title: WIBR2 hPSCs in HENSM medium, replication 2

description:
Poly-A RNA-seq
WIBR2 hPSCs in HENSM medium, batch 4, replication 2
counts_batch4.txt
WIBR2_HENSM_2

value: HENSM


title: WIBR2 hPSCs in tHENSM medium (titrated Erki 0.33mM), replication 1

status: Public on Mar 25 2021

type: SRA

city: Rehovot

first: Noa

last: Novershtern

address: Weizmann Institute

department: Molecular Genetics

country: Israel

institute: Weizmann Institute of Science

description:
Poly-A RNA-seq
WIBR2 hPSCs in tHENSM medium (titrated Erki 0.33mM), batch 4, replication 1
counts_batch4.txt
WIBR2_tHENSM_1

library_source: transcriptomic

data_processing:
We used Illumina CASAVA 1.8.2 software to generate fastq files.
reads were aligned to hg38 Genome using STAR aligner
counts were generated with HTSeq
Dataset was filtered to include genes that have at least one call > 10
All samples were normalized using DESeq 2 (default parameters)
Batch effect correction was done by substructing the minimal normzlied count of each gene in each batch.
Genome_build: hg38
Supplementary_files_format_and_content: matrix with counts of all genes and samples in the batch. Pre-normalization

molecule: total RNA

organism: Homo sapiens

source_name: human embryonic stem cells

growth_protocol: Maintenance of human naïve pluripotent cells were conducted using "Enhanced NHSM" (HENSM) as detailed in bayerl et.al in feeder free conditions on plates coated with 1% Matrigel (BD- FAL356231). Maintenance of human primed pluripotent cells were conducted using mTESR (Ludwing and Thomson: Curr. Protoc. Stem Cell Biol. 2:1C.2.1-1C.2.16) in feeder free conditions on plates coated with 1% Matrigel

extract_protocol:
Total RNA was isolated from indicated cell lines and extracted from Trizol pellets by chloroform-phenol extraction protocol.
Total RNA was then utilized for RNA-Seq by ScriptSeq Preparation Kit v2 (Illumina) according to manufacturer’s instruction.

tag: cell line

tag: culture conditions

value: tHENSM

tag: batch


title: WIBR2 hPSCs in mTeSR medium, replication 2

description:
Poly-A RNA-seq
WIBR2 hPSCs in mTeSR medium, batch 4, replication 2
counts_batch4.txt
WIBR2_primed_2

value: mTeSR (primed)


title: WIBR2 hPSCs in mTeSR medium, replication 1

description:
Poly-A RNA-seq
WIBR2 hPSCs in mTeSR medium, batch 4, replication 1
counts_batch4.txt
WIBR2_primed_1


title: WIBR2 hPSCs in OHENSM medium (no Erki), replication 2

description:
Poly-A RNA-seq
WIBR2 hPSCs in OHENSM medium (no Erki), batch 4, replication 2
counts_batch4.txt
WIBR2_OHENSM_2

value: OHENSM


title: WIBR2 hPSCs in OHENSM medium (no Erki), replication 1

description:
Poly-A RNA-seq
WIBR2 hPSCs in OHENSM medium (no Erki), batch 4, replication 1
counts_batch4.txt
WIBR2_OHENSM_1


title: WIBR2 hPSCs in HENSM medium, replication 1

description:
Poly-A RNA-seq
WIBR2 hPSCs in HENSM medium, batch 4, replication 1
counts_batch4.txt
WIBR2_HENSM_1


title: LIS41 hPSCs in tHENSM medium (titrated Erki 0.33mM), replication 2

description:
Poly-A RNA-seq
LIS41 hPSCs in tHENSM medium (titrated Erki 0.33mM), batch 4, replication 2
counts_batch4.txt
LIS41_tHENSM_2


title: LIS41 hPSCs in tHENSM medium (titrated Erki 0.33mM), replication 1

description:
Poly-A RNA-seq
LIS41 hPSCs in tHENSM medium (titrated Erki 0.33mM), batch 4, replication 1
counts_batch4.txt
LIS41_tHENSM_1


title: Healthy Control 2 - H3K4me3

city: Glasgow

first: John

middle: Joseph

last: Cole

address: University Avenue

country: United Kingdom

institute: University of Glasgow

library_source: genomic

data_processing:
The read quality of ChIP-seq dataset was verified using fastQC (v0.11.7) with each sample showing a mean per base quality > 30 at all read positions.
The data aligned to the human genome (GRCh38 version 94) using bowtie 2 (v2.3.5) with default parameters for indexing and alignment.
A mean alignment of 28 million uniquely mapping reads per sample (74%) was observed.
Per sample wig files were generated using the PeakRanger (1.18) wig command with --format bam. Bigwigs were generated from the wig files using UCSC tools wigToBigWig (v4), with chromosome sizes as determined by UCSC tools faSize.
The per sample H3K4me3 peaks were called with macs2 (v2.1.1.20160309) callpeak using the input BAM file for each sample as the control, a genome size of 2,945,849,067bp and specifying --format BAM.
Genome_build: Hg38
Supplementary_files_format_and_content: Peak text files

molecule: genomic DNA

source_name: Healthy control_H3K4me3

growth_protocol: Freshly isolated PBMCs were suspended in DPBS supplemented with 1% FBS, 0.1% NaN3 and 5mM EDTA and stained for flow cytometry.

extract_protocol:
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.
ChIP-seq libraries were prepared using the NEB NEXT UltraII DNA-library prep kit (E7645S for ChiP and E7600S for input) and samples were sequenced on an Illumina Next-Seq to a mean depth of 38 million reads. The read length was 75pb SE.

tag: subject status

value: Healthy control

tag: cell type

value: blood-derived monocytes

tag: chip antibody

value: H3K4me3 (Anti-trimethyl-Histone H3 (Lys4), Merck Millipore,07-473)


title: LIS41 hPSCs in OHENSM medium (no Erki), replication 2

description:
Poly-A RNA-seq
LIS41 hPSCs in OHENSM medium (no Erki), batch 4, replication 2
counts_batch4.txt
LIS41_OHENSM_2


title: LIS41 hPSCs in OHENSM medium (no Erki), replication 1

description:
Poly-A RNA-seq
LIS41 hPSCs in OHENSM medium (no Erki), batch 4, replication 1
counts_batch4.txt
LIS41_OHENSM_1


title: LIS41 hPSCs in mTeSR medium, replication 2

description:
Poly-A RNA-seq
LIS41 hPSCs in mTeSR medium, batch 4, replication 2
counts_batch4.txt
LIS41_primed_2


title: LIS41 hPSCs in HENSM + Activin medium, replication 2

description:
Poly-A RNA-seq
LIS41 hPSCs in HENSM + Activin medium, batch 4, replication 2
counts_batch4.txt
LIS41_HENSM_ACT_2

value: HENSM + Activin


title: LIS41 hPSCs in HENSM + Activin medium, replication 1

description:
Poly-A RNA-seq
LIS41 hPSCs in HENSM + Activin medium, batch 4, replication 1
counts_batch4.txt
LIS41_HENSM_ACT_1


title: LIS41 hPSCs in HENSM medium, replication 1

description:
Poly-A RNA-seq
LIS41 hPSCs in HENSM medium, batch 4, replication 1
counts_batch4.txt
LIS41_HENSM_1


title: WIBR3 hPSCs in HENSM + Activin medium, replication 8

description:
Poly-A RNA-seq
WIBR2 hPSCs in HENSM + Activin medium, replication 8
counts_batch2.txt
WIBR3_HENSM_ACT_8


title: LIS41 hPSCs in HENSM medium, replication 2

description:
Poly-A RNA-seq
LIS41 hPSCs in HENSM medium, batch 4, replication 2
counts_batch4.txt
LIS41_HENSM_2


description:
Poly-A RNA-seq
WIBR3 hPSCs in HENSM Xeno-free medium, replication 14
counts_batch2.txt
WIBR3_XF_HENSM_14


description:
Poly-A RNA-seq
WIBR3 hPSCs in HENSM Xeno-free medium, replication 13
counts_batch2.txt
WIBR3_XF_HENSM_13


description:
Poly-A RNA-seq
WIBR3 hPSCs in HENSM medium, replication 12
counts_batch2.txt
WIBR3_HENSM_12


description:
Poly-A RNA-seq
WIBR3 hPSCs in HENSM medium, replication 11
counts_batch2.txt
WIBR3_HENSM_11


description:
Poly-A RNA-seq
WIBR2 hPSCs in HENSM + Activin medium, replication 7
counts_batch2.txt
WIBR2_HENSM_ACT_7


description:
Poly-A RNA-seq
LIS49 hPSCs in HENSM medium, replication 16
counts_batch2.txt
LIS49_HENSM_16


description:
Poly-A RNA-seq
LIS49 hPSCs in HENSM + Activin medium, replication 4
counts_batch2.txt
LIS49_HENSM_ACT_4


description:
Poly-A RNA-seq
LIS49 hPSCs in HENSM medium, replication 7
counts_batch2.txt
LIS49_HENSM_7


description:
Poly-A RNA-seq
WIBR2 hPSCs in HENSM medium, replication 10
counts_batch2.txt
WIBR2_HENSM_10


description:
Poly-A RNA-seq
LIS41 hPSCs in HENSM medium, replication 4
counts_batch2.txt
LIS41_HENSM_4


description:
Poly-A RNA-seq
LIS41 hPSCs in HENSM medium, replication 3
counts_batch2.txt
LIS41_HENSM_3


description:
Poly-A RNA-seq
WIBR2 hPSCs in HENSM medium, replication 9
counts_batch2.txt
WIBR2_HENSM_9


description:
Poly-A RNA-seq
LIS49 hPSCs in mTeSR medium, replication 5
counts_batch2.txt
LIS49_primed_5


title: H9 hPSCs in HENSM medium, replication 2

description:
Poly-A RNA-seq
H9 hPSCs in HENSM medium, replication 2
counts_batch2.txt
H9_HENSM_2


description:
Poly-A RNA-seq
HUES64 (DNMT1-KO) hPSCs in HENSM medium, replication 2
counts_batch2.txt
DNMT1_KO_HENSM_2

value: HUES64 (DNMT1 KO)


title: LIS41 hPSCs in mTeSR medium, replication 1

description:
Poly-A RNA-seq
LIS41 hPSCs in mTeSR medium, batch 4, replication 1
counts_batch4.txt
LIS41_primed_1


title: H9 hPSCs in HENSM medium, replication 1

description:
Poly-A RNA-seq
H9 hPSCs in HENSM medium, replication 1
counts_batch2.txt
H9_HENSM_1


title: LIS49 hPSCs in HENSM medium, sample # 8

description:
ribo-zero RNA-seq
LIS49 hPSCs in HENSM medium, sample # 8
counts_batch3.txt
LIS49_HENSM_8


description:
ribo-zero RNA-seq
LIS49 hPSCs in HENSM medium, sample # 15
counts_batch3.txt
LIS49_HENSM_15


title: LIS49 hPSCs in mTeSR medium, sample # 6

description:
ribo-zero RNA-seq
LIS49 hPSCs in mTeSR medium, sample # 6
counts_batch3.txt
LIS49_primed_6


title: LIS41 hPSCs in HENSM medium, sample # 5

description:
ribo-zero RNA-seq
LIS41 hPSCs in HENSM medium, sample # 5
counts_batch3.txt
LIS41_HENSM_5


title: LIS41 hPSCs in HENSM medium, sample # 6

description:
ribo-zero RNA-seq
LIS41 hPSCs in HENSM medium, sample # 6
counts_batch3.txt
LIS41_HENSM_6


title: ko_setd2fl_3.batch2

city: Kansas City

first: Ning

last: Zhang

state: MO

address: 1000 E. 50th Street

country: USA

institute: Stowers Institute for Medical Research

description: processed data file: rsem_tpm.batch2.txt

data_processing:
Raw reads are demultiplexed into fastq format allowing up to one mismatch using Illumina bcl2fastq2 v2.18.
For RNA-seq samples, reads are aligned to UCSC genome hg38 with STAR aligner (version STAR_2.6.1c ), using Ensembl 96 gene models.
Transcript per million (TPM) values are generated by RSEM (version 1.3.0).
For ChIP-seq samples, reads are aligned to hg38 genome using Bowtie2 (version 2.3.4.1). For WT and KO ChIP-seq samples, reads are first aligned to spiked-in dm6 genome, and unmapped reads are then aligned to hg38 genome.
Bigwig files are normalized using reads per million (RPM) and extended to fragment length for individual IP samples. For merged bigwig files, reads are extended to 150bp and signals are RPM normalized. WT (except batch2) and KO merged bigwig files are also normalized to the spiked-in dm6 counts.
Genome_build: hg38 (GRCh38)
Supplementary_files_format_and_content: ChIP-seq in bigwig files.
Supplementary_files_format_and_content: RNA-seq TPM in tab-delimited text file.

source_name: HEK293T cells

growth_protocol: HEK293T were maintained as adherent cells in DMEM supplemented with 10% FBS and 2 mM L-glutamine at 37 °C with 5% CO2.

extract_protocol:
Total RNA was isolated from exponentially growing 293T cells and treated with DNaseI.
Sequencing libraries were prepared using High Throughput Library Prep Kit (KAPA Biosystems) following the manufacturer’s instructions. For RNA-Seq, ribodepletion and polyA enrichment was performed before library preparation.

tag: genotype/variation

value: SETD2 knockout full length rescued


title: ko_setd2fl_4.batch2


title: ko_setd2n3_2.batch2

value: SETD2 knockout N3 rescued


title: ko_setd2n3_1.batch2


title: ko_untreated_4.batch2

value: SETD2 knockout


title: wt_untreated_2.batch1

description: processed data file: rsem_tpm.batch1.txt

value: Wild type


title: ko_untreated_2.batch1


title: ko_untreated_2.batch2


description:
Poly-A RNA-seq
HUES64 (DNMT1-KO) hPSCs in HENSM medium, replication 1
counts_batch2.txt
DNMT1_KO_HENSM_1


title: wt_untreated_1.batch1


title: IMR90 MYC shSF3A3 RNA-seq #1

city: Lund

first: Phuong

last: Cao Thi Ngoc

address: BMC, B1222b, Klinikgatan 26

country: Sweden

institute: Lund University

data_processing:
RNA-seq datasets were aligned to the hg38 human genome using STAR v2.5.2b  with the parameter outFilterMultimapNmax set to 1.
Bioconductor package DESeq2  was used to analyze differential gene expression.
rMAT v4.0.2 was used to identify alternative splicing events
Genome_build: hg38
Supplementary_files_format_and_content: bigwig files

source_name: IMR90 cells

growth_protocol: IMR90 human primary cells cultured in EMEM+10%FBS+1%Penicilin/Streptomycin under standard conditions (5% CO2 humified chamber).

extract_protocol:
Total RNA from the cells was prepared using the Direct-zol™ RNA MicroPrep (Zymo Research Corporation) according to manufacturer's protocol. DNAse in column treatment was performed according to guidelines of the producer. Quality and quantity of the resulting RNA was confirmed by RNA Nano LabChip Bioanalyzer run (Agilent).
Libraries were constructed from 300 ng of total RNA using the TruSeq Stranded Total RNA LT Sample Prep (with  Ribo-Zero Gold treatment and single indexing). Quality of libraries was ensured with Bioanalyzer High Sensitivity DNA kit (Agilent). Sequencing was performed using the NextSeq 500 High Output v2 kit (300 cycles) Illumina platform.

treatment_protocol: Cells were subjected to subsequent lentiviral transduction with doxycycline (dox) inducible c-MYC oncogene vector and short hairpin RNA against SF3A3 splicing factor. After selection for pure populations of transduced cells, MYC was induced by 1 ug/ml dox and cells were harvested 24 hours afterwards into Trizol reagent.

tag: overexpression

value: MYC

tag: knockdown


title: IMR90 MYC shSF3A3 RNA-seq #3


title: IMR90 MYC shSF3A3 RNA-seq #2


title: IMR90 SF3A3 5'UTR DMS-MaPseq #2

data_processing:
Library strategy: DMS-MaPseq
All the relevant data analysis steps were performed using the RNA Framework suite.
Scoring and normalization of DMS signal was performed using respectively the Zubradt method  and 90% Winsorizing.
Genome_build: hg38
Supplementary_files_format_and_content: bw

extract_protocol:
Cells were collected by centrifugation and total RNA extracted with TRIzol Reagent (ThermoFisher Scientific, #15596018). After phase separation, the aqueous phase was added to 1 ml of 100% ethanol and the RNA purified on RNA Clean & Concentrator-5 columns (Zymo Research, #R1016). For reverse transcription, 2 ug of total RNA were heated at 70°C for 5 min, in the presence of 1 uM final gene specific primer and 1 mM final each dNTP. Sample was then immediately transferred to ice for 1 min, after which reaction was supplemented with RT buffer [50 mM Tris pH 8.3; 75 mM KCl; 3 mM MgCl2], 5 mM final DTT and 10 U SuperaseIN RNase Inhibitor (Invitrogen, #AM2694), and incubated at r.t. for 5 min. 100 U of TGIRT-III RT enzyme (InGex) were then added and the reaction was allowed to proceed at 50°C for 5 min, followed by 2 h at 57°C. The enzyme-cDNA-RNA complex was resolved by addition of 1 ul NaOH (5 N) followed by 3 min at 95°C. cDNA was then purified using RNA Clean & Concentrator-5 columns and 20% of cDNA was used for PCR using gene-specific primers and TaKaRa Taq™ DNA Polymerase (TaKaRa, #R0001A). To prepare libraries for the endogenous WT SF3A3 5' UTR, the PCR amplicon was first sheared into fragments of ~150-200 bp.
Library preparation was performed using 10 ng of sheared DNA and the NEBNext Ultra II DNA Library Prep kit (NEB, #E7645S), following manufacturer instructions. To prepare libraries for the Fluc constructs, gene-specific primers were fused with Illumina adaptor overhangs. After a first round of PCR, library barcodes were introduced by a second round of PCR. Libraries were then sequenced on a Illumina NextSeq 500 instrument.

treatment_protocol: ~10^6 cells were resuspended in RNA Probing Buffer [50 mM HEPES pH 7.9; 140 mM NaCl; 3 mM KCl] and pre-equilibrated at 37°C for 5 min. 1.76 M DMS in ethanol was added to a final concentration of 150 mM. After gentle vortexing, probing was allowed to proceed at 37°C for 2 min with moderate shaking. Reactions were quenched by addition of DTT to a final concentration of 0.7 M. Cells were collected at 2000 × g (4°C) for 3 min and subsequently washed once with PBS/0.7 M DTT.

tag: in vivo/in vitro transcribed

value: in vivo transcribed


title: RNA-seq in iNeuron rep6

city: Shanghai

first: Wei

last: Wu

state: Shanghai

address: 320 yueyang road

department: Center for Excellence in Molecular Cell Science

country: China

data_processing:
SAR-seq, END-seq, ChIP-seq, SEAL, and ATAC-seq reads were aligned to the reference genome (hg19 for human i3Neuron and iMuscle, mm10 for mouse pre B cells or rn6 for rat primary neurons) using bowtie (v1.1.2) with parameters -n 3 -l 50 -k 1 for END-seq and -n 2 -l 50 -m 1 for the rest. RNA-seq reads were aligned by STAR (v2.7.6a). Functions “view” and “sort” of samtools (v 1.6) were used to convert and sort the aligned sam files to sorted bam files. Bam files were further converted to bed files by the bedtools bamToBed command. Mitochondrial reads were removed in SAR-seq for intensity comparisons.
For RNA-seq, fragments per kilobase of transcript per million mapped reads (FPKM) was calculated by cufflinks based on the annotation from GENCODE v33. Mean values of replicates were used for analyses.
Genome_build: hg19
Supplementary_files_format_and_content: FPKM

molecule: polyA RNA

source_name: iNeuron

growth_protocol: For neuronal differentiation, 20-25 million iPSCs were plated on day 0 onto a 15 cm plate in N2 media composed of knockout DMEM/F12 media (Life Technologies Corporation, Cat. No. 12660012) with N2 supplement (Life Technologies Corporation, Cat. No. 17502048), 1x GlutaMAX (Thermofisher Scientific, Cat. No. 35050061), 1x MEM nonessential amino acids (NEAA) (Thermofisher Scientific, Cat. No. 11140050), 10 M ROCK inhibitor (Y-27632; Selleckchem, Cat. No. S1049), and 2 g/mL doxycycline (Clontech, Cat. No. 631311). N2 media was changed once a day for two more days. Day 3 cells were replated onto freshly-prepared poly-L-ornithine- (PLO; 0.1 mg/ml; Sigma, Cat. No. P3655-10MG) coated dishes as follows: Cells were washed with PBS, dissociated with accutase for 10 minutes at 37°C, washed and plated in i3Neuron Culture Media: BrainPhys media (STEMCELL Technologies, Cat. No. 05790) supplemented with 1x B27 Plus Supplement (ThermoFisher Scientific, Cat. No. A3582801), 10 ng/mL BDNF (PeproTech, Cat. No. 450-02), 10 ng/mL NT-3 (PeproTech, Cat. No. 450-03), 1 mg/mL mouse laminin (Sigma, Cat. No. L2020-1MG), and 2 g/mL doxycycline (Clontech, Cat. No. 631311).For 10 cm plates used in SAR-seq or CHIP-seq, 12-15 million neurons were plated. For 15 cm plates 30-45 million neurons were plated. For ibidi slides used in imaging experiments, 0.2 million neurons per well were plated. Unless otherwise noted, i3Neurons were fed on day 6 during a half media change and harvested on day 7. For i3Neurons cultured beyond 7 days, half media changes were conducted three times per week. In some experiments pre-differentiated i3Neurons were frozen on day 3 in 90% fetal bovine serum (Sigma Aldrich, Cat. No. ES-009-B) and 10% DMSO (Mediatech Inc., Cat. No. 25-950-CQC), and then thawed rapidly at 37°C, followed by removal of FBS/DMSO and plating in i3Neuron Culture Media. We did not detect any differences for experiments where day 3 neurons were thawed or plated immediately following differentiation.

extract_protocol: To extract RNA, cells were plated on 6-well dishes, washed with PBS, and then 500 L of tri-reagent (Zymo research corporation, Cat. No. R2050-1-200) was added directly to the cells. The lysed cells were collected using a cell scraper. To isolate RNA, we used a Direct-zol RNA miniprep kit (Zymo Research Corporation, Cat. No. R2052), following manufacturer’s instructions including the optional DNAse step.For RNA sequencing, six biological replicates were sequenced. Total RNA was enriched for polyA and sequenced 2x75 bp on a HiSeq machine.

tag: harvested day

value: neuron differentiated from iPSC


description:
ribo-zero RNA-seq
LIS49 hPSCs in HENSM + Activin medium, sample # 5
counts_batch3.txt
LIS49_HENSM_ACT_5


title: RNA-seq in iNeuron rep5

institute: Center for Excellence in Molecular Cell Science


title: RNA-seq in iNeuron rep4


title: DNMT1 KO, HENSM + Activin, sample 1 [WGBS_DNMT1_KO_1]

data_processing:
We used Illumina CASAVA 1.8.2 software to generate fastq files.
Reads were aligned to hg19 reference genome using proprietary software, which is based on bowtie2, and is available for download here: https://tanaylab.bitbucket.io/misha/. In cases where the two reads were not aligned in a concordant manner, the reads were discarded.
For each CpG site, the numbers of methylated and unmethylated reads were counted.
Genome_build: hg19
Supplementary_files_format_and_content: The tab file is the output of misha software. Each file consists of chromosomal location (like a bed file), the number of methylated reads and number of unmethylated reads in each location.

source_name: DNMT1 KO, HENSM + Activin

extract_protocol:
DNA was isolated from cells using the Quick-gDNA miniprep kit (Zymo). DNA (50ng) was then converted by bisulfite using the EZ DNA Methylation-Gold kit (Zymo).
Libraries were prepared using the TruSeq kit (Illumina) and length distribution of each library was measured using the Bioanalyzer and product concentration was measured using Qubit Fluorometric Quantitation.

value: HUE64 (Dnmt1-KO, positive control)

value: human embryonic stem cells

tag: passage (if available)


title: tHENSM, sample 9 [WGBS_tHENSM_9]

source_name: tHENSM

value: HENSM + NOTCHi, titrated Erki 0.33 microM


title: DNMT1 KO, HENSM + Activin, sample 2 [WGBS_DNMT1_KO_2]


title: IMR90 SF3A3 5'UTR DMS-MaPseq #1


title: RNA-seq in iNeuron rep3


title: RNA-seq in iNeuron rep2


title: tHENSM, sample 8 [WGBS_tHENSM_8]


title: ko_untreated_1.batch1


title: tHENSM, sample 6 [WGBS_tHENSM_6]


title: RNA-seq in iNeuron rep1


title: tHENSM, sample 7 [WGBS_tHENSM_7]


title: TF-1_sgMTSS1_2

city: Vienna

first: Rotraud

last: Wieser

address: Waehringer Guertel 18-20

department: Department of Medicine I

country: Austria

institute: Medical University of Vienna

data_processing:
Unmapped BAM-files were converted to FASTQ with SAMtools v1.10 and adapter trimming was performed using Bbduk of BBMap v38.70.
Sequence quality was checked using FASTQC v0.11.9.
Reads were aligned to the human genome build GRCh38 using hisat2 v2.1.0 (--threads 2 -N 1 -L 20 -i S,1,0.5 -D 25 -R 5 --pen-noncansplice 12 --mp 1,0 --sp 3,0--time --reorder --rna-strandness F -x)
Reads which were not uniquely aligned to the genome were remove with SAMtools.
DESeq2 was used to quantify raw gene counts according to Homo_sapiens.GRCh38.97.gtf
Genome_build: GCA_000001405.15 GRCh38 genome build
Supplementary_files_format_and_content: Raw counts for all samples are summarized as tab delimited txt file

source_name: AML cell line

extract_protocol:
Total RNA was extracted using Trizol reagent according to the manufacturer’s protocol.   RNA quality was measured on a Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA).
RNA-seq libraries were prepared using the QuantSeq 3’ mRNA-Seq Library Prep Kit FWD for Illumina (Lexogen, Vienna, Austria).

tag: group

value: MTSS1 knock-out


title: tHENSM, sample 5 [WGBS_tHENSM_5]


title: BT549 WT RNA-seq #3

data_processing:
RNA-seq datasets were aligned to the hg38 human genome using STAR v2.5.2b with the parameter outFilterMultimapNmax set to 1.
Bioconductor package DESeq2 was used to analyze differential gene expression.
Genome_build: hg38
Supplementary_files_format_and_content: bigwig files

source_name: BT549 cells

growth_protocol: BT549 human breast cancer cell line (ATCC) were cultured in RPMI+10%FBS+0.023U/ml Insulin+1%Penicilin/Streptomycin under standard conditions (5% CO2 humified chamber).

extract_protocol:
Total RNA from the cells was prepared using the Direct-zol™ RNA MicroPrep (Zymo Research Corporation) according to manufacturer's protocol. DNAse in column treatment was performed according to guidelines of the producer. Integrity and quantity of the resulting RNA was confirmed by RNA Nano LabChip Bioanalyzer run (Agilent).
Libraries were constructed from 300 ng of total RNA using the TruSeq Stranded Total RNA LT Sample Prep (with  Ribo-Zero treatment and single indexing). Quality of libraries was ensured with Bioanalyzer High Sensitivity DNA kit (Agilent). Sequencing was performed using the NextSeq 500 High Output v2 kit (75 cycles) Illumina platform.

treatment_protocol: Parental BT549 cell line was subjected to targeted editing of SF3A3 5'UTR locus with gRNAs against SL3 translational element. After single-cell sorting and expansion, clones were checked for type of editing by Sanger sequencing. For experiment, cells were seeded and  harvested at ~80% confluency 24 hours afterwards into Trizol reagent.

value: BT549 cells

tag: genotype

value: WT


title: TF-1_sgMTSS1_1


title: TF-1_sgCtrl_2

value: control


title: tHENSM, sample 4 [WGBS_tHENSM_4]


title: TF-1_sgCtrl_1


title: tHENSM, sample 2 [WGBS_tHENSM_2]


title: WIBR2 hPSCs in mTeSR medium, sample # 8

description:
ribo-zero RNA-seq
WIBR2 hPSCs in mTeSR medium, sample # 8
counts_batch1.txt
WIBR2_primed_8

value: mTeSR (primed)


title: primed/conventional, sample 7 [WGBS_primed_7]

source_name: primed/conventional

value: primed/conventional human stem cell


title: tHENSM, sample 1 [WGBS_tHENSM_1]


title: LIS49 hPSCs in mTeSR medium, sample # 4

description:
ribo-zero RNA-seq
LIS49 hPSCs in mTeSR medium, sample # 4
counts_batch1.txt
LIS49_primed_4


title: WIBR2 hPSCs in mTeSR medium, sample # 7

description:
ribo-zero RNA-seq
WIBR2 hPSCs in mTeSR medium, sample # 7
counts_batch1.txt
WIBR2_primed_7


title: primed/conventional, sample 6 [WGBS_primed_6]


title: H1 hPSCs in mTeSR medium, sample # 2

description:
ribo-zero RNA-seq
H1 hPSCs in mTeSR medium, sample # 2
counts_batch1.txt
H1_primed_2


title: primed/conventional, sample 5 [WGBS_primed_5]


title: LIS49 hPSCs in mTeSR medium, sample # 3

description:
ribo-zero RNA-seq
LIS49 hPSCs in mTeSR medium, sample # 3
counts_batch1.txt
LIS49_primed_3


title: H1 hPSCs in mTeSR medium, sample # 1

description:
ribo-zero RNA-seq
H1 hPSCs in mTeSR medium, sample # 1
counts_batch1.txt
H1_primed_1


title: primed/conventional, sample 3 [WGBS_primed_3]


title: TF-1_sgMTSS1_3


description:
ribo-zero RNA-seq
WIBR2 hPSCs in HENSM + Activin + CHIR medium, sample # 3
counts_batch1.txt
WIBR2_HENSM_ACT_CHIR_3

value: HENSM + Activin + CHIR


description:
ribo-zero RNA-seq
H1 hPSCs in HENSM + Activin  + CHIR medium, sample # 2
counts_batch1.txt
H1_HENSM_ACT_CHIR_2


title: primed/conventional, sample 2 [WGBS_primed_2]


description:
ribo-zero RNA-seq
WIBR2 hPSCs in HENSM + Activin medium, sample # 6
counts_batch1.txt
WIBR2_HENSM_ACT_6

value: HENSM + Activin


title: 0HENSM, sample 5 [WGBS_0HENSM_5]

value: HENSM + NOTCHi, no Erki


title: 0HENSM, sample 4 [WGBS_0HENSM_4]


title: primed/conventional, sample 1 [WGBS_primed_1]

value: P3 (early passage)


title: 0HENSM, sample 3 [WGBS_0HENSM_3]


description:
ribo-zero RNA-seq
LIS41 hPSCs in HENSM + Activin medium, sample # 1
counts_batch1.txt
LIS41_HENSM_ACT_1


title: 0HENSM, sample 2 [WGBS_0HENSM_2]


description:
ribo-zero RNA-seq
LIS41 hPSCs in HENSM + Activin medium, sample # 2
counts_batch1.txt
LIS41_HENSM_ACT_2


title: ENSHM, no Erki [WGBS_HENSM_noErki]

source_name: ENSHM, no Erki

value: HENSM, no Erki


title: mPB1

city: Toronto

first: Alexander

middle: James

last: Murison

state: Ontario

address: 101 College Street, TMDT room 11-706

country: Canada

institute: University Health Network

data_processing:
Reads were aligned using STAR 2.6.0c. Default parameters were used except for the following: sjdbOverhang 30
RNA velocity was run on the bam files using run_smartseq2 in velocyto 0.17.8 with default settings.
Cells with total read counts or total genes 4 median absolute deviations (MADs) below the median were removed, as were cells with a proportion of mitochondrial genes 4 MADs above the median.
Denoising was performed using dca 0.2.2 and batch corrected using mnncorrect within scanpy 1.3.3.
Genome_build: GRCh38

source_name: human mobilized peripheral blood

extract_protocol:
Single cells were immediately lysed when sorted into wells with a mix of 5× Maxima Transcription Buffer, dNTPs, and NXGen RNase inhibitor (Lucigen)
Nextera XT DNA Library Preparation Kit (Illumina)

tag: age

tag: gender

value: male

tag: tissue

value: human mobilized peripheral blood

tag: cell markers


title: mPB2


title: primed/conventional, sample 4 [WGBS_primed_4]

tag: cell line

tag: culture conditions


title: 0HENSM, sample 1 [WGBS_0HENSM_1]


title: mPB3

value: female


title: BM1

source_name: human bone marrow

value: human bone marrow


title: HENSM, sample 8 [WGBS_HENSM_8]

source_name: HENSM

value: human embryonic stem cells

value: HENSM


title: HENSM, sample 7 [WGBS_HENSM_7]


title: HENSM, sample 6 [WGBS_HENSM_6]


title: HENSM, sample 4 [WGBS_HENSM_4]

value: early


title: HENSM, sample 5 [WGBS_HENSM_5]


title: HENSM, sample 3 [WGBS_HENSM_3]


description:
ribo-zero RNA-seq
H1 hPSCs in HENSM + Activin  + CHIR medium, sample # 1
counts_batch1.txt
H1_HENSM_ACT_CHIR_1

tag: batch


title: HENSM, sample 2 [WGBS_HENSM_2]

tag: cell type


title: tHENSM, sample 3 [WGBS_tHENSM_3]

value: HENSM + NOTCHi, titrated Erki 0.33 microM


title: HENSM + Activin, sample 3 [WGBS_HENSM_ACT_3]

source_name: HENSM + Activin

value: p12 (late passage)


title: ST_INKA1_1

data_processing:
Reads were aligned with STAR v2.5.2b annotated with ensembl v90. Default parameters were used except for the following: --chimSegmentMin 12 --chimJunctionOverhangMin 12 --alignSJDBoverhangMin 10 --alignMatesGapMax 100000 --alignIntronMax 100000 --chimSegmentReadGapMax parameter 3 --alignSJstitchMismatchNmax 5 -1 5 5.
Read counts were generated using HTSeq v0.7.2 and general statistics were obtained from picard v2.6.0.
Genome_build: hg38
Supplementary_files_format_and_content: Read counts per gene per sample (tsv), and copiled, variance stabilized expression per gene in all samples

source_name: human cord blood hematopoietic stem cells

growth_protocol: Cells were cultured in 96-well round-bottom plates with  X-VIVO 10 media, 1 % BSA supplemented with 1x Pen/Strep, L-Glutamine and the the following cytokines: SCF (100 ng/ml), Flt3L (100 ng/ml), TPO (50 ng/ml) and IL7 (10 ng/ml)

extract_protocol:
PicoPure RNA Isolation Kit (Thermo Fisher). Samples that passed quality control according to integrity (RIN>7) and concentration as verified on a Bioanalyzer were further processed. cDNA conversion was performed using SMART-Seq v4 Ultra Low Input RNA Kit for Sequencing (Takara)
Nextera XT DNA Library Preparation Kit (Illumina)

treatment_protocol: CD112high and CD112low LT-HSC, total LT-HSC and ST-HSC were FACS-sorted from 3 independent CB pools and either directly resuspended and frozen (-80°C) in PicoPure RNA Isolation Kit Extraction Buffer or after transduction (after 16 h prestimulation) followed by a second sort (PI-BFP+) on day 6 post-transduction (average cell count: 104; range 0.25-3x10^4)

value: hematopoietic stem cells

tag: donor pool

value: cord blood pool 1

tag: lentiviral vector

tag: culture and second sort (bfp+)

value: yes


title: ST_INKA1_2

value: cord blood pool 2


title: HENSM + Activin, sample 2 [WGBS_HENSM_ACT_2]

value: HENSM + Activin


title: ST_INKA1_3

value: cord blood pool 3


title: HENSM, sample 1 [WGBS_HENSM_1]


title: ST_CTRL_3

value: CTRL


title: HENSM, sample 9 [WGBS_HENSM_9]


title: LT_INKA1_3


title: LT_INKA1_2


title: ST_CTRL_1


title: HENSM + Activin, sample 1 [WGBS_HENSM_ACT_1]


title: ST_CTRL_2


title: Whole Cell Extract in WIBR2 cell line, maintained in PRIMED conditions [WCE_PRIMED_WIBR2_4]

data_processing:
We used Illumina bcl2fastq version 2.17.1.14 software to generate fastq files.
rreads were aligned to human hg19 reference genome using bowtie2 software, with default parameters.
for transcription factors, peaks were identified with MACS version 1.4.2-157. Whole-cell extract was used as control to define a background model. Duplicate reads aligned to the exact same location are excluded by MACS default configuration.
Supplementary_files_format_and_content: bed file, contains the peaks detected by MACS software

source_name: hESCs, WIBR2 cell line

extract_protocol:
Cells were crosslinked in formaldehyde (1% final concentration, 10 min at room temperature), and then quenched with glycine (5 min at room temperature). Fixated detailed in the table below were then lysed in 50 mM HEPES KOH pH 7.5, 140 mM NaCl, 1 mM EDTA, 10% glycerol, 0.5% NP-40 alternative, 0.25% Triton supplemented with protease inhibitor at 4 °C (Roche, 04693159001) for 10 min, and later centrifuged at 950g for 10 min. Supp was discarded and pellet was resuspended in RIPA-1 (0.2% SDS, 1 mM EDTA, 0.1% DOC, 140 mM NaCl and 10 mM Tris-HCl) with protease inhibitor. Cells were then fragmented with a Branson Sonifier (model S-450D) at −4 °C to size ranges between 200 and 800 bp and centrifugation at max speed for 10 min. Supp lysate was extracted and diluted with RIPA 2-3 fold (0.1% SDS, 1 mM EDTA, 0.1% DOC, Triton 1%, 140 mM NaCl and 10 mM Tris-HCl). Small amount of lysate were saved for whole cell extract at this point. Antibody was pre-bound by incubating with Protein-G Dynabeads (Invitrogen 10004D) in blocking buffer (PBS supplemented with 0.5% TWEEN and 0.5% BSA) for 1 h at room temperature. Washed beads were added to the lysate for incubation as detailed in the table below. Samples were washed five times with RIPA buffer, twice with RIPA buffer supplemented with 500 mM NaCl, twice with LiCl buffer (10 mM TE, 250mM LiCl, 0.5% NP-40, 0.5% DOC), once with TE (10Mm Tris-HCl pH 8.0, 1mM EDTA), and then eluted in 0.5% SDS, 300 mM NaCl, 5 mM EDTA, 10 mM Tris HCl pH 8.0. Eluate was incubated treated sequentially with RNaseA (Roche, 11119915001) for 30 min in 37°C  and proteinase K (NEB, P8102S) for 2 h in 37°C  and de-crosslinked in 65 °C for 8 h. DNA was purified with The Agencourt AMPure XP system (Beckman Coulter Genomics, A63881)
120ul SPRI AMPure XP beads (Agencourt) were added to the reverse-crosslinked samples, pipette-mixed 15 times and incubated for 2 minutes. Supernatant were separated from the beads using a magnet for 4 minutes. Beads were washed on the magnet with 70% ethanol and then air dried for 4 minutes. The DNA was eluted in 40 ul EB buffer (10 mM Tris-HCl pH 8.0) by pipette mixing 25 times. For the remainder of the library construction process (DNA end-repair, A-base addition, adaptor ligation and enrichment) a general SPRI cleanup involves addition of buffer containing 20% PEG and 2.5 M NaCl to the DNA reaction products (without moving them from their original well position). After thorough mixing and a 2-minute incubation at room temperature, plates are transferred to a magnet plate, incubated for 4 minutes and supernatant removed. Beads are then washed on the magnet with 150ul 70% ethanol and then air dried for 4 minutes. The DNA is eluted with 40ul of EB buffer by pipette mixing 25 times. Reagent kits are prepared in advance for all enzymatic steps (New England Biolabs). The DNA end-repair was performed by adding 27 µl of a master mix (17 µl master mix (5 ul T4 buffer, 5ul BSA-1mg/ml, 5ul ATP-10mM -2ul dNTPs 10 mM), 5 ul T4 PNK enzyme, 5 µl T4 polymerase (3 units) to each well. Samples were incubated in a thermal cycler at 12C for 15 min, 25C for 15 min, and finally cooled to 4C. The SPRI bead clean up method was used to purify the product (147 µl of 20% PEG, 2.5 M NaCl was added to each sample and eluted in 40 µl EB). The A-base addition was performed by adding 20 µl master mix (17 µl A-base add mix, 3 µl Klenow (3’->5’ exonuclease) to each well and incubated at 37C for 30 min. in a thermal cycler. SPRI bead clean up method was used to purify the product (132 µl of 20% PEG, 2.5 M NaCl was added to each sample and eluted in 19 µl EB). Adaptor ligation was performed by adding 34 µl of a master mix (29 µl 2x DNA ligase buffer, 5 µl DNA ligase) to each well. Finally 5 µl PE Indexed oligo adaptors (0.75 uM ) was added to each well and samples were incubated 25C for 15 min in a thermal cycler. SPRI bead clean up with size selection was used to purify the ligated products (15.5 µl of 20% PEG, 2.5 M NaCl was added to each sample and eluted in 40 µl EB). Finally, enrichment PCR was performed by adding 10 µl of a master mix (2 µl Forward/Reverse Index Primer, 0.5 µl dNTP mix, 5 µl 10x Pfu Ultra Buffer, 1 µl Pfu Ultra-II Fusion, 1.5 µl Nuclease free water) to each well. Plate was transferred to a thermal cycler and ran a Pfu amplification program at 95C for 2 min, 16 cycles of: 95C for 30 sec, 55C for 30 sec, 72C for 60 sec, and finally 72C for 10 min. The final SPRI clean up coupled to size selection was performed (35 µl SPRI beads was added to each sample and eluted in 40 µl).

value: WIBR2, 29-8 cell line

value: PRIMED

tag: target protein

value: WCE


title: Whole Cell Extract in LIS49 cell line, maintained in PRIMED conditions [WCE_PRIMED_LIS49_6]

source_name: hESCs, LIS49 cell line

value: LIS49 cell line


title: LT_INKA1_1


title: LT_CTRL_2


title: LT_CTRL_1


title: Whole Cell Extract in LIS49 cell line, maintained in PRIMED conditions [WCE_PRIMED_LIS49_1]


title: Whole Cell Extract in WIBR2 cell line, maintained in HENSM conditions [WCE_HENSM_WIBR2_8]


title: Whole Cell Extract in LIS49 cell line, maintained in PRIMED conditions [WCE_PRIMED_LIS49_11]


title: Whole Cell Extract in WIBR2 cell line, maintained in HENSM conditions [WCE_HENSM_WIBR2_7]


title: ATAC_Ery_iPSC_C-SNV_LA06_rep1

city: Oxford

first: Yavor

last: Bozhilov

state: Oxfordshire

address: John Radcliffe Hospital, Headington, Weatherall Institiute of Molecular Medicine

institute: WIMM, Oxford University

description: Genome-wide library of tagmented fragments

data_processing:
Mapping : bowtie -m 2 --maxIns 350, genome
For un-mapping reads : trimming adaptors trim_galore -- length 10, combining overlapping R1-R2 reads : flash -m 9 -x 0.125
Combining trimmed+flashed and originally mapped reads, mapping again with  bowtie -m 2 --maxIns 350
Removing read pairs overlapping Blacklisted regions
Removing duplicates : samtools rmdup
Reconstructing sequenced fragments from R1+R2 read pairs ( bedtools bedpe | cut -f 1,2,6) - for visualisation
Pileup of fragments (bedtools genomecov -counts)
Generating bigwig tracks
Genome_build: hg19; custom chr16 sequence fasta files: chr16_hg19_INV.fa.gz, chr16_hg19_Vas.fa.gz, chr16_hg19_Vs.fa.gz
Supplementary_files_format_and_content: bigWig : (DEEPtools) bamCoverage converison of filtered fragments (reconstructed, duplicate-filtered fragments : see above) from bam to bigwig,  (--binSize 10 --normalizeUsingRPKM --minMappingQuality 30)

source_name: iPSC diffrentiation to Erythroid cells

growth_protocol: Prior to the initiation of differentiation protocol, human iPSCs were cultured for at least 15 days on Vitronectin (Invitrogen) coated plates (Corning; TC treated) in STEMPRO hESC media (Invitrogen) supplemented with 20ng/ml bFGF (RnD). Cultures were maintained in this way for 5-6 passages at high confluency and split 1 in 4 when over 85% confluent. Human iPSCs were differentiated as published by Olivier et al., 2016 and harvested on day 21 of the differentiation protocol. Flow cytometry analysis was performed on 2x105 cells resuspended in 200μl of 2% bovine serum albumin (SIGMA) in phosphate buffered saline and labelled for 20 minutes at 4oC with fluorescein isothiocyanate (FITC) conjugated anti-CD71 (BD Biosciences; 555536) and phycoerythrin (PE) conjugated anti-CD235a (BD Biosciences; 340947). After staining cells were harvested and resuspended in PBS containing 0.02% Hoechst 33258 pentahydrate nucleic acid stain (Invitrogen). Analysis was performed on an Attune NxT Flow Cytometer (Invitrogen) and subsequently using FlowJo software for gating on viable single cell events and representing the data as a dot plot. Morphological analysis was preformed using a modified Wright stain on a Hemateck 03564647 slide strainer (BAYER). The slides were then imaged on a Nikon inverted microscope.

extract_protocol:
Assay for transposition of active chromatin sequencing (ATAC-Seq) was performed as previously published (Buenrostro, 2013) on single cell suspensions. 60000-80000 cells were used per biological replicate. Cells were lysed and nuclei were isolated prior to transposition with Tn5 transposase (Nextera, Illumina) for 30 minutes at 37°C. DNA was purified using a MinElute kit (Qiagen).
Libraries were amplified and barcoded using the NEBNext 2xMastermix (NEB) and the custom primers as published in Buenrostro et al., 2013. ATAC-Seq libraries profiles were visualized using D1000 tape on the Tapestation (Agilent). The libraries were quantified using the universal library quantification kit (KAPA Biosystems).

value: Erythroid

tag: Sex

value: Female

tag: differentiation day

value: Day 21

value: C-SNV allele homozygous


title: Rheumatoid Arthritis 11 - input

source_name: Rheumatoid Arthritis_input

tag: subject status

value: Rheumatoid Arthritis

value: blood-derived monocytes


title: ATAC_Ery_iPSC_C-SNV_LA13_rep1


title: Whole Cell Extract in WIBR2 cell line, maintained in PRIMED conditions [WCE_PRIMED_WIBR2_7]


title: wt_1.h3k36me3.batch2

description:
DNA IP
processed data file: wt_merged.h3k36me3.batch2.rpm.bw

source_name: HEK293T cells

extract_protocol:
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.
Sequencing libraries were prepared using High Throughput Library Prep Kit (KAPA Biosystems) following the manufacturer’s instructions. For RNA-Seq, ribodepletion and polyA enrichment was performed before library preparation.

tag: genotype/variation

value: Wild type

tag: chip antibody


title: wt_2.h3.batch2

description:
DNA IP
processed data file: wt_merged.h3.batch2.rpm.bw


title: wt_2.h3k36me3.batch2


title: wt_1.h3.batch2


title: Whole Cell Extract in WIBR2 cell line, maintained in HENSM conditions [WCE_HENSM_WIBR2_10]

value: HENSM


title: Whole Cell Extract in WIBR2 cell line, maintained in HENSM conditions [WCE_HENSM_WIBR2_4]


title: Whole Cell Extract in LIS49 cell line, maintained in HENSM conditions [WCE_HENSM_LIS49_9]


title: Whole Cell Extract in WIBR2 cell line, maintained in HENSM conditions [WCE_HENSM_WIBR2_12]


title: ko_2.h3k36me3

description:
DNA IP
processed data file: ko_merged.h3k36me3.rpm.bw
processed data file: ko_merged.h3k36me3.spikein.bw

value: SETD2 knockout


title: Whole Cell Extract in LIS49 cell line, maintained in PRIMED conditions [WCE_PRIMED_LIS49_9]


title: LT_CTRL_3

value: hematopoietic stem cells

value: yes


title: wt_2.h3k36me3

description:
DNA IP
processed data file: wt_merged.h3k36me3.rpm.bw
processed data file: wt_merged.h3k36me3.spikein.bw


title: ko_1.h3k36me3


title: Whole Cell Extract in LIS49 cell line, maintained in HENSM conditions [WCE_HENSM_LIS49_6]


title: Whole Cell Extract in LIS49 cell line, maintained in HENSM conditions [WCE_HENSM_LIS49_13_2]


title: Whole Cell Extract in LIS49 cell line, maintained in HENSM conditions [WCE_HENSM_LIS49_13_1]


title: wt_1.h3k36me3


title: Whole Cell Extract in LIS49 cell line, maintained in HENSM conditions [WCE_HENSM_LIS49_12]


title: Whole Cell Extract in LIS49 cell line, maintained in HENSM conditions [WCE_HENSM_LIS49_10]


title: n3wosri_1.h3k36me3

description:
DNA IP
processed data file: n3wosri_merged.h3k36me3.rpm.bw

value: SETD2 knockout N3woSRI rescued


title: n3wosri_2.h3k36me3


title: Whole Cell Extract in LIS41 cell line, maintained in HENSM conditions [WCE_HENSM_LIS41_12]

source_name: hESCs, LIS41 cell line

value: LIS41 cell line


title: n3_2.h3k36me3

description:
DNA IP
processed data file: n3_merged.h3k36me3.rpm.bw

value: SETD2 knockout N3 rescued


title: Cattle_tissues_mixed

city: Fort Collins

first: Michelle

middle: M

last: Halstead

state: CO

address: 200 West Lake Street

department: Biomedical Sciences

institute: Colorado State University

data_processing:
Basecalling and demultiplexing were performed using ont-guppy-for-minknow (v3.0.5 for cattle data; v3.2.6 for pig and chicken data), and reads with quality score below 7 were discarded to obtain fastq files.
Demultiplexed fastq files were grouped together for each sample, and processed with Pychopper (v2.4.0) to identify and orient full-length reads. Barcodes used for demultiplexing can be found in the README.txt file.
Full-length strand-oriented reads for each sample were mapped to the respective genome assemblies (ARS-UCD1.2 for cattle; Sscrofa11.1 for pig; GRCg6a for chicken) with minimap2 (v2.16r922) with options “-ax splice -uf -k14” and modifying the maximum allowable intron size by species with option "-G 1000000" for pig and cattle, and "-G 400000" for chicken.
Uniquely mapped reads with a minimum quality score of 10 were extracted with Samtools (v1.7).
Uniquely mapped reads were used to obtain raw gene expression counts, based on the Ensembl v101 annotations for each species, using HTSeq (v0.11.2) with options "-i gene_id --type=exon --stranded=yes --mode=intersection-nonempty."
Uniquely mapped reads from all samples were pooled to predict transcripts using the Pinfish pipeline (v0.1.0). Briefly, reads with similar structure were grouped into clusters of three or more alignments, with an exon boundary tolerance of 20 bp and terminal exon boundary tolerance of 60 bp. Transcript clusters were then polished and mapped back to the genome to produce polished transcripts, which were grouped into “loci” based on 3’ ends and collapsed to remove likely products of RNA degradation, using an internal exon boundary tolerance of 5 bp, a 3’-exon boundary tolerance of 100 bp, and a 5’-exon boundary tolerance of 5,000 bp. Predicted transcripts were then compared to the Ensembl (v101) and NCBI RefSeq (release 106) annotations, and only single-exon transcripts that demonstrated same-strand overlap with reference exons of protein-coding genes, or which were strongly supported (cluster size ≥ 100 alignments), were retained in the final transcript set.
Genome_build: ARS-UCD1.2 (cattle), Sscrofa11.1 (pig), GRCg6a (chicken)
Supplementary_files_format_and_content: Raw gene counts, based on the Ensembl (v101) annotation for each species

organism: Bos taurus

source_name: Pooled tissues

extract_protocol:
Frozen tissues kept at -80°C were homogenized with a mortar and pestle in liquid nitrogen. Total RNA was extracted using Trizol (Invitrogen, Carlsbad, CA) followed by a column clean-up using the Direct-zol RNA Mini Prep Plus kit (Zymo Research, Irvine, CA) and performing an in-column DNA digestion. Integrity of the DNase-treated RNA was verified on the Experion electrophoresis system (Bio-Rad, Hercules, CA).
For each sample, 50 ng total RNA was transferred to 0.2 ml PCR tubes and adjusted to a final volume of 9µl with nuclease free water.  Reactions were prepared (9 μl total RNA, 1 μl 10 µM VNP primer , 1 μl 10mM dNTPs) and incubated for 5 min at 65°C, then snap cooled on a pre-chilled freezer block. Strand-switching buffer (4 μl 5x RT buffer, 1 μl RNaseOUT, 1 μl nuclease-free water, and 2 μl 10 μM strand-switching primer) was then added to the snap-cooled, annealed mRNA, and incubated at 42°C for 2 min. One μl of Maxima H Minus Reverse Transcriptase was added, and reactions were incubated at 42°C for 90 min, 85°C for 5 min, and held at 4°C. A round of PCR was used to introduce barcodes to the cDNAs using Oxford Nanopore PCR barcoding expansion 1-96 kit (Cat. No.EXP-PBC096). Barcoding PCR reactions were set up for each cDNA (1 μl PCR barcode, 19 μl first-strand cDNA, 20μl LongAmp Taq 2x master mix), and cycled for [3 min at 95°C]x1, [15 sec at 95°C, 15 sec at 62°C, 7 min at 65°C] x13 cycles, [15 min at 65°C]x1, then held at 4°C. Each barcoded cDNA was purified in 1x Ampure XP Beads, eluted in 20µl of nuclease free water and quantified in the Qubit. Barcoded cDNAs were pooled in a final volume of 47µl and the pool was taken to the DNA Technologies Core and Expression Analysis Laboratory at the University of California Davis where they performed the adapter ligation on the cDNA pool using SQK-DCS109 kit following manufacturer's guidelines. 50 fmol of adapter ligated library was loaded onto PromethION flow cell vR9.4.1.
Long-read Nanopore cDNA sequencing

value: pooled male and female

value: Pooled tissues


title: n3_1.h3k36me3


title: TFAP2C Chip-seq in WIBR2 cell line, maintained in HENSM conditions [TFAP2C_HENSM_WIBR2]

value: WIBR2, 29-8 cell line

tag: matched control file

tag: antibody

value: Santa-Cruz sc-8977


title: fl_1.h3k36me3

description:
DNA IP
processed data file: fl_merged.h3k36me3.rpm.bw

value: SETD2 knockout full length rescued


description:
ribo-zero RNA-seq
LIS49 hPSCs in HENSM + Activin medium, sample # 3
counts_batch1.txt
LIS49_HENSM_ACT_3

source_name: human embryonic stem cells

value: HENSM + Activin


title: TFAP2C Chip-seq in LIS49 cell line, maintained in HENSM conditions [TFAP2C_HENSM_LIS49_3]

value: LIS49 cell line


title: TFAP2C Chip-seq in LIS49 cell line, maintained in HENSM conditions [TFAP2C_HENSM_LIS49_2]


title: TFAP2C Chip-seq in LIS49 cell line, maintained in HENSM conditions [TFAP2C_HENSM_LIS49_1]


title: Whole Cell Extract in LIS49 cell line, maintained in HENSM conditions [WCE_HENSM_LIS49_11]

value: WCE


title: SOX2 Chip-seq in LIS49 cell line, maintained in PRIMED conditions [SOX2_PRIMED_LIS49_2]

value: PRIMED

value: R&D Systems AF2018


title: SOX2 Chip-seq in LIS49 cell line, maintained in PRIMED conditions [SOX2_PRIMED_LIS49_1]


title: LFY DAP-seq

city: Grenoble

first: Jérémy

last: LUCAS

address: 17 avenue des Martyrs

country: France

institute: CNRS

description: Recombinant proteins were produced by TnT in vitro transcription translation system from Promega

data_processing:
Library strategy: DAP-seq
Alignment to genome is done by Bowtie2
poor quality and multimapped reads are filtered out using samtools
peak-calling is done by MACS2 with parameters (-q 0.001 --call-summits)
Peaks called where Control read coverage is too high are removed from analysis
replicates are treated by MSPC to create consensus peaks
Consensus peaks are reworked around maximum of peaks (+/-200 bp).
Consensus bedgraphs are computed by the mean of the replicates bedgraphs
Genome_build: TAIR10
Supplementary_files_format_and_content: Bed files contain position of consensus peaks centered around maximum
Bedgraphs files contain profiles of binding intensity (cpm)

organism: Arabidopsis thaliana

source_name: 35S::LFY 2-weeks old seedlings (CA26 #15; Sayou et al., Nature Communication, 2016)

growth_protocol: Grow on 0.5 Murashige and Skoog medium in long-day conditions for 2-weeks.

extract_protocol:
Genomic DNA was extracted by chloroform isoamyl alcohol dna extraction protocol
Libraries were contructed using Truseq Illumina kits
Illumina TruSeq adaptors with single end index

tag: protein epitope tags

tag: molecule type

value: Sheared genomic DNA extracted from plants


title: LFY ampDAP-seq

source_name: 2-weeks old seedlings

value: PCR amplified genomic DNA


title: fl_2.h3k36me3

tag: cell line


title: SF3A3 5'UTR mut in vitro DMS-MaPseq

organism: synthetic construct

source_name: The reporter plasmid cloned SF3A3 5'UTR mut

tag: in vivo/in vitro transcribed

value: in vitro transcribed


title: SF3A3 5'UTR WT in vitro DMS-MaPseq

source_name: The reporter plasmid cloned SF3A3 5'UTR WT


title: SOX2 Chip-seq in WIBR2 cell line, maintained in HENSM conditions [SOX2_HENSM_WIBR2_2]

tag: culture conditions

value: HENSM


title: SF3A3 5'UTR res in vitro DMS-MaPseq

source_name: The reporter plasmid cloned SF3A3 5'UTR res


title: SOX2 Chip-seq in WIBR2 cell line, maintained in PRIMED conditions [SOX2_PRIMED_WIBR2]


title: SOX2 Chip-seq in WIBR2 cell line, maintained in HENSM conditions [SOX2_HENSM_WIBR2_1]


title: contol tissue 4 (C2)

type: RNA

city: Hyderabad

first: Smita

last: Pawar

state: Telangana

address: College of Science, Osmania University

department: Genetics

country: India

institute: Osmania University

hyb_protocol: Arrays were incubated for 16 h in an Affymetrix GeneChip 645 hybridization oven at 45°C with rotation at 60 rpm.

scan_protocol: GeneChips were scanned with an Affymetrix GeneChip Scanner 3000.

data_processing: Raw data were analyzed using Affymetrix Expression Console and Transcriptome Analysis Console software

label: biotin

source_name: normal cervical epithelium

label_protocol: Affymetrix GeneChip WT Pico Kit was used for cDNA preparation and biotin labeling.cRNA was purified using an Affymetrix magnetic bead protocol. (GeneChip™ WT Pico Reagent Kit manual)

extract_protocol: Kit based extraction of total RNA from tissue,according to the manfacture protocol

tag: Stage

value: control


title: cervical cancer squamous tissue 209 (P7)

source_name: cervical cancer squamous cell carsinoma tissue

value: IB


title: contol tissue 1 (C1)


title: VIAAT-TRAP_28_vHC_45min

city: Zürich

first: Lukas

middle: Matthias

last: von Ziegler

address: Winterthurerstrasse 190

department: D-HESZ

country: Switzerland

institute: ETH Zürich

description: ribosome bound RNA

data_processing:
Adaptor trimmed with cutadapt (v 1.15), maximum error rate of 0.05 and a minimum length of 15
Pseudoalignment using kallisto (version 0.44.0) on the GENCODE M17 transcriptome
Aggregation on the protein coding level
Genome_build: GRCm38
Supplementary_files_format_and_content: .h5 files with kallisto output (pseudoaligned read counts). Files are futher zipped

organism: Mus musculus

source_name: hippocampus

growth_protocol: Mice are originally all from a C57BL/6J Background. More details about mouselines can be found in the metadata. Age of the mice is between 2 and 3 months

extract_protocol:
Trizol
illumina TrueSeq or Illumina Smartseq2 (see samples)

treatment_protocol: Homecage (no stress, control group) or 6 min 18°C swim stress

tag: condition

value: Swim

tag: timepoint

tag: region

value: vHC

value: Male

tag: hemisphere

value: both

tag: animalnumber

tag: experiment

value: VIAAT-TRAP

tag: block

tag: mousetype

value: VIAAT-bacTRAP

tag: mouseline

tag: libraryprotocol

value: illumina Smartseq2

tag: sampleprocessing


title: VIAAT-TRAP_27_dHC_45min

description: ribosome bound RNA

value: dHC

tag: Sex


title: cervical cancer squamous tissue 102  (P3)

value: IIB


title: cervical cancer squamous tissue 180 (P5)


title: Dp16;D-KO/K-KO_M3

city: Guangzhou

first: Xiaoling

last: Jiang

state: Guangdong

address: 9 Jinsui Road, Tianhe District

department: Department of Genetics and Endocrinology

institute: Guangzhou Women and Children's Medical Center

data_processing:
The obtained raw data was filtered with SOAPnuke (https://github.com/BGI-flexlab/SOAPnuke) to remove adaptors and low quality reads
The obtained clean reads were then mapped to the mouse genome mm10 using HISAT
Differentially expressed (DE) genes between groups were identified using DEGseq
Genome_build: mm10
Supplementary_files_format_and_content: EXCEL files include RPKM values for each Sample

source_name: Hippocampus

extract_protocol:
The hippocampi were isolated from the brain on an ice-cold platform and fast frozen in liquid nitrogen. Total RNA was isolated using the TRIzolTM reagents. The quantity and quality of the RNA were determined by using Agilent 2100 bioanalyzer
One μg RNA from each sample was used for library construction. Briefly, mRNA was first enriched with Oligo(dT)-coupled beads and then fragmented. Random N6 primers were used to synthesis double strand cDNAs. Bubble adaptors were ligated onto the products before PCR amplification. The PCR products were denatured into single strands by heating and the circularized with splint oligos before subjected to sequencing

tag: genotype

tag: strain


title: SOX2 Chip-seq in LIS49 cell line, maintained in HENSM conditions [SOX2_HENSM_LIS49_1]

tag: cell line

value: LIS49 cell line

tag: target protein

tag: matched control file

tag: antibody


title: Dp16;D-KO/K-KO_F2

value: Female


title: cervical cancer squamous tissue 188 (P6)

tag: Stage

value: IIIB


title: VIAAT-TRAP_26_vHC_0min

description: ribosome bound RNA

tag: condition

value: Homecage

tag: timepoint

tag: region


title: contol tissue 9 (C3)


title: cervical cancer squamous tissue 103 (P4)

value: IIIA


title: Dp16;D-KO/K-KO_F1


title: VIAAT-TRAP_25_dHC_0min

description: ribosome bound RNA

tag: hemisphere

tag: animalnumber

tag: experiment


title: OCT4 Chip-seq in WIBR2 cell line, maintained in PRIMED conditions [OCT4_PRIMED_WIBR2]

source_name: hESCs, WIBR2 cell line

value: WIBR2, 29-8 cell line

tag: culture conditions

value: PRIMED

value: Santa-Cruz SC8628


title: Dp16/D-KO_M3


title: BMDM - DM - rep3

city: Chengdu

first: Lulingxiao

last: Nie

state: Sichuan

address: Department of Prosthodontics, West China Hospital of Stomatology, Sichuan University, 3rd Section S Renmin Road

institute: Sichuan University

description: Gene expression in high glucose clutured, and metformin treated BMDMs

hyb_protocol: 0.6 μg of Cy3-labelled cRNA (specific activity ＞ 10.0 pmol Cy3/μg cRNA) was fragmented at 60℃ for 30 minutes in a reaction volume of 22.5 μl containing 1×Agilent fragmentation buffer and 2× Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent-085631 for 17 hours at 65℃ in a rotating Agilent hybridization oven. After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37℃ GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately afger washing on the Agilent DNA Microarray Scanner (G2505C) using one color scan setting for 4×180k array slides (Scan Area 61×21.6mm, Scan resolution 3μm, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 10.7.1.1 (Agilent) using default parameters to obtain backgroud subtracted and spatially detrended Processed Signal intensities as the raw data. Raw data were normalized in quantile algorithm with Genespring 13.0 (Agilent). Probe that at least 1 out of 2 samples flagged as Detected were maintained.

source_name: bone marrow derived macrophages, high glucose and metformin, replicate 3

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.2 μg RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA). Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

extract_protocol: RNA was extracted by mirVanaTM RNA Isolation Kit (Applied Biosystem p/n AM1556) following the manufacturer's instructions.

tag: treatment

value: cultured with high glucose and metformin

tag: cell type

value: primary macrophage


title: BMDM - D - rep2

description: Gene expression in high glucose clutured BMDMs

source_name: bone marrow derived macrophages, high glucose, replicate 2

value: cultured with high glucose


title: BMDM - N - rep2

description: Gene expression in untreated BMDMs

source_name: bone marrow derived macrophages, untreated, replicate 2

value: untreated


title: VIAAT-TRAP_24_vHC_45min

description: ribosome bound RNA

value: Swim

value: vHC

tag: Sex

value: Male

value: both

value: VIAAT-TRAP

tag: block

tag: mousetype

tag: mouseline

tag: libraryprotocol

tag: sampleprocessing


title: BMDM - N - rep3

description: Gene expression in untreated BMDMs

source_name: bone marrow derived macrophages, untreated, replicate 3


title: cervical cancer squamous tissue 68 (P2)

value: IVA


title: Dp16/D-KO_F2

tag: genotype

tag: strain

value: Female


title: SOX2 Chip-seq in LIS49 cell line, maintained in HENSM conditions [SOX2_HENSM_LIS49_2]

source_name: hESCs, LIS49 cell line

tag: cell line

value: LIS49 cell line

value: HENSM

tag: target protein

tag: matched control file

tag: antibody

value: R&D Systems AF2018


title: cervical cancer squamous tissue 21 (P1)

tag: Stage

value: Recurent case IA


title: OCT4 Chip-seq in LIS49 cell line, maintained in PRIMED conditions [OCT4_PRIMED_LIS49_4]

value: PRIMED


title: BMDM - D - rep3

source_name: bone marrow derived macrophages, high glucose, replicate 3


title: Dp16_F2


title: BMDM - DM - rep1

source_name: bone marrow derived macrophages, high glucose and metformin, replicate 1


title: BMDM - D - rep1

source_name: bone marrow derived macrophages, high glucose, replicate 1


title: Dp16_M4


title: VIAAT-TRAP_22_vHC_0min

description: ribosome bound RNA

tag: condition

value: Homecage

tag: timepoint

tag: region

tag: hemisphere

tag: animalnumber

tag: experiment

value: VIAAT-bacTRAP

value: illumina Smartseq2


title: WT_F2

value: WT

tag: Sex


title: OCT4 Chip-seq in LIS49 cell line, maintained in PRIMED conditions [OCT4_PRIMED_LIS49_2]

tag: culture conditions

value: Santa-Cruz SC8628


title: VIAAT-TRAP_21_dHC_0min

description: ribosome bound RNA

value: dHC

tag: block

tag: mousetype

tag: mouseline

tag: libraryprotocol


title: VIAAT-TRAP_23_dHC_45min

description: ribosome bound RNA

value: Swim

tag: sampleprocessing


title: OCT4 Chip-seq in LIS49 cell line, maintained in PRIMED conditions [OCT4_PRIMED_LIS49_1]

tag: cell line

tag: target protein


title: Dp16_M3

tag: genotype

tag: strain

value: Male


title: WT_M4


title: Dp16_F3


title: BMDM - N - rep1

description: Gene expression in untreated BMDMs

source_name: bone marrow derived macrophages, untreated, replicate 1

tag: treatment

value: untreated

tag: cell type

value: primary macrophage


title: WT_M3


title: BMDM - DM - rep2

source_name: bone marrow derived macrophages, high glucose and metformin, replicate 2

value: cultured with high glucose and metformin


title: VIAAT-TRAP_20_vHC_45min

description: ribosome bound RNA

tag: condition

tag: timepoint

tag: region

value: vHC

value: both

value: VIAAT-TRAP


title: VIAAT-TRAP_19_dHC_45min

description: ribosome bound RNA

tag: hemisphere

tag: animalnumber

tag: experiment


title: OCT Chip-seq in WIBR2 cell line, maintained in HENSM conditions [OCT4_HENSM_WIBR2]

description: OCT4 Chip-seq in WIBR2 cell line, maintained in HENSM conditions

value: WIBR2, 29-8 cell line

tag: culture conditions

value: HENSM

tag: matched control file

tag: antibody


title: VIAAT-TRAP_18_vHC_0min

description: ribosome bound RNA

tag: Sex

tag: block

tag: mousetype

tag: mouseline

tag: libraryprotocol


title: wt2

city: Tianjin

first: Hanyang

last: Dong

state: Tianjin

address: Tianjin Medical university

institute: Tianjin Medical university,China

data_processing:
After the library construction was completed, the library was initially quantized using Qubit2.0 Fluorometer and diluted to 1.5ng/ul, followed by Agilent 2100 BioAnalyzer to detect the insert size of the library
The basic principle of Sequencing is Sequencing by Synthesis. In the sequencing of the flow cell with four kinds of fluorescence labeled dNTP, primers for amplification, DNA polymerase and joint in each sequence complementary chain clusters, each to join a fluorescently labeled dNTP can release the corresponding fluorescence, sequencing machine by capturing the fluorescent signal, and through the computer software to convert optical signals to sequencing peak, thereby gaining fragment awaiting testing sequence information.
Genome_build: ASM584v2
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

organism: Escherichia coli K-12

source_name: Escherichia coli

growth_protocol: E. coli strains were cultured in LB medium at 37℃ until OD 0.6

extract_protocol:
Total 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.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: E. coli strains were stimulated under acidic conditions (pH2.5 LB) for 2 h

tag: strain

value: acid stress (pH2.5) for two hours

tag: genotype

value: wildtype


title: R3

tag: treatment

value: H-NS KO strain covering mutated H-NS K121R


title: wt3


title: R1


title: VIAAT-TRAP_17_dHC_0min

description: ribosome bound RNA

tag: condition

value: Homecage

value: VIAAT-bacTRAP

value: illumina Smartseq2

tag: sampleprocessing


title: Q3

value: H-NS KO strain covering mutated H-NS K121Q


title: OCT4 Chip-seq in LIS49 cell line, maintained in HENSM conditions [OCT4_HENSM_LIS49_1]

tag: cell line

value: LIS49 cell line

tag: target protein

value: Santa-Cruz SC8628


title: Q2


title: VIAAT-TRAP_16_vHC_45min

description: ribosome bound RNA

value: Swim

tag: timepoint

tag: region

value: Male

tag: hemisphere

tag: animalnumber


title: O3

value: H-NS KO strain


title: O2


title: Q1


title: NANOG Chip-seq in LIS49 cell line, maintained in PRIMED conditions [NANOG_PRIMED_LIS49_2]

tag: culture conditions

value: PRIMED

value: NANOG

tag: matched control file

tag: antibody

value: R&D Systems AF1997


title: k3

value: H-NS KO strain covering wt H-NS


title: VIAAT-TRAP_14_vHC_0min

description: ribosome bound RNA

value: vHC

tag: Sex

value: both

tag: experiment

value: VIAAT-TRAP

tag: block

tag: mousetype


title: NANOG Chip-seq in LIS49 cell line, maintained in PRIMED conditions [NANOG_PRIMED_LIS49_1]


title: wt1

tag: strain

value: acid stress (pH2.5) for two hours

tag: genotype

value: wildtype


title: O1

tag: treatment


title: NANOG Chip-seq in WIBR2 cell line, maintained in HENSM conditions [NANOG_HENSM_WIBR2]

value: WIBR2, 29-8 cell line

value: HENSM


title: k2


title: OCT4 Chip-seq in LIS49 cell line, maintained in HENSM conditions [OCT4_HENSM_LIS49_2]


title: k1


title: VIAAT-TRAP_13_dHC_0min

description: ribosome bound RNA

tag: condition

value: Homecage

value: dHC

value: VIAAT-bacTRAP

tag: mouseline

tag: libraryprotocol

value: illumina Smartseq2

tag: sampleprocessing


title: NANOG Chip-seq in LIS49 cell line, maintained in HENSM conditions [NANOG_HENSM_LIS49_1]

tag: cell line

value: LIS49 cell line

tag: target protein


title: VIAAT-TRAP_12_vHC_45min

description: ribosome bound RNA

value: Swim

tag: timepoint

tag: region

value: Male

tag: hemisphere

tag: animalnumber


title: NANOG Chip-seq in WIBR2 cell line, maintained in PRIMED conditions [NANOG_PRIMED_WIBR2]

tag: culture conditions

value: PRIMED

value: NANOG

tag: matched control file

tag: antibody


title: VIAAT-TRAP_15_dHC_45min

description: ribosome bound RNA

tag: Sex

tag: experiment

tag: block

tag: mousetype


title: Lung_Cancer_miRNA_rep 1 (T_63_T)

city: Genova

first: Alessandra

last: Pulliero

state: Genova

address: Via A. Pastore 1

country: Italy

institute: Dipartimento di Scienze della Salute UNIGE

description: miRNA profiling

hyb_protocol: After adding Hyb Spike-In, each sample was hybridized at 55°C for 20 hours on G4872A-070156 Human miRNA Microarray, Release 21.0, 8 x 60K (Agilent Technologies).

scan_protocol: Microarrays were scanned (3 microns, 20 bit) on an Agilent microarray scanner (part number: G2565CA) and data extracted using Agilent feature extraction v.10. QC metrics from feature extraction were used to evaluate the success of the labeling and hybridization.

data_processing: GeneSpring software (GeneSpring Multi-Omic Analysis version 14.9 – Build 11939 by Agilent Technologies) was used for analysis of miRNA expression. miRNA raw data files from Agilent Technologies Microarray Scanner System G2505C were imported to GeneSpring using miRNA analysis type, AgilentmiRNA,  Threshold: 1.0, Logbase: 2, Technology: Agilent.miRNA.70156_v21_0, Normalization: None, Baseline Transformation: None .

label: Cyanine 3-pCp

source_name: Lung Cancer Tissue

label_protocol: 50 ng of total RNA was processed using the Agilent miRNA complete labeling and hybridization kit (part number 5190-0456) and Agilent miRNA spike-in kit (part number 5190-1934). The, the Cy3-labeled RNA was purified using Micro Bio-Spin P-6 Gel Column (Bio-Rad Laboratories, Inc., Hercules, CA, USA).

growth_protocol: No growth

extract_protocol: The total RNA was extracted from lung biopsies using standardized protocols that combined phenol/guanidine-based lysis of samples and silica-membrane-based purification and quantified by Qubit 2.0 Fluorometer using the Qubit™ RNA HS Assay Kit (Thermo Fisher Scientific).

treatment_protocol: No treatment

tag: gender

tag: age (years)

tag: histotype

value: small-cell-lung-cancer

tag: alive

value: yes

tag: tissue

value: Lung Cancer Tissue


title: Lung_Cancer_miRNA_rep 1 (T_64_T)

description: miRNA profiling

value: non-small-cell-lung-cancer


title: VIAAT-TRAP_11_dHC_45min

description: ribosome bound RNA

tag: condition

value: both

value: VIAAT-TRAP

tag: mouseline

tag: libraryprotocol

tag: sampleprocessing


title: KLF4 Chip-seq in WIBR2 cell line, maintained in HENSM conditions [KLF4_HENSM_WIBR2_2]

tag: cell line

value: WIBR2, 29-8 cell line

tag: target protein

value: R&D Systems AF3158


title: VIAAT-TRAP_10_vHC_0min

description: ribosome bound RNA

value: Homecage

tag: timepoint

tag: region

value: vHC

tag: hemisphere

tag: animalnumber


title: Lung_Cancer_miRNA_rep 1 (T_61_T)

description: miRNA profiling

value: Female

tag: smoke habit


title: KLF4 Chip-seq in WIBR2 cell line, maintained in HENSM conditions [KLF4_HENSM_WIBR2_1]

tag: culture conditions

value: HENSM

tag: matched control file

tag: antibody


title: VIAAT-TRAP_9_dHC_0min

description: ribosome bound RNA

value: dHC

tag: Sex

tag: experiment

tag: block

tag: mousetype

value: VIAAT-bacTRAP

value: illumina Smartseq2


title: KLF4 Chip-seq in LIS49 cell line, maintained in HENSM conditions [KLF4_HENSM_LIS49_1]

value: LIS49 cell line


title: Lung_Cancer_miRNA_rep 1 (T_60_T)

description: miRNA profiling

tag: gender

tag: age (years)

tag: alive

tag: tissue


title: VIAAT-TRAP_8_vHC_45min

description: ribosome bound RNA

tag: condition

value: Swim

value: Male

tag: mouseline

tag: libraryprotocol

tag: sampleprocessing


title: KLF4 Chip-seq in LIS49 cell line, maintained in HENSM conditions [KLF4_HENSM_LIS49_2]

tag: cell line

tag: target protein


title: Lung_Cancer_miRNA_rep 1 (T_59_T)

description: miRNA profiling

tag: histotype

value: small-cell-lung-cancer

tag: smoke habit

value: yes


title: Lung_Cancer_miRNA_rep 1 (T_58_T)

description: miRNA profiling

value: Lung Cancer Tissue


title: Lung_Cancer_miRNA_rep 1 (T_57_T)

description: miRNA profiling

value: no


title: VIAAT-TRAP_7_dHC_45min

description: ribosome bound RNA

tag: timepoint

tag: region

tag: hemisphere

value: both

tag: animalnumber

value: VIAAT-TRAP


title: Lung_Cancer_miRNA_rep 1 (T_56_T)

description: miRNA profiling


title: Lung_Cancer_miRNA_rep 1 (T_55_T)

description: miRNA profiling


title: Lung_Cancer_miRNA_rep 1 (T_54_T)

description: miRNA profiling


title: KLF4 Chip-seq in LIS41 cell line, maintained in HENSM conditions [KLF4_HENSM_LIS41]

source_name: hESCs, LIS41 cell line

value: LIS41 cell line

tag: culture conditions

tag: matched control file

tag: antibody

value: R&D Systems AF3158


title: VIAAT-TRAP_6_vHC_0min

description: ribosome bound RNA

value: Homecage

value: vHC

tag: Sex

tag: experiment

tag: block

tag: mousetype


title: Lung_Cancer_miRNA_rep 1 (T_53_T)

description: miRNA profiling

tag: gender

value: Female

tag: age (years)

tag: alive

tag: tissue


title: VIAAT-TRAP_5_dHC_0min

description: ribosome bound RNA

tag: condition

value: dHC

tag: mouseline

tag: libraryprotocol

tag: sampleprocessing


title: KLF17 Chip-seq in LIS49 cell line, maintained in HENSM conditions [KLF17_HENSM_LIS49_2]

tag: cell line

value: HENSM

tag: target protein

value: Sigma HPA024629


title: Lung_Cancer_miRNA_rep 1 (T_52_T)

description: miRNA profiling

tag: histotype

tag: smoke habit


title: KLF17 Chip-seq in LIS49 cell line, maintained in HENSM conditions [KLF17_HENSM_LIS49_1]

value: LIS49 cell line

tag: culture conditions

tag: matched control file

tag: antibody


title: Lung_Cancer_miRNA_rep 1 (T_48_T)

description: miRNA profiling


title: VIAAT-TRAP_4_vHC_45min

description: ribosome bound RNA

value: Swim

tag: timepoint

tag: region

tag: Sex

tag: hemisphere

tag: animalnumber

tag: experiment

tag: block

value: VIAAT-bacTRAP

value: illumina Smartseq2


title: Lung_Cancer_miRNA_rep 1 (T_50_T)

description: miRNA profiling

tag: gender

value: Male

tag: age (years)

value: non-small-cell-lung-cancer

tag: alive

value: yes

tag: tissue


title: Lung_Cancer_miRNA_rep 1 (T_49_T)

description: miRNA profiling

value: no

value: Lung Cancer Tissue


title: H3K27AC Chip-seq in WIBR2 cell line, maintained in PRIMED conditions [H3K27AC_PRIMED_WIBR2]

tag: cell line

value: WIBR2, 29-8 cell line

value: PRIMED

tag: target protein

value: ABCAM ab4729


title: VIAAT-TRAP_3_dHC_45min

description: ribosome bound RNA

tag: condition

value: both

value: VIAAT-TRAP

tag: mousetype

tag: mouseline

tag: libraryprotocol

tag: sampleprocessing


title: H3K27AC Chip-seq in WIBR2 cell line, maintained in HENSM conditions [H3K27AC_HENSM_WIBR2]

tag: culture conditions

tag: matched control file

tag: antibody


title: VIAAT-TRAP_1_dHC_0min

description: ribosome bound RNA

value: Homecage

tag: timepoint

tag: region

value: dHC

tag: Sex

tag: hemisphere

tag: animalnumber


title: Lung_Cancer_miRNA_rep 1 (T_45_T)

description: miRNA profiling

tag: gender

tag: age (years)

tag: histotype

tag: smoke habit

tag: alive


title: Lung_Cancer_miRNA_rep 1 (T_47_T)

description: miRNA profiling

value: Female

tag: tissue


title: WIBR3_ATAC_PRIMED

description: ATAC-seq from hESCs, maintained in conventional hESC/primed conditions

data_processing:
We used Illumina CASAVA 1.8.2 software to generate fastq files.
Reads were trimmed with Trim Galore version 0.4.5
Reads were aligned to hg19 human genome using Bowtie2 with the parameter -X2000 (allowing fragments up to 2 kb to align).
Duplicated aligned reads were removed using Picard MarkDuplicates tool with the command REMOVE_DUPLICATES=true.
To identify chromatin accessibility signal we considered only short reads (≤ 120bp) that correspond to nucleosome free region. To detect and separate accessible loci in each sample, we used MACS version 1.4.2-1 with --call-subpeaks flag (PeakSplitter version 1.0).
To generate the final ATAC loci of naïve and primed conditions, we selected peaks that appear in the majority of the replicates of each conditions, i.e. 3 out of 4 naïve samples, and 2 out of 3 primed samples.
Genome_build: hg19
Supplementary_files_format_and_content: bed files generated by MACS, including all ATAC-seq peaks identified in each sample.

source_name: hESCs, WIBR3 cell line

extract_protocol: Following purification, the library fragments were amplified using custom Nextera PCR primers 1 and 2 for a total of 12 cycles. Following PCR amplification, the libraries were purified using a QiagenMinElute Kit and sequenced.

treatment_protocol: Cells were trypsinized and counted, 50,000 cells were centrifuged at 500g for 3 min, followed by a wash using 50 μl of cold PBS and centrifugation at 500g for 3 min. Cells were lysed using cold lysis buffer (10 mM Tris-HCl, pH 7.4, 10 mM NaCl, 3 mM MgCl2 and 0.1% IGEPAL CA-630). Immediately after lysis, nuclei were spun at 500g for 10 min using a refrigerated centrifuge. Next, the pellet was resuspended in the transposase reaction mix (25 μl 2× TD buffer, 2.5 μl transposase (Illumina) and 22.5 μl nuclease-free water). The transposition reaction was carried out for 30 min at 37 °C and immediately put on ice. Directly afterwards, the sample was purified using a Qiagen MinElute kit.

tag: cell line

value: conventional/primed


title: Lung_Cancer_miRNA_rep 1 (T_43_T)

description: miRNA profiling

value: small-cell-lung-cancer


title: Lung_Cancer_miRNA_rep 1 (T_44_T)

description: miRNA profiling


title: BF1_ATAC_PRIMED

source_name: hiPSCs, BF1 cell line

value: BF1 (iPSCs)


title: Lung_Cancer_miRNA_rep 1 (T_41_T)

description: miRNA profiling


title: Lung_Cancer_miRNA_rep 1 (T_40_T)

description: miRNA profiling


title: Lung_Cancer_miRNA_rep 1 (T_46_T)

description: miRNA profiling


title: Lung_Cancer_miRNA_rep 1 (T_38_T)

description: miRNA profiling


title: Lung_Cancer_miRNA_rep 1 (T_37_T)

description: miRNA profiling


title: Lung_Cancer_miRNA_rep 1 (T_36_T)

description: miRNA profiling


title: TimeSeriesFST_88_dHC_0min

description: polyA RNA

source_name: hippocampus

tag: condition

tag: experiment

value: TimeSeriesFST

tag: block

tag: mousetype

value: WT

tag: mouseline

tag: libraryprotocol

value: illumina TruSeq

value: WholeRNA


title: LIS49_ATAC_HENSM

description: ATAC-seq from hESCs, maintained in HENSM culture conditions

tag: culture conditions

value: HENSM


title: WIBR2_299_ATAC_PRIMED

source_name: hESCs, WIBR2 29-9 cell line


title: VIAAT-TRAP_2_vHC_0min

description: ribosome bound RNA

tag: timepoint

tag: region

value: vHC

tag: Sex

value: Male

value: VIAAT-bacTRAP

value: illumina Smartseq2

tag: sampleprocessing


title: Lung_Cancer_miRNA_rep 1 (T_34_T)

description: miRNA profiling

tag: gender

tag: age (years)

value: no

value: Lung Cancer Tissue


title: Lung_Cancer_miRNA_rep 1 (T_33_T)

description: miRNA profiling

tag: histotype

tag: smoke habit

value: yes


title: Lung_Cancer_miRNA_rep 1 (T_35_T)

description: miRNA profiling

tag: alive

tag: tissue


title: WIBR3_ATAC_HENSM

tag: cell line


title: LIS41_ATAC_HENSM


title: TimeSeriesFST_86_dHC_45min

description: polyA RNA

tag: condition

value: Swim

value: dHC

tag: hemisphere

value: both

tag: animalnumber

tag: experiment


title: TimeSeriesFST_87_vHC_0min

description: polyA RNA

value: Homecage

tag: block

tag: mousetype

tag: mouseline

tag: libraryprotocol


title: Lung_Cancer_miRNA_rep 1 (T_42_T)

description: miRNA profiling

value: small-cell-lung-cancer


title: Lung_Cancer_miRNA_rep 1 (T_39_T)

description: miRNA profiling

value: Female


title: TimeSeriesFST_83_vHC_3h

description: polyA RNA

tag: timepoint

tag: region

tag: Sex

value: TimeSeriesFST

value: WT


title: Lung_Cancer_miRNA_rep 1 (T_32_T)

description: miRNA profiling

tag: gender

tag: age (years)


title: TimeSeriesFST_84_dHC_3h

description: polyA RNA

value: illumina TruSeq

tag: sampleprocessing

value: WholeRNA


title: Lung_Tissue_miRNA_rep 1 (T_18_N)

description: miRNA profiling

source_name: Lung Normal Tissue

tag: smoke habit

tag: alive

value: Lung Normal Tissue


title: Lung_Cancer_miRNA_rep 1 (T_30_T)

description: miRNA profiling

value: Male

tag: histotype

tag: tissue


title: ML171653 24H Post Saline

city: Parkville

first: Jane

middle: T

last: Seto

state: VIC

address: 50 Flemington Road

country: Australia

institute: Murdoch Children's Research Institute, Royal Children's Hospital

data_processing:
Raw read data was processed using the Illumina BaseSpace RNA Express application (Illumina Inc. 2016)
Sequencing reads were aligned using STAR ultrafast RNA seq aligner in the SAM file format
Reads were counted using HTSeq
genewise count data was analyzed using the R (3.6.0) statistical programming language
Differential expression (DE) was conducted using the voom precision weights approach in the limma (3.40.6) package from the Bioconductor (3.9) project
Genome_build: mm10
Supplementary_files_format_and_content: text

source_name: Skeletal muscle

extract_protocol:
Quadriceps muscles were removed and weighed, flash frozen in liquid nitrogen, and RNA extracted using Trizol reagent. RNA was purified using Qiagen RNA columns and Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols on a Illumina HiSeq 2500

tag: genotype

tag: treatment

value: Saline

tag: time point

value: 24H Post


title: Lung_Cancer_miRNA_rep 1 (T_26_T)

description: miRNA profiling


title: ML171654 24H Post Dex

value: Dex


title: Lung_Cancer_miRNA_rep 1 (T_27_T)

description: miRNA profiling

value: non-small-cell-lung-cancer

value: Lung Cancer Tissue


title: Lung_Tissue_miRNA_rep 1 (T_13_N)

description: miRNA profiling

value: no


title: OCT4 Chip-seq in LIS49 cell line, maintained in PRIMED conditions [OCT4_PRIMED_LIS49_3]

city: Rehovot

first: Noa

last: Novershtern

address: Weizmann Institute

institute: Weizmann Institute of Science

tag: cell line

value: LIS49 cell line

tag: culture conditions

value: PRIMED

tag: target protein

tag: matched control file

tag: antibody

value: Santa-Cruz SC8628


title: ML171652 24H Post Dex

value: KO


title: TimeSeriesFST_80_dHC_4h

description: polyA RNA

tag: condition

value: Swim

tag: timepoint

tag: region

value: dHC

tag: hemisphere

value: both

tag: animalnumber

tag: experiment

tag: block

tag: mousetype

tag: mouseline

tag: libraryprotocol


title: TimeSeriesFST_81_vHC_1h30min

description: polyA RNA

value: vHC

tag: Sex

value: TimeSeriesFST

value: WT

value: illumina TruSeq

tag: sampleprocessing


title: WIBR2_298_ATAC_HENSM

source_name: hESCs, WIBR2 29-8 cell line

tag: cell line

value: HENSM


title: TimeSeriesFST_85_vHC_45min

description: polyA RNA

value: Male

value: WholeRNA


title: Lung_Tissue_miRNA_rep 1 (T_14_N)

description: miRNA profiling

tag: gender

tag: age (years)

tag: smoke habit

tag: alive

value: yes

tag: tissue

value: Lung Normal Tissue


title: TimeSeriesFST_78_dHC_45min

description: polyA RNA

tag: condition

tag: timepoint


title: Lung_Tissue_miRNA_rep 1 (T_11_N)

description: miRNA profiling


title: Lung_Tissue_miRNA_rep 1 (T_09_N)

description: miRNA profiling

value: no


title: ML171651 24H Post Dex

tag: genotype

tag: treatment

value: Dex

tag: time point

value: 24H Post


title: Lung_Tissue_miRNA_rep 1 (T_15_N)

description: miRNA profiling

value: Female


title: TimeSeriesFST_79_vHC_4h

description: polyA RNA

tag: region

tag: hemisphere

tag: animalnumber

tag: experiment

tag: block


title: Lung_Tissue_miRNA_rep 1 (T_12_N)

description: miRNA profiling


title: TimeSeriesFST_77_vHC_45min

description: polyA RNA

tag: Sex

tag: mousetype

tag: mouseline

tag: libraryprotocol

tag: sampleprocessing


title: Dp16/D-KO_F3

source_name: Hippocampus

tag: strain


title: ML171571 24H Post Dex

tag: gender


title: ML171650 3H Post Dex

value: KO

value: 3H Post


title: TimeSeriesFST_76_dHC_2h

description: polyA RNA

tag: condition

value: Swim

value: dHC


title: ML171570 24H Post Dex


title: Lung_Tissue_miRNA_rep 1 (T_07_N)

description: miRNA profiling

tag: age (years)

tag: smoke habit

tag: alive

tag: tissue


title: ML171569 24H Post Dex

tag: genotype

tag: treatment

tag: time point


title: TimeSeriesFST_74_dHC_0min

description: polyA RNA

value: Homecage

tag: timepoint

tag: region

tag: hemisphere

value: both

tag: animalnumber

tag: experiment


title: TimeSeriesFST_75_vHC_2h

description: polyA RNA

value: vHC

tag: Sex

value: TimeSeriesFST

tag: block

tag: mousetype

value: WT

tag: mouseline

tag: libraryprotocol


title: Lung_Tissue_miRNA_rep 1 (T_06_N)

description: miRNA profiling

tag: gender

value: Male

tag: age (years)


title: Lung_Tissue_miRNA_rep 1 (T_05_N)

description: miRNA profiling

tag: smoke habit

tag: alive


title: Lung_Cancer_miRNA_rep 1 (T_06_T)

description: miRNA profiling

tag: histotype

value: small-cell-lung-cancer

tag: tissue

value: Lung Cancer Tissue


title: Lung_Cancer_miRNA_rep 1 (T_05_T)

description: miRNA profiling

value: yes


title: Lung_Tissue_miRNA_rep 1 (T_16_N)

description: miRNA profiling

value: Lung Normal Tissue


title: ML171568 24H Post Dex

tag: genotype

tag: treatment

value: Dex

tag: time point


title: ML171567 24H Post Saline

value: Saline

value: 24H Post


title: Lung_Tissue_miRNA_rep 1 (T_08_N)

description: miRNA profiling

value: Female


title: TimeSeriesFST_72_dHC_0min

description: polyA RNA

tag: condition

tag: timepoint

tag: region

tag: hemisphere

value: illumina TruSeq

tag: sampleprocessing

value: WholeRNA


title: NANOG Chip-seq in LIS49 cell line, maintained in HENSM conditions [NANOG_HENSM_LIS49_2]

source_name: hESCs, LIS49 cell line

tag: cell line

value: LIS49 cell line

tag: culture conditions

value: HENSM

tag: target protein

value: NANOG

tag: matched control file

tag: antibody

value: R&D Systems AF1997


title: TimeSeriesFST_73_vHC_0min

description: polyA RNA

value: Homecage

value: vHC

tag: Sex

value: both

tag: animalnumber

tag: experiment

value: TimeSeriesFST

tag: block

tag: mousetype

tag: mouseline

tag: libraryprotocol


title: Lung_Cancer_miRNA_rep 1 (T_08_T)

description: miRNA profiling

tag: gender

tag: age (years)

tag: histotype

value: small-cell-lung-cancer

tag: smoke habit

tag: alive

tag: tissue

value: Lung Cancer Tissue


title: R2

tag: strain

tag: treatment

value: acid stress (pH2.5) for two hours

tag: genotype

value: H-NS KO strain covering mutated H-NS K121R


title: TimeSeriesFST_71_vHC_0min

description: polyA RNA

tag: condition

tag: timepoint

tag: region

value: Male

tag: hemisphere

value: WT

tag: sampleprocessing


title: ML171566 24H Post Saline

value: Saline

tag: time point

value: 24H Post


title: ML171564 24H Post Saline


title: TimeSeriesFST_70_dHC_1h30min

description: polyA RNA

value: Swim

value: dHC

tag: Sex

tag: animalnumber

tag: experiment

tag: block

tag: mousetype

tag: mouseline

value: illumina TruSeq

value: WholeRNA


title: ML171563 24H Post Dex

tag: gender

value: KO

value: Dex


title: ML171562 24H Post Dex


title: TimeSeriesFST_68_dHC_3h

description: polyA RNA

tag: libraryprotocol


title: ML171559 24H Post Dex


title: TimeSeriesFST_67_vHC_3h

description: polyA RNA

value: vHC


title: ML171558 24H Post Saline


title: genomic DNA from Labial salivary gland tissue 26

type: genomic

city: Berkeley

first: Xiaorong

last: Shao

state: CA

address: 431 Stanley Hall

institute: University of California, Berkeley

description: Non-case

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation450K/Illumina Infinium Human MethylationEPIC Beadchip using standard Illumina protocol

scan_protocol: Arrays were imaged using HiScan Reader using standard recommended Illumina scanner setting

data_processing: Minfi

label: Cy5 and Cy3

source_name: Labial salivary gland tissue 26

label_protocol: Standard Illumina Protocol

extract_protocol: Qiagen Allprep DNA/RNA mini kit

value: Female

tag: tissue

value: Labial salivary gland tissue

tag: disease status

value: symptomatic not Sjogrens


title: genomic DNA from Labial salivary gland tissue 28

description: Case

source_name: Labial salivary gland tissue 28

value: Sjogrens Syndrome


title: genomic DNA from Labial salivary gland tissue 27

description: Non-case

source_name: Labial salivary gland tissue 27


title: TimeSeriesFST_69_vHC_1h30min

description: polyA RNA

value: both

value: TimeSeriesFST


title: genomic DNA from Labial salivary gland tissue 25

description: Non-case

source_name: Labial salivary gland tissue 25


title: TimeSeriesFST_66_dHC_45min

description: polyA RNA

value: Male


title: genomic DNA from Labial salivary gland tissue 24

description: Case

source_name: Labial salivary gland tissue 24


title: Lung_Cancer_miRNA_rep 1 (T_07_T)

description: miRNA profiling

tag: age (years)

tag: histotype

value: small-cell-lung-cancer

tag: smoke habit

tag: alive

value: yes

value: Lung Cancer Tissue


title: TimeSeriesFST_64_dHC_2h

description: polyA RNA

tag: condition

value: Swim

tag: timepoint

tag: region

tag: hemisphere

value: WT


title: TimeSeriesFST_65_vHC_45min

description: polyA RNA

tag: Sex

tag: animalnumber

value: illumina TruSeq

tag: sampleprocessing


title: ML171557 24H Post Saline

tag: genotype

tag: treatment

value: Saline

tag: time point

value: 24H Post


title: ML171554 3H Post Dex

tag: gender

value: Dex

value: 3H Post


title: genomic DNA from Labial salivary gland tissue 18

description: Case

source_name: Labial salivary gland tissue 18

value: Female

tag: tissue


title: ML171556 24H Post Saline

value: KO


title: genomic DNA from Labial salivary gland tissue 22

description: Non-case

source_name: Labial salivary gland tissue 22

value: Labial salivary gland tissue

tag: disease status

value: symptomatic not Sjogrens


title: genomic DNA from Labial salivary gland tissue 21

description: Case

source_name: Labial salivary gland tissue 21

value: Sjogrens Syndrome


title: TimeSeriesFST_62_dHC_4h

description: polyA RNA

value: dHC

value: both

tag: experiment

value: TimeSeriesFST

tag: block

tag: mousetype

tag: mouseline

tag: libraryprotocol

value: WholeRNA


title: ML171553 3H Post Dex

value: Male


title: genomic DNA from Labial salivary gland tissue 19

description: Case

source_name: Labial salivary gland tissue 19


title: TimeSeriesFST_63_vHC_2h

description: polyA RNA

tag: condition

value: Swim

tag: timepoint

value: vHC


title: genomic DNA from Labial salivary gland tissue 16

description: Non-case

source_name: Labial salivary gland tissue 16


title: genomic DNA from Labial salivary gland tissue 17

description: Case

source_name: Labial salivary gland tissue 17


title: genomic DNA from Labial salivary gland tissue 20

description: Case

source_name: Labial salivary gland tissue 20


title: genomic DNA from Labial salivary gland tissue 15

description: Case

source_name: Labial salivary gland tissue 15


title: ML171552 3H Post Dex

source_name: Skeletal muscle

value: WT


title: TimeSeriesFST_60_dHC_1h30min

description: polyA RNA

source_name: hippocampus

tag: region

tag: hemisphere

value: illumina TruSeq


title: TimeSeriesFST_61_vHC_4h

description: polyA RNA

tag: Sex

tag: animalnumber


title: Group2_t11a rep 3

city: Kansas City

first: Madelaine

last: Gogol

address: 1000 E. 50th Street

department: Computational Biology Core

institute: Stowers Institute

data_processing:
Samples were sequenced on 3 lanes total of a HiSeq and data was processed with Casava 1.8.2.
Reads were aligned to yeast genome sacCer3 from UCSC with ensembl transcript definition from Ensembl 72 using tophat (2.0.13) with -g 1
Downstream analysis was done in R using edgeR with TMM normalization.
Genome_build: sacCer3
Supplementary_files_format_and_content: tab-delimited text, edger RPKMs

organism: Saccharomyces cerevisiae

source_name: Yeast cells

growth_protocol: Cells were grown in YPD medium to an OD600 of 0.7-1.0

extract_protocol:
The RNA was extracted with Rneasy mini kit.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: genotype

tag: replicate

tag: technical replicate


title: ML171551 3H Post Dex

tag: gender

tag: treatment

tag: time point


title: Group2_t11a rep 3, technical rep 2


title: Group2_t11a rep 1, technical rep 2


title: TimeSeriesFST_59_vHC_1h30min

description: polyA RNA

tag: experiment

tag: sampleprocessing


title: Group2_t11a rep 1


title: ML171550 3H Post Saline

value: Saline


title: TimeSeriesFST_58_dHC_3h

description: polyA RNA

tag: block

tag: mousetype


title: ML171548 3H Post Saline


title: Group2_ybl574 rep 3, technical rep 2


title: ML171549 3H Post Saline


title: Group2_ck2 rep 2


title: Group2_ybl574 rep 2, technical rep 2


title: ML171555 3H Post Dex

value: Dex


title: Group2_ybl574 rep 2


title: Group2_ybl574 rep 3


title: Group2_ck2 rep 3


title: genomic DNA from Labial salivary gland tissue 9

description: Non-case

source_name: Labial salivary gland tissue 9

tag: tissue

tag: disease status


title: genomic DNA from Labial salivary gland tissue 23

description: Non-case

source_name: Labial salivary gland tissue 23


title: TimeSeriesFST_56_dHC_2h

description: polyA RNA

tag: condition

tag: timepoint

tag: mouseline

tag: libraryprotocol


title: genomic DNA from Labial salivary gland tissue 5

description: Non-case

source_name: Labial salivary gland tissue 5


title: genomic DNA from Labial salivary gland tissue 6

description: Case

source_name: Labial salivary gland tissue 6


title: genomic DNA from Labial salivary gland tissue 14

description: Non-case

source_name: Labial salivary gland tissue 14


title: genomic DNA from Labial salivary gland tissue 10

description: Non-case

source_name: Labial salivary gland tissue 10


title: genomic DNA from Labial salivary gland tissue 7

description: Non-case

source_name: Labial salivary gland tissue 7


title: genomic DNA from Labial salivary gland tissue 4

description: Case

source_name: Labial salivary gland tissue 4


title: genomic DNA from Labial salivary gland tissue 13

description: Non-case

source_name: Labial salivary gland tissue 13


title: Group2_wt rep 3

value: wt


title: Group2_serine treatment rep 2


title: Group2_wt rep 2


title: genomic DNA from Labial salivary gland tissue 11

description: Non-case

source_name: Labial salivary gland tissue 11

value: Female


title: Group2_serine treatment rep 3


title: TimeSeriesFST_54_dHC_4h

description: polyA RNA

tag: region

tag: Sex

tag: hemisphere

tag: animalnumber


title: genomic DNA from Labial salivary gland tissue 8

description: Non-case

source_name: Labial salivary gland tissue 8

tag: gender


title: Group2_control rep 3

tag: genotype

tag: replicate

tag: technical replicate


title: wt pyk1 rep 3

extract_protocol:
The RNA was extracted with Rneasy mini kit.
RNA libraries were prepared for sequencing using a Ribo-depletion stranded illumina RNA-seq protocol.

value: wt pyk1

tag: biological replicate

value: rep 3

value: tech rep 1


title: pyk1 rep 1

value: rep 1


title: pyk1 rep 2

value: rep 2


title: wt pyk1 rep 1


title: Group2_control rep 2


title: shm2 rep 2, technical rep 2

value: tech rep 2


title: genomic DNA from Labial salivary gland tissue 12

description: Non-case

source_name: Labial salivary gland tissue 12

value: Labial salivary gland tissue

value: symptomatic not Sjogrens


title: TimeSeriesFST_52_dHC_45min

description: polyA RNA

value: dHC

value: Male

value: both

tag: experiment

value: TimeSeriesFST

tag: block

tag: sampleprocessing

value: WholeRNA


title: genomic DNA from Labial salivary gland tissue 3

description: Case

source_name: Labial salivary gland tissue 3

tag: tissue

tag: disease status

value: Sjogrens Syndrome


title: TimeSeriesFST_51_vHC_45min

description: polyA RNA

tag: condition

value: Swim

tag: timepoint

value: vHC

tag: mousetype

value: WT

value: illumina TruSeq


title: genomic DNA from Labial salivary gland tissue 1

description: Case

source_name: Labial salivary gland tissue 1

value: Female


title: genomic DNA from Labial salivary gland tissue 2

description: Case

source_name: Labial salivary gland tissue 2


title: ML171543 3H Post Dex

source_name: Skeletal muscle

value: KO

tag: treatment

value: Dex

tag: time point

value: 3H Post


title: TimeSeriesFST_53_vHC_4h

description: polyA RNA

source_name: hippocampus

tag: region

tag: Sex

tag: hemisphere

tag: mouseline

tag: libraryprotocol


title: ML171541 3H Post Saline

tag: gender

tag: genotype

value: Saline


title: ML171542 3H Post Saline


title: TimeSeriesFST_50_dHC_0min

description: polyA RNA

value: Homecage

tag: animalnumber

tag: experiment


title: shm2 rep 2

source_name: Yeast cells

tag: biological replicate

value: rep 2

tag: technical replicate

value: tech rep 1


title: ML171540 3H Post Saline

value: Male


title: shm2 rep 1, technical rep 2

value: rep 1

value: tech rep 2


title: ML171545 3H Post Dex


title: TimeSeriesFST_49_vHC_0min

description: polyA RNA

value: both

value: TimeSeriesFST

tag: block

tag: sampleprocessing

value: WholeRNA


title: TimeSeriesFST_57_vHC_3h

description: polyA RNA

tag: condition

value: Swim

tag: timepoint

value: vHC


title: shm2 rep 1


title: ser33 rep 3, technical rep 2

value: rep 3


title: TimeSeriesFST_48_dHC_45min

description: polyA RNA

value: dHC

tag: mousetype

value: WT

value: illumina TruSeq


title: ser33 rep 3


title: sam1 rep 3, technical rep 2


title: sam1 rep 3


title: 391 D60 R2

city: Cuernavaca

first: Gamaliel

last: Lopez

state: Morelos

address: Ave. Universidad s/n, Chamilpa

department: Genómica Evolutiva

country: Mexico

institute: Centro de Ciencias Genómicas

description: 391 D60 R2

data_processing:
Raw reads were quality checked and trimmed using fastqc (version 0.11.9) and Trim_Galore (version 0.6.5)
Quality reads were aligned with the Mus musculus from NCBI (assembly GRCm38.p6) as the reference genome, using BWA_MEM (version 0.7.17)
Read counts were obtained using htseq-count (version 0.13.5)
The differential expressed genes were identified considering those with a p-value of <0.01 by DESeq2 (version 3.7)
Genome_build: Mus musculus from NCBI (assembly GRCm38.p6) was used as the reference genome
Supplementary_files_format_and_content: All the raw counts for each gene (and replicates) are in the spreadsheet processed_data.xlsx

source_name: lung

growth_protocol: The genetic material was obtained from BALB/c mouse lungs infected with ~250,000 bacteria per 100 uL of solution, for each of the Beijing strains.

extract_protocol:
RNA was obtained from lungs stored at -80 ° C using the Quick-RNA Miniprep Kit Zymo Research cat. R1054 / R1055 following the manufacturer's instructions.
cDNA_oligo_dT

treatment_protocol: The infected lungs were obtained after euthanasia at days 3, 14 and 28 post-infection for 323 Beijing-Like and at days 3, 14, 28 and 60 post-infection for 391 Beijing-Classic.

tag: strain

value: BALB/c

tag: age

value: six weeks

value: male

tag: infection

value: Classical-Beijing strain 391

tag: time

value: post-infection D60


title: TimeSeriesFST_43_vHC_0min

description: polyA RNA

value: Homecage

tag: region

tag: Sex

value: Male

tag: hemisphere

tag: mouseline


title: TimeSeriesFST_46_dHC_4h

description: polyA RNA

tag: animalnumber

tag: libraryprotocol


title: EHE 4

city: Cleveland

first: Brian

middle: P

last: Rubin

state: OH

address: 9620 Carnegie Ave NE2-215

department: Cancer Biology

institute: Cleveland Clinic

data_processing:
Gapped aligment was performed to the hg38 genome with HISAT2 v2.1.0
Raw counts were created with Featurescounts v1.6.4
FPKM abundance measurements were generated with Cufflinks v2.2.1.3
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: EHE Tumor

extract_protocol:
Tumors from either surgical resection or autopsy were cold preserved at -80˚C till sample processing. Total RNA was isolated with the Qiagen RNAeasy kit.
RNA libraries were prepared for sequencing using the standard DNBSeq protocol (BGI).

tag: tissue

value: Epithelioid hemangioendothelioma (EHE)


title: 391 D60 R3

description: 391 D60 R3


title: TimeSeriesFST_45_vHC_4h

description: polyA RNA

value: both

tag: experiment


title: TimeSeriesFST_42_dHC_2h

description: polyA RNA

value: TimeSeriesFST

tag: block


title: EHE 2


title: 391 D28 R3

description: 391 D28 R3

value: post-infection D28


title: EHE 6