title: Liver - HFD_O3 - Rep7 [s3214]

value: male

value: HFD

value: liver


title: Ovarian Clear Cell Carcinoma cell line TU-OC-1

status: Public on Nov 01 2020

type: genomic

city: London

first: Gabriel

middle: E

last: DiMattia

state: ONTARIO

address: 750 Base Line Rd E

department: Biochemistry

country: Canada

institute: Western University

description: Affymetrix CytoScan HD Reagent kit

hyb_protocol: 50°C, 60 rpm for 16 hr-18hr

scan_protocol: Affymetrix GeneChip Scanner 3000 (#3)

data_processing:
ChAS
Genotype Call (SNP call)

label: Biotin

molecule: genomic DNA

organism: Homo sapiens

label_protocol: Affymetrix CytoScan HD Reagent kit

growth_protocol: Cell lines were cultured in Dulbecco’s modified Eagle medium/Ham’s F12 (Wisent) and supplemented with 10% FBS (Wisent). Cells were maintained in at 37 °C and a CO2 concentration of 5%. Cells were allowed to reach ~90% confluency at which point the media was aspirated and cells were washed with phosphate buffered saline (PBS) and exposed to 2 mL of trypsin/EDTA until cells detached from plate. Cells were resuspended in 10 mL of media and then split onto new plates at a minimum of a 1:3 dilution.

extract_protocol: Wizard Genomic DNA Purification Kit (Promega) was used to isolate DNA from cells as per manufacturers protocol.

treatment_protocol: No treatment

tag: cell type

value: Ovarian Clear Cell Carcinoma cell line


title: MSR-2 (Clostridium thermocellum 1313 ∆hpt∆SO3R: sulfate)

type: SRA

city: Oak Ridge

first: Dawn

middle: Marie

last: Klingeman

state: TN

address: 1 Bethel Valley Rd building 15056 Rm 366  MS 6038

department: Biosciences Division

country: USA

institute: Oak Ridge National Lab

library_source: transcriptomic

data_processing:
Demultiplexing and file conversion performed by DRAGEN,  version 01.003.043.02.01.02.25767
RNAseq reads were aligned to the C. thermocellum DSM1313 (NC_017304.1) genome assembly using Fastq files imported into the CLCBio RNA-sequencing pipeline. Default settings were used for mismatch, insertion, and deletion costs.
Unique gene counts from the CLCBio mapping (DESeq_input.txt) were used for DESeq2 analysis to normalize and determine significant gene expression differences (DeSeq_output_all_pairwise_comparisons.xlsx)
Genome_build: NC_017304.1
Supplementary_files_format_and_content: Tab deliminated file includes unique read counts for each gene across the 4 conditions (with 3 biological replicates each) used in this study

molecule: total RNA

organism: Acetivibrio thermocellus DSM 1313

source_name: Clostridium thermocellum_1313_ culture

growth_protocol: Strains were grown to mid-exponential phase (OD ~ 0.6) in sealed, N2 sparged 162 ml serum bottles containing 50 ml MTC (initial pH of 7.1) supplemented with 5 g/l cellobiose

extract_protocol:
Pelleted cells were  resuspended in TRIzol (Invitrogen, CA), throughly mixed and then refrozen.  The frozen TRIzol cell suspension was used for cell lysis by bead beating with 0.8 g of 0.1mm glass beads (Biospec Products) with 3 X 20 s bead beating treatments at 6,500 rpm in a Precellys 24 high-throughput tissue homogenizer (Bertin Technologies, Montigny-le-Bretonneux, France). The RNA from each cell lysate was purified and DNaseI treated (on column) using the Qiagen RNeasy kit. The RNA quantity and quality assessed by Nanodrop and Bioanalyzer respectively. Purified RNA was depleted of rRNA using the Ribo-Zero rRNA Removal kit for Bacteria (Epicentre/Illumina). The sample was then concentrated with RNA Clean & Concentrator-5 (Zymo Research, CA) following the manufacturer’s protocol.
Depleted RNA was used as the starting material for the Epicentre ScriptSeq™ v2 RNA-Seq Library preparation kit (Illumina compatible) utilising Epicentres Fail Safe PCR Enzyme mix (Epicentre, WI) and following the manufacturer’s protocol. cDNA, tagged with ScriptSeq adaptors (1-12), was purified with Agencourt AMPure XP magnetic beads (Beckman Coulter, IN ) and  eluted in water according to the ScriptSeq™ v2 RNA -Seq Library preparation kit protocol.  Twelve PCR cycles were used during library amplification and samples were purified with Agencourt AmPureXP magnetic beads and eluted with 20 µl of water. The final mRNA Seq library was quantified with a Qubit Fluorometer (Invitrogen, CA) and library quality was assessed with an Agilent Bioanalyzer DNA Chip (Agilent, CA). Samples were pooled and the concentration determined.  Pools of barcoded samples were sent to Hudson Alpha for SR50 sequencing run on an Illumina Hiseq 2500 platform.

treatment_protocol: Samples for RNA-seq were taken from mid-exponential phase (OD ~ 0.6) batch cultures grown in MTC on 5 g/l cellobiose. Control strain (∆hpt) and sulfite-reductase-mutant strain (∆hpt∆SO3R) were grown in the presence of either 5.7mM cysteine or 28.2mM sodium sulfate as the only sulfur source

tag: genotype/variation

tag: sulfur source

value: sulfate

tag: strain

value: sulfite reductase knockout strain


title: miR-155 C-3

type: RNA

city: Bangalore

first: Genotypic

last: technology

state: Karnataka

address: 259, Apoorva 4th cross,80 feet Road,RMV 2ND STAGE

country: India

institute: Genotypic Technology

description:
SNB19 cells were transfected with  miRNA cloned pLemiR construct
SNB19 miR-155 C-3_(Cy5)Vs. SNB19 CTL  (Cy3)

hyb_protocol: Cy3 labeled samples and of Cy5 labeled samples were pooled. Fragmentation of labeled cRNA and hybridization were done using the Gene Expression Hybridization kit of Agilent (Part Number 5190-0404). Hybridization was carried out in Agilent’s Surehyb Chambers at 65º C for 16 hours. The hybridized slides were washed using Agilent Gene Expression wash buffers (Part No: 5188-5327)

scan_protocol: Scanned using Agilent Scanner (Agilent Technologies G2600D ).

data_processing: The Lowess Normalization was done using GeneSpring GX Software.

source_name: SNB19 CTL cells

label_protocol: The samples for Gene expression were labeled using Agilent Quick Amp Kit PLUS (Part number: 5190-0444). Each of the Control and test samples were reverse transcribed at 40°C and  converted to double stranded cDNA primed by oligodT tagged with a T7 polymerase promoter. The double stranded cDNA were used as template for cRNA synthesis. cRNA was generated by in vitro transcription. The dye Cy3 CTP (Agilent) for control samples and Cy5 CTP(Agilent) for test samples were incorporated during this step. The cDNA synthesis and in vitro transcription steps were carried out at 40°C. Labeled cRNA was cleaned up and quality assessed for yields and specific activity using Nanodrop.

growth_protocol: SNB19 cells were transfected with  miRNA cloned pLemiR construct. Cells were  cultured in RPMI-1640 medium supplemented with 10% Fetal Bovine Serum (FBS), 0.5% Penicillin Streptomycin (Pen-Strep) and Puromycin (0.5 µg/mL).

extract_protocol: Total RNA from each condition were isolated using Qaigen miRNeasy mini Kit (Cat: 217004) according to the manufacturer protocol.

value: Glioblastoma cells

tag: cell line

tag: genotype

value: wildtype

source_name: SNB19 miR-155 cells

value: miR-155 overexpression


title: Liver - STD_Cont - Rep4 [s3150]

city: clermont ferrand

first: frederic

last: capel

address: 28 place henri dunant

department: alimentation humaine

country: France

institute: INRA

hyb_protocol: 600 ng of Cy3-labelled cRNA (specific activity >6 pmol Cy3/µg cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 25 µl containing 10x Agilent fragmentation buffer and 25x Agilent blocking agent following the manufacturer's instructions (Agilent Technologies, Santa Clara, CA). On completion of the fragmentation reaction, 25 µl of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to SurePrint G3 Mouse GE v2 microarray (8X60K, Design 074809  enclosed in Agilent SureHyb-enabled hybridization chambers for 17 hours at 65°C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed sequentially in Wash buffer 1 (Agilent Technologies, 1 min) and Wash buffer 2 (Agilent Technologies, 37°C, 1 min).

scan_protocol: Slides were scanned immediately after washing on a Agilent G2505C Microarray Scanner with Agilent Scan Control A.8.5.1 software

data_processing: The scanned images were analyzed with Feature Extraction Software 10.10.1.1 (Agilent Technologies, Santa Clara, CA) using default parameters (protocol GE1_1010_Sep10 and Grid: 074809_D_F_20150624). All subsequent data analyses were done under R (www.r-project.org) using packages of Bioconductor (www.bioconductor.org). Raw data (median of pixels intensity) were imported into R using the read.maimages function from the limma package with the following weight function (assigning a weight of 1 or 0 to each spot): myfunw<-function(x) {okType<-x$ControlType==0; okFoundGreen<-x$gIsFound==1; okPos=x$gIsPosAndSignif==1; okWellAbove<- x$gIsWellAboveBG==1; as.numeric(okType & okFoundGreen & okPos & okWellAbove);} We selected the spots with a minimal weight of 1 for 20 out of 24 microarrays or with a minimal weight of 4 per group from at least one experimental group. At this step, 34807 spots out of 62976 were selected. Data were then stored in an ExpressionSet object and normalized by the quantile method using the normalize.quantiles function from the preprocessCore R library. Replicated probes on the array (identical ProbeName) were resolved by taking the median normalized signal of each set of replicated probes. The resulting matrix has 32176 rows each corresponding to a unique ProbeName (provided as data Matrix).

organism: Mus musculus

source_name: Liver - STD_Cont

label_protocol: For each sample, Cyanine-3 (Cy3) labeled cRNA was prepared from 200 ng of total RNA using the One-Color Quick Amp Labeling kit (Agilent Technologies, Santa Clara, CA) according to the manufacturer's instructions, followed by Agencourt RNAClean XP (Agencourt Bioscience Corporation, Beverly, Massachusetts) purification. Dye incorporation and cRNA yield were checked using Dropsense™ 96 UV/VIS droplet reader (Trinean, Belgium).

extract_protocol: RNA were isolated using the Trizol reagent and washing steps with Isopropanol/Ethanol procedure before solubilization in sterile water

tag: Sex

tag: group id

tag: lineage

value: Control fatty acid

tag: diet

value: STD

tag: tissue


title: Liver - HFD_Cont - Rep8 [s3199]

source_name: Liver - HFD_Cont


title: MSR-1 (Clostridium thermocellum 1313 ∆hpt∆SO3R: sulfate)


title: Liver - HFD_O3 - Rep1 [s3136]

source_name: Liver - HFD_O3


title: Liver - STD_Cont - Rep9 [s3196]


title: H27634_cerebellum_sciRNA

city: Seattle

first: Junyue

last: Cao

state: WA

address: Foege Building S-210, 3720 15th Ave NE

department: Department of Genome Sciences

institute: University of Washington

data_processing:
Read alignment and gene count matrix generation for the single cell RNA-seq was performed using the pipeline that we developed for sci-RNA-seq3 (Cao et al. 2019) with minor modifications: Duplicates were removed using the unique molecular identifier (UMI) sequence (ED < 2, including insertions and deletions), reverse transcription (RT) index, hairpin ligation adaptor index and read 2 end-coordinate.
Genome_build: human reference genome (hg19)
Supplementary_files_format_and_content:
S1_metadata_cells.txt: Metadata of high-quality cells. Includes sample metadata and various per-cell QC stats, Louvain cluster id and cell type annotation, for each of the 4,062,965 high-quality cells used in the downstream analyses.
S2_Metadata_genes.txt: Metadata of genes. Includes gene id, short name and gene type information for each gene.
S3_gene_count.loom: Gene count matrix of cells. Includes expression UMI values for each gene in each cell. The gene count is stored in loom-formatted hdf5 file (read with function "scanpy.read_loom" in python)
S4_gene_expression_tissue.txt: Matrix of gene expression values across tissues. Includes normalized gene expression values (transcripts per million) for each tissue.
S5_gene_fraction_tissue.txt: Matrix of positive cell ratio for each gene across tissues. Includes the ratio number of cells expressing each gene in each tissue.
S6_gene_expression_celltype.txt: Matrix of positive cell ratio for each gene across tissues. Includes the ratio number of cells expressing each gene in each tissue.
S7_gene_fraction_celltype.txt: Matrix of positive cell ratio for each gene across main cell types. Includes the ratio number of cells expressing each gene for each type in each tissue.
S8_DE_gene_cells.txt: Differential gene expression test results for main cell types within each organ. For each gene, the “max_cell_type” is the cell type with the highest expression within the organ by transcripts per million (TPM) (“max.expr”). The “second_cell_type” is the cell type with the second highest expression within the organ by transcripts per million (TPM) (“second.expr”). The “fold.change” is the fold change between the max expression and second max expression. The “qval” is the false detection rate (one-sided likelihood ratio test with adjustment for multiple comparisons) for the differential gene expression test across different cell types within the organ.

molecule: polyA RNA

source_name: RNA-seq of Homo sapiens: Fetus cerebellum

growth_protocol: Human fetal tissues were obtained by the UW Birth Defects Research Laboratory (BDRL) under a protocol approved by the University of Washington Institutional Review Board. Gestational age, reported as the number of weeks post-fertilization, was estimated from fetal foot length. Tissues of interest were isolated and rinsed in 1X HBSS (with Ca2+ and Mg2+) then blotted dry on a semi-damp gauze. Dried tissue was placed on a heavy-duty foil or in cryotube, snap frozen in liquid nitrogen, and then stored at -80°C.

extract_protocol:
On the day of nuclei isolation, aliquots of tissue powder (0.1-1g) were first incubated with 1 mL ice-cold cell lysis buffer (10 mM Tris-HCl, pH 7.4, 10 mM NaCl, 3 mM MgCl2 and 0.1% IGEPAL CA-630 from (Buenrostro et al. 2013), modified to also include 1% SUPERase In (Thermo Fisher Scientific, AM2696) and 1% BSA (NEB, B9000S)) and then transferred to the top of a 40 µm cell strainer (VWR, 10199-654). Tissues were homogenized through the strainer with the rubber tip of a syringe plunger (VWR, BD309646) in 4 ml cell lysis buffer. The filtered nuclei were then transferred to a new 15 ml tube (VWR, 21008-936) and pelleted by centrifuge at 500xg for 5 min and washed once with 1 ml cell lysis buffer. The nuclei were fixed in 5 ml ice-cold 4% paraformaldehyde (EMS, 15-4-100) for 15 min on ice. After fixation, the nuclei were washed twice in 1 ml nuclei wash buffer (cell lysis buffer without IGEPAL), and re-suspended in 500 µl nuclei wash buffer. The samples were split into two tubes with 250 µl in each tube and flash frozen in liquid nitrogen. For human cell extraction in renal and digestive organs (kidney, pancreas, intestine, and stomach) and paraformaldehyde fixation, we followed the procedure described in (Thomsen et al. 2016).
sci-RNA-seq3 library: The paraformaldehyde fixed nuclei were processed similarly to the published sci-RNA-seq3 protocol (Cao et al. 2019). For paraformaldehyde fixed cells, frozen fixed cells were thawed on 37°C water bath, spun down at 500xg for 5 min, and incubated with 500ul PBSI (1 x PBS, pH 7.4, 1% BSA, 1% SuperRnaseIn)  including 0.2% Triton X-100 for 3min on ice. Cells were pelleted and resuspended in 500ul nuclease free water including 1% SuperRnaseIn. 3ml 0.1N HCl were added into the cells for 5min incubation on ice (Rosenberg et al. 2018). 3.5ml Tris-HCl (pH = 8.0) and 35ul 10% Triton X-100 were added into cells to neutralize HCl. Cells were pelleted and washed with 1ml PBSR. Cells were pelleted and resuspended in 100ul PBSI. The following steps were similar with the sci-RNA-seq3 protocol (with paraformaldehyde fixed nuclei) with slight modifications: (1) We distributed 20,000 fixed cells (instead of 80,000 nuclei) per well for reverse transcription. (2) We replaced all nuclei wash buffer in following steps with PBSI. (3) All nuclei dilution buffer were replaced with PBS + 1% BSA.

tag: development stage

value: Fetus tissues

value: Fetus cerebellum


title: Liver - HFD_O3 - Rep5 [s3209]


title: H27772_kidney_sciRNA

source_name: RNA-seq of Homo sapiens: Fetus kidney

value: Fetus kidney


title: miR-155 C-2

description:
SNB19 cells were transfected with  miRNA cloned pLemiR construct
SNB19 miR-155 C-2 (Cy5) Vs. SNB19 CTL (Cy3)


title: H27620_eye_sciRNA

source_name: RNA-seq of Homo sapiens: Fetus eye

value: Fetus eye


title: untreated HBV LDB_16

city: Bethesda

first: Barbara

last: Rehermann

state: Maryland

address: 10 Center Drive

department: Liver Diseases Branch

institute: National Institutes of Health

description: nothing special

hyb_protocol: Hybridization was performed according to hybridization protocol for nCounter XT CodeSet Gene Expression Assays Including Panels. Briefly, hybridization buffer and reporter codeset were mixed first, and this mastermix was added to samples (total RNA), finally hybridization reaction was completed by adding capture probeset.

scan_protocol: The cartridge was read with maximum sensitivity (280 FOV).

data_processing: Data from all runs were imported into nSolver version 4.0 (NanoString Technologies), matched to corresponding Reporter Library File (RLF), and subjected to quality control using the software quality metrics with default cutoff criteria

source_name: peripheral blood mononucler cells

extract_protocol: Total RNA was extracted from PBMC using QIAshredder and RNeasy Mini Kit (Qiagen, Germantown, MD), and 100 ng of total RNA was used for hybridization.

treatment_protocol: Frozen PBMCs were thawed and total RNA was extracted.

tag: diseases

value: chronic HBV

tag: hbeag (+/-)

value: HBeAg+

tag: therapy that the patient received

value: untreated


title: uninfected control LDB_24

description: nothing special

value: uninfected control


title: H27552_thymus_sciRNA

source_name: RNA-seq of Homo sapiens: Fetus thymus

value: Fetus thymus


title: MTR-2 (Clostridium thermocellum 1313 ∆hpt∆SO3R: cysteine)

value: cysteine


title: untreated HBV LDB_17

description: nothing special


title: H27552_spleen_sciRNA

source_name: RNA-seq of Homo sapiens: Fetus spleen

value: Fetus spleen


title: untreated HBV LDB_15

description: nothing special


title: H27552_pancreas_sciRNA

source_name: RNA-seq of Homo sapiens: Fetus pancreas

value: Fetus pancreas


title: untreated HBV LDB_13

description: nothing special


title: untreated HBV LDB_14

description: nothing special

value: HBeAg-


title: Liver - STD_Cont - Rep5 [s3163]

value: male

value: liver


title: PSR-3 (Clostridium thermocellum 1313 ∆hpt: sulfate)

value: {delta}hpt

value: sulfate

value: wild-type parental strain


title: Liver - HFD_Cont - Rep5 [s3171]

value: Control fatty acid

value: HFD


title: PSR-2 (Clostridium thermocellum 1313 ∆hpt: sulfate)


title: MTR-1 (Clostridium thermocellum 1313 ∆hpt∆SO3R: cysteine)

value: sulfite reductase knockout strain


title: Liver - HFD_Cont - Rep1 [s3127]


title: MTR-3 (Clostridium thermocellum 1313 ∆hpt∆SO3R: cysteine)


title: Liver - STD_Cont - Rep2 [s3133]

value: STD


title: untreated HBV LDB_12

description: nothing special

value: chronic HBV

value: HBeAg+


title: PSR-1 (Clostridium thermocellum 1313 ∆hpt: sulfate)


title: H27552_adrenal_sciRNA

source_name: RNA-seq of Homo sapiens: Fetus adrenal

value: Fetus tissues

value: Fetus adrenal


title: H27477_muscle_sciRNA

source_name: RNA-seq of Homo sapiens: Fetus muscle

value: Fetus muscle


title: Liver - STD_Cont - Rep1 [s3129]


title: Liver - HFD_O3 - Rep6 [s3213]


title: Liver - HFD_Cont - Rep3 [s3159]


title: PTR-3 (Clostridium thermocellum 1313 ∆hpt: cysteine)

value: cysteine


title: uninfected control LDB_10

description: nothing special

value: uninfected control


title: uninfected control LDB_9

description: nothing special


title: H27477_lung_sciRNA

source_name: RNA-seq of Homo sapiens: Fetus lung

value: Fetus lung


title: H27477_cerebellum_sciRNA

value: Fetus cerebellum


title: PTR-1 (Clostridium thermocellum 1313 ∆hpt: cysteine)


title: uninfected control LDB_8

description: nothing special


title: H27474_placenta_sciRNA

source_name: RNA-seq of Homo sapiens: Fetus placenta

value: Fetus placenta


title: H27474_muscle_sciRNA


title: NOR2: Trauma patient 2

city: Wenzhou

first: Li

last: Sun

address: South Baixiang, Ouhai District

department: Department of Rheumatology and Immunology

country: China

institute: The first Affiliated Hospital of Wenzhou Medical University

data_processing:
Adapters and reads with lower mapping quility were trimed by trim_galore.
Reads were aligned to the human hg19 reference genomes using the Hisat2.
Raw counts were quantified against Ensemble transcript and including small and lncRNA annotations by featureCount.
Differentially expressing genes were detected by DESeq2.
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text files include raw count for each sample.

source_name: FLS from trauma patient 2

extract_protocol:
Total RNA from synovium tissues were extracted by using Trizol reagent (Invitrogen, USA), the concentration (>= 500ng/ul is qualified), purity (OD260/OD280 range from 1.8 to 2.2) and integrity (28S:18S >=1.5) were detected using Qubit® RNA Assay Kit with Qubit® 2.0 Flurometer (Life Technologies, USA), NanoPhotometer® spectrophotometer (IMPLEN, USA) and RNA Nano 6000 Assay Kit with Bioanalyzer 2100 system (Agilent Technologies, USA), respectively.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: synovial tissue

value: fibroblast-like synoviocytes


title: NOR3: Trauma patient 3

source_name: FLS from trauma patient 3


title: uninfected control LDB_11

description: nothing special


title: NOR1: Trauma patient 1

source_name: FLS from trauma patient 1


title: H27474_lung_sciRNA


title: uninfected control LDB_7

description: nothing special


title: uninfected control LDB_6

description: nothing special


title: PTR-2 (Clostridium thermocellum 1313 ∆hpt: cysteine)

source_name: Clostridium thermocellum_1313_ culture

value: {delta}hpt

value: wild-type parental strain


title: WT-5

city: Boston

first: KLaus

last: Schmitz-Abe

state: MA

address: 300 Longwood Avenue

department: Asthma, Allergy and Immunology

institute: Children's Hospital Boston

description:
B
WT Treg

data_processing:
Trim raw data
Trimmomatic (version 0.39)
Default parameters
fastq file to bam file to count file
Rsubread (version 2.0.1)
Default parameters
Count file to Gene differential expression file
Lima (version 3.42.2)
Default parameters
Count file to Gene differential expression file
edgeR (version 3.28.1)
Default parameters
Count file to Gene differential expression file
DESeq2 (version 1.26.0)
Default parameters
Join results
Results_RNASeq.xlsx
Genome_build: Ensambl (GRCm38.R101)
Supplementary_files_format_and_content: vcf files and excel file

source_name: Lung

extract_protocol:
The cells were sorted our using Foxp3YFP reporter, then they were lysed using RLT buffer. The RNA was extracted using the Qiagen miniRNasy kit as per manufacturer's protocol
RNA to cDNA was performed using the SMART-Seq v4 Ultra Low Input RNA kit using the manufacturer's protocol

value: WT


title: WT-3

description:
B
WT Treg


title: uninfected control LDB_5

description: nothing special


title: Liver - HFD_O3 - Rep3 [s3203]

source_name: Liver - HFD_O3

value: male

value: HFD

value: liver


title: WT-4

description:
B
WT Treg


title: Liver - HFD_Cont - Rep2 [s3142]

source_name: Liver - HFD_Cont

value: Control fatty acid


title: Liver - STD_Cont - Rep7 [s3175]

source_name: Liver - STD_Cont

value: STD


title: untreated HBV LDB_4

description: nothing special

value: chronic HBV

value: HBeAg-

value: untreated


title: WT-2

description:
B
WT Treg


title: RA3: RA patient3

source_name: FLS from rheumatoid arthritis patient 3


title: WT-1

description:
B
WT Treg


title: untreated HBV LDB_3

description: nothing special

source_name: peripheral blood mononucler cells


title: RA1: RA patient1

source_name: FLS from rheumatoid arthritis patient 1


title: H27474_brain_sciRNA

source_name: RNA-seq of Homo sapiens: Fetus brain

value: Fetus tissues

value: Fetus brain


title: N4-4

description:
A
N4 Treg


title: H27474_adrenal_sciRNA

value: Fetus adrenal


title: IKK2 KO MEF TNF 90 rep2

city: Singapore

first: Vinay

last: Tergaonkar

address: 61 Biopolis Drive,  Proteos

country: Singapore

institute: Institute of Molecular and Cell Biology

data_processing:
Base quality assessment of raw sequence was performed using FastQC v0.11.8 and Trimmomatic v0.321 was used to filter low quality bases and adapter sequences.
Spliced alignment was performed using HISAT2 with reference to Mus musculus (GRCm38) genome index.
Gene-level expression counts were quantified (strand-specific read counting) using featureCounts (subread-v1.6.2 package).
Differential genes expression analysis was performed by using edgeR v3.26.4 package.
Genome_build: GRCm38
Supplementary_files_format_and_content: Tab-delimited text files include raw counts of every genes for all samples.

source_name: Mouse Embryonic Fibroblast

growth_protocol: Cells were cultured in DMEM media supplemented with 10% FBS and antibiotics.

extract_protocol:
RNA was isolated using Trizol followed by column purification.
RNA-Seq library was prepared by NEBNext® Ultra™ II Directional RNA library preparation kit according to manufacturer instructions.
Paired-end sequencing was performed using Illumina NextSeq, 2x76bp.

treatment_protocol: Immortalized wild-type, p65 knock-out and IKK beta knock-out MEFs were stimulated with TNF alpha (10ng/ml) for 0, 45 and 90 mins.

value: Immortalized

value: IKK2 KO

tag: treatment

value: TNFα treated 90mins


title: H27474_liver_sciRNA

source_name: RNA-seq of Homo sapiens: Fetus liver

value: Fetus liver


title: N4-3

description:
A
N4 Treg


title: H27473_placenta_sciRNA

value: Fetus placenta


title: H27473_muscle_sciRNA

source_name: RNA-seq of Homo sapiens: Fetus muscle

value: Fetus muscle


title: Roots 55N1 rep 1

city: Villa Elisa-La Plata

first: Maria

middle: Eugenia

last: Zanetti

state: BUENOS AIRES

department: Instituto de Biotecnología y Biología Molecular

country: Argentina

institute: Universidad Nacional de La Plata

description: Phaseolus vulgaris accession NAG12

data_processing:
sRNA-seq analysis was performed using the UEA Workbench, small RNA Workbench Version 3.2 (Stocks et al., 2012; Beckers et al., 2017; Mohorianu et al., 2017). Fastq sequences were filtered by size and quality. Only read with QC> 30 and sizes between 18-26 nucleotides in length were used for further analysis. Free adapters were removed using the Adapter Removal tool of UEA Workbench. Ribosomal and transfer RNA fragments were removed using the Filter Tool selecting the Discard T-R RNA parameter.
Reads were mapped to the Mesoamerican BAT93 and Andean Race Peru G19833 (Vlasova et al., 2016; Schmutz et al., 2014) using Bowtie2 (Langmead and Salzberg, 2012).
miRNAs were identified using the UEA Workbench Tools miRCat v21 (Moxon et al., 2008) with default parameters for plant miRNAs.
Genome_build: Mesoamerican BAT93 and Andean Race Peru G19833 (Vlasova et al., 2016; Schmutz et al., 2014)
Supplementary_files_format_and_content: Conserved and new miRNAs normalized abundance.txt

organism: Phaseolus vulgaris

source_name: Roots

growth_protocol: P. vulgaris seedlings were grown on acrylic boxes (17 cm x 22 cm x 4.5 cm) containing slanted agar-Fahraeus media and incubated for 7 days in a Persival Intellus Control System growth chamber at 25°C and 75% humidity with a long-day period (16-h-day/8-h-night cycle) and a photosynthetically active radiation of 200 μmol. s-1.cm-2 using mixed lighting containing four OSRAM cool daylight L36W/765 tubesand one OSRAM FLUORA L36W/77 tube.

extract_protocol:
RNA was extracted with Trizol following manufacture´s recommendations (Thermo Fisher). RNA quality was evaluated by capillary gel electrophoresis on an Agilent 2100 Bioanalyzer using the AgilentRNA6000 Pico kit. Separation of low and high molecular weight RNAs was performed with polyethylene glycol (PEG) precipitation essentially as described by Lu et al (2007). Low molecular RNAs were further separated into a denaturing 15% (w/v) polyacrylamide gel containing 0.48 % (w/v) of urea. The population of sRNAs ranging from 18 to 35 nucleotides was excised from the gel and eluted with 250 μl of 0.3M NaCl by incubating overnight at 4°C. Eluted RNAs were filtered through 5 µm spin-X filter by centrifuging at 16,000 xg. sRNAs (18-35 nucleotides) were precipitated by adding 3 μg of glycogen as a carrier and 2 volumes of 95% (v/v) ethanol and incubating at -80°C for two hours. Samplers were centrifuged for 30 min at 16,000 xg at 4°C and washed with 200 μl of cold 80% ethanol. The supernatants were discharged, and pellets containing the small RNAs were air dry and resuspended into 10 μl of MiliQ water.
sRNA-seq libraries were generated using kit TruSeq Small RNA preparation kit following manufacture’s recommendations (Illumina). SuperScript II reverse transcriptase (Thermo Fisher Scientific) was used for cDNA synthesis. DNA fragments were purified using AMPure XP beads (Beckman Coulter Genomics) and their size was verified onan Agilent 2100 Bioanalyzer using the DNA-1000 kit (Agilent).

treatment_protocol: Roots were inoculated with 5 ml of Yeast Extract-Manitol (YEM) media as a control or with 5 ml of a suspension of strain SC15 or 55N1 grown in YEM media until they reached an OD600=0.8

tag: accession

value: Wild type

value: Roots

value: inoculated with 55N1, a less-efficient strain of R. etli


title: Roots 55N1 rep 2

description: Phaseolus vulgaris accession NAG12


title: H27473_liver_sciRNA


title: H27474_cerebellum_sciRNA

source_name: RNA-seq of Homo sapiens: Fetus cerebellum

value: Fetus cerebellum


title: Roots SC15 rep 1

description: Phaseolus vulgaris accession NAG12

value: inoculated with SC15, a highly-efficient strain of R. etli


title: N4-1

description:
A
N4 Treg


title: Roots SC15 rep 2

description: Phaseolus vulgaris accession NAG12


title: IKK2 KO MEF TNF 45 rep2

value: TNFα treated 45mins


title: IKK2 KO MEF TNF 45 rep1


title: IKK2 KO MEF UT rep2

value: Untreated


title: Roots CTL rep 2

description: Phaseolus vulgaris accession NAG12

value: control


title: untreated HBV LDB_2

description: nothing special

value: chronic HBV

value: HBeAg-

value: untreated


title: H27473_heart_sciRNA

source_name: RNA-seq of Homo sapiens: Fetus heart

value: Fetus tissues

value: Fetus heart


title: IKK2 KO MEF UT rep1

value: Immortalized

value: IKK2 KO


title: Roots CTL rep 1

description: Phaseolus vulgaris accession NAG12


title: untreated HBV LDB_1

description: nothing special


title: H27472_placenta_sciRNA

source_name: RNA-seq of Homo sapiens: Fetus placenta

value: Fetus placenta


title: p65 KO MEF TNF90 rep2

value: p65 KO

value: TNFα treated 90mins


title: IKK2 KO MEF TNF 90 rep1


title: N4-2

description:
A
N4 Treg


title: H27472_muscle_sciRNA

value: Fetus muscle


title: p65 KO MEF TNF90 rep1


title: H27472_lung_sciRNA

source_name: RNA-seq of Homo sapiens: Fetus lung

value: Fetus lung


title: p65 KO MEF TNF45 rep2


title: MD_2K_NovaSeq

city: San Francisco

first: Daniel

last: Nguyen

address: 513 Parnassus Ave

institute: University of California San Francisco

library_source: genomic

data_processing:
Aligned with Bismark version 0.14.3 and --non_directional parameter
Genome_build: mm10
Supplementary_files_format_and_content: Read coverage (one bigWig file per sample)
Supplementary_files_format_and_content: CpG methylation percentage (one bigWig file per sample)

source_name: male germ cells

extract_protocol:
E13.5 testes were digested in 0.05% Trypsin-EDTA and immunostained with antibodies to PE-PECAM1 (Biolegend, 102407)and APC-c-Kit (Biolegend, 313205). Germ cells were identified on the basis of OCT4-GFP+ and further separated into AP (PECAM1-high;cKit-high) or MD (PECAM1-low;cKit-low) populations. Cells were lysed using EZ DNA Methylation-DirectTM Kit (Zymo D5020).
Bisulfite conversion and library preparation was carried out with the Pico Methyl-Seq Library prep kit (Zymo D5455).
Libraries were sequenced on NextSeq 500 High Output and NovaSeq 6000 S1 flow cells 484 yielding to 75-bp, and 50-bp paired-end reads, respectively for whole-genome bisulfite sequencing by post-bisulfite adapter tagging.

value: C57BL/6 x CD1

tag: age

value: Embryonic day 13.5

tag: cell type

value: Male-differentiated (MD) germ cell

value: male


title: AP_6K_NovaSeq

value: Apoptosis-poised (AP) germ cell


title: MD_6K_NovaSeq


title: p150DN 2-cell H3.3 ChIP-seq rep2

city: Fukuoka

first: Takashi

last: Ishiuchi

address: 3-1-1 Maidashi, Higashi-ku

department: Medical Institute of Bioregulation

country: Japan

institute: Kyushu University

description:
processed data file:
2C_p150DN_input-normalized-H33_bin1k.bw

data_processing:
For ChIP-seq data, paired-end reads were aligned to the mouse genome (mm10) using Bowtie2 with a default setting after removing adaptor sequences and low-quality reads by Trim Galore!.
Reads from PCR duplicates were removed by using Samtools ‘markdup’ with an option ‘-r’.
Input-normalized log2 fold enrichment in each bin was computed using deepTools bamCompare with an option '--binSize 1000'.
For CUT&RUN data, paired-end reads were aligned to the mouse genome (mm10) using Bowtie2 with an option '-X 700' after removing adaptor sequences and low-quality reads by Trim Galore!.
Reads from PCR duplicates were removed by using Samtools ‘markdup’ with an option ‘-r’.
Normalized read counts were computed using deepTools bamCoverage with options '--normalizeUsing RPKM' and '--binSize 1000'.
Genome_build: mm10
Supplementary_files_format_and_content: bigWig

source_name: p150DN 2-cell H3.3 ChIP-seq

growth_protocol: Male mouse ESCs (JM8A3N1) were cultured with the medium that consists of GMEM containing 15% FBS, 0.1 mM 2-mercaptoethanol, nonessential amino acid, sodium pyruvate, penicillin/streptomycin, LIF, 0.5 uM PD0325901, and 3 uM CHIR99021 on gelatin-coated plates. For ChIP-seq after mRNA injection, in vitro fertilization was performed.

extract_protocol:
For ChIP-seq, MNase-digested chromatin was used. For CUT&RUN, chromatin digested by protein A- protein G-MNase was used.
ULI-NChIP-seq protocol was used to prepare ChIP-seq libraries. CUT&RUN libraries were prepared as described before (Skene et al., eLife 2017).

treatment_protocol: For ULI-NChIP-seq for mRNA-injected 2-cell embryos, mRNA for EGFP or EGFP-p150DN (a dominant negetive p150) was injected into the cytoplasm of 1-cell embryos at 11 h post-insemination. Those developed to the late 2-cell stage were collected for ULI-N-ChIP-seq at 34 h post-insemination. For H3.3 CUT&RUN, wild-type or siRNA-transfected mESCs  were used.

value: hybrid C57BL/6 / DBA

tag: tissue/cell type

value: Embryo

tag: antibody


title: AP_2K_NovaSeq

tag: strain


title: p65 KO MEF TNF45 rep1

tag: cell line

tag: genotype

value: TNFα treated 45mins


title: H27472_liver_sciRNA

value: Fetus tissues

value: Fetus liver


title: p65 KO MEF UT rep2

value: Immortalized

value: Untreated


title: H27472_heart_sciRNA

value: Fetus heart


title: VN (notrogen stress)

city: Gurugram

first: Mandira

last: Kochar

state: Haryana

address: Nanobiotechnology Centre, Sustainable Agriculture Division, TERI Gram, Gual Pahari, Gurugram-Faridabad Highway

department: Sustainable Agriculture Division

institute: The Energy and Resources Institute, New Delhi

data_processing:
Sequenced reads were trimmed for adaptor sequence, and masked for low-quality sequence using CutAdapt and Trimmomatic  v0.36
Filtered reads mapped to A. brasilense Sp245 whole genome (GenBank Assembly accession: GCA_000237365.1) using Bowtie v2.1.0
The aligned reads were used to generate counts data using Rsubread package (Version 1.16.1) in R using the GCF file of the reference genome
The gene counts were converted into RPKM values using the edgeR package in R.
Genome_build: A. brasilense Sp245 (GenBank Assembly accession: GCA_000237365.1)
Supplementary_files_format_and_content: tab-delimited text files include count values of the sequenced RNA reads in each Sample

organism: Azospirillum baldaniorum

source_name: isolated from surface sterilized wheat root

growth_protocol: The wild-type strain Sp245 was grown in buffered standard succinate medium (SSM) under two nutritional conditions: control (SSM with full strength of nitrogen) and stress-inducing (SSM with half strength of nitrogen). The temperature used for incubation was 30 degrees C and cells were grown for 12h prior to RNA  extraction.

extract_protocol:
Total RNA was extracted using the Ambion PureLink RNA Mini kit (Invitrogen).
Small RNA libraries were constructed for sequencing according to the Illumina TruSeq Small RNA library protocol

value: pure bacterial culture

tag: growth condition

value: strain Sp245 grown in Nitrogen stress


title: p65 KO MEF UT rep1

value: p65 KO


title: p150DN 2-cell input rep2

description: processed data file:

source_name: p150DN 2-cell input


title: WT MEF TNF 90 rep2

value: Wildtype

value: TNFα treated 90mins


title: H27472_spleen_sciRNA

source_name: RNA-seq of Homo sapiens: Fetus spleen

value: Fetus spleen


title: H27472_eye_sciRNA

source_name: RNA-seq of Homo sapiens: Fetus eye

value: Fetus eye


title: Liver - STD_Cont - Rep6 [s3169]

source_name: Liver - STD_Cont

tag: Sex

value: male

tag: group id

tag: lineage

value: Control fatty acid

value: STD

value: liver


title: p150DN 2-cell H3.3 ChIP-seq rep1

value: hybrid C57BL/6 / DBA

value: Embryo


title: WT MEF TNF 90 rep1


title: WT MEF TNF 45 rep2

value: TNFα treated 45mins


title: H27472_adrenal_sciRNA

source_name: RNA-seq of Homo sapiens: Fetus adrenal

tag: development stage

value: Fetus tissues

tag: tissue

value: Fetus adrenal


title: H27471_thymus_sciRNA

source_name: RNA-seq of Homo sapiens: Fetus thymus

value: Fetus thymus


title: H27471_spleen_sciRNA


title: EGFP 2-cell H3.3 ChIP-seq rep2

description:
processed data file:
2C_GFP_input-normalized-H33_bin1k.bw

source_name: EGFP 2-cell H3.3 ChIP-seq


title: H2B MEF High_3

city: New Haven

first: Xiao

last: Hu

state: CT

address: 10 Amistad ST

department: Cell Biology

institute: Yale University

data_processing:
RNA-seq reads were mapped to mouse genome (mm10) or human genome (hg38) with TopHat2. Gene abundance was calculated using cuffnorm, which outputs read counts and the number of mapped fragments per kilobase of exon per million fragments (RPKM). Genes with RPKM ≥1 in two or more samples were selected for further analysis. Differentially expressed genes were identified by Cuffdiff followed by cutting off with FDR-adjusted P value < 0.05 and fold change > 2.
Genome_build: mm10, hg38

source_name: Reprogramming MEFs

growth_protocol: Reprogramming MEFs were cultured in mES medium + Dox (2 ug/mL). Medium was changed every other day. Reprogramming human secondary fibroblasts were cultured in mTeSRTM1 complete kit (STEMCELL technologies, 85850). Medium was changed every other day.

extract_protocol:
Total RNA was extracted with Trizol (ThermoFisher Scientific, invitrogen).
RNA-seq libraries were prepared with TruSeq Stranded mRNA Library Prep Kit (Illumina, RS-122-2101).

treatment_protocol: GFP low (10%) and GFP high (10%) cells were FACS-sorted.

value: mouse embryonic fibroblasts

tag: reprogramming day

value: Day 4


title: p150DN 2-cell input rep1

description: processed data file:


title: EGFP 2-cell input rep2

description: processed data file:

source_name: EGFP 2-cell input


title: WT MEF UT rep2

source_name: Mouse Embryonic Fibroblast

value: Immortalized

value: Untreated


title: H2B MEF High_2


title: WT MEF TNF 45 rep1

value: Wildtype


title: H27471_pancreas_sciRNA

source_name: RNA-seq of Homo sapiens: Fetus pancreas

value: Fetus pancreas


title: H27471_placenta_sciRNA

value: Fetus placenta


title: WT MEF UT rep1


title: EGFP 2-cell H3.3 ChIP-seq rep1


title: H27472_cerebellum_sciRNA

source_name: RNA-seq of Homo sapiens: Fetus cerebellum

value: Fetus cerebellum


title: EGFP 2-cell input rep1

description: processed data file:


title: H2B MEF High_1


title: p150KD ESC IgG CUTandRUN rep2

description:
processed data file:
p150KDES_IgG_CR_rep-merged_RPKM_bin1k.bw

source_name: p150KD ESC IgG CUTandRUN

value: Embryonic stem cell


title: H2B MEF Low_3


title: H27471_lung_sciRNA

source_name: RNA-seq of Homo sapiens: Fetus lung

value: Fetus lung


title: H2B MEF Low_2


title: H27471_muscle_sciRNA

source_name: RNA-seq of Homo sapiens: Fetus muscle

value: Fetus muscle


title: p150KD ESC IgG CUTandRUN rep1


title: EVI_Wild type replicate 1

city: Manchester

first: Adam

last: Stevens

address: Oxford Road

department: Medicine

country: United Kingdom

institute: University of Manchester

data_processing:
Ordered BAM files were generated against the mouse genome feature file Mus_musculus.GRCm38.75.gtf downloaded from Ensembl (ftp://ftp.ensembl.org/pub/current_gtf).
Data analysis for heatmaps was performed using Qlucore Omics Explorer 3.3 (Qlucore, Lund, Sweden) with a FPKM (Fragments Per Kilobase Million) cut-off of 10.
Further analysis used Deseq2, which converts read counts to a normalised value based using size factors to normalise for difference in the depth of sequence between samples (geometric size factor normalisation method) to calculate fold changes.
Genome_build: Mus_musculus.GRCm38.75.gtf
Supplementary_files_format_and_content: Deseq2 abundance matrix

source_name: murine haematopoietic progenitor cells

growth_protocol: Murine haematopoietic progenitor cells where isolated, purified and maintained as described previously (Paredes et al, 2018)

extract_protocol:
For Poly-A RNA sequencing (RNAseq) analysis of Evi1-mediated modulation of gene expression RNA was extracted from murine haematopoietic progenitor cells at 48 hrs after lentiviral transduction with Evi1-WT, Evi1-S436A or vector only and untransduced cells using the RNA/DNA Purification Micro Kit (Norgen Biotek Corp.).
Libraries were prepared with the Lexogen QuantSeq 3’ mRNA-Seq Library Prep Kit for Illumina (FWD) using an input of 200 ng and performing 14 cycles of amplification. Indexed libraries were then quantified using the Kapa Illumina Library quantification kit (Cat 07960336001) and pooled. 1 x 75bp sequence reads were generated by clustering 2.0pM of the library pool on a NextSeq500 High throughput run

tag: time

value: 48 hrs after lentiviral transduction

tag: vector


title: EVI_Wild type replicate 2


title: Liver - HFD_O3 - Rep2 [s3202]

source_name: Liver - HFD_O3

value: male

tag: diet

value: HFD

value: liver


title: EVI_Wild type replicate 3


title: controlKD ESC IgG CUTandRUN rep2

description:
processed data file:
contKDES_IgG_CR_rep-merged_RPKM_bin1k.bw

source_name: controlKD ESC IgG CUTandRUN


title: H2B MEF Low_1


title: H27471_liver_sciRNA

source_name: RNA-seq of Homo sapiens: Fetus liver

value: Fetus tissues

value: Fetus liver


title: H27471_heart_sciRNA

source_name: RNA-seq of Homo sapiens: Fetus heart

value: Fetus heart


title: EVI_S436A replicate 2


title: controlKD ESC IgG CUTandRUN rep1


title: cKO - Astrocyte specific TDP-43 homozygous conditional knockout mouse, ID-1649 [F1649_SPC]

first: Shuo-Chien

last: Ling

state: Singapore

address: 12 Science Drive 2, MD1, 16-03-H

department: Physiology

institute: National University of Singapore

description:
processed data file:
normTPM.csv
cKO_vs_cHet.csv
cKO_vs_control.csv

data_processing:
Sequenced reads filtered for low quality reads with skewer 0.2.2. (-Q 5)
The RNA-Seq reads were aligned and quantified using Kallisto v.0.44.0 with standard parameters and 100 bootstraps
DEG calling was performed using Sleuth v.0.30.0
Genome_build: GRCm38 ENSEMBL 94
Supplementary_files_format_and_content: csv file with gene abundance (TPM) for all samples
Supplementary_files_format_and_content: csv files with DE calls for pairwise comparisons of conditions

source_name: cKO - Astrocyte specific TDP-43 homozygous conditional knockout_spinal cord

extract_protocol:
Spinal cords were removed from 3-month old mice and flash frozen under liquid nitrogen. The RNA was harvested using Trizol reagent
RNA-Seq libraries were contructed using the Illumina TruSeq Sample Prep Kit

value: Gfap-Cre; Tardbp-fl/fl

tag: age

value: M

value: Spinal Cord


title: H27471_cerebellum_sciRNA


title: cKO - Astrocyte specific TDP-43 homozygous conditional knockout mouse, ID-1639 [F1639_SPC]

value: F


title: H27471_brain_sciRNA

source_name: RNA-seq of Homo sapiens: Fetus brain

value: Fetus brain


title: cKO - Astrocyte specific TDP-43 homozygous conditional knockout mouse, ID-1718 [F1718_SPC]


title: H27471_adrenal_sciRNA

source_name: RNA-seq of Homo sapiens: Fetus adrenal

value: Fetus adrenal


title: HP1gKO_Rep2_RNA-Seq

city: Madison

first: Rupa

last: Sridharan

state: WI

address: 330 N. Orchard Street

department: Wisconsin Institute for Discovery

institute: University of Wisconsin

data_processing:
Sequenced reads were trimmed, cropped, filtered by quality, and adapter sequence clipped using Trimmomatic paired-end mode, with the options “LEADING:3 TRAILING:3 CROP:95 HEADCROP:13 SLIDINGWINDOW:4:15 MINLEN:36”
Quality reads were aligned to mouse reference genome mm9 (and human reference genome hg18 to be used for normalization) via RSEM-1.2.4 with a mismatch per seed set to 2 and seed length set to 28
Differentially Expressed (DE) genes (PPDE > 0.95) was determined using EBSeq with median normalization using the human aligned reads matrix (MedianNorm(human_matrix))
TPM values for all genes was calculated using RSEM
Genome_build: mm9
Supplementary_files_format_and_content: text file containing genes, transcript ID, length, counts, transcripts per million (TPM), and FPKM.

source_name: V6.5 Mouse Embryonic Stem Cells

growth_protocol: Cells were maintained on irradiated mouse embryonic fibroblasts (MEFs) in ESC media (KnockOut DMEM, 15% fetal bovine serum (FBS), L-glutamine, Penicillin/Streptomycin, non-essential amino acids, 2-mercaptoethanol, and leukemia inhibitory factor)

extract_protocol:
RNA was extracted using TriZol followed by purification on Qiagen RNeasy Mini Kit. 1 ug of RNA was used for each sample, combined with 20ng of RNA from 293T (human) cells, prepared as above, as a spike-in control for sequencing normalization
cDNA library was constructed using TruSeq RNA Sample Preparation Kit (Illumina, RS-122-2002) according to the manufacturer’s instructions

treatment_protocol: 24 hrs prior to harvesting, cells were passaged onto gelatinized dish without irradiated MEFs in ESC media with 0.1% DMSO

value: HP1gamma KO ESCs


title: HP1gKO_Rep1_RNA-Seq


title: Vector Control replicate 3


title: H27464_spleen_sciRNA

source_name: RNA-seq of Homo sapiens: Fetus spleen

value: Fetus spleen


title: cHet - Astrocyte specific TDP-43 hemizygous conditional knockout mouse, ID-1844 [F1844_SPC]

description:
processed data file:
normTPM.csv
cHet_vs_control.csv
cKO_vs_cHet.csv

source_name: cHet - Astrocyte specific TDP-43 hemizygous conditional knockout_spinal cord

value: Gfap-Cre; Tardbp-fl/+


title: Vector Control replicate 1


title: WT_Rep2_RNA-Seq

value: WT ESCs


title: WT_Rep1_RNA-Seq


title: H27464_placenta_sciRNA

source_name: RNA-seq of Homo sapiens: Fetus placenta

value: Fetus placenta


title: RA2: RA patient2

source_name: FLS from rheumatoid arthritis patient 2

value: synovial tissue

tag: cell type

value: fibroblast-like synoviocytes


title: cKO - Astrocyte specific TDP-43 homozygous conditional knockout mouse, ID-1703 [F1703_SPC]


title: H27464_pancreas_sciRNA

source_name: RNA-seq of Homo sapiens: Fetus pancreas

value: Fetus pancreas


title: cHet - Astrocyte specific TDP-43 hemizygous conditional knockout mouse, ID-1720 [F1720_SPC]


title: cHet - Astrocyte specific TDP-43 hemizygous conditional knockout mouse, ID-1642 [F1642_SPC]


title: FGO input rep2

data_processing:
Paired-end reads were aligned to the mouse genome (mm10) using Bowtie2 with a default setting after removing adaptor sequences and low-quality reads by Trim Galore!.
Reads from PCR duplicates were removed by using Samtools ‘markdup’ with an option ‘-r’.
Normalized ChIP read counts was divided by normalized input read counts to compute fold enrichment in each bin.
Genome_build: mm10
Supplementary_files_format_and_content: bigWig

source_name: Oocyte

growth_protocol: Growing oocytes and fully-grown oocytes were collected from P10 and adult (8-12 weeks old) mouse ovaries, respectively.

extract_protocol:
MNase-digested chromatin was used for ULI-N-ChIP-seq.
ULI-N-ChIP-seq protocol was used for ChIP-seq.


title: EVI_S436A replicate 3

value: 48 hrs after lentiviral transduction


title: Vector Control replicate 2


title: Untreated replicate2

value: Untransfected


title: EVI_S436A replicate 1


title: FGO H3.3 ChIP-seq rep2

tag: chip antibody


title: H27464_lung_sciRNA

source_name: RNA-seq of Homo sapiens: Fetus lung

value: Fetus tissues

value: Fetus lung


title: FGO H3.3 ChIP-seq rep1


title: cHet - Astrocyte specific TDP-43 hemizygous conditional knockout mouse, ID-1700 [F1700_SPC]

value: M


title: Untreated replicate1


title: Control - TDP-43 floxed mouse, ID-1641 [F1641_SPC]

description:
processed data file:
normTPM.csv
cHet_vs_control.csv
cKO_vs_control.csv

source_name: Control - TDP-43 floxed_spinal cord

value: Tardbp-fl/fl

value: Spinal Cord


title: H27464_liver_sciRNA

value: Fetus liver


title: FGO input rep1


title: H27464_heart_sciRNA

value: Fetus heart


title: GO H3.3 ChIP-seq rep2


title: Naive-mouse-brain-3

city: Lexington

first: Ann

last: Stowe

state: Kentucky

address: 741 S. Limestone

department: Neurology

institute: University of Kentucky

data_processing:
Paired-end 150 bp read length Fastq files were checked for quality using fastqc (v0.11.2) and fastq_screen (v0.4.4)
Fastq files were mapped to human genome using STAR(v2.5.3a)
Read counts were generated using featureCounts (subread)
Differential expression was performed using edgeR
Normalized read counts generated using edgeR
mm10
Genome_build: tab delimited files that includes normalized read counts for each sample per gene

growth_protocol: Mouse husbandry and animal procedures were completed in conformation with guidelines and approved protocols by the Institutional Animal Care and Use Committee at UT Southwestern Medical Center.

extract_protocol:
Cells sorted into Clontech lysis buffer
Samples were processed using services of Omega Bioservices. Clontech SMART-Seq_v4 Ultra Low Input RNA was used for library preparation

treatment_protocol: Spleens were dissociated into single cell suspensions and processed through fluorescence-activated cell sorting   for isolating CD8 T cells.

value: CD8 T cells

value: brain


title: Control - TDP-43 floxed mouse, ID-1663  [F1663_SPC]

value: F


title: H27464_brain_sciRNA

value: Fetus brain


title: Control - TDP-43 floxed mouse, ID-1738 [F1738_SPC]


title: H27552_eye_sciRNA

source_name: RNA-seq of Homo sapiens: Fetus eye

value: Fetus eye


title: Naive-mouse-brain-1


title: Untreated replicate3

source_name: murine haematopoietic progenitor cells


title: H27458_eye_sciRNA


title: GO input rep2


title: Control - TDP-43 floxed mouse, ID-1734 [F1734_SPC]


title: GO H3.3 ChIP-seq rep1


title: FOLR2 positive TAMs from mouse #155

city: Philadelphia

first: Alba

last: Rodriguez Garcia

state: Pennsylvania

address: 3400 civic center boulevard

institute: Upenn

description:
expression_values.xls
FOLR2p_vs_FOLR2n_TAMs_paired_dex_processed_data_file.xls

data_processing:
100bp single-read sequencing was performed on an Illumina HiSeq 4000 sequencer. Illumina’s bcl2fastq version v2.17.1.14 software was used to convert bcl to fastq files.
Reads were filtered to retain only high quality reads. In addition, ribosomal reads and repeats were eliminated by alignment to a generic set of ribosomal/repeat sequences. Remaining reads were processed with RNA-Seq Unified Mapper (RUM) (Grant et al., Bioinformatics, 2011). Following RUM alignments to mouse genome (build mm10) and known transcripts (RefSeq, UCSC, ENSEMBL, etc.), a feature-level quantitation (transcript, exon, and intron) was output as a result.
To analyze global gene expression profiles, the number of uniquely aligning reads to transcripts in RefSeq were extracted from the RUM output. MDS plots, PCA plots and K-means heatmaps were generated using quantile normalization of log2 counts for evaluating clustering between samples and for outlier identification. A strong mouse-to-mouse bias was revealed in the samples. Consequently, differential expression analysis was performed (R library edgeR (Robinson et al. 2010)) using a design formula that included the mouse identifier as well as the FOLR2 status of the cells, i.e., the mouse-specific expression pattern is separated from the differential expression. Standard processing steps using dispersion estimation, GLM fit, and log-ratio testing were performed. The resulting p-values were adjusted for multiple testing using the default method (Benjamini and Hochberg) for the topTags function.
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: expression_values.xls: Excel file with expression values before differential expression analysis.
Supplementary_files_format_and_content: FOLR2p_vs_FOLR2n_TAMs_paired_dex_processed_data_file.xls: Excel file with information on differential expression analysis, including FC, CPM, LR, Pvalue and FDR for each gene transcript.

source_name: Tumor-associated macrophages from ID8 ovarian ascites

growth_protocol: 5 million ID8 mouse ovarian cancer cells were inoculated intraperitoneally in C57Bl/6 mice. 4 weeks later, ascites were collected through peritoneal wash.

extract_protocol:
Total RNA from FACS-sorted FRβ+ or FRβ- TAMs was obtained by using an RNeasy Plus Mini kit (QIAGEN) according to manufacturer’s instructions.
Libraries were prepared using TruSeq Stranded mRNA HT Sample Prep Kit (Illumina, Part number 20020595) as per standard protocol in the kit’s sample prep guide. Libraries were assayed for overall quality using HS D5000 ScreenTape assay (Agilent Technologies, Part numbers 5067-5592 and 5067-5593) of Agilent 2200 TapeStation System. Average library molarity was 13.9+/-4.2 nM.

treatment_protocol: Cells from the peritoneal wash were pelleted by centrifugation and lysed with ACK buffer. CD11b+ cells were then isolated by using magnetic beads (milteny) and subsequently stained by flow cytometry for live cells, CD45, F480 and FRb. Stained cells from each mouse were sorted by flow cytometry into 2 samples: FRb+ TAMs (Cd45+F480+FRb+) and FRb- TAMs (Cd45+F480+FRb-).

value: FRb+ TAMs (Cd45+F480+FRb+)

tag: mouse id


title: Naive-mouse-blood-2

value: blood


title: H27432_brain_sciRNA


title: GO input rep1

tag: strain


title: Naive-mouse-blood-3


title: H27431_thymus_sciRNA

source_name: RNA-seq of Homo sapiens: Fetus thymus

value: Fetus thymus


title: FOLR2 negative TAMs from mouse #155

value: FRb- TAMs (Cd45+F480+FRb-)


title: H27431_spleen_sciRNA

value: Fetus spleen


title: FOLR2 positive TAMs from mouse #58


title: sample_9

city: Helsinki

first: Jukka

last: Jernvall

address: P.O. Box 56 (Viikinkaari 9)

country: Finland

institute: University of Helsinki

data_processing:
10x genomics “cellranger” and R package “Seurat” were used to process the data.
Genome_build: mm10
Supplementary_files_format_and_content: Tab-delimited gene expression count values of each cell

source_name: Molar 1

growth_protocol: Tooth germs were dissected carefully under microscope from E14.5 C57BL/6JOlaHsd mice.

extract_protocol:
Each tooth was processed individually in the single-cell dissociation. The tooth germ was treated with 0.1 mg/ml liberase (Roche, Basel, Schwitzerland) in Dulbecco's solution for 15 min at 28°C in shaking at 300 rpm followed by gentle pipetting to detach the mesenchymal cells. Then the tissue preparation was treated with TrypLE Select (Life Technologies, Waltham, USA) for 15 min at 28°C in shaking at 300 rpm followed by gentle pipetting to detach the epithelial cells. The cells were washed once in PBS with 0,04% BSA. The cells were resuspended in 50 µl PBS with 0.04% BSA.
Library prepartion was done according to the manufacturer's instructions in Chromium single cell 3' library & gel bead Kit v3 (10x Genomics, Pleasanton, USA).

value: mandibular molar 1

value: wild type


title: 3-days-post-stroke-mouse-brain-3


title: H27431_placenta_sciRNA

data_processing:
Read alignment and gene count matrix generation for the single cell RNA-seq was performed using the pipeline that we developed for sci-RNA-seq3 (Cao et al. 2019) with minor modifications: Duplicates were removed using the unique molecular identifier (UMI) sequence (ED < 2, including insertions and deletions), reverse transcription (RT) index, hairpin ligation adaptor index and read 2 end-coordinate.
Genome_build: human reference genome (hg19)
Supplementary_files_format_and_content:
S1_metadata_cells.txt: Metadata of high-quality cells. Includes sample metadata and various per-cell QC stats, Louvain cluster id and cell type annotation, for each of the 4,062,965 high-quality cells used in the downstream analyses.
S2_Metadata_genes.txt: Metadata of genes. Includes gene id, short name and gene type information for each gene.
S3_gene_count.loom: Gene count matrix of cells. Includes expression UMI values for each gene in each cell. The gene count is stored in loom-formatted hdf5 file (read with function "scanpy.read_loom" in python)
S4_gene_expression_tissue.txt: Matrix of gene expression values across tissues. Includes normalized gene expression values (transcripts per million) for each tissue.
S5_gene_fraction_tissue.txt: Matrix of positive cell ratio for each gene across tissues. Includes the ratio number of cells expressing each gene in each tissue.
S6_gene_expression_celltype.txt: Matrix of positive cell ratio for each gene across tissues. Includes the ratio number of cells expressing each gene in each tissue.
S7_gene_fraction_celltype.txt: Matrix of positive cell ratio for each gene across main cell types. Includes the ratio number of cells expressing each gene for each type in each tissue.
S8_DE_gene_cells.txt: Differential gene expression test results for main cell types within each organ. For each gene, the “max_cell_type” is the cell type with the highest expression within the organ by transcripts per million (TPM) (“max.expr”). The “second_cell_type” is the cell type with the second highest expression within the organ by transcripts per million (TPM) (“second.expr”). The “fold.change” is the fold change between the max expression and second max expression. The “qval” is the false detection rate (one-sided likelihood ratio test with adjustment for multiple comparisons) for the differential gene expression test across different cell types within the organ.

extract_protocol:
On the day of nuclei isolation, aliquots of tissue powder (0.1-1g) were first incubated with 1 mL ice-cold cell lysis buffer (10 mM Tris-HCl, pH 7.4, 10 mM NaCl, 3 mM MgCl2 and 0.1% IGEPAL CA-630 from (Buenrostro et al. 2013), modified to also include 1% SUPERase In (Thermo Fisher Scientific, AM2696) and 1% BSA (NEB, B9000S)) and then transferred to the top of a 40 µm cell strainer (VWR, 10199-654). Tissues were homogenized through the strainer with the rubber tip of a syringe plunger (VWR, BD309646) in 4 ml cell lysis buffer. The filtered nuclei were then transferred to a new 15 ml tube (VWR, 21008-936) and pelleted by centrifuge at 500xg for 5 min and washed once with 1 ml cell lysis buffer. The nuclei were fixed in 5 ml ice-cold 4% paraformaldehyde (EMS, 15-4-100) for 15 min on ice. After fixation, the nuclei were washed twice in 1 ml nuclei wash buffer (cell lysis buffer without IGEPAL), and re-suspended in 500 µl nuclei wash buffer. The samples were split into two tubes with 250 µl in each tube and flash frozen in liquid nitrogen. For human cell extraction in renal and digestive organs (kidney, pancreas, intestine, and stomach) and paraformaldehyde fixation, we followed the procedure described in (Thomsen et al. 2016).
sci-RNA-seq3 library: The paraformaldehyde fixed nuclei were processed similarly to the published sci-RNA-seq3 protocol (Cao et al. 2019). For paraformaldehyde fixed cells, frozen fixed cells were thawed on 37°C water bath, spun down at 500xg for 5 min, and incubated with 500ul PBSI (1 x PBS, pH 7.4, 1% BSA, 1% SuperRnaseIn)  including 0.2% Triton X-100 for 3min on ice. Cells were pelleted and resuspended in 500ul nuclease free water including 1% SuperRnaseIn. 3ml 0.1N HCl were added into the cells for 5min incubation on ice (Rosenberg et al. 2018). 3.5ml Tris-HCl (pH = 8.0) and 35ul 10% Triton X-100 were added into cells to neutralize HCl. Cells were pelleted and washed with 1ml PBSR. Cells were pelleted and resuspended in 100ul PBSI. The following steps were similar with the sci-RNA-seq3 protocol (with paraformaldehyde fixed nuclei) with slight modifications: (1) We distributed 20,000 fixed cells (instead of 80,000 nuclei) per well for reverse transcription. (2) We replaced all nuclei wash buffer in following steps with PBSI. (3) All nuclei dilution buffer were replaced with PBS + 1% BSA.

value: Fetus tissues

value: Fetus placenta


title: sample_7


title: sample_4


title: Naive-mouse-brain-2


title: 3-days-post-stroke-mouse-brain-2


title: H27431_muscle_sciRNA

source_name: RNA-seq of Homo sapiens: Fetus muscle

value: Fetus muscle


title: FOLR2 positive TAMs from mouse #47


title: 3-days-post-stroke-mouse-brain-1


title: FOLR2 positive TAMs from mouse #3


title: H27431_lung_sciRNA

value: Fetus lung


title: 30-days-post-stroke-mouse-brain-3


title: H27431_liver_sciRNA

source_name: RNA-seq of Homo sapiens: Fetus liver

value: Fetus liver


title: p150DN 8-cell rep3

description:
8C_DN3_S16_L002
processed data file: RNAseq_p150DN_embryo_read_counts.txt

data_processing:
Paired-end reads were aligned to the mouse genome (mm10) using Bowtie2 with a default setting after removing adaptor sequences and low-quality reads by Trim Galore!.
Reads from PCR duplicates were removed by using Samtools ‘markdup’ with an option ‘-r’.
Normalized ChIP read counts was divided by normalized input read counts to compute fold enrichment in each bin.
RNA-seq reads were aligned to the mouse genome (mm10) using Hisat2 after removing adaptor sequences and low quality reads by Trim Galore!.
After the reads were aligned, the reads correspond to rRNA were removed. featureCounts was then used to assign the mapped reads to a transcriptional model file.
Genome_build: mm10
Supplementary_files_format_and_content: bigWig

source_name: p150DN 8-cell

growth_protocol: Early embryos were cultured in KSOM. Male mouse embryonic stem cells were cultured with the medium that consists of GMEM (Sigma-Aldrich) containing 15% FBS, 0.1 mM 2-mercaptoethanol, nonessential amino acid, sodium pyruvate, penicillin/streptomycin, LIF, 0.5 uM PD0325901, and 3 uM CHIR99021 on gelatin-coated plates.

extract_protocol:
MNase-digested chromatin was used for ULI-N-ChIP-seq. Total RNA in cell lysates was directly used for RNA-seq sample preparation according to the manufacturer's  instructions (SMART-seq stranded kit, TAKARA).
ULI-N-ChIP-seq protocol was used for ChIP-seq. For RNA-seq, SMART-seq stranded kit was used.

value: hybrid C57BL/6 / C3H

tag: tissue/cell type

value: Embryo


title: p150DN 8-cell rep2

description:
8C_DN2_S15_L002
processed data file: RNAseq_p150DN_embryo_read_counts.txt


title: FOLR2 negative TAMs from mouse #47


title: H27431_heart_sciRNA

source_name: RNA-seq of Homo sapiens: Fetus heart

value: Fetus heart


title: FOLR2 negative TAMs from mouse #3


title: 30-days-post-stroke-mouse-brain-2

value: CD8 T cells

value: brain


title: 30-days-post-stroke-mouse-brain-1


title: Naive-mouse-blood-1


title: p150DN 8-cell rep1

description:
8C_DN1_S11_L002
processed data file: RNAseq_p150DN_embryo_read_counts.txt


title: H27431_brain_sciRNA

source_name: RNA-seq of Homo sapiens: Fetus brain

value: Fetus brain


title: MD_6K_NextSeq

source_name: male germ cells

value: C57BL/6 x CD1

tag: genotype

value: Embryonic day 13.5

value: Male-differentiated (MD) germ cell

value: male


title: EGFP 8-cell rep3

description:
8C_cont3_S12_L002
processed data file: RNAseq_p150DN_embryo_read_counts.txt

source_name: EGFP 8-cell


title: FOLR2 negative TAMs from mouse #58

value: FRb- TAMs (Cd45+F480+FRb-)


title: H27423_thymus_sciRNA

value: Fetus thymus


title: FCCL23

first: frederic

last: capel

institute: INRA

data_processing:
Image analysis and base calling were performed using RTA 2.7.3 and bcl2fastq 2.17.1.14.
Genome_build: mm10

source_name: total RNA isolated from mouse liver using the Trizol extraction technique and suspended in water

extract_protocol:
RNA were isolated using the Trizol reagent and washing steps with Isopropanol/Ethanol procedure before solubilization in sterile water
Small RNA-Seq librairies were generated from 800 ng of total RNA (or from --- ng of purified small RNA fraction) using TruSeq Small RNA Library Prep Kit (Illumina, San Diego, CA), according to manufacturer's instructions. The protocol takes advantage of the natural structure common to most microRNA molecules that have a 3' hydroxyl group resulting from enzymatic cleavage by Dicer or other RNA processing enzymes. Briefly, in the first step, RNA adapters were sequentially ligated to each end of the RNA, first the 3' RNA adapter that is specifically modified to target microRNAs and other small RNAs, then the 5' RNA adapter. Small RNA ligated with 3' and 5' adapters were reverse transcribed and PCR amplified (30 sec at 98oC; [10 sec at 98oC, 30 sec at 60oC, 15 sec at 72oC] x 13 cycles; 10 min at 72oC) to create cDNA constructs. Amplified cDNA constructs of 140 to 160 nt were selectively isolated by acrylamide gel purification followed by ethanol precipitation.  The final cDNA libraries were checked for quality and quantified using capillary electrophoresis.

tag: sample id

value: Control fatty acid

value: HFD

value: Liver


title: FCCL22


title: MD_2K_NextSeq

tag: Sex


title: EGFP 8-cell rep1

description:
8C_cont1_S9_L002
processed data file: RNAseq_p150DN_embryo_read_counts.txt


title: FCCL21

tag: group id


title: EGFP 8-cell rep2

description:
8C_cont2_S10_L002
processed data file: RNAseq_p150DN_embryo_read_counts.txt


title: H27423_placenta_sciRNA

first: Junyue

last: Cao

institute: University of Washington

source_name: RNA-seq of Homo sapiens: Fetus placenta

value: Fetus tissues

value: Fetus placenta


title: H27423_lung_sciRNA

value: Fetus lung


title: sample_1

value: mandibular molar 1

value: wild type


title: AP_2K_NextSeq

value: Apoptosis-poised (AP) germ cell


title: H27423_liver_sciRNA

value: Fetus liver


title: AP_6K_NextSeq


title: EGFP blastocyst rep2

description:
Blast_cont2_S14_L002
processed data file: RNAseq_p150DN_embryo_read_counts.txt

source_name: EGFP blastocyst

value: hybrid C57BL/6 / C3H

value: Embryo


title: H27423_heart_sciRNA

value: Fetus heart


title: FCCL18

tag: lineage


title: H27423_brain_sciRNA

tag: development stage

value: Fetus brain


title: FCCL17

tag: tissue


title: 2-cell H3.1/H3.2 CUT&RUN rep2

description:
2C_H312_CR_rep2_S5_L002
processed data file: 2C_H312_CR_bin100.bw

source_name: 2-cell H3.1/H3.2 CUT&RUN


title: H27295_thymus_sciRNA


title: 2-cell H3.1/H3.2 CUT&RUN rep1

description:
2C_H312_CR_rep1_S7_L002
processed data file: 2C_H312_CR_bin100.bw


title: FCCL19


title: HCSD_H3K36me3_ChIP-Seq_R2

data_processing:
FASTQ files were aligned to the mm9 genome (and hg19 to be used for normalization) using Bowtie aligner with default parameters
BAM and index files were generated using SAMtools with the “view” and “index” commands, respectively
Total reads aligning to the human genome, hg19 were quantified, and a Scaling Factor was determined such that the total human mapped reads would be the same across samples
ChIP samples were normalized by the Scaling Factor using Deeptools "bamCoverage" command (using default 50bp bins) to generate bigWig files
Genome_build: mm9
Supplementary_files_format_and_content: peak call files generated using MACS2

source_name: V6.5 Mouse Embryonic Stem Cells

extract_protocol:
ESCs were harvested and MEF-depleted. Chromatin was prepared by cross-linking cells with 1% formaldehyde for 5 min, followed by adding glycine to 0.125M for 5 min. Cells were washed and resuspended in ChIP Lysis Buffer (50mM Tris-HCl pH8.0, 20mM EDTA,1% SDS, protease inhibitor cocktail) and sonicated using Covaris S220 for 14 cycles of alternating 45s on/off with peak power = 170, duty factor = 5, cycles per burst = 200, 10-13x106 cells at a time. Soluble chromatin was collected by centrifuging at 12,000 x g for 10 min. 20ug of chromatin was used for each sample, together with a 0.4ug spike-in of human chromatin from 293T cells (50:1 of sample to spike-in chromatin ratio). The combined chromatin was diluted with 9 parts volume of Dilution Buffer (16.7mM Tris pH8.0, 0.01% SDS, 1.1% Triton-X-100, 1.2mM EDTA, 167mM NaCl), and incubated with 3ug of H3K36me3 antibody (Active Motif, 61101) overnight at 4°C. Equal portions of protein A and protein G magnetic beads (Thermo Fisher Scientific, 1002D and 1004D, respectively) were washed and added to each sample for 2 hrs at 4°C. Following IP, beads were washed twice with low salt buffer (50 mM HEPES, 0.1% SDS, 1% Triton X-100, 0.1% deoxycholate, 1 mM EDTA, and 140 mM NaCl), high salt buffer (50 mM HEPES, 0.1% SDS, 1% Triton X-100, 0.1% deoxy- cholate, 1 mM EDTA, and 500 mM NaCl), LiCl buffer (20 mM Tris, 0.5% NP-40, 0.5% deoxycholate, 1 mM EDTA, and 250 mM LiCl), and TE. Elution of DNA was performed by incubating beads with elution buffer (50 mM Tris, 1 mM EDTA, and 0.1% SDS) followed by reverse cross-linking at 65°C overnight with 1% SDS. Samples were treated with RNase A for 30 min followed by 2 h of proteinase K digestion. Magnetic beads were removed, and DNA was purified by phenol:chloroform extraction followed by ethanol precipitation.
Libraries were prepared using the Ovation Ultralow System V2 (NuGen, 0344) according to manufacturer's protocol

treatment_protocol: Expression of rescue constructs were induced growing cells in ESC media containing 1ug/ml doxycyline for 72hrs.

value: V6.5 Mouse Embryonic Stem Cells

tag: genotype/variation

value: HP1g HCSD

tag: treatment

value: Doxycycline (1ug/ml) for 72 hrs


title: CD_H3K36me3_ChIP-Seq_R2

value: HP1g CD


title: FCCL16

value: HFD


title: sip150 mESC H3.3ChIP-seq rep2

description:
ES_H33_KD_rep2_S8_L001
processed data file: ESC_sip150_H33_bin100.bw

source_name: sip150 mESC H3.3ChIP-seq

value: Embryonic stem cell


title: FCCL20

value: Liver


title: H27295_heart_sciRNA

value: Fetus tissues


title: W174A_H3K36me3_ChIP-Seq_R2

value: HP1g W174A


title: H27098_placenta_sciRNA

value: Fetus placenta


title: I165E_H3K36me3_ChIP-Seq_R2

value: HP1g I165E


title: FCCL14

value: Control fatty acid


title: sip150 mESC input rep2

description:
ES_input_KD_rep2_S4_L001
processed data file: ESC_sip150_H33_bin100.bw

source_name: sip150 mESC input


title: V32M_H3K36me3_ChIP-Seq_R2

value: HP1g V32M


title: FCCL15


title: H27098_muscle_sciRNA

value: Fetus muscle


title: CSD_H3K36me3_ChIP-Seq_R2

value: HP1g CSD


title: FCCL13


title: Full-length_H3K36me3_ChIP-Seq_R2

value: HP1g Full length


title: FCCL12


title: Uninduced_H3K36me3_ChIP-Seq_R2

value: uninduced-KO


title: EGFP blastocyst rep1

description:
Blast_cont1_S13_L002
processed data file: RNAseq_p150DN_embryo_read_counts.txt

value: hybrid C57BL/6 / C3H

value: Embryo


title: FCCL11


title: siControl mESC input rep2

description:
ES_input_cont_rep2_S2_L001
processed data file: ESC_siCont_H33_bin100.bw

source_name: siControl mESC input


title: H27098_heart_sciRNA

value: Fetus heart


title: HP1gKO_H3K36me3_ChIP-Seq_R2

value: V6.5 Mouse Embryonic Stem Cells

value: HP1g KO


title: FCCL10

value: HFD


title: H27098_brain_sciRNA

value: Fetus brain


title: C3-/- GLY4

city: Paris

first: Anne

last: Grunenwald

state: Ile-de-France

address: 15 rue de l'Ecole de Médecine, Escalier E, 3ème étage

institute: INSERM UMRS1138 Cordeliers Research Center

data_processing:
Alignment STAR 2.7.1, Ensembl database mus musculus GRCm38 release 96
Quality control QC STAR
Normalized expression DESeq2 Package R
R 3.6.1
Genome_build: Ensembl database mus musculus GRCm38 release 96
Supplementary_files_format_and_content: Normalized matrix counts for all samples in tsv file, Differential analysis using DESeq2 for WT PBS vs Gly and Gly WT vs C3 KO in csv file

extract_protocol:
Thirty-μm-thick frozen sections of kidneys were cut with a Cryostat at -20°C (Leica AS-LMD, Leica Biosystem) and homogenized in 200μL of 1-Thioglycerol/Homogenization Solution (Maxwell® 16 LEV simplyRNA Tissue Kit Promega AS1280). The quality and quantity of mRNA were evaluated with the Agilent 2100 bioanalyzer using the Agilent TNA 6000 NanoKit, followed by retrotranscription to cDNA. All RNA Integrity Numbers superior to 7 were eligible for reverse transcription in cDNA
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: To induce rhabdomyolysis, we injected mice intramuscularly in the right thigh caudal muscle with 7.5 ml/kg 50% glycerol (>99,5% m/v G5516, Sigma, MO, USA). Glycerol was diluted in sterile water or PBS1X as control at day 0 and autoclaved to 108°C.

tag: strain background

value: 8 weeks old mice

value: glycerol

value: kidney


title: siControl mESC H3.3ChIP-seq rep1

description:
ES_H33_cont_rep1_S5_L001
processed data file: ESC_siCont_H33_bin100.bw

source_name: siControl mESC H3.3ChIP-seq

value: Embryonic stem cell


title: FCCL9

city: clermont ferrand

address: 28 place henri dunant

value: Control fatty acid

tag: diet

value: Liver


title: sip150 mESC H3.3ChIP-seq rep1

description:
ES_H33_KD_rep1_S7_L001
processed data file: ESC_sip150_H33_bin100.bw


title: H27058_placenta_sciRNA

city: Seattle

address: Foege Building S-210, 3720 15th Ave NE

value: Fetus tissues

value: Fetus placenta


title: FCCL8

value: STD


title: H3.3K36M midshaft rep2

data_processing:
Single-end reads were aligned to the mouse genome (mm10) using Hisat2  with options '--rna-strandness R' and '--dta' after removing adaptor sequences and low-quality reads by Trim Galore! with an option '-q 30'.
Reads aligned to ribosomal DNA were eliminated by using Bedtools intersect with an option '-v'
Assembly and quantification of transcripts were performed by StringTie with options '-e' and '-B'.
Normalized read counts was computed with igvtools in IGV.
Genome_build: mm10
Supplementary_files_format_and_content: tdf

source_name: Bone (tibia)

growth_protocol: E14.5 embryos were collected by crossing H3f3b(K36M-flox/K36M-flox) x Prx1-Cre, and tibias were isolated under a microscope.

extract_protocol:
mRNA was isolated by poly (dT) beads (Dynabeads mRNA DIRECT Micro Kit (Thermo Fisher Scientific))
NEBnext Ultra II Directional RNA library Prep Kit for Illumina (New England Biolabs) was used.

treatment_protocol: Isolated E14.5 tibias were trisected along the longitudinal axis and allocated to tibial end or midshaft samples.

value: tibia bone

tag: tissue region

value: midshaft

tag: developmental stage


title: C3-/- GLY3

tag: age


title: H3.3K36M midshaft rep3


title: H27098_liver_sciRNA

value: Fetus liver


title: H27058_pancreas_sciRNA

source_name: RNA-seq of Homo sapiens: Fetus pancreas

value: Fetus pancreas


title: H27098_lung_sciRNA

source_name: RNA-seq of Homo sapiens: Fetus lung

value: Fetus lung


title: WT_H3K36me3_ChIP-Seq_R2

tag: cell type

value: V6.5 Mouse Embryonic Stem Cells

value: WT


title: sip150 mESC input rep1

description:
ES_input_KD_rep1_S3_L001
processed data file: ESC_sip150_H33_bin100.bw

tag: strain


title: H27098_adrenal_sciRNA

source_name: RNA-seq of Homo sapiens: Fetus adrenal

value: Fetus adrenal


title: FCCL6


title: siControl mESC H3.3ChIP-seq rep2

description:
ES_H33_cont_rep2_S6_L001
processed data file: ESC_siCont_H33_bin100.bw

tag: tissue/cell type

tag: chip antibody


title: C3-/- GLY2

value: 8 weeks old mice


title: H27058_lung_sciRNA


title: FCCL5

tag: sample id


title: siControl mESC input rep1

description:
ES_input_cont_rep1_S1_L001
processed data file: ESC_siCont_H33_bin100.bw


title: Control midshaft rep3

tag: genotype

value: control


title: WT GLY4

value: glycerol

value: kidney


title: H27058_liver_sciRNA

source_name: RNA-seq of Homo sapiens: Fetus liver


title: FCCL4

tag: group id

value: Control fatty acid


title: Control midshaft rep2


title: Control midshaft rep1


title: FCCL3

tag: lineage

value: Liver


title: FCCL7


title: H26547_thymus_sciRNA

source_name: RNA-seq of Homo sapiens: Fetus thymus

tag: development stage

value: Fetus tissues

value: Fetus thymus


title: WT GLY2

tag: tissue


title: FCCL2

value: STD


title: WT GLY1

tag: genotype/variation


title: H3.3K36M end rep3

value: tibia bone

value: end


title: H26547_spleen_sciRNA

source_name: RNA-seq of Homo sapiens: Fetus spleen

value: Fetus spleen


title: H3.3K36M end rep2


title: H26547_placenta_sciRNA

value: Fetus placenta


title: C3-/- PBS4

tag: treatment

value: PBS


title: H3.3K36M midhsft rep1

value: midshaft


title: C3-/- PBS3

tag: strain background


title: H3.3K36M end rep1


title: Infected #5 Female

city: Salt Lake City

first: Keke

middle: Celeste

last: Fairfax

state: UT

address: 15 N Medical Drive East

department: Pathology

institute: University of Utah

data_processing:
The sequencing data were first assessed using FastQC (Babraham Bioinformatics, Cambridge, UK) for quality control
Then all sequenced libraries were mapped to the mouse genome (UCSC mm10) using STAR RNA-seq aligner with the following parameter: “--outSAMmapqUnique 60”
The reads distribution across the genome was assessed using bamutils (from ngsutils)
Uniquely mapped sequencing reads were assigned to mm10 refGene genes using featureCounts (from subread) with the following parameters: “-s 2 –p –Q 10
Quality control of sequencing and mapping results was summarized using MultiQC . Genes with read count per million (CPM) > 0.5 in more than 2 of the samples were kept
The data was normalized using TMM (trimmed mean of M values) method.
Differential expression analysis was performed using edgeR. False discovery rate (FDR) was computed from p-values using the Benjamini-Hochberg procedure
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample

source_name: bone marrow derived macrophages

growth_protocol: Mice we fed high fat diet for 10 days before either infection or mock infection (For controls) and maintained on HFD throughout. At 10 weeks post infection bones marrow was harvested and cultured in M-CSF for 6 days to generate macrophages.

extract_protocol:
cells were harvested, washed in 1X PBS and then RNA was harvested using Trizol reagent. RNA was DNase treated (NEB) and then cleaned with Qiagen MinElute Cleanup kit.
200 nanograms of RNA per sample were used to prepared dual-indexed strand-specific cDNA library using KAPA mRNA Hyperprep Kit (Roche)

treatment_protocol: Cells are unstimulated Day 6 bone marrow derived macrophages

value: Bone marrow

tag: gender

value: female

tag: infection

value: 5 schistosoma mansoni


title: Infected #4 Female


title: H26547_pancreas_sciRNA

value: Fetus pancreas


title: C3-/- GLY1

value: 8 weeks old mice

value: glycerol


title: Control end rep3

tag: tissue region

tag: developmental stage

value: control


title: C3-/- PBS2

tag: age

value: kidney


title: H27058_brain_sciRNA

source_name: RNA-seq of Homo sapiens: Fetus brain

value: Fetus tissues

value: Fetus brain


title: WT GLY3

value: WT


title: Infected #3 Female

tag: strain


title: C3-/- PBS1


title: H26547_lung_sciRNA

value: Fetus lung


title: H26547_heart_sciRNA

source_name: RNA-seq of Homo sapiens: Fetus heart

value: Fetus heart


title: Control end rep2

value: tibia bone

value: end


title: FCCL1

source_name: total RNA isolated from mouse liver using the Trizol extraction technique and suspended in water

value: Control fatty acid

tag: diet

value: STD

value: Liver


title: Infected #2 Female

value: Bone marrow

value: female


title: WT PBS4

value: PBS


title: Infected #1 Female

value: 5 schistosoma mansoni


title: WT PBS3

value: 8 weeks old mice


title: Uninfected #4 Female


title: H3.3K36M H3K27me3 ChIP-seq rep2

data_processing:
Single-end reads were aligned to the mouse genome (mm10) using Bowtie2 with a default setting after removing adaptor sequences and low-quality reads by Trim Galore! with an option '-q 30'.
Reads from PCR duplicates were removed by using Samtools 'markdup' with an option '-r'.
After confirming reproducibility between replicates, they were merged by using 'divide_bam.py' in RSeQC and Samtools 'merge' so that each replicate data contributes equally to the merged file.
Normalized ChIP read counts was divided by normalized input read counts to compute fold enrichment in each bin using deepTools 'bamCompare'.
Genome_build: mm10
Supplementary_files_format_and_content: bigWig

growth_protocol: E14.5 embryos were collected by crossing H3f3b(K36M-flox/K36M-flox) mice with Prx1-Cre mice, and tibias were isolated .

extract_protocol:
MNase-digested chromatin was used for ChIP-seq.
ULI-N-ChIP-seq protocol was used for ChIP-seq.

treatment_protocol: Isolated tibias were trisected along the longitudinal axis and the tibial samples at the center (tibial midshaft) were used for ChIP-seq.

tag: chip antibody


title: H3.3K36M H3K27me3 ChIP-seq rep1


title: H26350_thymus_sciRNA

value: Fetus thymus


title: H26547_adrenal_sciRNA

value: Fetus adrenal


title: WT PBS1

value: kidney


title: WT PBS2


title: Control H3K27me3 ChIP-seq rep1

value: control


title: Uninfected #2 Female


title: H26350_placenta_sciRNA

source_name: RNA-seq of Homo sapiens: Fetus placenta

value: Fetus tissues

value: Fetus placenta


title: Control H3K27me3 ChIP-seq rep2


title: H26350_pancreas_sciRNA

value: Fetus pancreas


title: Uninfected #3 Female


title: PAI1het_Rep3

city: Chicago

first: Douglas

last: Vaughan

state: IL

address: Arkes Pavilion, Suite 2330, 676 N. St. Clair Street

institute: Northwestern University Feinberg School of Medicine

description: PAI-1 heterozygous ad lib fed liver mRNA

data_processing:
Alignment:  Sequenced reads were aligned to the mm10 reference mouse genome using STAR
Quantification of gene expression: gene expression at exons was quantified as integer counts using HOMER
Differenial expression analysis: differentially expressed exonic RNAs were identified using DESeq2 (FDR-adjusted p-value <0.05 and |LFC| > 2).
Genome_build: mm10
Supplementary_files_format_and_content: Excel file with differential expression and individual replicate normalized rlog values

source_name: Liver

extract_protocol:
Liver was flash frozen with liquid nitrogen.  RNA harvested from frozen liver using Qiagen RNA Easy Mini Kit (Cat#: 74104, Qiagen)
mRNA libraries were constructed using KAPA mRNA HyperPrep kits (Cat#kk8580, KAPA)

value: 21 Weeks

value: PAI-1 heterozygous


title: H3.3K36M H3K36me3 ChIP-seq rep2

value: tibia bone


title: H26350_adrenal_sciRNA


title: PAI1Het_Rep1


title: H3.3K36M H3K36me3 ChIP-seq rep1


title: Control end rep1

value: end


title: Infected #4 Male

value: male


title: PAI1het_Rep2


title: Control H3K36me3 ChIP-seq rep2


title: WT_Rep3

description: Male WT ad lib fed liver mRNA

value: wild type


title: H26350_lung_sciRNA

value: Fetus lung


title: Control H3K36me3 ChIP-seq rep1


title: Infected #5 Male

value: Bone marrow


title: Untransfected_293T_3

city: La Jolla

first: Gene

last: Yeo

state: CA

address: 2880 Torrey Pines Scenic Dr. Room 3805/Yeo Lab

institute: UCSD

description: poly(A)+ RNA

data_processing:
Raw reads were adapter-trimmed using Cutadapt (version 1.14)
Sequenced reads were aligned to hg19 genome using STAR (version 2.5.2b) and sorted using samtools (version 1.5)
Gene counts were quantified from sorted BAM files using featureCounts (version 1.5.0) of the Subread (Liao et al., Nucleic Acids Research 2013) package using "gene" as a metafeature. Annotated gene length and gene counts were subsequently used to calculate transcript per-million (TPM) for each gene in each library.
For downsampling prior to downstream editing analysis, samtools view -bs INT.FRAC was used for proportional downsampling of read pairs to achieve sampling depth between 15-35 million aligned reads
Aligned BAM files were run through SAILOR (v1.0.4) using the following parameters-- min_variant_coverage: 5, alpha: 0, beta: 0, edit_fraction: 0.01
BED files that are output corresponding to positive and negative strands of the genome from SAILOR are combined into one BED file and filtered based upon confidence score (Washburn et al., Cell Reports 2014)
Recurrent sites between replicates were determined using pybedtools (version 0.8.0) intersect with the following options: wo=True, s=True
Genome_build: hg19
Supplementary_files_format_and_content: Matrix tables containing normalized transcripts per-million (TPM) data for every annotated gene; BED files containing editing events per library

source_name: HEK293T cells

growth_protocol: HEK293T cells were maintained in DMEM supplemented with 10% Fetal Bovine Serum and routinely passaged 2-3 times per week upon reaching confluency

extract_protocol:
Total RNA was collected with TRIzol reagent using manufacturers' protocol
Libraries were constructed using the TruSeq Stranded mRNA Library Prep kit (Cat# 20020594) according to manufacturers' instructions
poly(A)+ RNA-seq

treatment_protocol: In a 24 well-plate format, cells were transfected with 100 ng Cas-ADAR2DD plasmid and 400 ng gRNA plasmid using Lipofectamine 3000 reagent and allowed to incubate for 48 hours

tag: cell type

value: Immortalized human epithelial kidney cell

tag: treatmant

value: untreated


title: Untransfected_293T_2

description: poly(A)+ RNA


title: WT_Rep2

description: Male WT ad lib fed liver mRNA


title: H26350_spleen_sciRNA

growth_protocol: Human fetal tissues were obtained by the UW Birth Defects Research Laboratory (BDRL) under a protocol approved by the University of Washington Institutional Review Board. Gestational age, reported as the number of weeks post-fertilization, was estimated from fetal foot length. Tissues of interest were isolated and rinsed in 1X HBSS (with Ca2+ and Mg2+) then blotted dry on a semi-damp gauze. Dried tissue was placed on a heavy-duty foil or in cryotube, snap frozen in liquid nitrogen, and then stored at -80°C.

value: Fetus spleen


title: WT_Rep1

description: Male WT ad lib fed liver mRNA


title: Infected #1 Male

value: 5 schistosoma mansoni


title: ME13E10M1L

data_processing:
Illumina bcl2fastq2 v2.17.1.14 for basecalling
The quality control of the rna-seq reads were done by AfterQC, Trimmomatic , MultiQC and FastQC
The ribosomal rRNA were filtered out using SortMeRna
The reads where aligned to mouse genome using STAR (1.5) with default parameters (GRCm38/mm10/Ensembl release 79 - March 2015) )
The gene expression was measured by counting the corresponding reads of the exons. This step was performed by htseq-count with parameters (-s reverse -t exon -i gene_id)
Genome_build: mm10
Supplementary_files_format_and_content: Tab-delimited gene expression count values of each samples

source_name: Molar 1

growth_protocol: Tooth germs were dissected carefully under microscope from E13.5, E14.5 or E16.5 C57BL/6JOlaHsd mice.

extract_protocol:
The tooth germ was homogenised into TRI Reagent (Merck, Darmstadt, Germany) using Precellys 24 -homogenizer (Bertin Instruments, Montigny-le-Bretonneux, France). The RNA was extracted by guanidium thiocyanate-phenol-chloroform method and then further purified by RNeasy Plus micro kit (Qiagen GmbH, Hilden, Germany) according to manufacturer's instructions.
The cDNA libraries were prepared with Ovation Mouse Universal RNAseq System (Tecan, Zürich, Schwitzerland).

tag: embryonic day

value: Molar 1 tooth germ


title: H3.3K36M H3K36me2 ChIP-seq rep1

tag: genotype

value: H3K36me2 (Cell Signaling Technology, #2901, lot 5)


title: Cas13d_NT_gRNA_2

description: poly(A)+ RNA

value: Transfected with dCas13d-ADAR2(E488Q) + NT gRNA for 48 hours


title: Uninfected #1 Female

value: female


title: Uninfected #4/#5 Pooled Male


title: Control H3K36me2 ChIP-seq rep2

value: control


title: ME13-E9M1R


title: Untransfected_293T_1

description: poly(A)+ RNA


title: Uninfected #3 Male


title: Infected #3 Male


title: ME13-E7M1L


title: Cas13d_NT_gRNA_1

description: poly(A)+ RNA


title: Cas13d_CYFIP2_gRNA_2

description: poly(A)+ RNA

value: Transfected with dCas13d-ADAR2(E488Q) + CYFIP2 gRNA for 48 hours


title: Uninfected #2 Male


title: H3.3K36M input rep2


title: ME13-E5M1R


title: Cas13d_CYFIP2_gRNA_1

description: poly(A)+ RNA


title: Uninfected #1 Male


title: H3.3K36M H3K36me2 ChIP-seq rep2


title: Infected #2 Male


title: ME13-E3M1L


title: Control input rep2


title: H3.3K36M input rep1


title: Stomach sci-ATAC-seq3

first: Silvia

last: Domcke

address: William H. Foege Hall, 3720 15th Ave NE

department: Genome Sciences

data_processing:
Please see associated publication for details on data processing.
Seurat object with both gene by cell matrix used for cell type annotation (RNA assay) and peak by cell matrix (peaks assay) used for downstream analyses
Genome_build: hg19
Supplementary_files_format_and_content:
tissue_filtered.seurat.RDS files: Seurat object for each tissue, containing only high-quality cells remaining after all filtering steps, including peak module-based filtering of doublets as described in the Cicero part of the methods section of the associated publication. Contain both gene by cell matrix used for cell type annotation (RNA assay) and peak by cell matrix (peaks assay) used for downstream analyses. Include the following metadata information for each cell: number of reads in gene bodies + 2kb upstream of TSS (nCountRNA), number of gene bodies + 2 kb upstream of TSS that contain at least one read (nFeature_RNA), cell barcode, sample name, donor ID, estimated gestational age based on foot length (day_of_pregnancy), sex, tissue, experimental batch, total number of reads, total number of deduplicated reads, total number of deduplicated reads that fall into peaks, total number of deduplicated reads that fall into a 2 kb window centered on TSS, fraction of reads in peaks (frip), fraction of reads in 2 kb window centered on TSS (frit), number of 5 kb windows of the X, Y and autosomal chromosomes respectively containing reads, fraction of unique reads falling in ENCODE blacklist regions, Louvain cluster ID (resolution = 0.3), number of reads in peaks (nCount_peaks), number of peaks that contain at least one read (nFeature_peaks), tissue UMAP coordinates based on the peaks assay, assigned cell type.
File_S1.Master_list_of_sites.txt.gz: Chromosomal location, width, read number in the object evenly subsampled across cell types, and indication of whether this site was z-score filtered for downstream analyses, for each site within a merged set of 1.05 M peaks of accessibility.
File_S2.Metadata_of_high_quality_cells.txt.gz: Cell metadata for all high-quality cells remaining after all filtering steps, including peak module-based filtering of doublets as described in the Cicero part of the methods section of the associated publication cells. Includes tissue of origin, donor ID, estimated gestational age, sex, experimental batch, total number of reads, total number of deduplicated reads, total number of deduplicated reads that fall into peaks, total number of deduplicated reads that fall into a 2 kb window centered on TSS, fraction of reads in peaks (frip), fraction of reads in 2 kb window centered on TSS (frit), number of peaks that contain at least one read (nFeature_peaks), Louvain cluster ID and UMAP coordinates of per tissue (not combined) UMAP visualizations and cell type annotation.
File_S3.Motif_enrichments_across_cell_types.txt.gz: For each of the 579 motifs from the JASPAR vertebrate database, the enrichment in accessible sites in each of the main 54 cell types was determined using a linear regression model. Fold-change of the mean motif occurrence in sites of a given cell type relative to the rest of the dataset and matching Benjamini Hochberg-adjusted p-values are reported for each motif-cell type pair.
File_S4.Specificity_scores_for_top_10000_sites_per_cell_type.txt.gz: The top 10,000 specific sites for each of the 54 cell types were calculated for each site/cell type pair using Jensen-Shannon divergence. A higher score indicates a peak that is more specific to a given cell type.
File_S5.Cicero_coaccessibility_scores_by_cell_type.csv.gz: Comma-separated table of Cicero co-accessibility scores greater than 0.1, generated for each of 101 cell type/tissue pairs. The first two columns are the coordinates in hg19 of the two tested sites. Each of the remaining columns represents the co-accessibility scores for each of the cell types. NA values indicate that the pair of sites was not tested because of insufficient depth or that the co-accessibility value was less than 0.1.
File_S6.Cicero_gene_activity_scores_by_cell_type.csv.gz: Comma-separated combined triplet sparse matrix table of Cicero gene activity scores for each of 101 cell type/tissue pairs. The first column is gene symbols, the second column is cell IDs with cell type and tissue, and the third column is the associated gene activity score. NA values indicate that there was insufficient accessibility to calculate a gene activity score.
File_S7.Motif_enrichment_across_clusters_in_UMAP_of_sites.txt.gz: For each of the 579 motifs from the JASPAR vertebrate database, the enrichment in each of the 15 Louvain clusters in the UMAP of sites was determined using a linear regression model. Fold-change of the mean motif occurrence in a given cluster relative to the rest of the dataset and matching Benjamini Hochberg-adjusted p-values are reported for each motif-cluster pair.

source_name: Stomach

extract_protocol:
Nuclei were extracted directly from cryopreserved tissues (please see associated publication for more details). A detailed version of the full sci-ATAC-seq3 workflow is also available on protocols.io.
Please see associated publication for details on library construction. A detailed version of the full sci-ATAC-seq3 workflow is also available on protocols.io.

value: estimated gestational age 89-125d

value: Stomach


title: RNA_Eomes_null_rep_2

city: Oxford

first: Luke

middle: Thomas Gilbert

last: Harland

address: South Parks Road

department: Sir William Dunn School of Pathology

institute: Oxford University

data_processing:
Paired-end reads were aligned against the mm10 genome using the STAR RNA-seq aligner with default parameters outputting bam files using --outSAMtype BAM SortedByCoordinate (Dobin et al., 2013).
BAM file primary alignments with a mapping quality of > 254 were treated as RNA-Seq data and imported into Seqmonk 1.45.4.  (https://www.bioinformatics.babraham.ac.uk/projects/download.html#seqmonk).
The RNA-Seq quantitation pipeline (p<0.05 and multiple testing correction applied) in SeqMonk utilizing DESeq2 (Love et al., 2014) was performed to identify significantly differentially expressed genes (p<0.05, fold change > 1.5 and FPKM >1).
Genome_build: mm10
Supplementary_files_format_and_content: [.txt] Read Counts and DESeq2 Results from SeqMonk

source_name: Day 4 Flk-1hi/PdgfRa- EB cells

growth_protocol: WT (CCE) and Eomes-null (CCE, clone 6A6) ESC lines were maintained in feeder free culture conditions in serum + LIF as previously described(Costello et al., 2011). 48-72 hrs prior to induction of hematopoietic differentiation cells were washed with PBS and cultured in serum free ES media containing 50% Neurobasal Media (Gibco, Cat # 21103049), 50% DMEM/F12 (Gibco, Cat # 11320033), supplemented with 0.5X of both N2 (Gibco, Cat#17502048) and B27 (Gibco, Cat# 17504044), 1%Pen/Strep, 1% glutamine, 0.05% BSA (Gibco, Cat# 15260037), 1 uM PD0325091, 3 uM CHIR99021 and 1000 U/ml LIF. At D0 cells were dissociated using Trypsin-LE (Gibco) and seeded at a density of 1×10^5 cells ml in serum-free differentiation (SF-D) media(Nostro et al., 2008) and cultured on an orbital shaker at 70 rpm for ~18 hrs in the absence of growth factors to form EBs. At D2, EBs were split 1:3 in SF-D media containing recombinant human (rh) VEGF (5 ng ml-1; R&D Systems), rhBMP4 (10 ng ml-1; R&D Systems) and Activin A (5 ng ml-1; R&D Systems) for 48 hr. At D4, EBs were dissociated, stained with Flk-1-APC (Cat# 17-5821-81) and PdgfRa-PECy7 (Cat# 25-1401-82) antibodies and FACS sorted.

extract_protocol:
RNA was isolated from Flk-1hi/PdgfRa- single cell suspensions (1.5x105 cells) from three independent hematopoietic differentiations of WT (CCE) and Eomes-null (clone 6A6, CCE) cells using the RNeasy Micro Kit (QIAGEN, Cat#74004). These cell samples were taken from the same cells that were also used for ATAC-seq (see below).
Total RNA was normalized to 800ng per sample, depleted of cytoplasmic and mitochondrial ribosomal RNA sequences (Ribo-Zero Gold rRNA Removal Kit (H/M/R), Cat: #MRZG12324) and library preparation was performed using the Illumina TruSeq Stranded Total RNA Library Prep (H/M/R) (Cat: #20020597), followed by sequencing (75-cycle paired end) on the Illumina HiSeq4000 platform.

value: hematovascular mesoderm

value: Eomes-null


title: RNA_Eomes_null_rep_3


title: Control input rep1

first: Takashi

last: Ishiuchi

address: 3-1-1 Maidashi, Higashi-ku

source_name: Bone (tibia)

value: tibia bone


title: Spleen sci-ATAC-seq3

description: Seurat object with both gene by cell matrix used for cell type annotation (RNA assay) and peak by cell matrix (peaks assay) used for downstream analyses

source_name: Spleen

value: Spleen


title: ME14-E8M1L


title: a-ama 2-cell H3.3 ChIP-seq rep2

description:
H33_ama2C_rep2_S6
processed data file: ama2C_H33_bin100.bw

source_name: a-ama 2-cell H3.3 ChIP-seq

value: hybrid C57BL/6/JF-1

tag: tissue/cell type

value: Embryo


title: ME13-E1M1R

tag: tissue


title: RNA_Eomes_null_rep_1


title: Placenta sci-ATAC-seq3

source_name: Placenta

value: Placenta


title: RNA_WT_rep_3

value: wildtype


title: Control H3K36me2 ChIP-seq rep1


title: a-ama 2-cell input rep2

description:
input_ama2C_rep2_S8
processed data file: ama2C_H33_bin100.bw

source_name: a-ama 2-cell input


title: Pancreas sci-ATAC-seq3

source_name: Pancreas

value: Pancreas


title: RNA_WT_rep_2


title: Muscle sci-ATAC-seq3

source_name: Muscle

value: Muscle


title: a-ama 2-cell H3.3 ChIP-seq rep1

description:
H33_ama2C_rep1_S5
processed data file: ama2C_H33_bin100.bw


title: ME14-E6M1R

value: Molar 1 tooth germ


title: Thymus sci-ATAC-seq3

source_name: Thymus

value: Thymus


title: ME13-E2M1L


title: ME14-E5M1R