title: human neutrophils-1h C5a-#3

city: Ulm

first: Markus

last: Huber-Lang

address: Helmholtzstrasse 8/1

department: Institute of Clinical and Experimental Trauma-Immunology

institute: University Hospital Ulm

description: Gene expression data from human neutrophils after C5a exposure

hyb_protocol: according to Affymetrix Whole Transcript (WT) Sense Target Labeling Assay

scan_protocol: according to Affymetrix protocols using a GeneChip 3000 Scanner

data_processing: Affymetrix® Expression Console™ Software for RMA normalization, BRB Array Tools for statistical analysis

source_name: neutrophil, C5a incubation, 60min

growth_protocol: PMNs were isollated from whole blood. CD9+ eosinophils were seprated from PMNs by MACS, eosinophil-free neutrophils were resuspended in RPMI medium and were used for experiments. Incubation/treatment was performed in RPMI medium supplemented with 0.1% BSA.

extract_protocol: After incubation, RNA extraction was performed by Guanidinium Thiocyanate–Phenol–Chloroform (TRIZOL) according to the manufacturer's instructions RNA was resuspended in nuclease-free water.

treatment_protocol: 1 x10e7 neutrophils/ml were incubated with native human complement anaphylatoxin C5a (100ng/ml) for 60min at 37°C on a rotating wheel to simulate blood circulation. Untreated neutrophils served as controls.

value: neutrophil

value: C5a incubation


title: human neutrophils-1h C5a-#2

status: Public on Sep 23 2020

type: RNA

country: Germany

label: biotin

molecule: total RNA

organism: Homo sapiens

label_protocol: Whole Transcript (WT) Sense Target Labeling Assay

tag: gender

value: male

tag: cell type

tag: treatment


title: MA2_Male_35_days

type: SRA

city: Birmingham

first: julia

last: constantinou

address: Edgebaston

department: Biosciences

country: United Kingdom

institute: University of Birmingham

library_source: transcriptomic

data_processing:
The reads were mapped to reference genome of Daphnia magna (GCA_001632505.1) with TopHat2 (2.1.1) with preset b2-sensitive.
The read counts were extracted with Rsubread (1.30.9), with default settings, using the reference gene models (GCA_001632505.1).
Expression changes were analysed at gene levels using DESeq2 (1.20) with default settings. Genes  with significant expression difference between males and females, chages during normal ageing or interaction with sex and age are reported in processed files.
Genome_build: GCA_001632505.1
Supplementary_files_format_and_content: csv (differential expression analysis results at gene level: RSeq_results_age only_age in days_ordered by padj.csv.gz, RSeq_results_sex-age_interaction_age in days_ordered by padj.csv.gz, RSeq_results_sex only_age in days_ordered by padj.csv.gz)
Supplementary_files_format_and_content: csv (read counts at gene level: readcounts_combined.csv.gz)

organism: Daphnia magna

source_name: whole organism

growth_protocol: Cultures of Daphnia magna, strain Bham2, were maintained in a 16:8 h light:dark photoperiod and temperature of 20 ± 1 °C, in high hardness COMBO medium (COMBO). Media were prepared using a protocol adapted from Kilham et al. (1998), and renewed every other day. Animals were fed every other day with Chlorella vulgaris at a concentration of ~27,550 cells of algae per individual Daphnia. Daphnia samples were monitored every 2 hours during the light period once the appropriate age was reached.

extract_protocol:
Total RNA was extracted from the samples using RNeasy micro kit ((Qiagen Ltd, UK) according to the manufactures protocol.
The RNA-seq libraries were prepared using the Illumina TruSeq standard mRNA kit and sequenced (2x100bp) using Illumina Hi-Seq 4000 platform at BGI, Denmark.

treatment_protocol: Samples were flash frozen in liquid nitrogen when brood pouch was empty and stored in -80C until further use.

tag: tissue

value: whole organism

tag: strain

value: Male

tag: notes

tag: age

value: Maintained under normal conditions

tag: culturing media

value: High Hardness COMBO


title: human neutrophils-1h C5a-#1


title: CEMBA181023_6B_3_CEMBA181023_6B_4_H11_ad001

city: La Jolla

first: Joseph

middle: R

last: Ecker

state: CA

address: 10010 North Torrey Pines Road

department: Genomic Analysis Laboratory

country: USA

institute: HHMI-Salk-Institute

library_source: genomic

data_processing:
Library strategy: snmC-seq2
Reads trimed with Cutadapt for adapters and low quality bases (Phred score >= 20)
The resulting files are mapped to in-silico bisulfite converted mm10 reference genome using Bismark.
The raw BAM file will be filtered using samtools to filter reads by MAPQ > 10 and use Picard to remove PCR duplicates
Tab-delimited files (ALLC files) describing the quantity of unmethylated and methylated cytosine base calls will be generated with in-house developing package using the filtered BAM files
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited files (ALLC files) describing the quantity of unmethylated and methylated cytosine base calls. Columns are: 1. Chromosome, 2. Position, 3. Strand, 4. Cytosin Context, 5. methylated base call, 6. total mapped base call, 7. not used, place holder column

molecule: genomic DNA

organism: Mus musculus

source_name: C57BL/6J Male P56 Mouse Brain

growth_protocol: All mice are C57BL/6J Male, brain dissected in P56

extract_protocol:
the brain of P56 male C57BL/6J mouse will be removed and cut into 600 microns thick coronal sections using a tissue matrix. Then each region will be microdissected from the coronal tissue sections based on identified landmarks and brain atlas coordinates, as defined in Allen brain atlas CCF3 (Avaliable at: http://atlas.brain-map.org). For each dissection region, the tissue from several littermate mice will be combined together into to separate replicate groups. The number of animals in a replicate depends on the size of the tissue. Nuclei preparation will be stained with the fluorescently labeled anti-NeuN body and nucleic acid stain Hoechst 33342.
Library prepared following protocol discribed in Luo, Chongyuan, Angeline Rivkin, Jingtian Zhou, Justin P. Sandoval, Laurie Kurihara, Jacinta Lucero, Rosa Castanon, et al. 2018. “Robust Single-Cell DNA Methylome Profiling with snmC-seq2.” Nature Communications 9 (1): 3824.

tag: brain region

value: SSp

tag: Sex


title: 44_SMG_C_S14

city: Buffalo

first: Jonathan

middle: E

last: Bard

state: New York

address: 701 Ellicott Street

department: Genomics and Bioinformatics Core

institute: University at Buffalo

data_processing:
Reads were mapped to the Mus musculus genome (mm9 build) with TopHat2 (v2.1.1),using Bowtie2 (v2.2.6) as the underlying aligner.
Reads aligning to the UCSC mm9 build were quantified with featureCounts (v1.5.1) , which disregarded any read/read pair that aligned to more than one location, or more than one gene at a single location.
DESeq2 (v1.20.0) was used to normalize the read counts, and TPM values were calculated by normalising read counts were further normalised by gene length and total counts to generate Transcript Per Million (TPM) values.
Genome_build: mm9
Supplementary_files_format_and_content: TPM values were generated by normalizing raw counts for both library size and gene length.

source_name: Mouse Submandilar Salivary Gland

extract_protocol:
Mouse submandibular salivary gland epithelial cells were isolated from adult wildtype  and p63 knockout mice and RNA was extracted using the Direct-zol RNA Mini-Prep kit.
Library preparation was carried out using the Illumina TruSeq RNA Sample Prep Kit protocol. 1 ug of total RNA from each sample was used in the the construction of sequencing libraries.

value: Adult (12wk)

value: Salivary Gland

tag: genotype/variation

value: p63 WildType mouse


title: M3_Female_35_days

value: Female


title: CEMBA181023_6B_3_CEMBA181023_6B_4_H10_ad004


title: 76_SMG_KO_S30

description: TPM values were generated by normalizing raw counts for both library size and gene length.

value: p63 Knockout Mouse


title: M2_Female_35_days


title: 6594_KO_SMG_S20


title: human neutrophils-control-#2

description: Gene expression data from human neutrophils without treatment.

source_name: neutrophil, untreated, 60min

value: control


title: M1_Female_35_days


title: MA1_Male_35_days


title: CEMBA181023_6B_3_CEMBA181023_6B_4_H10_ad008


title: human neutrophils-control-#1


title: 41_SMG_KO_S15


title: L2_Female_75_days


title: CEMBA181023_6B_3_CEMBA181023_6B_4_H10_ad007


title: CEMBA181023_6B_3_CEMBA181023_6B_4_H10_ad006


title: CEMBA181023_6B_3_CEMBA181023_6B_4_H10_ad002


title: L3_Female_75_days


title: L1_Female_75_days


title: GM12878_4C_rep1

city: WEST LAFAYETTE

first: Majid

last: Kazemian

state: IN

address: 201 S. University Street

department: Biochemistry and Computer Science

institute: Purdue University

description: Blood

data_processing:
Library strategy: 4C-seq
Reads with 5’ end mapped to the forward inverse PCR primer sequence were selected.
Selected reads were mapped to hg19 assembly by Burrows-Wheeler Aligner (BWA).
Mapped fragments were further aligned to a reduced in silico digestion “library” containing DpnII sites genome wide.
A “binarization” step was taken to minimize the PCR duplication bias.
A window-based model was used to identify significantly interacting regions. Sites with only one read were eliminated to filter out random noise.
Reproducible sites were defined as exact match of 4C sites with coverage >1 in both biological replicates.
Differential 4C-seq interactions identified using the W4Cseq package.
Genome_build: hg19 (GRCh37)
Supplementary_files_format_and_content: *.peak.bed: Peak files

source_name: B-Lymphocyte cells

growth_protocol: All Lymphoblastoid Cell Lines (GM12878) were grown in RPMI supplemented with 1% L-glutamate, 1% Pen/Strep and 10% FBS.

extract_protocol:
The cells were treated with 1% formaldehyde to crosslink, and the nuclei were isolated via resuspension in lysis buffer (500 μl 10 mM Tris-HCl pH 8.0, 10 mM NaCl, 0.2% Igepal CA-630 and 50 μl protease inhibitors). Nuclei were resuspended in 500 μl restriction enzyme buffer and permeabilized by incubation with 10% SDS (final concentration: 0.3%) for 37°C overnight.
500 units DpnII restriction enzyme were added and incubated overnight at 37 °C with shaking. Digestion was stopped after adding 1.6% SDS and incubated at 65 °C for 25 minutes. Samples were then diluted in 7.5 ml 1x ligation buffer and 100 Weiss unit of T4 DNA ligase was added. Samples were kept at 16 °C for 24 hours. The ligated chromatin was digested by proteinase K at 65 °C overnight.
After purification, 16 parallel inverse PCR reactions, each containing 3.2 ug of circularized DNA, were performed.

tag: cell line

value: Lymphoblastoid cell line


title: T06_CI

city: Linköping

first: Rada

last: Ellegård

state: Ostergotlands Lan

address: Vallmogatan 16

country: Sweden

institute: Linköping University

data_processing:
trimmomatic
STAR
featureCounts
Genome_build: GRCh38
Supplementary_files_format_and_content: counts

source_name: colon biopsy

extract_protocol:
MinElute Reaction Cleanup Kit (Qiagen)
Ovation RNA-Seq V2 kit (Tecan)

tag: donor

tag: condition

value: complement and antibody opsonized HIV

tag: time


title: K3_Female_45_days


title: CEMBA181023_6B_3_CEMBA181023_6B_4_H10_ad001


title: T06_M

value: mock


title: K2_Female_45_days


title: CEMBA181023_6B_3_CEMBA181023_6B_4_H1_ad001


title: GM12878_4C_rep2

description: Blood


title: CEMBA181023_6B_3_CEMBA181023_6B_4_H10_ad010


title: Healthy donor pool

city: Botucatu

first: Juliana

middle: Ravelli Baldassarre

last: Martins

state: SP

address: Rua Mansueto Lunardi, 37

country: Brazil

institute: Faculdade de Medicina de Botucatu

description:
control
SAMPLE 29

data_processing:
Comparative Ct analysis was used for quantification of microRNAs gene expression and differences were evaluated by Student´s t test; p<0,05 was considered to indicate statistical significance; maximun allowed Ct value: 35. Input data for class comparison, permutations and prediction analysis consisted of the raw miR expression CT values normalized to the endogenous Mammalian U6. [delta] CT = CTsample - CTreference.
fold change ≤ 0,5 and fold change ≥ 2,0

label: FAM

source_name: peripheral blood sample

label_protocol:
A sample of 5 mL peripheral blood were collected from the patients. For RNA isolation, was used QIAamp RNA Blood Mini Kit (QIAGEN). After purification, a NanoDrop (Thermo Scientific Waltham) was used for quantification, quality and control of RNA. Quantification and sizing were analyzed using RNA 2100 Bioanalyzer (Agilent Technologies)
The miRNA cDNA was prepared  using the TaqMan TM MicroRNA Reverse Transcription Kit, Catalog No. 4366597, combined with Megaplex TM RT Primers, Human Pools A+B Set v2.0, catalog No. 4400928. The qPCR reaction was performed using the mix TaqMan TM Universal Master Mix II, catalog No 4440040 in combination with TaqMan TM Array Human MicroRNA A+B Cards Set v2.0, catalog No. 4400238. The reactions were amplified using the  ViiA7 equipment (ThermoFisher). For all steps, the manufacturer´s  protocol was followed.

growth_protocol: Human samples were obtained from patients treated with bone marrow tranplantation and from newly diagnosed patients that did not start treatment. Control was constituted by a pool of healthy donors.  HUMAN SAMPLES OBTAINED FROM PATIENTS TREATED WITH BONE MARROW TRANSPLANTATION AND FROM NEWLY DIAGNOSTIC PATIENTS THAT DID NOT START TREATMENT. CONTROL WAS CONSTITUTED BY A POOL OF HEALTHY DONORS

extract_protocol: Total RNA was extracted with QIAamp RNA Blood Mini Kit (QIAGEN)

tag: disease state

value: Healthy donor

value: peripheral blood


title: T06_C

value: complement opsonized HIV


title: K1_Female_45_days

value: whole organism


title: CEMBA181023_6B_3_CEMBA181023_6B_4_H1_ad012

value: male


title: Achilles tendon at P 6-8w,biological rep2

city: Beijing

first: yu

last: Wang

state: Beijing

address: 22 South Zhongguancun Street, Haidian District

department: Peking University School and Hospital of Stomatology

country: China

institute: Peking University

description: Gene expression data from Achilles tendon of  rat at 6-8 week

hyb_protocol: Following labeling, cDNA was hybridized on a GeneChip Rat Gene 2.0.

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Command Console installed in the GeneChip® Scanner 3000 7G.

data_processing: The data was analyzed with the Robust Multichip Analysis (RMA) algorithm, using the Affymetrix default analysis settings.

organism: Rattus norvegicus

source_name: Rattus norvegicus Achilles tendon

label_protocol: Biotinylated cDNA was prepared from 150 ng total RNA according to the manufacturer’s standard protocol (Affymetrix).

growth_protocol: The achilles tendon that was harvested individually from the left hindlimb were stored at liquid nitrogen temperature at once with protected by Rnasin inhibitor.

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions.

treatment_protocol: After grinded under the ice，achilles tendon tissue were collected for further total RNA extraction.

value: Skin-removed achilles tendon

value: 6-8 week


title: Achilles tendon at P 6-8w,biological rep3


title: Philadelphia negative 14

description:
tested
SAMPLE 28

treatment_protocol: A sample of 5 mL peripheral blood were collected from the patients. For RNA isolation, was used QIAamp RNA Blood Mini Kit (QIAGEN). After purification, a NanoDrop (Thermo Scientific Waltham) was used for quantification, quality and control of RNA. Quantification and sizing were analyzed using RNA 2100 Bioanalyzer (Agilent Technologies)

value: Philadelphia negative CML


title: Achilles tendon at P 6-8w,biological rep1


title: J3_Female_20_days

value: mislabelled samples, excluded

value: Maintained under normal conditions

value: High Hardness COMBO


title: Philadelphia negative 13

description:
tested
SAMPLE 27


title: human neutrophils-control-#3

value: neutrophil


title: T27_M


title: T27_CI


title: J1_Female_20_days

value: Female


title: CEMBA181023_6B_3_CEMBA181023_6B_4_H1_ad008

value: SSp


title: CEMBA181023_6B_3_CEMBA181023_6B_4_H1_ad007


title: T27_C


title: Philadelphia negative 12

description:
tested
SAMPLE 26


title: Achilles tendon at P 1d,biological rep1

description: Gene expression data from Achilles tendon of neonatal rat at 1th day after birth

value: 1 day


title: Achilles tendon at P 1d,biological rep2


title: Achilles tendon at P 1d,biological rep3


title: H2_Female_40_days


title: I2_Female_70_days


title: Philadelphia negative 10

description:
tested
SAMPLE 24


title: T06_F

value: free HIV


title: CEMBA181023_6B_3_CEMBA181023_6B_4_H1_ad004


title: Philadelphia negative 9

description:
tested
SAMPLE 23


title: T10_M

value: mock


title: H1_Female_40_days


title: T10_CI

value: complement and antibody opsonized HIV


title: CEMBA181023_6B_3_CEMBA181023_6B_4_H1_ad010


title: G3_Female_15_days


title: J2_Female_20_days


title: CEMBA181023_6B_3_CEMBA181023_6B_4_H1_ad002


title: T10_C


title: CEMBA181023_6B_3_CEMBA181023_6B_4_G9_ad001


title: Philadelphia negative 8

description:
tested
SAMPLE 22

value: peripheral blood


title: G2_Female_15_days


title: T27_F


title: T10_F


title: CEMBA181023_6B_3_CEMBA181023_6B_4_G9_ad010


title: CEMBA181023_6B_3_CEMBA181023_6B_4_H1_ad006


title: G1_Female_15_days


title: Philadelphia negative 7

description:
tested
SAMPLE 21


title: Philadelphia negative 6

description:
tested
SAMPLE 20


title: CEMBA181023_6B_3_CEMBA181023_6B_4_G9_ad008


title: Philadelphia negative 5

description:
tested
SAMPLE 19


title: Philadelphia negative 11

description:
tested
SAMPLE 25


title: c30ag77

city: Kyoto

first: Yukihiro

last: Yabuta

state: Kyoto

address: Yoshida-Konoe-cho, Sakyo-ku

department: Anatomy and Cell Biology

country: Japan

institute: Kyoto University, Graduate school of medicine

description: Bisulfite-seq (PBAT)

data_processing:
All reads were processed with Trim_galore program (http://www.bioinformatics.babraham.ac.uk/projects/trim_galore/) to remove 4 bases from 5’-ends, 1 base from 3’-ends, adaptor sequences, and low-quality reads (quality score < 20).
The processed reads were mapped onto human genome (GRCh38.p2) with bismark program from Bismark (v0.17.0) with “--pbat” option (Krueger and Andrews, 2011).
Mapped data (BAM format) were converted to methylation levels using bismark_methylation_extractor program from Bismark.
Samtools (v1.3) (Li et al., 2009) and IGVTools (v2.3.52) (James et al., 2011) were used to manipulate BAM files and create wig files. Only CpGs, whose read depth are between 4 and 200, are included in the bigWig files.
Genome_build: GRCh38.p2
Supplementary_files_format_and_content: bigWig
Supplementary_files_format_and_content: *_bismark_CpG_report.txt: Tab-delimited bismark reports.

source_name: BT+AG+ cells from ag77 xrOvary derived from c30 expanded hPGCLC

growth_protocol: The defined hPGCLC expansion culture medium is: DMEM (1.0 g/L glucose; GIBCO, 11054-020) with 15% of KSR, 2.5% of FBS, 1% of NEAA, 2mM of GlutaMAX (GIBCO, 35050-061), 1% penicillin & streptomycin, and 0.1 mM of 2-Mercaptoethanol (GIBCO, 21985-023) supplemented with 10 µM of forskolin, 100 ng/mL of SCF and 20 ng/mL of bFGF.

extract_protocol:
10,000-15,000 cells were lysed in the lysis buffer [0.1% of SDS and 1 µg/µL of Proteinase K in DNase-free water (GIBCO, 15230-160)] containing unmethylated lambda phage DNA (Promega, D1521) at 37°C for 60 min and then incubated at 98°C for 15 min to inactivate proteinase K. Assuming that a single cell bears 6 pg of genome DNA, we added the unmethylated lambda phage DNA equivalent to 0.5% of the input DNA. For the bisulfite treatment, the cell lysate was treated with EZ DNA Methylation-Gold Kit (Zymogen, D5005) according to the manufacturer’s instruction.
To construct sequence libraries, the bisulfite-treated DNA was subjected to the serial synthesis of the single-end adaptor-tagged complementary DNA fragments (http://www.crest-ihec.jp/english/epigenome/index.html).

tag: transgene

value: BLIMP1-tdTomato, TFAP2C-EGFP


title: F3_Female_65_days

value: whole organism

tag: gender


title: CEMBA181023_6B_3_CEMBA181023_6B_4_G9_ad012

value: male


title: c120_2

description: Bisulfite-seq (PBAT)

source_name: expanded hPGCLC derived from 585B1-BTAG iPSC, BT+AG+ cells were collected at expansion culture day 120, rep2


title: Philadelphia negative 4

description:
tested
SAMPLE 18


title: c120_1

description: Bisulfite-seq (PBAT)

source_name: expanded hPGCLC derived from 585B1-BTAG iPSC, BT+AG+ cells were collected at expansion culture day 120, rep1


title: F2_Female_65_days


title: c70_2

description: Bisulfite-seq (PBAT)

source_name: expanded hPGCLC derived from 585B1-BTAG iPSC, BT+AG+ cells were collected at expansion culture day 70, rep2


title: Philadelphia negative 3

description:
tested
SAMPLE 17


title: E2_Female_30_days


title: CEMBA181023_6B_3_CEMBA181023_6B_4_G9_ad007


title: c70_1

description: Bisulfite-seq (PBAT)

source_name: expanded hPGCLC derived from 585B1-BTAG iPSC, BT+AG+ cells were collected at expansion culture day 70, rep1


title: E3_Female_30_days


title: Philadelphia negative 2

description:
tested
SAMPLE 16


title: E1_Female_30_days


title: Philadelphia negative 1

description:
tested
SAMPLE 15


title: Newly diagnosed Chronic Myeloid Leukemia 14

description:
control
SAMPLE 14

value: Newly diagnosed CML


title: D3_Female_10_days


title: c10_1

description: Bisulfite-seq (PBAT)

source_name: expanded hPGCLC derived from 585B1-BTAG iPSC, BT+AG+ cells were collected at expansion culture day 10, rep1


title: c10_2

description: Bisulfite-seq (PBAT)

source_name: expanded hPGCLC derived from 585B1-BTAG iPSC, BT+AG+ cells were collected at expansion culture day 10, rep2


title: D2_Female_10_days


title: Newly diagnosed Chronic Myeloid Leukemia 13

description:
control
SAMPLE 13


title: Adrb3-/-_ICH_rep3

city: Tianjin

first: Kaibin

last: Shi

address: 154 Anshan Rd, Heping District

department: Neurology

institute: Tianjin Medical University

description: HSCs were flow cytometric sorted from bone marrow of mice

hyb_protocol: Each mRNA was hibridized with two ~50 base probes in the hybidize solution. The reporter probe carries the signal, the capture probe allows the complex to be immobilized for data collection.

scan_protocol: After hybridization, excess probes are removed and the probe/target complexes aligned and immobilized in the nCounter Cartrige. Sample cartriges are placed in the Digital Analyzer. Color codes on the surface of the cartrige are counted and tabulated for each target mRNA.

data_processing: Data were processed on the nSolver software. Data were normalized to the 14 reference genes including positive and negative controls and housekeeping genes probes using nSolver software

source_name: HSCs

extract_protocol: HSC were sorted from femur bone marrow of ICH and sham mice at day 3 after surgery. Cells were directly sorted into Trizol LS (ThermoFisher)-containing tubes, and total RNA was then extracted.

value: bone marrow

tag: genotype

tag: agent

value: ICH

value: Male


title: D1_Female_10_days

tag: tissue

tag: treatment

value: Maintained under normal conditions


title: d6hPGCLC

description: Bisulfite-seq (PBAT)

source_name: day6 human PGCLC, from 585B1-BTAG iPSC


title: POM_GSK-2

city: Daejeon

first: Jong Hwan

last: Kim

address: 125 Gwahak-ro, Yuseong-gu

department: Genome structure research center

country: South Korea

institute: Korea Research Institute of Bioscience and Biotechnology

description:
derived from the pleural effusion of a 41-year-old Caucasian man with B-cell non-Hodgkin lymphoma (B-NHL, diffuse large cell lymphoma non-cleaved type, intermediate grade
1μM of pomalidomide and GSK126 were co-treated

data_processing:
Illumina Casava1.7 software used for basecalling.
The reads were mapped to hg19 using STAR v2.5.1.
Read counts were calculated using a STAR standard protocol.
Heat map was constructed using Mev (v. 4.9.0). Statistical analyses were performed using R (v. 3.3.0) and PYTHON (v. 2.7.6).
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include log2CPM (count per million) values for each sample

source_name: follicular small cleaved cell, low grade

growth_protocol: WSU-DLCL2 were cultured in RPMI 1640 supplemented with 10% fetal bovine serum. 5X104 cells /ml were seed at 150mm dish and harvested

extract_protocol:
Total RNA was isolated from cells using the RNeasy RNA extraction Mini-Kit (Qiagen) and the quality of the RNA was confirmed by agarose gel electrophoresis.
TruSeq Stranded mRNA Sample Preparation Guide, Part #15031047 Rev. The sequencing library was prepared using the IlluminaTruSeq Stranded mRNA LT Sample Prep Kit (Illumina).
The mRNA derived from total RNA using poly-T oligo-attached magnetic beads was fragmented and converted into cDNA. Adapters were ligated to the cDNA and the fragments were amplified by PCR.

treatment_protocol: co-treated by 1μM of GSK126 and 1μM of pomalidomide for 2day  and each treatment alone were treated and DMSO was added for the same volumes.

tag: cell type

value: EZH2 Y641F mutation lymphoma cell line

value: 1uM of pomalidomide and GSK126


title: Newly diagnosed Chronic Myeloid Leukemia 12

description:
control
SAMPLE 12


title: Newly diagnosed Chronic Myeloid Leukemia 11

description:
control
SAMPLE 11


title: Adrb3-/-_ICH_rep1


title: Adrb3-/-_ICH_rep2


title: C3_Female_60_days

source_name: whole organism

tag: strain

value: Female

tag: notes

tag: age

value: High Hardness COMBO


title: Wild type_ICH_rep2

value: Wild type

tag: Sex


title: Wild type_ICH_rep3


title: CEMBA181023_6B_3_CEMBA181023_6B_4_G9_ad006

source_name: C57BL/6J Male P56 Mouse Brain

tag: brain region

value: SSp


title: POM_GSK-1

tag: cell line


title: POM-2

description:
derived from the pleural effusion of a 41-year-old Caucasian man with B-cell non-Hodgkin lymphoma (B-NHL, diffuse large cell lymphoma non-cleaved type, intermediate grade
1μM of pomalidomide was treated alone and DMSO was added for the same volume

value: 1uM of pomalidomide


title: C1_Female_60_days

tag: culturing media


title: Newly diagnosed Chronic Myeloid Leukemia 10

description:
control
SAMPLE 10


title: Wild type_ICH_rep1


title: B3_Female_25_days


title: Adrb3-/-_sham_rep3

value: sham


title: B2_Female_25_days


title: Adrb3-/-_sham_rep2


title: POM-1


title: Newly diagnosed Chronic Myeloid Leukemia 8

description:
control
SAMPLE 8

value: peripheral blood


title: GSK-2

description:
derived from the pleural effusion of a 41-year-old Caucasian man with B-cell non-Hodgkin lymphoma (B-NHL, diffuse large cell lymphoma non-cleaved type, intermediate grade
1μM of GSK126 was treated alone and DMSO was added for the same volume

value: 1uM of GSK126


title: Newly diagnosed Chronic Myeloid Leukemia 9

description:
control
SAMPLE 9


title: Newly diagnosed Chronic Myeloid Leukemia 7

description:
control
SAMPLE 7


title: B1_Female_25_days

value: whole organism


title: GSK-1


title: Newly diagnosed Chronic Myeloid Leukemia 6

description:
control
SAMPLE 6


title: Adrb3-/-_sham_rep1


title: Wild type_sham_rep3


title: A2_Female_55_days


title: DMSO-1

description:
derived from the pleural effusion of a 41-year-old Caucasian man with B-cell non-Hodgkin lymphoma (B-NHL, diffuse large cell lymphoma non-cleaved type, intermediate grade
DMSO was treated as vehicle control

value: DMSO


title: A1_Female_55_days


title: Wild type_sham_rep2


title: Newly diagnosed Chronic Myeloid Leukemia 5

description:
control
SAMPLE 5

value: Newly diagnosed CML


title: Newly diagnosed Chronic Myeloid Leukemia 4

description:
control
SAMPLE 4


title: Treatment Patient 3

city: Clayton

first: Shanti

last: Gurung

state: Vic

address: 27-31 Wright Street

country: Australia

institute: Hudson Institute of Medical Research

data_processing:
Transcriptomic maps of paired-end reads were generated using bowtie-2.2.3, samtools-0.1.19, and tophat-2.0.12 against the hg19 reference genome (2014)
Transcript counts were assessed by HTSeq-0.6.1 using the reverse strand setting and intersection-non-empty mode and counts were assigned to gene ids.
Genome_build: hg19
Supplementary_files_format_and_content: Count and TPM data in .XLS format

source_name: Endometrial mesenchyme stem cells

growth_protocol: Endometrial biopsies were processed and single-cell suspensions of eMSCs obtained as described previously (Masuba et al. 2012).

extract_protocol:
Total RNA was extracted from untreated and A83-01 treated eMSCs using Rneasy Mini kit (Qiagen) according to the manufacturer's instructions, with some variations. Briefly, eMSCs were trypsinised using TryLE (Life Technologies), cells resuspended in DMEM/F12 containing 5% heat-inactivated newborn calf serum and then centrifuged at 300g for 5 min. RNeasy Lysis (RLT) Buffer was added followed by 70% ethanol and centrifugation (>= 8000g) for 15 sec in an RNeasy spin column (Qiagen). Genomic DNA contamination was minimized by washing in RNA wash buffer (RW1), 80ul DNase I incubation mix was added to the spin column membrane and incubated at RT for 15 min, then washed in RW1 Buffer, followed by two washes in RPE buffer and RNA eluted with 30-50 ul RNase-free water. RNA quality was assessed on an Agilent Bioanalyzer. RNA samples with RNA Integrity Number (RIN) >8 were used to generate RNA libraries according to the Illumina Stranded mRNA protocol.
RNA libraries were sequenced on the Illumina HiSeq 300. Fifty million single-end reads were sequenced per sample.

treatment_protocol: eMSCs were cultured in DMEM/F12 medium containing 10% FCS, 1% primocin and 2mM glutamine (Invitrogen), supplemented with 10 ng/ml basic fibroblast growth factor (bFGF) (Peprotech) and slowly scaled-down to an in-house DMEM/F12 serum free medium (SFM) and incubated at 37 C in 5%CO2/5% O2/90% N2 with 1uM TGFbeta-R inhibitor (A83-01 - Trocis Bioscience) or without (0.01% DMSO). Cells were seeded at 5,000 cells/cm2 with medium changed every 48h and passaged on days 15, 22, 29 and 36 onto fibronectin-coated clusture flasks as described previously (Gurung et al. 2015). Treated and untreated eMSC cultures were subjected to RNA-seq at passage 4 after 36 days in culture.

value: Endometrial mesenchyme stem cells

tag: passage

tag: patient id

value: Patient 3

value: A83-01 treated


title: Newly diagnosed Chronic Myeloid Leukemia 3

description:
control
SAMPLE 3

tag: disease state


title: Met-3

city: Shanghai

first: Hailiang

last: Liu

address: NO 1239, siping road

institute: Tongji university

description: Cultured hADSC

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence and low-quality sequence, then mapped to hg18 whole genome using tophat2
Genes expression level is quantified by cuffquant.
Reads aligned to genes were calculated using cufflinks.
Genome_build: hg18
Supplementary_files_format_and_content: Read count and FPKM ( Fragments Per Kilobase Million) for each Sample

source_name: Human adipose-derived mesenchymal stem cells

extract_protocol:
Total RNA was extracted using the TRIZOL following the manufacturer's instructions.
Libraries were prepared according to Nextera® XT DNA Library Prep Kit for Illumina

tag: origin

value: China

value: adipose-derived mesenchymal stem cells

value: adult

value: Metformin treatment 6 days


title: Wild type_sham_rep1

value: bone marrow

value: Male


title: Treatment Patient 2

value: Patient 2


title: ASFVΔE66L-2

city: Wuhan

first: Zhou

last: Shen

state: Hubei

address: 1 Shi-zi-shan Street

institute: Huazhong agriculture university

description:
PAM
E66.2

data_processing:
FastQC
Hisat2
Samtools
StringTie
Deseq2
Genome_build: Sscrofa11(Ensembl)
Supplementary_files_format_and_content: raw counts matrix

organism: Sus scrofa

source_name: porcine alveolar macrophages

extract_protocol:
Using TRIzol based method following manufactures instruction
Using VAZYME NR612 following manufactures instruction

value: porcine alveolar macrophages

tag: group

value: ASFV missing pE66L infected


title: ASFVΔE66L-3

description:
PAM
E66.3


title: Met-2

description: Cultured hADSC


title: Newly diagnosed Chronic Myeloid Leukemia 2

description:
control
SAMPLE 2

source_name: peripheral blood sample

value: peripheral blood


title: Treatment Patient 1

value: Patient 1


title: Newly diagnosed Chronic Myeloid Leukemia 1

description:
control
SAMPLE 1


title: ASFVΔE66L-1

description:
PAM
E66.1


title: Control Patient 3

value: control


title: ASFV-3

description:
PAM
WT3

value: ASFV infected


title: Ctrl-3

description: Cultured hADSC


title: A3_Female_55_days

value: whole organism

tag: gender

value: Female

value: Maintained under normal conditions

value: High Hardness COMBO


title: Control Patient 2

value: Endometrial mesenchyme stem cells


title: Ctrl-2

description: Cultured hADSC

value: China

value: adipose-derived mesenchymal stem cells


title: DMSO-2

value: EZH2 Y641F mutation lymphoma cell line

value: DMSO


title: ASFV-2

description:
PAM
WT2


title: miR-122_metastasis

city: Chapel Hill

first: Hossein

last: Sendi

state: NC

address: 125 Mason Farm Rd

department: Radiation Oncology

institute: University of North Carolina at Chapel Hill

description:
Test
This sample represents the average of 4 replicates.

data_processing:
Thermal cycling was performed using QuantStudio 6 Pro RT PCT System (Applied Biosystems, USA) with an initial denaturation at 95⁰C for 10 minutes, 40 cycles at 95⁰C for 15 seconds, and 60⁰C for 1 minute. Values of cycle threshold (Ct) obtained in quantification were used for calculations of fold changes in mRNA abundance using 2-ΔΔCt method. Data was analyzed using RT2 profiler PCR array data analysis at GeneGlobe Data Analysis Center online (GeneGlobe, Qiagen, MD).
For normalization, 4 housekeeping genes (Actb, Gapdh, Gusb,Hsp90ab1) were used

label: CYBR Green

source_name: miR-122 treated liver

label_protocol: Then, mixed with RT2 SYBR Green/ROX qPCR Master Mix added into a 384-well RT2 PCR Arrays of mouse tumor metastasis (Qiagen, PMAM-028Z)

growth_protocol: Liver tissue from balb/c mice with CT26 hemi-splenectomy induction of liver metastasis

extract_protocol: Total RNA was extracted with miRNAeasy kit and cDNA was made using RT2, First Strand kit (Qiagen, MD)

treatment_protocol: Mice were treated with LCP nanoparticle containing miR-122 or miRNC 3 times a week for 3 weeks

value: liver

value: balb/c


title: Ctrl-1

description: Cultured hADSC

value: adult


title: Control Patient 1


title: miRNC_metastasis

description:
Control
This sample represents the average of 4 replicates.

source_name: miRNC treated liver


title: D0-10-Crl

first: Jian

last: Zheng

state: Tianjin

address: QiXiangTai Road，He Ping district

department: Immunology

institute: TIanjin Medical University

data_processing:
The Cell Ranger Single Cell Software Suite v3.1.0 was used to perform sample demultiplexing, barcode processing, and single cell 3' gene counting (https://support.10xgenomics.com/single-cell/software/pipelines/latest/what-is-cell-ranger).
Genome_build: GRCh38
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every cell

source_name: Human periperal blood NK cells

extract_protocol:
Cells were loaded on a Chromium Single Cell Controller (10x Genomics) to generate single-cell Gel Bead-In-Emulsions (GEM) by using Single Cell 3′ Library and Gel Bead Kit v3 (10X Genomics, San Francisco, CA) and run through the library preparation procedures following guidance from the Chromium Single Cell 3′ Library Reagent Kits v3. The libraries were quantified using Agilent 2100 High Sensitivity DNA kit (Agilent, California, U.S.) and sequenced via Illumina NovaSeq6000 with pair end 150 bp (PE150) (Illumina, San Diego, CA).
Chromium Single Cell 3′ Library Reagent Kits v3 was used for library construction, following the kit user guide.

value: Human NK cells

value: No treatment

tag: time point

value: Day 0


title: D7-10-Stim

value: Day 7


title: NAC NSC 13

status: Public on Sep 22 2020

city: New york

first: Jihye

last: Paik

state: NY

address: 1300 York Ave.

department: Pathology

institute: Weill Cornell Medical College

data_processing:
Basecalls performed using BaseCall  version 1.1.2
Sequenced reads with adaptor sequence or low-quality sequence (we define the low quality read as the percentage of base which quality is lesser than 15 is greater than 20% in a read) are discarded and then mapped to mm10 whole genome using HISAT2 v2.0.4 with parameters:  --phred64 --sensitive --no-discordant --no-mixed -I  1 -X 1000, mapped to gene reference using Bowtie2 v2.2.5 with parameters: -q --phred64 --sensitive --dpad 0 --gbar 99999999 --mp 1,1 --np 1 --score-min L,0,-0.1 -I 1 -X 1000 --no-mixed --no-discordant -p 1 -k 200 and then calculate gene expression level with RSEM. RSEM is a software package for estimating gene and isoform expression levels from RNA-Seq data.
Screening DEGs using EBSeq,we defined a gene as a DEG (differentially expressed gene) when foldchange ≥2 and PPEE ≤ 0.05.
Genome_build: mm10
Supplementary_files_format_and_content: Tab-delimited txt files include FPKM values for each Sample.

source_name: Neural progenitor cells

growth_protocol: N2 media with EGF and bFGF

extract_protocol:
TRIZOL
1) Total RNA treatment  a) RNase H Probe (rRNA depletion): Hybridize the rRNA with DNA probe and digest the DNA/RNA  hybrid strand, followed by DNase I reaction to remove DNA probe. Then obtain the target RNA after  purification.  b) Oligo dT Selection (mRNA enrichment): Use oligo dT beads to select mRNA with poly A tail.  2) RNA fragment and reverse transcription  Fragment the RNA and reverse transcription to double-strand cDNA (dscDNA) by N6 random primer.  3) End repair and adaptor ligation  End repair the dscDNA to blunt end and phosphate at 5’ end, 3’ end forms an “A” cohesive end. And  then ligate to the bubble adapter with protruding T of 3’ end.  4) PCR amplification  5) Single strand separation and cyclization  Denature the PCR product by heat and the single strand DNA is cyclized by splint oligo and DNA  ligase.  6)DNA nanoball making7) Sequencing on BGISEQ-500 platform

treatment_protocol: 48 hrs with PQ or NAC

value: Neural progenitor cells

value: NAC


title: PQ NSC 9

value: PQ


title: NAC NSC 10


title: control NSC 8

value: control


title: Met-1

description: Cultured hADSC

tag: tissue

value: Metformin treatment 6 days


title: KO-TCR

city: Xinxiang

first: Genshen

last: Zhong

state: Henan Province

address: Jinsui Road, 601#

institute: Xinxiang Medical University

description: 10x Genomics TCR library

data_processing:
Library strategy: TCR-seq
Following sequencing, the raw data from each sample were demultiplexed, aligned to the mm10 reference genome, and UMI counts were quantified using the 10x Genomics Cell Ranger pipeline (v3.1.0, 10X Genomics). Then, we continued the data analysis with the raw barcode matrix files using the Seurat package (v3.2.0). Cells more than 100 detected genes and less than 10% mitochondrial reads were considered valid cells and were kept for downstream analysis. In order to prevent clusters from being biased by mitochondrial transcript content, gene expression values were scaled based on  the cell mitochondrial transcript content. Next, "LogNormalize" and "vst" was applied to normalize and find variable features within the single cell gene expression data. Clustering and differential expression analysis was performed using R package Seurat with default parameters. Based on the PC ElbowPlot, we picked a certain number of principal components (PCs) for the clustering analysis when the number reached the baseline of the standard deviation of PC. We generally used the cluster resolution that higher one did not result in increasing clusters linearly. Cell clusters were visualized using UMAP. For differential gene expression, we used model-based analysis of single-cell Transcriptomics (MAST) (log fc ≥0.25, min.pct = 0.1, min.diff.pct > -Inf) and only selected the genes with adjusting p value <0.05. In order to predict cellular differentiation, cells were ordered in pseudotime using Monocle2 (v2.14.0) with default parameters. All analyses were carried out in R 3.6.1 environment.
Genome_build: mm10

molecule: polyA RNA

source_name: B16 melanoma tumor

extract_protocol:
Single cells were collected from tumor tissues as described previously (Zhang et al., 2020). Briefly, tumor tissues were cut into approximately 1-2 mm3 pieces in the RPMI-1640 medium (Gibco), and enzymatically digested with gentleMACS (Miltenyi) using program 37C_m_TDK_1 on a rotor at 37°C, according to manufacturer’s instruction. The dissociated cells were subsequently passed through a 100 µm SmartStrainer and centrifuged at 400 g for 5 min. After the supernatant was removed, the pelleted cells were suspended in red blood cell lysis buffer (Miltenyi) and incubated on ice for 1-2 min to lyse red blood cells. After washing twice with 1× PBS (Gibco), the cell pellets were re-suspended in sorting buffer (PBS supplemented with 2% fetal bovine serum (FBS, Gibco)).
Cells were loaded around 17,400 cells/chip position using the 10x Chromium Single cell 5’ Library, Gel Bead & Multiplex Kit and Chip Kit (10x Genomics, V1.0 barcoding chemistry) according to the manufacturer’s instructions.

value: B16 melanoma tumor

value: male

tag: genotype

value: ATPIF1 knock-out


title: KO-5

description: 10x Genomics 5' library

data_processing:
Following sequencing, the raw data from each sample were demultiplexed, aligned to the mm10 reference genome, and UMI counts were quantified using the 10x Genomics Cell Ranger pipeline (v3.1.0, 10X Genomics). Then, we continued the data analysis with the raw barcode matrix files using the Seurat package (v3.2.0). Cells more than 100 detected genes and less than 10% mitochondrial reads were considered valid cells and were kept for downstream analysis. In order to prevent clusters from being biased by mitochondrial transcript content, gene expression values were scaled based on  the cell mitochondrial transcript content. Next, "LogNormalize" and "vst" was applied to normalize and find variable features within the single cell gene expression data. Clustering and differential expression analysis was performed using R package Seurat with default parameters. Based on the PC ElbowPlot, we picked a certain number of principal components (PCs) for the clustering analysis when the number reached the baseline of the standard deviation of PC. We generally used the cluster resolution that higher one did not result in increasing clusters linearly. Cell clusters were visualized using UMAP. For differential gene expression, we used model-based analysis of single-cell Transcriptomics (MAST) (log fc ≥0.25, min.pct = 0.1, min.diff.pct > -Inf) and only selected the genes with adjusting p value <0.05. In order to predict cellular differentiation, cells were ordered in pseudotime using Monocle2 (v2.14.0) with default parameters. All analyses were carried out in R 3.6.1 environment.
Genome_build: mm10


title: IP_C7eIF2α cKICaMKIIα 1hr post-FC_rep3 [D706-D503]

city: Montreal

first: Nahum

last: Sonenberg

state: Quebec

address: Goodman Cancer Research Centre 1160 Pine Avenue West, Room 614

department: Department of Biochemistry

country: Canada

institute: McGill University

data_processing:
Adaptor sequence GATCGGAAGAGCACACG was removed from reads using Cutadapt. Reads shorter than 25 nucleotides were discarded.
Reads were aligned to ribosomal RNA using Bowtie37 allowing for 2 mismatches and no ambiguous mapping, aligned reads were discarded.
Remaining forward pair reads were then aligned to the mouse transcriptome (Gencode version 14) using Bowtie allowing for 2 mismatches and no ambiguous mapping
Differential expression analysis was carried out using DESeq2 version 1.26.039
Genome_build: Gencode M14
Supplementary_files_format_and_content: csv, count table

source_name: IP_eIF2α cKICaMKIIα 1hr post-FC

growth_protocol: Neuronal subtypes-specific eIF2α conditional knock-in (cKI) mice were generated by breeding eIF2αA/A;fTg+ floxed mice15 with a Cre+ transgenic line driven by either the CaMKIIα, GAD65, parvalbumin (Pvalb), or somatostatin (Sst) promoters. The genetic background of these strains is C57BL/6. We first bred eIF2αA/A;fTg+ with neuronal subtypes-specific Cre mice to generate Cre-positive, eIF2αA/S;fTg+ heterozygous mice. eIF2αA/S;fTg+;Cre positive mice were then bred with eIF2αA/A;fTg+ mice to generate homozygous eIF2α cKI mice and Cre-negative, eIF2αA/A;fTg+ or neuronal subtypes-specific X-Cre-positive control mice . Adult (2- to 3-month-old, weight range 26-30 g) males were used in the studies. Mice were housed in standard laboratory cages of 4 to 5 mice in each cage and kept on a 12-hour light (between 7:00 AM and 7:00 PM), 12-hour dark cycle. Mice were given water and standard rodent chow ad libitum. Cages were maintained in ventilated racks in temperature (20-21°C) and humidity (~55%) controlled rooms.

extract_protocol:
Frozen hippocampi from one mouse were pooled and homogenized in 1 ml of buffer as described27. After centrifugation, 4 μl of anti-HA antibody (Extended Data Table 2) were added to 800 μl of the cleared lysate and incubated for 4 h at 4 °C. Remaining lysate was saved as input sample. After incubation, 200 μl of protein A/G magnetic beads (Thermo Fisher Scientific) were added and incubated overnight at 4 °C with rotation. Immunoprecipitates (IPs) were washed in high salt buffer and RNA from inputs and IPs extracted as described in the original protocol
RNA-Seq libraries were prepared from 200 ng of total RNA using the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina with the NEBNext Poly(A) mRNA Magnetic Isolation Module and NEBNext Multiplex Oligos (New England Biolabs). Libraries were pair-end sequenced (2 × 50 bp) on an Illumina Illumina Novaseq 6000 Instrument.

treatment_protocol: Prior to the experiment, mice were handled for 5 min per day for three consecutive days. Habituation was done by exposing mice to two distinct contexts; Context A (grid floor with transparent cage walls) and Context B (grid floor and cage walls were covered with yellow plastic to create another context) for 20 min for 2 days. The two habituation sessions were separated by at least 4 h. During training, mice explored Context A for 2 min, then received one pairing of a tone (Sound-1, frequency of 2800 Hz and amplitude of 85 dB for 30 s) co-terminated by a foot shock (0.35 mA, 1 s) in the weak training protocol or two pairings of a tone (2800 Hz, 85 dB, 30 s) with a co-terminating foot shock (0.7 mA, 2 s) for the strong training protocol. Sixty seconds later, they were returned to their home cage. Contextual fear was tested 1 h (STM) and 24 h (LTM) after conditioning by placing the animals in the conditioning context (Context A) for a 5 min period, and time spent freezing was used as an indicator of fear learning and memory. For auditory fear conditioning, the test consisted of a 2 min acclimatizing period to the context (Context B; pre-CS period), followed by a 3 min period during which the tone was delivered (CS). Mice were returned to their cages 30 s after the end of the tone. For all tests, each mouse was assessed at 5 s intervals as either freezing or not freezing. Data are expressed as the percent of 5 s intervals in which freezing was observed. Statistical analysis was based on repeated measures ANOVA and between-group comparisons by Tukey’s pos hoc test.

tag: strain background

tag: genetic modification

value: CaMKIIα-Cre+ conditional knock-in

tag: treatment

value: 1hr post FC

value: Hippocampus

tag: sample type

value: RiboTag IP


title: IP_C6eIF2α cKICaMKIIα 1hr post-FC_rep2 [D705-D503]


title: IP_C24Standard CaMKIIα-Cre+1hr post-FC_rep2 [D705-D504]

source_name: IP_Standard CaMKIIα-Cre+1hr post-FC

value: Control


title: IP_C2eIF2α cKICaMKIIα Naive_rep2 [D702-D503]

source_name: IP_eIF2α cKICaMKIIα Naive

value: Naive


title: IP_C5eIF2α cKICaMKIIα 1hr post-FC_rep1 [D704-D503]


title: IP_C1eIF2α cKICaMKIIα Naive_rep1 [D701-D503]


title: IP_C25Standard CaMKIIα-Cre+1hr post-FC_rep3 [D706-D504]


title: IP_C18Standard CaMKIIα-Cre+Naive_rep1 [D701-D504]

source_name: IP_Standard CaMKIIα-Cre+Naive


title: Input_C25Standard CaMKIIα-Cre+1hr post-FC_rep3 [D706-D502]

source_name: Input_Standard CaMKIIα-Cre+1hr post-FC

value: INPUT RNA-Seq


title: Input_C20Standard CaMKIIα-Cre+Naive_rep3 [D703-D502]

source_name: Input_Standard CaMKIIα-Cre+Naive


title: ASFV-1

description:
PAM
WT1

tag: cell type

value: porcine alveolar macrophages

value: ASFV infected


title: Input_C23Standard CaMKIIα-Cre+1hr post-FC_rep1 [D704-D502]


title: IP_C20Standard CaMKIIα-Cre+Naive_rep3 [D703-D504]


title: Input_C24Standard CaMKIIα-Cre+1hr post-FC_rep2 [D705-D502]


title: Input_C18Standard CaMKIIα-Cre+Naive_rep1 [D701-D502]


title: IP_C3eIF2α cKICaMKIIα Naive_rep3 [D703-D503]


title: WT-5

description: 10x Genomics 5' library

tag: strain

tag: Sex

value: wild-type


title: Input_C6eIF2α cKICaMKIIα 1hr post-FC_rep2 [D705-D501]

source_name: Input_eIF2α cKICaMKIIα 1hr post-FC


title: Input_C7eIF2α cKICaMKIIα 1hr post-FC_rep3 [D706-D501]


title: Input_C3eIF2α cKICaMKIIα Naive_rep3 [D703-D501]

source_name: Input_eIF2α cKICaMKIIα Naive


title: IP_C23Standard CaMKIIα-Cre+1hr post-FC_rep1 [D704-D504]


title: Input_C1eIF2α cKICaMKIIα Naive_rep1 [D701-D501]


title: Input_C19Standard CaMKIIα-Cre+Naive_rep2 [D702-D502]


title: Input_C2eIF2α cKICaMKIIα Naive_rep2 [D702-D501]


title: Input_C5eIF2α cKICaMKIIα 1hr post-FC_rep1 [D704-D501]


title: IP_C19Standard CaMKIIα-Cre+Naive_rep2 [D702-D504]


title: DT rep3

city: Nagoya

first: Hiroyuki

last: Konishi

state: Aichi

address: 65, Tsurumai-cho, Showa-ku

department: Department of Functional Anatomy and Neuroscience

institute: Nagoya University

data_processing:
Adapter sequences and low quality (quality value < 20) bases were trimmed from 3’-ends of the RNA-seq reads with the Trim Galore v0.5.0.
The reads were qualified with FastQC v0.11.8 before and after trimming.
The processed reads were mapped on the mouse genome version mm10 using HISAT2 v2.1.0 by employing strand specificity information, followed by removal of reads mapped to rDNA regions using BEDTools v2.25.0.
From the mapping data, expressions of individual genes were quantified with StringTie v1.3.5 using the mm10 gene annotation.
Analysis of differential expression between the PBS and DT groups was performed with edgeR v3.24.3 implemented in R v3.5.1, and the q-value was calculated as the false discovery rate for multiple testing correction of the p-values by the qvalue package v2.24.1 in R.
Transcripts per million (TPM) and counts per million (CPM) values were computed with StringTie and edgeR, respectively.
Genome_build: mm10
Supplementary_files_format_and_content: Tab-delimited text file includes counts per million (CPM) and transcripts per million (TPM) values for each sample.

source_name: Astrocytes

extract_protocol:
Astrocytes were isolated from hippocampus using magnetic-activated cell sorting system with anti-astrocyte cell surface antigen-2 MicroBeads (Miltenyi Biotec). Total RNA was purified using RNeasy Micro Kit (QIAGEN). Total RNA was quantified by 2100 Bioanalyzer with RNA 6000 Pico Kit (Agilent Technologies).
Libraries were prepared using the SMARTer Stranded RNA-seq Kit (Clontech Laboratories).

treatment_protocol: PBS or DT (50 µg/kg) was intraperitoneally injected to Siglechdtr/dtr mice 2 days before sampling.

value: hippocampus

value: Astrocytes

value: Siglechdtr/dtr

value: 2d after DT injection


title: WT-TCR

description: 10x Genomics TCR library

value: B16 melanoma tumor


title: DT rep1


title: DT rep2


title: PBS rep1

value: 2d after PBS injection


title: PBS rep3


title: CEMBA181022_6B_3_CEMBA181022_6B_4_H9_ad008

city: La Jolla

first: Joseph

last: Ecker

address: 10010 North Torrey Pines Road

institute: HHMI-Salk-Institute

data_processing:
Library strategy: snmC-seq2
Reads trimed with Cutadapt for adapters and low quality bases (Phred score >= 20)
The resulting files are mapped to in-silico bisulfite converted mm10 reference genome using Bismark.
The raw BAM file will be filtered using samtools to filter reads by MAPQ > 10 and use Picard to remove PCR duplicates
Tab-delimited files (ALLC files) describing the quantity of unmethylated and methylated cytosine base calls will be generated with in-house developing package using the filtered BAM files
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited files (ALLC files) describing the quantity of unmethylated and methylated cytosine base calls. Columns are: 1. Chromosome, 2. Position, 3. Strand, 4. Cytosin Context, 5. methylated base call, 6. total mapped base call, 7. not used, place holder column

source_name: C57BL/6J Male P56 Mouse Brain

extract_protocol:
the brain of P56 male C57BL/6J mouse will be removed and cut into 600 microns thick coronal sections using a tissue matrix. Then each region will be microdissected from the coronal tissue sections based on identified landmarks and brain atlas coordinates, as defined in Allen brain atlas CCF3 (Avaliable at: http://atlas.brain-map.org). For each dissection region, the tissue from several littermate mice will be combined together into to separate replicate groups. The number of animals in a replicate depends on the size of the tissue. Nuclei preparation will be stained with the fluorescently labeled anti-NeuN body and nucleic acid stain Hoechst 33342.
Library prepared following protocol discribed in Luo, Chongyuan, Angeline Rivkin, Jingtian Zhou, Justin P. Sandoval, Laurie Kurihara, Jacinta Lucero, Rosa Castanon, et al. 2018. “Robust Single-Cell DNA Methylome Profiling with snmC-seq2.” Nature Communications 9 (1): 3824.

tag: brain region

value: SSp

value: male

tag: age


title: CEMBA181022_6B_3_CEMBA181022_6B_4_H9_ad004


title: CEMBA181022_6B_3_CEMBA181022_6B_4_H8_ad007


title: CEMBA181022_6B_3_CEMBA181022_6B_4_H8_ad006


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title: CEMBA181022_6B_3_CEMBA181022_6B_4_H8_ad012


title: CEMBA181022_6B_3_CEMBA181022_6B_4_H9_ad001


title: CEMBA181022_6B_3_CEMBA181022_6B_4_H9_ad002


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title: CEMBA181022_6B_3_CEMBA181022_6B_4_H7_ad012


title: CEMBA181022_6B_3_CEMBA181022_6B_4_H7_ad006


title: CEMBA181022_6B_3_CEMBA181022_6B_4_H9_ad006


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title: CEMBA181022_6B_3_CEMBA181022_6B_4_H6_ad006


title: PBS rep2


title: CEMBA181022_6B_3_CEMBA181022_6B_4_H9_ad007


title: CEMBA181022_6B_3_CEMBA181022_6B_4_H6_ad002


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