


title: F0-Exposed4 miRNA seq


title: F0-Exposed2 miRNA seq


title: Infected_Donor1_BDQ2

value: infected


title: Uninfected_Donor2_DMSO


title: Uninfected_Donor2_Untreated


title: Uninfected_Donor2_BDQ1


title: Infected_Donor1_BDQ1


title: F0-Exposed1 miRNA seq


title: Infected_Donor1_DMSO


title: RNA-seq DEX 3 naïve

city: Seoul

first: Jaechul

last: Lim

state: CT

address: 1 Gwanak-ro, 1 Gwanak-gu

country: South Korea

institute: Seoul National University

description:
RNA-seq
Naive_processed.txt

data_processing:
The sequences were basecalled by Illumina RTA embedded in NextSeq Control Software by the standard workflow.
Reads were aligned to the mouse genome (mm10) using STAR (v2.5.3a) and annotated with Ensembl Transcripts release 91 in Partek® Genomics Suite® software, version 7.0 (2018).
Genome_build: mm10(GRCm38)
Supplementary_files_format_and_content: a tab-delimited file including Gene symbol, Gene type and CPM (counts per million).

source_name: Naïve CD8 T cells

growth_protocol: Naïve OT-I (CD45+, CD8+, CD62L+, CD44-) or stimulated (CD4-, CD8+) CD8 T cells were sorted from spleen and/or LNs. T cells were enriched before FACS by utilizing Pan T cell MACS kit (Miltenyi Biotec) and sorted with BD FACS Aria (BD Bioscience).

extract_protocol:
RNA was purified from T cells using QIAGEN RNeasy columns (74106) with on-column DNase digestion according to the manufacturer’s instructions.
RNA-seq libraries were constructed following Illumina Tru-seq stranded mRNA protocol (20020594).

value: Naive CD8 T cells

tag: surface marker

value: Perinatal DEX treated


title: Infected_Donor1_Untreated


title: Uninfected_Donor1_DMSO


title: RNA-seq DEX 1 naïve

description:
RNA-seq
Naive_processed.txt


title: RNA-seq DEX 2 naïve

description:
RNA-seq
Naive_processed.txt


title: F0-Trained4 miRNA seq


title: RNA-seq Control 3 naïve

description:
RNA-seq
Naive_processed.txt

value: Control


title: ReSt_d14_3

city: Lyon

first: Zdenko

last: Herceg

address: 25 avenue Tony Garnier CS 90627

department: EGM

institute: IARC

data_processing:
Fastq files were trimmed usinf TrimGalore for Q>30
Mapping with hisat2
Splice jonction was improved with SplitNCigarReads from GATK
Read counts were generated from bam files using htseq-count function and genes with ≤10 counts-per-million in at least two samples were eliminated
Normalized count obtained with edgeR
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include read count and  logCPM values for each Sample

growth_protocol: For maintainance, cells were cultured in DMEM/F-12 supplemented with 10% (v/v) charcoal-stripped fetal bovine serum, 1% nonessential amino acids, sodium pyruvate and penicillin/streptomycin and with a daily addition of 10nM E2 in 0.1% DMSO

extract_protocol:
AllPrep DNA/RNA Mini kit (Qiagen)
1 µg of RNA was processed with a TruSeq RNA library preparation kit and sequenced on HiSeq 2500  (Illumina)

treatment_protocol: 10nM 17β-estradiol in 0.1% DMSO (CTR and ReSt) or only 0.1% DMSO (E2D)

tag: cell line

value: MCF-7 HTB22 (ATCC)

value: ReSt

tag: time point


title: Uninfected_Donor1_BDQ1

value: BDQ 0.5 microg/mL


title: Uninfected_Donor1_Untreated


title: RNA-seq Control 2 naïve

description:
RNA-seq
Naive_processed.txt


title: ReSt_d14_2


title: F0-Exposed3 miRNA seq


title: E2D_d14_3


title: ReSt_d14_1


title: RNA-seq Control 1 naïve

description:
RNA-seq
Naive_processed.txt


title: E2D_d14_2


title: Uninfected_Donor1_BDQ2


title: E2D_d14_1


title: RNA-seq DEX 2 stim

description:
RNA-seq
Stim_processed.txt

source_name: Stimulated CD8 T cells

value: Stimulated CD8 T cells


title: RNA-seq DEX 3 stim

description:
RNA-seq
Stim_processed.txt


title: RNA-seq DEX 1 stim

description:
RNA-seq
Stim_processed.txt


title: RNA-seq Control 3 stim

description:
RNA-seq
Stim_processed.txt


title: E2D_d4_3


title: RNA-seq Control 1 stim

description:
RNA-seq
Stim_processed.txt


title: CTR_d14_3

value: CTR


title: CTR_d14_2


title: ATAC-seq DEX 2

description: ATAC-seq

data_processing:
The sequences were basecalled by Illumina RTA embedded in NextSeq Control Software by the standard workflow.
Sequenced reads were trimmed with adaptor sequences (cutadapt v1.9.1, (Martin, 2011)) and mapped to the mouse genome (GRCm38, emsembl release 93) by Bowtie2 (v2.3.4.1, (Langmead and Salzberg, 2012)). Mitochondrial and duplicated reads were removed by SAMtools (v1.9, (Li et al., 2009)) and Picard (v2.9.0, https://broadinstitute.github.io/picard/), respectively.
Peaks were found by MACS2 (v.2.1.1, (Zhang et al., 2008)) and visualized by deepTools (v3.1.1, Ramirez et al., 2014, NAR).
Genome_build: mm10(GRCm38)
Supplementary_files_format_and_content: a narrowPeak file including Chrom, ChromStart, ChromEnd, Name, Score, Strand, SignalValue, pValue, qValue, and Peak.
Supplementary_files_format_and_content: a bigWig file

growth_protocol: Naive OT-I (CD45+, CD8+, CD62L+, CD44-) CD8 T cells were sorted from spleen and/or LNs. T cells were enriched before FACS by utilizing Pan T cell MACS kit (Miltenyi Biotec) and sorted with BD FACS Aria (BD Bioscience).

extract_protocol:
Genomic DNAs were extracted by DNA Clean & Concentrator (Zymo).
ATAC-seq libraries were constructed with 50K cells from each condition following Omni-ATAC protocol (Illumina FC-121-1031(Corces et al., 2017))


title: ATAC-seq DEX 1

description: ATAC-seq


title: CTR_d14_1


title: CTR_d4_3


title: ATAC-seq Control 3

description: ATAC-seq


title: CTR_d4_2


title: ATAC-seq Control 2

description: ATAC-seq


title: CTR_d4_1


title: ATAC-seq Control 1

description: ATAC-seq


title: input of myotube without pyruvate

city: Beijing

first: Yong

last: Zhang

address: 5 Dong Dan San Tiao

institute: School of Basic Medicine, Peking Union Medical College

data_processing:
Illumina bcl2fastq v2.19 software used for basecalling.
ChIP-seq reads were aligned to the mm9 genome assembly using bowtie2-2.1.0 with the following parameters  -N 1 -p 4 -x -U
peaks were called using macs2 2.1.1 with the following setting:  -t  --extsize --call-summits --nomodel -c  -g  -n  -p 1e-5.
Genome_build: mm9
Supplementary_files_format_and_content: bw files were generated using UCSC, tab-delimited text files include Peak and genes

source_name: Myotube

growth_protocol: Primary myoblasts isolated from 2-week-old mice were cultured in  F-10 medium containing 20% FBS, 1% penicillin-streptomycin, 1% glutamine at 37 °C in a 5% CO2 atmosphere. At 70–80% confluence, the myoblasts were switched to differentiation medium (DMEM with 2% horse serum). After 5 days of differentiation, the myotubes were cultured in differentiation medium with or without pyruvate for 24 hr.

extract_protocol:
Lysates were clarified from sonicated nuclei and protein-DNA complexes were isolated with related antibody.
Libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit (Part# 0801-0303). Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (32 to 52 exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation DNA was PCR amplified with Illumina primers for 15 cycles and library fragments of ~250 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Genome Analyzer following the manufacturer's protocols.

treatment_protocol: Cultured in medium with or without pyruvate

value: Myotube differentiated from primary myoblasts

tag: antibody


title: MDA-LM2_SRSF1_CLIP_r2

city: San Francisco

first: Hani

last: Goodarzi

state: CA

department: Biochemistry and Biophysics

institute: UCSF

description: HITS-CLIP

data_processing:
After linker sequence removal and quality trimming (cutadapt; -u 5 -q 15 -m 20 -a GTGTCAGTCACTTCCAGCGG), sequence mapping was performed using BWA (v.0.7; -t 12 -n 0.06 -q 20) with default parameters (build hg19).
The binding sites were identified using the CTK package (Zhang and Darnell, Nature biotech, 2011).
Genome_build: hg19
Supplementary_files_format_and_content: Identified HITS-CLIP peaks

growth_protocol: Cells were grown in DMEM-based media supplemented with 10% FBS, 1% L-glutamine, 1% Sodium Pyruvate, and 1% Pen/Strep

extract_protocol:
Cells were UV cross-linked and prepared as described previously (Licatalosi D, et al. 2008, Nature 456:464-U22).
Samples were prepared for sequencing as described previously (Licatalosi D, et al. 2008, Nature 456:464-U22).

tag: rep


title: input of myotube with pyruvate


title: MDA-LM2_SRSF1_CLIP_r1

description: HITS-CLIP


title: MyoD Chip-seq on myotube without pyruvate

value: MyoD (SC-760)


title: E2D_d4_2


title: MyoD Chip-seq on myotube with pyruvate


title: ATAC-seq DEX 3

description: ATAC-seq


title: RNA-seq Control 2 stim

description:
RNA-seq
Stim_processed.txt


title: UACC-DHA-B

city: La Jolla

first: Haoxin

last: Li

address: 10550 North Torrey Pines Road

institute: The Scripps Research Institute

description:
UACC257_count_normalized_processed_data.txt
raw data file contains sequencing reads for the sgRNAs in the library

data_processing:
Library strategy: CRISPR screen
Sequence mapping and counting: For CRISPR screen data analysis, the sgRNA sequences were mapped to a reference file containing all SpCas9 sgRNAs in the library and the sgRNA-associated barcodes were counted and mapped to the barcode reference file. The reference file containing all the sgRNAs in the Brunello library is included in this submission, and can be found publicly at https://media.addgene.org/cms/filer_public/8b/4c/8b4c89d9-eac1-44b2-bb2f-8fea95672705/broadgpp-brunello-library-contents.txt .
Read count normalization: The read count matrix was normalized to reads per million reads (RPM) within each condition.
Supplementary_files_format_and_content: The read count matrix is presented as a txt file.

source_name: Human cancer cell line

growth_protocol: UACC257 cells were cultured in RPMI-1640 (Gibco) media supplemented with 10% fetal bovine serum (Sigma) and normocin (Invivogen) in a humidified incubator at 37°C with 5% CO2.

extract_protocol:
Genomic DNA from cell pellets was purified using the QIAamp DNA Blood Maxi/Midi/Mini kits (Qiagen) according to the manufacturer’s protocols and quantified using a Nanodrop 2000 (Thermo Fisher Scientific).
sgRNA cassettes were PCR-amplified and barcoded with sequencing adaptors utilizing ExTaq DNA Polymerase (Clontech). PCR products were purified with Agencourt AMPure XP SPRI beads (Beckman Coulter A63880) according to the manufacturer’s instructions, quantified using a Nanodrop 2000, pooled into a master sequencing pool, and sequenced (Illumina) with 300nt single-end reads, loaded at 60% with a 5% spike-in of PhiX DNA.

treatment_protocol: Prior to screening, the viral titer and volume was pre-determined with pilot experiments to ensure about 30-40% infection rate in the screening experiment and caution was taken to minimize multiple constructs transduced into the same cell. Optimized surface area for cell growth was pre-determined in pilot experiments to avoid over-confluence during screening. Puromycin concentrations were pre-determined with pilot experiments before the screen. For the screening experiment, 180 million UACC257-Cas9 cells were infected with a lentiviral library (Brunello, purchased from the Broad Institute) containing 77,441 sgRNA targeting ~18,000 genes in human genome to ensure each sgRNA is represented by at least 500 cells on average. For the infection, cells added with the calculated lentivirus volume were supplemented with 8 µg/mL of polybrene and centrifuged at 950g for 2 hours. Infected cells were selected with 2 µg/mL of puromycin for 96 hours, expanded to reach the desired cell number and split for polyunsaturated fatty acid treatment or control incubation. After 3 days, DMSO or 5 µM ML210 was added to corresponding groups. The resistant cells were cultured for further sequencing.

value: Melanoma

tag: pufa

value: DHA


title: E2D_d4_1

tag: treatment


title: esiBrd2, biological rep2

city: Sevilla

first: Jose

middle: C.

last: Reyes

address: Av. Américo Vespucio

department: Genome biology

country: Spain

institute: CABIMER

data_processing:
RNA-Seq data were primarily filtered using the FASTQ Toolkit v1.0.0 program
The RNA-seq data were aligned using Subjunc function from Rsubread [1] v.1.28.1 bioconductor package, to map reads to the mm9 mouse reference genome, using TH1=2 and unique=TRUE parameters. The downstream analysis was performed on bam files with duplicates removed using the samtools [2] v.0.1.19 rmdup command. FeatureCounts() function from Rsubread v.1.28.1 bioconductor package was used to assign reads to UCSC mm9 genes using GTF.featureType="exon" and GTF.attrType="gene_id" parameters on duplicate removed bam files. Then differential gene expression analysis was performed using the voom/limma [6] v.3.34.9 and edgeR [7,8] v.3.20.9 bioconductor packages. Genes that were expressed at > 1 counts per million mapped reads in ≥2 replicates were analyzed. CalcNormFactors() function using TMM method was used to normalize samples.
Genome_build: mm9 mouse reference genome
Supplementary_files_format_and_content: Raw counts per UCSC knownGenes at exon level for all treatments.

source_name: P19 mouse teratocarcinoma cell line

growth_protocol: Mouse P19 cells were cultured in α-modified Minimum Essential Medium (HyClone, Logan, UT, USA) supplemented with 7.5% calf serum (HyClone) and 2.5% fetal bovine serum

extract_protocol:
Total RNA was isolated using RNeasy Mini Kit (Qiagen)
The libraries were prepared with the TruSeq Stranded TOTAL RNA kit (Illumina, San Diego, CA, USA) and the sequencing was performed with the NextSeq500 HIGH-Output and 1x75bp length parameters

treatment_protocol: Two independent cultures (replicates) were treated with each one of the following siRNA: siControl, siNipbl, siBrd4, siBrd2

value: Cells transfected  with siBrd2 RNA

tag: tissue origin

value: teratocarcinoma


title: UACC-EPA-B

value: EPA


title: UACC-DHA-A


title: esiBrd4, biological rep2

value: Cells transfected  with esiBrd4 RNA


title: esiBrd2, biological rep1


title: UACC-EPA-A


title: UACC-DPA-A

value: DPA


title: Tumor_WT

city: Pittsburgh

first: Wei

last: Chen

state: PA

address: 4401 Penn Ave., Rangos Research Building, Room 9125

department: Division of Pulmonary Medicine, Allergy and Immunology, Department of Pediatrics

institute: Children’s Hospital of Pittsburgh of UPMC

description: B16-tumor infiltrating CD45+ cells

data_processing:
10X Genomics Cell Ranger v1.3
Gene-cell UMI matrix was generated for downstream analyses, which was filtered such that only the cells expressing at least 500 genes, including gene Ptprc (encoding CD45), were retrieved for data normalization and Log2 transformation.
A total of 1491 genes after filtering were used for the PCA analysis.
Genome_build: mm10
Supplementary_files_format_and_content: for each sample, there are one mtx file with filtered gene expressing UMI counts for each sample; a tsv file containing gene names; a tsv file with cell barcodes.

source_name: B16-tumor infiltrating CD45+ cells

growth_protocol: Cell were isolated directly ex vivo and immediately subjected to cDNA and library generation

extract_protocol:
Freshly sorted CD45+ cells from B16 tumors implanted in Foxp3Cre-YFP or Nrp1L/LFoxp3Cre-YFP mice (female, 5 week of age) on day 14 post inoculation were re-suspended in 1xPBS containing 0.04% BSA. Precisely 2,600 cells were mixed with reverse transcription master mix, gel beads and partition oil were loaded on the GemCode Single-Cell Instrument to generate single-cell gel-beads in emulsion (GEMs). The reaction mixture/emulsion was removed from the Chromium instrument, and reverse transcription performed, followed by the Dynabead cDNAs clean up and amplification (14 cycles).
cDNAs were sheared (Covaris) into ~ 200 bp length. DNA fragment ends were repaired, A-tailed and adaptors ligated. The library was quantified using KAPA Universal Library Quantification Kit (KK4824) and further characterized for cDNA length on a Bioanalyzer using a High Sensitivity DNA kit.

treatment_protocol: No in vitro treatment

value: B16 tumor

tag: genotype


title: Tumor_NRP1

description: B16-tumor infiltrating CD45+ cells


title: UACC-C204-B


title: UACC-C204-A


title: siNipbl, biological rep2

value: Cells transfected  with siNipbl RNA


title: esiBrd4, biological rep1


title: UACC-C182-B


title: UACC-C183-A


title: UACC-C183-B


title: UACC-C182-A


title: UACC_DMSO

value: DMSO


title: UACC-DPA-B


title: siNipbl, biological rep1


title: siControl, biological rep1

value: Cells transfected with siControl RNA


title: siControl, biological rep2

value: Cells transfected  with siControl RNA


title: input DNA

data_processing:
The ChIP-Seq reads were aligned using align function from Rsubread53 v.1.28.1 bioconductor package, to map reads to the mm9 mouse reference genome, using TH1=2 and unique=TRUE parameters. The downstream analysis was performed on bam files with duplicates removed using the samtools54 v.0.1.19 rmdup command. MACS258 version 2.1.1 was used to call NIPBL narrow peaks against input with a cutoff of -log10(q-value) = 15 and mfold = 5.
Genome_build: mm9 mouse reference genome
Supplementary_files_format_and_content: bigwig format. Tag density data

extract_protocol:
Nuclei were isolated using lysis buffer 1 [5 mM Pipes pH 8, 85Mm KCl, 0.5% NP40, complete protease inhibitor cocktail (Roche)] and were lysed using lysis buffer 2 [1% SDS, 10 mM EDTA, 50 mM Tris-HCl pH 8.1, complete protease inhibitor cocktail (Roche)]. Chromatin was sheared into an average size of 500 pb by 8 30s pulses (30s pause between pulses) for P19 cells at 4º C in the waterbath sonicator Bioruptor (Diagenode, Liège, Belgium). 30 µg of chromatin from P19 cells, were incubated overnight at 4º C in rotation diluted 1:10 in IP buffer [0.01% SDS, 1.1% Triton X-100, 1.2 mM EDTA, 16.7 mM Tris-HCl pH 8.1, 167 mM NaCl] and with 3 µg of anti-NIPBL (A301-779A, Bethyl Laboratories, Inc.). IPs were incubated for 2h at 4º C in rotation with protein A or G Dynabeads (Invitrogen) for rabbit or mouse antibodies, respectively, and then washed with wash buffer 1 (0.1% SDS, 1% Triton X-100, 2 mM EDTA, 20 mM Tris-HCl pH 8.1, 150 mM NaCl), wash buffer 2 (0.1% SDS, 1% Triton X-100, 2 mM EDTA, 20 mM Tris-HCl pH 8.1, 500 mM NaCl), wash buffer 3 (0.25 M LiCl, 1% NP40, 1% sodium deoxycholate, 1 mM EDTA, 10 mM Tris-HCl pH 8.1), and twice with TE buffer (10 mM Tris-HCl pH 8.0, 1 mM EDTA). The complexes were eluted from the beads with elution buffer (1% SDS in TE buffer) by incubating twice 10 min at 65º C. The eluates and the inputs (3 or 1 µg of chromatin from P19 cells or human fibroblasts, respectively) were incubated overnight at 65º C for de-crosslinking. All the samples were treated with proteinase K (Roche) for 1h at 37ºC and purified using the ChIP DNA Clean and & Concentrator kit (Zymo Research, Irvine, CA, USA).
Libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit

treatment_protocol: Cell growing under normal conditions. No treatment was applied.

value: Normal proliferation

tag: chip antibody


title: Mouse 2 Skin Nfil3(GFP)posKlrg1pos Treg

city: Mainz

first: Michael

last: Delacher

state: Rhineland-Palatinate

address: Langenbeckstrasse 1

department: Institute for Immunology

institute: University Medical Center of the Johannes Gutenberg-University Mainz

description:
scTCR-sequencing
clonotypes_summary.tsv, consensus_summary.tsv, metric_summary.tsv
Skin tisTregST2 (mouse2)

data_processing:
Fastq files were processed using Cell Ranger (version 2.2.0) based on 10xGenomics provided mm10 reference genome (refdata-cellranger-vdj-GRCm38-alts-ensembl-2.2.0). Clones were matched by TRA and TRB sequence and clonal diversity was estimated using the inverse Simpson index. Samples from each mouse were compared in a pairwise fashion using the Jaccard index. Clonal abundance pie charts were generated using ggplot2 (version 2.2.1) and R (version 3.4.2). R1 fastq is technical, R2 fastq biological. R1 is built with partial Illumina Read 1 sequence (22nucleotides) followed by 10x barcode (16 nucleotides) followed by UMI (10 nucleotides) and switch oligo (13 nucleotides).
Genome_build: mm10

source_name: skin

growth_protocol: Mice were housed at DKFZ or UKR central animal facility

extract_protocol: Samples for scTCR-seq were loaded on the Chromium Single cell Controller using the Single Cell 5’ Library & Gel Bead Kit (10x Genomics #1000014) and the Single Cell V(D)J Enrichment Kit, Mouse T Cell (10x Genomics #1000071). TCR samples were sequenced on an Illumina NextSeq 500 with 300 cycles paired-end sequencing.

treatment_protocol: For scTCR-seq, we sorted 15000 (mouse 1) and 15000 (mouse 2) spleen CD25+Klrg1-Nfil3(GFP)- Treg, 15000 (mouse 1) and 15000 (mouse 2) spleen CD25+Klrg1-Nfil3(GFP)+ Treg, 8000 (mouse 1) and 15000 (mouse 2) spleen CD25+Klrg1+Nfil3(GFP)+ Treg, 3000 (mouse 1) and 15000 (mouse 2) skin CD25+Nfil3(GFP)+ Treg, 3000 (mouse 1) and 15000 (mouse 2) skin CD25+Nfil3(GFP)+ Treg, and 3000 (mouse 1) and 15000 (mouse 2) skin CD25+Nfil3(GFP)+ Treg. Samples were sorted from single male Nfil3(GFP) animals.

value: Skin

value: Nfil3(GFP)positive Klrg1positive


title: Mouse 2 Fat Nfil3(GFP)posKlrg1pos Treg

description:
scTCR-sequencing
clonotypes_summary.tsv, consensus_summary.tsv, metric_summary.tsv
Fat tisTregST2 (mouse2)

source_name: fat

value: Fat


title: Mouse 2 Colon Nfil3(GFP)posKlrg1pos Treg

description:
scTCR-sequencing
clonotypes_summary.tsv, consensus_summary.tsv, metric_summary.tsv
Colon tisTregST2 (mouse2)

source_name: colon

value: Colon


title: MCF10A_HER2_0.5KPa_siAS

city: Padova

first: Silvio

last: Bicciato

address: via U. Bassi 59/b

department: Molecular Medicine

country: Italy

institute: University of Padova

data_processing:
Raw reads were aligned using STAR (Dobin et al., 2013) version 2.5.3a to build version hg19 of the human genome.
Counts for UCSC annotated genes were calculated from the aligned reads using featureCounts function of the Rsubread R package (Liao et al., 2014).
Normalization and differential analysis were carried out using edgeR package (Robinson et al., 2010).
Genome_build: hg19
Supplementary_files_format_and_content: Expression matrix of raw counts for each sample

source_name: MCF10A human breast epithelial cell line

growth_protocol: Cells were cultured in DMEM/F12 (Gibco) with 5% horse serum, glutamine and antibiotics, freshly supplemented with insulin (Sigma-Aldrich), EGF (Peprotech), hydrocortisone (Sigma-Aldrich) and cholera toxin (Sigma-Aldrich).

extract_protocol:
Cells were harvested by the RNeasy Mini Kit (Qiagen) for total RNA extraction and contaminant DNA was removed by the RNase-Free DNase Set (Qiagen).
RNA-seq libraries for deep-sequencing were prepared with the Illumina TruSeq Standard Total RNA with Ribo-Zero GOLD kit.

treatment_protocol: MCF10A cells were  transducted with retroviral constructs (pBABEpuro-HER2-CAV659E or pBABEpuro). siRNA transfections were done with Lipofectamine RNAi-MAX (Thermo Fisher Scientific) in antibiotics-free medium according to the manufacturer’s instructions.

tag: transduction

tag: substrate

value: 0.5 Kpa PAAm hydrogel

tag: transfection

value: Control siRNA


title: MCF10A_HER2_plastic_siYT1

value: plastic

value: YAP/TAZ siRNA #1


title: MCF10A_HER2_plastic_siYT3

value: YAP/TAZ siRNA #3


title: MCF10A_empty_0.5KPa_siAS

value: empty


title: MCF10A_empty_plastic_siYT1


title: Mouse 2 Spleen Nfil3(GFP)posKlrg1neg Treg

description:
scTCR-sequencing
clonotypes_summary.tsv, consensus_summary.tsv, metric_summary.tsv
Spleen tisTregST2 progenitor (mouse2)

source_name: spleen

value: Spleen

value: Nfil3(GFP)positive Klrg1negative


title: Mouse 1 Colon Nfil3(GFP)posKlrg1pos Treg

description:
scTCR-sequencing
clonotypes_summary.tsv, consensus_summary.tsv, metric_summary.tsv
Colon tisTregST2 (mouse1)


title: MCF10A_empty_plastic_siAS_repB


title: Mouse 2 Spleen Nfil3(GFP)negKlrg1neg Treg

description:
scTCR-sequencing
clonotypes_summary.tsv, consensus_summary.tsv, metric_summary.tsv
Spleen DN Treg (mouse2)

value: Nfil3(GFP)negative Klrg1negative


title: MCF10A_empty_plastic_siAS_repA


title: Mouse 1 Fat Nfil3(GFP)posKlrg1pos Treg

description:
scTCR-sequencing
clonotypes_summary.tsv, consensus_summary.tsv, metric_summary.tsv
Fat tisTregST2 (mouse1)


title: Mouse 1 Spleen Nfil3(GFP)posKlrg1neg Treg

description:
scTCR-sequencing
clonotypes_summary.tsv, consensus_summary.tsv, metric_summary.tsv
Spleen tisTregST2 progenitor (mouse1)


title: Mouse 1 Spleen Nfil3(GFP)posKlrg1pos Treg

description:
scTCR-sequencing
clonotypes_summary.tsv, consensus_summary.tsv, metric_summary.tsv
Spleen tisTregST2 (mouse1)


title: NIPBL_ChIPSeq

value: teratocarcinoma

value: anti-NIPBL (A301-779A Bethyl)