title: 22M_H3K27Me3

city: wuhan

first: dong

last: chen

state: Hubei

address: GaoXin 2nd Road

institute: ablife

description: the ipsilateral brain tissue of intracerebral hemorrhage rats with 22-mon rat plasma treatment

data_processing:
Illumina Casava1.9 software used for basecalling.
3' adapter (end1:AGATCGGAAGAGC;end2:AGATCGGAAGAGC) trimmed with cutadapt
Reads were mapped using bowtie2 -N 1. Uniq mapped reads were remained.
macs14 was used to peakcalling with  default parameters
homer was used to find motifs with options -len 5,6,7,8,9,10,11,12
Genome_build: Rattus norvegicus 6.0
Supplementary_files_format_and_content: peaks

source_name: Rat brain tissues

extract_protocol:
Lysates were clarified from sonicated cell and histone-DNA complexes were isolated with antibody.
he libraries were prepared following the manufacturer's instructions （ThruPLEX DNA-seq 48S Kit, R400427）and applied to Illumina NextSeq 500 system for 150nt pair-end sequencing by ABlife Inc.

value: ipsilateral brain

tag: age

value: 21 mon old

tag: agent

value: rat plasma

tag: time point

tag: chip antibody

value: H3K27Me3 (Millipore,07-449)

tag: disease

value: intracerebral hemorrhage


title: 22M_H3K27Me3-input

status: Public on Nov 30 2020

type: SRA

country: China

library_source: genomic

molecule: genomic DNA

organism: Rattus norvegicus

tag: tissue


title: 3M_H3K27Me3

description: the ipsilateral brain tissue of intracerebral hemorrhage rats with 3-month rat plasma treatment


title: N1006

city: New York

first: Aarthi

last: Ramakrishnan

state: New York

address: 1425 Madison Avenue

department: Neuroscience

country: USA

institute: Icahn School of Medicine at Mount Sinai

library_source: transcriptomic

data_processing:
Paired-end sequencing reads were aligned to mouse genome GRCm38.95 using STAR aligner (Dobin et al., 2013)
FeatureCounts (Liao et al., 2014) was then used to assign reads to genes for quantifying gene expression levels based on GENCODE (Frankish et al., 2019) release M20
Limma was applied to the normalized expression levels to identify DEGs between Crym OE and GFP in males and in females, as well as DEGs between male GFP vs. female GFP, and male Crym OE vs. female Crym OE
Genome_build: mm10
Supplementary_files_format_and_content: raw counts

molecule: total RNA

organism: Mus musculus

source_name: Brain

extract_protocol:
RNA was isolated as described previously (Walker et al., 2018) using RNAeasy Mini Kit (Qiagen, Fredrick, MD) with a modified protocol from the manufacturer allowing for the separation and purification of small RNAs from total RNA. Briefly, after cell lysis and extraction with QIAzol (Qiagen, Fredrick, MD), small RNAs were collected in the flow-through and purified using the RNeasy MinElute spin columns and total RNA was purified using RNeasy Mini spin columns. Samples were treated with DNAse to rid them of genomic DNA and run on nanodrop and an Agilent Bioanalyzer 2100 to confirm RNA purity, integrity and concentration.
Libraries were prepared using the TruSeq Stranded mRNA HT Sample Prep Kit protocol (Illumina, San Diego, CA). Briefly, poly A selection and fragmentation of 300 ng of RNA was performed, and the resulting RNA was converted to cDNA with random hexamers. Adapters were ligated and samples were size-selected with AMPur XP beads (Beckman Coulter, Brea, CA). Barcode bases (6 bp) were introduced at one end of the adaptors during PCR amplification steps. Library size and concentration were assessed using Tape Station (Life Technologies, Grand Island, NY) before sequencing. Libraries were pooled for multiplexing (pool of 21 samples) and sequenced on a HighSeq2500 System using V4 chemistry with 50 base pair single-end reads at UCLA Neuroscience Genomics core. Each pool was sequenced 3 times with the goal of obtaining ~30 million reads per sample.

tag: region

value: Nac

tag: Sex

value: M

tag: housing

value: G

tag: treatment (mg/kg cocaine)

tag: acute/chronic

value: A


title: E3.75_MUT_04_03_A_PrE

city: Cambridge

first: Giuliano

middle: Giuseppe

last: Stirparo

state: Cambridgeshire

address: 418 Cambridge Science Park Milton Rd

country: United Kingdom

institute: Cerevance ltd

description:
ICM
ICM from E3.5 mouse embryos

data_processing:
STAR alignment (ensembl 87)
--sjdbOverhang 149 --twopassMode Basic -–seedSearchStartLmax 10 --outFilterMismatchNoverLmax 0.3 --outFilterMismatchNmax 10 --outFilterMultimapNmax 100 --alignSJoverhangMin 12 --outSJfilterOverhangMin 30 10 10 10 --sjdbScore 1 --clip3pAdapterSeq
htseq-count
-s no -a 20 -m intersection-nonempty
Genome_build: mm10
Supplementary_files_format_and_content: counts

source_name: ICM from E3.5 mouse embryos

extract_protocol: none provided by the submitter

tag: sample type

value: PrE

tag: genotype

value: Stat3 -/-


title: N1005


title: 22M_H3K9ac

value: H3K9Ac (Millipore,06-942)


title: 3M_H3K27Me3-input


title: N1003

value: F


title: E3.75_MUT_02_02_B_PrE

description:
ICM
ICM from E3.5 mouse embryos


title: E3.75_MUT_02_03_B_PrE

description:
ICM
ICM from E3.5 mouse embryos


title: N1002


title: E3.75_MUT_05_01_A_PrE

description:
ICM
ICM from E3.5 mouse embryos


title: E3.75_MUT_02_01_B_EPI

description:
ICM
ICM from E3.5 mouse embryos

value: EPI


title: 22M_H3K9ac-input


title: N1013

value: SI


title: N1000


title: E3.75_MUT_01_04_B_PrE

description:
ICM
ICM from E3.5 mouse embryos


title: 3M_H3K9ac

description: the ipsilateral brain tissue of intracerebral hemorrhage rats with 3-mon rat plasma treatment


title: 3M_H3K9ac-input


title: m21_R_H3K9ac-2

description: the contralateral brain tissue of intracerebral hemorrhage rats

value: contralateral brain


title: A579

value: AMY

value: CHR


title: A577


title: E3.75_MUT_01_02_B_PrE

description:
ICM
ICM from E3.5 mouse embryos


title: m21_R_H3K9ac-1

value: 21 mon old


title: A571


title: m21_R_H3K9ac-input-2


title: A563


title: m21_R_H3K9ac-input-1


title: A565


title: E3.5_WT_22_13_E

description:
ICM
ICM from E3.5 mouse embryos

value: ICM

value: Stat3 +/+


title: E3.5_WT_22_12_E

description:
ICM
ICM from E3.5 mouse embryos


title: m21_L_H3K9ac-2

description: the ipsilateral brain tissue of intracerebral hemorrhage rats

value: ipsilateral brain

value: intracerebral hemorrhage


title: A537

value: M


title: m21_L_H3K9ac-input-2


title: E3.5_WT_22_11_E

description:
ICM
ICM from E3.5 mouse embryos


title: A527


title: A536

value: G


title: m21_L_H3K9ac-input-1


title: E3.5_WT_22_08_D

description:
ICM
ICM from E3.5 mouse embryos


title: E3.75_MUT_01_03_B_EPI

description:
ICM
ICM from E3.5 mouse embryos


title: A525


title: E3.5_WT_22_09_D

description:
ICM
ICM from E3.5 mouse embryos


title: A524


title: m13_R_H3K9ac-2

value: 13 mon old


title: m13_R_H3K9ac-1


title: E3.5_WT_22_07_H

description:
ICM
ICM from E3.5 mouse embryos


title: A521


title: E3.5_WT_22_14_E

description:
ICM
ICM from E3.5 mouse embryos


title: E3.75_MUT_01_01_B_EPI

description:
ICM
ICM from E3.5 mouse embryos


title: m13_R_H3K9ac-input-2


title: m13_R_H3K9ac-input-1


title: E3.5_WT_22_02_F

description:
ICM
ICM from E3.5 mouse embryos


title: A511


title: m13_L_H3K9ac-2


title: E3.5_WT_22_01_F

description:
ICM
ICM from E3.5 mouse embryos


title: m21_L_H3K9ac-1


title: A1239


title: E3.5_WT_21_19_E

description:
ICM
ICM from E3.5 mouse embryos


title: E3.5_WT_22_01_D

description:
ICM
ICM from E3.5 mouse embryos


title: A1238


title: m13_L_H3K9ac-input-2


title: m13_L_H3K9ac-input-1


title: m13_L_H3K9ac-1


title: A1237


title: E3.5_WT_21_18_D

description:
ICM
ICM from E3.5 mouse embryos


title: A1236


title: E3.5_WT_21_17_D

description:
ICM
ICM from E3.5 mouse embryos


title: m21_R_H3K4Me3-2


title: E3.5_WT_22_03_F

description:
ICM
ICM from E3.5 mouse embryos


title: E3.5_WT_21_15_H

description:
ICM
ICM from E3.5 mouse embryos


title: A1235


title: A1233


title: E3.5_WT_21_09_F

description:
ICM
ICM from E3.5 mouse embryos


title: m21_L_H3K4Me3-2


title: E3.5_WT_21_16_H

description:
ICM
ICM from E3.5 mouse embryos


title: E3.5_WT_21_08_E

description:
ICM
ICM from E3.5 mouse embryos


title: m21_R_H3K4Me3-1


title: m21_R_H3K4Me3-input-2


title: A514


title: m21_L_H3K4Me3-input-1


title: A1227


title: A1234


title: A1226


title: m21_R_H3K4Me3-input-1


title: E3.5_WT_21_14_H

description:
ICM
ICM from E3.5 mouse embryos


title: A1231


title: E3.5_WT_21_04_H

description:
ICM
ICM from E3.5 mouse embryos


title: m21_L_H3K4Me3-input-2


title: m21_L_H3K4Me3-1


title: E3.5_WT_21_11_F

description:
ICM
ICM from E3.5 mouse embryos


title: A1229


title: A1230


title: E3.5_WT_21_06_D

description:
ICM
ICM from E3.5 mouse embryos


title: A1222


title: m13_R_H3K4Me3-input-1


title: E3.5_WT_21_02_H

description:
ICM
ICM from E3.5 mouse embryos


title: m13_L_H3K4Me3-2


title: m13_R_H3K4Me3-1


title: E3.5_WT_21_05_D

description:
ICM
ICM from E3.5 mouse embryos


title: A1220


title: A1216


title: m13_R_H3K4Me3-2


title: E3.5_WT_21_02_E

description:
ICM
ICM from E3.5 mouse embryos


title: A1223


title: A1224


title: m13_L_H3K4Me3-1


title: m13_R_H3K4Me3-input-2


title: Larva_Zebrafish_3

city: Seattle

first: Joshua

middle: William

last: Hahn

state: WA

address: 3747 W Stevens Wy NE

department: Department of Neurobiology & Biophysics

institute: University of Washington

description:
ConsolidatedCounts_Zebrafish_Larva.csv
The third replicate of 200 manually dissected larva retinas.

data_processing:
Sample demultiplexing for each of 15 adult and 3 larval samples with the mkfastq function from Cell Ranger software(version 2.1.0, 10X Genomics)
Sample alignment to the zebrafish reference transcriptome (ENSEMBL zv10, release 82) using “cellranger count” with default parameters to obtain a digital gene expression (DGE) matrix (genes x cells) summarizing transcript counts.
Genome_build: ENSEMBL zv10, release 82
Supplementary_files_format_and_content: Csv files including gene expression matrix from all larval samples and all adult samples

organism: Danio rerio

source_name: Zebrafish retina, 5 days post-fertilization

growth_protocol: Adult and larval zebrafish were maintained on a 14:10 hour light:dark cycle at 28°C. Embryos were bred in Danieau’s solution (17 mM NaCl, 2 mM KCl, 0.12 mM MgSO4, 1.8 mM Ca(NO3)2, 1.5 mM HEPES).

extract_protocol:
Retinas were digested in papain 20U/ml in ox Ames at 28°C for 30 (larval retinas) or 45 minutes (adult retinas). To stop the digestion, the papain solution was replaced by papain inhibitor solution containing ovomucoid 15mg/ml and BSA 15mg/ml. Tissue was gently dissociated by trituration using a flamed glass pipette in papain inhibitor solution. To wash the cell suspension, cells were pelleted at 250g for 8 minutes and resuspended in ox. Ames containing 0.4% BSA. The cell suspension was filtered through a 30µm strainer prior to fluorescence-activated cell sorting (FACS) purification. Non-transgenic wildtype retinas were used to determine background fluorescence levels and adjust sorting gates. Calcein blue was added to distinguish live RFP+ RGCs. Cells were washed and resuspended in PBS 0.04% BSA and loaded onto the microfluidic device within ~45 minutes after FACS enrichment.
Droplet RNA sequencing experiments using the 10X chromium platform were performed according to the manufacturer's instructions with no modifications. The cDNA libraries were sequenced on the Illumina HiSeq 2500 to a depth of ~30,000 reads per cell.
10x Chromium 3’ v2 platform (10X Genomics, Pleasanton, CA)

treatment_protocol: All zebrafish used were anesthetized in a lethal overdose of tricaine and rapidly euthanized by immersion in ice water for 10 min. Retinas from larval or adult fish were dissected in oxygenated (ox) Ames and transferred into ox Ames on ice until tissue collection was completed.

value: retina


title: E3.5_WT_21_07_E

description:
ICM
ICM from E3.5 mouse embryos


title: E3.5_WT_21_01_F

description:
ICM
ICM from E3.5 mouse embryos


title: A1228


title: m13_L_H3K4Me3-input-2


title: A1210


title: A1206


title: m21_R_H3K27Me3-2

value: H3K27Me3 (Millipore,07-449)


title: m13_L_H3K4Me3-input-1


title: A1205


title: m21_R_H3K27Me3-input-2


title: E3.5_WT_20_12_E

description:
ICM
ICM from E3.5 mouse embryos


title: A1215


title: E3.5_WT_21_03_H

description:
ICM
ICM from E3.5 mouse embryos


title: Larva_Zebrafish_2

description:
ConsolidatedCounts_Zebrafish_Larva.csv
The second replicate of 200 manually dissected larva retinas.


title: E3.5_WT_20_11_E

description:
ICM
ICM from E3.5 mouse embryos


title: A1202


title: E3.5_WT_20_14_F

description:
ICM
ICM from E3.5 mouse embryos


title: Larva_Zebrafish_1

description:
ConsolidatedCounts_Zebrafish_Larva.csv
The first replicate of 200 manually dissected larva retinas.


title: A1200


title: E3.5_WT_20_15_F

description:
ICM
ICM from E3.5 mouse embryos


title: Adult_Zebrafish_14

description:
ConsolidatedCounts_Zebrafish_Adult.csv
4th replicate of the fifth experiment containing about 20 adult zebrafish retinas.

source_name: Zebrafish retina, 4-6 month old


title: E3.5_WT_20_08_H

description:
ICM
ICM from E3.5 mouse embryos


title: Adult_Zebrafish_15

description:
ConsolidatedCounts_Zebrafish_Adult.csv
5th replicate of the fifth experiment containing about 20 adult zebrafish retinas.


title: A1177

value: A


title: A1204

value: F


title: E3.5_WT_20_07_H

description:
ICM
ICM from E3.5 mouse embryos


title: Adult_Zebrafish_9

description:
ConsolidatedCounts_Zebrafish_Adult.csv
1st replicate of the fourth experiment containing about 20 adult zebrafish retinas.


title: E3.5_WT_20_06_H

description:
ICM
ICM from E3.5 mouse embryos


title: E3.5_WT_20_09_D

description:
ICM
ICM from E3.5 mouse embryos


title: Adult_Zebrafish_13

description:
ConsolidatedCounts_Zebrafish_Adult.csv
3rd replicate of the fifth experiment containing about 20 adult zebrafish retinas.


title: Adult_Zebrafish_12

description:
ConsolidatedCounts_Zebrafish_Adult.csv
2nd replicate of the fifth experiment containing about 20 adult zebrafish retinas.


title: m21_R_H3K27Me3-input-1


title: A1173


title: m21_L_H3K27Me3-1


title: Adult_Zebrafish_10

description:
ConsolidatedCounts_Zebrafish_Adult.csv
2nd replicate of the fourth experiment containing about 20 adult zebrafish retinas.


title: E3.5_WT_20_04_G

description:
ICM
ICM from E3.5 mouse embryos


title: m21_L_H3K27Me3-2


title: Adult_Zebrafish_7

description:
ConsolidatedCounts_Zebrafish_Adult.csv
3rd replicate of the third experiment containing about 20 adult zebrafish retinas.


title: A1171


title: m21_L_H3K27Me3-input-2


title: A1178


title: Adult_Zebrafish_11

description:
ConsolidatedCounts_Zebrafish_Adult.csv
1st replicate of the fifth experiment containing about 20 adult zebrafish retinas.


title: m21_R_H3K27Me3-1


title: m21_L_H3K27Me3-input-1


title: E3.5_WT_20_13_F

description:
ICM
ICM from E3.5 mouse embryos


title: m13_R_H3K27Me3-input-1


title: A1158


title: A1176


title: A1170


title: m13_R_H3K27Me3-2


title: A1155


title: Adult_Zebrafish_4

description:
ConsolidatedCounts_Zebrafish_Adult.csv
2nd replicate of the second experiment containing about 20 adult zebrafish retinas.


title: E3.5_WT_20_03_F

description:
ICM
ICM from E3.5 mouse embryos


title: Adult_Zebrafish_2

description:
ConsolidatedCounts_Zebrafish_Adult.csv
2nd replicate of the first experiment containing about 20 adult zebrafish retinas.


title: m13_R_H3K27Me3-input-2


title: E3.5_WT_20_02_F

description:
ICM
ICM from E3.5 mouse embryos


title: m13_R_H3K27Me3-1


title: Adult_Zebrafish_6

description:
ConsolidatedCounts_Zebrafish_Adult.csv
2nd replicate of the third experiment containing about 20 adult zebrafish retinas.


title: m13_L_H3K27Me3-input-2


title: Adult_Zebrafish_5

description:
ConsolidatedCounts_Zebrafish_Adult.csv
1st replicate of the third experiment containing about 20 adult zebrafish retinas.


title: A1150


title: E3.5_WT_20_01_F

description:
ICM
ICM from E3.5 mouse embryos


title: m13_L_H3K27Me3-input-1


title: m13_L_H3K27Me3-2


title: E3.5_WT_16_18_H

description:
ICM
ICM from E3.5 mouse embryos


title: A1154


title: E3.5_WT_20_01_D

description:
ICM
ICM from E3.5 mouse embryos


title: Adult_Zebrafish_3

description:
ConsolidatedCounts_Zebrafish_Adult.csv
1st replicate of the second experiment containing about 20 adult zebrafish retinas.


title: A1147


title: T6_4

city: Atlanta

first: Muralidhar

last: Padala

state: GA

address: 380B Northyards Blvd NW

institute: Emory University

data_processing:
Partek Flow, version rn6 rat reference genome, was used to map reads.
Mapped reads were quantified using the RefSeq transcripts 2019-02-02 annotation, using the Partek E/M method using GSA to compare each experimental group against Sham
Data were filtered using the following specifications: p≤0.05 and 2 ≤ fold change ≤ -2.
Functional enrichment analysis was performed using Protein Analysis Through Evolutionary Relationships (PANTHER version 15), Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) databases, to identify molecular and biochemical pathways
Genome_build: rn6
Supplementary_files_format_and_content: The processed data files is a text file (.txt) and contain normalized counts for each feature for each individual sample

molecule: polyA RNA

source_name: Myocardium

extract_protocol:
Myocardial tissue was section, snap frozen in liquid nitrogen and stored at -80 degress celcius. RNA was harvested using the miRNeasy mini kit. RNA sequencing was performed using the Illumina platform (Novogene).
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Rats were subjected to an MI surgery (left thoracotomy and ligation of the left coronary artery) or an MI surgery followed by a second surgery to implant the TRD device, and followed until 12 weeks

value: Myocardium

tag: strain

value: Sprague-Dawley

tag: treatment

value: 6wk post op MI+TRD surgery


title: E3.5_WT_16_19_D

description:
ICM
ICM from E3.5 mouse embryos


title: m13_L_H3K27Me3-1

description: the ipsilateral brain tissue of intracerebral hemorrhage rats


title: A1146

value: AMY


title: E3.5_WT_16_17_H

description:
ICM
ICM from E3.5 mouse embryos


title: A1152

value: SI


title: T6_3


title: E3.5_WT_16_16_H

description:
ICM
ICM from E3.5 mouse embryos


title: E3.5_WT_16_14_G

description:
ICM
ICM from E3.5 mouse embryos


title: T6_5


title: A1143


title: T6_2


title: T6_1


title: A1145


title: THP-1_48h_Bio-Acetoxime_1µM_rep2

type: RNA

city: Duesseldorf

first: Karl

last: Koehrer

address: Universitaetsstr. 1

department: BMFZ

country: Germany

institute: University of Duesseldorf

description: X 2

hyb_protocol: After fragmentation labeled cRNA was hybridized to Affymetrix PrimeView Human Gene Expression Microarrays for 16h at 45 °C, stained by streptavidin/phycoerythrin conjugate and scanned as described in the manufacturers´ protocol.

scan_protocol: Gene ChIP Scanner 3000 7G (Affymetrix Inc.); AGCC (Vers. 3.3)

data_processing: Data analyses on Affymetrix CEL files were conducted with GeneSpring GX software (Vers. 12.5; Agilent Technologies). Probes within each probeset were summarized by RMA after quantile normalization of probe level signal intensities across all samples to reduce inter-array variability . Input data pre-processing was concluded by baseline transformation to the median of all samples

label: biotin

organism: Homo sapiens

source_name: differentiated THP-1_1µM Bio-Acetoxime for 48h

label_protocol: Synthesis of cDNA and subsequent biotin labeling of cRNA was performed according to the manufacturers´ protocol (3´ IVT Plus Kit; Affymetrix, Inc.). Briefly, 100 ng of total RNA were converted to cDNA, followed by in vitro transcription and biotin labeling of cRNA.

growth_protocol: Monocyte THP-1 cells were grown in RPMI 1640 medium supplemented with 10% FCS, 1 mM sodium pyruvate, antibiotics (5 units/ml penicillin, 5 μg/ml streptomycin), 2 mM L-glutamine and 50 μM 2-β-mercaptoethanol. The cells were cultured in T75 cell culture flasks in a humidified incubator at 37°C in the presence of 5% CO2.

extract_protocol: Total RNA was extracted from cells using the Trizol Plus RNA Purification Kit (Thermo Fisher Scientific) according to the manufacturer's instructions.

treatment_protocol: Monocyte THP-1 cells were seeded in six-well plates at a density of 700000 cells in 3 ml medium per well containing 10 nM PMA for the differentiation of THP-1 monocytes into adherent macrophage-like cells. 24h after seeding the cells were treated for 48h with GSK3ß inhibitors in the presence of 10 nM PMA

tag: cell type source

value: Monocyte THP-1

tag: cell type

value: differentiated THP-1 cells

tag: treated with

value: 1µM Bio-Acetoxime for 48h

tag: differentiation using

value: RPMI medium containing 10nM PMA


title: E3.5_WT_16_09_E

description:
ICM
ICM from E3.5 mouse embryos

value: ICM

value: Stat3 +/+


title: Adult_Zebrafish_8

description:
ConsolidatedCounts_Zebrafish_Adult.csv
4th replicate of the third experiment containing about 20 adult zebrafish retinas.


title: THP-1_48h_SB216763_10µM_rep2

description: SB 2

source_name: differentiated THP-1_10µM SB216763 for 48h


title: A1140

value: G


title: THP-1_48h_Bio-Acetoxime_1µM_rep1

description: X 1


title: E3.5_WT_16_08_D

description:
ICM
ICM from E3.5 mouse embryos


title: E3.5_WT_16_06_H

description:
ICM
ICM from E3.5 mouse embryos


title: THP-1_48h_SB216763_10µM_rep1

description: SB 1


title: A1126

value: M


title: E3.5_WT_16_07_D

description:
ICM
ICM from E3.5 mouse embryos


title: A1125


title: E3.5_WT_16_04_H

description:
ICM
ICM from E3.5 mouse embryos


title: S6_6

value: 6wk post op MI surgery


title: A1121


title: stricta pistil, meiosis, rep 2

city: Logan

first: John

middle: G.

last: Carman

state: UT

address: 4820 Old Main Hill

department: Plants, Soils and Climate Department

institute: Utah State University

description:
excised 9 A.M - 12 Noon
SP2b

hyb_protocol: ATH1 arrays were hybridized for 16 h at 45 °C using 15 µg of labeled and fragmented cRNA (Affymetrix Technical Analysis Manual).

scan_protocol: Arrays were stained with streptavidin-phycoerythrin in an Affymetrix GeneChip® Fluidics Workstation 400 and scanned with a GeneChip® Scanner 3000.

data_processing:
Cel files were removed if they exceeding the 99 % cutoff of the RLE-NUSE T2 multivariate statistic (RMAExpress, http://rmaexpress.bmbolstad.com/). The remaining files were RMA normalized using BRB-ArrayTools (4.6.0-Beta-2, Dr. Richard Simon and the BRB-ArrayTools Development Team, http://linus.nci.nih.gov/BRB-ArrayTools.html). Low variability genes (< 10% of expression values exceeding 1.5-fold change from the median) or genes missing > 50 % of their expression data were removed. The BRB-ArrayTools class comparison option (random variance model with a normalized significance level of 0.001 for univariate tests) was used to identify differentially expressed genes (DEGs). Where multiple ATH1 probe sets identified the same gene (~ 0.8 % of probe sets), probe sets producing the greatest fold change were retained. For Panther gene ontology term (GO) overrepresentation tests (2020-04-07 release), two tests were performed per comparison, one with DEGs upregulated in one treatment and one with DEGs upregulated in the other treatment. Gene trimming criteria were relaxed for Panther GO enrichment analyses (version 14.1, http://www.pantherdb.org/, 2019-12-16 release; GO Ontology database released 2020-03-23). Here, genes were removed if < 0-40 % of sample values differed from the median by ≥ 8 % (percentages of sample values meeting the threshold was varied so as to retain 10-16 thousand genes). GO categories from the Araport11 genome release (TAIR, 2020-01-01) were used to compare all GOs across treatments.
RMA normalized log2 transformed expression values are presented. RMA normalizations and log2 transformations were performed individually for the samples of each of 16 matrices (16 different combinations of 20 samples, including 3-8 samples each). Matrices containing only three samples  (no replication for one of the treatments)  were used for Panther gene ontology enrichment analyses only. Values in each matrix are those remaining after trimming. Genes were removed if no more than 0-40 % of sample values differed from the median by ≥ 8 %. The percentage of sample values meeting the threshold was varied so as to retain 10,000 to 16,000 genes. For example, if only one of the four gene values for a gene in a matrix comparison involving four samples (two sets of replicate samples) differed from the median value by > 8 %, that gene would be trimmed if the trim percentage were <25 %. However, this gene would be retained if the trim value were between 25 and 40 % (at least 1 of 4 values differs from the median by > 8 %). GO categories from the Araport11 genome release (TAIR, 2020-01-01) were used to compare all GOs across treatments.

organism: Boechera stricta

source_name: ~ 80 excised pistils from healthy plants

label_protocol: RNA was extracted and purified from ovules using TRIzol reagent (Invitrogen, Life Technologies Corporation) and RNeasy columns (Qiagen, Germantown, MD) and from pistils using PureLink® RNA Mini Kits (Ambion, Austin, TX) and TURBO DNA-free™ Kits (Ambion, Austin, TX). NanoDrop (Thermo Scientific, Wilmington, DE) and Bioanalyzer (Agilent, Santa Clara, CA) instruments were used to determine RNA yield and integrity. Affymetrix two-cycle cDNA synthesis kits (P/N 900494) were used for cDNA synthesis and RNA amplification of ovule RNA. The MEGAscript T7 kit (Ambion) with unlabeled nucleotides was used for first-cycle cRNA amplifications. For in vitro transcription (IVT), 20 μL cDNA was mixed with 30 μL first-cycle IVT master mix, and reactions were incubated at 37 oC for 24 h. Second-cycle first and second strand cDNA syntheses were performed as above. The Affymetrix GeneChip IVT labeling kit (P/N 900449) was used for the second IVT. First and second cycle cRNA was purified using Affymetrix sample cleanup modules P/N 900371, and cRNA was fragmented at 94 oC for 35 min. Pistil RNA (500 ng) was amplified, labeled and fragmented using GeneChip® 3’ IVT Express Kits (Affymetrix).

growth_protocol: Plants were obtained from native habitats or grown from seed. Potted seedlings or transplants were grown in pots that contained Sunshine Mix #1 potting soil (Sun Gro Horticulture Canada Ltd, Vancouver, BC). Vernalization was accomplished by cold incubation for 10-12 weeks with minimal lighting (8/16 day/night photoperiod). Vernalized plants were transferred to controlled-environment greenhouses or growth chambers that maintained a 16/8 h day/night photoperiod using supplemental light provided by a combination of cool white florescent bulbs, incandescent bulbs, and high-pressure sodium-vapor lamps. These provided a minimum photosynthetic photon flux of 400 µmol m 2 sec 1 at the tops of the canopies. Day/night temperatures were maintained at 22/16 C, and plants were watered regularly with a dilute solution (250 mg per L) of Peters Professional 20:20:20 fertilizer (Scotts, Maryville, OH, USA).

extract_protocol: Ovules and pistils were collected from 9:00 A.M. to 12:00 noon, placed in Nuclease-Free water (Ambion, Life Technologies Corporation, Carlsbad, CA) and measured. Needles from 1.0 mL syringes were used to excise ovules. Instruments and work surfaces were cleaned with RNAse ZAP (Ambion) prior to dissection and at 20-30 min intervals. Ovules and pistils were immediately placed in RNAlater (Ambion) and stored at  80 °C.

treatment_protocol: Plants were grown under ideal conditions.

value: pistil

tag: Stage

value: meiosis

tag: reproductive mode

value: sexual


title: S6_5

value: Myocardium


title: stricta pistil, meiosis, rep 1

description:
excised 9 A.M - 12 Noon
SP2a


title: E3.5_WT_16_02_G

description:
ICM
ICM from E3.5 mouse embryos


title: A1127

value: A


title: S6_4

value: Sprague-Dawley


title: Adult_Zebrafish_1

description:
ConsolidatedCounts_Zebrafish_Adult.csv
1st replicate of the first experiment containing about 20 adult zebrafish retinas.

value: retina


title: THP-1_48h_DMSO_rep1

description: DMSO 1

source_name: differentiated THP-1_DMSO control for 48h

value: DMSO control for 48h


title: S6_2


title: microphylla ovule, mature gametophyte, rep2

description:
excised 9 A.M - 12 Noon
MO4b

organism: Boechera microphylla

source_name: ~ 800 excised ovules from healthy plants

value: ovule

value: mature gametophyte

value: facultatively diplosporous and aposporous


title: A1120

value: AMY

value: F


title: microphylla ovule, mature gametophyte, rep1

description:
excised 9 A.M - 12 Noon
MO4a


title: A1114

value: SI


title: E3.5_WT_16_01_E

description:
ICM
ICM from E3.5 mouse embryos

value: ICM

value: Stat3 +/+


title: THP-1_48h_CHIR99021_5µM_rep2

description: CHIR 2

source_name: differentiated THP-1_5µM CHIR99021 for 48h

value: Monocyte THP-1

value: differentiated THP-1 cells

value: 5µM CHIR99021 for 48h

value: RPMI medium containing 10nM PMA


title: E3.5_WT_16_02_D

description:
ICM
ICM from E3.5 mouse embryos


title: S6_3

value: Myocardium

value: 6wk post op MI surgery


title: microphylla ovule, young gametophyte, rep 2

description:
excised 9 A.M - 12 Noon
MO3b

source_name: ~ 1200 excised ovules from healthy plants

value: young gametophyte


title: THP-1_48h_DMSO_rep2

description: DMSO 2


title: THP-1_48h_CHIR99021_5µM_rep1

description: CHIR 1


title: E3.5_WT_13_11_F

description:
ICM
ICM from E3.5 mouse embryos


title: E3.5_WT_16_05_H

description:
ICM
ICM from E3.5 mouse embryos


title: E3.5_WT_16_01_F

description:
ICM
ICM from E3.5 mouse embryos


title: S6_1

value: Sprague-Dawley


title: T12_4

value: 12wk post op MI+TRD surgery


title: A1107

value: M

value: G

value: A


title: E3.5_WT_13_08_E

description:
ICM
ICM from E3.5 mouse embryos


title: A1104

value: AMY


title: T12_5


title: T12_6


title: A1101

value: F


title: E3.5_WT_13_09_E

description:
ICM
ICM from E3.5 mouse embryos


title: E3.5_WT_13_07_D

description:
ICM
ICM from E3.5 mouse embryos


title: microphylla ovule, young gametophyte, rep 1

description:
excised 9 A.M - 12 Noon
MO3a

value: ovule

value: facultatively diplosporous and aposporous


title: A1112

value: SI


title: T12_2


title: T12_3


title: A1109


title: E3.5_WT_13_05_H

description:
ICM
ICM from E3.5 mouse embryos

value: ICM

value: Stat3 +/+


title: microphylla ovule, meiosis, rep 1

description:
excised 9 A.M - 12 Noon
MO2a

source_name: ~ 1400 excised ovules from healthy plants

value: meiosis


title: microphylla ovule, MMC, rep 1

description:
excised 9 A.M - 12 Noon
MO1a

source_name: ~ 1600 excised ovules from healthy plants

value: MMC


title: T12_1

value: Myocardium


title: microphylla ovule, MMC, rep 2

description:
excised 9 A.M - 12 Noon
MO1b


title: A1097

value: CHR


title: E3.5_WT_13_01_F

description:
ICM
ICM from E3.5 mouse embryos


title: S12_6

value: 12wk post op MI surgery


title: microphylla ovule, meiosis, rep 2

description:
excised 9 A.M - 12 Noon
MO2b


title: E3.5_WT_13_04_H

description:
ICM
ICM from E3.5 mouse embryos


title: lignifera ovule, mature gametophyte, rep2

description:
excised 9 A.M - 12 Noon
LO4b

organism: Boechera lignifera

value: mature gametophyte

value: facultatively diplosporous


title: S12_5

value: Sprague-Dawley


title: A1094


title: A1095

value: M


title: A1093


title: E3.5_MUT_24_14_D

description:
ICM
ICM from E3.5 mouse embryos

value: Stat3 -/-


title: lignifera ovule, mature gametophyte, rep1

description:
excised 9 A.M - 12 Noon
LO4a


title: lignifera ovule, young gametophyte, rep 2

description:
excised 9 A.M - 12 Noon
LO3b

value: young gametophyte


title: S12_4


title: S12_2


title: S12_3


title: lignifera ovule, young gametophyte, rep 1

description:
excised 9 A.M - 12 Noon
LO3a


title: A1091

value: AMY

value: F


title: lignifera ovule, meiosis, rep 1

description:
excised 9 A.M - 12 Noon
LO2a

value: ovule


title: E3.5_MUT_24_13_H

description:
ICM
ICM from E3.5 mouse embryos


title: A1086

value: G


title: E3.5_MUT_24_09_D

description:
ICM
ICM from E3.5 mouse embryos

value: ICM


title: S12_1


title: lignifera ovule, meiosis, rep 2

description:
excised 9 A.M - 12 Noon
LO2b


title: lignifera ovule, MMC, rep 2

description:
excised 9 A.M - 12 Noon
LO1b


title: 2532-DG

city: Gainesville

first: Tom

last: Foster

state: FL

address: 1149 Newell Drive

institute: University of Florida

description: LPS-Study-Normalized-Counts-DG.csv

data_processing:
Data was analyzed using Partek Flow (Partek Inc.). Reads were trimmed based on quality score.
Reads were aligned using STAR against the rat genome reference (rn6). All parameters were kept default.
Gene-level counts were generated and annotated in Partek using  rn6-Ensembl Transcripts release 92.
Genes were normalized using DESeq2 and genes with an average read count less than 5 were removed.
Genome_build: rn6
Supplementary_files_format_and_content: Comma separated values files which contain the normalized counts for each sample.

source_name: DG region of the hippocampus

extract_protocol:
Hippocampi were collected 48 hours after a seventh injection. Rats were anesthetized with isoflurane and swiftly decapitated. The brains were rapidly removed and one hippocampus was subdivided into CA1 and dentate gyrus (DG) for RNA sequencing. All brain samples were flash frozen in liquid nitrogen and were stored at -80 C.
Sequencing libraries were constructed using the library preparation kit Ion Total RNA-Seq kit v2 (Thermo Fisher, Cat# 4475936). Ion Xpress barcodes (Thermo Fisher, catalog number4475485) were added for multiplex sequencing.

tag: age

value: Aged (14-16 months)

value: Vehicle (saline i.p. injection once a week for 7 weeks)

value: Male


title: formosa ovule, young gametophyte, rep 2

description:
excised 9 A.M - 12 Noon
FO3b

organism: Boechera formosa x Boechera sp. JC-2020

tag: tissue

value: highly diplosporous


title: A1085

tag: region

value: CHR


title: 2420-DG

description: LPS-Study-Normalized-Counts-DG.csv

tag: Sex


title: 2531-DG

description: LPS-Study-Normalized-Counts-DG.csv


title: formosa ovule, young gametophyte, rep 1

description:
excised 9 A.M - 12 Noon
FO3a


title: E3.5_MUT_24_08_E

description:
ICM
ICM from E3.5 mouse embryos


title: E3.5_MUT_24_06_E

description:
ICM
ICM from E3.5 mouse embryos


title: E3.5_MUT_24_15_D

description:
ICM
ICM from E3.5 mouse embryos


title: A1083

tag: housing


title: A1076

value: SI

tag: treatment (mg/kg cocaine)


title: 2415-DG

description: LPS-Study-Normalized-Counts-DG.csv


title: formosa ovule, meiosis, rep 2

description:
excised 9 A.M - 12 Noon
FO2b

value: meiosis


title: E3.5_MUT_24_03_H

description:
ICM
ICM from E3.5 mouse embryos


title: E3.5_MUT_24_05_D

description:
ICM
ICM from E3.5 mouse embryos


title: 2411-DG

description: LPS-Study-Normalized-Counts-DG.csv


title: A1090

tag: acute/chronic


title: E3.5_MUT_23_06_D

description:
ICM
ICM from E3.5 mouse embryos

tag: sample type


title: E3.5_MUT_24_04_D

description:
ICM
ICM from E3.5 mouse embryos

tag: genotype


title: 2532-CA1

source_name: CA1 region of the hippocampus


title: A1071


title: A1075


title: 2531-CA1


title: A1077


title: A1074


title: A1070


title: E3.5_MUT_23_04_D

description:
ICM
ICM from E3.5 mouse embryos


title: 2420-CA1


title: E3.5_MUT_23_05_D

description:
ICM
ICM from E3.5 mouse embryos


title: A1084


title: E3.5_MUT_24_07_E

description:
ICM
ICM from E3.5 mouse embryos


title: 2412-DG

description: LPS-Study-Normalized-Counts-DG.csv


title: E3.5_MUT_23_03_H

description:
ICM
ICM from E3.5 mouse embryos


title: Paired contralateral cervical DRGs, Static sham, rep 2

city: Newark

first: Joseph

middle: R.

last: Loverde

state: NJ

address: 111 Lock Street

department: Department of Biomedical Engineering

institute: New Jersey Institute of Technology

description: Gene expression data from cultured DRG neurons grown in the static sham condition

hyb_protocol: The Affymetrix GeneChip WT Terminal Labeling and Hybridization protocol was used following the format for Array type 169 to hybridize cDNA to the arrays for 16 hours at 45C in the GeneChip Hybridization Oven 640.

scan_protocol: Affymetrix GCS 3000 Scanner w/AGCC v1.1.0.845 software

data_processing: Partek Genomic Suite software (Partek Inc., St. Louis, MO) was used to analyze the array data.  The arrays were normalized using the robust multi-array average (RMA) algorithm and principal component analysis was performed to check for chip outliers.  Fold changes were calculated and a paired two-tailed t-test was performed to generate p-values. Up and downregulation of genes in stretch-grown samples relative to shams were expressed as positive and negative changes, respectively. In addition to p-values, Significance Analysis of Microarrays (SAM) v4.0 was used to generate q-values (Tusher et al., 2001). Normalized data from Partek was analyzed pairwise using SAM to generate q-values for all genes.

label: Biotin

source_name: Rat DRG, 0 % strain 13 days in vitro

label_protocol: cDNA was generated from total RNA using the Ambion WT Expression Kit according to the manufacturer's protocol.   The cDNA was fragmented and end labeled following the GeneChip Whole Transcript Terminal Labeling and Hybridization protocol.

growth_protocol: C1-C7 cervical DRG explants were bilaterally isolated from E15.5 rat embryos removed from a single timed-pregnant Sprague-Dawley rat and seeded into matching stretch and sham cultures.  DRGs were seeded onto 1.5 x 2.5 cm Aclar (Honeywell, Morristown NJ) manipulating substrates which overlaid a large Aclar stationary substrate.  Explants were seeded individually utilizing a stereo microscope along the edges of the manipulating substrates; ensuring outgrowth of all explants onto the underlying substrates.  Aclar substrates consisted of 2.00 mil (51 μm thickness) UltRx 2000 Aclar washed with 50 % acetone-soaked cotton swabs and rinsed thoroughly 2 days prior to coating.  On the day of seeding, substrates were coated with high molecular weight poly-d-lysine (354210, Becton Dickinson, Bedford MA) at 60 μg/cm2 in PBS w/Ca2+ & Mg2+ for 1 hour at 37°C.  Culture media consisted of Neurobasal (Gibco 21103) supplemented with 2 % B-27 (Gibco 17504), 1 % FBS-HI, 20 ng/mL NGF (Gibco 13290-010), 0.5 mM L-glutamine (Gibco 25030081), 2.5 g/L D-glucose (Sigma G-7528), 20 µM FdU (Sigma F-0503), and 20 µM Uridine (Sigma U-3003), which was changed the day after seeding and every 3 to 4 days thereafter.

extract_protocol: Messenger RNA was isolated by detaching the Aclar substrates containing DRG explants and immersing directly into microcentrifuge tubes containing lysis buffer.  Utilizing a standard silica-based RNA isolation kit (RNeasy, Qiagen, Valencia CA), DNA was digested on-column and eluted mRNA was frozen.

treatment_protocol: Following seeding, and growth of axons across the substrates, mechanotransduced cultures underwent 25 % daily cumulative strain until a maximum stretch-growth rate of 3 mm/day was reached and sustained for 2 days.

tag: strain

value: Sprague dawley

tag: developmental stage

value: Embryonic day 15.5 + 13 days in vitro

value: Cervical dorsal root ganglia


title: Paired contralateral cervical DRGs, Static sham, rep 5


title: E3.5_MUT_18_22_D

description:
ICM
ICM from E3.5 mouse embryos

value: Stat3 -/-


title: E3.5_MUT_18_21_D

description:
ICM
ICM from E3.5 mouse embryos


title: 2412-CA1

tag: treatment


title: Paired contralateral cervical DRGs, Static sham, rep 3


title: 2415-CA1


title: 2411-CA1


title: E3.5_MUT_18_18_H

description:
ICM
ICM from E3.5 mouse embryos


title: A1065

source_name: Brain

value: M


title: A1066

value: AMY


title: 2717-DG

description: LPS-Study-Normalized-Counts-DG.csv

value: Young (5-7 months)

value: LPS (1mg/kg i.p. injection once a week for 7 weeks)


title: A1063

value: F

value: G


title: E3.5_MUT_18_19_H

description:
ICM
ICM from E3.5 mouse embryos

source_name: ICM from E3.5 mouse embryos

value: ICM


title: E3.5_MUT_18_17_G

description:
ICM
ICM from E3.5 mouse embryos


title: A1062


title: 2573-DG

description: LPS-Study-Normalized-Counts-DG.csv


title: A1060


title: Paired contralateral cervical DRGs, Static sham, rep 4


title: NELF-A*/+_Rep2 [BX_r2]

city: Singapore

first: Chin Tong

last: Ong

address: 1 Research Link, National University of Singapore

country: Singapore

institute: Temasek Life Sciences Laboratory

data_processing:
Read quality check was performed using FASTQC and adaptors were trimmed using Trim Galore. Reads were aligned to Drosophila reference genome (BDGP6.22.98) using STAR (v2.5). HTSeq-count was used to identify read counts per gene. Differentially expressed genes (DEGs) were determined using DESeq2 (v1.22.1) on Galaxy platform. The data was visualised by Heatmap2 (v3.0.1). Gene Ontology analysis was performed using DAVID Functional Annotation Bioinformatics (v6.8).
Genome_build: Drosophila melanogaster reference genome (BDGP6.22.98)
Supplementary_files_format_and_content: Tab-delimited raw count contains the raw gene count matrix for all samples and genes.
Supplementary_files_format_and_content: Tab-delimited Deseq output contains the differentially expressed genes for overexpression and control flies.

organism: Drosophila melanogaster

source_name: Heterozygous NELFA mutant BX

growth_protocol: Drosophila melanogaster were cultured in standard fly media (6% cornmeal, 5% dextrose, 2.4% brewer’s yeast, 0.8% agarose and 0.3% nipagin) at 25◦C with 12-hour light/dark cycle.

extract_protocol:
Fly heads were dissected and frozen by liquid nitrogen. Total RNA was isolated from the pooled fly heads at the age of day 50 using RNAzol®RT (Sigma).
RNA-sequencing was carried at BGI (Hong Kong) according to company’s protocol. RNA quality was assessed with Agilent 2100 bioanalyzer. Following DNAse I treatment, mRNA enriched by magnetic beads coupled to Oligo-dT was fragmented and used as template for cDNA library construction. Short DNA fragments were then subjected to end-repair, A-tailing, adaptor ligation, size selection and sequenced on Illumina HiSeq 4000.

treatment_protocol: Twenty flies were housed in one vial (diameter of 2.5 cm, height of 9.5 cm) and the food was changed every two days until the desired age of day 50.

value: Day 50 adult

value: Head


title: Ipsilateral cervical DRGs, Stretch-induced axon growth, rep 3

description: Gene expression data from cultured DRG neurons undergoing stretch-mediated axon growth

source_name: Rat DRG, 0 % strain 5 days, 25 % strain 8 days in vitro


title: 2547-DG

description: LPS-Study-Normalized-Counts-DG.csv

value: Male


title: Ipsilateral cervical DRGs, Stretch-induced axon growth, rep 5


title: A1067

value: CHR


title: Ipsilateral cervical DRGs, Stretch-induced axon growth, rep 4


title: A1048

value: A


title: Paired contralateral cervical DRGs, Static sham, rep 1


title: Ipsilateral cervical DRGs, Stretch-induced axon growth, rep 1


title: 2543-DG

description: LPS-Study-Normalized-Counts-DG.csv


title: E3.5_MUT_18_15_F

description:
ICM
ICM from E3.5 mouse embryos


title: A1046


title: E3.5_MUT_18_13_F

description:
ICM
ICM from E3.5 mouse embryos


title: E3.5_MUT_18_14_F

description:
ICM
ICM from E3.5 mouse embryos


title: NELF-A*/+_Rep1 [BX_r1]


title: E3.5_MUT_18_11_E

description:
ICM
ICM from E3.5 mouse embryos


title: NELF-A*/+_Rep2_input

description:
H3K9me2 Input genomic DNA
H3K9me2_BX_Input2_DKDL192000771-1a_H77N5CCX2_L1

data_processing:
Read quality check was performed using FASTQC and adaptors were trimmed using Trim Galore
Reads were mapped to Drosophila reference genome (BDGP6.22.98) using STAR (v2.5) with following parameters: --alignEndsType EndToEnd --alignIntronMax 1
Downstream analysis was performed using Galaxy platform. Peak calling was performed using MACS2 (v2.1.1), using an effective genome size of 120000000 --no model --extsize 200 --broad --keep-dup auto --bdg
Differential peaks between NELF-A*/+ (BX) and control siblings (Sib) was performed using MACS2 bdgdiff with following parameters: -g 100 -l 200
Genome_build: Drosophila melanogaster reference genome (BDGP6.22.98)
Supplementary_files_format_and_content: Alignment files (bam format) were transformed into read coverage files (bigwig format) using DeepTools: bamCompare (v3.3.2), normalized by readcount, scores representing ChIP minus Input.
Supplementary_files_format_and_content: peak files generated from MACS2 bdgdiff (Condition1:Sib>BX; Condition2:BX>Sib; Condition3:Sib=BX)

extract_protocol:
Fly heads were dissected and frozen by liquid nitrogen. Fly heads were fixed and homogenized for nuclei isolation. Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with indicated antibody.
ChIP-sequencing was carried at Novogene (Singapore) according to company’s protocol. Libraries were prepared according to Illumina's instructions. Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (32 to 52 exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation DNA was PCR amplified using KAPA library amplification kit (KK2702) with Illumina primers for 11 cycles and library fragments of ~200-500 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Illumina HiSeq 4000.

tag: chip antibody


title: NELF-A*/+_Rep1_input

description:
H3K9me2 Input genomic DNA
H3K9me2_BX_Input1_DKDL192000769-1a_H77N5CCX2_L1


title: 2527-DG

description: LPS-Study-Normalized-Counts-DG.csv


title: E3.5_MUT_18_09_D

description:
ICM
ICM from E3.5 mouse embryos


title: Control_Sib_Rep2 [Sib_r2]

source_name: control sibling


title: 2408-DG

description: LPS-Study-Normalized-Counts-DG.csv


title: A1045


title: A1041


title: Control_Sib_Rep1 [Sib_r1]


title: 2404-DG

description: LPS-Study-Normalized-Counts-DG.csv


title: E3.5_MUT_18_04_G

description:
ICM
ICM from E3.5 mouse embryos


title: NELF-A*/+_Rep2_H3K9me2

description:
H3K9me2 ChIP genomic DNA
H3K9me2_BX_IP2_DKDL192000775-1a_H77N5CCX2_L1

value: H3K9me2 (abcam, ab1220)


title: A1043


title: 2543-CA1


title: E3.5_MUT_18_07_H

description:
ICM
ICM from E3.5 mouse embryos


title: 2717-CA1


title: 2573-CA1


title: E3.5_MUT_18_03_F

description:
ICM
ICM from E3.5 mouse embryos


title: NELF-A*/+_Rep1_H3K9me2

description:
H3K9me2 ChIP genomic DNA
H3K9me2_BX_IP1_DKDL192000773-1a_H77N5CCX2_L1


title: Control_Sib_Rep2_input

description:
H3K9me2 Input genomic DNA
H3K9me2_Sib_Input2_DKDL192000770-1a_H77N5CCX2_L1


title: Ipsilateral cervical DRGs, Stretch-induced axon growth, rep 2

value: Sprague dawley


title: E3.5_MUT_18_06_H

description:
ICM
ICM from E3.5 mouse embryos


title: 2547-CA1


title: A1038

value: SI


title: A1040


title: E3.5_MUT_18_05_G

description:
ICM
ICM from E3.5 mouse embryos


title: A1036


title: 2403-DG

description: LPS-Study-Normalized-Counts-DG.csv


title: A1044


title: E3.5_MUT_18_01_D

description:
ICM
ICM from E3.5 mouse embryos


title: 2404-CA1


title: A1037


title: E3.5_MUT_18_02_H

description:
ICM
ICM from E3.5 mouse embryos


title: 2527-CA1


title: E3.5_MUT_10_23_E

description:
ICM
ICM from E3.5 mouse embryos


title: Control_Sib_Rep1_input

description:
H3K9me2 Input genomic DNA
H3K9me2_Sib_Input1_DKDL192001143-1a_H77N5CCX2_L1


title: A1034


title: 2731-DG

description: LPS-Study-Normalized-Counts-DG.csv

value: Vehicle (saline i.p. injection once a week for 7 weeks)


title: 2722-DG

description: LPS-Study-Normalized-Counts-DG.csv


title: A1032


title: E3.5_MUT_10_24_F

description:
ICM
ICM from E3.5 mouse embryos

value: Stat3 -/-


title: 2408-CA1


title: A1016

value: M


title: Control_Sib_Rep1_H3K9me2

description:
H3K9me2 ChIP genomic DNA
H3K9me2_Sib_IP1_DKDL192000772-1a_H77N5CCX2_L1


title: E3.5_MUT_10_18_H

description:
ICM
ICM from E3.5 mouse embryos


title: A1015

value: AMY


title: A1030


title: E3.5_MUT_10_22_E

description:
ICM
ICM from E3.5 mouse embryos


title: Control_Sib_Rep2_H3K9me2

description:
H3K9me2 ChIP genomic DNA
H3K9me2_Sib_IP2_DKDL192000774-1a_H77N5CCX2_L1


title: E3.5_MUT_10_21_D

description:
ICM
ICM from E3.5 mouse embryos


title: A1033


title: A1018


title: E3.5_MUT_10_17_G

description:
ICM
ICM from E3.5 mouse embryos


title: 2572-DG

description: LPS-Study-Normalized-Counts-DG.csv

value: Young (5-7 months)


title: A1014


title: E3.5_MUT_10_16_G

description:
ICM
ICM from E3.5 mouse embryos


title: 2571-DG

description: LPS-Study-Normalized-Counts-DG.csv


title: 2728-DG

description: LPS-Study-Normalized-Counts-DG.csv


title: A1013


title: 2523-DG

description: LPS-Study-Normalized-Counts-DG.csv


title: E3.5_MUT_10_19_H

description:
ICM
ICM from E3.5 mouse embryos


title: E3.5_MUT_10_12_F

description:
ICM
ICM from E3.5 mouse embryos


title: A1017


title: 2410-DG

description: LPS-Study-Normalized-Counts-DG.csv


title: A1008


title: 2403-CA1

value: LPS (1mg/kg i.p. injection once a week for 7 weeks)


title: A1011

value: F


title: A1006

value: G


title: A1007


title: E3.5_MUT_10_09_D

description:
ICM
ICM from E3.5 mouse embryos

value: ICM


title: E3.5_MUT_10_11_E

description:
ICM
ICM from E3.5 mouse embryos


title: 2572-CA1


title: 2731-CA1


title: E3.5_MUT_10_08_D

description:
ICM
ICM from E3.5 mouse embryos


title: 2728-CA1


title: A1004


title: 2722-CA1


title: E3.5_MUT_10_05_G

description:
ICM
ICM from E3.5 mouse embryos


title: 2571-CA1


title: E3.5_MUT_10_07_H

description:
ICM
ICM from E3.5 mouse embryos


title: 2526-DG

description: LPS-Study-Normalized-Counts-DG.csv


title: E3.5_MUT_10_06_H

description:
ICM
ICM from E3.5 mouse embryos


title: A1003


title: 2526-CA1


title: 2523-CA1


title: A1000


title: E3.5_MUT_10_02_D

description:
ICM
ICM from E3.5 mouse embryos


title: E3.5_MUT_10_03_G

description:
ICM
ICM from E3.5 mouse embryos


title: E3.5_MUT_02_05_H

description:
ICM
ICM from E3.5 mouse embryos


title: E3.5_MUT_02_03_G

description:
ICM
ICM from E3.5 mouse embryos


title: E3.5_MUT_10_01_E

description:
ICM
ICM from E3.5 mouse embryos


title: 2410-CA1


title: Tex_RNAseq_rep2

city: Beijing

first: Jingzhe

last: Lu

state: Beijing

address: No.30 shuangqing road

department: School of medicine

institute: Tsinghua University

description:
Raw_gene_counts_matrix.txt
Normalized_gene_expression_matrix.txt

data_processing:
Hi-C data was aligned to the mm10 genome assembly using BWA with parameters mem -t 16
Hi-C reads were filtered by the Juicer preprocessing protocol
The chromatin interactions were detected by Chrom-Lasso from preprocessed Hi-C data.
RNA-seq data was aligned to the mm10 genome assembly using Hisat2 with parameters -p 16 --mm --dta -x
The raw read counts were called by HTseq with parameters -count -s no -i gene_name after mapping
The normalized gene expression level were called by R package DESeq2 rlog function using the raw read counts from all samples
Genome_build: mm10
Supplementary_files_format_and_content: Preprocessed files including preserved reads after filtering are used as the input files for Chrom-Lasso to call interactions
Supplementary_files_format_and_content: The result files include interactions called by Chrom-Lasso for each Hi-C sample with the interacting loci information and P value showing significance level
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every RNA-seq sample
Supplementary_files_format_and_content: Matrix table with normalized gene expression level for every gene and every RNA-seq sample

source_name: CD8+ T cells

growth_protocol: Naïve CD8+ T cells were isolated from single-cell suspensions of splenocytes using EasySep™ Mouse Naïve CD8+ T Cell Isolation Kit (STEMCELL technologies, 19858 ) according to the manufacturer’s instructions.

extract_protocol:
RNA of T cells (0.2 million cells per sample) were extracted using the Monarch Total RNA Miniprep Kit (NEB, T2010S).
Bulk RNA-seq libraries were constructed using NEBNext Ultra RNA Library Prep Kit for Illumina (NEB, E7530L).

treatment_protocol: Freshly purified naïve CD8+ T cells were stimulated with anti-mouse CD3e ( 10μg/ml ) (BioLegend, 100314 )and anti-mouse CD28 ( 10μg/ml ) (BioLegend, 102112). Overnight, recombinant mouse IL-2 (PeproTech, AF212-12-20) was added to the culture at 300U/ml. T cells were used for further experiments after 2d or 5d of in vitro activation.

tag: cell type

value: CD8+ T cells

tag: time

value: day 5 of culture

tag: sorting criteria


title: Teff2_RNAseq_rep3


title: Tex_RNAseq_rep3


title: E3.5_MUT_02_04_H

description:
ICM
ICM from E3.5 mouse embryos


title: E3.5_MUT_02_01_G

description:
ICM
ICM from E3.5 mouse embryos


title: m-Tyr 60 min treatment Rep 3

city: Los Angeles

first: Beth

last: Lazazzera

state: CA

address: 405 Hilgard Ave.

department: MIMG

institute: UCLA

description:
processed data file:
ann_t60t0.result.txt
11_S11_L001

data_processing:
Sequence results were aligned to E. coli str. K-12 substr. MG1655 ASM584v2.32 genome sequence using TopHat
Transcript read counts were determined using HTSeq version 0.6.1p1
Normalization of read counts and differential gene expression analysis were performed using R package DESeq2
Results were analyzed by pairwise comparison of time-points t=30, 60, and 120 to t=0.
Supplementary_files_format_and_content: tab-delimited text files include gene_symbol, ID, baseMean, log2FoldChange, lfcSE, stat, pvalue, and padj

organism: Escherichia coli

source_name: m-Tyr 60 min treatment_whole cells

growth_protocol: A 5 ml LB culture was inoculated from a single colony of BAL4703 (pheT(G318W)) strain and grown until it reached mid-log phase (OD600 0.4-0.6).   A 1 ml sample of the cells were then washed in 0.9% NaCl and used to inoculate a 100 ml, M9 minimal media culture in a 500 ml flask to an OD600 of 0.001. The M9 culture was allowed to grow with shaking at 37°C until it reached an OD600 of 0.5.

extract_protocol:
RNA purification was performed using the Qiagen®  RNeasy® Mini Kit.  One-ml of culture was removed for each time point and mixed with 2 ml of RNAprotect® Bacterial Reagent.  RNA was then purified accound to the Qiagen® protocols for “Enzymatic Lysis of Bacteria” and “Purification of Total RNA from Bacterial Lysate Using the RNeasy® Mini Kit”. Ribosomal RNA was removed from the RNA samples using the Thermo Fisher Scientific RiboMinus™ Transcriptome Isolation Kit for bacteria.  The resulting rRNA-depleted samples were then concentrated using the Qiagen® RNeasy® columns using the “RNA Clean Up” protocol.
cDNA libraries were then created using New England Biolabs’ (Ipswich, MA, USA) NEBNext® Ultra™ Directional RNA Library Prep Kit for Illumina® and the Primer Set 1 of NEBNext® Multiplex Oligos for Illumina (Ipswich, MA, USA).
Sequencing of the 12 cDNA libraries was performed using the Illumina MiSeq Personal Sequencer System with paired end 150 bp reads.

treatment_protocol: A sample of cells was taken at this time (t=0) for RNA purification and CFU/ml determination.  A m-Tyr solution was then added to the culture to 0.5 mM.  The culture was then allowed to continue growing at 37°C with shaking.  Additional sampling for RNA purification and CFU/ml measurements was done at 30, 60, and 120 minutes after m-Tyr addition.

value: m-Tyr

tag: time point

value: Time 60


title: E3.5_MUT_02_02_G

description:
ICM
ICM from E3.5 mouse embryos


title: Teff1_RNAseq_rep3

value: day 2 of culture


title: A1002

value: A


title: Tex_RNAseq_rep1


title: m-Tyr 30 min treatment Rep 3

description:
processed data file:
ann_t30t0.result.txt
10_S10_L001

source_name: m-Tyr 30 min treatment_whole cells

value: Time 30


title: Teff2_RNAseq_rep2


title: Teff2_RNAseq_rep1


title: E3.5_MUT_10_04_G

description:
ICM
ICM from E3.5 mouse embryos


title: m-Tyr 120 min treatment Rep 3

description:
processed data file:
ann_t120t0.results.txt
12_S12_L001

source_name: m-Tyr 120 min treatment_whole cells

value: Time 120


title: Teff1_RNAseq_rep2


title: m-Tyr 0 min treatment Rep 3

source_name: m-Tyr 0 min treatment_whole cells

value: Time 0


title: Teff1_RNAseq_rep1


title: m-Tyr 120 min treatment Rep 2

description:
processed data file:
ann_t120t0.results.txt
8_S8_L001


title: YM_Naive2_S15: Naive_rep2

city: Philadelphia

first: E

middle: JOHN

last: WHERRY

state: PA

address: 421 Curie Blvd,354 BRB II/III

department: Systems Pharmacology       and Translational Therapeutics,Institute for Immunology

institute: University of Pennsylvania

data_processing:
Raw FASTQ files from RNAseq paired-end sequencing were aligned to the  GRCm38/mm10 reference genome using STAR2.5.2a
Counts were corrected/normalized using PORT(github.com/itmat/normalization)
Genes with differential  expression across samples (DEGs) were assessed using the R package Limma
Differential genes were calculated using a FDR cutoff of 0.05 and Log2 fold change of 1 otherwise indicated
Genome_build: GRCm38/mm10
Supplementary_files_format_and_content: tab-delimited text file with normalized counts

source_name: CD8 T cells

growth_protocol: At D8 post infection. with LCMV Armstrong strain, p14 CD8 T cells were isolated from spleens of infected recipients and CD62Lhi, IL-7Rαhi and KLRG1hi subsets were sorted, Naive P14 CD8+ T cells from uninfected mice were used as controls

extract_protocol:
mRNA was extracted using RNeasy Plus Micro kit  (Qiagen) following manufacturer’s protocol and eluted in 14μl of RNAse free water.  mRNA quality was assessed on a 2200 TapeStation (Agilent Technologies) using  High Sensitivity RNA ScreenTape (Agilent Technologies).mRNA from each  biological replicate (5ng/sample) was converted into cDNA and amplified (9 cycles)  using the SMART-Seq V4 Ultra Low Input RNA Kit (Takara Bio).
10ng of cDNA  was used to prepare DNA libraries using Nextera XT DNA Library Prep Kit  (Illumina). Barcoded samples were pooled, diluted at 1.8pM, loaded onto a TG  NextSeq 500/550 High Output Kit v2 (150 cycles, 400M reads, Illumina) and  paired-end sequencing was performed on a NextSeq 550 (Illumina)

treatment_protocol: Sorted cells were centrifuged, resuspended in 350μl of RLT buffer (RNeasy Plus  Micro kit, Qiagen) in DNA LoBind tubes (Eppendorf), vortexed for 30s, flash-frozen  on dry ice and stored at -80oC

tag: background strain

value: Uninfected

value: CD8 T cells


title: YM_Naive3_S19: Naive_rep3

tag: tissue


title: YM_Red1_S14: KLRG1_rep1

value: LCMV Armstrong infection


title: m-Tyr 0 min treatment Rep 2


title: m-Tyr 30 min treatment Rep 2

description:
processed data file:
ann_t30t0.result.txt
6_S6_L001


title: Tn_RNAseq_rep3

value: day 0 of culture


title: Tn_RNAseq_rep2


title: YM_Red2_S18: KLRG1_rep2


title: m-Tyr 60 min treatment Rep 1

description:
processed data file:
ann_t60t0.result.txt
3_S3_L001


title: YM_Red3_S22: KLRG1_rep3


title: YM_Green3_S21: IL-7Rahi_rep3


title: YM_Green2_S17: IL-7Rahi_rep2


title: Tn_RNAseq_rep1


title: YM_Blue3_S20: CD62Lhi_rep3


title: YM_Blue2_S16: CD62Lhi_rep2


title: m-Tyr 30 min treatment Rep 1

description:
processed data file:
ann_t30t0.result.txt
2_S2_L001


title: m-Tyr 60 min treatment Rep 2

description:
processed data file:
ann_t60t0.result.txt
7_S7_L001


title: YM_Naive1_S11: Naive_rep1


title: m-Tyr 0 min treatment Rep 1


title: G1

city: La Tronche

first: Alexandre

last: Bougdour

state: Isère

address: Domaine de la Merci, Campus santé

department: Prevention and Therapy of Chronic diseases

country: France

institute: Centre de Recherche Inserm U1209 / CNRS UMR5309 / UGA

data_processing:
The RNA-Seq reads (FASTQ) were processed and analyzed using the Lasergene Genomics Suite version 15 (DNASTAR, Madison, WI, USA) using default parameters.
The paired-end reads were uploaded onto the SeqMan NGen (version 15, DNASTAR. Madison, WI, USA) platform for reference-based assembly using the Toxoplasma Type I GT1 strain (ToxoDB-36, GT1 genome) as reference template.
The ArrayStar module (version 15, DNASTAR. Madison, WI, USA) was used for normalization, variant detection and statistical analysis of uniquely mapped paired-end reads using the default parameters.
The expression data quantification and normalization were calculated using the RPKM (Reads Per Kilobase of transcript per Million mapped reads) normalization method.
Variant calls were filtered to select variants present in coding regions with the following criteria: SNP% ≥ 90%, variant depth ≥ 30, and absent in the parental wild-type strain (Supplementary Table S2). SNVs, insertions and deletions present in regulatory or intergenic regions were filtered out as they are unlikely to contribute to drug resistance.
Genome_build: Toxoplasma Type I GT1 strain (ToxoDB-36, GT1 genome).
Supplementary_files_format_and_content: xlsx format. The matrix table includes RNA-Seq report, RPKM values and raw counts of T. gondii transcripts for each sample. Variants detected in each strain when compared to the GT1 reference genome are also provided.

organism:
Toxoplasma gondii
Homo sapiens

source_name: HFF and parasites

growth_protocol: Cells were maintained in Dulbecco’s modified Eagle’s medium (DMEM, Invitrogen) supplemented with 10% heat-inactivated FBS (Invitrogen), 10 mM HEPES buffer, pH 7.2, 2 mM L-glutamine, and 50 μg/ml penicillin and streptomycin (Thermo Fisher Scientific). Cells were incubated at 37°C in 5% CO2.

extract_protocol:
18 hours post-infection, cells were harvested and total RNAs were extracted and purified using TRIzol (Invitrogen, Carlsbad, CA, USA) and RNeasy Plus Mini Kit (Qiagen). RNA quantity and quality were measured by NanoDrop 2000 (Thermo Scientific). RNA integrity was assessed by standard non-denaturing 1.2% TBE agarose gel electrophoresis. The ribosomal large subunits from Toxoplasma and the host cells was used to verify that the ratio between Toxoplasma RNA versus host RNA was equivalent between the different biological samples, thus indicating that the samples had equivalent infection rates.
RNA libraries were prepared using polyA selected RNAs for sequencing using standard Illumina protocols (Illumina TruSEQ RNA library prep).

tag: t. gondii genotype

value: mutant G1

tag: t. gondii strain background

value: RH

value: HFF


title: m-Tyr 120 min treatment Rep 1

description:
processed data file:
ann_t120t0.results.txt
4_S4_L001


title: IgG-3

first: Jason

last: Weinstein

address: New Jersey Medical School Cancer Center 205 South Orange Ave

department: Center for Immunity and Inflmmation

institute: Rutgers New Jersey Medical School

data_processing:
Sequenced reads were mapped to the mouse genome (mm10 NCBI Build 38) using the BWA version 0.7.9a alignment program.
Reads mapping to the ENCODE project blacklist of repetitive regions and mitochondrial regions were removed
The MACS2 program version 2.1.0.20150420 was used to identify peaks using parameters --nomodel --shift -100 --extsize 200 with a q value of <0.05.
Read counts for open chromatin regions in all samples were obtained using the DiffBind version 2.0.7 package (Ross-Innes et al., 2012)with DESEQ2 normalization utilizing read counts in analyzed regions (parameter bFullLibrarySize=FALSE). Statistically significant differentially accessible regions were identified by DiffBind using the DESEQ2 method with default parameters.
Bigwig files were created using bedtools genomeCoverageBed scaling per million read, followed by conversion to bigwig format using the UCSC bedGraphToBigWig program.
Genome_build: Genome_build: mm10
Supplementary_files_format_and_content: Comma delimited file (csv) for differential gene expression counts via DESeq2.

source_name: Spleen

extract_protocol:
Sorted cells were lysed in buffer (10mM Tris-HCl, 10mM NaCl 3mM MgCL2 and 0.1% IGEPAL) for 15 minutes at 4C, then centrifuged and re-suspended with transposase reaction mix (2x tagmented DNA buffer, transposase [Ilumina Nextera]), and nuclease-free water) and incubated for 30 min at 37 degrees.  Cells were then added to MinElute column (Qiagen) and PCR amplified in KAPA HiFi 2x mix (Kapa Biosystems) with barcoding primers(Buenrostro et al., 2013) at 98C for 45 sec (45s) + 5 x at (98C for 15s + 63C for 30s + 72C for 30s) + 72C for 1 min. PCR products were cleaned with MinElute columns and size exclusion was performed with magJet NGS Cleanup and Size Selection kit (Thermo Fisher). Q-PCR library amplification test and PCR library amplification was performed as previously described(Buenrostro et al., 2015).
Paired end strand-specific libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: B6/Sle1.Yaa mice treated twice a week for 4 weeks with either anti-IFNA1 or anti-rat IgG

tag: infected with

value: anti-rat IgG

tag: timepoint

value: 5 months 4 weeks after txt

value: Sorted Tfh cells (CD4+CD44+GITR-PSGL-1loCXCR5hiPD-1hi)


title: YM_Green1_S13: IL-7Rahi_rep1


title: IgG-2


title: IFN-4


title: CM+hCF+EC3

city: Hannover

first: Monika

last: Szepes

address: Carl-Neuberg Str. 1

department: Department of Cardiac, Thoracic, Transplantation and Vascular Surgery

institute: Hannover Medical School

data_processing:
BCL files were converted to FASTQ files using bcl2fastq Conversion Software version v2.20.0.422 (Illumina).
Raw data processing was conducted by use of nfcore/rnaseq (version 1.3). Sequenced reads were trimmed for adaptor sequence (Trim Galore! 0.5.0), the reads were aligned (STAR2.6.1d) and RNA reads were assigned and counted (featureCounts1.6.4). Report was generated by MultiQC1.7.
Normalization and differential expression analysis was performed with DESeq2 (Galaxy Tool Version 2.11.40.2) with default settings except for “Output normalized counts table” which was set to “Yes”.
Genome_build: Homo sapiens; Reference data coming from GENCODE (www.gencodegenes.org); Genome sequence (GRCh38.p12) - Release 29 (ftp://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_human/release_29/GRCh38.primary_assembly.genome.fa.gz); Comprehensive gene annotation (ftp://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_human/release_29/gencode.v29.annotation.gtf.gz)
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample

source_name: hESC-CM BCT with hCF+EC

growth_protocol: CMs and ECs differentiated in suspension culture (Dahlman et al. 2013 Biomaterials; Olmer et al. 2018 Stem Cell Reports), BCTs were prepared and cultivated as described (Halloin et al. 2019 Stem Cell Reports).

extract_protocol:
RNA was harvested using Trizol reagent and purified through sodium-acetate precipitation.
200ng of total RNA per sample were utilized as input for mRNA enrichment procedure with ‘NEBNext® Poly(A) mRNA Magnetic Isolation Module’ (E7490L; New England Biolabs) followed by stranded cDNA library generation using ‘NEBNext® Ultra II Directional RNA Library Prep Kit for Illumina’ (E7760L; New England Biolabs).

value: hESC-CMs + induced pluripotent stem cell-derived ECs +  human cardiac fibroblasts (PromoCell C-12375)

tag: age

value: Tissue cultivation day 21

tag: batch number


title: E1

value: mutant E1


title: CM+hCF+EC2


title: IFN-3


title: CM+hCF+EC1


title: D1

value: mutant D1


title: CM+PC+EC 3

source_name: hESC-CM BCT with PC+EC

value: hESC-CMs + induced pluripotent stem cell-derived ECs +   induced pluripotent stem cell-derived PCs


title: IFN-1


title: IgG-1


title: B1

value: mutant B1


title: F1

value: mutant F1


title: C1

value: mutant C1


title: IFN-2


title: CM+PC+EC 2


title: WT

value: wild-type


title: heart_Treg_MIRI_1

city: Wuhan

first: Muyang

last: Gu

address: 1277 Jiefang Road, Jianghan District

institute: Union Hospital, Tongji Medical College, Huazhong   University of Science and Technology

data_processing:
The primary sequencing output (FASTQ) is produced by a combination of Illumina software (CASAVA v. 1.8.2) and EA developed tools. Low quality reads, bases, homopolymers and adapter sequences were removed with fastq-mcf (Expression Analysis).
Reads were then mapped to mm10 using Hisat2 (http://ccb.jhu.edu/software/hisat2；Kim D et al., 2015).
Reads were counted with HTSeq v0.6.0 using the settings union and stranded=no.
Genome_build: mm10
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: heart Tregs

extract_protocol:
Tregs from 3-day post-IR injury heart, spleen or heart draining MLN of the Foxp3-GFP transgenic mice were double-sorted by magnetic-activated cell sorting (MACS) and fluorescence activated cell sorting (FACS) into special cell lysates (provided by Novogene, Beijing, China). RNA was extracted, and RNA degradation and contamination were monitored on 1% agarose gels. RNA purity was checked using a NanoPhotometer® spectrophotometer (IMPLEN, CA, USA), and the concentration was measured by a Qubit® RNA Assay Kit in a Qubit® 2.0 Fluorometer (Life Technologies, CA, USA). The integrity was assessed using the RNA Nano 6000 Assay Kit of the Bioanalyzer 2100 system (Agilent Technologies, CA, USA). RNA samples were converted into cDNA libraries using the Illumina SMARTer Ultra Low Input sample preparation kit.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: heart

value: 8 weeks

tag: disease state

value: 3 days post-I/R injury

value: Tregs


title: A1

value: mutant A1

value: RH

value: HFF


title: CM+hFF+EC3

source_name: hESC-CM BCT with hFF+EC

value: hESC-CMs + induced pluripotent stem cell-derived ECs +  human foreskin fibroblasts (ATCC-SCRC-1041)


title: heart_Treg_MIRI_3

tag: strain


title: heart_Treg_MIRI_2


title: s1154rDeletion_Uberis_T24_Macrophagerep2

city: Loughborough

first: Nathan

last: Archer

state: East Midlands

address: Sutton Bonington

department: School of Veterinary Medicine and Sciences

institute: University of Nottingham

description: UMI included in second strand synthesis and is the first 6 nucleotides of the read.

data_processing:
BCL2FASTQ for Basecalling and Demultiplexing
Bluebee Genomics Pipeline for UMI-corrected alignments in brief:
The 6 nt UMI is the first 6 nucleotides of the read.
umi2index is used to add the UMI to the read name
bbduk used to trim adapters
STAR alignment to Bos_taurus_UMD_3.1.1
collapse_UMI to collapse the UMI into the bam file
samtools_index
htseq-count (stranded = yes)
data downloaded for local analysis with DESEQ2 multifactor differential expression
DESEQ2 for differential expression (bluebee genomics online)
mutifactor DESEQ2 analysis, i.e: where assay was timepoint and treatment was strain of s.uberis:  ddsHTSeq = DESeqDataSetFromHTSeqCount(sampleTable=[matrix_of_samples&filenames], design= ~ assay + treatment + assay:treatment, directory=directory)  dds <- DESeq(ddsHTSeq)  dds <- DESeq(dds, test="LRT", reduced= ~ assay + treatment).
data converted to CSV and imported into R for further analysis (not included here)
Genome_build: UMD_3.1.1
Supplementary_files_format_and_content: bam files provided for UMI collapsed alignments, .txt files provided for non-normalised read counts, .xlsx files provided for differential expression outputs, .gz-zipped fastq files provided for raw sequencing data.

organism: Bos taurus

source_name: Ex vivo bovine milk CD14+ Cells

growth_protocol: Somatic cells were isolated from untreated milk collected from a bulk tank as follows: 1L of milk was mixed with 1L of P.A.E buffer and centrifuged for 40 minutes at 1000g. The resultant cell pellet was then washed thrice with PBS before CD14+ cells were isolated with magnetic beads. Isolated CD14+ cells were cultured overnight in IMDM media supplemented with 20% FBS before challenge with s.uberis strains.

extract_protocol:
Trizol
Lexogen (Vienna) Quantseq 3'-FWD with UMI add-in for second strand synthesis, following the manufacturer's instructions

treatment_protocol: challenged with heat killed strains of s.uberis

value: milk

value: CD14+ macrophage

tag: s. uberis strain

value: Deletion

tag: timepoint (hours)


title: CM+PC+EC 1

value: Tissue cultivation day 21


title: s1154rDeletion_Uberis_T24_Macrophagerep1


title: CM+hFF+EC2


title: s1154rDeletion_Uberis_T24_Macrophagerep3


title: MLN_Treg_MIRI_3

source_name: mediastinal lymph node Tregs

value: mediastinal lymph nodes


title: CM+hFF+EC1


title: hESC-CM 3

source_name: hESC-CM

growth_protocol: CMs differentiated in suspension culture (Dahlman et al. 2013 Biomaterials)

value: CMs differentiated from embrionic stem cells

value: Differentiation day 18


title: YM_Blue1_S12: CD62Lhi_rep1

tag: treatment

value: LCMV Armstrong infection

value: CD8 T cells


title: MLN_Treg_MIRI_1

tag: cell type


title: s1154rDeletion_Uberis_T0_Macrophagerep3


title: s1154rDeletion_Uberis_T0_Macrophagerep2


title: SD140_GBM002-cA10-p58-Rx-XChIP1_SUZ12

city: Montreal

first: Carol

last: Chen

state: QC

address: 1001 Decarie Boulevard, Rm E01.4380

department: Human Genetics

country: Canada

institute: Research Institute of McGill University Hospital Centre

data_processing: Datasets were processed using the ChIP-seq or RNA-seq module of GenPipes (Bourgey, 2019). Briefly, raw reads are trimmed using Trimmomatic to remove adaptor and sequencing-primer associated reads, then aligned to hg19 using bwa-mem for ChIP-seq, and STAR for RNA-seq using default parameters. PCR duplicate reads as defined by reads with identical mapping coordinates are then collapsed by Picard to produce uniquely aligned reads. Reads were then filtered for mapping quality of > 5. For SE75 ChIP datasets, reads were extended by 250bp. Wiggle tracks depicting coverage are then generated using uniquely aligned reads. Analysis of Hi-C generated libraries and downloaded files was performed using Juicer and the associated Juicer Tools (Durand et al. 2016). Contact maps were generated using Juicer with the following parameters: -s DpnII -g hg19. Map resolution was determined by using Juicer’s “calculate_map_resolution.sh” script. Hi-C contact maps and associated annotations were visualized using Juicebox (Durand et al. 2016)

source_name: patient-derived glioma cell line

growth_protocol: Tumor-derived cell lines HSJD-GBM002 were cultured in NeuroCult NS-A proliferation media (StemCell Technologies) supplemented with bFGF (10 ng/mL), rhEGF (20 ng/mL), and heparin (0.0002%) (StemCell Technologies) and on plates coated with poly-L-ornithine (0.01%) (Sigma) and laminin (0.01 mg/mL) (Sigma). KNS-42 and PS10-801 cell lines were cultured in DMEM containing 4.5 g/L glucose, L-glutamine, phenol red, and 10% FBS (Wisent). All lines were tested monthly for mycoplasma contamination (MycoAlert Mycoplasma Detection kit by Lonza), and STR fingerprinting was regularly performed.

extract_protocol:
For ChIP-seq, cells were fixed with 1% formaldehyde (Sigma). Fixed cell preparations were washed, pelleted and stored at -80°C. Sonication of lysed nuclei (lysed in a buffer containing 1% SDS) was performed on a BioRuptor UCD-300 for 60 cycles, 10s on 20s off, centrifuged every 15 cycles, chilled by 4°C water cooler. Samples were checked for sonication efficiency using the criteria of 150-500bp by gel electrophoresis. After the sonication, the chromatin was diluted to reduce SDS level to 0.1% and before ChIP reaction ~5% of sonicated drosophila S2 cell chromatin was spiked-in the samples for quantification of total levels of histone mark after the sequencing (see below). ChIP reaction for histone modifications was performed on a Diagenode SX-8G IP-Star Compact using Diagenode automated Ideal ChIP-seq Kit. 25ul Protein A beads were washed and then incubated with 6ug of H3K27ac antibody (Diagenode, C15410196), and 2 million cells of sonicated cell lysate combined with protease inhibitors for 10 hr, followed by 20 min wash cycle with provided wash buffers. Reverse cross linking took place on a heat block at 65°C for 4 hr. ChIP samples were then treated with 2ul RNase Cocktail (Life Technologies) at 65°C for 30 min followed by 2ul Proteinase K (Thermo Fisher Scientific) at 65°C for 30 min. Samples were then purified with QIAGEN MiniElute PCR purification kit as per manufacturers’ protocol. In parallel, input samples (chromatin from about 50,000 cells) were reverse crosslinked and DNA was isolated following the same protocol. For RNA-seq, total RNA was extracted from cell pellets and mouse tumors using the AllPrep DNA/RNA/miRNA Universal Kit (Qiagen) according to instructions from the manufacturer. Library preparation was performed with ribosomal RNA (rRNA) depletion according to instructions from the manufacturer (Epicentre) to achieve greater coverage of mRNA and other long non-coding transcripts. Paired-end sequencing was performed on the Illumina HiSeq 2500/4000 platform. For Hi-C, libraries were generated from 5 million cultured G34 glioblastoma cell lines KNS-42, HSJD-GBM002 and PS10-801 as described in (Rao et al., 2014) with minor modifications. Briefly, in situ Hi-C consists of 7 steps: (1) crosslinking cells with formaldehyde, (2) digesting the DNA using a 4-cutter restriction enzyme (e.g., DpnII) within intact permeabilized nuclei, (3) filling in, biotinylating the resulting 5′-overhangs and ligating the blunt ends, (4) shearing the DNA, (5) pulling down the biotinylated ligation junctions with streptavidin beads, (6) library amplification and (7) analyzing these fragments using paired end sequencing. As quality control (QC) steps, we checked for efficient sonication with an agarose DNA gel and for appropriate size selection using the Agilent Bioanalyzer on final amplified libraries. For the final QC, we performed superficial sequencing on the Illumina Hiseq 2500 (~30M reads/sample) to assess quality of the libraries using percent of reads passing filter, percent of chimeric reads, and percent of forward-reverse pairs.  125bp paired-end sequencing was performed on the Illumina HiSeq 4000.
For ChIP-seq, library preparation was carried out using Kapa HTP Illumina library preparation reagents. Briefly, 25ul of ChIP sample was incubated with 45ul end repair mix at 20°C for 30 min followed by Ampure XP bead purification. A tailing: bead bound sample was incubated with 50ul buffer enzyme mix for 30°C 30 min, followed by PEG/NaCl purification. Adaptor ligation: bead bound sample was incubated with 45ul buffer enzyme mix and 5ul of different TruSeq DNA adapters (Illumina) for each sample, for 20°C 15 min, followed by PEG/NaCl purification (twice). Library enrichment: 12 cycles of PCR amplification. Size selection was performed after PCR using a 0.6x/0.8x ratio of Ampure XP beads (double size selection) set to collect 250-450bp fragments. Single-end or paired-end 50bp sequencing was performed on the Illumina HiSeq 4000 or NovaSeq 6000 platform.
For RNA-seq, RNA-seq library preparation was performed with ribosomal RNA (rRNA) depletion according to instructions from the manufacturer (Epicentre) to achieve greater coverage of mRNA and other long non-coding transcripts, paired-end sequencing (100 bp) was performed on the Illumina HiSeq 4000 platform.

treatment_protocol:
CRISPR-Cas9 editing of HSJD-GBM002 cell line was performed by designing a synthetic ALT-R crRNA (IDT) guide targeting the H3F3A G34R mutation. Nucleofection was performed using program A-023 on the Amaxa Nucleofector 2b (Lonza) device, following manufacturer’s instructions to introduce crRNA, tracrRNA and recombinant Alt-R S.p. Cas9 Nuclease V3. Single cell clones were isolated by limiting dilution, expanded and screened for editing events at the target locus by Sanger sequencing and confirmed through targeted deep sequencing using Illumina MiSeq.
For IUE - the piggyBac donor and helper vector system (CAG-PBase, PBCAG-GFP) was used to transduce NPCs in utero as described previously (Chen and LoTurco, 2012). Two ATRX shRNA vectors, cDNA encoding murine Pdgfra and cDNA encoding C-terminal HA-tagged Drosophila His3.3A (highly conserved orthology of mammalian H3f3a) were cloned into the PBCAG-GFP vector to generate shAtrx-PdgfraWT-H3f3aWT constructs, previously described in Pathania et al., 2017. CRISPR/Cas9 pX330 vectors containing Trp53-targeted gRNA were similarly used. G34R and PdgfraD842V mutants were generated using Quikchange Lightning site-directed mutagenesis (Agilent). In utero electroporation was performed using sterile technique on isoflurane/oxygen-anesthetized pregnant females at E13.5 (cortex), and ex vivo isolation of NPCs were as described in Panathia et al. 2017.

value: patient-derived glioma cell line

tag: genotype

tag: cell line name

tag: clone name

tag: passage

tag: media

value: stem

tag: chip antigen


title: hESC-CM 2


title: hESC-CM 1

value: Differentiation day 21


title: Human RV 3

source_name: Right ventricle 16183/18

tag: tissue type

value: Right ventricle

value: adult


title: s1154rDeletion_Uberis_T0_Macrophagerep1

tag: tissue


title: GBM002-cC08-p57-Rx-ChIP1_Input

value: Input


title: MLN_Treg_MIRI_2

value: 8 weeks

value: 3 days post-I/R injury

value: Tregs


title: GBM002-cA10-p58-Rx-ChIP1_Input


title: spleen_Treg_MIRI_1

source_name: spleen Tregs

value: spleen


title: Wildtype_Uberis_T24_Macrophagerep2

value: milk

value: CD14+ macrophage

value: Wildtype


title: GBM002-cF06-p58-Rx-ChIP1_Input


title: Heart_Tconv3

source_name: heart Tconvs

extract_protocol:
Tregs and Tconvs from 7-day post-MI heart, spleen, NDLN or heart draining MLN of the Foxp3-GFP transgenic mice were double-sorted by magnetic-activated cell sorting (MACS) and fluorescence activated cell sorting (FACS) into special cell lysates (provided by Novogene, Beijing, China). RNA was extracted, and RNA degradation and contamination were monitored on 1% agarose gels. RNA purity was checked using a NanoPhotometer® spectrophotometer (IMPLEN, CA, USA), and the concentration was measured by a Qubit® RNA Assay Kit in a Qubit® 2.0 Fluorometer (Life Technologies, CA, USA). The integrity was assessed using the RNA Nano 6000 Assay Kit of the Bioanalyzer 2100 system (Agilent Technologies, CA, USA). RNA samples were converted into cDNA libraries using the Illumina SMARTer Ultra Low Input sample preparation kit.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: strain genotype/variation

tag: time point

value: 7 days post-MI

value: heart


title: Human RV 2

source_name: Right ventricle 13705/18

tag: age

tag: batch number


title: GBM002-cA09-p60-Rx-ChIP1_Input


title: GBM002-cA09-p60-Rx-ChIP1_H3K27me3


title: Wildtype_Uberis_T0_Macrophagerep3


title: Wildtype_Uberis_T24_Macrophagerep1


title: Heart_Tconv1


title: spleen_Treg_MIRI_3

tag: strain

tag: disease state


title: Human RV 1

source_name: Right ventricle 22350/18


title: Heart_Tconv2


title: spleen_Treg_MIRI_2


title: Wildtype_Uberis_T0_Macrophagerep2

tag: s. uberis strain

tag: timepoint (hours)


title: NDLN_Tconv2

source_name: non-draining lymph node Tconvs

value: non-draining lymph nodes


title: GBM002-cA09-p60-Rx-ChIP1_H3K36me3


title: NDLN_Tconv3


title: Wildtype_Uberis_T0_Macrophagerep1

tag: cell type


title: GBM002-cF06-p58-Rx-ChIP1_H3K36me3

tag: genotype


title: Spleen_Tconv3

source_name: spleen Tconvs


title: SD141_GBM002-cC08-p57-Rx-XChIP1_SUZ12

tag: cell line name


title: PI_wt (Preimmune) ChIP-seq

city: Moscow

first: Natalia

last: Klimenko

address: 34/5 Vavilova Street

country: Russia

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

data_processing:
Adapters, poly-N and poly-A read ends were removed using cutadapt software (Martin 2011). Cutadapt was also used for trimming low-quality ends (quality threshold was set to 20, reads with the length less than 20 bp after trimming were discarded).
The remaining reads were aligned to build version dm6 of the Drosophila melanogaster genome using Bowtie version 2 (Langmead and Salzberg 2012). Only reads that aligned concordantly exactly one time were passed to further analysis.
After alignment, read duplicates were removed using Picard MarkDuplicates function (http://broadinstitute.github.io/picard/). Also, peaks overlapping with blacklist regions were discarded (blacklist regions were previously converted from dm3 to dm6 genome built version) (https://sites.google.com/site/anshulkundaje/projects/blacklists)
Peak calling was performed using MACS version 2 against preimmune control (Zhang et al. 2008) in paired-end mode (option format=BAMPE).
Peaks with p value less than 1x10-2 were passed to the IDR pipeline to access reproducibility of chip-seq replicates (https://sites.google.com/site/anshulkundaje/projects/idr).
Optimal set of reproduced peaks (IDR p value < 0.05) was chosen for each sample and passed to further analysis.
Genome_build: dm6
Supplementary_files_format_and_content: Processed data was obtained by MACS2 and deeptools bamCoverage and includes: extended bed (narrowPeak) peak calls regions and coverage (bedGraph)

source_name: whole organism

growth_protocol: Transgenic lines of Drosophila melanogaster expressed Pita wt and Pita dCP1dCP2 fused with 3xFLAG  were grown in population cages at 25 degrees. Embryos were collected for 12 hours. The collected embryos were dechorionated using 50% bleach and fixed in 10 ml cross-linking solution (50 mM HEPES pH 8.0, 1 mM EDTA, 0.5 mM EGTA, 100 mM NaCl, 1.8 % formaldehyde, pH 8.0) with 30ml n-heptane on a shaker table at RT for 15 minutes. The reaction was terminated with 125 mM glycine, 0.1% Triton X-100 in PBS. After washing out the fix, the embryos were blotted dry and frozen in liquid nitrogen. A small number of embryos from each collection were set aside for staging.

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

treatment_protocol: Approximately 1g of Drosophila embryos were resuspended in 15ml ice-cold 0.1% Triton X-100 in PBS with protease inhibitors (PIs) and dounced 20x with loose pestle on ice, followed by centrifugation at 400g for 1min at 4 degrees. The supernatant was transferred to a fresh tube and centrifuged at 1100g for 10min at 4 degrees. The pellet was resuspended in 15ml ice-cold Cell lysis buffer with PIs (5 mM HEPES pH 8.0, 85 mM KCl, 0.5% NP40) and dounced 20x with tight pestle. Two equal aliquots were transferred into 15ml falcon tubes and centrifuged at 2000g for 4min at 4 degrees. The pellets consisting of nuclei were resuspended in 1ml of ice-cold Nuclear Lysis Buffer with PIs (50 mM HEPES pH 8.0, 10 mM EDTA, 0.5% N-laurylsarcosine) and incubated for 20min at RT. 1ml ice-cold Nuclear Lysis Buffer with PIs was added to each tube and sonicated using the bioruptor. Chromatin was then transferred to 1.5 ml-eppendorf tubes and centrifuged at 14000 rpm for 10 min at 4 degrs. Finally, supernatants were pooled, aliquoted and frozen in liquid nitrogen. Chromatin (50 ug of DNA) was brought to RIPA conditions (140mM NaCl / 10mM Tris-HCl pH8,0 / 1mM EDTA / 1% TritonX100 / 0,1% SDS / 0,1% sodium deoxycholate, 1mM PMSF) and incubated with anti-FLAG, anti-CP190 antibodies and mouse IgG at 4 degrees on a rotary shaker overnight. The antibody/antigen complexes were precipitated with 40 ul protein G sepharose at 4 degrees for 3 hrs and washed 1x with RIPA buffer, 3x with RIPA buffer with 500 mM NaCl.

value: whole organism

tag: development stage

value: embryonic

tag: antibody source

value: mouse

value: Oregon-R

value: Pita wt


title: GBM002-cA09-p60-Rx-ChIP1_H3K27ac

value: patient-derived glioma cell line

tag: clone name

tag: passage

tag: media

value: stem


title: GBM002-cF06-p58-Rx-ChIP1_H3K27ac

tag: tissue

tag: chip antigen


title: NDLN_Tconv1

tag: strain genotype/variation

value: 8 weeks

tag: time point


title: CP190_PITA_wt_repl2 ChIP-seq


title: Spleen_Tconv2

tag: age


title: Wildtype_Uberis_T24_Macrophagerep3


title: GBM002-cC08-p57-Rx-ChIP1_H3K27ac


title: Spleen_Tconv1


title: CP190_PITA_wt_repl1 ChIP-seq

tag: strain


title: Heart_Treg2


title: GBM002-cA10-p58-Rx-ChIP1_H3K27me3


title: GBM002-cC08-p57-Rx-ChIP1_H3K27me3


title: GBM002-cA10-p58-Rx-ChIP1_H3K27ac


title: Heart_Treg1


title: GBM002-cF06-p58-Rx-ChIP1_H3K27me3


title: GBM002-cC08-p57-Rx-ChIP1_H3K36me3


title: Heart_Treg3


title: CP190_PITA_delta_repl2 ChIP-seq

value: Pita {delta}CP1+2


title: Flag_PITA_wt_repl1 ChIP-seq


title: CP190_PITA_delta_repl1 ChIP-seq


title: Flag_PITA_delta_repl2 ChIP-seq


title: MLN_Treg2

value: mediastinal lymph nodes


title: MLN_Treg3


title: Flag_PITA_wt_repl2 ChIP-seq


title: Flag_PITA_delta_repl1 ChIP-seq


title: NDLN_Treg3

source_name: non-draining lymph node Tregs


title: GBM002-cA10-p58-Rx-ChIP1_H3K36me3


title: MLN_Treg1


title: ym12

city: Bielefeld

first: Christian

last: Kaltschmidt

address: Universitätstraße 25

department: Department of Cell Biology

institute: University of Bielefeld

data_processing:
Mapping: Tophat, Version V2.0.9, Parameter: mismatch = 2
Quantification: HTseq, Version v0.6.1, Parameter: -m union
reference: hg19
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample ...

source_name: human cardiac stem cells

extract_protocol:
RNA was harvested using Macherey Nagel RNA isolation Kit
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: culture

value: cultured in DMEM-F12 + 10% FCS + 5ng/ml FGF2 + 10ng/ml EGF

tag: treatment

value: DMEM-F12 + 10% young male blood serum + 5ng/ml FGF2 + 10ng/ml EGF


title: ym15


title: Naïve synovial fibroblasts 2

city: Glasgow

first: Miguel

last: Pineda

address: University Avenue

institute: University of Glasgow

data_processing:
FastQC was used for initial quality control checks on raw sequence data coming from high throughput sequencing pipelines.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to GRCM38 mouse reference using Hisat2 v2.1.0.
Featurecounts version 1.4.6 was used to quantify reads counts.
Genome_build: GRCM38
Supplementary_files_format_and_content: tab-delimited text files include read counts values for each sample generated with feature counts.

source_name: mouse synovium

extract_protocol:
Mouse synovium was digested with collagenase. Single cell suspension were stained with anti CD31, anti CD45 and anti Podoplanin antibodies to sort synovial fibroblasts by FACs. Cells were collected in lysis buffer and RNA was immediately extracted.
library preparation using polyA selection (TruSeq stranded mRNA kit)

value: synovium

value: synovial fibroblast

tag: condition

value: naïve healthy


title: Naïve synovial fibroblasts 3

tag: cell type


title: NDLN_Treg1

value: 7 days post-MI


title: om20

value: DMEM-F12 + 10% old male blood serum + 5ng/ml FGF2 + 10ng/ml EGF


title: NDLN_Treg2

value: non-draining lymph nodes


title: om11


title: Naïve synovial fibroblasts 1


title: Spleen_Treg2

value: spleen


title: om14


title: c

value: DMEM-F12 + 5ng/ml FGF2 + 10ng/ml EGF


title: Spleen_Treg1


title: CIA synovial fibroblasts 6-3

value: Arthritic (experimental)


title: ym17


title: CIA synovial fibroblasts 5-4


title: Spleen_Treg3


title: AML Day 14 mTORC1 HIgh 4

status: Public on Nov 29 2020

city: Boston

first: Toshihiko

last: Oki

state: MA

address: 185 Cambridge Street

department: Center for Regenerative Medicine

institute: Massachusetts General Hospital

data_processing:
Library strategy: DNA sequencing
Illumina software used to basecalling.
The data was analyzed with the Python program provided by Addgene for alignment.
Supplementary_files_format_and_content: Tab-deliniated files include raw counts for each barcde for each sample.
Supplementary_files_format_and_content: The matrix file with raw counts for every barcode and every sample.

source_name: Bone marrow

extract_protocol:
Two million FM4-Venus cells were subjected to lentiviral infection of the Clontracer library plasmid with DsRed selection marker (Addgene (Cambridge, MA, USA)) with MOI < 10%. They were incubated for 3 days and sorted with FACS AriaII (BD). One million sorted cells were obtained. The sorted cells were expanded up to 1 billion by culturing for 10 days. One million cells were transplanted into each of the four groups of the four mice.  Four hundred thousand mVenus-high or low AML cells were sorted from the mouse bone marrow by sacrificing the mice immediately before (day 0) or at either of the 3 different time after chemotherapy (day 5, 7, and 14).
Genomic DNA was extracted with the DNA/RNA mini kit (Qiagen) and sequencing libraries were constructed according to the protocol from Addgene.

value: mouse AML cell line with MLL-AF9 (mFM4-mVenus)

value: Day 14 of Chemothrapy (Ara-C and Doxo)


title: CIA synovial fibroblasts 5-1


title: AML Input cell 5

source_name: Cultured cells

value: AML cells before transplantation


title: AML Day 14 mTORC1 High 3


title: AML Input cell 6


title: AML Day 14 mTORC1 Low 4


title: AML Input cell 3


title: AML Input cell 4


title: AML Input cell 1


title: AML Day 14 mTORC1 High 2


title: AML Day 14 mTORC1 Low 3


title: A549-IVA-12H_moi1_rep1

city: Los Alamos

first: Sofiya

middle: N

last: Micheva-Viteva

state: New Mexico

address: Los Alamos National Lab

department: Bioscience

institute: Los Alamos National Laboratory

data_processing:
Illumina Casava1.7 software used for basecalling.
With the PiReT application (https://github.com/mshakya/piret) we performed quality control on the RNA-seq data using FaQC v2.09. The reads that passed the QC were mapped using HISAT2 v2.1.0 against its graph FM index (GFM) human reference genome
Using htseq-count v0.11.1 we calculated the number of reads that mapped to coding sequences: Anders, S.;  Pyl, P. T.; Huber, Bioinformatics 2015, 31 (2), 166-169.
Applying count data, we calculated transcripts per kilobase per million (TPM) and found differentially expressed genes using R package DESeq2 v1.18.1.
Genome_build: human reference genome GRCh38
Supplementary_files_format_and_content: DESeq2 output

organism:
Homo sapiens
Influenza A virus (A/Port Chalmers/1/1973(H3N2))

source_name: Lung epithelial cells

growth_protocol: A549 carcinoma human alveolar epithelial cells were maintained in high-glucose DMEM (Gibco-Thermo Fisher, Grand Island, NY) supplemented with 10% (v/v) fetal bovine serum (Gibco-Thermo Fisher, Grand Island, NY).

extract_protocol:
At indicated time points post initiation of infection cells were washed with cold phosphate buffered saline (PBS) and lysed in the well with 350 µL 1% beta-mercaptoethanol supplemented RLT buffer from the RNeasy Plus Mini kit (QIAGEN, Maryland). Total RNA was isolated according to the manufacturer’s protocol including on-column removal of gDNA. After elution total RNA was treated with Turbo DNA-free Kit (AM1907, Thermo Fisher Scientific) for complete elimination of gDNA. RNA quality was determined by both direct observation of rRNA on 1% denaturing agarose gel and by Agilent bioanalyzer scan. For the preparation of Illumina libraries 5µg total RNA per sample were processed with the TruSeq Stranded Total RNA Ribo-Zero H/M/R kit (RS-122-2201, Illumina). Following rRNA removal polyA-mRNA species were separated from the non-polyA RNA pool with the polyA Spin mRNA Isolation Kit (S1560S, NEB). The two RNA sample pools were further quantified by Qubit (Invitrogen) and 15 ng were subjected to size fragmentation followed by cDNA synthesis and the addition of a terminal tagged oligonucleotide.
Tagged cDNA was purified with Agencourt AMpure XP beads and amplified with 15 cycles of PCR. Fragment length distributin of all libraries was analyzed on a BioAnalyzer high-sensitivity LabChip. Diluted libraries (5 pmol) were multiplex sequenced on the Illumina MiSeq (2- by 250-bp paired-end run, 3 to 4 million reads/sample).

treatment_protocol: The virus work was performed in compliance with CDC guidelines for biosafety level 2 agents. Virus stocks (harvested from MDCK producer cells in serum free media) were treated with 20 µg/mL TPCK trypsin for 10 min at 37◦C to activate cleavage of viral HA glycoprotein to HA1 and HA2, followed by dilution in high glucose DMEM supplemented with 10% Fetal clone III serum (10%DMEM) to neutralize the trypsin. For this infection method, A549 cells were plated 18h prior to infection in 10%-DMEM at 1x106 per well in 6-well format dishes.  Pre-activated virus stock was adjusted to the required MOI in 10% DMEM and was layered on target cells. After 2 hours of incubation of A549 cells with mock infected media or 250 µL virus containing 10%DMEM at 37◦C the media was topped with fresh 10%DMEM to a total volume of 2ml and cells were incubated at 37◦C prior to harvest.

tag: cell line

value: Influenza A/Port Chalmers/1/73 (H3N2) infected at MOI1

tag: treatment time

value: 12 hour post infection [hpi]


title: A549-IVA-12H_moi5_rep2

value: Influenza A/Port Chalmers/1/73 (H3N2) infected at MOI5


title: A549-IVA-12H_moi5_rep1


title: A549-IVA-8H_moi5_rep2

value: 8 hour post infection [hpi]


title: A549-IVA-8H_moi1_rep1


title: AML Day 14 mTORC1 High 1


title: AML Day 14 mTORC1 Low 1


title: AML Day 7 mTORC1 High 3

value: Day 7 of Chemothrapy (Ara-C and Doxo)


title: AML Input cell 2


title: A549-IVA-6H_moi1_rep1

value: 6 hour post infection [hpi]


title: A549-IVA-8H_moi5_rep1


title: AML Day 7 mTORC1 Low 3


title: AML Day 7 mTORC1 Low 2


title: AML Day 7 mTORC1 High 2


title: A549-IVA-6H_moi5_rep2


title: A549-IVA-6H_moi5_rep1


title: A549-IVA-4H_moi5_rep2

value: 4 hour post infection [hpi]


title: A549-IVA-4H_moi1_rep1


title: AML Day 7 mTORC1 High 1


title: AML Day 7 mTORC1 Low 1


title: AML Day 14 mTORC1 Low 2


title: A549-IVA-3H_moi1_rep1

value: 3 hour post infection [hpi]


title: A549-IVA-3H_moi5_rep2


title: AML Day 5 mTORC1 High 4

value: Day 5 of Chemothrapy (Ara-C and Doxo)


title: A549-IVA-4H_moi5_rep1


title: AML Day 5 mTORC1 Low 4