title: Embryo stage 12-14 WT_for_chiffon_rep4

city: West Lafayette

first: Vikki

middle: Marie

last: Weake

state: IN

address: 175 South University Street

department: Biochemistry

institute: Purdue University

data_processing:
Illumina Casava software used for basecalling.
Sequenced reads were trimmed for adaptor sequence with Trimmomatic, then mapped to dm6 whole genome using Hisat2  with parameters -p 8 --rna-strandness FR -x
Counts were identified for each gene using Htseq-count (v0.11.1) with default parameters.
Genome_build: dm6
Supplementary_files_format_and_content: raw counts

organism: Drosophila melanogaster

source_name: Drosophila embryo

extract_protocol:
Embryos were collected and 100ul of Trizol were added and  embryos were flashed frozen in liquid nitrogen. RNA was extracted using Direct-zol RNA microPrep (Zymo Research)
Libraries were prepared following the Ovation RNA-seq System V2 (NuGEN)

tag: developmental stage

value: Embryo stage 12-14

value: WT (act-gal4 x GFP)


title: Lib_FUN-18

status: Public on Dec 21 2021

type: SRA

city: Milano

first: Luca

last: Massimino

state: MI

address: Via Olgettina, 58

department: Gastroenterology

country: Italy

institute: Ospedale San Raffaele

library_source: transcriptomic

data_processing:
Fastq files were mapped to the hg38 human reference genome with the STAR aligner v2.7 (Dobin et al., 2013).
Differential gene expression and Functional enrichment analyses were performed with DESeq2 (Love et al., 2014) and geneSCF (Subhash et.al. 2016), respectively.
hg38

molecule: polyA RNA

organism: Homo sapiens

source_name: Control Colon HILEC

extract_protocol:
RNA was isolated with Trizol (Thermo Fisher), and treated with DNase I (NEB) according to manufacturer's instructions.
Library preparation was done with TruSeq RNA Library Prep Kit v2 (Illumina) according to manufacturer's instructions.

tag: disease state

value: Control

tag: tissue

value: Colon

tag: cell type

value: HILEC


title: Naïve KO rep2

city: SAN FRANCISCO

first: SUJIT

last: KASHYAP

state: CA

address: 513 Parnassus Ave

department: Pediatric Rheumatology

country: USA

institute: UNIVERSITY OF CALIFORNIA, SAN FRANCISCO

data_processing:
Data Analysis : Downstream analysis was performed using a combination of programs including STAR, HTseq, dEseq2 and our wrapped scripts. Alignments were parsed using STAR program and differential expressions were determined through DESeq2/edgeR. GO and KEGG enrichment were implemented by the ClusterProfiler. Gene fusion and difference of alternative splicing event were detected by Star-fusion and rMATS software
Reads mapping to the reference genome : Reference genome and gene model annotation files were downloaded from genome website browser (NCBI/UCSC/Ensembl) directly. Indexes of the reference genome was built using STAR and paired-end clean reads were aligned to the reference genome using STAR (v2.5). STAR used the method of Maximal Mappable Prefix(MMP) which can generate a precise mapping result for junction reads.
Differential expression analysis (For DESeq2 with biological replicates) Differential expression analysis between two conditions/groups (two biological replicates per condition) was performed using the DESeq2 R package (2_1.6.3). DESeq2 provide statistical routines for determining differential expression in digital gene expression data using a model based on the negative binomial distribution. The resulting P-values were adjusted using the Benjamini and Hochberg’s approach for controlling the False Discovery Rate(FDR). Genes with an adjusted P-value <0.05 found by DESeq2 were assigned as differentially expressed.
Correlations To allow for log adjustment, genes with 0 FPKM are assigned a value of 0.001. Correlation were determined using the cor test function in R with options set alternative =”greater” and method = “Spearman”.
GO and KEGG enrichment analysis of differentially expressed genes Gene Ontology (GO) enrichment analysis of differentially expressed genes was implemented by the cluster Profiler R package, in which gene length bias was corrected. GO terms with corrected P value less than 0.05 were considered significantly enriched by differential expressed genes. KEGG is a database resource for understanding high-level functions and utilities of the biological system, such as the cell, the organism and the ecosystem, from molecular level information, especially large-scale molecular datasets generated by genome sequencing and other high-through put experimental technologies (http://www.genome.jp/kegg/). cluster Profiler R package was used to test the statistical enrichment of differential expression genes in KEGG pathways.
Alternative splicing analysis Alternative Splicing is an important mechanism for regulate the expression of genes and the variable of protein. rMATS(3.2.1) software was used to analysis the ASevent.
Genome_build: Mus Musculus(GRCm38/mm10)
Supplementary_files_format_and_content: tab-delimited xls files include count values for all samples along with the list of differentially expressed genes in the respective RNAseq expriment.

molecule: total RNA

organism: Mus musculus

source_name: Spleenocyte, Lymph node

growth_protocol: Cells were grown in complete media when ever required using standard procedure

extract_protocol:
Briefly, spleen and lymph node from mice were extracted followed by isolation of CD8 T cells. RNA was isolated using Qiagen RNeasy Mini Kit as per manufacturers protocol. A total amount of 1 μg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample.
Briefly, mRNA was purified from total RNA using poly-T oligo-attached magnetic beads. Fragmentation was carried out using divalent cations under elevated temperature in NEBNext First Strand Synthesis Reaction Buffer (5X). First strand cDNA was synthesized using random hexamer primer and M-MuLV Reverse Transcriptase (RNase H-). Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and RNase H. Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. After adenylation of 3’ ends of DNA fragments, NEBNext Adaptor with hairpin loop structure were ligated to prepare for hybridization. In order to select cDNA fragments of preferentially 150~200 bp in length, the library fragments were purified with AMPure XP system (Beckman Coulter, Beverly, USA). Then 3 μl USER Enzyme (NEB, USA) was used with size-selected, adaptor ligated cDNA at 37 °C for 15 min followed by 5 min at 95 °C before PCR. Then PCR was performed with Phusion High-Fidelity DNA polymerase, Universal PCR primers and Index (X) Primer. At last, PCR products were purified (AMPure XP system) and library quality was assessed on the Agilent Bioanalyzer 2100 system.
The clustering of the index-coded samples was performed on a cBot Cluster Generation System using PE Cluster Kit cBot-HS (Illumina) according to the manufacturer’s instructions. After cluster generation, the library preparations were sequenced on an Illumina platform and paired-end reads were generated.

treatment_protocol: Stimulated RNAseq was done after treatment of cells with CD3/CD28 for 48 hrs

tag: strain

value: Spleen, lymph node

tag: age

value: 4-6 week

tag: genotype


title: mNPC_Cyto_rep 1_Small

city: LOS ANGELES

first: Chia-ho

last: Lin

address: 6577 MRL. 675 CHARLES E YOUNG DR. SOUTH

institute: UCLA

description:
small RNA (ribominus)
Cytoplasmic small RNA im mNPC biological replicate 1

data_processing: none provided by the submitter

source_name: mouse neuronal progenitor cell (mNPC)

growth_protocol: E14 mESC line was cultured on 0.1 % gelatin-coated dishes in mESC media supplemented with LIF. mNPC line were  were grown in DMEM/F12 supplemented with B27 (without vitamin A), 1 mM GlutaMax, and antibiotics. EGF and FGF were added every day at 10 ng/ml concentration. Primary cortical neurons (mCtx) were plated on 0.1 mg/ml poly-L-lysine coated dishes and culture media for 5 days.

extract_protocol:
Total RNA was collected with the Trizol LE regent for cytoplasmic RNAs, and Trizol reagent for soluble nucleoplasmic and chromatin-associated RNAs. Short RNA below 200 nt was selected using RNeasy MinElute Cleanup Kit (Qiagen). RNA was processed with Ribo-minus kit to remove ribosomal RNA.
Libraries were constructed with the Illumina TruSeq Small RNA sample Prep Kit. A final library of 120-160 bp was size selection with an TBE gel.
The libraries were subjected to 100 bp single-end sequencing (MiSeq).

tag: sample type


title: Naive Het rep1


title: Embryo stage 12-14 WT_for_chiffon_rep3


title: Lib_FUN-23

source_name: UC Colon HILEC

value: UC


title: Lib_FUN-17


title: mNPC_Chr_rep 3_Small

description:
small RNA (ribominus)
Chromatin-associated small RNA im mNPC biological replicate 3


title: Embryo stage 12-14 WT_for_chiffon_rep2


title: Naïve KO rep1


title: SCR_GSK_2

type: RNA

city: Paris

first: Franck

last: Letourneur

address: 22 rue mechain

country: France

institute: INSERM

hyb_protocol: cDNA were hybridized for 16 h at 45°C on GeneChip ClariomS Human from Affymetrix GeneChips, washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the GCS 3000 scanner (Affymetrix).

data_processing: Raw fluorescence intensity values were normalized using Robust Multiarray Average (RMA) algorithm in R to generate the normalized data matrix by performing background correction, quantile normalization and log2 transformation of raw fluorescence intensity values of each gene. All quality controls and statistics were performed using Partek® Genomics Suite software (Partek, St. Louis, MO, USA). Data were normalized using custom brainarray CDF files (v22 ENTREZG). To identify differentially expressed genes, we applied a classical analysis of variance (ANOVA) with a FDR permutation-base for each gene. We created a new matrix with only the significant ANOVA site and performed Z-scoring of rows. Hierarchical clustering by Pearson's dissimilarity and average linkage and principal components analysis (PCA) were conducted in an unsupervised fashion to control for experimental bias or outlier samples. We set a filter for those genes that displayed at least a ≥1,5 or ≤-1,5 fold difference in expression between groups and achieved an FDR of <0.05. Data were then interrogated for evidence of biologic pathway dysregulation using Gene set enrichment analysis (GSEA, Broad Institute). Enrichment rates were considered as significant for P-value <0.05 and FDR ≤0.1.

label: Biotin

source_name: MOLM-14 cells incubated with GSK621

label_protocol: Biotinylated cDNA were prepared according to the standard Affymetrix protocol from 100 ng total RNA (Following the GeneChip whole transcript Sense Target labelling assay kit Affymetrix, Santa Clara, CA).

growth_protocol: AML cells were cultured in 10% fetal calf serum supplemented minimum essential medium Eagle (MEM, α-modification, Gibco, Lifetechnologies, Carlsbad, CA, USA, reference 41090028).

extract_protocol: RNA was extracted using a RNeasy Mini Kit (Qiagen, Redwood City, CA, USA) and quality was evaluated with a Bioanalyzer 2100 (using Agilent RNA6000 nano chip kit), and 100 ng of total RNA was reverse transcribed using the GeneChip® WT Plus Reagent Kit according to the manufacturer’s instructions (Affymetrix, Thermo Fischer Scientific).

treatment_protocol: PERK WT and PERK KO MOLM-14 cells were cultured 6h with vehicle (DMSO) or 30mM GSK621 before RNA extraction

value: hematopoietic

tag: cell line

value: acute myeloid leukemia

value: SCR control

tag: treated with


title: PERK_GSK

source_name: MOLM-14 PERK KO cells incubated with GSK621

value: PERK KO


title: Lib_FUN-16


title: SCR_GSK


title: LCMV KO rep3


title: mNPC_Chr_rep 1_Small

description:
small RNA (ribominus)
Chromatin-associated small RNA im mNPC biological replicate 1


title: Embryo stage 12-14 WT_for_chiffon_rep1


title: mESC_Cyto_rep 3_Small

description:
small RNA (ribominus)
Cytoplasmic small RNA im mESC biological replicate 3

source_name: mouse embryonic stem cell (mESC)


title: LCMV KO rep2


title: mESC_Nuc_rep 3_Small

description:
small RNA (ribominus)
Nucleoplasmic small RNA im mESC biological replicate 3


title: Lib_FUN-14


title: LCMV KO rep1


title: Embryo stage 12-14 chiffon ΔN_rep3

value: chiffon  delta_N


title: Embryo stage 12-14 chiffon ΔN_rep4


title: Lib_FUN-15


title: Lib_FUN-13


title: Embryo stage 12-14 chiffon ΔN_rep2


title: Lib_FUN-12

source_name: CD Ileum HILEC

value: CD

value: Ileum


title: mESC_Chr_rep 3_Small

description:
small RNA (ribominus)
Chromatin-associated small RNA im mESC biological replicate 3


title: mESC_Cyto_rep 2_Small

description:
small RNA (ribominus)
Cytoplasmic small RNA im mESC biological replicate 2


title: mNPC_Nuc_rep 1_Small

description:
small RNA (ribominus)
Nucleoplasmic small RNA im mNPC biological replicate 1


title: mESC_Nuc_rep 2_Small

description:
small RNA (ribominus)
Nucleoplasmic small RNA im mESC biological replicate 2


title: Embryo stage 12-14 chiffon ΔN_rep1


title: LCMV Het rep2


title: Lib_FUN-11


title: LCMV Het rep1


title: Embryo stage 12-14 chiffon FLWF24_rep4

value: chiffon FLWF24


title: mESC_Chr_rep 2_Small

description:
small RNA (ribominus)
Chromatin-associated small RNA im mESC biological replicate 2


title: In vitro 3D EB differentiation day 30 (NCAM1-High-sorted)

city: Lausanne

first: Gioele

last: La Manno

state: Vaud

address: Station 19

department: BMI

country: Switzerland

institute: EPFL

data_processing:
Cell Ranger 2.1.1 or 3.1.0 was used to convert Illumina base call files to FASTQ format.
Cell Ranger 3.1.0 was used to map FASTQ sequencing reads to the human GRCh38 reference transcriptome with the STAR aligner and to generate feature-barcode count matrices.
For cells isolated from rabbit retina were generated using a custom-built hybrid reference transcriptome combining both the human GRCh38 reference and the rabbit reference (Oryctolagus cuniculus 2.0.99, EMBL-EBI). FASTQ files were mapped to this hybrid reference with Cell Ranger 3.1.0 to generate count matrices. Reads were exclusively assigned either to a human or rabbit transcript.
The velocyto run10x command was used to produce loom files containing spliced and unspliced RNA count matrices
Downstream analyses, including dimensionality reduction and cell type annotation, were performed using both velocyto and scanpy in Python (version 3.7)
Genome_build: GRCh38 human reference, Oryctolagus cuniculus 2.0.99 EMBL-EBI rabbit reference
Supplementary_files_format_and_content: Processed data were stored in loom file format (http://loompy.org/) containing spliced and unspliced count matrices. For the human-rabbit cell mixture (rabbit1.tar.gz, rabbit2.tar.gz), processed data is provided as the 10X count matrices in mtx file format).

source_name: In vitro hESC-derived culture (HS980)

growth_protocol: A step-by-step protocol describing the differentiation procedure has been reported previously (Plaza Reyes et al., 2020a, 2020b). hESCs were plated at a cell density of 2.4x104 cells/cm2 on hrLN-521 (20 μg/mL) using NutriStem hPSC XF medium. A Rho-kinase inhibitor (Millipore, Y-27632) at a concentration of 10 μM was added during the first 24h, while cells were kept at 37°C, 5% CO2/5% O2. After 24h, hPSC medium was replaced with differentiation medium NutriStem hPSC XF without bFGF and TGFβ and cells were placed at 37°C, 5% CO2/21%O2. From day 6 after plating, 100 ng/mL of Activin A (R&D Systems, 338-AC-050) was added to the media. Cells were fed three times a week and kept for 30 days. Monolayers were then trypsinized using TrypLE Select (ThermoFisher Scientific, 12563011) for 10 min at 37°C, 5% CO2. The enzyme was carefully removed and the cells were collected in fresh pre-warmed NutriStem hPSC XF medium without bFGF and TGFβ by gentle pipetting to obtain a single cell suspension. Cells were centrifuged at 300 g for 4 min, the pellet was resuspended, passed through a cell strainer (ø 40 μm, VWR, 732-2757), and seeded on laminin coated dishes (hrLN-521 at 20μg/mL) at different cell densities ranging from 1.4x106 to 1.4x104 cells/cm2. Cell sorting was performed on hPSC-RPE cultures after 30 days of differentiation. Cells were incubated with the mentioned conjugated antibodies on ice for 30 min. Fluorescence minus one (FMO) controls were included for each condition to identify and gate negative and positive cells. Stained cells were then sorted using a BD FACS Aria Fusion Cell Sorter (BD Bioscience) using FACSDiva Software v8.0.1. After sorting, specific cell populations (NCAM1-High, CD140b-High and unsorted counterparts) were cultured under RPE conditions. Replated cells were fed three times a week during the subsequent 30 days with NutriStem hPSC XF medium without bFGF and TGFβ.

extract_protocol: Cells were transported at 4°C to the Eukaryotic Single Cell Genomics Facility (ESCG, SciLifeLab, Stockholm, Sweden) where a 3’ cDNA library was prepared for single cell RNA sequencing (scRNA-seq) using the 10X Genomics platform and NovaSeq 6000 software.


title: Lib_FUN-10


title: Embryo stage 12-14 chiffon FLWF24_rep3


title: Lib_FUN-09


title: Embryo stage 12-14 chiffon FLWF24_rep2


title: In vitro 3D EB differentiation day 30 (CD140b-High-sorted)


title: mESC_Nuc_rep 1_Small

description:
small RNA (ribominus)
Nucleoplasmic small RNA im mESC biological replicate 1


title: mESC_Cyto_rep 1_Small

description:
small RNA (ribominus)
Cytoplasmic small RNA im mESC biological replicate 1


title: LCMV Het rep3


title: R.227_Spleen_GEX

city: Boston

first: Jim

last: Kaminski

state: MA

address: 1 Blackfan Circle

institute: Boston Children's Hospital

description:
Single-cell RNA – scRNA-Seq
Initial_10x_GEX_filtered_feature_bc_matrix.h5

data_processing:
Samples were aligned using the Cellranger multi pipeline (v6.0.2), with VDJ libraries listed as “vdj-t” to indicate T cell libraries. Samples were aggregated with the Cellranger aggr pipeline (v6.0.2) with normalize=none
We analyzed the total transcripts detected and total genes detected for each sample to determine appropriate thresholds and retained cells with 500 to 6,000 genes detected and 1,800 to 40,000 transcripts detected, and less than 5% of aligned reads originating from the mtDNA. We then applied SCTransform(52) to normalize the data, reduced the dimensionality of the dataset using PCA (retained 22 PC’s after check of ElbowPlot), clustered the data using Seurat’s FindClusters function with a resolution of 0.2, and subsetted the dataset to T cells by removing two clusters that were not enriched for the T cell genes CD3E, CD4, CD8A, or TRAC.
This resulted in a dataset with 28,646 cells by 15,904 genes. We then repeated the above procedure from SCTransform to clustering using 23 PC’s.
We then limited the dataset to samples from the PBMC, the MLR experiments, and the GVHD target organs. We then removed genes present in less than 5 cells, resulting in a dataset with 23,618 cells by 15,195 genes. This dataset was normalized using the same pipeline previously described, retaining 22 PC’s from the PCA.
Genome_build: MMul 10
Supplementary_files_format_and_content: h5 matrix of single-cell RNA-Seq

organism: Macaca mulatta

source_name: T Cells obtained from Spleen

extract_protocol:
Blood and MLR Samples: RM PBMCs were isolated from whole blood by Ficoll gradient centrifugation, and then used for MLR assays either immediately, or after liquid nitrogen cryopreservation in 10% dimethyl sulfoxide (DMSO)/90% fetal bovine serum (FBS). Frozen samples were thawed using RPMI-1640 media prior to resuspension in X-vivo-15 medium (BioWhitaker) supplemented with with 10% FBS (Irvine Scientific) for MLR incubation. At the time of the MLR, stimulator PBMCs were irradiated with 3500 cGy of (137Cs) radiation. Responder PBMCs were stained with cell trace violet (CTV, Invitrogen) as per manufacturer’s instructions. 2× 105 T cell-enriched responder PBMCs along with an equal number of stimulator PBMCs were added to each well in a 96-well plate (Corning) in X-vivo-15 medium supplemented with 10% FBS and incubated at 37°C for a total of 5 days. Cell culture media change was performed on day 3 of the culture. At the end of 5 days, cells were stained with an extracellular antibody for CD3 (clone SP34-2), CD20 (clone 2H7) and CD14 (clone M5E2, all antibodies from BD Bioscience) for 20min at 4°C, and high-, medium- and non-proliferating CD3+ T cells (identified based on the dilution of CTV) were sorted and processed for single cell sequencing using the Chromium Next GEM Single Cell 5’ Reagent Kit with optimized RM primers as described below.
GvHD Organ Samples: Viable LIVE/DEAD Violet-negative CD45-positive cells were sorted from two out of four GVHD-derived samples into host and donor fractions, based on MAMU-A001 expression.
10x Genomics Single Cell 5’ Reagent Kit for Single-cell RNA-Seq and with custom RM primers for single-cell TCR-Seq

tag: modality

value: GEX

tag: source

value: Spleen


title: In vitro 3D EB differentiation day 60, non-replated

growth_protocol: A step-by-step protocol describing the differentiation procedure has been reported previously (Plaza Reyes et al., 2020a, 2020b). hESCs were plated at a cell density of 2.4x104 cells/cm2 on hrLN-521 (20 μg/mL) using NutriStem hPSC XF medium. A Rho-kinase inhibitor (Millipore, Y-27632) at a concentration of 10 μM was added during the first 24h, while cells were kept at 37°C, 5% CO2/5% O2. After 24h, hPSC medium was replaced with differentiation medium NutriStem hPSC XF without bFGF and TGFβ and cells were placed at 37°C, 5% CO2/21%O2. From day 6 after plating, 100 ng/mL of Activin A (R&D Systems, 338-AC-050) was added to the media. Cells were fed three times a week and kept for 60 days. Cells were not replated after 30 days as in the standard protocol.


title: Lib_FUN-08


title: Embryo stage 12-14 chiffon FLWF24_rep1

value: Embryo stage 12-14


title: mESC_Chr_rep 1_Small

description:
small RNA (ribominus)
Chromatin-associated small RNA im mESC biological replicate 1


title: In vitro 3D EB differentiation day 38, non-replated


title: Lib_FUN-07


title: Embryo stage 12-14 chiffon FL_rep3

value: chiffon FL


title: Lib_FUN-06

source_name: CD Colon HILEC

value: Colon


title: In vitro hESC-RPE differentiation days 60 (KARO1)

source_name: In vitro hESC-derived culture (KARO1)

growth_protocol: A step-by-step protocol describing the differentiation procedure has been reported previously (Plaza Reyes et al., 2020a, 2020b). hESCs were plated at a cell density of 2.4x104 cells/cm2 on hrLN-521 (20 μg/mL) using NutriStem hPSC XF medium. A Rho-kinase inhibitor (Millipore, Y-27632) at a concentration of 10 μM was added during the first 24h, while cells were kept at 37°C, 5% CO2/5% O2. After 24h, hPSC medium was replaced with differentiation medium NutriStem hPSC XF without bFGF and TGFβ and cells were placed at 37°C, 5% CO2/21%O2. From day 6 after plating, 100 ng/mL of Activin A (R&D Systems, 338-AC-050) was added to the media. Cells were fed three times a week and kept for 30 days. Monolayers were then trypsinized using TrypLE Select (ThermoFisher Scientific, 12563011) for 10 min at 37°C, 5% CO2. The enzyme was carefully removed and the cells were collected in fresh pre-warmed NutriStem hPSC XF medium without bFGF and TGFβ by gentle pipetting to obtain a single cell suspension. Cells were centrifuged at 300 g for 4 min, the pellet was resuspended, passed through a cell strainer (ø 40 μm, VWR, 732-2757) and seeded on laminin coated dishes (hrLN-521 at 20μg/mL) at different cell densities ranging from 1.4x106 to 1.4x104 cells/cm2. Replated cells were fed three times a week during the subsequent 30 days with NutriStem hPSC XF medium without bFGF and TGFβ.


title: Lib_FUN-05

value: HILEC


title: DETC Tcrd-/- C

city: Hannover

first: Christoph

last: Binz

state: Niedersachsen

address: Carl-Neuberg-Straße 1

department: Institut für Immunologie

country: Germany

institute: Medizinische Hochschule Hannover

data_processing:
Fastq files were obtained after demultiplexing, basecalling and quality filtering during the sequencing run on a MiSeq machine.
Data were aligned to the IMGT database from 22.05.2018 using MiXCR (Bolotin, D. A., S. Poslavsky, I. Mitrophanov, M. Shugay, I. Z. Mamedov, E. V. Putintseva, and D. M. Chudakov. 2015. MiXCR: software for comprehensive adaptive immunity profiling. Nature methods 12: 380-381.)
Afterwards the samples were analyzed using VDJTOOLS (Shugay, M., D. V. Bagaev, M. A. Turchaninova, D. A. Bolotin, O. V. Britanova, E. V. Putintseva, M. V. Pogorelyy, V. I. Nazarov, I. V. Zvyagin, V. I. Kirgizova, K. I. Kirgizov, E. V. Skorobogatova, and D. M. Chudakov. 2015. VDJtools: Unifying Post-analysis of T Cell Receptor Repertoires. PLoS Comput. Biol. 11: e1004503.) and OLGA (Sethna, Z., Elhanati, Y., Callan, C. G., Walczak, A. M. & Mora, T. OLGA: Fast computation of generation probabilities of B-and T-cell receptor amino acid sequences and motifs. Bioinformatics 35, 2974–2981 (2019)).
Supplementary_files_format_and_content: VDJTOOLS.txt files were generated using MiXCR.

source_name: ear skin_DETC Tcrd-/-

extract_protocol:
The desired populations were sorted and the RNA was isolated employing the "RNeasy Plus Micro kit" from Qiagen (Hilden, Germany).
The cDNA was generated by employing ingredients from the TAKARA cDNA Synthesis Kit (TAKARA Bio Europe, France) according to an in-house modified protocol based on the manufacturer’s protocol. The DNA-amplicons for the Illumina sequencing were generated by using Advantage 2 PCR Kit (TAKARA Bio Europe, France). The DNA was then purified using Qiaquick Gel Extraction Kit (Qiagen Hilden, Germany). The purified product of each sample was indexed by an indexing-PCR with Nextera-Primers. Finally a pool of the samples was sequenced employing Illumina MiSeq v2 Reagent Kit (Illumina Inc, San Diego, CA, USA).

tag: strain/genotype

value: B6.129P2-Tcrdtm1Mom/J (Tcrd-/-)

value: ear skin

tag: group

value: TRB


title: In vitro 3D EB differentiation days 7, 14, 28

description: CellPlex; CMO301 (EB_D28), CMO302 (EB_D14), CMO303 (EB_D7)

source_name: In vitro hESC-derived embryoid body culture

growth_protocol: For hPSC-RPE in vitro differentiation in 3D suspension embryoid bodies see our previous publication (Plaza Reyes et al., 2016).


title: Embryo stage 12-14 chiffon FL_rep1


title: DETC Tcrd-/- B


title: In vitro hESC-RPE differentiation days 38, 45 (KARO1)

description: CellPlex; CMO308 (KARO1_D45), CMO309 (KARO1_D38)


title: Lib_FUN-04


title: Embryo stage 12-14 chiffon null_rep4

value: chiffon null mutant


title: dermal Tcrd-/- CD103hi

source_name: ear skin_dermal Tcrd-/- CD103hi


title: Embryo stage 12-14 chiffon null_rep3


title: In vitro hESC-RPE differentiation days 7, 14 (KARO1)

description: CellPlex; CMO305 (KARO1_D14), CMO304 (KARO1_D7)


title: dermal Tcrd-/- CD103+

source_name: ear skin_dermal Tcrd-/- CD103+


title: Embryo stage 12-14 chiffon null_rep2

source_name: Drosophila embryo


title: In vitro hESC-RPE differentiation day 60 (NCAM1-High-sorted, CD140b-High-sorted, Unsorted)

description: CellPlex; CMO301 (Unsorted_D60), CMO302 (CD140b-High_D60), CMO303 (NCAM1-High_D60)


title: shCBX82

city: Tianjin

first: Chenghao

last: Xuan

address: 22 Qixiangtai Road

country: China

institute: Tianjin Medical University

data_processing:
Adapters and low-quality sequences were trimmed using Trimmomatic (0.36).
Trimmed reads were mapped to the human genome (UCSC hg38) using STAR (2.6.1d) with the following parameters: --outSAMtype BAM SortedByCoordinate --outSAMattributes All --chimSegmentMin 10 --outSAMattrIHstart 0 --outWigStrand Stranded --outSAMstrandField intronMotif --quantMode GeneCounts
Gene expression levels were quantified as read counts and FPKM. Unstranded read counts was directly collected from STAR output. FPKM was calculated by dividing read count by the gene length and the total number of reads mapped to protein-coding genes, according to the formula in GDC mRNA Analysis Pipeline.
edgeR (3.22.5) was used to perform different gene expression analyses
Genome_build: hg38
Supplementary_files_format_and_content: FPKM for every gene and every sample was calculated as descirbed above
Supplementary_files_format_and_content: Read counts for every gene and every sample was calculated by STAR (2.6.1d)

source_name: human ovarian cancer cell

growth_protocol: SKOV3 cells were cultured in Dulbecco's modified Eagle’s medium supplemented with 10% fetal bovine serum at 37 ℃ in a humidified atmosphere with 5% CO2.

extract_protocol:
RNA was harvested using Trizol reagent.
RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: The lentiviruses expressing control or shCBX8 shRNA were employed to infect SKOV3 cells to obtain stable expression cells

value: ovary

value: human ovarian cancer cell

tag: treatment

value: CBX8 shRNA2


title: Lib_FUN-02


title: dermal Tcrd-/- B

source_name: ear skin_dermal Tcrd-/-


title: Lib_FUN-01


title: Embryo stage 12-14 chiffon null_rep1


title: Embryo stage 12-14 chiffon FL_rep2


title: dermal Tcrd-/- A


title: pLN Tcrd-/-

source_name: peripheral lymph-node_pLN Tcrd-/-

value: peripheral lymph-node


title: PLKONC

value: control


title: DETC Tcrd-/- A


title: Embryo stage 12-14 WT_rep3

value: Embryo stage 12-15

value: WT (elav-gal4 x GFP)


title: Embryo stage 12-14 WT_rep2


title: dermal WT beta

source_name: ear skin_dermal WT beta

value: C57BL/6-N/Crl (WT)


title: siNEK2 1

first: Pierre

last: de la Grange

address: 29, rue du Faubourg Saint-Jacques

department: Paris Biotech Santé

institute: GenoSplice technology

data_processing:
Sequencing, data quality, reads repartition (e.g., for potential ribosomal contamination), and insert size estimation were performed using FastQC, Picard-Tools, Samtools and rseqc
Reads were mapped using STAR_2.4.0
Genome_build: hg19
Supplementary_files_format_and_content: Tab-delimited text file includes deseq2 normalized expression values for each gene and for each sample. Annotations from Human FAST DB v2016_1 were also provide

growth_protocol: MDA-MB-231 breast cancer cells were cultured in Dulbecco's Modified Eagle Medium, high-glucose, 25mM Hepes, containing 10% FBS and 1%Penicillin/streptomycin.

extract_protocol:
RNA was extracted and DNAse treated using the miRNeasy Mini Kit (Qiagen).
Libraries were prepared using the TruSeq Stranded mRNA kit protocol (Illumina technology) with an input total RNA of 1µg

treatment_protocol: MDA-MB-231 cells were transfected twice with control or NEK2-targeting siRNAs, using  Lipofectamine RNA iMAX (Thermofisher) according to manufacturer's protocol, and harvested 24h after the second round of transfection.

value: breast cancer cell line

value: transfected with NEK2 targeting siRNA


title: DETC WT gamma

source_name: ear skin_DETC WT gamma

value: TRG


title: Embryo stage 12-14 WT_rep4

value: Embryo stage 12-14


title: siCTRL 3

value: transfected with no-targeting control siRNA


title: Lib_FUN-03

value: CD

value: Colon

value: HILEC


title: siNEK2 2


title: 7SNB

city: Portland

first: Timothy

middle: J

last: Nice

state: OR

address: 3181 SW Sam Jackson Park Rd

department: Molecular Microbiology and Immunology

institute: Oregon Health & Science University

data_processing:
Reads were aligned to the human reference genome using STAR version 2.5.3a
Total read counts for annotated genes were determined using the featureCounts program.
Genome_build: GRCh38 version 89
Supplementary_files_format_and_content: count matrix output from featureCounts program

source_name: IEC organoid

growth_protocol: Organoid generation and maintenance was performed as previously described (VanDussen et al., 2015, doi:10.1136/gutjnl-2013-306651).

extract_protocol:
RNA was isolated from cells using the ZR Viral RNA Kit (Zymoresearch)
mRNA sequencing libraries were prepared using the Ilumina Stranded polyA+ Library Prep Kit

treatment_protocol: Recombinant cytokines purchased from the following suppliers were added to culture media: IFN-β1a (Sigma, #IF014); IFN-γ (Sigma, #I17001); IFN-λ2 (IL28b; Sigma #I1288);

tag: subject

tag: biopsy site

value: sigmoid colon


title: Input

city: Tokyo

first: Takuro

last: Nakamura

address: 3-8-31 Ariake, Koto-ku

department: The Cancer Institute

country: Japan

institute: Japanese Foundation for Cancer Research

library_source: genomic

data_processing:
Base calls were performed using Bowtie 1.1.1.
ChIP-seq reads were aligned to the mm9 genome assembly using samtools 1.2.
Peak call was performed using MACS1.4.
Genome_build: mm9
Supplementary_files_format_and_content: tdf file:  For every 300 bp window, the mapped tag count for ChIP, Cc and that for Input, Ci were used for calculation. Ec and Ei indicates the estimate count for 300 bp window for ChIP and Input. Signal ratio of ‘target TF’ was calculated as, Cc/Ec + 1 ÷ Max(1, Ci/Ei + 1).

molecule: genomic DNA

source_name: Trib1/Bcl11a AML

growth_protocol: AML cells are maintained in IMDM supplemented with 10% FBS and 5 ng/ml IL3

extract_protocol:
Lysates were clarified from sonicated nuclei and immunoprecipitated with each antibodies
Libraries were prepared according to Illumina's instructions accompanying the ThruPLEX DNA-seq 6S (12) Kit (R400523). Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (32 to 52 exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation DNA was PCR amplified with Illumina primers for 15 cycles and library fragments of ~250 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on an Illumina instrument following the manufacturer's protocols.

treatment_protocol: Trib1 and Bcl11a cDNAs were introduced by retrovirus-mediated gene transfer

value: Trib1- and Bcl11a-expressing murine AML cells

tag: chip antibody


title: 7SNC


title: 7SNA


title: Embryo stage 12-14 WT_rep1

tag: developmental stage


title: siCTRL 2


title: H3K27ac

value: Histone H3K27ac (Active Motif, catalog# 39133, lot# 28518012)


title: Embryo stage 12-14 Ada2b-PA + Ada2b_PB_rep4

value: ada2b_PA + ADa2b_PB


title: shCBX81

tag: tissue

value: ovary

value: human ovarian cancer cell

value: CBX8 shRNA1


title: Embryo stage 12-14 Ada2b-PA + Ada2b_PB_rep3


title: PU.1

value: PU.1 (Cell Signaling. catalog# 2258, lot# 3)


title: siCTRL 1

tag: cell type


title: siNEK2 3


title: 7SLB

value: IFN-III


title: Embryo stage 12-14 Ada2b-PA + Ada2b_PB_rep2


title: 7SLA


title: 10nM MT rep2

city: Wuhan

first: Zhulong

last: Chan

state: Hubei Province

address: No. 1, Shizishan St, Nanhu

department: College of Horticulture and Forestry Sciences

institute: Huazhong Agricultural University

data_processing:
Illumina Casava1.7 software used for base calling.
Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts. In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data. At the same time, Q20, Q30and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality.
Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using Bowtie v2.2.3 and paired-end clean reads were aligned to the reference genome using TopHat v2.0.12. We selected TopHat as the mapping tool for that TopHat can generate a database of splice junctions based on the gene model annotation file and thus a better mapping result than other non-splice mapping tools.
HTSeq v0.6.1 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene. FPKM, expected number of Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced, considers the effect of sequencing depth and gene length for the reads count at the same time, and is currently the most commonly used method for estimating gene expression levels
Differential expression analysis of MT or IAA treatment vs control (two biological replicates) was performed using the DESeq R package (1.18.0). DESeq provide statistical routines for determining differential expression in digital gene expression data using a model based on the negative binomial distribution. The resulting P-values were adjusted using the Benjamini and Hochberg’s approach for controlling the false discovery rate . Genes with an adjusted P-value <0.05 found by DESeq were assigned as differentially expressed
Supplementary_files_format_and_content: raw counts of sequencing reads

organism: Arabidopsis thaliana

source_name: seedlings

growth_protocol: Arabidopsis seeds were surface-sterilized with 2%(v/v) sodium hypochlorite (NaClO) containing 0.1%(v/v) TritonX-100 for 3 minutes, then washed for five times with sterile water and sown on plates containing Murashige and Skoog (MS) medium with 3%（w/v) sucrose and 0.8% (w/v) agar. After 3 days stratification at 4oC in the dark, plates were transferred to a growth chamber. The growth chamber was set at 23oC with 16 hours light and 8 hours dark cycles, 100 µmol photons m−2 s−1 light intensity and 60% relative humidity.

extract_protocol:
The seedlings of control and MT or IAA treated Col plants were collected for RNA isolation following the standard Qiagen RNeasy mini kit protocol. RNA purity and integrity was checked using the NanoPhotometer® spectrophotometer (IMPLEN, CA, USA) and RNA Nano 6000 Assay Kit of the Bioanalyzer 2100 system (Agilent Technologies, CA, USA), respectively.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: MT and IAA were dissolved in 100% ethanol (v/v) to obtain stock concentrations which were further diluted to the desired working concentrations. Ethanol with the final concentration of 0.1% was used as control treatment.  Four-day-old Arabidopsis seedlings on control MS medium plates were transferred to MS plates containing MT or IAA.

value: seedlings

tag: treatment time

value: 72h after MT treatment

value: WT


title: Bcl11a

tag: strain

value: Bcl11a ( Abcam, catalog# ab191401, lot# GR3260079-1)


title: Embryo stage 12-14 Ada2b-PA + Ada2b_PB_rep1

value: Embryo stage 12-14

tag: genotype


title: 7SGC

value: IFN-II


title: 1nM IAA rep2

value: 72h after IAA treatment


title: Embryo stage 12-14 Ada2b-PB_rep4


title: 10nM MT rep1


title: 1nM IAA rep1


title: 7SLC


title: 72h without treatment control rep2

value: 72h without treatment


title: 7SBC

value: sigmoid colon

value: IFN-I


title: 72h without treatment control rep1


title: Embryo stage 12-14 Ada2b-PB_rep1


title: Embryo stage 12-14 Ada2b-PA_rep4


title: 7SBB


title: Embryo stage 12-14 Ada2b-PA_rep3


title: 7SBA


title: 7SGA


title: 1000µM melatonin rep1

data_processing:
Illumina Casava1.7 software used for base calling.
Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts. In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing poly-N and low quality reads from raw data. At the same time, Q20, Q30and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality.
Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using Bowtie v2.2.3 and paired-end clean reads were aligned to the reference genome using TopHat v2.0.12. We selected TopHat as the mapping tool for that TopHat can generate a database of splice junctions based on the gene model annotation file and thus a better mapping result than other non-splice mapping tools.
HTSeq v0.6.1 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene. FPKM, expected number of Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced, considers the effect of sequencing depth and gene length for the reads count at the same time, and is currently the most commonly used method for estimating gene expression levels
Differential expression analysis of two conditions/groups (two biological replicates per condition) was performed using the DESeq R package (1.18.0). DESeq provide statistical routines for determining differential expression in digital gene expression data using a model based on the negative binomial distribution. The resulting P-values were adjusted using the Benjamini and Hochberg’s approach for controlling the false discovery rate . Genes with an adjusted P-value <0.05 found by DESeq were assigned as differentially expressed
Genome_build: TAIR10
Supplementary_files_format_and_content: raw counts of sequencing reads

source_name: leaf

extract_protocol:
The rosette leaves  were collected for RNA isolation following the standard Qiagen RNeasy mini kit protocol. RNA purity and integrity was checked using the NanoPhotometer® spectrophotometer (IMPLEN, CA, USA) and RNA Nano 6000 Assay Kit of the Bioanalyzer 2100 system (Agilent Technologies, CA, USA), respectively.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: leaf

value: 12h after 1000microM melatonin treatment


title: 1000µM melatonin rep2


title: 5SNC

value: control


title: Embryo stage 12-14 Ada2b-PA_rep2


title: 5SNB


title: 100µM melatonin rep2

value: 12h after 100microM melatonin treatment


title: Embryo stage 12-14 Ada2b-PB_rep3


title: Embryo stage 12-14 Ada2b-PA_rep1


title: 100µM melatonin rep1


title: 7SGB


title: Embryo stage 12-14 Ada2b-PB_rep2


title: control rep2

value: 12h without melatonin treatment


title: Embryo stage 12-14 ada2b null_rep4

value: ada2b null mutant


title: 5SLC

value: IFN-III


title: 5SNA


title: control rep1


title: 5SLA


title: Embryo stage 12-14 ada2b null_rep3


title: vehicle-treated, rep 3

city: Freiburg

first: Geoffroy

last: Andrieux

address: Breisacherstr 153

institute: University clinics Freiburg

description:
Gene expression from WT mouse CXCL12-abundant reticular cells
vehicle_59

hyb_protocol: Labeled fragments were hybridized to Affymetrix Mouse Gene ST 1.0 arrays for 16h at 45°C with 60 rpm in an Affymetrix Hybridization oven 645.

scan_protocol: After washing and staining, the arrays were scanned with the Affymetrix GeneChip Scanner 3000 7G. CEL-files were produced from the raw data with Affymetrix GeneChip Command Console Software.

data_processing: CEL files were analysed using the oligo R package. RMA method, log2 transformed were used to normalized the probe intensities.

source_name: small intestine, mice treated with vehicle, d14 after allo-HCT

label_protocol: We used the Affymetrix WT Pico kit for cDNA synthesis, amplification, and second-cycle cDNA synthesis, as well as fragmentation and labeling with Biotin, as described by the manufacturer.

growth_protocol: BALB/c mice were subjected to total body irradiation and were injected with 5x10e6 BM cells and 3x10e5 T cells from a C57BL/6N donor. Mice were kept under standard pathogen-free conditions for 14 days after transplantation.

extract_protocol: RNA was isolated using the miRNeasy Mini Kit from Qiagen according to the manufacturer's instructions.

treatment_protocol: Mice were treated with 200 mg/kg body weight TUDCA (dissolved in aqua ad iniectabilia) or an equal volume (200 µl) of vehicle by a daily intraperitoneal injection.

value: small intestine

value: BALB/c

value: wild type


title: vehicle-treated, rep 5

description:
Gene expression from WT mouse CXCL12-abundant reticular cells
vehicle_153

value: treated with vehicle, d14 after allo-HCT


title: vehicle-treated, rep 4

description:
Gene expression from WT mouse CXCL12-abundant reticular cells
vehicle_60


title: vehicle-treated, rep 1

description:
Gene expression from WT mouse CXCL12-abundant reticular cells
vehicle_57


title: vehicle-treated, rep 6

description:
Gene expression from WT mouse CXCL12-abundant reticular cells
vehicle_155


title: vehicle-treated, rep 2

description:
Gene expression from WT mouse CXCL12-abundant reticular cells
vehicle_58


title: TUDCA-treated, rep 6

description:
Gene expression from WT mouse CXCL12-abundant reticular cells
drug_166

source_name: small intestine, mice treated with TUDCA, d14 after allo-HCT

value: treated with TUDCA, d14 after allo-HCT


title: TUDCA-treated, rep 5

description:
Gene expression from WT mouse CXCL12-abundant reticular cells
drug_165


title: TUDCA-treated, rep 4

description:
Gene expression from WT mouse CXCL12-abundant reticular cells
drug_164


title: 5SGB

value: IFN-II


title: 5SGC


title: Embryo stage 12-14 chiffon FL_rep3 H3k14ac

data_processing:
Illumina Casava software used for basecalling.
Sequenced reads were trimmed for adaptor sequence with Trimmomatic, then mapped to dm6 whole genome and yeast using Bowtie2 (v2.3.5.1) using -sensitive settings.
scaleFactor was calculated as in Orlando et al. 2014. "Quantitative ChIP-Seq normalization reveals global modulation of the epigenome"
Bam files were used to normalize to spike-in controls (yeast) using bamCoverage(deepTools) to generate bigwig files.
Genome_build: dm6 (drosophila), S288C (yeast)
Supplementary_files_format_and_content: Bigwig files already normalized to spike-in control

extract_protocol:
Protein-DNA complexes were eluted from the magnetic beads with Elution buffer (1X TE, 1% SDS, 250 mM NaCl), treated with RNAse A (ThermoFisher #EN0531) at 37°C for 30 min and Proteinase K (ThermoFisher #AM2546) at 55°C overnight. DNA purification was performed using Zymo Research  194 ChIP DNA clean & concentrator kit (Zymo Research, Catalog #D5205)
Libraries were prepared following the Ovation Ultralow library system (NuGEN) with unique dual indices for multiplexing

value: Embryo stage 12-14

value: chiffon FL

value: H3K14ac (rabbit; 07353, Millipore)


title: Embryo stage 12-14 ada2b null_rep1


title: Embryo stage 12-14 chiffon FL_rep2 H3k14ac


title: Embryo stage 12-14 ada2b null_rep2


title: Rec12_wt

type: genomic

city: New York

first: Shintaro

last: Yamada

state: New York

address: 1275 York Avenue

department: MOLECULAR BIOLOGY PROGRAM

institute: MEMORIAL SLOAN-KETTERING CANCER CENTER

description: Rec12 / WCE, meiosis 5h, wild type cells.

hyb_protocol: 16 h at 45C using a hybridization oven 640 (Affymetrix) as described in the Affymetrix Chromatin Immunoprecipitation Assay Protocol (P/N 702238).

scan_protocol: Fluidics Station 400 protocol EukGE-WS2v5 (Affymetrix) was performed to wash and stain arrays. The arrays were scanned on GeneChip Scanner 3000 7G (Affymetrix).

data_processing:
Data were quantile normalized and smoothed with Affymetrix Tiling Analysis Software.
Processed data files: *.bar

label: biotin

organism: Schizosaccharomyces pombe

source_name: FLAG ChIP DNA from rec12+-FLAG wild type cells harvested 5h after meiosis induction

label_protocol: Amplified DNA were labeled with biotin as described (Katou et al., Nature 424:1078-83).

growth_protocol: Cells in a pat1-114 background were induced to enter meiosis by the haploid meiosis system, and harvested four or five hours after the induction.

extract_protocol: Cells were crosslinked with formaldehyde and ChIPs were performed as previously described (Yamada et al., EMBO J 23: 1792-803) except for using anti-FLAG antibodies from Sigma-Aldrich.

tag: genotype/variation

value: pat1-114 rad50S rec12+-FLAG wild type

value: meiosis induction

value: anti-FLAG

source_name: Input DNA from pat1-114 cells in the wild-type background harvested 4h after meiosis induction

value: pat1-114 wild type


title: 5SGA

value: sigmoid colon


title: Rec12_pht1D

description: Rec12 / WCE, meiosis 5h, pht1D cells.

source_name: FLAG ChIP DNA from rec12+-FLAG pht1 deletion cells harvested 5h after meiosis induction

value: pat1-114 rad50S rec12+-FLAG pht1 deletion


title: TUDCA-treated, rep 3

description:
Gene expression from WT mouse CXCL12-abundant reticular cells
drug_163


title: TUDCA-treated, rep 2

description:
Gene expression from WT mouse CXCL12-abundant reticular cells
drug_70


title: 5SBB

value: IFN-I


title: Embryo stage 12-14 chiffon null_rep3 H3k14ac

value: chiffon null mutant


title: Embryo stage 12-14 chiffon null_rep2 H3k14ac


title: 5SBC


title: 5INF

value: ileum

value: control


title: Embryo stage 12-14 chiffon null_rep1 H3k14ac


title: Embryo stage 12-14 chiffon FL_rep3 H3

value: H3 (rabbit; ab1791, Abcam)


title: Embryo stage 12-14 chiffon FL_rep2 H3


title: 5INE


title: 5SBA


title: 5IND


title: TUDCA-treated, rep 1

description:
Gene expression from WT mouse CXCL12-abundant reticular cells
drug_67

value: small intestine

value: BALB/c

value: wild type


title: TB14-4

description: Gene expression data from mouse AML

hyb_protocol: Following fragmentation, 7.5 ug of aRNA were hybridized for 16 hr at 45C on GeneChip Mouse Genome 430 PM Array. GeneChips were washed and stained in the Affymetrix GeneAtlas Fluidics Station.

scan_protocol: GeneChips were scanned using the Affymetrix GeneAtlas Imaging Station.

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100.

source_name: AML cell line expressing Trib1 and Bcl11a

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 100 ng total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: Trib1, TB13 and TB14 cells were grown in IMDM supplemented with 10% fetal bovine serum, and 5 ng/ml IL-3.

extract_protocol: Total RNA was purified using RNA Easy kit (QIAGEN) according to the manufacturer's protocol

treatment_protocol: No treatment was provided.

tag: cell line

value: Trib1- and Bcl11a-expressing murine AML cells


title: Embryo stage 12-14 chiffon FL_rep1 H3

value: Embryo stage 12-14

value: chiffon FL


title: Embryo stage 12-14 chiffon FL_rep1 H3k14ac

value: H3K14ac (rabbit; 07353, Millipore)


title: Embryo stage 12-14 chiffon null_rep3 H3


title: TB14-3

description: Gene expression data from mouse AML


title: TB14-2

description: Gene expression data from mouse AML


title: Embryo stage 12-14 chiffon null_rep2 H3


title: TB14-1

description: Gene expression data from mouse AML


title: 5INA


title: 5INC


title: TB13-2

description: Gene expression data from mouse AML


title: TB13-4

description: Gene expression data from mouse AML


title: Embryo stage 12-14 chiffon null_rep1 H3


title: 5INB


title: LPPA5

city: Cleveland

first: Pratima

last: Karnik

state: Ohio

address: 10900 Euclid Ave., BRB547A

department: Dermatology

institute: Case Western Reserve University

description: Gene expression data from occipital skin biopsy of individuals with LPP from affected area

hyb_protocol: 15 ug of biotinylated cRNA were fragmented and added to a hybridization cocktail along with bacterial hybridization controls and buffers.This hybridization cocktail was hybridized  overnight at 45°C at  to the U133 plus 2.0 Affymetrix human 3’-array chips in a Genechip Hybridization Oven 320. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Affymetrix Genechip 3000 scanner A.

data_processing: The data were analyzed with Affymetrix proprietary MAS 5.0 (Microarray Suite 5.0) using Affymetrix default analysis settings and global scaling to 500 as normalization method.

source_name: Skin biopsy from occipital scalp of individuals with LPP (affected area)

label_protocol: Biotinylated cRNA were prepared according to the standard 2007 era  (3' labelling ) Affymetrix protocol from  total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

extract_protocol: The total RNA from each skin biopsy was extracted using TRIzol reagent (Life Technologies, Inc., Gaithersburg, MD, USA) per the manufacturer's instructions.

value: skin biopsy from affected area

tag: disease state

value: LPP


title: LPPA6


title: LPPA7


title: LPPA2


title: 5ILC

value: IFN-III


title: LPPA3


title: LPPA1


title: LPPA4


title: LPPU7

description: Gene expression data from occipital skin biopsy of individuals with LPP from unaffected area

source_name: Skin biopsy from occipital scalp of individuals with LPP (unaffected area)

value: skin biopsy from unaffected area


title: TB13-3

description: Gene expression data from mouse AML


title: LPPU6


title: ≥16N megakaryocytes from Pf4Cre-Srsf3fl/fl mice, replicate 3

city: Clayton

first: Minna-Liisa

last: Anko

state: VIC

address: 15 Innovation Walk

department: Department of Anatomy and Developmental Biology

country: Australia

institute: Monash University

data_processing:
For megakaryocyte data, the raw read were trimmed using Trimmomatic with default parameters. The reads were aligned with STAR to Ensembl mm10 reference genome. The aligned files were deduplicated using the Picard MarkDuplicates function, ["Picard Toolkit." 2019 Broad Institute, Github Repository. http://broadinstitute.github.io/picard/; Broad Institute]. To obtain levels of gene expression, read counts were generated with the Subread function FeatureCounts. Genes with 1 count per million (CPM) in at least two samples were kept for further analysis.  Normalisation and differential gene expression was conducted with EdgeR.
For platelet data, Torrent Suite Software v5.6 (Thermo Fisher) was used for read processing, base calling, alignment to the reference transcriptome (mm10) and gene expression counts. Differential gene expression analysis was performed using DESeq2.
Genome_build: mm10
Supplementary_files_format_and_content: .csv file containing log-fold change, p-value, FDR and read counts for DEGs

source_name: ≥16N megakaryocytes

extract_protocol:
Following fluorescence associated cell sorting based on CD41 and ploidy, low ploidy (8N only) and high ploidy (≥16N) megakaryocytes were pooled (52k±32k per sample) for RNA isolation using RNeasy Mini kit (Qiagen). RNA from washed platelets was isolated using TriReagent (Sigma-Aldrich).
Megakaryocyte RNA-seq libraries were prepared using SMARTer Stranded Total RNA Low Input Sample Prep kit (Clontech) and RNA-sequencing by Illumina HiSeq1500. Platelet RNA-seq libraries were prepared from 10ng of total RNA using an Ion AmpliSeq Transcriptome Mouse Gene Expression Kit and libraries were sequenced on an Ion Proton Sequencer (Thermo Fisher)

value: ≥16N megakaryocytes


title: 5ILB


title: LPPU5


title: LPPU4


title: Embryo stage 12-14 chiffon FL_rep2 INPUT

first: Vikki

last: Weake

address: 175 South University Street

institute: Purdue University

source_name: Drosophila embryo


title: Trib1 4

description: Gene expression data from mouse AML

source_name: AML cell line expressing Trib1

value: Trib1-expressing murine AML cells


title: Embryo stage 12-14 chiffon FL_rep3 INPUT


title: LPPU3


title: ≥16N megakaryocytes from Pf4Cre-Srsf3fl/fl mice, replicate 2


title: Embryo stage 12-14 chiffon null_rep2 INPUT

value: chiffon null mutant


title: 5IBC

value: ileum

value: IFN-I


title: Embryo stage 12-14 chiffon FL_rep1 INPUT


title: ≥16N megakaryocytes from Pf4Cre-Srsf3fl/fl mice, replicate 1


title: Embryo stage 12-14 chiffon null_rep1 INPUT


title: TB13-1

description: Gene expression data from mouse AML


title: Embryo stage 12-14 chiffon null_rep3 INPUT


title: TFAm knockdown stimulated with TGFβ rep3

city: Erlangen

first: Thuong

middle: Minh

last: Trinh

address: Ulmenweg 18

institute: University of Erlangen-Nuremberg

data_processing:
Paired-end clean reads were mapped to the reference genome (grch38) using Spliced Transcripts Alignment to a Reference (STAR) method
featureCounts function in useGalaxy platform was used to count the read numbers mapped of each gene, including known and novel genes
Genome_build: grch38
Supplementary_files_format_and_content: text document containing raw counts from each sample

source_name: Primary dermal fibroblast

growth_protocol: The fibroblasts were cultured in DMEM/F12 with 10% FBS, 1% penicillin-streptomycin, 2 mM l-glutamine and 2.5 μg ml−1 amphotericin B until reaching 90% confluence. Cells were transfected with TFAM siRNA or non-target siRNA then seeded to 6-well plate (3x105 cells per well). Incubate the plate for 24 hours at 37oC, 5% CO2.

extract_protocol:
Total RNA was extracted from adherent cells using the Nucleo Spin RNA isolation kit (Macherey-Nagel).
A total amount of 1 μg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample. Briefly, mRNA was purified from total RNA using poly-T oligo-attached magnetic beads. Fragmentation was carried out using divalent cations under elevated temperature in NEBNext First Strand Synthesis Reaction Buffer (5X). First strand cDNA was synthesized using random hexamer primer and M-MuLV Reverse Transcriptase (RNase H-). Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and RNase H. Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. After adenylation of 3’ ends of DNA fragments, NEBNext Adaptor with hairpin loop structure were ligated to prepare for hybridization. In order to select cDNA fragments of preferentially 150~200 bp in length, the library fragments were purified with AMPure XP system (Beckman Coulter, Beverly, USA). Then 3 μl USER Enzyme (NEB, USA) was used with size-selected, adaptorligated cDNA at 37 °C for 15 min followed by 5 min at 95 °C before PCR. Then PCR was performed with Phusion High-Fidelity DNA polymerase, Universal PCR primers and Index (X) Primer. At last, PCR products were purified (AMPure XP system) and library quality was assessed on the Agilent Bioanalyzer 2100 system.

treatment_protocol: Starve the cells with serum-free DMEM/F12 for 24 hours at 37oC, 5% CO2. Stimulate the cells with TGFβ  (10ng/mL at final concentration) for 24 hours at 37oC, 5% CO2.

value: Primary dermal fibroblast

value: TGFbeta

tag: batch of rna isolation

tag: knockdown target

value: TFAM siRNA

tag: donor fibroblasts

value: Donor 3


title: ≥16N megakaryocytes from Cre-negative control mice, replicate 3

value: Cre- control


title: ≥16N megakaryocytes from Cre-negative control mice, replicate 1


title: 8N megakaryocytes from Pf4Cre-Srsf3fl/fl mice, replicate 3

source_name: 8N megakaryocytes

value: 8N megakaryocytes


title: Control stimulated with TGFβ rep3

value: non-target siRNA


title: 5ILA

source_name: IEC organoid


title: TFAm knockdown rep3

value: PBS


title: 8N megakaryocytes from Pf4Cre-Srsf3fl/fl mice, replicate 2


title: 5IBA


title: 5IBB


title: LPPU2


title: ≥16N megakaryocytes from Cre-negative control mice, replicate 2


title: Trib1 2

description: Gene expression data from mouse AML


title: Trib1 3

description: Gene expression data from mouse AML


title: 8N megakaryocytes from Pf4Cre-Srsf3fl/fl mice, replicate 1


title: Trib1 1

description: Gene expression data from mouse AML


title: CCCAA1

description: Gene expression data from occipital skin biopsy of individuals with CCCA from affected area

source_name: Skin biopsy from frontal scalp of individuals with CCCA (affected area)

value: skin biopsy from affected area

value: CCCA


title: LPPU1

value: LPP


title: CCCAA2


title: CCCAA3


title: TFAm knockdown stimulated with TGFβ rep2

value: Donor 2


title: Control rep3


title: 8N megakaryocytes from Cre-negative control mice, replicate 3


title: Control stimulated with TGFβ rep2


title: CCCAU2

description: Gene expression data from occipital skin biopsy of individuals with CCCA from unaffected area

source_name: Skin biopsy from occipital scalp of individuals with CCCA (unaffected area)

value: skin biopsy from unaffected area


title: Linc01133 overexpression

city: Jinan

first: Yujing

last: Sun

state: Shandong

address: 44 Wen Hua Xi Road

department: Department of pathology

institute: School of Basic Medical Sciences, Shandong University

data_processing:
Perl script was used to  filter the original data and to get the clean data. Steps are:1.Trim Smart-seq2 public primer sequence from the Reads ; 2. Remove the contaminated reads for adapters ;3. Remove the low quality reads; 4.Remove the reads whose N base more than 5% for total bases .
Reference genomes and the annotation file were downloaded from ENSEMBL database. Bowtie2 v2.2.3 was used for building the genome index, and Clean Data was then aligned to the reference genome using HISAT2 v2.1.0.
Reads Count for each gene in each sample was counted by HTSeq v0.6.0, and FPKM was then calculated to estimate the expression level of genes in each sample
Genome_build: GRCh38.94.chr
Supplementary_files_format_and_content: FPKMs

source_name: human gastric cancer cell line

growth_protocol: HGC27 cells were cultured in RPMI-1640 medium (HyClone, Logan, UT, USA) supplemented with 10% fetal bovine serum (Gibco) and were incubated at 37 °C in a humidified incubator at 5% CO2.

extract_protocol:
Total RNA were extracted using Trizol reagent (TaKaRa, Dalian, China) according to the manufacturer's instruction. mRNA was purified from total RNA using poly-T oligo-attached magnetic beads.
Sequencing libraries were generated using NEBNext® Ultra™ RNA Library Prep Kit for Illumina® (#E7530L, NEB, USA) following the manufacturer’s recommendations a

treatment_protocol: HGC27 cells were transfected by Turbofect with pcDNA3.1-control or  pcDNA3.1-linc01133  48h before harvest

value: human gastric cancer cell line

tag: passage

value: linc01133 overexpression


title: K6H

city: Sendai

first: Shin

last: Hamada

state: Miyagi

address: 1-1 Seiryo-machi, Aobaku

department: Division of Gastroenterology

institute: Tohoku University Graduate School of Medicine

hyb_protocol: cRNA was hybridized to a 60K 60-mer oligomicroarray (SurePrint G3 Mouse Gene Expression Microarray 8x60K v2 ; Agilent Technologies) according to the manufacturer's instructions.

scan_protocol: The hybridized microarray slides were scanned using an Agilent scanner. The relative hybridization intensities and background hybridization values were calculated using Feature Extraction Software version 9.5.1.1 (Agilent Technologies).

data_processing: The scanned images were analyzed with Feature Extraction Software 9.5.1.1 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities. The raw signal intensities and flags for each probe were calculated from the hybridization intensities and spot information according to the procedures recommended by Agilent Technologies using the Flag criteria in the GeneSpring Software. The raw signal intensities of all samples were  normalized by the quantile algorithm with the Bioconductor.

source_name: mouse cancer cell, treated with halofuginone 100 nM for 24 hours

label_protocol: cRNA was amplified and labelled using a Low input Quick Amp Labelling Kit (Agilent Technologies).

extract_protocol: The total RNA was isolated from cells using Rneasy kit (QIAGEN).

value: pancreatic cancer


title: 8N megakaryocytes from Cre-negative control mice, replicate 2


title: Control

value: control


title: 8N megakaryocytes from Cre-negative control mice, replicate 1


title: TFAm knockdown rep2

value: Primary dermal fibroblast

tag: treatment


title: Control rep2


title: CCCAU1


title: TFAm knockdown stimulated with TGFβ rep1

value: TGFbeta

value: Donor 1


title: KO-2 RPE

first: Ching-Hwa

last: Sung

address: 1300 York Ave

institute: Weill Cornell Medicine

data_processing:
The samples were sequenced using Illumina HiSeq4000 or NovaSeq6000 sequencer with either single-read or paired-end 50 bps reads. The raw sequencing reads in BCL format were processed through bcl2fastq 2.19 (Illumina) for FASTQ conversion and demultiplexing.
The RNA reads were aligned and mapped to the GRCm38 human reference genome by STAR (Version2.5.2).
The transcriptome reconstruction was performed by Cufflinks (Version 2.1.1). The reads counts were conducted with HTSeq(Version 0.11.2).
Genome_build: GRCm38
Supplementary_files_format_and_content: tab-delimited text file include read counts at gene level for each samples

source_name: RPE

extract_protocol:
The total RNAs of the loosened mouse RPE cell pellets were isolated using the Absolutely RNA Nanoprep kit (Agilent).
The messenger RNA was prepared using the TruSeq Stranded mRNA Sample Library Preparation kit (Illumina, San Diego, CA), according to the manufacturer’s instructions.

value: Retinal pigment epithelium

tag: age

value: Best1-Cre+/-; Clic4f/f


title: KO-1 RPE


title: CCCAU3

source_name: Skin biopsy from frontal scalp of individuals with CCCA (unaffected area)


title: K6C

source_name: mouse cancer cell, control treatment


title: CreCtrl-2 RPE


title: Spinal cord-VANCO-2

city: Goettingen

first: Gabriela

last: Salinas

state: Lower-Saxony

address: Kreuzbergring 57

department: Department of Pathology

institute: Universitaetsmedizin Goettingen

data_processing:
Sequence images were transformed with Illumina software BaseCaller to BCL files, which was demultiplexed to fastq files with bcl2fastq v2.20.0.422
STAR version 2.5.2a was used to align the reads to the rn6 genome using 2 mismatches within 50 bases
featureCounts version 1.5.0-p1 was used to quantify reads for genes in rn6 version 97
Genome_build: rn6 version 97
Supplementary_files_format_and_content: Tab-delimited gene counts

organism: Rattus norvegicus

source_name: Total spinal cord

growth_protocol: not applicable

extract_protocol: RNA was extracted from TRI Reagent (Merck) according to the manufacturer’s instructions.

treatment_protocol: Spinal cord were homogenized, and myelin was removed by Percoll gradient.The pellet was then suspended in 300 µL TRI reagent (Merck) and 1 µL glycogen (Roche). The samples were stored at -80 °C until further processing. For microglial samples, spinal cord were homogenized and myelin was removed as above. Antibody-stained CD45low CD11b+ microglial cells were sorted out of the tissue and then stored in TRI reagent until further processing.

value: Spinal cord

value: Total spinal cord

value: 6-8 weeks old

value: LEW/Crl

value: wild type

value: VANCO


title: RRBS Non-Cond rep4

city: Rishon LeZion

first: Tatiana

last: Kisliouk

address: 68 HaMaccabim Road

department: Animal Sciences

country: Israel

institute: ARO

data_processing:
For RRBS, Bioinformatic trimming of Illumina adapters, as well as quality trimming, were performed with Trimmomatic. Reads were mapped to the chick genome (galGal5.0, UCSD) using Bismark (v0.22.3) bowtie mode. Differentially methylated regions (DMRs) were extracted and analyzed by Metilene (v0.2-8) package. 300-bp windows with cutoff criteria of padj less than 0.01 and minimum average difference of 0.25 were used for data analysis. DMR annotation was performed by HOMER software.
Genome_build: galGal5.0, UCSD
Supplementary_files_format_and_content: tab-delimited text files include segmented DMR avg /per group
Supplementary_files_format_and_content: tab-delimited text files include raw DMR (% methylation) per sample

organism: Gallus gallus

source_name: Anterior hypothalamus

extract_protocol:
DNA was isolated with the RNA/DNA Purification Micro Kit (Norgen Biotek, Thorold, ON, Canada)
Libraries were prepared from 15-30 ng of DNA with Zymo-Seq RRBS Library Kit (Zymo Research, Irvine, CA). The libraries were sequenced on Illumina NextSeq HO machine 75 cycles.

treatment_protocol: Chicks were heat‐conditioned on day 3 posthatch at 39°C for 24 h. One week later (day 10), LPS or saline was injected into the third ventricle. Chicks were sacrificed on day 11 and their AH dissected. Microglial cell population from hypothalamic cell pools of 10–12 chicks each was collected by FACS. Total RNA was isolated from each sample and subjected to RNA-Seq. DNA was extracted from microglia of 10-day-old heat-conditioned and non-conditioned chicks before LPS-challenge and subjected to RRBS.

value: microglia

value: Non-Conditioned

value: day 10 posthatch


title: RRBS Cond rep3

value: Conditioned


title: RRBS Cond rep1-2


title: RRBS Cond rep4


title: Spinal cord-VANCO-3


title: Spinal cord-VANCO-1


title: TFAm knockdown rep1

value: PBS

value: TFAM siRNA


title: Control rep1

value: Primary dermal fibroblast

value: non-target siRNA


title: RRBS Non-Cond rep2


title: KO#3 RPE


title: s104188-001-023

city: Rijswijk

first: Eveline

last: Gart

state: Zuid-Holland

address: Van vredenburchweg 659

country: Netherlands

institute: TNO

data_processing:
Quality filtering and adapter-trimming of the Illumina NovaSeq6000 fastq files was performed by TRIMMOMATIC software
Trimmed Fastq files were merged (in case of Paired-end reads) and aligned to the reference genome using the STAR 2.5 algorithm with default settings (https://github.com/alexdobin/STAR).
Based on the mapped read locations and the gene annotation, Htseq-count 0.6.1p1 was used to count the read mapping frequency/gene (transcript region) resulting in count.files.
Genome_build: Homo_sapiens.GRCh38.gencode.v29
Supplementary_files_format_and_content: The count files contain the # reads mapped per gene (not normalised per sample). These counts serve as input for the statistical analysis using DEseq2 package.

growth_protocol: Primary human hepatic stellate cells (HSC) (BioIVT, West Sussex, United Kingdom) were seeded on fibronectin-coated (Roche, Woerden, the Netherlands) 24-well culture plates and maintained overnight in stellate cell medium (STECM) supplemented with 2% (v/v) fetal bovine serum (FBS), 1% (v/v) antibiotic solution and 1% (v/v) stellate cell growth supplement (all HSC seeding medium materials were from ScienCell, Carlsbad, Canada).

extract_protocol:
Next generation sequencing was performed in RNA samples extracted from n=6 unstimulated; n=8 TGF-β; n=8 TGF-β+BU conditioned HSC. RNA was isolated using the RNAqeous Microkit (Thermo Fisher Scientific) and obtained RNA concentration were determined spectrophotometrically using the Nanodrop 1000 (Isogen Life Science, De Meern, the Netherlands).
To assess the quality of the samples, the concentration of the sample was determined using the Fragment Analyzer. The NEBNext Ultra II Directional RNA Library Prep Kit for Illumina was used to process the sample(s). The sample preparation was performed according to the protocol "NEBNext Ultra II Directional RNA Library Prep Kit for Illumina" (NEB #E7760S/L). Briefly, mRNA was isolated from total RNA using the oligo-dT magnetic beads. After fragmentation of the mRNA, a cDNA synthesis was performed. This was used for ligation with the sequencing adapters and PCR amplicification of the resulting product. The quality and yield after sample preparation was measured with the Fragment Analyzer (see appendices). The size of the resulting products was consistent with the expected size distribution (a broad peak between 300-500 bp).
Clustering and DNA sequencing using the NovaSeq6000 v1.5 was performed according to manufacturer's protocols. A concentration of 1.1 nM of DNA was used yielding paired end reads (2x 150bp). NovaSeq control software NCS v1.7 was used. Image analysis, base calling, and quality check was performed with the Illumina data analysis pipeline  RTA3.4.4 and Bcl2fastq v2.20.

treatment_protocol: HSC were incubated for 4 days in STECM supplemented with 1% (v/v) FBS and 1% (v/v) antibiotic solution with or without TGF-β1 (2 ng/mL; rh-TGFB1 R&D systems, Minneapolis, USA), and TGF-β1 co-treated with BU (Sodium Butyrate, Sigma Aldrich).

value: TB

value: TGF-β1 (2 ng/mL) + Sodium Butyrate (1mM)


title: Spinal cord-PBS-3


title: Control stimulated with TGFβ rep1

value: TGFbeta

value: Donor 1


title: Spinal cord-PBS-2

value: Spinal cord

value: Total spinal cord


title: KO#1 RPE

value: Retinal pigment epithelium

value: Best1-Cre+/-; Clic4f/f


title: RRBS Non-Cond rep1


title: KO#2 RPE


title: RRBS Non-Cond rep3


title: CreCtr-1 RPE


title: WT#3 RPE

value: wild type


title: Spinal cord-PBS-1

value: 6-8 weeks old

value: LEW/Crl


title: s104188-001-021

source_name: Primary human hepatic stellate cells (HSC)


title: s104188-001-019


title: WT#2 RPE


title: Spinal cord-NEO-3

value: NEO


title: WT#1 RPE


title: K5C

value: pancreatic cancer


title: s104188-001-020


title: Spinal cord-NEO-1


title: 19a_DMSO

first: Gregory

middle: Hunter

last: Babunovic

address: 665 Huntington Ave., SPH 1, Room 802

department: Immunology and Infectious Diseases

institute: Harvard T.H. Chan School of Public Health

description: mRNA

data_processing:
Reads were aligned with STAR aligner (version 2.6.0) in the RSEM program (version 1.2.29).
RNAseq counts were analyzed in R (version 3.6.3) with DESeq2 (version 1.24.0).
During analysis in R, gene names were retrieved with biomaRt (version 2.40.5) and log2 fold-changes were shrunk with apeglm (version 1.6.0).
Genome_build: hg38 (GRCh38)
Supplementary_files_format_and_content: SuppTable1-ext_RNAseq-Data-ext.xlsx: Raw counts are included in two sheets of the Excel document (one with and one without donor 18p counts); donors 18k, 18o, and 19a were used to calculate the log2 fold-changes and significance values in the other sheet.

source_name: Human macrophages (MO-GMCSF)

growth_protocol: Human primary monocytes were positively selected (CD14) from healthy donor peripheral blood mononuclear cells, then matured in 50 ng/mL GM-CSF for 6 days to create MO-GMCSF.

extract_protocol:
RNA was extracted with buffer RLT (Qiagen) and purified on Zymo columns with off-column DNA digestion.
Libraries were constructed using the KAPA mRNA HyperPrep kit.

treatment_protocol: MO-GMCSF were infected for 12 hours with Mycobacterium tuberculosis at MOI=1 (or left uninfected), then treated with the indicated compounds at 10 μM, 0.2% DMSO or plain media for 11 hours prior to lysis.

value: Macrophages (MO-GMCSF)

tag: infection status

value: Infected with Mycobacterium tuberculosis

value: 0.2% DMSO

tag: donor


title: 19a_EC23

description: mRNA

value: 10 uM EC 23


title: 19a_Uninfected

description: mRNA

value: Uninfected

value: media


title: 19a_ATRA

description: mRNA

value: 10 uM all-trans-retinoic acid


title: 19a_TTNPB

description: mRNA

value: 10 uM TTNPB


title: s104188-001-017

value: TB

value: TGF-β1 (2 ng/mL) + Sodium Butyrate (1mM)


title: s104188-001-018


title: s104188-001-022


title: Spinal cord-MICRO-VANCO-5

source_name: Spinal cord microglia

value: Spinal cord

value: Spinal cord microglia

value: VANCO


title: K5H


title: FFAA1

description: Gene expression data from frontal skin biopsy of individuals with FFA from affected area

hyb_protocol: Following fragmentation, 15 ug of cRNA were hybridized overnight at 45°C at  on U133 plus 2.0 Affymetrix human 3’-array chips in a Genechip Hybridization Oven 320. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Affymetrix Genechip 3000 scannerA.

data_processing:
The data were analyzed with Affymetrix proprietary MAS 5.0 (Microarray Suite 5.0) using Affymetrix default analysis settings and global scaling as normalization method.
* P means Present ( <=0.05 P value)
* M means Marginally present ( 0.05 to 0.065 P value)
* A means Absent ( > 0.065 P value)

source_name: Skin biopsy from frontal scalp of individuals with FFA (affected area)

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from  total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

extract_protocol: The total RNA from each biopsy was extracted using TRIzol reagent (Life Technologies, Inc., Gaithersburg, MD, USA) per the manufacturer's instructions. (Karnik, P., Tekeste, Z., McCormick, T.S., Gilliam, A.C., Price, V.H., Cooper, K.D., and Mirmirani, P. (2009). Hair follicle stem cell-specific PPARgamma deletion causes scarring alopecia. The Journal of investigative dermatology 129, 1243-1257).

treatment_protocol: No Treatment

value: FFA

value: affected skin biopsy


title: 18p_Uninfected

description: mRNA


title: FFAU1

description: Gene expression data from occipital skin biopsy of  individuals with FFA from unaffected area

source_name: Skin biopsy from occipital scalp of individuals  with FFA (unaffected area)

value: unaffected skin biopsy


title: FFAU2


title: FFAA2


title: Normal (10 samples pooled)

description: Gene expression data from occipital skin biopsy of healthy individuals

source_name: Skin biopsy from occipital scalp of healthy individuals

value: healthy

value: normal skin biopsy


title: FFAA3


title: kidney cortex-control diet (Sample4_S4)

city: Los Angeles

first: Janos

last: Peti-Peterdi

address: 1501 San Pablo Street

institute: University of Southern California

data_processing:
Raw sequencing reads with adaptors trimmed were mapped mm10 genome using Star 2.6.1 and quantified using Gencode M25 annotation to generate gene level counts.
The gene counts were subjected to QA/QC and the low-quality cells were filtered using the following criteria: (1) contained less than 300 or more than 8000 detected genes, (2) mitochondrial counts higher than 15% of total counts.
Gene level read counts in all samples were the filtered to only retain counts from protein coding genes as defined by Gencode25 annotation.
The counts were normalized using the Partek Flow recommended method (divided by 1 million, Add:1 and log2).
The normalized counts were then filtered so that only cells actively expressing Nos1 and Pappa2 genes were retained for further analysis.
Genome_build: mm10
Supplementary_files_format_and_content: 10X Genomics CellRanger HDF5 files

source_name: kidney cortex-control diet

growth_protocol: C57BL6 nNos CreERT2-mTmG (MD-GFP) animals were raised in animal facilities according to protocol approved by the Institutional Animal Care and Use Committee at the University of Southern California.

extract_protocol:
MD cells (green)  were isolated by FACS. RNA sequencing was prepared using 10x Genomics 3' v3.1 (cat# 1000092) following manufacturer’s protocol.  MD-GFP mice on C57BL6/J background were generated by intercrossing nNOS/CreERT2 and mTmG/fl mice resulting in membrane-targeted eGFP expression in MD cells (green), and membrane-targeted tdTomato expression in all other kidney cell types (red).
Samples were parsed into single cells using 10x Genomics Chromium Controller and libraries were simultaneously prepared. Prepared single cell RNA sequencing libraries were sequenced on the Illumina Novaseq 6000 platform at a read length of 28x90 and read depth of 100,000 reads/cell for 2000-4000 cells.
single cell RNAseq

treatment_protocol: Animals were given either control diet or low salt diet (TD 90228, Harlan Teklad, Madison, WI). After 14 days of treatment kidney cortex was digested, MD and control cells were FACS sorted based on their genetic fluorescent labeling for RNA extraction.

value: kidney

value: macula densa

tag: genetic model

value: Control diet


title: kidney cortex-LS diet (Sample3_S3)

source_name: kidney cortex-LS diet

tag: tissue

value: low salt (LS)


title: Spinal cord-NEO-2

tag: cell type

value: Total spinal cord

value: 6-8 weeks old

value: LEW/Crl

value: wild type

value: NEO


title: s104188-001-016

value: TB

value: TGF-β1 (2 ng/mL) + Sodium Butyrate (1mM)


title: Spinal cord-MICRO-VANCO-3

value: Spinal cord

value: Spinal cord microglia

value: VANCO


title: 18p_TTNPB

city: Boston

description: mRNA

value: Macrophages (MO-GMCSF)

value: Infected with Mycobacterium tuberculosis

value: 10 uM TTNPB


title: Spinal cord-MICRO-VANCO-2


title: s104188-001-015

value: T

value: TGF-β1 (2 ng/mL)


title: 18p_EC23

description: mRNA

value: 10 uM EC 23


title: s104188-001-014


title: kidney cortex-control diet (4414-S1)

value: kidney

value: macula densa

value: Control diet


title: Spinal cord-MICRO-VANCO-1

value: 6-8 weeks old

value: LEW/Crl


title: s104188-001-013


title: Triple combo 2

city: San Diego

first: Wenjing

last: Yanf

address: 10770 Science Center Drive

department: Oncology

institute: Pfizer

description: CD45+ cells sorted from B16 tumor after treatment with combinatoin of anti-PD1/anti-4-1BB/antiOX40 antibodies

data_processing:
Data were processed using the Cell Ranger v2.1.1 (10x Genomics) to generate count-level cell by gene matrix for further analysis.
Genome_build: mm10

source_name: CD45+ cells sorted from B16 tumor

growth_protocol: 5x10^5 B16-F10 tumor cells were implanted s.c into mice and  tumor resected 21 days post s.c. implantation.

extract_protocol:
TILs were isolated by digesting tumor fragments using Mylteni mouse tumor disassociation kit with enzyme R at 1:10 per manufacturer's guidelines. 1 to 5 × 106 cells were stained using fluorescently labeled mouse CD45 antibody (clone 30F11) and Fixable Viability Dye eFluor 506 (Thermo Fisher Scientific; Waltham, MA) to sort for live CD45+ and CD45− cells using the FACSAria II cell sorter.
RNA sequencing by standard protocol

treatment_protocol: Mice were treated with isotype or triple combinatorial therapy at days 10, 13 and 16 post-tumor implantation

value: B16-F10 tumor bearing mice


title: Spinal cord-MICRO-PBS-5

value: wild type

value: PBS


title: 18p_DMSO

description: mRNA

value: 0.2% DMSO


title: 18p_ATRA

description: mRNA

value: 10 uM all-trans-retinoic acid


title: kidney cortex-LS diet (Sample2_S2)

value: low salt (LS)


title: Spinal cord-MICRO-PBS-2

value: Spinal cord

value: Spinal cord microglia


title: s104188-001-011


title: Spinal cord-MICRO-PBS-1


title: Triple combo 1


title: 18o_Uninfected

description: mRNA

value: Macrophages (MO-GMCSF)

value: Uninfected

value: media


title: Spinal cord-MICRO-PBS-3


title: s104188-001-012

value: T

value: TGF-β1 (2 ng/mL)


title: s104188-001-009


title: s104188-001-010


title: 18o_TTNPB

description: mRNA

value: Infected with Mycobacterium tuberculosis

value: 10 uM TTNPB


title: Isotype 2

description: CD45+ cells sorted from B16 tumor after treatment with isotype antibody

value: Isotype antibody


title: Spinal cord-MICRO-NEO-5

value: 6-8 weeks old

value: LEW/Crl

value: NEO


title: 18o_DMSO

description: mRNA


title: Visium 4

city: Farmington

first: Dylan

last: Baker

state: CT

address: 10 Discovery Dr

institute: The Jackson Laboratory

data_processing:
Library strategy: Spatial Transcriptomics
Fastq files were generated from BCL by bcl2fastq
Counts matrices were generated from Fastqs processed via Cellranger or Spaceranger with the mm10 reference
Bulk RNA mapped with star to mm10 subread featureCounts used to generate counts for each gene
Genome_build: mm10
Supplementary_files_format_and_content: raw counts matrices of single cell gene expression

source_name: Mouse urinary bladder

extract_protocol: Standard Visium Spatial Gene Expression

value: Frozen Section of Whole Mouse Bladder

value: 14 Months

tag: sample group (sex/number)

value: 4X Male


title: s104188-001-008


title: Isotype 1

tag: strain

value: B16-F10 tumor bearing mice


title: 18o_EC23

description: mRNA

value: 10 uM EC 23


title: Spinal cord-MICRO-NEO-3

value: Spinal cord

value: Spinal cord microglia

tag: genotype

value: wild type


title: s104188-001-006

value: U

value: Unstimulated Control


title: 18o_ATRA

description: mRNA

value: Macrophages (MO-GMCSF)

value: 10 uM all-trans-retinoic acid


title: Spinal cord-MICRO-NEO-2


title: 18k_Uninfected

description: mRNA

value: Uninfected

value: media


title: Visium 2

value: 22 Months


title: s104188-001-005


title: Spinal cord-MICRO-NEO-1

value: 6-8 weeks old

value: LEW/Crl


title: Isotype 3

description: CD45+ cells sorted from MC38 tumor after treated with PBS

source_name: CD45+ cells sorted from MC38 tumor

extract_protocol:
TILs were isolated by digesting tumor fragments using Mylteni mouse tumor disassociation kit with enzyme R at 1:10 per manufacturer's guidelines. 1 to 5 × 106 cells were stained using fluorescently labeled mouse CD45 antibody (clone 30F11) and Fixable Viability Dye eFluor 506 (Thermo Fisher Scientific; Waltham, MA) to sort for live CD45+ cells using the FACSAria II cell sorter.
standard RNA-seq protocols

treatment_protocol: Mice were treated with isotype antibody at days 10, 13 and 16 post-tumor implantation

value: MC38 tumor bearing mice

value: isotype antibody


title: P18_CUT&RUN_IgG_Ino80cKO_rep3

city: Chapel Hill

first: Prabuddha

last: Chakraborty

state: NC

address: 120 Mason Farm Road5023 B, Genetic Medicine Building, CB#7264

department: Genetics

institute: University of North Carolina at Chapel Hill

data_processing:
Library strategy: CUT&RUN
CUT&RUN reads were aligned to the reference genome mm10 using Bowtie2 with very-sensitive setting allowing dovetail alignment.
Duplicates were marked by Picard and replicates were merged using Samtools.
Bigwig files were prepared from merged files with 1X normalization using Deeptools.
Genome_build: mm10
Supplementary_files_format_and_content: Bigwig files for genomic tracks.

source_name: spermatogenic cells from Testes

extract_protocol:
Seminiferous tubules from P18 testes were digested with collagenase and trypsin to obtain spermatogenic cells followed by filtration through 40 micron filter. Cells were prepared for CUT&RUN library by previously published protocol (Skene et al., 2018; Meers et al., 2019).
Libraries were generated using Kapa hyperprep DNA library kit for Illumina sequencing with modifications from CUT&RUN protocol (Skene et al., 2018; Meers et al., 2019).

value: Mixed background

value: Spermatogenic cells

value: Testis

tag: antibody

value: Rabbit-IgG, Sigma (I5006)


title: s104188-001-004


title: 18k_EC23

description: mRNA

value: Infected with Mycobacterium tuberculosis

value: 10 uM EC 23


title: P18_CUT&RUN_IgG_Ino80cKO_rep2


title: 18k_TTNPB

description: mRNA

value: 10 uM TTNPB


title: s104188-001-002

value: U

value: Unstimulated Control


title: P18_CUT&RUN_IgG_Ino80WT_rep3


title: 18k_ATRA

description: mRNA

value: Macrophages (MO-GMCSF)

value: 10 uM all-trans-retinoic acid


title: s104188-001-001


title: s104188-001-003


title: Visium 3

value: Frozen Section of Whole Mouse Bladder

value: 14 Months

value: 4X Male


title: 18k_DMSO

description: mRNA

value: 0.2% DMSO


title: P18_CUT&RUN_IgG_Ino80WT_rep1


title: NEO-d1-lung3

description: Rattus norvegicus domestica

data_processing:
Sequence images were transformed with Illumina software BaseCaller to BCL files, which was demultiplexed to fastq files with bcl2fastq v2.17.1.14
STAR version 2.5.2a was used to align the reads to the rn6 genome using 2 mismatches within 50 bases
featureCounts version 1.5.0-p1 was used to quantify reads for genes in rn6 version 100
Genome_build: rn6 version 100
Supplementary_files_format_and_content: Tab-delimited gene counts

source_name: Lung

treatment_protocol: Lungs were chopped, digested with collagenase and homogenized using a gentleMACS Dissociator. Lung-derived cell suspensions were further homogenized using a cell strainer. The pellet was enriched in leukocytes by Percoll gradient. Finally, fluorescently labeled MBP-reactive T cells were sorted and kept in TRI Reagent at -80° until further processing.

value: MBP-reactive T cells

value: LEW/Crl

value: wild type

value: 6-8 weeks old

value: NEO

tag: time

value: Lung


title: NEO-d1-lung2

description: Rattus norvegicus domestica


title: CTBTerm #3

city: TauYau

first: Yun-Shien

last: Lee

state: Taiwan

address: TauYau

department: Dept. Biotechnology

country: Taiwan

institute: Ming Chuan Univ

description: Total RNA by depleting ribosomal RNA

data_processing:
CLC Genomics Workbench v10 software used for base-calling.
Sequenced reads were trimmed for adaptor sequence, low quality sequence (QV³20), and ambiguous nucleotides, then mapped to Homo sapiens GRCh38 (hg38).
The expression value was calculated in FPKM (Fragments Per Kilobase of exon model per Million mapped fragments) using a protocol from Mortazavi et al., Nature Methods, 2008
Genome_build: hg38
Supplementary_files_format_and_content: Matrix table with FPKM for every gene and every sample
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: Placenta

extract_protocol:
Total RNA was extracted with the RNeasy mini Kit and RNase-free DNase (QIAGEN)
RNA libraries were prepared for sequencing using Universal RNA Seq Library Preparation Kit with NuQuant (Tecan Trading AG) according to the manufacturer's protocol.

value: Cytotrophoblast cell

tag: Stage

value: cytotrophoblast from placenta


title: P18_CUT&RUN_IgG_Ino80WT_rep2

value: Mixed background

value: Spermatogenic cells

value: Testis

value: Rabbit-IgG, Sigma (I5006)


title: NEO-d1-lung1

description: Rattus norvegicus domestica


title: Visium 1

value: 22 Months


title: P18_CUT&RUN_SUZ12_Ino80cKO_rep3

value: Rabbit anti-SUZ12; Cell signaling (3737)


title: CTBTerm #1

description: Total RNA by depleting ribosomal RNA


title: P18_CUT&RUN_SUZ12_Ino80cKO_rep2


title: EVT-TSTerm #3

description: Total RNA by depleting ribosomal RNA

value: Extravillous trophoblast

value: differentiated into EVT


title: ST-TSTerm #3

description: Total RNA by depleting ribosomal RNA

value: Syncytiotrophoblast

value: differentiated into STB


title: P18_CUT&RUN_SUZ12_Ino80cKO_rep1


title: P18_CUT&RUN_IgG_Ino80cKO_rep1


title: P18_CUT&RUN_SUZ12_Ino80WT_rep3


title: TSTerm #3

description: Total RNA by depleting ribosomal RNA

value: Trophoblast stem cell

value: undifferentiated


title: CTBTerm #2

description: Total RNA by depleting ribosomal RNA


title: P18_CUT&RUN_SUZ12_Ino80WT_rep2


title: NEO-d0-lung3

description: Rattus norvegicus domestica

value: MBP-reactive T cells

value: LEW/Crl

value: wild type

value: 6-8 weeks old


title: NEO-d0-lung1

description: Rattus norvegicus domestica

value: NEO

value: Lung


title: A549-HOXB9 KO_2 RNASeq

city: Beijing

first: Qianchen

last: Li

address: Beijing

institute: PKU

data_processing:
Illumina Casava2.19 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to GRCh38 whole genome using HISAT2 v2.0.5 with parameters -p 4 --dta -t --phred33 -1
Genome_build: GRCh38
Supplementary_files_format_and_content: The quantitative software was Featurecounts (1.5.0-P3) and got the FPKM value.
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: Lung adenocarcinoma

growth_protocol: A549 cell line was cultured in RPMI 1640 supplemented with 10% FBS

extract_protocol:
Trizol，RNA libraries were prepared for sequencing using standard Illumina protocols
RNA libraries were prepared for sequencing using standard Illumina protocols

value: A549 cells stably infected with lentivirus carrying PLVX-HOXB9 KO

value: Lung adenocarcinoma

tag: cell line


title: P18_CUT&RUN_SUZ12_Ino80WT_rep1

value: Mixed background

value: Spermatogenic cells

value: Testis


title: A549-HOXB9 KO_1 RNASeq


title: P18_CUT&RUN_H3K27me3_Ino80cKO_rep3

value: Rabbit anti-H3K27me3; Cell signaling (9733)


title: NEO-d0-lung2

description: Rattus norvegicus domestica


title: A549-HOXB9-T133A_2 RNASeq

value: A549 cells stably infected with lentivirus carrying PLVX-HOXB9-T133A


title: Leaf C [J.procumbens L_3]

city: Duluth

first: Marshall

last: Hampton

state: MN

address: 1117 University Drive

institute: University of Minnesota Duluth

description: RNA-Seq sample

data_processing:
Contigs assembled with Trinity v.2.12
Reads quantified using kallisto 0.46.1
Contigs mapped to Arabidopsis thaliana with NCBI’s blastn
Genome_build: N/A
Supplementary_files_format_and_content: Jaltomata_hp_tpms.xlsx

organism: Jaltomata procumbens

source_name: Leaf tissue

extract_protocol: Jaltomata procumbens and Jaltomata herrerae plants were grown in Sun Gro LC8 soil in the MAES/MDA Plant Growth Facilities at the University of Minnesota with typical daytime highs of 25C and nighttime lows of 15C. Three types of RNA samples were separately prepared in triplicate from the floral nectaries of both species, including: ‘pre-secretory’ (~24-48 hours prior to anthesis/nectar secretion), ‘secretory’ (full anthesis, at ~3-6 hours after dawn), and ‘post-secretory’ (after petal abscission). RNA from fully expanded leaf tissue was also isolated in triplicate for both species. All tissues were manually dissected by hand with the RNA being immediately extracted by mechanical disruption with a microcentrifuge pestle and using an RNAqueous® RNA isolation kit (Thermo Fisher) with Plant RNA Isolation Aid (Thermo Fisher). Agarose gel electrophoresis and UV spectrophotometry were used to assess RNA quality for all samples prior to submission to the University of Minnesota Genomics Center for mRNA isolation, barcoded library creation and Illumina NovaSeq 6000 sequencing. Twenty-four TruSeq stranded mRNA libraries were created (triplicate samples for nectaries at three timepoints each, as well as leaf tissue, for each species) and sequenced via 150 bp, paired-end runs on the NovaSeq 6000 using Rapid chemistry. All libraries were pooled and sequenced. All expected barcodes were detected and mean depth for the libraries was ≥ 20 M reads. The average quality scores were all above Q30.

value: Leaf


title: A549-HOXB9-T133A_1 RNASeq


title: Muscle_Overload_1wk_Mutant3

city: Paris

first: Franck

last: Letourneur

address: 22 rue mechain

institute: INSERM

hyb_protocol: After control of fragmentation using Bioanalyzer 2100, cDNA is then hybridized to GeneChip® ClariomS Mouse (LifeTechnologies) at 45°C for 17 hours.

scan_protocol: After overnight hybridization, chips are washed on the fluidic station FS450 following specific protocols (Affymetrix) and scanned using the GCS3000 7G

data_processing: The scanned images are then analyzed with Expression Console software (Thermofischer) to obtain raw data (cel files) and metrics for Quality Controls. The observations of some of these metrics and the study of the distribution of raw data show no outlier experiment.  RMA normalization is performed using R with CDF v22 of EntrezGene (Brian Array).

source_name: Plantaris muscle_Overload_1wk_Mutant3

label_protocol: 100 ng of total RNA is reverse transcribed following the GeneChip® WT Plus Reagent Kit (Thermofisher) .  Briefly, the resulting double strand cDNA is used for in vitro transcription with T7 RNA polymerase . After purification according to Affymetrix protocol, 5.5 ug of Sens Target DNA are fragmented and biotin labelled.

extract_protocol: The muscles were collected and freezed in liquid nitrogen. 1ml of Trizol was added for each muscle and TRIzol™ Reagent experimental protocol for RNA isolation by Invitrogen/Thermo scientific was used. The samples were all treated with DNAsi.

value: adult plantaris muscle

value: mutants lacking RhoA


title: Secretory floral nectary B [J.procumbens 1_1]

description: RNA-Seq sample

source_name: Nectary tissue

value: Secretory floral nectary


title: Muscle_Overload_1wk_Mutant4

source_name: Plantaris muscle_Overload_1wk_Mutant4


title: Muscle_Overload_1wk_Mutant2

source_name: Plantaris muscle_Overload_1wk_Mutant2


title: A549-HOXB9_2 RNASeq

value: A549 cells stably infected with lentivirus carrying PLVX-HOXB9


title: Muscle_Overload_1wk_Control4

source_name: Plantaris muscle_Overload_1wk_Control4

value: wildtype


title: Muscle_Overload_1wk_Control2

source_name: Plantaris muscle_Overload_1wk_Control2


title: P18_CUT&RUN_H3K27me3_Ino80cKO_rep1


title: Pre-secretory floral nectary D [J.procumbens 0_3]

description: RNA-Seq sample

value: Pre-secretory floral nectary D


title: Muscle_Overload_1wk_Mutant1

source_name: Plantaris muscle_Overload_1wk_Mutant1


title: Muscle_Overload_1wk_Control3

source_name: Plantaris muscle_Overload_1wk_Control3


title: Leaf B [J.procumbens L_2]

description: RNA-Seq sample


title: Muscle_sham operated_1wk_Mutant4


title: A549-HOXB9_1 RNASeq


title: Muscle_Overload_1wk_Control1

source_name: Plantaris muscle_Overload_1wk_Control1


title: Muscle_sham operated_1wk_Mutant3


title: Leaf A [J.procumbens L_1]

description: RNA-Seq sample


title: Muscle_sham operated_1wk_Mutant2


title: P18_CUT&RUN_H3K27me3_Ino80WT_rep2


title: ST-TS#1 GCM1-KO

description:
Total RNA by depleting ribosomal RNA.
RAWcount.txt
FPKM.txt

data_processing:
CLC Genomics Workbench v10 software used for base-calling.
Sequenced reads were trimmed for adaptor sequence, low quality sequence (QV³20), and ambiguous nucleotides, then mapped to Homo sapiens GRCh38 (hg38).
The expression value was calculated in FPKM (Fragments Per Kilobase of exon model per Million mapped fragments) using a protocol from Mortazavi et al., Nature Methods, 2008.
Genome_build: hg38 (GRCh38)
Supplementary_files_format_and_content: FPKM.txt: Matrix table with FPKM for every gene and every sample.
Supplementary_files_format_and_content: RAWcount.txt: Matrix table with raw gene counts for every gene and every sample.

extract_protocol:
Total RNA was extracted with the RNeasy mini Kit and RNase-free DNase (QIAGEN).
RNA libraries were prepared for sequencing using Universal RNA Seq Library Preparation Kit with NuQuant (Tecan Trading AG) according to the manufacturer's protocol.

value: Syncytiotrophoblast

value: Differentiated into STB


title: Post-secretory floral nectary C [J.procumbens 2_1]

description: RNA-Seq sample

value: Post-secretory floral nectary


title: Muscle_sham operated_1wk_Mutant1


title: P18_CUT&RUN_H3K27me3_Ino80WT_rep1


title: P18_CUT&RUN_H3K27me3_Ino80cKO_rep2


title: TS#1 GCM1-KO

value: Trophoblast stem cell

value: Undifferentiated


title: Muscle_sham operated_1wk_Control3