title: treatment 3 input


title: Pool-1ab

status: Public on May 18 2020

type: SRA

city: London

first: Davide

last: Zecchin

address: Gower Street

country: United Kingdom

institute: University College London

description: Please note that the raw (fastq) files uploaded here contain multiplexed data: The included README.txt file describes how the individual samples may be demultiplexed from each GEO sample.

library_source: genomic

data_processing:
Demultiplex each lane of sequencing using internal barcodes (nucleotides 1-6) & extract nuclotides 31-51 as the shRNA within the backone vector
Please see README.txt file for sample-barcode associations
Collapse reads to unique "tags" along with count of ocurrences of each tag in full file -- in-house software
Align tags to shRNA library using bwa 0.5.9, -n 4, -l 90, -k 4
Summarise number of reads mapping to each target, weighted by ocurrences of each tag - in-house code
Discard off-target reads (wrong pool or unmapped) and scale counts to maximum total reads aligned across all samples for that pool
Genome_build: MISSION Lentiplex Human Pooled shRNA library sequences (Sigma-Aldrich Cat. SHPH01)
Supplementary_files_format_and_content: _RawCounts.txt: tab delimited text file containing un-normalised counts of reads aligning to each feature

molecule: genomic DNA

organism: Homo sapiens

growth_protocol: MDA-MB-468 were grown in DMEM supplemented with 10% FBS and 1% pen/strep.

extract_protocol:
Genomic DNA was extracted and shRNA inserts were retrieved by PCR amplification
PCR primers contained Indexes and adaptors for deep sequencing: P5_Illuseq, P7 and barcodes.

treatment_protocol:
MDA-MB-468 cells were infected the whole-genome shRNA library, MISSION Lentiplex Pooled shRNA library from Sigma (SHPH01). The library was divided in 10 pools (treated individually) and the infection was done in triplicate.
Selected cells were treated with vehicle control, 250 nM AZD8186, 250 nM GDC0941 or 450 nM MK2206 for 12 days. One fraction of cells was frozen at time 0 (before drug treatment).

tag: cell line


title: treatment 1-1

city: Duarte

first: Haiqing

last: Li

state: CA

address: 1500 East Duarte Road

department: Department of Computational & Quantitative Medicine

country: USA

institute: Beckman Research Institute of City of Hope, Center for Informatics

data_processing:
Basecalls performed using CASAVA version 1.8
The ChiP-Seq sequence reads were mapped to Homo sapiens genome assembly GRCh37 (hg19) using open source DNA-seq alignment tool BWA version 0.7.15
only keep the high quality unique alignments using SAM Tag (XA:Z and SA:Z) as filter
remove the duplicated alignments caused by PCR duplication using SAMTools (ver 0.1.19) ; the unmapped reads and the reads that is not the primary alignment are also removed using SAMTools based on the alignment quality tag (-F 4 -F 256).
ChiP-Seq peak calling was performed using MACS2 (v2.1.2) with broad option to detect the H3K4me3 binding sites with FDR<0.005 cutoff.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files for ChIP-seq Peaks

source_name: Melanoma_glutamine supplemented diet

growth_protocol: Tumor TM00702 was purchased from The Jackson Lab and propagated in NSG mice. Briefly, tumors were sectioned into 5 mm^3 pieces, and engrafted subcutaneously in 5 weeks old NSG mice.

extract_protocol:
10 mg of frozen tumor tissue was used for ChIP and pull down using H3K4me3
ChIP-seq libraries were prepared with Kapa DNA HyperPrep Kit (Cat No. KK 8700, Kapa) according to the manufacturer's protocol; A 10 cycles of PCR was performed on 5-10 ng of immunoprecipitated DNA to produce the final sequencing library. The libraries were validated with the Agilent Bioanalyzer DNA High Sensitivity Kit and quantified with Qubit.

treatment_protocol: When tumor reached a volume of 50 mm^3, mice were placed in to 2 groups receiving either control or glutamine supplemented diet. Tumors were collected at the end of the study and used for pull down with HeK4me3 antibody and ChIP-seq analysis.

tag: tumor model

value: Melanoma PDX TM00702 model (Jackson Lab)

tag: chip antibody

value: H3K4me3 Millipore 17-614

tag: tissue

value: melanoma


title: S_ctrl_4

type: RNA

city: Derio

first: Ana

middle: Maria

last: Aransay

state: BIZKAIA

address: Parque tecnologico de Bizkaia, Building 801-A

department: Genome Analysis Platform

country: Spain

institute: CIC bioGUNE

description:
Healthy
S_ctrl_4

hyb_protocol: Standard, as recommended by illumina

scan_protocol: Standard, as recommended by illumina

data_processing: The data was preprocessed by Bioconductor lumi package (version 2.22.1). It was log2 transformed and quantile normalized. The normalized data table does not contain all the probes since the ones that do not follow the established criteria are filtered out. Only probes with a detection p-value lower than 0.01 in at least one sample are analzyed.

label: Biotin

molecule: total RNA

source_name: serum Evs

label_protocol: Whole-Genome Gene Expression DASL®HT Assay Guide (Part#15018210 Rev. D)

growth_protocol: NHC, H69, EGI and TFK cell lines were cultured in collagen-coated plates: NHC, H69 and EGI cells in FLASK media (as described in DOI: 10.1136/gutjnl-2013-305281) and TFK cells in DMEM/F12+Glutamax media suplemented with FBS10%

extract_protocol: RNA was extracted from the described samples by  using miRCURY RNA Isolation kit - Biofluids (EXIQON; ref #300112). Quality control was performed with 2100 Bioanalyzer.

tag: disease

value: Healthy


title: control 3-1

source_name: Melanoma _control


title: control 3-2


title: control 1-2


title: control 1 input


title: control 2-1


title: control 2 input


title: control 1-1


title: scRNA-seq_CTRL

city: Bruxelles

first: Cedric

last: Blanpain

address: 808, route de Lennik, CP 637

country: Belgium

institute: Université Libre de Bruxelles (ULB)

library_source: transcriptomic

data_processing:
Read Alignment - CellRanger (version 3.0.2)
Cell-cycle assignment - Scran (1.10.1)
UMAP dimensionality reduction - Seurat (3.0.1)
Normalization - Seurat (3.0.1)
Gene regulatory network analysis - SCENIC (0.9.9+2.gcaded79)
Genome_build: mm10-1.2.0
Supplementary_files_format_and_content: R Rds objects

organism: Mus musculus

source_name: dorsal skin interfollicular epidermal basal cells in CTRL

growth_protocol: Mouse colonies were maintained in a certified animal facility in accordance with the European guidelines.

extract_protocol:
To separate epidermis from dermis, the samples were incubated in HBSS (Gibco) 0,25% trypsin  (Gibco) at 4°C overnight. Epidermis was mechanical separated from the dermis with scalpel first and then by pipetting and trypsin was neutralized by adding DMEM medium (Gibco) supplemented with 2% Chelex Fetal Calf Serum (FCS). Samples were filtrated on 70 and 40µm filter (Falcon). Cells were incubated in 2% FCS/PBS with primary antibodies for 30 min on ice, protected from the light, with shaking every 10 min. Immunostaining for isolating basal IFE and infundibulum cells was performed using FITC-conugated anti-α6-integrin (clone GoH3; BD biosciences). CD34 staining was used to exclude bulge cells from the sorted cells (clone RAM34; BD Biosciences). Primary antibodies were washed with 2% FCS/PBS and cells incubated for 30 min in APC conjugated streptavidin (BD Biosciences), on ice, with shaking every 10 min. Living epidermal cells were gated by forward scatter, side scatter and negative staining for Hoechst dye. Basal cells from the interfollicular epidermis were targeted using CD34 negative and α6 integrin positive gating. Fluorescence-activated cell sorting analysis was performed using FACSAria I at high pressure (70 psi) and FACSDiva software (BD Biosciences). After sorting, 6000 cells were loaded onto each channel of the Chromium Single Cell 3’ microfluidic chips (V2-chemistry, PN-120232, 10X Genomics) and individually barcoded with a 10X Chromium controller according to the manufacturer’s recommendations (10X Genomics). RNA from the barcoded cells was reverse transcribed, followed by amplification, shearing 5′ adaptor and sample index attachment.
The libraries were prepared using the Chromium Single Cell 3’ Library Kit (V2-chemistry, PN-120233, 10X Genomics), quantified using a low coverage Illumina NextSeq 550 run and sequenced on an Illumina NovaSeq

treatment_protocol: For the stretching condition, mice were anesthetized (5% xylazine 10% ketamine in PBS) and the dorsal skin was disinfected with 10% Iso-Betadine (Meda Pharma), an incision was created in the most caudal part of the dorsal skin to minimize any tension in the wound as the expansion progressed and to maximise the distance from the access wound, to the location of the expander. A subcutaneous pocket was created with forceps and a 4ml Hemispher Self-inflating tissue expander (OsmedTM) was placed in the most rostral part under the dorsal skin in proximity of the neck. Stiches were used to close the subcutaneous pocket, to limit the hydrogel movement and to close the access incision.   All analyses were performed in the area on the top of the dome of the hemisphere induced by the skin expander, since this region experiences the highest strainFor TPA treatments, TPA (200 μl of 0.02 mg/ml solution in acetone) was administered daily to shaved mouse back skin for 2 days. To inhibit MEK1/2 activity, mice were treated with Trametinib 2mg per kg body weight by daily oral gavage. To inhibit MAL activity, mice received drug treatment via IP injection daily using 100mg CCG203971 (Cayman Chemical) per kg body weight for 2 or 4 days as indicated in the figures.

tag: strain

tag: treatment

value: no

tag: cell type


title: scRNA-seq_TPA

source_name: dorsal skin interfollicular epidermal basal cells under TPA treatment

value: tpa


title: scRNA-seq_EXPD1

source_name: dorsal skin interfollicular epidermal basal cells upon stretching at D1

value: stretching at D1


title: Male germ cells, E18.5.Tex15KO.rep2

city: Philadelphia

first: Yemin

last: Lan

state: PA

address: 3400 Civic Center Blvd

institute: University of Pennsylvania

description:
read_count_E18.5.txt
repeat_family_E18.5.txt

data_processing:
Sequenced reads were mapped to reference genome either in unique or multiple mapping mode.
The alignments in the unique mapping mode were used to evaluate expression of protein coding genes and individual repeats. For this, we used STAR for alignment with the default parameters. The annotation of genes and individual repeats were acquired from UCSC RefSeq annotation and RepeatMasker, separately. Number of reads mapping to genes and repeats were determined by using FeatureCount. Differential gene and repeat expression was determined by using edgeR, with a FDR cutoff of 5%.
The alignments in the multiple mapping mode were used to evaluate repeat families. Before alignment, adapters were trimmed and reads mapping to ribosomal RNA (GenBank identifiers: 18S NR_003278.3, 28S NR_003279.1, 5S D14832.1, 5.8S K01367.1) by up to three mismatches were discarded. We used Bowtie for alignment, keeping reads that map up to 10,000 sites. Each mapping read was assigned a score of 1/N, where N is the number of sites in the genome the read mapped to. Expression values for each repeat family was calculated by adding the scores contained within the repeat body, divided by the total million reads mapped and average length of repeats (kb) within the family. Differential expression for each repeat family was determined by simple t-test and FDR correction.
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files include raw read counts for each Sample ...

source_name: male germ cells

growth_protocol: Male germ cells were flow-sorted based on green fluorescence (Oct4-GFP).

extract_protocol:
RNA extraction by PicoPure RNA Isolation Kit (Cat# KIT0202) from ARCTURS
RNA-seq libraries were made by using Ovation RNA-Seq System V2 (Part No.7102) and Ovation Ultralow System V2 1-16 (Part No.0344) from NuGEN

tag: strain background

value: mixed

tag: age

value: embryonic day 18.5 (e18.5)

tag: Sex

value: male

value: germ cells

tag: isolation

value: GFP flow sorting

tag: genotype


title: scRNA-seq_EXPD4

source_name: dorsal skin interfollicular epidermal basal cells upon stretching at D4

value: stretching at D4


title: treatment 1-2


title: Male germ cells, E18.5.Tex15KO.rep3


title: control 2-2


title: Male germ cells, E18.5.Tex15HT.rep1


title: Male germ cells, E18.5.Tex15HT.rep2


title: Male germ cells, E18.5.Tex15HT.rep3


title: control 3 input


title: Male germ cells, E16.5.Tex15KO.rep3

description:
read_count_E16.5.txt
repeat_family_E16.5.txt

value: embryonic day 16.5 (e16.5)


title: Male germ cells, E16.5.Tex15KO.rep1


title: Male germ cells, E16.5.Tex15HT.rep3


title: Male germ cells, E16.5.Tex15KO.rep2


title: Male germ cells, E16.5.Tex15HT.rep2


title: Male germ cells, E16.5.Tex15HT.rep1


title: Male germ cells, D2.5.Tex15WT.rep3

description:
read_count_D2.5.txt
repeat_family_D2.5.txt

value: postnatal day 2 (d2.5)


title: Pool-8ab


title: Male germ cells, D2.5.Tex15KO.rep2


title: Male germ cells, D2.5.Tex15WT.rep2


title: Male germ cells, D2.5.Tex15KO.rep3


title: Male germ cells, E18.5.Tex15KO.rep1


title: Male germ cells, D2.5.Tex15HT.rep2


title: Male germ cells, Tex15WT-2.5d-9 (BS-seq)

data_processing:
Sequenced reads were mapped to mouse rRNA using BSMAP in order to exclude them.
Unmapped reads were mapped to reference genome using Bismark.
Methylation ratio were counted using MethylKit R package. CpG sites with 3X coverage per group were retained.
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text file includes coverage/methylated/unmethylated  counts of each CpG sites with 3X coverage per group for each sample.

extract_protocol:
DNA extraction was made with QIAamp DNA Micro Kit
Bisulfite DNA libraries were prepared using the Ovation Ultralow Methyl-Seq Library Systems (Part No. 0335).

treatment_protocol: About 10 ng DNA of germ cells from individual embryo or pup was subjected to bisulfite treatment. Unmethylated Lambda phage DNA (NEB) was spiked in at 0.5% input DNA to test bisulfite conversion efficiency.


title: Male germ cells, D2.5.Tex15HT.rep1


title: Male germ cells, Tex15WT-2.5d-8 (BS-seq)


title: Male germ cells, Tex15KO-2.5d-3 (BS-seq)


title: Male germ cells, Tex15HT-2.5d-18 (BS-seq)


title: Male germ cells, D2.5.Tex15KO.rep1


title: Male germ cells, D2.5.Tex15HT.rep3


title: treatment 2-1


title: S_ctrl_5

description:
Healthy
S_ctrl_5


title: Sox100B_Dam_rep3

city: Beijing

first: huanwei

last: huang

address: 7 Science Park Rd., ZGC life science park

country: China

institute: NIBS

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to BDGP6 genome using Bowtie v1.1.2 with -v 3 -m 1 parameters.
Genome_build: Ensemble Drosophila melanogaster BDGP6.
Supplementary_files_format_and_content: bigwig files were generated using Homer package.

organism: Drosophila melanogaster

extract_protocol:
Drosophila DamID was carried out according to iDamIDseq based on a method from Gutierrez-Triana JA et al.2016
Libraries were prepared for sequencing using standard Illumina protocols

tag: genotype/variation

value: Sox100B overexpression

value: adult stage day 2

value: midgut

value: intestinal stem cells


title: Male germ cells, Tex15HT-2.5d-7 (BS-seq)


title: Sox100B_Dam_rep1


title: Sox100B_Dam_rep2


title: Sox100B-IR-rep3

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to BDGP6 genome using STAR v020201 with default parameters
featureCounts v1.6.3 was run for calculating reads counts of genes and relative quantitation of expression. Differential genes expression was analyzed by DESeq2
Genome_build: Ensemble Drosophila melanogaster BDGP6
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample

extract_protocol:
Drosophila midgut were removed and digested using Elastase (Sigma, cat. no. E0258). About 10000 green fluorescent protein (GFP) labled cells were sorted using FACSAria II cell sorter (Becton Dickinson) and RNA was harvested using the  Arcturus PicoPure RNA isolation kit (Applied Biosystems). The RNA was then amplified using Arcturus RiboAmp HS PLUS RNA ampliﬁcation kit (Applied Biosystems).
RNA libraries were prepared for sequencing using standard Illumina protocols

value: adult stage day 3

value: intestinal progenitor cells


title: Ctrl_Dam_rep3

value: Wild type


title: Ctrl_Dam_rep2


title: ESG-rep5

source_name: Wild type_intestinal progenitor cells


title: Male germ cells, D2.5.Tex15WT.rep1


title: Ctrl_Dam_rep1


title: EE-rep1

source_name: Wild type_intestinal enteroendocrine cells

value: intestinal enteroendocrine cells


title: ESG-rep1


title: Sox100B-OE1-rep3

source_name: Sox100B overexpression_intestinal progenitor cells


title: Sox100B-OE1-rep2


title: C_11_04_1

city: La Jolla

first: Sheng

last: Zhong

state: California

address: 9500 Gilman Drive MC 0412

department: Bioengineering

institute: University of California, San Diego

data_processing:
Base-calling by bcl2fastq v2.20.0.422.
Sequencing data cleaning with Trimmomatic v0.36 and seqtk v1.2.
Reads alignment by STAR v2.5.4b.
UMI based de-duplication of aligned BAM files by in-house script.
Gene level read counts by featureCounts v1.6.1.
Calculate gene expression level in TPM.
Expression levels (TPM) of transposons were calculated by SalmonTE (version 0.4) with default parameters on UMI-deduplicated FASTQ files.
Genome_build: hg38 with Ensembl gene annotation release 84
Supplementary_files_format_and_content: gene TPM table of all the samples, TE TPM table of all the samples

source_name: plasma

extract_protocol:
Total extracellular RNA from plasma samples were extracted following SILVER-seq protocol
Sequencing libraries were constructed following SILVER-seq protocol

value: plasma

tag: sampling year

tag: donor id

tag: donor group

value: C

tag: donor age at death

tag: donor gender

value: F

tag: donor braak stage

tag: donor diagnosis year

tag: molecule subtype

value: extracellular RNA


title: C_11_01_1

tag: tissue


title: C_11_09_1


title: Sox100B-IR-rep1


title: Sox100B-OE1-rep1


title: ESG-rep3


title: Male germ cells, Tex15KO-2.5d-16 (BS-seq)

value: mixed

value: male

value: germ cells


title: ESG-rep4


title: C_10_10_1


title: C_10_08_1


title: EE-rep3


title: C_10_03_1


title: C_9_07_1


title: C_9_05_1


title: C_9_10_1


title: C_11_03_1


title: C_10_14_1


title: C_10_13_1


title: EE-rep2


title: C_8_00_1

value: M


title: C_10_05_1


title: C_7_00_1


title: WT

city: Nanchang

first: Yi

last: Sang

state: Jiangxi

address: No.128,Xiangshan North Road

institute: Nanchang University

description: WT

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to Homo_sapiens.GRCh37 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Genome_build: Alignment was initially to the transcriptome (hg19, GRCh37.72), and then to the genome (hg19, GRCh37).
Supplementary_files_format_and_content: raw read count

source_name: nasopharyngeal carcinoma cell lines

growth_protocol: 10% FBS in DMEM

extract_protocol:
RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
Libraries were prepared according to Illumina's instructions

value: nasopharyngeal carcinoma cell lines

tag: passages

tag: cell line

value: WT


title: C_7_01_1


title: C_7_04_1


title: S_UC_12

description:
UC
S_UC_12

tag: disease

value: Ulcerative Colitis


title: Sox100B-IR-rep2

tag: age

value: midgut

tag: cell type


title: ESG-rep2


title: C_6_12_1


title: C_8_04_1


title: C_10_01_1


title: C_9_00_1


title: C_8_06_1


title: C_6_06_1


title: C_5_05_1


title: C_8_01_1


title: TPA_2: Tpa treated basal cells Biological rep2

address: route de Lennik, 808

institute: Université Libre De Bruxelles

description: Gene expression data from basal cells of the interfollicular epidermis

hyb_protocol: Affymetrix MG-430 PM array strips were hybridized with 8 mg of labeled cDNA, washed, stained and scanned according to the protocol described in GeneAtlas 3’IVT express kit User Manual.

scan_protocol: Arrays were scanned with GeneAtlasImaging station scanner (Affymetrix, Santa Clara, CA)

data_processing: Normalized expression signals were calculated from Affymetrix CEL files using RMA algorithm (Irizarry et al., 2003)

source_name: Back skin inetrfollicular epidermis

label_protocol: cDNA was labeled using GeneChip Mapping 250K Nsp Assay Kit (Affymetrix; catalog # 900766), according to manufacturer's instructions.

extract_protocol: RNA isolation and cDNA amplification was performed as described by Gonzalez-Roca et al. (2010).In brief, 300 cells were sorted into lysis buffer and RNA was purified using magnetic beads (RNAClean XP beads, Agencourt).RNA was reverse transcribed and cDNA was amplified using Whole Transcriptome Amplification chemistry (WTA2, Sigma Aldrich). For monitoring amplification, SYBR Green was added to the reaction; it was stopped after 25 cycles when SYBR Green signal reached a plateau. cDNA was purified using Genelute PCR Clean-Up kit (Sigma Aldrich).

treatment_protocol: To separate epidermis from dermis, the samples were incubated in HBSS (Gibco) 0,25% trypsin  (Gibco) at 4°C overnight. Epidermis was mechanical separated from the dermis with scalpel first and then by pipetting and trypsin was neutralized by adding DMEM medium (Gibco) supplemented with 2% Chelex Fetal Calf Serum (FCS). Samples were filtrated on 70 and 40µm filter (Falcon). Cells were incubated in 2% FCS/PBS with primary antibodies for 30 min on ice, protected from the light, with shaking every 10 min. Immunostaining for isolating basal IFE and infundibulum cells was performed using FITC-conugated anti-α6-integrin (clone GoH3; BD biosciences). CD34 staining was used to exclude bulge cells from the sorted cells (clone RAM34; BD Biosciences). Primary antibodies were washed with 2% FCS/PBS and cells incubated for 30 min in APC conjugated streptavidin (BD Biosciences), on ice, with shaking every 10 min. Living epidermal cells were gated by forward scatter, side scatter and negative staining for Hoechst dye. Basal cells from the interfollicular epidermis were targeted using CD34 negative and α6 integrin positive gating. Fluorescence-activated cell sorting analysis was performed using FACSAria I at high pressure (70 psi) and FACSDiva software (BD Biosciences).

value: Back skin inetrfollicular epidermis

tag: treatment

value: tpa


title: C_6_13_1


title: C_7_08_1


title: C_5_02_1


title: C_6_08_1


title: T47D_Both_rep1_RNAseq

city: San Antonio

first: Zhijie

middle: Jason

last: Liu

state: TEXAS

address: 7703 Floyd Curl Drive

department: Department of Molecular Medicine

institute: Universality of Texas Health Science Center at San Antonio

data_processing:
Basecalls were performed using Illumina Casava software.
Reads were aligned to hg19 genome assembly using STAR 2.5.2b. Refseq transcripts were supplied in GTF format file.
featureCounts package was used to count the uniquely mapped reads in union mode.
Differentially expressed genes were detected by DESeq2 with FDR thresold 0.05
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include reads counts for each Sample

source_name: breast cancer cells

growth_protocol: T47D cells were maintained in RPMI/1640 supplemented with 10% heat-inactivated FBS (Sigma) and 1% penicillin-streptomycin (P/S).  All cells were kept at 37 °C in a humified incubator with 5% CO2. The hormone-independent HBCx-124 ED PDX was established from a HBCx-124 xenograft that escaped after 3 months of estrogen deprivation (ED).

extract_protocol:
Total RNA was extracted by RNeasy Mini Kit from Qiagen(Cat no 74106).
RNA-seq library were prepared by the KAPA mRNA HyperPrep Kit (KK8580), according to the manufacturer’s instructions.

treatment_protocol: For knockdown of GATA3, T47D cells were infected with shRNA lentiviruses and selected by puromycin (1 μg/ml) for 3 days to establish GATA3 knockdown T47D stable cell lines. For the Dox-inducible JUN-overexpressing cell lines, JUN cDNAs (Open Biosystems) were cloned into the pInducer 20 destination vector (Meerbrey et al., 2011) using the Gateway system (Invitrogen). Lentivirus was produced in 293T cells and used to infect cells in media containing polybrene (8 μg/ml). Cells were selected for 4 days by 500 μg/mL G418 (Invitrogen) after virus infection to get inducible overexperssion stable lines. To induce JUN protein expression, 1 μg/ml doxycycline was added into culture media for about 48 h before collection for experiments. For knockdown of GATA3 and overexpression of JUN in T47D cells at the same time, Dox-inducible JUN-overexpressing T47D stable cell line was further infected with shGATA3 lentiviruses and selected by puromycin (1 μg/ml) for 24 h, then 1 μg/ml doxycycline was added into culture media to induce JUN overexpression for about 48 h before collection for experiments.

value: GATA3 shRNA (sh9301) for T47D cells with DOX-inducible expression of JUN-with DOX treatment

tag: growth medium

value: Full media


title: T47D_Both_rep2_RNAseq


title: EXPD4_1: Expanded basal cells Biological rep1

value: tissue stretching


title: TPA_1: Tpa treated basal cells Biological rep1


title: C_4_05_1

value: plasma


title: C_5_01_1

value: C


title: C_4_07_1

value: F


title: T47D_oeJUN_rep2_RNAseq

value: Control shRNA (scramble) for T47D cells with DOX-inducible expression of JUN-with DOX treatment


title: C_8_03_1

value: extracellular RNA


title: T47D_Ctrl_rep2_RNAseq

value: Control shRNA (scramble) for T47D cells with DOX-inducible expression of JUN-without DOX treatment


title: CTRL_1: Control basal cells Biological rep1


title: C_4_03_1


title: EXPD4_3: Expanded basal cells Biological rep3


title: T47D_shGATA3_rep2_RNAseq

value: GATA3 shRNA (sh9301) for T47D cells with DOX-inducible expression of JUN-without DOX treatment


title: T47D_shGATA3_rep1_RNAseq


title: T47D_Ctrl_rep1_RNAseq


title: CTRL_3: Control basal cells Biological rep3


title: C_3_06_1


title: EXPD4_2: Expanded basal cells Biological rep2


title: C_2_11_1

value: M


title: CTRL_2: Control basal cells Biological rep2


title: C_3_02_1


title: HBCX124_ED_rep2_RNAseq

value: PDX

value: Estrogen deprivation


title: C_3_04_1


title: HBCX124_ctrl_rep2_RNAseq

value: Estrogen supplementation


title: C_2_07_1


title: C_2_12_1


title: C_2_10_1


title: HBCX124_ED_rep1_RNAseq


title: C_1_12_1


title: C_1_11_1


title: HBCX124_ctrl_rep1_RNAseq


title: T47D_shGATA3_GROseq

description: Nascent RNA

data_processing:
Library strategy: GRO-seq
Basecalls performed using Illuminal CASAVA software.
GRO-seq reads were aligned to human genome (hg19) using bowtie with “--best --strata –m 1 –v 2” parameters. Duplicated reads were eliminated for subsequent analysis.
To balance the clonal amplification bias and total useful reads, only at most three reads was allowed for each unique genomic position.
edgeR 3.16.5 was used to call the differential eRNAs.
Genome_build: hg19
Supplementary_files_format_and_content: bigWig

growth_protocol: T47D cells were maintained in RPMI/1640 supplemented with 10% heat-inactivated FBS (Sigma) and 1% penicillin-streptomycin (P/S). All cells were kept at 37 °C in a humified incubator with 5% CO2.

extract_protocol:
Cells were subjected to nuclear run-on for 5minutes at 30°C with BrU labeling. The run-on RNAs were pull down by BrU beads and subjected to library preparation for deep sequencing.
We followed a previous published protocol (Ingolia et al., 2009 Science; Wang et al., 2011 Nature). Briefly, the run-on RNA were first added with a polyA tracts by RNA polyA polymerase. This polyA tail enables the run-on RNA to be reverse transcribed into single strand cDNA by Reverse Transcriptase. The cDNA was circularized by CircLigase (Epicentre) and re-linearized by APE I, subsequently subjected to PCR amplification and deep sequencing.


title: T47D_oeJUN_rep1_RNAseq


title: T47D_oeJUN_GROseq

description: Nascent RNA


title: C_1_08_1


title: C_1_04_1


title: T47D_ctrl_GROseq

description: Nascent RNA


title: T47D_both_GROseq

description: Nascent RNA


title: AD_15_06_1

value: AD


title: AD_15_03_1


title: C_1_03_1


title: ZR75_Both_K27ac_Chipseq

data_processing:
Basecalls performed using Illuminal CASAVA software.
ChIP-seq reads were aligned to the hg19 genome assembly using bowtie v1.1.2 with only uniquely mapped reads retained.
Peaks were called using MACS2 with q-value less than 1e-5. The peaks overlapped with the blacklist regions downloaded from UCSC were removed
Genome_build: hg19
Supplementary_files_format_and_content: bigWig file

growth_protocol: T47D and ZR75-1 cells were maintained in RPMI/1640 supplemented with 10% heat-inactivated FBS (Sigma) and 1% penicillin-streptomycin (P/S). All cells were kept at 37 °C in a humified incubator with 5% CO2.

extract_protocol:
Lysates were clarified from sonicated nuclei and protein-DNA complexes were isolated with antibody.
The extracted ChIP DNA was ligated to specific adaptors using  KAPA Hyper Prep Kit (KK8504), according to the manufacturer’s instructions.

treatment_protocol: For knockdown of GATA3, T47D or ZR75-1 cells were infected with shRNA lentiviruses and selected by puromycin (1 μg/ml) for 3 days to establish GATA3 knockdown T47D or ZR75-1 stable cell lines. For the Dox-inducible JUN-overexpressing cell lines, JUN cDNAs (Open Biosystems) were cloned into the pInducer 20 destination vector (Meerbrey et al., 2011) using the Gateway system (Invitrogen). Lentivirus was produced in 293T cells and used to infect cells in media containing polybrene (8 μg/ml). Cells were selected for 4 days by 500 μg/mL G418 (Invitrogen) after virus infection to get inducible overexperssion stable lines. To induce JUN protein expression, 1 μg/ml doxycycline was added into culture media for about 48 h before collection for experiments. For knockdown of GATA3 and overexpression of JUN in T47D or ZR75-1 cells at the same time, Dox-inducible JUN-overexpressing T47D or ZR75-1 stable cell line was further infected with shGATA3 lentiviruses and selected by puromycin (1 μg/ml) for 24 h, then 1 μg/ml doxycycline was added into culture media to induce JUN overexpression for about 48 h before collection for experiments.

value: GATA3 shRNA (sh9301) for ZR75-1 cells with DOX-inducible expression of JUN-with DOX treatment

tag: chip antibody

value: H3K27ac(Abcam, ab4729)


title: ZR75_shGATA3_K27ac_Chipseq

value: GATA3 shRNA (sh9301) for ZR75-1 cells with DOX-inducible expression of JUN-without DOX treatment


title: C_1_01_1

tag: sampling year


title: T47D_shGATA3_K27ac_Chipseq

tag: treatment GATA3 shRNA (sh9301) for T47D cells with DOX-inducible expression of JUN-without DOX treatment

value: Full media


title: ZR75_oeJUN_K27ac_Chipseq

value: Control shRNA (scramble) for ZR75-1 cells with DOX-inducible expression of JUN-with DOX treatment


title: T47D_oeJUN_K27ac_Chipseq


title: ZR75_Ctrl_K27ac_Chipseq

value: Control shRNA (scramble) for ZR75-1 cells with DOX-inducible expression of JUN-without DOX treatment


title: T47D_Both_K27ac_Chipseq

value: GATA3 shRNA (sh9301) for T47D cells with DOX-inducible expression of JUN-with DOX treatment


title: T47D_Ctrl_K27ac_Chipseq


title: AD_14_14_1

value: plasma

tag: donor id

tag: donor group

value: F


title: AD_15_00_1

tag: donor age at death

tag: donor gender

value: extracellular RNA


title: T47D_Both_ATACseq

description: GATA3 shRNA (sh9301) for T47D cells with DOX-inducible expression of JUN-with DOX treatment

data_processing:
Basecalls performed using Illuminal CASAVA software.
The adaptor was removed by using cutadapt v1.11 with parameters "-m 20 -e 0.1". The clean reads were aligned to the hg19 genome assembly using bowtie2 v2.2.9 with parameters "-mm --very-sensitive --no-discordant -X 2000", and only primary alignments were retained. The alignments were shifted with +4 for plus strand and -5 for minus strand.
Peaks were called using MACS2 with q-value less than 1e-5. The peaks overlapped with the blacklist regions downloaded from UCSC were removed
Genome_build: hg19
Supplementary_files_format_and_content: bigWig file

growth_protocol: MCF7 and T47D parental cells were maintained in RPMI/1640 supplemented with 10% heat-inactivated FBS (Sigma) and 1% penicillin-streptomycin (P/S). The TamR cells were kept in phenol-red free RPMI/1640 medium supplemented with 10% heat-inactivated charcoal-stripped-FBS and 1% P/S with the addition of 100 nM 4-hydroxytamoxifen (4-OHT, H7904, Sigma). All cells were kept at 37 °C in a humified incubator with 5% CO2.

extract_protocol: 50,000 cells were harvested for each condition. After purification of nuclei, transposition was performed with Tn5 transposase from Nextera DNA Library Prep Kit (Illumina, catalog # FC-121-1030). ATAC-seq library prep was performed as in Buenrostro et al, 2015. Libraries were sequenced  with Mid 75bp PE on Illumina NextSeq 500 (4 samples in one lane).


title: AD_15_04_1

tag: donor braak stage

tag: donor diagnosis year


title: T47D_Ctrl_ATACseq

description: Control shRNA (scramble) for T47D cells with DOX-inducible expression of JUN-without DOX treatment


title: AD_14_07_1

tag: tissue

tag: molecule subtype


title: AD_14_03_1


title: AD_14_01_1


title: C_5_07_1

value: C


title: AD_14_13_1


title: AD_14_05_1


title: AD_14_00_1


title: AD_15_01_1


title: MCF7R_ATACseq

description: MCF7 resistant cells_full media_ATAC-seq

tag: cell line

tag: growth protocol

value: resistant cell


title: AD_13_04_1


title: AD_13_06_1


title: T47DP_ATACseq

description: T47D parental cells_full media_ATAC-seq

value: control (parental cell)


title: MCF7P_ATACseq

description: MCF7 parental cells_full media_ATAC-seq


title: T47D_shGATA3_ATACseq

description: GATA3 shRNA (sh9301) for T47D cells with DOX-inducible expression of JUN-without DOX treatment


title: AD_14_10_1


title: TamR_rep4_RNAseq

data_processing:
Basecalls were performed using Illumina Casava software.
Reads were aligned to hg19 genome assembly using STAR 2.5.2b. Refseq transcripts were supplied in GTF format file.
featureCounts package was used to count the uniquely mapped reads in union mode.
Differentially expressed genes were detected by DESeq2 with FDR thresold 0.05
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text file includes reads counts for each Sample

growth_protocol: MCF7 parental cells were maintained in RPMI/1640 supplemented with 10% heat-inactivated FBS (Sigma) and 1% penicillin-streptomycin (P/S). The TamR cells were kept in phenol-red free RPMI/1640 medium supplemented with 10% heat-inactivated charcoal-stripped-FBS and 1% P/S with the addition of 100 nM 4-hydroxytamoxifen (4-OHT, H7904, Sigma). All cells were kept at 37 °C in a humified incubator with 5% CO2.

extract_protocol:
Total RNA was extracted by RNeasy Mini Kit from Qiagen(Cat no 74106).
RNA-seq library were prepared by the KAPA RNA HyperPrep Kits with RiboErase (KK8560) or KAPA mRNA HyperPrep Kit (KK8580), according to the manufacturer’s instructions.

treatment_protocol: For knockdown of GATA3 or JUN, MCF7 parental or TamR cells were infected with shRNA lentiviruses and selected by puromycin (1 μg/ml) for 3 days to establish GATA3 knockdown MCF7 parental or JUN knockdown TamR stable cell lines. For the Dox-inducible GATA3, JUN-overexpressing cell lines, GATA3 and JUN cDNAs (Open Biosystems) were cloned into the pInducer 20 destination vector (Meerbrey et al., 2011) using the Gateway system (Invitrogen). Lentivirus was produced in 293T cells and used to infect cells in media containing polybrene (8 μg/ml). Cells were selected for 4 days by 500 μg/mL G418 (Invitrogen) after virus infection to get inducible overexperssion stable lines. To induce GATA3 or JUN protein expression, 1 μg/ml doxycycline was added into culture media for about 48 h before collection for experiments. For knockdown of GATA3 and overexpression of JUN in MCF7 parental cells at the same time, Dox-inducible JUN-overexpressing MCF7 parental stable cell line was further infected with shGATA3 lentiviruses and selected by puromycin (1 μg/ml) for 24 h, then 1 μg/ml doxycycline was added into culture media to induce JUN overexpression for about 48 h before collection for experiments.

value: TamR

value: TamR as a reference


title: C_2_09_1

value: M


title: TamR_rep3_RNAseq


title: MCF7_shGATA3_Dox_rep2_RNAseq

value: GATA3 shRNA (sh9301) for MCF7 parental cells with DOX-inducible expression of JUN-with DOX treatment


title: T47DR_ATACseq

description: T47D resistant cells_full media_ATAC-seq


title: AD_13_00_1

value: AD


title: T47D_oeJUN_ATACseq

description: Control shRNA (scramble) for T47D cells with DOX-inducible expression of JUN-with DOX treatment


title: AD_12_03_1


title: MCF7_shGATA3_Dox_rep1_RNAseq


title: MCF7_shGATA3_noDox_rep2_RNAseq

value: GATA3 shRNA (sh9301) for MCF7 parental cells with DOX-inducible expression of JUN-without DOX treatment


title: MCF7_shGATA3_noDox_rep1_RNAseq


title: AD_12_02_1


title: AD_11_08_1


title: MCF7_shCtrl_Dox_rep1_RNAseq

value: Control shRNA (scramble) for MCF7 parental cells with DOX-inducible expression of JUN-with DOX treatment


title: AD_11_04_1


title: MCF7_shCtrl_noDox_rep2_RNAseq

value: Control shRNA (scramble) for MCF7 parental cells with DOX-inducible expression of JUN-without DOX treatment

value: Full media


title: AD_11_03_1


title: AD_11_10_1


title: MCF7_shCtrl_Dox_rep2_RNAseq


title: AD_11_02_1


title: AD_10_10_1


title: AD_12_07_1


title: AD_13_03_1


title: AD_12_05_1


title: TamR_shJUN_rep2_RNAseq

value: TamR cells were infected with JUN shRNA(sh9591)


title: MCF7_Dox_rep1_RNAseq

value: MCF7 parental cells with DOX-inducible expression of JUN-with DOX treatment


title: AD_10_06_1

value: plasma


title: MCF7_Dox_rep2_RNAseq


title: MCF7_noDox_rep2_RNAseq

value: MCF7 parental cells with DOX-inducible expression of JUN-without DOX treatment


title: AD_9_06_1

value: F

value: extracellular RNA


title: AD_10_04_1


title: MCF7_noDox_rep1_RNAseq


title: AD_9_09_1


title: AD_8_12_1


title: MCF7_shCtrl_noDox_rep1_RNAseq


title: TamR_shJUN_rep1_RNAseq


title: AD_9_04_1


title: AD_8_09_1


title: AD_8_07_1


title: TamR_shCtrl_rep1_RNAseq

value: TamR cells were infected with Control shRNA (scramble)


title: AD_8_05_1


title: AD_8_11_1


title: AD_10_09_1


title: MCF7_shGATA3_rep2_RNAseq

value: control (parental cell)

value: MCF7 cells were infected with GATA3 shRNA(sh9301)


title: AD_7_12_1


title: MCF7_shGATA3_rep1_RNAseq


title: AD_7_09_1


title: MCF7_shCtrl_rep2_RNAseq

value: MCF7 cells were infected with Control shRNA (scramble)


title: AD_7_06_1

value: M


title: AD_7_08_1


title: T2DM with CVD dVSMC3

city: Basel

first: Filip

last: Roudnicky

state: Basel

address: Grenzacherstrasse 124

department: Chemical Biology

country: Switzerland

institute: F.Hoffmann-La Roche Ltd

description: RNA from cellular lysate

hyb_protocol: Samples were hybridized using Affymetrix hybridization kit materials using standard Affymetrix protocol

scan_protocol: Affymetrix Gene ChIP Scanner

data_processing:
Generated CEL files were imported into Partek Genomics Suite software.6.6 for subsequent analysis.
HuGene-2_0-st

source_name: With cardiovascular disease

label_protocol: Samples were enzymatically fragmented and biotinylated following the standard Affymetrix protocol

growth_protocol: iPSCs were plated at a density of 47,000-67,000 cells cm-2 in mTeSR1 with 10 μM Y-27632 dihydrochloride. On day one, mesoderm induction medium was added, consisting of N2B27 medium (1:1 mixture of DMEM:F12 (1:1) with Glutamax and Neurobasal media supplemented with N2 and B27: all Life Technologies), 8 μM CHIR99021 (Cayman Chem) and 25 ng ml-1 Bone morphogenetic protein (BMP) 4 (R&D Systems). On day four and five, medium was replaced with EC induction medium consisting of StemPro 34 SFM medium (Life Technologies), 200 ng ml-1 Vascular endothelial growth factor (VEGF) (Aldevron) and 2 μM forskolin (Sigma-Aldrich). On day six of differentiation, ECs were AutoMACS-enriched using CD144 MicroBeads (Miltenyi Biotec). CD 144+ cells were re-plated on human fibronectin (Sigma-Aldrich)-coated plates at a density of 25,000 cells cm-2 in EC expansion Medium (1:1 mixture of day six medium and StemPro-34 SFM supplemented with 50 ng ml-1 VEGF). For VSMC differentiations, medium was replaced on day four and five by VSMC induction medium, consisting of N2B27 medium with 12.5 ng ml-1 platelet-derived growth factor (PDGF)-BB (PeproTech) and 12.5 ng ml-1 Activin A (PeproTech). On day six, cells were dissociated and plated at 35,000 cells cm-2 on gelatin-coated plates in Medium 231 (Thermo Fisher) supplemented with smooth muscle growth supplement (SMGS) (Thermo Fisher). Microarray analysis was performed with dECs and dVSMCs at passage 3. Other experiments described in this manuscript were performed with dVSMCs at passage 4-5.

extract_protocol: RNA extraction was done using RNeasy mini kit (Qiagen) according to the manufacturer’s instructions. RNA quality was verified using the Agilent Bioanalyzer and the 6000 nano kit. Total RNA samples were processed according to the GeneChip® WT PLUS Reagent kit (Affymetrix). Affymetrix Human Gene 2.1 Array Strips were hybridized, processed and scanned using the appropriate Affymetrix protocols.

treatment_protocol: not applicable

value: Vascular smooth muscle cells

tag: condition

value: With cardiovascular disease


title: T2DM with CVD dVSMC5

description: RNA from cellular lysate

tag: cell type


title: T2DM with CVD dVSMC4

description: RNA from cellular lysate


title: T2DM with CVD dVSMC7

description: RNA from cellular lysate


title: T2DM with CVD dVSMC2

description: RNA from cellular lysate


title: AD_6_12_1

value: AD


title: AD_6_11_1


title: TamR_shCtrl_rep2_RNAseq

value: TamR

tag: treatment


title: T2DM with CVD dVSMC6

description: RNA from cellular lysate


title: T2DM with CVD dVSMC1

description: RNA from cellular lysate


title: TamR_rep2_RNAseq

tag: growth medium


title: AD_6_10_1


title: AD_6_09_1


title: AD_8_03_1


title: MCF7_shCtrl_rep1_RNAseq


title: AD_5_12_1


title: AD_5_13_1


title: AD_7_11_1


title: TamR_rep1_RNAseq


title: MCF7_rep2_RNAseq


title: AD_6_13_1


title: AD_5_10_1


title: T2DM without CVD dVSMC4

description: RNA from cellular lysate

source_name: Without cardiovascular disease

value: Without cardiovascular disease


title: AD_5_11_1


title: MCF7_rep1_RNAseq

value: Full media


title: AD_4_11_1


title: T2DM without CVD dVSMC6

description: RNA from cellular lysate


title: AD_4_10_1


title: AD_4_12_1


title: TamR_shJUN_GROseq

description: Nascent RNA

value: TamR cells were infected with JUN shRNA(sh9591)


title: T2DM without CVD dVSMC5

description: RNA from cellular lysate


title: T2DM without CVD dVSMC3

description: RNA from cellular lysate


title: T2DM without CVD dVSMC7

description: RNA from cellular lysate


title: AD_3_05_1


title: TamR_shCtrl_GROseq

description: Nascent RNA


title: AD_3_07_1


title: MCF7_shGATA3_GROseq

description: Nascent RNA


title: AD_4_13_1


title: AD_3_03_1


title: AD_3_00_1


title: MCF7_shCtrl_GROseq

description: Nascent RNA


title: T2DM without CVD dVSMC2

description: RNA from cellular lysate


title: T2DM without CVD dVSMC1

description: RNA from cellular lysate


title: AD_5_09_1


title: AD_2_07_1


title: AD_2_05_1


title: AD_2_03_1


title: MCF7_shGATA3_Dox_GROseq

description: Nascent RNA

value: GATA3 shRNA (sh9301) for MCF7 parental cells with DOX-inducible expression of JUN-with DOX treatment


title: TamR_rep3_GROseq

description: Nascent RNA

value: TamR as a reference


title: AD_3_01_1

value: plasma


title: AD_1_11_1

value: F


title: AD_2_02_1

value: extracellular RNA


title: AD_1_13_1


title: T2DM with CVD dEC7

description: RNA from cellular lysate

value: Endothelial cells


title: T2DM with CVD dEC6

description: RNA from cellular lysate


title: MCF7_shCtrl_noDox_GROseq

description: Nascent RNA

value: control (parental cell)

value: Control shRNA (scramble) for MCF7 parental cells with DOX-inducible expression of JUN-without DOX treatment


title: AD_2_01_1


title: T2DM with CVD dEC5

description: RNA from cellular lysate


title: MCF7_shCtrl_Dox_GROseq

description: Nascent RNA

value: Control shRNA (scramble) for MCF7 parental cells with DOX-inducible expression of JUN-with DOX treatment


title: AD_1_09_1


title: AD_1_04_1


title: TamR_rep2_GROseq

description: Nascent RNA

value: Full media for MCF7-TamR (100nM 4_OHT)


title: AD_1_02_1


title: T2DM with CVD dEC4

description: RNA from cellular lysate


title: AD_1_08_1


title: N_9_12_1

value: N


title: N_9_03_1


title: N_9_08_1


title: MCF7_shGATA3_noDox_GROseq

description: Nascent RNA

value: GATA3 shRNA (sh9301) for MCF7 parental cells with DOX-inducible expression of JUN-without DOX treatment


title: TamR_rep1_GROseq

description: Nascent RNA


title: MCF7_rep2_GROseq

description: Nascent RNA

value: Full media for MCF7-P


title: N_9_06_1


title: T2DM with CVD dEC2

description: RNA from cellular lysate

value: With cardiovascular disease


title: T2DM with CVD dEC1

description: RNA from cellular lysate


title: T2DM without CVD dEC6

description: RNA from cellular lysate

value: Without cardiovascular disease


title: T2DM without CVD dEC7

description: RNA from cellular lysate


title: N_8_07_1


title: MCF7_rep1_GROseq

description: Nascent RNA


title: N_9_00_1


title: N_8_01_1


title: N_7_07_1


title: N_8_05_1


title: N_7_01_1


title: N_7_02_1


title: N_7_04_1


title: TamR_JUN_CST9165_Chipseq

extract_protocol:
Lysates were clarified from sonicated nuclei and protein-DNA complexes were isolated with antibody.
The extracted ChIP DNA was ligated to specific adaptors using KAPA LTP Library Preparation Kit (KK8230) or KAPA Hyper Prep Kit (KK8504), according to the manufacturer’s instructions.

value: TamR

value: Full media

tag: chip antibody

value: JUN (Cell Signaling, CST9165)


title: MCF7_JUN_BD610326_Chipseq


title: TamR_JUN_BD610326_Chipseq


title: Control

city: São Paulo

first: Helder

middle: I.

last: Nakaya

address: 438, Av. Prof. Lúcio Martins Rodrigues, 374 - Butantã

country: Brazil

institute: Universidade de São Paulo

data_processing:
Quality control using FASTQC
Paired-end reads were aligned to the human genome, ENSEMBL GRCh38.89, by STAR v.2.5.3.a,
Genome_build: GRCh38.89
Supplementary_files_format_and_content: Comma-separated text file include raw counts table for each sample.

source_name: Post-mortem brain

extract_protocol:
Brain samples were frozen in RNALater (Ambion®) and stored at -80 ° C until extraction. The tissue was broken and homogenized by TissueRupter® (QIAGEN) and RNA extraction was performed with the RNAeasy Plus (QIAGEN), following the protocol suggested by the manufacturer. Mini® kit
The libraries were diluted to 4nM with 15% PhiX. The cDNA library was sequenced with MySeq System (Illumina®, San Diego, CA) using the MiSeq Reagent kit (150 cycles, 2 x 75 paired-end).

tag: infection

value: control

value: post-mortem brain from infant with microcephaly


title: N_6_08_1

value: plasma

tag: sampling year

value: F


title: Zika_05 infected

value: ZIKV


title: Zika_08 infected


title: N_6_03_1

tag: donor id

value: extracellular RNA


title: MCF7_JUN_CST9165_Chipseq

value: control (parental cell)


title: N_6_06_1

tag: donor group


title: Zika_03 infected


title: T2DM without CVD dEC5

description: RNA from cellular lysate

value: Endothelial cells


title: T2DM without CVD dEC2

description: RNA from cellular lysate


title: N_5_10_1

tag: donor age at death

value: M


title: T2DM without CVD dEC4

description: RNA from cellular lysate


title: MCF7_shGATA3_noDox_K27ac_Chipseq

value: H3K27ac(Abcam, ab4729)


title: N_5_08_1

value: N

tag: donor gender


title: T2DM without CVD dEC1

description: RNA from cellular lysate


title: T2DM without CVD dEC3

description: RNA from cellular lysate


title: B. subtilis_SMM-1.2M NaCl-1mM GB_rep3

city: Greifswald

first: Ulrike

last: Mäder

address: F.-L.-Jahn-Str. 15A

department: Functional Genomics

country: Germany

institute: University Medicine Greifswald

description:
NaCl-GB_3
Bacillus subtilis BSB1

hyb_protocol: 1200 ng of Cy3-labeled cDNA were hybridized to the tiling array following Agilent’s hybridization, washing and scanning protocol (One-Color Microarray-based Gene Expression Analysis, version 5.5).

scan_protocol: The microarray was scanned using an Agilent Microarray Scanner G2505C (Agilent Technologies).

data_processing: Data were extracted using the Agilent Feature Extraction software (version 11.5.1.1, Agilent Technologies). Probe intensities were computed from the raw intensity data using a model of signal shift and drift and correcting for probe affinity variations as described before (Nicolas et al., 2009; PMID 19561016). An aggregated expression value was computed for each annotated CDS and previously identified RNA feature (Nicolas et al., 2012; PMID 22383849) as the median log2 intensity of probes lying entirely within the corresponding region.

organism: Bacillus subtilis

source_name: B. subtilis_ SMM with 1.2 M NaCl and 1 mM glycine betaine_OD1.0

label_protocol: For cDNA synthesis, 10 µg of total RNA were mixed with random primers (FairPlay III Microarray Labeling Kit) and spike-ins (One-Color RNA Spike-In Kit, Agilent Technologies) and incubated at 70°C for 10 min followed by 5 min incubation on ice. Then, first-strand Master Mix, Actinomycin D (final conc. 40 µg/ml) and AffinityScript HC Reverse Transcriptase were added. The reaction was incubated for 60 min at room temperature and for 60 min at 42°C. After hydrolyzing the RNA, cDNA was precipitated overnight at -20°C. NHS-ester dye coupling (CyDye Mono-Reactive Dye, GE Healthcare) and purification of labeled cDNA were performed according to the FairPlay III instructions. cDNA and Cy-dye concentrations were quantified by means of a NanoDrop spectrophotometer.

growth_protocol: B. subtilis BSB1 was grown aerobically at 37 °C in Spizizen's minimal medium either supplemented with 1 mM glycine betaine, 1.2 M NaCl or 1.2 M NaCl and 1 mM glycine betaine. Cells were harvested at OD at 600 nm of 1.0.

extract_protocol: Cells were harvested and total RNA was isolated by the mechanical cell disruption/ acid phenol method (Eymann et al., 2002; PMID 11948165).

tag: strain

value: BSB1 (Trp+ derivative of strain 168)

tag: medium

value: SMM + 1.2M NaCl + 1mM GB


title: N_5_06_1

tag: tissue

tag: donor braak stage

tag: donor diagnosis year


title: MCF7_shCtrl_Dox_K27ac_Chipseq

tag: cell line

tag: growth protocol

value: Control shRNA (scramble) for MCF7 parental cells with DOX-inducible expression of JUN-with DOX treatment


title: N_5_04_1

tag: molecule subtype


title: N_5_03_1


title: TamR_GATA3_Chipseq

value: TamR

value: GATA3 (Cell Signaling, CST5852)


title: N_4_08_1


title: N_4_06_1


title: N_6_02_1


title: MCF7_GATA3_Chipseq

value: Full media


title: MCF7_shGATA3_Dox_K27ac_Chipseq

tag: treatment

value: GATA3 shRNA (sh9301) for MCF7 parental cells with DOX-inducible expression of JUN-with DOX treatment


title: N_3_06_1


title: MCF7_shCtrl_noDox_K27ac_Chipseq

value: Control shRNA (scramble) for MCF7 parental cells with DOX-inducible expression of JUN-without DOX treatment

tag: growth medium


title: TamR_shJUN_P300_Chipseq

value: TamR cells were infected with JUN shRNA(sh9591)

tag: chip antibody

value: P300(Active motif, 61401)


title: B. subtilis_SMM-1.2M NaCl-1mM GB_rep2

description:
NaCl-GB_2
Bacillus subtilis BSB1


title: N_4_01_1

value: plasma


title: N_3_04_1

value: extracellular RNA


title: TamR_shJUN_BRG1_Chipseq

value: BRG1(Abcam, ab4081)


title: N_3_01_1


title: TamR_shCtrl_P300_Chipseq

value: TamR cells were infected with Control shRNA (scramble)


title: B. subtilis_SMM-1.2M NaCl_rep1

description:
NaCl_1
Bacillus subtilis BSB1

source_name: B. subtilis_ SMM with 1.2 M NaCl_OD1.0

value: SMM + 1.2M NaCl


title: B. subtilis_SMM-1.2M NaCl_rep2

description:
NaCl_2
Bacillus subtilis BSB1


title: B. subtilis_SMM-1.2M NaCl_rep3

description:
NaCl_3
Bacillus subtilis BSB1


title: N_2_08_1

value: F


title: T2DM with CVD dEC3

description: RNA from cellular lysate

tag: cell type

value: Endothelial cells

tag: condition

value: With cardiovascular disease


title: N_2_06_1

tag: sampling year

tag: donor id

value: N


title: N_4_04_1

tag: donor group

tag: donor age at death

value: M


title: TamR_shCtrl_BRG1_Chipseq

value: TamR


title: N_6_01_1

tag: donor gender


title: B. subtilis_SMM-1mM GB_rep3

description:
GB_3
Bacillus subtilis BSB1

source_name: B. subtilis_ SMM with 1 mM glycine betaine_OD1.0

tag: strain

value: BSB1 (Trp+ derivative of strain 168)

tag: medium

value: SMM + 1mM GB


title: N_2_01_1

tag: tissue

tag: donor braak stage


title: N_2_03_1

tag: donor diagnosis year


title: B. subtilis_SMM-1.2M NaCl-1mM GB_rep1

description:
NaCl-GB_1
Bacillus subtilis BSB1

value: SMM + 1.2M NaCl + 1mM GB


title: N_4_02_1


title: N_2_00_1


title: N_1_09_1


title: TamR_shJUN_ARID1B_Chipseq

tag: cell line

tag: growth protocol

value: Full media

value: ARID1B(Bethyl, A301-046A)


title: N_3_03_1

tag: molecule subtype


title: B. subtilis_SMM-control_rep3

description:
SMM-control_3
Bacillus subtilis BSB1

source_name: B. subtilis_ SMM_OD1.0

value: SMM control


title: B. subtilis_SMM-1mM GB_rep1

description:
GB_1
Bacillus subtilis BSB1


title: B. subtilis_SMM-1mM GB_rep2

description:
GB_2
Bacillus subtilis BSB1


title: MCF7_oeJUN_K27ac_Chipseq

value: control (parental cell)

tag: treatment

value: MCF7 parental cells with DOX-inducible expression of JUN-with DOX treatment

tag: growth medium

value: H3K27ac(Abcam, ab4729)


title: N_1_07_1

value: plasma

value: extracellular RNA


title: TamR_shCtrl_ARID1B_Chipseq

value: TamR cells were infected with Control shRNA (scramble)

tag: chip antibody


title: N_1_05_1


title: N_1_01_1


title: MCF7_oeCtrl_K27ac_Chipseq

value: MCF7 parental cells with DOX-inducible expression of JUN-without DOX treatment


title: PBMCs from healthy control HIP045

city: Stanford

first: Aaron

middle: James

last: Wilk

address: 300 Pasteur Dr Bldg S131, Grant

institute: Stanford University

data_processing:
mRNA reads in read 2 FASTQ files tagged with cell barcode and UMI from read 1 file with dropTag (dropEst)
Tagged reads aligned with STAR using GRCh37 reference that included the complete genome sequences for all SARS-CoV-2 strains sequenced from California before March 24, 2020
Count matrices built from BAM files using dropEst
Genome_build: GRCh37 including the complete genome sequences for all SARS-CoV-2 strains sequenced from California before March 24, 2020
Supplementary_files_format_and_content: .rds files containing exonic, intronic, and spanning count matrices

molecule: polyA RNA

source_name: PBMCs from healthy control

growth_protocol: No growth or treatment performed

extract_protocol:
Immediately after Ficoll separation, 50,000 PBMCs were resuspended in RPMI + 10% FCS at a concentration of 75,000 cells/mL. 200 μL of this cell suspension (15,000 cells) was then loaded onto Seq-Well arrays pre-loaded with mRNA capture beads (ChemGenes). Following four washes with DPBS to remove serum, the arrays were sealed with a polycarbonate membrane (pore size of 0.01 µm) for 30 minutes at 37°C and then frozen at -80°C for no less than 24 hours and no more than 14 days to allow batching of samples processed at irregular hours. Next, arrays were thawed, cells lysed, transcripts hybridized to the mRNA capture beads, and beads recovered from the arrays and pooled for downstream processing.
Library preparation was performed with a Nextera XT DNA library preparation kit (Illumina FC-131-1096) with 1 ng of pooled library using dual-index primers. Tagmented and amplified libraries were again purified by Agencourt AMPure XP beads with a 0.6x volume wash followed by a 1.0x volume wash, and quality and concentration determined by Fragment Analysis. Libraries between 400-1000bp with no primer peaks were considered successful and pooled for sequencing. Sequencing was performed on a NovaSeq S2 instrument (Illumina; Chan Zuckerberg Biohub). The read structure was paired-end with read 1 beginning from a custom read 1 primer11 containing a 12bp cell barcode and an 8 bp unique molecular identifier (UMI), and with read 2 containing 50bp of mRNA sequence.

treatment_protocol: No growth or treatment performed

tag: sample origin

value: Healthy control

tag: cell type

value: Un-cryopreserved peripheral blood mononuclear cells (PBMCs)


title: TamR_oeCtrl_K27ac_Chipseq

value: TamR cells with DOX-inducible expression of GATA3-without DOX treatment


title: TamR_oeGATA3_K27ac_Chipseq

value: TamR

value: TamR cells with DOX-inducible expression of GATA3-with DOX treatment


title: B. subtilis_SMM-control_rep2

description:
SMM-control_2
Bacillus subtilis BSB1

value: BSB1 (Trp+ derivative of strain 168)


title: MCF7_oeJUN_ER_Chipseq

value: ERalpha (Santa Cruz, sc-543)


title: PBMCs from healthy control HIP023


title: PBMCs from healthy control HIP015


title: PBMCs from healthy control HIP002


title: TamR_P300_Chipseq

value: Full media

value: P300(Santa Cruz, sc-585)


title: MCF7_oeCtrl_ER_Chipseq


title: MCF7_P300_Chipseq


title: N_1_08_1

tag: sampling year

tag: donor id

value: N

value: M


title: B. subtilis_SMM-control_rep1

description:
SMM-control_1
Bacillus subtilis BSB1

value: SMM control


title: PBMCs from COVID-19 sample covid_561

source_name: PBMCs from COVID-19 sample

value: Patient with confirmed COVID-19


title: PBMCs from COVID-19 sample covid_558


title: MCF7_shGATA3_K27ac_Chipseq

value: control (parental cell)

value: MCF7 cells were infected with GATA3 shRNA(sh9301)

value: H3K27ac(Abcam, ab4729)


title: PBMCs from COVID-19 sample covid_559


title: PBMCs from COVID-19 sample covid_557


title: MCF7_shCtrl_K27ac_Chipseq

value: MCF7 cells were infected with Control shRNA (scramble)


title: MCF7_shGATA3_ER_Chipseq


title: PBMCs from healthy control HIP044

value: Healthy control


title: PBMCs from healthy control HIP043

value: Un-cryopreserved peripheral blood mononuclear cells (PBMCs)


title: PBMCs from COVID-19 sample covid_556


title: MCF7_shCtrl_ER_Chipseq


title: PBMCs from COVID-19 sample covid_555_2


title: TamR_shJUN_K27ac_Chipseq

value: TamR cells were infected with JUN shRNA(sh9591)


title: TamR_shCtrl_K27ac_Chipseq

value: TamR

value: TamR cells were infected with Control shRNA (scramble)


title: PBMCs from COVID-19 sample covid_555_1


title: TamR_shJUN_ER_Chipseq


title: PoKI10_input_GEX [10x 3' Gene Expression] invivo_well8

city: San Francisco

first: Eric

last: Shifrut

address: 513 Parnassus Ave, HSW 1033

institute: University of California, San Franscisco

description: 10x 3' Gene Expression

data_processing:
Fastq files from 10x gene expression library were processed with Cell Ranger, using default parameters.
Fastq files for TCR KI barcodes were matched to the reference barcodes in the pooled library.
Genome_build: GRCh38
Supplementary_files_format_and_content: For each sample, gene expression (GEX) tar file contains a named count matrix of genes by cells for all cells passing filter. For TCR KI barcode files, tsv files contain a two column table of the identified KI gene(s) for each cell barcode in

source_name: pan T cells

growth_protocol: CD3+ cells were stimulated, edited by electroporation two days later, and then grown in IL-2.

extract_protocol: ChromiumTM Single Cell 3’ v3 Protocol (CG000183)

treatment_protocol: TCR stimulus with or without TGFB ; In vivo TILs vs ex vivo input cells

value: T cells


title: TamR_shCtrl_ER_Chipseq

value: ERalpha (Santa Cruz, sc-543)


title: PoKI10_input_TCR [Enrichment PCR of TCR KI] invivo_well8

description: Enrichment PCR of TCR KI


title: TamR_FOXA1_Chipseq

value: Full media

value: FOXA1(Abcam, ab5068)


title: PoKI10_input_GEX [10x 3' Gene Expression] invivo_well7

description: 10x 3' Gene Expression


title: MCF7_FOXA1_Chipseq


title: JP15

type: genomic

city: Hangzhou

first: Daoqiong

last: Zheng

state: Zhejiang

address: 866 Yuhangtang Road

department: Institute of Microbiology

institute: College of Life Sciences, Zhejiang University

hyb_protocol: The hybridization reactions were prepared using an Agilent Oligo aCGH/ChIP-on-Chip Hybridization kit (5188-5220) following kit instructions. Arrays were incubated for 24 hours at 62°. Following hybridization, the arrays were washed for 5 minutes in Oligo aCGH/ChIP-on-Chip Wash Buffer 1 (Agilent 5188-5221) and 1 minute in Oligo aCGH/ChIP-on-Chip Wash Buffer 2 (Agilent 5188-5222) that was pre-warmed to 37°. The arrays were then scanned at wavelengths of 635 and 532 nm using the GenePix scanner and the GenePix Pro software using settings recommended by the manufacturer.Microarrays could be re-used approximately 4-6 times by removing the hybridized labeled DNA sequences from the oligonucleotides. Microarrays and gasket slides were stripped separately in 1x stripping buffer (10 mM potassium phosphate, pH6.6). The slides were slowly heated to the boiling point in the stripping buffer for 30-45 minutes. After stripping, they were transferred to deionized water, and then slowly removed and stored in a nitrogen cabinet. The gasket slides were centrifuged at 500 rpm to remove excess liquid. Labels on microarrays were removed prior to stripping.

scan_protocol: The data generated by GenePix Pro were exported as .gpr files and analyzed with a homemade software pipeline. Probes that were flagged by the software were deleted from the analysis.

data_processing: The data generated by GenePix Pro were exported to text files and analyzed with Microsoft Excel. The 635 nm/532 nm ratio was analyzed for each oligonucleotide. The average value of the median ratios of the control probes was calculated and used to normalize the ratios of the experimental probes to a value of 1 by dividing each probe ratio by the average control probe ratio. The Whole genome arrays were completed with Agilent platform with Design ID Agilent-027438 was used. Sectored colonies were mapped using Agilent platforsm with Design IDs Agilent-031671, which contains probes specific only to chromosome IV, and Agilent-047217, which contains many probes on chromsome IV, but few probes near the telomere and centromere of all chromosomes.

organism: Saccharomyces cerevisiae

source_name: cell culture of strain JP15

label_protocol: DNA from these colonies was labeled with Cy5, and mixed with control DNA (DNA from the strain JSC24) labeled with Cy3. The two samples were mixed and competitively hybridized to the SNP microarrays.

growth_protocol: Yeast cells were grown in YPD medium at 30 degree.

extract_protocol: Genomic DNA were prepared by standard procedures (St. Charles et al., 2012)

treatment_protocol: The JSC25-1 cells were cultured in liquid YPD to an OD600 of 0.25 (initial OD600 was 0.05), then cells at a concentration of 1 OD600 were heat-shocked at 52℃ for 4 min.

tag: ploidy

value: diploid strain

source_name: cell culture of JSC24-2

value: control strain JSC24-2


title: JP17

source_name: cell culture of strain JP17


title: PoKI10_input_TCR [Enrichment PCR of TCR KI] invivo_well7

description: Enrichment PCR of TCR KI


title: JP18

source_name: cell culture of strain JP18


title: JP21

source_name: cell culture of strain JP21


title: TamR_input_Chipseq

value: Input


title: PoKI9_input_GEX [10x 3' Gene Expression] invivo_well6

description: 10x 3' Gene Expression


title: JP19

source_name: cell culture of strain JP19


title: JP14

source_name: cell culture of strain JP14


title: JP10

source_name: cell culture of strain JP10


title: JP16

source_name: cell culture of strain JP16


title: JP12

source_name: cell culture of strain JP12


title: PoKI9_input_TCR [Enrichment PCR of TCR KI] invivo_well6

description: Enrichment PCR of TCR KI


title: JP11

source_name: cell culture of strain JP11


title: JP20

source_name: cell culture of strain JP20


title: JP13

source_name: cell culture of strain JP13


title: JP09

source_name: cell culture of strain JP09


title: PoKI9_input_GEX [10x 3' Gene Expression] invivo_well5

description: 10x 3' Gene Expression


title: MCF7_K27ac_rep2_Chipseq

source_name: breast cancer cells


title: PoKI9_input_TCR [Enrichment PCR of TCR KI] invivo_well5

description: Enrichment PCR of TCR KI


title: JP07

source_name: cell culture of strain JP07


title: TamR_K27ac_rep1_Chipseq


title: MCF7_input_Chipseq


title: PoKI10_invivo_GEX [10x 3' Gene Expression] invivo_well4

description: 10x 3' Gene Expression

source_name: pan T cells


title: PoKI10_invivo_TCR [Enrichment PCR of TCR KI] invivo_well4

description: Enrichment PCR of TCR KI


title: TamR_K4me1_Chipseq

value: H3K4me1(Abcam, ab8895)


title: Endothelial cells from B16F10 melanomas grown on mice with Shb conditionally inactivated in endothelial cells 2

city: Uppsala

first: L.

last: He

address: Dag Hammarskjölds Väg 20

country: Sweden

institute: Uppsala University

data_processing:
The sequence reads were aligned to the Ensembl mouse gene assembly (GRCm38) using Tophat2 software (version 2.1.1).
FPKM summary was performed using the Cufflinks tool (version 2.2.1)
Genome_build: GRCm38
Supplementary_files_format_and_content: tab-delimited text files with RPKM values for each sample

source_name: Tumors and lungs

extract_protocol:
Total RNA from tumors or from magnetic cell sorting (MACS®)-isolated cells was isolated using the RNeasy mini-kit (Quiagen, Hilden, Germany).
EC (CD31+ cells after pre-depletion of CD11b+ cells) RNA concentration and quality were assessed using the Agilent 2100 Bioanalyzer, and RNA library preparation was done TruSeq stranded total RNA library preparation kit (#15031048) with Ribo Zero Gold treatment.

value: Shbflox/flox/Cdh5-CreERt2 mice

value: Tumors

tag: age

value: adult


title: Endothelial cells from B16F10 melanomas grown on mice with Shb conditionally inactivated in endothelial cells 1

tag: strain


title: PoKI10_invivo_GEX [10x 3' Gene Expression] invivo_well3

description: 10x 3' Gene Expression


title: TamR_K27ac_rep2_Chipseq

value: H3K27ac(Abcam, ab4729)


title: JP06

source_name: cell culture of strain JP06

source_name: cell culture of JSC24-2


title: MCF7_K27ac_rep1_Chipseq

value: control (parental cell)


title: PoKI10_invivo_TCR [Enrichment PCR of TCR KI] invivo_well3

description: Enrichment PCR of TCR KI


title: JP03

source_name: cell culture of strain JP03


title: PoKI9_invivo_GEX [10x 3' Gene Expression] invivo_well2

description: 10x 3' Gene Expression


title: MCF7_K4me1_Chipseq


title: Endothelial cells from B16F10 melanomas grown on wild type mice 1


title: MCF7_Full_ER_Chipseq


title: PoKI9_invivo_TCR [Enrichment PCR of TCR KI] invivo_well2

description: Enrichment PCR of TCR KI


title: JP05

source_name: cell culture of strain JP05


title: JP04

source_name: cell culture of strain JP04


title: JP08

source_name: cell culture of strain JP08


title: JP02

source_name: cell culture of strain JP02


title: JP01

source_name: cell culture of strain JP01


title: RNA data from human PBMC (RNA-seq)

city: Pittsburgh

first: Xinjun

last: Wang

address: 4401 Penn Ave., Rangos Research Building

institute: Children’s Hospital of Pittsburgh of UPMC

description:
single cell RNA
scRNA data from human PBMC

data_processing:
Standard 10X Genomics CellRanger pipeline
Match RNA data and ADT data with common cell barcodes
Genome_build: GRCh38
Supplementary_files_format_and_content: For each sample, the raw UMI count matrix is stored in a csv file with features as row names and cell barcodes as column names.

source_name: PBMC RNA

extract_protocol:
Sorted cells were loaded into the Single Cell Chip and processed through the 10X controller for droplet generation, resulting in droplets containing a single cell and bead per droplet
Chromium Single Cell 3' RNA-seq libraries were prepared for sequencing using standard 10X Genomics protocols

value: blood

value: Peripheral blood mononuclear cells


title: TamR_Full_ER_Chipseq

value: TamR


title: TamR_ATACseq

description: TamR_full media_ATAC-seq


title: PoKI9_invivo_TCR [Enrichment PCR of TCR KI] invivo_well1

description: Enrichment PCR of TCR KI


title: MCF7_ATACseq

description: MCF7_full media_ATAC-seq


title: Donor2_GFP_Rep_TCR_TCR

description: Enrichment PCR of TCR KI


title: DME #2

city: Daejeon

first: Bong Ihn

last: Koh

address: 291 Daehakro

country: South Korea

institute: Korea Advanced Institute of Science and Technology

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence(using fastx_trimmer), then mapped to mm10 whole genome using Bowtie2
Read count extraction and nomalization were performed using edgeR.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include read count values for each Sample

source_name: Dura mater endothelial cells (Dura mater ECs)

extract_protocol:
RNA was harvested using Trizol reagent (Invitrogen). 500 ng of total RNA was used for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using LEXOGEN Quant-Seq Library Prep Kit (Cat#001.24) standard protocols.

value: 8 weeks

value: Dura mater

value: endothelial cell (EC)


title: Donor1_mCherry_Rep_TCR_TCR

description: Enrichment PCR of TCR KI

value: T cells


title: BPE #2

source_name: Brain parenchyma endothelial cells (Brain PC ECs)

value: Brain parenchyma


title: INJ_dura_CD45pos

description:
single cell RNA
CD45+ dura single cell RNA library

data_processing:
Cell Ranger (v3.1.0) was used to process single cell 3' RNA-seq ouput. Breifly, first the cell ranger mkfastq was used to demultiplex illumina BCLs into fastq files.
Then, using cell ranger count, reads were aligned to mm10 mouse reference genome.
Aligned reads were then read by Seurat (v3.1.0) and cell-gene raw expression matrices were made. Potential doublets were removed by Scrublet.  Low quality cells (less than 1000 detected genes) were removed. Also, cells with high mitochondrial gene associated UMI count (>7% of total UMI counts) were removed.
After quality control, expression matrices were log normalized and variables such as number of UMIs and mitochondrial gene percentage were regressed out and scaled with Seurat to produce processed data files.
Identification of differentially expressed genes and dimensionality reductions were performed by Seurat.
Genome_build: mm10
Supplementary_files_format_and_content: Cell-gene expression matrix of log normalized UMI counts for WT and LATS1/2 KO datasets

source_name: CD45+ dura single cells

extract_protocol:
FACS sorted CD45+ or CD45- cells were processed on the 10X chromium system following the manufacturer's protocols.
Using Chromium Single cell 3' v3 Reagent Kit (10X genomics), cDNA libraries were constructed

tag: sample type

value: FACS sorted

value: Adult


title: A3

city: NEW DELHI

first: Anurag

middle: Singh

last: Rathore

state: DELHI

address: Lab no. 356, Block III

department: Chemical Engineering

country: India

institute: Indian Institute of Technology

data_processing:
The raw data generated was checked for the quality using FastQC. Reads were pre processed to remove the adapter sequences and removal of the low quality bases (<q30). Pre-processing of the data is done with Cutadapt. The pre-processed high quality data was aligned to reference genome using Bowtie2. Bowtie with  default parameter was run to identify the alignment percentage.
Genome_build: Escherichia coli_BL21(DE3), GCF_000022665.1 assembly was downloaded from NCBI
Supplementary_files_format_and_content: HTSeq4 was used to estimate and calculate gene abundance. Absolute counts for each genes were   identified ,which were used in differential expression calculations. DESeq5 was used to calculate the differentially expressed genes using Amino acid supplemented conditions (A3 and A7) as test and without amino acid supplemention (C3 and C7) as control. Genes were categorized into UP, Down and Neutrally regulated based on the log2fold change cutoff of 1 value.

organism: Escherichia coli

source_name: bacterial cell

growth_protocol: A chemically defined medium (CDM) is used for E. coli culture. Control (only CDM) and Test cultivation (CDM + 5 mM of all amino acids)  of  E.coli BL21(DE3) expressing recombinant protein was carried out. Sample at 3rd hour (growth phase) and 7th hour (protein production phase) was taken for RNA-seq analysis.

extract_protocol:
Total RNA was isolated using RNeasy Mini Kit (Qiagen) using manufacturer’s instructions.
RNA sequencing libraries were prepared with Illumina-compatible NEBNext® UltraTM Directional RNA Library Prep Kit (New England BioLabs, MA, USA) at Genotypic Technology Pvt. Ltd., Bangalore, India. ~2.5μg of total RNA was taken for rRNA depletion using Ribo-Zero rRNA Removal Kit (Bacteria). ~50 ng of Qubit quantified ribodepleted RNA was taken for fragmentation and priming. The fragmented and primed mRNA was further subjected to first strand synthesis in the presence of Actinomycin D (Gibco, life technologies, CA, USA) followed by second strand synthesis. The double stranded cDNA was purified using HighPrep PCR magnetic beads (Magbio Genomics Inc, USA). The purified cDNA was end-repaired, adenylated and ligated to Illumina multiplex barcode adapters as per NEBNext® UltraTM Directional RNA Library Prep Kit protocol.

treatment_protocol: Not required

tag: age of culture

value: growth phase of  cultures (3rd Hour)

value: supplementation of amino acids


title: ADT data from human PBMC (CITE-seq)

description:
single cell surface protein
single cell protein data from human PBMC

data_processing:
Library strategy: CITE-seq
Standard 10X Genomics CellRanger pipeline
Match RNA data and ADT data with common cell barcodes
Genome_build: GRCh38
Supplementary_files_format_and_content: For each sample, the raw UMI count matrix is stored in a csv file with features as row names and cell barcodes as column names.

molecule: other

source_name: PBMC ADT (Antibody Derived Tag)

tag: tissue


title: Donor2_mCherry_Rep_TCR_TCR

description: Enrichment PCR of TCR KI


title: PoKI9_invivo_GEX [10x 3' Gene Expression] invivo_well1

description: 10x 3' Gene Expression


title: A7

value: protein production phase of cultures (7th Hour)


title: C3

value: growth phase of cultures (3rd Hour)

value: control


title: C7


title: INJ_brain_CD45pos

description:
single cell RNA
CD45-+ brain single cell RNA library

source_name: CD45-+ brain single cells


title: CT_dura_CD45pos


title: BPE #1


title: Donor2_TGFB_Rep_3_TCR

description: Enrichment PCR of TCR KI

source_name: pan T cells


title: Donor1_GFP_Rep_TCR_TCR

description: Enrichment PCR of TCR KI


title: CT_brain_CD45pos


title: Aero

city: Freiburg im Breisgau

first: Galina

last: Erikson

address: Stübeweg 51

institute: Max Planck Institute of Immunobiology and Epigenetics

data_processing:
RNAs were sequenced on Illumina HiSeq2000 with 50 bp paired-end reads
Sequenced reads were quality-tested using FASTQC and aligned to the hg19 human genome using the STAR aligner version 2.4.0k. Mapping was carried out using default parameters (up to 10 mismatches per read, and up to 9 multi-mapping locations per read). The genome index was constructed using the gene annotation supplied with the hg19 Illumina iGenomes collection  and sjdbOverhang value of 100.
Raw gene expression was quantified across all gene exons using the top-expressed isoform as proxy for gene expression. Transcripts per million (TPM) values were calculated for each sample. The length of the transcript was determined by querying the Ensembl mart with dataset = “hsapiens_gene_ensembl”, using biomaRt in R version 3.5.1. TPM values were log2 + 1 transformed for downstream analyses.
Genome_build: hg19
Supplementary_files_format_and_content: Raw counts matrix and TPM matrix provided as CSV files

source_name: iPSC-derived neurons

extract_protocol:
At 15 days post-differentiation, the neurons positive for PSA-NCAM (Anti PSA-NCAM Antibody, Miltenyi Biotec) were sorted using flow cytometry to ensure isolation of a more homogeneous population of neuronal fate-committed cells. RNA was extracted after cell sorting on TRIzol LS reagent (Invitrogene) from 15 neuronal samples (7 neurotypical controls and 8 idiopathic ASD patients with early brain overgrowth). Total RNA was extracted using DNA Free RNA Kit (Zymo Research) according to the manufacturer’s instructions.
RNA quality was assayed using Agilent Technologies 2200 TapeStation and samples with integrity superior to RIN 8.5 were used for library preparation. Stranded mRNA sequencing libraries were prepared using the Illumina TruSeq Stranded mRNA Library Prep Kit according to the manufacturer’s instructions. Briefly, RNA with a poly A tail was isolated using magnetic beads conjugated to polyT oligos. mRNA was then fragmented and reverse transcribed into cDNA. dUTPs were incorporated, followed by second strand cDNA synthesis. The dUTP-incorporated second strand was not amplified. cDNA was then end repaired, index adapter ligated and PCR amplified. AMPure XP beads (Beckman Coulter) were used to purify nucleic acid after each step of the library prep. All sequencing libraries were then quantified, pooled and sequenced at single-end 50 base-pair (bp) on Illumina HiSeq 2500 at the Salk Institute Next Generation Sequencing Core. One thousand ng of RNA was used for library preparation with the Illumina TruSeq RNA Sample Preparation Kit. The RNAs were sequenced on Illumina HiSeq2000 with 50 bp paired-end reads, generating 50 million high-quality sequencing fragments per sample, on average.

tag: group

value: Autism

value: 15 days post-differentiation

tag: sorting

value: PSA-NCAM


title: Aqua


title: Donor2_TGFB_Rep_2_TCR

description: Enrichment PCR of TCR KI


title: Donor2_TGFB_Rep_3_GEX

description: 10x 3' Gene Expression


title: Ahoy


title: WT2

city: SINGAPORE

first: LONG

middle: NAM

last: NGUYEN

address: 28 Medical Drive

department: BIOCHEMISTRY

country: Singapore

institute: NUS YONG LOO LIN SCHOOL OF MEDICINE

data_processing:
RNA-seq datasets of three control samples and three knockout samples were aligned to the mm10 mouse genome using STAR 2.5.2a with the parameter outFilterMultimapNmax set to 1.
featureCount was used for the mapped reads in .bam files to generate count tables based on the hg19 Ensembl gene annotation
Bioconductor package DESeq2 v1.12.4 was used to analyze differential gene expression.
Genome_build: mm10
Supplementary_files_format_and_content: txt file for differentially expressed genes

source_name: Wild-type 2

extract_protocol: Whole mouse brain of embryos were dissected and proceeded to total RNA purification using TRIzol reagent. 1µg of RNA sample was submitted to NovogeneAIT (Singapore) and used for RNA sequencing.

value: brain

tag: genotype/variation

value: wild type

tag: developmental stage


title: WT3

source_name: Wild-type 3


title: Donor2_TGFB_Rep_2_GEX

description: 10x 3' Gene Expression


title: WT1

source_name: Wild-type 1


title: Donor2_TGFB_Rep_1_TCR

description: Enrichment PCR of TCR KI


title: Donor2_TGFB_Rep_1_GEX

description: 10x 3' Gene Expression


title: Acai


title: KO2

source_name: Knock-out 2

value: Mfsd7c-/- knock out


title: Able


title: Donor2_Stim_Rep_3_TCR

description: Enrichment PCR of TCR KI


title: Apex


title: Avid


title: KO3

source_name: Knock-out 3


title: pfkfb3-ko-3d_HLI_-macrophage2

city: schwerzenbach

first: jing

last: zhang

state: Schwerzenbach

address: schorenstrasse 16

department: Department Health Sciences and Technology

institute: DHEST

data_processing:
For mapping and trimming of FASTQ format sequences was performed using Trim Galore, and sequence quality control was assessed using FastQC. Alignment to the Ensembl reference genome GRCm38 was performed using the Hisat2 aligner. Gene expression values were computed with the function featureCounts from the R package Rsubread. Differential expression was computed using Negative Binomial model implemented in the Bioconductor package DESeq.
Genome_build: GRCm38
Supplementary_files_format_and_content: raw counts of sequencing reads for the features of interest for each Sample ...

source_name: muscle macrophage

extract_protocol:
Tissues were removed, cell were FACS sorted and 7,000-50,000cells were collected into lysis buffer from RNeasy Plus Micro Kit, which was used to collect total RNA.
Sequencing libraries were prepared following SMARTer® Universal Low Input RNA Kit for Sequencing

treatment_protocol: intraperitoneal administration of 1mg tamoxifen_T5648, Sigma-Aldrich_ dissolved in 1:10 ethanol: corn oil solution for 5 consecutive days to the mice. A wash out period of at least 7 days was allowed before starting the experiments.

value: calf muscle

value: macrophage

tag: genotype

tag: development stage

value: 3days after hindlimb ischemia


title: KO1

source_name: Knock-out 1


title: Clue

value: Control


title: Cent


title: Donor2_Stim_Rep_2_GEX

description: 10x 3' Gene Expression

value: T cells


title: Donor2_Stim_Rep_2_TCR

description: Enrichment PCR of TCR KI


title: pfkfb3-ko-3d_HLI_-macrophage1


title: Donor2_Stim_Rep_1_TCR

description: Enrichment PCR of TCR KI


title: pfkfb3-3d_HLI_-macrophage2

value: WT


title: Donor2_Stim_Rep_1_GEX

description: 10x 3' Gene Expression


title: Chap


title: Clay


title: pfkfb3-3d_HLI_-macrophage1


title: pfkfb3-ko-3d_HLI_-macrophage


title: Arch


title: Cove3


title: Donor1_TGFB_Rep_3_TCR

description: Enrichment PCR of TCR KI


title: pfkfb3-3d_HLI_-macrophage


title: WT126


title: scRNA-seq_MAL inbibitor

city: Bruxelles

first: Cedric

last: Blanpain

address: 808, route de Lennik, CP 637

institute: Université Libre de Bruxelles (ULB)

data_processing:
Read Alignment - CellRanger (version 3.0.2)
Cell-cycle assignment - Scran (1.10.1)
UMAP dimensionality reduction - Seurat (3.0.1)
Normalization - Seurat (3.0.1)
Gene regulatory network analysis - SCENIC (0.9.9+2.gcaded79)
Genome_build: mm10-1.2.0
Supplementary_files_format_and_content: R Rds objects

source_name: dorsal skin interfollicular epidermal basal cells under stretching and under CCG203971 treatment

extract_protocol:
To separate epidermis from dermis, the samples were incubated in HBSS (Gibco) 0,25% trypsin  (Gibco) at 4°C overnight. Epidermis was mechanical separated from the dermis with scalpel first and then by pipetting and trypsin was neutralized by adding DMEM medium (Gibco) supplemented with 2% Chelex Fetal Calf Serum (FCS). Samples were filtrated on 70 and 40µm filter (Falcon). Cells were incubated in 2% FCS/PBS with primary antibodies for 30 min on ice, protected from the light, with shaking every 10 min. Immunostaining for isolating basal IFE and infundibulum cells was performed using FITC-conugated anti-α6-integrin (clone GoH3; BD biosciences). CD34 staining was used to exclude bulge cells from the sorted cells (clone RAM34; BD Biosciences). Primary antibodies were washed with 2% FCS/PBS and cells incubated for 30 min in APC conjugated streptavidin (BD Biosciences), on ice, with shaking every 10 min. Living epidermal cells were gated by forward scatter, side scatter and negative staining for Hoechst dye. Basal cells from the interfollicular epidermis were targeted using CD34 negative and α6 integrin positive gating. Fluorescence-activated cell sorting analysis was performed using FACSAria I at high pressure (70 psi) and FACSDiva software (BD Biosciences). After sorting, 6000 cells were loaded onto each channel of the Chromium Single Cell 3’ microfluidic chips (V2-chemistry, PN-120232, 10X Genomics) and individually barcoded with a 10X Chromium controller according to the manufacturer’s recommendations (10X Genomics). RNA from the barcoded cells was reverse transcribed, followed by amplification, shearing 5′ adaptor and sample index attachment.
The libraries were prepared using the Chromium Single Cell 3’ Library Kit (V2-chemistry, PN-120233, 10X Genomics), quantified using a low coverage Illumina NextSeq 550 run and sequenced on an Illumina NovaSeq

tag: treatment

value: stretching and CCG203971


title: Donor1_TGFB_Rep_2_TCR

description: Enrichment PCR of TCR KI


title: Donor2_Stim_Rep_3_GEX

description: 10x 3' Gene Expression


title: Donor1_TGFB_Rep_3_GEX

description: 10x 3' Gene Expression


title: Endothelial cells from B16F10 melanomas grown on mice with Shb conditionally inactivated in endothelial cells 6

source_name: Tumors and lungs

value: Shbflox/flox/Cdh5-CreERt2 mice

value: Tumors

value: adult


title: scRNA-seq_Trametinib

source_name: dorsal skin interfollicular epidermal basal cells under stretching and under Trametinib treatment

value: stretching and trametinib


title: Donor1_TGFB_Rep_2_GEX

description: 10x 3' Gene Expression


title: Endothelial cells from B16F10 melanomas grown on mice with Shb conditionally inactivated in endothelial cells 5


title: Donor1_TGFB_Rep_1_TCR

description: Enrichment PCR of TCR KI


title: Donor1_Stim_Rep_3_TCR

description: Enrichment PCR of TCR KI


title: Smel_CoIP-Ctrl-3

city: Cologne

first: Konrad

middle: U.

last: Förstner

state: North Rhine-Westphalia

address: Gleueler Str. 60

department: Information Services

institute: ZB MED - Information Centre for Life Sciences

data_processing:
Quality trimming : cutadapt 1.15
Read mapping : READemption (0.4.3) and segemehl (0.2.0)
Coverage plot generation: READemption (0.4.3)
Genome_build: CP004140.1, EF437940.1
Supplementary_files_format_and_content: nucleotide wise coverage in wiggle format

organism: Sinorhizobium meliloti

growth_protocol: 3 L-Erlenmeyer flasks were filled with 1 l TY medium containing streptomycin (250µg/ml) and Tc (10 µ/ml). Cultures were grown at 30 °C and 140 r. p. m. till an OD600 nm of 0.5. IPTG was added to a final concentration of 1 mM and after 10 min of incubation at 30 °C and 140 r. p. m., cells were harvested.

extract_protocol:
Cell pellet was resuspended in 5 ml lysis buffer containing 20 mM Tris, pH of 7.5, 150 mM KCl, 1 mM MgCl2, 1 mM DTT, lysozyme, 2 µg/ml Tc and 1 pill protease inhibitor per 40 ml buffer. Cells were lysed by sonication and 40 µl anti-FLAG antibody-bound magnetic beads were added to the cleared lysate. After incubation at 4 °C for 2 h, the beads were collected and washed 3 times with 500 µl lysis buffer containing 2 µg/ml Tc. Purification of CoIP RNA was performed using TRIzol,
The total RNA samples were first fragmented using ultrasound (1 pulse of 30 sec at 4°C). First, an oligonucleotide adapter was ligated to the 3' end of the RNA molecules. First-strand cDNA synthesis was performed using M-MLV reverse transcriptase and the 3’ adapter as primer. The first-strand cDNA was purified and the 5' Illumina TruSeq sequencing adapter was ligated to the 3' end of the antisense cDNA. The resulting cDNA was PCR-amplified to about 10-20 ng/μl using a high fidelity DNA polymerase (cycle numbers are indicated in Table 2). The TruSeq barcode sequences which are part of the 5' and 3' TruSeq sequencing adapters are included in Table 2. The cDNA was purified using the Agencourt AMPure XP kit (Beckman Coulter Genomics) and was analyzed by capillary electrophoresis For Illumina NextSeq sequencing, the samples were pooled in approximately equimolar amounts. The cDNA pool was size fractionated in the size range of 200 - 500 bp using a preparative agarose gel. An aliquot of the size fractionated pool was analyzed by capillary electrophoresis. The cDNA pool was sequenced on an Illumina NextSeq 500 system using 75 bp read length.

treatment_protocol: Cells were harvested by centrifugation at 6,000 g and 4 °C and immediately used for cell disruption and CoIP.

tag: strain background

value: pSRKGm-peTrpL, pRK4352

value: Liquid culture

tag: molecule subtype

value: mock CoIP total RNA


title: Smel_FLAG-CoIP1

value: pSRKGm-3xFlag-peTrpL, pRK4352

value: CoIP total RNA


title: Endothelial cells from B16F10 melanomas grown on mice with Shb conditionally inactivated in endothelial cells 4


title: Endothelial cells from B16F10 melanomas grown on mice with Shb conditionally inactivated in endothelial cells 3


title: ADRC40

value: 15 days post-differentiation

value: PSA-NCAM


title: Donor1_Stim_Rep_3_GEX

description: 10x 3' Gene Expression


title: Endothelial cells from B16F10 melanomas grown on wild type mice 4


title: Endothelial cells from B16F10 melanomas grown on wild type mice 3


title: Smel_CoIP-Ctrl-1


title: Donor1_Stim_Rep_2_TCR

description: Enrichment PCR of TCR KI


title: Donor1_Stim_Rep_2_GEX

description: 10x 3' Gene Expression


title: Smel_CoIP-Ctrl-2


title: Endothelial cells from B16F10 melanomas grown on wild type mice 2


title: RcsR1-OE-3

growth_protocol: 50 ml-Erlenmeyer flasks were filled with 30 TY medium containing streptomycin (250 µg/ml).  For strains OE and EVC, Tc (10 µ/ml) was added . Cultures were grown at 30 °C and 140 r. p. m. to an OD600 nm of 0.5.

extract_protocol:
Total RNA  was extracted with 1 ml TRIzol (cell disruption was performed  in the cell suspension using glass beads in a shaking mill). Precipitated RNA was dissolved in cold ultrapure water and imediately subjected to additional hot-phenol purification. 10 µg RNA was treated with TURBO DNase and used for RNAseq.  RNA from three independent biological samples was pooled. Each pool was used for three independent cDNA libraries.
The total RNA samples were first fragmented using ultrasound (4 pulses of 30 sec at 4°C). Each sample was used for three independent cDNA synthesis. First, an oligonucleotide adapter was ligated to the 3' end of the

treatment_protocol: 15 ml culture was added to a 50 ml-tube filled with ice rocks an centrifuged at 6,000 g at 4 °C. The cell pellet was dissolved in 1 ml cold TY medium, transferred to an Eppendorf tube and centrifuged for 5 min and 6,000 r.p.m.at 4 °C. The pellet was used immediately for isolation of total RNA  .

tag: genoypte/variation

value: overexpressing strain (OE; pRK-RcsR1)


title: Smel_FLAG-CoIP3


title: RcsR1-OE-2


title: Donor1_Stim_Rep_1_GEX

description: 10x 3' Gene Expression


title: RcsR1-OE-1


title: Exp-D2

address: route de Lennik, 808

institute: Université Libre De Bruxelles

data_processing:
Adaptors sequences were removed with TrimmomaticPE using options “ILLUMINACLIP:adaptor.file:2:30:10 HEADCROP:10 CROP:70 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:60”.
ATAC-seq paired-end reads were then aligned to mouse genome Grcm38 using Bowtie2 (version 2.2.6) using options “-X 2000 --fr --very-sensitive --no-discordant --no-unal --no-mixed –non-deterministic”.
Mitochondrial reads, reads from unmapped or random contigs and reads with a mapping quality less than 20 were removed using samtools.
Duplicate reads were removed by Picard tools (http://broadinstitute.github.io/picard/).
Peak calling was performed on each individual sample by macs2 (version 2.1.0.20151222)  using options “-f BAMPE -g mm -q 0.05 --nomodel --call-summits -B –SPMR”. TDF files were generated with IGVtools from the treat_pileup.bdg
Peaks from the different subpopulations were merged for downstream analysis.
Reads counts of each merged peaks for each individual sample were calculated by HTSeq-count using options “-r pos -m intersection-nonempty”. These counts were normalized for one million of mapped reads in merged peaks and fold<
Peaks were associated to genes with GREAT software with the following association rules : “basal plus extension” with parameters : 5.0kb in proximal upstream, 1.0kb in proximal downstream and 100.0kb in distal.
Genome_build: Grcm38
Supplementary_files_format_and_content: tdf
Supplementary_files_format_and_content: peaks
Supplementary_files_format_and_content: counts

source_name: Back skin  inetrfollicular epidermis

extract_protocol: Cells were centrifuged and cell pallets were resuspended in 100ul of lysis buffer (TrisHCl 10mM, NaCl 10mM, MgCl2 3mM, Igepal 0.1%) and centrifuged at 500g for 25 minutes at 4ºC. Supernatant was carefully discarded and nuclei were resuspended in 50ul of reaction buffer (Tn5 transposase 2.5ul, TD buffer 22.5ul, from Nextera DNA sample preparation kit, Illumina, and 25ul H20). The reaction was performed at 37ºC for 30min and was stopped by addition of 5ul of clean up buffer (NaCl 900mM, EDTA 300mM). DNA was purified using the MiniElute purification kit (QIAGEN) following manufacturer protocol. DNA libraries were PCR amplified (Nextera DNA Sample Preparation Kit, Illumina), and size selected from200 to 800bp (BluePippin, Sage Sciences), following manufacturer ́s recommendations.

value: tissue stretching


title: Donor1_TGFB_Rep_1_GEX

description: 10x 3' Gene Expression


title: Smel_FLAG-CoIP2


title: EVC-pRK-3

source_name: EVC-pRK

value: empty vector control (EVC; pRK4352)


title: EVC-pRK-2


title: Embryos, mzoep_90_3

city: Saint Louis

first: Bo

last: Zhang

state: Missouri

address: 4515 McKinley Research Bldg 03212

department: Developmental Biology

institute: Washington University School of Medicine

data_processing:
Raw reads were trimmed with cutadapt to remove low quality bases
Trimmed reads were aligned to danio rerio genome GRCz10 using STAR_2.5.4b with Ensembl v83 annotation
Aligned reads were quantified using featureCounts 1.6.3 from the subreads package
Genome_build: GRCz10
Supplementary_files_format_and_content: gene counts text file

organism: Danio rerio

source_name: 50 pooled MZoep-/- embryos at 90% epiboly

growth_protocol: Embryos obtained from natural mating were maintained at 28.5C until 90% epiboly stage

extract_protocol:
Embryos were lysed and total RNA isolated using Trizol, then cleaned up using a Qiagen Rneasy kit.
Samples were depleted of ribosomal RNA using the Illumina Ribo-Zero kit and libraries prepared using TruSeq stranded total RNA reagents.

value: embryo

value: MZoep mutant


title: Embryos, mzoep_90_1


title: Embryos, mzoep_90_2


title: EVC-pRK-1


title: A14

data_processing:
The raw data generated was checked for the quality using FastQC. Reads were pre processed to remove the adapter sequences and removal of the low quality bases (<q30). Pre-processing of the data is done with Cutadapt. The pre-processed high quality data was aligned to reference genome using Bowtie2. Bowtie with  default parameter was run to identify the alignment percentage.
Genome_build: Escherichia coli_BL21(DE3), GCF_000022665.1 assembly was downloaded from NCBI
Supplementary_files_format_and_content: HTSeq4 was used to estimate and calculate gene abundance. Absolute counts for each genes were  identified ,which were used in differential expression calculations. DESeq5 was used to calculate the differentially expressed genes using Microaerobic conditions (M10, M12, M14) as test and Aerobic conditions ( A10, A12, A14) as control. Genes were categorized into UP, Down and Neutrally regulated based on the log2fold change cutoff of 1 value.

organism: Escherichia coli BL21(DE3)

source_name: bacterial cell

growth_protocol: Aerobic (A) and Microaerobic (M) fermentation was carried out in E.coli BL21(DE3) and E.coli cells were grown in Kortz based media (containing 100g/l lactose) in bioreactor under strict oxygen control conditions to late log phase, cells were collected at different time points (10th,12th,14th hour) and proceeded for RNA isolation

value: Aerobic (A) fermentation

tag: growth phase

value: late log phase cultures

tag: time point

value: 14th hour