title: Skeletal muscle Lane 1

city: Baltimore

first: Marc

middle: K

last: Halushka

state: MD

address: 720 Rutland Avenue / Ross Rm 632B

department: Pathology

institute: Johns Hopkins University SOM

description: scRNA-seq

data_processing:
Reads were mapped and counted using zUMIs 2.2.3 with default settings and barcodes provided as a list. zUMIs utilizes STAR (2.5.4b) to map reads to an input reference genome and featureCounts through Rsubread (1.28.1) to tabulate counts and UMI tables.
Initial data processing was performed using the Cell Ranger version 3.1.0 pipeline (10x Genomics, Pleasanton, California). Reads were mapped to the mm10 version of the mouse genome. We used GRCm38 from Ensembl concatenated with ERCC spike-in references for the reference genome and gene annotations
Genome_build: mm10
Supplementary_files_format_and_content: raw gene count

source_name: flexor digitorus brevis

growth_protocol: Normal care of the mus musculus.

extract_protocol:
A collagenase digestion was performed on the flexor digitorum brevis muscle in a dish containing DMEM with 1% penicillin/streptomycin, 1% fetal bovine serum, and 2mg/mL Collagenase Type II, kept at 37C for 1.5 hours. After 1.5 hours the muscle was transfered to a non-collagenase media and titurated. Single myocytes were isolated using a large particle fluorescent activated cell sorter using a flow channel size of 500 um. The COPAS SELECT Flow Pilot Platform was used to isolate cell populations. These sorted cells were placed individually into 96-well plates. Capture plate wells contained 5 µl of capture solution (1:500 Phusion High-Fidelity Reaction Buffer, New England Biolabs; 1:250 RnaseOUT Ribonuclease Inhibitor, Invitrogen).
Single cell libraries were then prepared using the mcSCRB-seq protocol. Briefly, cells were subjected to proteinase K treatment followed by RNA desiccation to reduce the reaction volume. RNA was subsequently reverse transcribed using a custom template-switching primer as well as a barcoded adapter primer. The customized mcSCRB-seq barcode primers contain a unique 6 base pair cell-specific barcode as well as a 10 base pair unique molecular identifier (UMI). Transcribed products were pooled and concentrated, with unincorporated barcode primers subsequently digested using Exonuclease I treatment. cDNA was PCR-amplified using Terra PCR Direct Polymerase (Takara Bio). Final libraries were prepared using 1ng of cDNA per library with the Nextera XT kit (Illumina) using a custom P5 primer.

treatment_protocol: No treatment of the mus musculus.

value: >3 months of age

value: flexor digitorus brevis


title: Skeletal muscle Lane 2

status: Public on Jan 15 2020

type: SRA

country: USA

description: scRNA-seq

library_source: transcriptomic

molecule: total RNA

organism: Mus musculus

tag: strain

tag: age

tag: tissue


title: L4_DB08_Tumor_Cisplatin_ES28E

city: RTP

first: John

middle: S.

last: House

state: NC

address: 111 TW Alexander Drive

department: Biostatistics & Computational Biology Branch

institute: National Instititute of Environmental Health Sciences

description:
ES28E
S1500 TempOseq RNA
L4_DB08_S88_L001_R1_001.fastq.gz
processed data file: TCTC_Mapped_Reads.csv

data_processing:
.gz files were concatenated from Lane1/2.
Reads Aligned against s1500+ Manifest (BioSpyder) Human. This was a TempOseq experiment with the s1500+ probeset (January 2018).
Unambiguous Counts assigned for n = 2977 Probes.
Supplementary_files_format_and_content: TCTC_Mapped_Reads.csv: Comma-separated file

organism: Homo sapiens

source_name: Ewing's Sarcoma Cells 2D

extract_protocol:
Cell lysates from plates or 3D tumors were prepared using lysis buffer (provided with TempO-seq probes). After 10-min incubation at room temperature, lysates were stored at −80 °C until testing.
RNA libraries were prepared for sequencing using standard Illumina protocols.

tag: cell type

value: Ewing's Sarcoma Cells 2D

tag: exposure

value: Cisplatin

tag: treatment concentration


title: L4_DA12_Tumor_MAP_ES210F

description:
ES210F
S1500 TempOseq RNA
L4_DA12_S48_L001_R1_001.fastq.gz
processed data file: TCTC_Mapped_Reads.csv

value: MAP

value: low


title: L4_DC12_Tumor_MAP_ES310E

description:
ES310E
S1500 TempOseq RNA
L4_DC12_S144_L001_R1_001.fastq.gz
processed data file: TCTC_Mapped_Reads.csv

value: high


title: L4_DA11_Tumor_Vincristine_ES34G

description:
ES34G
S1500 TempOseq RNA
L4_DA11_S46_L001_R1_001.fastq.gz
processed data file: TCTC_Mapped_Reads.csv

value: Vincristine


title: bmECs replicate 2

city: Muenster

first: Kishor Kumar

last: Sivaraj

address: Roentgenstrasse 20

department: Department of Tissue Morphogenesis

country: Germany

institute: Max Planck Institute for Molecular Biomedicine

description: processed data file: all_FPKM.txt

data_processing:
Illumina RTA v2 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm10 whole genome using TopHat-2 v2.0.13 with parameters -g 2
HTSeq was used to count the aligned reads on a per gene basis (Version: HTSeq-0.6.1). The count data were normalized, Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using the DESeq2 package
Genome_build: mm10
Supplementary_files_format_and_content: abundance measurements

source_name: bmECs

extract_protocol:
Endothelial cells isolated by FACS. RNA was isolated with RNeasy Plus Micro kit(QIAGEN). Illumina TruSeq Stranded Total RNA Library Prep Kit (Cat#RS-122-2203) was used with 100 ng of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: strain background

tag: genetype/variation

value: wildtype

value: bone

value: FACS-sorted bone endothelial cells


title: bmECs replicate 1

description: processed data file: all_FPKM.txt


title: L4_DA09_Tumor_Dexamethasone_ES46F

description:
ES46F
S1500 TempOseq RNA
L4_DA09_S42_L001_R1_001.fastq.gz
processed data file: TCTC_Mapped_Reads.csv

value: Dexamethasone


title: L4_DA10_Tumor_Methotrexate_ES16E

description:
ES16E
S1500 TempOseq RNA
L4_DA10_S44_L001_R1_001.fastq.gz
processed data file: TCTC_Mapped_Reads.csv

value: Methotrexate


title: mpECs replicate 3

description: processed data file: all_FPKM.txt

source_name: mpECs


title: mpECs replicate 1

description: processed data file: all_FPKM.txt


title: L2_DF10_Tumor_Linsitinib_TC-2DD-F2

description:
TC-2DL-F2
S1500 TempOseq RNA
L2_DF10_S284_L001_R1_001.fastq.gz
processed data file: TCTC_Mapped_Reads.csv

value: Linsitinib


title: L2_DE10_Tumor_Linsitinib Control_TC-2DD-B4

description:
TC-2DL-B4
S1500 TempOseq RNA
L2_DE10_S236_L001_R1_001.fastq.gz
processed data file: TCTC_Mapped_Reads.csv

value: Linsitinib Control


title: Ser5-RNAPII-S-WT

city: Granada

first: Jordi

last: Martorell-Marugan

address: Avenida de la Ilustración 114

department: Bioinformatics Unit

country: Spain

institute: GENyO

description: ChIP-seq

library_source: genomic

data_processing:
bcl2fastq v2.18.0.12 used for basecalling
Cutadapt 1.9.1 with parameters -q 20 -m 30 used for quality-trimming sequences
STAR_2.5.2b used for aligning sequences to mm9 reference genome
Samtools 1.3.1 used to discard alignments with quality < 200 and to sort bam files
BamCompare 3.1.3 used to normalize with BPM method and to apply a smoothing of 10 bp. For ChIP-Seq samples, signal from input samples was sustracted to the samples signal. For RNA-Seq samples, signal from the reverse strand was sustracted to the signal in the forward strand.
Genome_build: mm9
Supplementary_files_format_and_content: Bigwig files containing Reads per Million (RPM) with a 10 bp smoothing. ChIP-Seq signal was normalized against input signal. For RNA-Seq, signal in forward strand has positive values, while signal in reverse strand has negative values.

molecule: genomic DNA

source_name: Fucci-Jarid2 fl/fl mESCs

growth_protocol: Fucci-mESCs were cultured in 5% CO2 at 37 ºC on 0.1% gelatin-coated dishes in DMEM KO (Gibco) media supplemented with 10% FCS, leukaemia-inhibiting factor (LIF), penicillin/streptomycin (Gibco), L-glutamine (Gibco) and 2-mercaptoethanol (Gibco) as described previously (Landeira et al. 2015) and hygromycin B (InvivoGen)

extract_protocol:
ChIP assays were mainly performed as described previously (Stock et al, 2007) with minor modifications to optimize the protocol for an input of 1 million cells and suspension conditions.
ChIP-seq libraries were generated from 1-5 ng of immunoprecipitated DNA with the NEBNext Ultra DNA Library Prep kit for Illumina (#7370) according to manufacturer’s instructions.

treatment_protocol: Cell-cycle sorting using an Aria Fusion cell sorter

value: Fucci-Jarid2 fl/fl mESCs

value: Mouse embryonic stem cells

value: Mixed background:129/Sv / C57BL/C6

tag: developmental stage


title: L2_DD10_Tumor_Linsitinib Control_TC-2DD-B3

description:
TC-2DL-B3
S1500 TempOseq RNA
L2_DD10_S188_L001_R1_001.fastq.gz
processed data file: TCTC_Mapped_Reads.csv


title: L2_DG10_Tumor_Linsitinib_TC-2DD-F3

description:
TC-2DL-F3
S1500 TempOseq RNA
L2_DG10_S332_L001_R1_001.fastq.gz
processed data file: TCTC_Mapped_Reads.csv


title: L2_DH10_Tumor_Linsitinib_TC-2DD-F4

description:
TC-2DL-F4
S1500 TempOseq RNA
L2_DH10_S380_L001_R1_001.fastq.gz
processed data file: TCTC_Mapped_Reads.csv


title: Ser5-RNAPII-S-Input

description: ChIP-seq


title: Ser5-RNAPII-S-KO

description: ChIP-seq

source_name: Fucci-Jarid2 -/- mESCs

value: Fucci-Jarid2 -/- mESCs


title: L4_DA07_Tumor_Control_ES32E

description:
ES32E
S1500 TempOseq RNA
L4_DA07_S38_L001_R1_001.fastq.gz
processed data file: TCTC_Mapped_Reads.csv

value: Ewing's Sarcoma Cells 2D

value: Control


title: L1_CH10_Tumor_Doxorubicin_TC-2DD-F4

description:
TC-2DD-F4
S1500 TempOseq RNA
L1_CH10_S356_L001_R1_001.fastq.gz
processed data file: TCTC_Mapped_Reads.csv

value: Doxorubicin


title: Ser5-RNAPII-G2-M-WT

description: ChIP-seq


title: L1_CF10_Tumor_Doxorubicin_TC-2DD-F2

description:
TC-2DD-F2
S1500 TempOseq RNA
L1_CF10_S260_L001_R1_001.fastq.gz
processed data file: TCTC_Mapped_Reads.csv


title: L2_DC10_Tumor_Linsitinib Control_TC-2DD-B2

description:
TC-2DL-B2
S1500 TempOseq RNA
L2_DC10_S140_L001_R1_001.fastq.gz
processed data file: TCTC_Mapped_Reads.csv


title: Ser5-RNAPII-G2-M-KO

description: ChIP-seq


title: Ser5-RNAPII-G1-WT

description: ChIP-seq


title: L1_CG10_Tumor_Doxorubicin_TC-2DD-F3

description:
TC-2DD-F3
S1500 TempOseq RNA
L1_CG10_S308_L001_R1_001.fastq.gz
processed data file: TCTC_Mapped_Reads.csv


title: L1_CE10_Tumor_Doxorubicin Control_TC-2DD-B4

description:
TC-2DD-B4
S1500 TempOseq RNA
L1_CE10_S212_L001_R1_001.fastq.gz
processed data file: TCTC_Mapped_Reads.csv

value: Doxorubicin Control


title: L1_CD10_Tumor_Doxorubicin Control_TC-2DD-B3

description:
TC-2DD-B3
S1500 TempOseq RNA
L1_CD10_S164_L001_R1_001.fastq.gz
processed data file: TCTC_Mapped_Reads.csv


title: RNA-G2-M-KO

data_processing:
Library strategy: 4sU-seq
bcl2fastq v2.18.0.12 used for basecalling
Cutadapt 1.9.1 with parameters -q 20 -m 30 used for quality-trimming sequences
STAR_2.5.2b used for aligning sequences to mm9 reference genome
Samtools 1.3.1 used to discard alignments with quality < 200 and to sort bam files
BamCompare 3.1.3 used to normalize with BPM method and to apply a smoothing of 10 bp. For ChIP-Seq samples, signal from input samples was sustracted to the samples signal. For RNA-Seq samples, signal from the reverse strand was sustracted to the signal in the forward strand.
Genome_build: mm9
Supplementary_files_format_and_content: Bigwig files containing Reads per Million (RPM) with a 10 bp smoothing. ChIP-Seq signal was normalized against input signal. For RNA-Seq, signal in forward strand has positive values, while signal in reverse strand has negative values.

extract_protocol:
4su experiments were carried out as described in Rutkowski and Dölken, 2017 with minor modifications to optimize the protocol to cell-cycle sorting and for a reduced number of cells.
Libraries were generated from 75 ng of 4Su-RNA using the NextFlex Rapid Directional RNA-seq kit (Bioo Scientific #NOVA-5138-07) according to manufacturer’s instructions.

treatment_protocol: 4-thiouridine labelling during 1 hour 37ºC. Cell-cycle sorting using an Aria Fusion cell sorter


title: RNA-S-WT


title: Ser5-RNAPII-G1-KO

description: ChIP-seq


title: RNA-G2-M-WT


title: L4_DA08_Tumor_Cisplatin_ES26G

description:
ES26G
S1500 TempOseq RNA
L4_DA08_S40_L001_R1_001.fastq.gz
processed data file: TCTC_Mapped_Reads.csv

value: Cisplatin


title: RNA-S-KO


title: mpECs replicate 2

description: processed data file: all_FPKM.txt


title: RNA-G1-WT


title: ru226_3

city: New York

first: Brandoch

last: Cook

state: NY

address: 1300 York Ave LC-711

department: Surgery

institute: Weill Cornell Medicine

description: RNA-seq

data_processing:
Raw reads were aligned using STAR v2.3.0e_r291
Read counting was performed using htseq-count v0.6.0
Genome_build: mm10
Supplementary_files_format_and_content: counts

source_name: murine C2C12 cells

growth_protocol: Cells were cultured at 37 degrees C in 5% carbon dioxide in Dulbecco's modifed Eagle media using 10 % fetal bovine serum.

extract_protocol:
Total RNA was isolated from 12-well plates using Trizol reagent, then 100 ng was used per sample to generate stranded mRNA library.
Illumina TruSeq RNA Library Prep Kit v2 with poly-A selection and stranded RNA-seq.

treatment_protocol: Cells were treated with either 10 μM final concentration of the screening compound or with the equivalent volume of DMSO for a period of 2 days before RNA extraction.

tag: cell line

value: C2C12 myoblast cell line bipotential for muscle and osteoblast

tag: agent


title: RNA-G1-KO


title: ru226_2

description: RNA-seq


title: ru226_1

description: RNA-seq


title: Distal- Microglia ablated 13

city: Calgary

first: Jeff

last: Biernaskie

state: Alberta

address: 3330 Hospital Drive NW

department: Comparative Biology and Experimental Medicine

country: Canada

institute: University of Calgary

description: Males and females grouped

data_processing:
After sequencing, the bcl data was converted to fastq data files using the Illumina BCL2FASTQ utility. Alignment was performed using BWA-MEM Galaxy Version 0.7.17.1 in “mem” alignment mode against mm10 reference genome with default parameters.
R programming language for GenomicAlignments, Pheatmap, and DESeq2 packages; Ingenuity Pathway Analysis. Expression was summarized at the gene level using the “union” mode of summarize overlaps of transcriptsByGene. A false discovery rate corrected p-value of 0.1 for the Wald test was used for linear model of factors; genes passing this threshold were used in subsequent analysis in Ingenuity Software, using default parameters.
Genome_build: mm10
Supplementary_files_format_and_content: Excel file including size-factor normalized values for each sample

source_name: Spinal cord-distal uninjured

extract_protocol:
All tissue was collected, and storage at -80 until RNA extraction. For RNA extractions, all samples were processed together following manufacturers recommendations (RNeasy mini kit, 74104, Qiagen). Total RNA extracts were quantitated and quality assessed using a TapeStation assay. All RNA integrity (RIN) values were greater than 0.68.  All samples were subjected to reverse transcription and Multiple Displacement Amplification (MDA) with the Qiagen FX Single Cell RNA Library preparation kit (150073) and the manufacturer’s protocol.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: 75 cycle high-output nextSeq kit

tag: genotype/variation

value: Cx3cr1-CreER :Rosa26-iDTR+/-

value: Ventral spinal cord

tag: sample type

value: Distal uninjured control

value: 14 months

tag: Sex

value: pooled male and female


title: dmso_3

description: RNA-seq

value: DMSO


title: dmso_1

description: RNA-seq


title: LPC lesion- Microglia ablated 12

description: Males and females grouped

source_name: Spinal cord-LPC lesion

value: LPC lesion

value: 13 months


title: LPC lesion- Microglia ablated 14

description: Males and females grouped

value: 15 months


title: Distal- Microglia ablated 11

description: Males and females grouped

value: 12 months


title: dmso_2

description: RNA-seq


title: Uninjured aged-matched control

description:
10X Genomics Single Cell RNAseq v2
# FACS sorted cells: 2,500 cells; Recovered: 705 cells

data_processing:
All raw FASTQs reads were aligned to the mouse GRCm38.p5 (primary assembly) reference genome using the STAR algorithm and quantified through the 10X Genomics cellranger v2.0.1 single cell pipeline, with default and recommended parameter. ANNOTATIONS!! Only mapped reads were used for normalization before aggregating cells. The resulting gene-barcode matrix was imported into Seurat (v2.1.0 ) R toolkit for quality control and all downstream analysis. All functions were run with default or recommended parameters, unless specified otherwise. Low quality cells (<400 genes/cell and <20 cells/gene) were excluded from the overall experiment. Gene expression was log normalized to a scale factor of 10,000. To begin unsupervised clustering of cells, a selection of highly variable genes was obtained and used to calculate up to 75 principle components. Significance of principle components was determined using JackStraw analysis and by creating a PCElbowPlot. PCs 1 to 20 were used to run and plot a tSNE plot for all cells.
Genome_build: mm10 (GRCm38.p5)
Supplementary_files_format_and_content: Filtered gene - barcode matrix output from CellRanger

molecule: polyA RNA

source_name: Uninjured

extract_protocol:
4 weeks following tamoxifen, spinal cords were dissected and enzymatically dissociated with 2mg/ml collagenase-4 for 1 hour at 37 oC. Cell suspensions were subsequenty strained and centrifuged before removing debris (Mytlenyi debris removal kit). Liberated single cells were re-suspended in 1% bovine serum album in HBSS before FACS purification. For FACS purification, forward and side scatter gates were used to exclude debris, and cell doublets, then tdTomato cells were purified.
Libraries were prepared according to 10X Genomics ChromiumTM Single Cell 3’ Reagent Guidelines v2 Chemistry as per the manufacturer’s protocol. In brief, single cells were sorted into 1% BSA–PBS and partitioned into Gel Bead-In-EMulsions (GEMs) using 10xTM GemCodeTM Technology. This process lysed cells and enabled barcoded reverse transcription of RNA, generating full-length cDNA from poly-adenylated mRNA. DynaBeads® MyOneTM Silane magnetic beads were used to remove leftover biochemical reagents, then cDNA was amplified by PCR over 10 cycles. Quality control size gating was used to select cDNA amplicon size prior to library construction. Read 1 primer sequences were added to cDNA during GEM incubation. P5 primers, P7 primers, i7 sample index, and Read 2 primer sequences were added during library construction. Quality control and cDNA quantification was performed using Agilent High Sensitivity DNA Kit. Sequencing was performed first using Illumina MiSeq SR50 to approximate the number of recovered cells in each sample.

treatment_protocol: Cre-recombination was initiated with two intraperitoneal injections of 4-hydroxy-tamoxifen (4-OHT; 1mg in sterile sunflower oil, Sigma-Aldrich) at postnatal week 4.

value: spinal cord

tag: transgenic strain

tag: background strain

tag: facs strategy

value: tdTomato+positive


title: Distal- Microglia ablated 7

description: Males and females grouped

value: 8 months


title: LPC lesion- Microglia ablated 8

description: Males and females grouped

value: 9 months


title: Distal- non microglia ablated 5

description: Males and females grouped

value: Cx3cr1-CreER :Rosa26-iDTR-/-

value: 6 months


title: LPC lesion- non microglia ablated 4

description: Males and females grouped

value: 5 months


title: LPC lesion- non microglia ablated 2

description: Males and females grouped

value: 3 months


title: Sample_PSJorrT96R2

city: University Park

last: Carlson

state: Pennsylvania

address: 323 Forest Resources Building

department: Ecosystem Science and Management

institute: Pennsylvania State University

data_processing:
The raw sequencing reads were trimmed and filtered by using Trimmomatic v0.36
Clean reads were mapped to the Salix purpurea transcriptome reference sequence using Bowtie2 version 2.2.8, with parameters set to --local and --sensitive mode.
Counts of mapped and unmapped reads were extracted from bam files by using Samtool v1.3 stat function
Genome_build: Salix purpurea reference genome predicted transcript sequences (Salix purpurea v1.0, DOE-JGI, Phytozome 12.0 https://phytozome.jgi.doe.gov/pz/portal.html#!info?alias=Org_Spurpurea)
Supplementary_files_format_and_content: tab-delimited text files includes raw counts of sequencing reads mapped to each transcript

organism: Salix x rubra

source_name: Leaf

extract_protocol:
One single young, expanded leaf was collected near the top of a dominant shoot of each plant, folded and pushed into a 2 mL grinding tube, and quick frozen in liquid nitrogen, then stored in a -80°C freezer.Total RNA was extracted from each leaf sample using a Spectrum™ Plant Total RNA Kit (Sigma-Aldrich, St. Louis, MO) and checked for quality using an Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA 95051, USA)
RNA-Seq bar-coded libraries were prepared on a robotic platform using the Illumina Trueseq Library Kit 2

value: Leaf

tag: time course

value: 96 hours

tag: replicate

tag: genotype id

value: PSJorr


title: Sample_PSJorrT24R1

tag: tissue

value: 24 hours


title: Sample_PSJorrT6R2

value: 6 hours


title: Sample_PSJorrT24R3


title: Sample_PSJorrT6R3


title: L1_CC10_Tumor_Doxorubicin Control_TC-2DD-B2

description:
TC-2DD-B2
S1500 TempOseq RNA
L1_CC10_S116_L001_R1_001.fastq.gz
processed data file: TCTC_Mapped_Reads.csv

tag: cell type

value: Ewing's Sarcoma Cells 2D

tag: exposure

value: Doxorubicin Control


title: Distal- non microglia ablated 1

description: Males and females grouped

value: Ventral spinal cord

value: Distal uninjured control

tag: age

value: 2 months

value: pooled male and female


title: Sample_PSJorrT0R3

value: 0 hour


title: Distal- Microglia ablated 9

description: Males and females grouped

value: Cx3cr1-CreER :Rosa26-iDTR+/-

value: 10 months


title: Sample_PSJorrT0R2


title: Sample_PSJorrT96R3


title: Day 5 post-lysolecithin injury

description:
10X Genomics Single Cell RNAseq v2
# FACS sorted cells: 2,500 cells; Recovered: 580 cells

source_name: Injured

value: spinal cord

value: tdTomato+positive


title: Sample_PS94006T6R3


title: 43TGFBpluspLZRSCEBPa

city: Utrecht

first: Ana

last: Lourenço

address: Uppsalalaan 8

country: Netherlands

institute: UMC Utrecht

data_processing:
Sequencing reads were mapped against the reference genome (hg19 assembly) using TopHat v2.0.9 as previously described (Trapnell et al., 2012). Only uniquely mapped reads were selected for further analysis.
guide transcripts were assembled using CuffLinks v2.2.1. Reads were quartile normalized using the –library-norm-method quartile option.
Differential gene analysis was performed using CuffDiff.
Genome_build: hg19
Supplementary_files_format_and_content: Tab-delimited text files containing  average differential gene expression FPKM normalized values

source_name: Immortalized human mammary epithelial cells

growth_protocol: Upon lentiviral transduction HMLEs were grown and expanded under puromycin selection before RNA-isolation (0.5 µg/mL)

extract_protocol:
total RNA-isolation with RNAeasy kit (Qiagen)
TruSeq stranded ribo-zero kit (Illumina)
Samples were sequenced on the NextSeq 500 (Illumina), SE75

treatment_protocol: Cells were left untreated or treated with TGF-β (2.5ng/ml) for 24 hours

tag: vector

tag: treatment

value: Plus TGF-β


title: 33TGFBminpLZRSCEBPa

value: Immortalized human mammary epithelial cells

value: Minus TGF-β


title: Sample_PS94006T6R2

value: Leaf


title: Sample_PS94006T6R1


title: 32TGFBminpLZRSCEBPa


title: 42TGFBpluspLZRSCEBPa


title: LPC lesion- non microglia ablated 6

description: Males and females grouped

value: Cx3cr1-CreER :Rosa26-iDTR-/-

value: LPC lesion

value: 7 months


title: 23TGFBpluspLZRS

value: pLZRS


title: Sample_PS94006T24R2

value: 24 hours


title: Distal- non microglia ablated 3

description: Males and females grouped

value: Ventral spinal cord

value: Distal uninjured control

value: 4 months


title: 22TGFBpluspLZRS


title: Sample_PS94006T0R3

value: 0 hour


title: 13TGFBminpLZRS


title: Sample_PS94006T24R1


title: Sample_PS94006T0R2


title: 12TGFBminpLZRS


title: Sample_PS94006T0R1


title: Sample_PS4006T96R2

value: 96 hours


title: Uninfected host foreskin fibroblast (1 week) replicate 3

city: Parkville

first: Alexandra

last: Garnham

state: Victoria

address: 1G Royal Parade

country: Australia

institute: Walter and Eliza Hall Institute of Medical Research

data_processing:
The base calling and quality scoring were determined using Real-Time Analysis on board software v2.4.6
The human and toxoplasma genomes were combined. Reads were aligned to this combined genome by Rsubread version 1.24.1
Reads counts were summarized using the Rsubread featureCounts function.  Human genes were identified by Entrez Gene ID and NCBI annotation. Toxoplasma genes were identified using annotation available through ToxoDB (http://toxodb.org/toxo/)
Genome_build: hg38 (Homo sapien), ME49 (Toxoplasma gondii)
Supplementary_files_format_and_content: tab-delimited text files wre written from the R prompt; columns represent Entrez Gene ID (human)/ToxoDB ID (Toxoplasma), total gene length (total base count of all exons) and the number of reads mapping to that gene

source_name: Foreskin

growth_protocol: Parasites were lysised and incoluated (or not) onto confluent HFF (host cells) at an MOI of 0.2 in either D1 ot iM media for 24 hours or 1 week.

extract_protocol:
RNA was extracted using the RNeasy kit (Qiagen)
100ng of total RNA was prepared and indexed separately for IlluminaTM sequencing using the TruSeq RNA sample Prep Kit (Illumina) as per manufacturer’s instruction.  Each library was quantified using the Agilent Tapestation and the Qubit™ DNA BR assay kit for Qubit 3.0® Fluorometer (Life technologies).  The indexed libraries were pooled and diluted to 1.5pM for paired end sequencing (2x 81 cycles) on a NextSeq 500 instrument using the v2 150 cycle High Output kit (Illumina) as per manufacturer’s instructions (generating 80bp paired-ends)

treatment_protocol: host cells were washed with PBS and dislodged with trypsin before being FACS sorted for the presence of mCherry.

tag: infection

value: Uninfected

tag: toxoplasma stage

tag: toxoplasma strain

tag: incubation time

value: 1 week

tag: incubation media

value: iM - RPMI-HEPES  supplemented with 5% v/v fetal calf serum at pH 8.1-8.2


title: Uninfected host foreskin fibroblast (1 week) replicate 2


title: Sample_PS4006T96R3


title: Sample_PS122T96R3


title: Uninfected host foreskin fibroblast (24 hours) replicate 3

value: D1 - Dulbecco's Modified Eagle medium supplemented with 1% v/v fetal calf serum and 1% v/v Glutamax


title: Uninfected host foreskin fibroblast (24 hours) replicate 2


title: Sample_PS4006T96R1


title: LPC lesion- Microglia ablated 10

description: Males and females grouped

tag: genotype/variation

value: Cx3cr1-CreER :Rosa26-iDTR+/-

tag: sample type

value: 11 months

tag: Sex

value: pooled male and female


title: Uninfected host foreskin fibroblast (1 week) replicate 1


title: mRNAs from Fusarium graminearum ∆GzZC190 mutant under toxoflavin condition

city: Busan

first: Jungwook

last: Park

address: Pusan National University, 2, Busandaehak-ro 63beon-gil, Geumjeong-gu, Busan 609-735, Korea

department: Microbiology

country: South Korea

institute: Pusan National University

data_processing:
The filtered reads of raw data were processed using the BWA-MEM algorithm with default parameters.
SAM files were converted to BAM files of binary format, and then sorted by chromosomal coordinates using the SAMtools program.
Mapped reads per annotated gene were counted by Bamtoreadcount.
Reads per kilobase of exon per million mapped sequence reads were calculated for normalization.
RPK100M = 100 x RPKM
Genome_build: Fusarium graminearum PH-1 ASM24013v3
Supplementary_files_format_and_content: *txt: Tab-delimited text files include gene information, raw count, RPKM, and RPK100M for each Sample.

organism: Fusarium graminearum

source_name: Fungal culture containing toxoflavin (100 mg l-1), ∆GzZC190 mutant

growth_protocol: Fusarium graminearum wild-type strain GZ03639 and toxoflavin-sensitive mutant strain (∆GzZC190) were grown in 50 ml of complete medium at 25°C with shaking at 200 rpm for 72 h.

extract_protocol:
The mycelia were grinding in liquid nitrogen and total RNAs were extracted with NucleoSpin RNA Plant Kit (Machey-Nagel GmbH & Co. KG) according to the manufacturer’s protocol.
RNA-sequencing libraries were prepared using an Illumina TruSeqTM RNA sample prep kit (Illumina), according to the manufacturer’s protocols. Sequencing was performed on an Illumina HiSeq2000 instrument at the National Instrumentation Center for Environmental Management (NICEM).

treatment_protocol: The filtrated mycelia were incubated in 50 ml of minimal medium with presence of toxoflavin 100 mg l-1 for 24 h at 200 rpm.

tag: strain/background

value: FGSG_07589 deletion mutant

value: toxoflavin

tag: toxoflavin sensitivity

value: sensitive


title: mRNAs from Fusarium graminearum GZ03639 wild-type under toxoflavin condition

source_name: Fungal culture containing toxoflavin (100 mg l-1), wild-type

value: wild-type

value: resistant


title: Sample_PS122T6R1

value: Leaf

tag: time course

value: 6 hours

tag: replicate

tag: genotype id


title: Sample_PS122T24R3

tag: tissue

value: 24 hours


title: Uninfected host foreskin fibroblast replicate 1

data_processing:
The base calling and quality scoring were determined using Real-Time Analysis on board software v2.4.6
The human and toxoplasma genomes were combined. Reads were aligned to this combined genome by Rsubread version 1.27.4
Reads counts were summarized for human genes by Entrez Gene ID using the Rsubread featureCounts function and NCBI annotation
Genome_build: hg38 (Homo sapien), ME49 (Toxoplasma gondii)
Supplementary_files_format_and_content: tab-delimited text files wre written from the R prompt; columns represent Entrez Gene ID, total gene length (total base count of all exons) and the number of reads mapping to that gene

growth_protocol: Parasites were lysised and incoluated (or not) onto confluent HFF (host cells) at an MOI of 0.2 in iM media for 1 week.

treatment_protocol: host cells were washed with PBS and dislodged with trypsin before being FACS sorted on the absence (bystander) or presence (infected) of mCherry.


title: Sample_PS122T6R2


title: Sample_PS122T24R1


title: Uninfected host foreskin fibroblast replicate 3


title: Sample_PS122T0R3

value: 0 hour


title: Uninfected host foreskin fibroblast replicate 2


title: ECKO3

data_processing:
Illumina RTA v1.18.54 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to GRCm38 whole genome using TopHat-2 v2.0.13 with parameters -g 2
HTSeq was used to count the aligned reads on a per gene basis (Version: HTSeq-0.6.1). The count data were normalized, Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using the DESeq2 package
Genome_build: GRCm38
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample.

source_name: bone

tag: strain background

tag: age

value: post natal day 21

tag: genetype/variation

value: bone

tag: cell type

value: bone endothelial cells


title: ECKO1


title: Sample_PS122T0R2


title: ECKO2


title: Sample_PS102T96R3

value: 96 hours


title: Sample_PS122T96R1


title: control3


title: control2


title: Uninfected host foreskin fibroblast (24 hours) replicate 1

tag: infection

value: Uninfected

tag: toxoplasma stage

value: D1 - Dulbecco's Modified Eagle medium supplemented with 1% v/v fetal calf serum and 1% v/v Glutamax


title: Sample_PS102T96R2


title: control1


title: Sample_PS122T6R3


title: Sample_PS122T24R2


title: Sample_PS102T6R2


title: Sample_PS122T0R1


title: Sample_PS102T24R3


title: Sample_PS102T0R3


title: Sample_PS102T24R1


title: Sample_PS102T0R2


title: Sample_PS102T0R1


title: MGSP6 MUT

city: Toronto

first: Norman

middle: D

last: Rosenblum

address: 686 Bay Street

institute: The Hospital for Sick Children

data_processing:
Sequencing platform used: Illumina HiSeq 2500. Depth of 150 million reads
Transcripts aligned to the reference mouse genome mm9 using TopHat
Subsequent analysis performed following the pipeline published by Anders et al., 2013 (Nature protocols, 8:1765-1786). Htseq was used to generate the count matrix and DESeq2 to identify differentially expressed genes
Genome_build: UCSC mm9
Supplementary_files_format_and_content: tab-delimited text files listing read count either by DEXSeq (dxsqct) or HTSeq (htsqct).

source_name: P2 Math1-Cre; Sufu flox/- cerebellum

growth_protocol: Math1-Cre; Sufu +/- mice were mated with Sufu flox/flox; Math1 mgfp/mgfp mice. The day of birth was designated P0 and pups were collected at 2 days post-birth for this experiment

extract_protocol:
Tissue lysis and RNA extraction was performed using TRIzol reagent.
Library preparation was performed using Illumina TruSeq RNA library prep kit using polyA selection. Qubit RNA HS assay used for RNA quantitation.

treatment_protocol: Pups were sacrificed by decapitation. Cerebella were dissected in ice-cold sterile HBSS solution and collected individually from each pup.

tag: strain

tag: developmental stage

value: brain/cerebellum

tag: genotype

value: Math1-Cre; Sufu flox/-


title: MGSP7 MUT


title: MGSP3 CRL

source_name: P2 control cerebellum

value: control


title: MGSR7 CRL


title: MGSP4 CRL


title: MGSR5 MUT


title: MGSR6 CRL


title: bmECs replicate 3

description: processed data file: all_FPKM.txt

source_name: bmECs

value: wildtype

value: FACS-sorted bone endothelial cells


title: Sample_PS089T96R2


title: CZ-Front-Balb_C-18

city: Rochester

first: Asha

last: Nair

address: 200 1ST ST SW

institute: Mayo Clinic

description: CZ-Front-Balb_C-18.FCHTYFKBBXX_L1_R*_IGGCTAC

data_processing:
Base calling was performed with the Illumina bcl2fastq
QC was performed on the FASTQ files using RSeQC software (http://rseqc.sourceforge.net/)
The paired end reads were aligned by TopHat 2.0.6
Gene counts were generated using HTseq (http://www-huber.embl.de/users/anders/HTSeq/doc/overview.html)
Genome_build: mm10
Supplementary_files_format_and_content: abundance measurements; DESeq2 differential expression results

extract_protocol:
Dissected cranial tissues were immeidately digested in 2mg/ml collagenase type II + 0.05% trypsin in aMEM media. Digested samples were homogenized with zirconium oxide beads and Trizol reagent. RNA was extracted from spun supernatant using Direct-zol RNA MiniPrep (Zymo Research).
mRNA version 2 library prep kit (Illumina)

value: BALB/c

tag: genotype/variation

value: postnatal day 3

value: frontal bone (including nasal bone, coronal and frontonasal sutures)


title: CZ-Front-Balb_C-17

description: CZ-Front-Balb_C-17.FCHTYFKBBXX_L1_R*_ITAGCTT


title: CZ-Front-Balb_C-16

description: CZ-Front-Balb_C-16.FCHTYFKBBXX_L1_R*_IGATCAG


title: Sample_PS089T96R1

value: Leaf


title: Sample_PS102T24R2

value: 24 hours


title: WT-Front-Balb_C-14

description: WT-Front-Balb_C-14.FCHTYFKBBXX_L1_R*_ITTAGGC

value: Wild Type


title: Sample_PS102T6R3

value: 6 hours


title: Sample_PS089T6R3


title: Sample_PS102T6R1


title: WT-Front-Balb_C-13

description: WT-Front-Balb_C-13.FCHTYFKBBXX_L1_R*_IATCACG


title: Sample_PS089T6R2


title: MGSR1 MUT


title: Sample_PS089T6R1


title: WT-Front-Balb_C-15

description: WT-Front-Balb_C-15.FCHTYFKBBXX_L1_R*_IACTTGA


title: Sample_PS089T96R3


title: CZ-Front-C57-6

description: CZ-Front-C57-6.FCH2WC2BBXY_L1_R*_IGGCTAC


title: Sample_PS089T24R3


title: CZ-Front-C57-4

description: CZ-Front-C57-4.FCH2WC2BBXY_L1_R*_IGATCAG


title: Sample_PS089T24R1


title: WT-Front-C57-3

description: WT-Front-C57-3.FCH2WC2BBXY_L1_R*_IACTTGA


title: Sample_PS089T0R2

value: 0 hour


title: WT-Front-C57-1

description: WT-Front-C57-1.FCH2WC2BBXY_L1_R*_IATCACG


title: EloB-S

value: Mixed background:129/Sv / C57BL/C6

value: Mouse embryonic stem cells

value: Fucci-Jarid2 fl/fl mESCs

tag: cell-cycle fraction

value: S

tag: chip antibody

value: EloB antibody is a gift from Luciano Di Croce referenced in Beringer et al, 2016, Molecular Cell.


title: Sample_PS084T6R3


title: EloB-G1

description: ChIP-seq


title: Sample_PS084T6R2


title: Sample_PS084T96R3

value: 96 hours


title: EloB-Input

description: ChIP-seq


title: Jarid2-Input

description: ChIP-seq


title: Jarid2-S

description: ChIP-seq


title: Sample_PS084T24R3


title: Jarid2-G2-M

description: ChIP-seq


title: Sample_PS084T24R2


title: Sample_PS084T24R1


title: WT-Front-C57-2

description: WT-Front-C57-2.FCH2WC2BBXY_L1_R*_ITTAGGC


title: Ezh2-Input

description: ChIP-seq


title: Jarid2-G1

description: ChIP-seq


title: Sample_PS084T0R2


title: Sample_PS089T0R1


title: Ezh2-S

description: ChIP-seq


title: Sample_PS084T0R1


title: Sample_PS084T6R1


title: Ezh2-G2-M

description: ChIP-seq


title: Sample_PS059T96R3


title: Sample_PS084T96R2


title: Sample_PS089T24R2


title: EPOP-Input

description: ChIP-seq


title: Sample_PS059T96R2


title: CZ-Front-C57-5

description: CZ-Front-C57-5.FCH2WC2BBXY_L1_R*_ITAGCTT


title: EPOP-G2-M

description: ChIP-seq


title: EPOP-G1

description: ChIP-seq


title: Sample_PS059T6R2


title: Sample_PS059T6R3


title: EloB-G2-M

description: ChIP-seq


title: Sample_PS059T24R2


title: rpoB no Ab control B

city: Paris

first: Alaksh

last: Choudhury

address: 16 Rue Henri Huchard

department: IAME

country: France

institute: INSERM

data_processing:
Library strategy: DNA-seq
Reads were assembled using PandaSeq tool
The merged reads were aligned to a database of known sequences using usearch to map reads to a sequence
Genome_build: N/A
Supplementary_files_format_and_content: Text Format with a table containing query, target, alignment length, number of mismatches, alignment consensus and qrowdots.

organism: Escherichia coli

source_name: Escherichia coli genome

growth_protocol: The cells were grown at 30 deegrees C on LB+Agar plates overnight.

extract_protocol:
Fifty µL of the scraped cell suspension was subjected to centrifugation in a 1.5 mL tube. The cells were washed twice with PBS and as much of the supernatant was removed as possible. Finally, the cells were suspended in 50 µL TE buffer (pH 8.0). The resuspended cells were boiled at 100 OC for 10 minutes.
The genomic region to be sequenced was amplified using primers with Illumina Nextera adapters

treatment_protocol: Cells for genome sequencing were scraped from LB agar plates with 1X PBS after overnight growth of the recovery mixture. Care was taken to collect at least 250-500 colonies for adequate representation of the population.

tag: mutl e32k

value: MutLE32K Present

tag: end homology length


title: Sample_PS059T24R1

tag: time course

tag: replicate


title: rpoB 4h incubation B


title: rpoB genome library A


title: rpoB genome library B


title: Sample_PS059T0R2

tag: tissue

tag: genotype id


title: rpoB linear donor


title: rpoB plasmid


title: Sample_PS044T96R3


title: Sample_PS059T96R1


title: Sample_PS044T96R2


title: mreB plasmid


title: rpoB no Ab control A


title: Sample_PS044T96R1


title: Crp linear donor


title: mreB genomic mutation library


title: Crp plasmid library


title: Sample_PS059T6R1


title: Sample_PS044T24R3


title: Sample_PS044T24R2


title: Sample_PS044T6R1


title: Sample_PS059T0R1


title: Rifampicin selection 100 ug/mL SPM-only library


title: Sample_PS044T24R1


title: Rifampicin selection 50 ug/mL SPM-only library


title: Sample_PS044T6R2


title: Sample_PS089T0R3


title: Rifampicin selection 10 ug/mL SPM-only library


title: Rifampicin selection 100 ug/mL replicate C


title: Sample_PS044T6R3


title: Ezh2-G1

description: ChIP-seq

source_name: Fucci-Jarid2 fl/fl mESCs


title: Sample_PS059T0R3


title: Rifampicin selection 50 ug/mL replicate C


title: Sample_PS044T0R1


title: Sample_PS004T96R3


title: Sample_PS044T0R2


title: mreB linear donor


title: Rifampicin selection 100 ug/mL replicate B


title: Sample_PS004T6R3


title: Rifampicin selection 50 ug/mL replicate B


title: Sample_PS004T6R2


title: Rifampicin selection 10 ug/mL replicate B


title: Sample_PS004T6R1


title: Sample_PS004T24R3


title: Sample_PS044T0R3


title: Rifampicin selection 100 ug/mL replicate A


title: Rifampicin selection 50 ug/mL replicate A


title: Sample_PS004T24R1


title: Sample_PS004T0R2


title: Rifampicin rpoB preselection library B and C


title: Sample_PS004T96R2


title: galK High diversity 250 BP end homology-mutLE32K A


title: Sample_PS004T0R1


title: galK High diversity 250 BP end homology A

value: MutLE32K Absent


title: galK High diversity 250 BP end homology B


title: galK High diversity 250 BP end homology-mutLE32K B


title: 171_galK low diversity donor library


title: 172_galK high diversity donor library


title: 169_galK low diversity donor library


title: Sample_PS004T24R2


title: Rifampicin selection 10 ug/mL replicate A


title: 167_galK High diversity 250 BP end homology A


title: Rifampicin rpoB preselection library A


title: 166_galK High diversity 150 BP end homology B


title: 165_galK High diversity 150 BP end homology A


title: 170_galK high diversity donor library


title: 163_galK High diversity 50 BP end homology A


title: 164_galK High diversity 50 BP end homology B


title: Sample  32 Normal progesterone

type: RNA

city: nottingham

first: Sutham

last: Suthaporn

state: UK

address: Derby road

department: Ob&Gyn

country: United Kingdom

institute: University of Nottingham

description: Gene expression data from women with normal progesterone

hyb_protocol: A mixture of purified, and fragmented biotinylated and labelled sscDNA, and hybridisation controls (Affymetrix) was hybridised on Affymetrix' Clariom S array followed by staining and washing in a GeneChip® fluidics station 450 (Affymetrix) according to the manufacturer’s procedures.

scan_protocol: Detection was performed using a GeneChip Scanner 3000 7G (Affymetrix).

data_processing: Gene expression data were analysed using Partek Genomics Suite 6.6 software (Partek). The raw CEL files were normalized using the robust multiarray average (RMA) background correction with quantile normalization, log base 2 transformation and mean probe-set summarization with adjustment for guanine-cytosine content

label: biotin

source_name: Women with normal progesterone (32)

label_protocol: RNA concentration and purity were determined spectrophotometrically using the Nanodrop ND-1000 (Nanodrop Technologies) and RNA integrity was assessed using a Bioanalyser 2100 (Agilent). Per sample, an amount of 100 ng of total RNA spiked with RNA transcript positive controls (Affymetrix) was amplified and labeled using the GeneChip WT Plus Reagent Kit (Affymetrix). All steps were carried out according to the manufacturers protocol (Affymetrix).

growth_protocol: not applicable

extract_protocol: Total RNA was extracted from human endometrium by using the RNeasy Mini Kit (QIAGEN) according to the manufacturer’s instructions.

treatment_protocol: not applicable

value: human endometrium at the receptive phase

tag: condition

value: normal progesterone


title: Sample  33 Normal  progesterone

source_name: Women with normal progesterone (33)


title: Sample  36 Normal progesterone

source_name: Women with normal progesterone (36)


title: 162_galK Low diversity 250 BP end homology B


title: Sample  40 Normal progesterone

source_name: Women with normal progesterone (40)


title: Sample  39 Normal progesterone

source_name: Women with normal progesterone (39)


title: Sample  27 Low progesterone

description: Gene expression data from women with low progesterone

source_name: Women with Low progesterone (27)

value: Low progesterone


title: Sample  26 Low progesterone

source_name: Women with Low progesterone (26)


title: Sample  31 Normal progesterone

source_name: Women with normal progesterone (31)


title: Sample  54 Low progesterone

source_name: Women with Low progesterone (54)


title: Patient 101

type: protein

city: Groningen

first: Sanne

last: Arjaans

address: Hanzeplein 1

institute: University Medical Center Groningen

hyb_protocol: Two sequential bead-based immobilization and washing steps eliminated unbound or non-specifically bound proteins and the unbound SOMAmer reagents, leaving only protein target-bound SOMAmer reagents.

scan_protocol: SOMAmers are hybridized to complementary sequences on a microarry chip and quantified by fluorescence.

data_processing: The amount of each SOMAmer measured was quantitatively proportional to the protein concentration in the original sample.

label: Photocleavable linker

molecule: protein

source_name: Plasma

label_protocol: SOMAmers are labeled with a fluorophore, photocleavable linker, and biotin.

extract_protocol: Blood was placed into an EDTA-plasma tube, which was centrifuged after phlebotomy. The supernatant was removed, aliquoted and stored at −80°C until assay.

value: Plasma

tag: gender

value: Male

tag: bpd

value: Mild


title: Patient 102


title: Sample  55 Low progesterone

source_name: Women with Low progesterone (55)


title: Patient 100


title: 168_galK High diversity 250 BP end homology B


title: 161_galK Low diversity 250 BP end homology A


title: 159_galK Low diversity 150 BP end homology A


title: 160_galK Low diversity 150 BP end homology B


title: Sample  24 Low progesterone

source_name: Women with Low progesterone (24)


title: 158_galK Low diversity 50 BP end homology B


title: Sample  25 Low progesterone

source_name: Women with Low progesterone (25)


title: Patient 97

value: Female


title: Patient 99

value: Severe


title: Patient 98

value: Moderate


title: 157_galK Low diversity 50 BP end homology A


title: Patient 95


title: Patient 96


title: Patient 92


title: Patient 89

data_processing: The amount of each SOMAmer measured was quantitatively proportional to the protein concentration in the original sample. The relative fluorescent units provided by the company are included in the sample tables. Statistical analysis output is available on the series record.


title: Patient 90


title: Patient 93


title: Patient 91


title: Patient 94


title: Patient 87


title: crp genomic mutation library


title: Patient 86


title: Patient 85


title: Patient 84


title: B71 line: Water Stress: Aerial Part. Rep. 4

city: Río Cuarto

first: Sergio

middle: Gabriel

last: Alemano

state: Cordoba

address: Ruta 36. Km 601

department: Ciencias Naturales

country: Argentina

institute: Universidad Nacional de Río Cuarto

description: Gene expression of B71 line aerial part after 20 days in water stress

hyb_protocol: 1.5 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 250 ml containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 250 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Human Genome Oligo Microarrays (G4112A) for 17 hours at 65°C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 1x44k array slides (Scan Area 61x21.6 mm, Scan resolution 10um, Dye channel is set to Green and Green PMT is set to 100%)

data_processing: The scanned images were analyzed with Feature Extraction Software 9.1 (Agilent) using default parameters (protocol GE1-v1_91 and Grid: 027480_D_F_20100303) to obtain background subtracted and spatially detrended Processed Signal intensities. Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

organism: Helianthus annuus

source_name: B71 line: Water Stress: Aerial Part. Replicate. 4

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.5 ug RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA). Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: Germination and early growth assays were performed as described previously (Andrade et al. 2013). Seedlings were planted in sand and four days after were watered to field capacity (FC) with solutions (treatments): (1) Hoagland’s solution, 50% full-strength (irrigated - control); (2) mannitol 400 mM (water stress). Irrigation with each of the four solutions was performed every three days throughout the experiment. The seedlings were harvested 20 day after germination, when a significant decrease in stomatal conductance was observed relative to the control.

extract_protocol: Samples were immediately frozen in liquid nitrogen and conserved at -80°C until their processing. High quality total RNA was isolated from 100 mg of frozen tissue using extraction kit of RNAqueous Plant RNA Isolation Aid (Ambion, Life Technologies Corporation. USA) according to the manufacturer’s instructions. The obtained RNA was precipitated with lithium chloride (LiCl) overnight at 4°C to remove the polyphenols (Ling et al. 2013). The genomic DNA was eliminated after treatment with DNase I (Invitrogen, Buenos Aires, Argentina) for 20 min at room temperature. The RNA concentration was measured using a Nanodrop ND-1000 spectrophotometer (NanoDrop Technologies, Wilmington, DE). The integrity of total RNA was checked in agarose gel electrophoresis. The quality of total RNA was determined using a NanoBioanalyzer RNA-6000 analysis (Agilent Technologies, Palo Alto, CA).

treatment_protocol: Mannitol (400 mM; Biopack) was used as a drought simulator to generate a moderate water stress level (-0.989 MPa). Hoagland’s solution, 50% full-strength (irrigated - control).

tag: inbred line

tag: phenotype

value: tolerant of water stress

value: Aerial Part

tag: age


title: B71 line: Water Stress: Root. Rep. 4

description: Gene expression of B71 line root after 20 days in water stress

source_name: B71 line: Water Stress: Root. Replicate 4

value: Root


title: B71 line: Water Stress: Aerial Part. Rep. 3

source_name: B71 line: Water Stress: Aerial Part. Replicate. 3


title: B71 line: Water Stress: Root. Rep. 1

source_name: B71 line: Water Stress: Root. Replicate 1


title: Patient 88


title: B71 line: Water Stress: Root. Rep. 2

source_name: B71 line: Water Stress: Root. Replicate 2


title: B71 line: Water Stress: Root. Rep. 3

source_name: B71 line: Water Stress: Root. Replicate 3


title: B71 line: Control: Aerial Part. Rep.4

description: Gene expression of B71 line aerial part after 20 days in control

source_name: B71 line: Control: Aerial Part. Replicate 4


title: B71 line: Control: Root. Rep.1

description: Gene expression of B71 line root after 20 days in control

source_name: B71 line: Control: Root. Replicate 1


title: B71 line: Control: Root. Rep.4

source_name: B71 line: Control: Root. Replicate 4


title: Rifampicin selection 10 ug/mL replicate C

source_name: Escherichia coli genome


title: Patient 82


title: Patient 81


title: B71 line: Water Stress: Aerial Part. Rep. 1

source_name: B71 line: Water Stress: Aerial Part. Replicate. 1


title: B71 line: Water Stress: Aerial Part. Rep. 2

source_name: B71 line: Water Stress: Aerial Part. Replicate. 2


title: Patient 79


title: Patient 80


title: Patient 78


title: B71 line: Control: Root. Rep.3

source_name: B71 line: Control: Root. Replicate 3


title: B71 line: Control: Root. Rep.2

source_name: B71 line: Control: Root. Replicate 2


title: rpoB 4h incubation A


title: Patient 77

source_name: Plasma


title: Patient 76


title: Patient 75


title: Patient 73


title: B59 line: Water Stress: Root. Rep. 4

description: Gene expression of B59 line root after 20 days in water stress

source_name: B59 line: Water Stress: Root. Replicate 4

value: sensitive to water stress


title: B71 line: Control: Aerial Part. Rep.2

source_name: B71 line: Control: Aerial Part. Replicate 2


title: Patient 74


title: B71 line: Control: Aerial Part. Rep.3

source_name: B71 line: Control: Aerial Part. Replicate 3


title: B71 line: Control: Aerial Part. Rep.1

source_name: B71 line: Control: Aerial Part. Replicate 1


title: Patient 72


title: B59 line: Water Stress: Root. Rep. 3

source_name: B59 line: Water Stress: Root. Replicate 3


title: B59 line: Water Stress: Root. Rep. 1

source_name: B59 line: Water Stress: Root. Replicate 1


title: Patient 71


title: B59 line: Water Stress: Root. Rep. 2

source_name: B59 line: Water Stress: Root. Replicate 2


title: B59 line: Water Stress: Aerial Part. Rep. 3

description: Gene expression of B59 line aerial part after 20 days in water stress

source_name: B59 line: Water Stress: Aerial Part. Replicate 3


title: Hypothalamus_Wildtype_Rep4

city: Guildford

first: Emma

last: Laing

address: Stag Hill

institute: University of Surrey

hyb_protocol: Labelled cRNA (1.65 μg) was hybridized on a Whole Mouse Genome 4 x 44K oligonucleotide microarray (G4122F, AMADID 014868; Agilent Technologies). Standard manufacturer's instructions for one-colour gene expression hybridization and washing steps were followed. The microarrays were hybridized at 65°C for 17 h in an Agilent hybridization oven with rotisserie at 10 rpm. The microarrays were washed with Agilent Wash Buffer 1, pre-warmed Wash Buffer 2 (37C) and acetonitrile according to the manufacturer’s instructions. The last washing step was performed with Agilent Stabilization and Drying Solution for 30 sec.

scan_protocol: The processed microarrays were scanned using an Agilent Microarray Scanner with a resolution of 5 μm, exploiting the extended dynamic range feature. The two images derived from each slide scanned at 10% and 100% PMT were imported into Agilent Feature Extraction software (Version 10.7.1.1) for image analysis.

data_processing: Expression levels were analysed using the standard protocol of GeneSpring version 12 (Agilent).

source_name: Hypothalamic block

label_protocol: Two hundred ng of total RNA was used to synthesize cRNA labelled with Cy3

growth_protocol: Mouse total brains and whole eye were collected after in the 17th ultradian cycle, and immediately placed in a RNA stabilising solution and frozen to -80 degrees Celsius.

extract_protocol: RNA extraction from hypothalamus with the RNeasy kit (Qiagen)

treatment_protocol: Whole eye and tissue blocks of the hypothalamus were dissected and RNA was extracted

value: WT

value: Brain

value: male

value: adult


title: Hypothalamus_Wildtype_Rep6


title: B59 line: Water Stress: Aerial Part. Rep. 2

source_name: B59 line: Water Stress: Aerial Part. Replicate 2


title: B59 line: Water Stress: Aerial Part. Rep. 1

source_name: B59 line: Water Stress: Aerial Part. Replicate 1


title: Hypothalamus_Wildtype_Rep5


title: Hypothalamus_Wildtype_Rep7


title: Hypothalamus_Wildtype_Rep3


title: Hypothalamus_Per3_KO_Rep6


title: Hypothalamus_Per3_KO_Rep8


title: Hypothalamus_Wildtype_Rep8


title: Patient 70


title: Hypothalamus_Per3_KO_Rep4


title: Hypothalamus_Per3_KO_Rep5


title: Hypothalamus_Per3_KO_Rep3


title: B59 line: Water Stress: Aerial Part. Rep. 4

source_name: B59 line: Water Stress: Aerial Part. Replicate 4


title: Patient 69


title: Patient 68


title: B59 line: Control: Root. Rep.4

description: Gene expression of B59 line root after 20 days in control

source_name: B59 line: Control: Root. Replicate 4


title: Patient 67


title: Hypothalamus_Per3_KO_Rep2


title: Hypothalamus_Per3_KO_Rep1


title: Eye_Per3_KO_Rep8

source_name: Whole eye

value: Whole eye


title: Hypothalamus_Wildtype_Rep1


title: Hypothalamus_Wildtype_Rep2


title: Patient 66


title: Eye_Per3_KO_Rep7


title: Eye_Wildtype_Rep8


title: B59 line: Control: Root. Rep.2

source_name: B59 line: Control: Root. Replicate 2


title: B59 line: Control: Root. Rep.1

source_name: B59 line: Control: Root. Replicate 1


title: Patient 65

source_name: Plasma


title: Eye_Per3_KO_Rep6


title: B59 line: Control: Root. Rep.3

source_name: B59 line: Control: Root. Replicate 3


title: Patient 64


title: KO.1mon.Sample8

city: Seoul

first: Jiyeon

address: 222, Banpo-daero

department: Catholic Center for Precision Medicine Research

institute: The Catholic University of Korea

data_processing:
Basecalls performed using Illumina CASAVA
Sequenced reads were trimmed for adaptor sequence, and then mapped to mm10 genome using HiSAT2 (Nat Methods. 2015;12(4):357-60)
mRNA expression was normalized and mRNA regulation between samples was calculated using edgeR
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include log2(CPM)

source_name: Trx1 flox/flox/MHC-Cre 1 Month-old

extract_protocol:
RNA was extracted from the heart at 1 month of age using TRIzol Reagent.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: heart

value: 1 month old

value: Trx1 flox/flox/MHC-Cre

tag: strain


title: Patient 83

value: Plasma

value: Male


title: Patient 63

value: Female


title: B59 line: Control: Aerial Part. Rep.4

description: Gene expression of B59 line aerial part after 20 days in control

source_name: B59 line: Control: Aerial Part. Replicate 4


title: Eye_Wildtype_Rep4

tag: genotype


title: B59 line: Control: Aerial Part. Rep.3

source_name: B59 line: Control: Aerial Part. Replicate 3


title: B59 line: Control: Aerial Part. Rep.2

source_name: B59 line: Control: Aerial Part. Replicate 2


title: Eye_Wildtype_Rep7


title: Eye_Per3_KO_Rep3


title: Eye_Per3_KO_Rep4


title: Eye_Wildtype_Rep3


title: Eye_Wildtype_Rep5


title: Eye_Wildtype_Rep6


title: Eye_Per3_KO_Rep5


title: Eye_Per3_KO_Rep2


title: B59 line: Control: Aerial Part. Rep.1

source_name: B59 line: Control: Aerial Part. Replicate 1


title: Patient 62

value: Mild


title: KO.1mon.Sample6


title: KO.1mon.Sample7


title: Eye_Wildtype_Rep1


title: CT.1mon.Sample5

source_name: Trx1 flox/flox 1 Month-old

value: Trx1 flox/flox


title: Patient 61

value: Severe


title: CT.1mon.Sample4


title: Patient 59


title: CT.1mon.Sample3


title: Patient 60

value: Moderate


title: Patient 58


title: Patient 57


title: Patient 56


title: Patient 55


title: Patient 54


title: 46 dpi LCMV Arm 3h stim., repl.3

first: Avi

last: Ma'ayan

address: One Gustave L. Levy Place, Box 1603

department: Pharmacological Sciences

institute: Icahn School of Medicine at Mount Sinai

hyb_protocol: Hybridization to Affymetrix 430.2 arrays and quality control were performed by the Affymetrix Core Dacility at the University of Colorado Cancer Center according to standard protocols.

scan_protocol: Affymetrix standard protocols

data_processing: Data processing and analyses were conducted at the University of Colorado as detailed in Eberlein et al., J Clin Invest 2016 (PMID: 27617858) and independently at the Icahn School of Medicine at Mount Sinai. The Mount Sinai analysis included the following steps: CEL files were imported by 'read.celfiles' function from Bioconductor package 'oligo'  (Bioinformatics, 26(19), 2363-7, 2010). Background correction, normalization and summarization with RMA (robust multichip average) (Biostatistics. 4 (2), 249–64, 2003) were performed with the 'rma' function from Bioconductor package 'oligo.'

source_name: 46 dpi LCMV Arm 3h stim

label_protocol: Amplification and labeling of mRNA was performed according to maufacturer's instruction using the NuGen Ovation Biotin RNA Amplification and Labeling System.

growth_protocol: p14 chimeras were generated by i.v. injection of 5e4 purified, naive and CD90.1-congenic p14 T cells (TCRtg CD8+T cells specific for the LCMV GP33-41 determinant) into B6 recipients followed by infection with 2e5 plaque forming units of LCMV Armstrong i.p.; spleens were harvested 8 dpi (for p14 TE) and 46 dpi (for p14 TM), and p14 TE and TM from individual mice (n=3-4) were enriched to >90% purity by sequential magnetic and fluorescence activated cell sorting.

extract_protocol: DNA-digested total RNA was extracted from p14 TE and TM either directly after purification (ex vivo) or after a 3h aCD3/aCD28 stimulation (see above) using a MinElute kit (Qiagen) and RNA integrity was confirmed by PicoCHip RNA technology (Agilent) according to manufacturer's instruction.

treatment_protocol: An aliquot of each sorted p14 TE and TM poulation was stimulated for 3h with plate-bound aCD3 (10ug/ml) and solubel aCD28 (2ug/ml) antibodies.

tag: cell type

value: memory p14 TM

tag: time point

value: 46 days post infection/dpi

tag: treatment

value: 3h stimulation with aCD3/aCD28 prior to RNA extraction


title: 46 dpi LCMV Arm 3h stim., repl.4


title: Methylation data from Oligodendroglioma tissue 15

type: genomic

city: New York City

first: Matija

last: Snuderl

address: 240 E 38th St

institute: New York University Langone Medical Center

description:
Oligodendroglioma_15
RD-15-1044
Bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation450 BeadChip using standard Illumina protocol.

hyb_protocol: The DNA is bisulfite-converted using the EZ-96 DNA Methylation Kit from Zymo Research. After bisulfite conversion, the DNA then undergoes restoration using the Illumina Infinium HD FFPE DNA Restore Kit. The DNA then undergoes a whole-genome overnight amplification. The amplified DNA is then enzymatically fragmented using end-point fragmentation. The DNA is then isolated and precipitated in isopropanol and re-suspended in Illumina RA1 buffer. The re-suspended DNA is then denatured at 95⁰C, and the resulting single-stranded DNA is dispensed directly onto the Illumina Array for hybridization. The DNA hybridizes with the array overnight in an oven at 48⁰C. After hybridization, the BeadChips are then washed with Illumina PB1 buffer to remove any unhybridized and non-specifically hybridized DNA.

scan_protocol: Arrays were imaged using iScan using standard recommended Illumina scanner setting.

data_processing: The Minfi R package was used to analyze the data. Data was preprocessed, quantile normalized and poor samples and probes were removed based on mean detection Pvalues per sample. 'dmpFinder' was used to identify the differentially methylated probes between MPNSTs and DMs. qvalue < 0.01 are considered significant.

label: Cy5 and Cy3

source_name: IDH Mutant Oligodendroglioma sample

label_protocol: Standard Illumina Protocol.

extract_protocol: Using a Promega Maxwell 16 instrument, DNA was extracted from formalin-fixed paraffin-embedded (FFPE) specimens with the Maxwell® 16 FFPE Plus LEV DNA Purification Kit.

tag: disease state

value: Oligodendroglioma

tag: genotype/variation

value: IDH Mutant

value: Oligodendroglioma tissue


title: 46 dpi LCMV Arm 3h stim., repl.2


title: 46 dpi LCMV Arm 3h stim., repl.1


title: Patient 53


title: Methylation data from Oligodendroglioma tissue 9

description:
Oligodendroglioma_9
RD-15-882
Bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation450 BeadChip using standard Illumina protocol.


title: Patient 52


title: Methylation data from Oligodendroglioma tissue 10

description:
Oligodendroglioma_10
RD-15-1152
Bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation450 BeadChip using standard Illumina protocol.


title: Methylation data from Oligodendroglioma tissue 14

description:
Oligodendroglioma_14
RD-15-1033
Bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation450 BeadChip using standard Illumina protocol.


title: Hypothalamus_Per3_KO_Rep7

source_name: Hypothalamic block

value: Brain

value: male

value: adult


title: Methylation data from Oligodendroglioma tissue 13

description:
Oligodendroglioma_13
RD-15-1028
Bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation450 BeadChip using standard Illumina protocol.


title: Methylation data from Oligodendroglioma tissue 11

description:
Oligodendroglioma_11
RD-15-1113
Bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation450 BeadChip using standard Illumina protocol.


title: Methylation data from Oligodendroglioma tissue 12

description:
Oligodendroglioma_12
RD-15-963
Bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation450 BeadChip using standard Illumina protocol.


title: Methylation data from TCGA Cholangiocarcinoma tissue 8

description:
Cholangiocarcinoma_8
TCGA-W5-AA2G
Bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation450 BeadChip using standard Illumina protocol.

source_name: IDH Mutant Cholangiocarcinoma sample

value: Cholangiocarcinoma

value: Cholangiocarcinoma tissue


title: Methylation data from Oligodendroglioma tissue 4

description:
Oligodendroglioma_4
RD-15-665
Bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation450 BeadChip using standard Illumina protocol.


title: Methylation data from Oligodendroglioma tissue 7

description:
Oligodendroglioma_7
RD-15-880
Bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation450 BeadChip using standard Illumina protocol.


title: Methylation data from Oligodendroglioma tissue 6

description:
Oligodendroglioma_6
RD-15-875
Bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation450 BeadChip using standard Illumina protocol.


title: Methylation data from Oligodendroglioma tissue 3

description:
Oligodendroglioma_3
RD-15-428
Bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation450 BeadChip using standard Illumina protocol.


title: Methylation data from Oligodendroglioma tissue 5

description:
Oligodendroglioma_5
RD-15-666
Bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation450 BeadChip using standard Illumina protocol.


title: Methylation data from Oligodendroglioma tissue 2

description:
Oligodendroglioma_2
RD-15-335
Bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation450 BeadChip using standard Illumina protocol.


title: 46 dpi LCMV Arm ex vivo, repl.4 [re-analysis]

source_name: 46 dpi LCMV Arm ex vivo

value: direct extraction of total DNA-digested RNA (ex vivo)


title: Patient 50

value: Plasma

value: Female


title: Patient 49

value: Male


title: Methylation data from TCGA Cholangiocarcinoma tissue 9

description:
Cholangiocarcinoma_9
TCGA-W5-AA2I-2
Bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation450 BeadChip using standard Illumina protocol.


title: Methylation data from TCGA Cholangiocarcinoma tissue 6

description:
Cholangiocarcinoma_6
TCGA-W5-AA2I
Bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation450 BeadChip using standard Illumina protocol.


title: Patient 51

value: Severe


title: 46 dpi LCMV Arm ex vivo, repl.1 [re-analysis]


title: Methylation data from Oligodendroglioma tissue 1

description:
Oligodendroglioma_1
RD-15-296
Bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation450 BeadChip using standard Illumina protocol.


title: Methylation data from Oligodendroglioma tissue 8

description:
Oligodendroglioma_8
RD-15-881
Bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation450 BeadChip using standard Illumina protocol.


title: 46 dpi LCMV Arm ex vivo, repl.3 [re-analysis]


title: Methylation data from TCGA Cholangiocarcinoma tissue 7

description:
Cholangiocarcinoma_7
TCGA-W6-AA0S
Bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation450 BeadChip using standard Illumina protocol.


title: Methylation data from TCGA Cholangiocarcinoma tissue 3

description:
Cholangiocarcinoma_3
TCGA-W5-AA2O
Bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation450 BeadChip using standard Illumina protocol.


title: Patient 48


title: 46 dpi LCMV Arm ex vivo, repl.2 [re-analysis]


title: Methylation data from TCGA Cholangiocarcinoma tissue 5

description:
Cholangiocarcinoma_5
TCGA-YR-A95A
Bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation450 BeadChip using standard Illumina protocol.


title: Patient 47


title: 8 dpi LCMV Arm 3h stim., repl.2

source_name: 8 dpi LCMV Arm 3h stim

value: splenic CD90.1+ effector p14 TE

value: 8 days post infection/dpi


title: Methylation data from TCGA Cholangiocarcinoma tissue 4

description:
Cholangiocarcinoma_4
TCGA-W5-AA34
Bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation450 BeadChip using standard Illumina protocol.


title: Patient 45

value: Mild


title: 8 dpi LCMV Arm 3h stim., repl.3

value: 3h stimulation with aCD3/aCD28 prior to RNA extraction


title: Patient 44


title: 8 dpi LCMV Arm ex vivo, repl.3 [re-analysis]

source_name: 8 dpi LCMV Arm ex vivo


title: Methylation data from Astrocytoma tissue 22

description:
Astrocytoma_22
RD-15-822
Bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation450 BeadChip using standard Illumina protocol.

source_name: IDH Mutant Astrocytoma sample

value: Astrocytoma

value: Astrocytoma tissue


title: Methylation data from Astrocytoma tissue 24

description:
Astrocytoma_24
RD-15-967
Bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation450 BeadChip using standard Illumina protocol.

value: IDH Mutant


title: Methylation data from TCGA Cholangiocarcinoma tissue 2

description:
Cholangiocarcinoma_2
TCGA-3X-AAVA
Bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation450 BeadChip using standard Illumina protocol.


title: Patient 42


title: 8 dpi LCMV Arm ex vivo, repl.1 [re-analysis]


title: Methylation data from Astrocytoma tissue 25

description:
Astrocytoma_25
RD-15-1051
Bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation450 BeadChip using standard Illumina protocol.


title: Patient 43

value: Moderate


title: 8 dpi LCMV Arm 3h stim., repl.1


title: Patient 41


title: Adenocarcinoma from Apc mice, replicate 3

city: Lyon

first: Michelina

last: Plateroti

address: 28 rue Laennec

institute: Cancer Research Center of Lyon

description: Gene expression analysis

hyb_protocol: Labeling, hybridization and detection were carried out by the Biopuces et Sequençage platform at IGBMC (Illkirch, France). Gene expression was determined by hybridization to the Mouse GE 4x44K v2 Microarray Kit (Agilent Technologies). Three independent samples were hybridized for each experimental condition.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 1x44k array slides (Scan Area 61x21.6 mm, Scan resolution 10um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 9.1 (Agilent) using default parameters (protocol GE1-v1_91 and Grid: 012391_D_20060331) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

source_name: Intestinal tumor

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.5 ug RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

extract_protocol: Total RNA was extracted from tumors using the RNeasy mini kit and treated with DNAse (Qiagen) according to the manufacturer’s instructions. RNA samples were analyzed quantitatively and qualitatively by NanoDrop ND-2000 UV (Thermo Scientific) and using the BioAnalyzer 2100 (Agilent Technologies)

treatment_protocol: Animals were sacrificed and tumors were quickly removed under a binocular microscope. Samples were frozen in liquid nitrogen and stored at -80°C until use for RNA extraction

value: Apc

value: Intestinal tumor

value: 9/12-month old


title: Adenocarcinoma from Apc mice, replicate 2

description: Gene expression analysis


title: Methylation data from Astrocytoma tissue 21

description:
Astrocytoma_21
RD-15-818
Bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation450 BeadChip using standard Illumina protocol.


title: Methylation data from Astrocytoma tissue 19

description:
Astrocytoma_19
RD-15-637
Bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation450 BeadChip using standard Illumina protocol.


title: Methylation data from Astrocytoma tissue 20

description:
Astrocytoma_20
RD-15-812
Bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation450 BeadChip using standard Illumina protocol.


title: 8 dpi LCMV Arm ex vivo, repl.2 [re-analysis]


title: Patient 46

source_name: Plasma


title: Methylation data from Astrocytoma tissue 17

description:
Astrocytoma_17
RD-15-585
Bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation450 BeadChip using standard Illumina protocol.


title: Methylation data from Astrocytoma tissue 23

description:
Astrocytoma_23
RD-15-1155
Bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation450 BeadChip using standard Illumina protocol.


title: Methylation data from Astrocytoma tissue 16

description:
Astrocytoma_16
RD-15-577
Bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation450 BeadChip using standard Illumina protocol.


title: Methylation data from Astrocytoma tissue 15

description:
Astrocytoma_15
RD-15-382
Bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation450 BeadChip using standard Illumina protocol.


title: Patient 39


title: Methylation data from Astrocytoma tissue 13

description:
Astrocytoma_13
RD-15-554
Bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation450 BeadChip using standard Illumina protocol.


title: Methylation data from Astrocytoma tissue 14

description:
Astrocytoma_14
RD-15-584
Bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation450 BeadChip using standard Illumina protocol.


title: Methylation data from Astrocytoma tissue 11

description:
Astrocytoma_11
RD-15-583
Bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation450 BeadChip using standard Illumina protocol.


title: Methylation data from Astrocytoma tissue 12

description:
Astrocytoma_12
RD-15-606
Bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation450 BeadChip using standard Illumina protocol.


title: Adenocarcinoma from vil-TRa1/Apc mice, replicate 3

description: Gene expression analysis


title: Methylation data from TCGA Cholangiocarcinoma tissue 1

description:
Cholangiocarcinoma_1
TCGA-W5-AA35
Bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation450 BeadChip using standard Illumina protocol.

value: Cholangiocarcinoma

value: Cholangiocarcinoma tissue


title: Methylation data from Astrocytoma tissue 18

description:
Astrocytoma_18
RD-15-629
Bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation450 BeadChip using standard Illumina protocol.


title: Patient 38

value: Plasma


title: Adenocarcinoma from Apc mice, replicate 1

description: Gene expression analysis


title: Patient 40

value: Female


title: Methylation data from Astrocytoma tissue 10

description:
Astrocytoma_10
RD-15-290
Bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation450 BeadChip using standard Illumina protocol.


title: Patient 37

value: Male


title: Patient 35


title: HK2_17_OTA100

city: Halle (Saale)

first: Virginie

last: Dubourg

address: Magdeburger Str. 6

department: Julius Bernstein Institute for Physiology

institute: Martin Luther University - Halle-Wittenberg

description: processed data file: HK2_rawCounts.txt

data_processing:
Adaptor removal (Cutadapt - v1.8.1)
Alignment (tophat - 2.0.14)
Counting (featureCounts - 1.4.6)
Genome_build: hg38
Supplementary_files_format_and_content: txt files containing raw counts obtained after Counting with featureCounts

source_name: HK-2_100 nM OTA

growth_protocol: HK-2 and HEK293-T were cultivated in DMEM/F12 media with 5% FCS. Prior to incubation with OTA, cells were incubated for 24h with serum-free media.

extract_protocol:
Total RNA was isolated with TriZol Reagent, following the manufacturer's instructions. Eventual gDNA contaminations were removed using Turbo DNAse (ambion, Life Technologies).
rRNA were removed using RiboMinus (Life Technologies) according to the manufacturer's instructions. RNA was fragmented (w/ Tris-acetate, Potassium acetate and Magnesium acetate) and precipitated (w/ 100% Ethanol, Ammonium acetate and glycogen).
Resulting RNAs were used to generate cDNA libraries using Illumina index adapters.  10nM of pools of up to 10 libraries were used for cluster generation (Illumina cBot). Paired end sequencing (2x100bp) was performed on Illumina HiScanHQ and HiSeq 2000.

treatment_protocol: Cells were incubated for 48h with 0, 10 or 100nM OTA in serum-free media.

tag: cell line

tag: tissue source

value: Kidney

value: Proximal tubule epithelial cell line

value: 100 nM OTA


title: stopdIEC_3

city: Providence

first: Shipra

last: Vaishnava

state: Rhode Island

address: 171 Meeting street, Box G-B5, MMI dept

department: Molecular Microbiology and Immunology

institute: Brown University

data_processing:
Illumina platform. Fastq generated by Casava
Sequences were trimmed and aligned to Mus_musculus.GRCm38.dna.primary_assembly.fa using Bowtie
FPKM values generated using Cuffdiff on Galaxy platform
Genome_build: GRCm38
Supplementary_files_format_and_content: FPKM

source_name: Distal ileum epithelial cells

extract_protocol:
Laser capture microdissection from fresh frozen sections
NuGen Ovation Mouse RNAseq kit

treatment_protocol: Homeostatic stopFlox and stopdIEC littermate mice

value: VillinCre+;dnRAR

value: 7-9 weeks


title: Patient 34

tag: tissue

value: Mild


title: Adenocarcinoma from vil-TRa1/Apc mice, replicate 1

description: Gene expression analysis


title: Patient 36


title: HK2_16_OTA10

description: processed data file: HK2_rawCounts.txt

source_name: HK-2_10 nM OTA

value: 10 nM OTA


title: HK2_18_OTA100

description: processed data file: HK2_rawCounts.txt


title: HK2_15_OTA10

description: processed data file: HK2_rawCounts.txt


title: Methylation data from Astrocytoma tissue 7

description:
Astrocytoma_7
RD-15-33
Bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation450 BeadChip using standard Illumina protocol.

value: Astrocytoma

value: IDH Mutant

value: Astrocytoma tissue


title: stopdIEC_1


title: Patient 33

value: Moderate


title: Adenocarcinoma from vil-TRa1/Apc mice, replicate 2

description: Gene expression analysis

value: Intestinal tumor

value: 9/12-month old


title: stopdIEC_2


title: stopFlox _3

value: VillinCre-;dnRAR


title: Methylation data from Astrocytoma tissue 6

description:
Astrocytoma_6
RD-15-103
Bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation450 BeadChip using standard Illumina protocol.


title: stopFlox _2


title: HK2_12_OTA100

description: processed data file: HK2_rawCounts.txt


title: Patient 32

value: Plasma


title: HK2_14_Ctrl

description: processed data file: HK2_rawCounts.txt

source_name: HK-2_0 nM OTA

value: 0 nM OTA


title: HK2_13_Ctrl

description: processed data file: HK2_rawCounts.txt


title: Patient 31

value: Male


title: stopFlox _1


title: Patient 30

value: Female


title: Methylation data from Astrocytoma tissue 2

description:
Astrocytoma_2
RD-14-87
Bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation450 BeadChip using standard Illumina protocol.


title: Methylation data from TCGA AML tissue 20

description:
AML_20
TCGA-AB-2959
Bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation450 BeadChip using standard Illumina protocol.

source_name: IDH Mutant AML sample

value: AML

value: AML tissue


title: Methylation data from TCGA AML tissue 21

description:
AML_21
TCGA-AB-2990
Bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation450 BeadChip using standard Illumina protocol.


title: Methylation data from Astrocytoma tissue 1

description:
Astrocytoma_1
RD-15-250
Bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation450 BeadChip using standard Illumina protocol.


title: Methylation data from TCGA AML tissue 17

description:
AML_17
TCGA-AB-2901
Bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation450 BeadChip using standard Illumina protocol.


title: Methylation data from Astrocytoma tissue 5

description:
Astrocytoma_5
RD-15-83
Bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation450 BeadChip using standard Illumina protocol.


title: HK2_11_OTA100

description: processed data file: HK2_rawCounts.txt

value: Kidney

value: Proximal tubule epithelial cell line

value: 100 nM OTA


title: Methylation data from TCGA AML tissue 18

description:
AML_18
TCGA-AB-2874
Bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation450 BeadChip using standard Illumina protocol.


title: Methylation data from TCGA AML tissue 19

description:
AML_19
TCGA-AB-2936
Bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation450 BeadChip using standard Illumina protocol.


title: Patient 29


title: mlh3_2

city: NEW YORK

first: Xiaojing

last: Mu

state: New York

address: 1275 York Ave

department: Molecular Biology

institute: Memorial Sloan kettering cancer center

description:
Spo11-associated DNA oligonucleotides
AS_5h_2_IGO_09181_2_S2

data_processing:
Base calls perfomed using HiSeq Control Software v.2.0.10.0 for samples sequenced on Illumina HiSeq 2500
Adapters (AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC) were clipped from reads using fastx_clipper, part of the FASTX Toolkit 0.0.13.2, with parameters -l 15 -n -v -Q33 -i
First five bases (diffusion primer added in library prep) in each sequence were trimmed and trimmed sequence was recorded in the FASTQ ID tag for downstream tracking
Clipped reads were mapped using SHRiMP 2.1.1b with parameters -N 15 -U -g -1000 -q -1000 -m 10 -i -20 -h 100 -r 50% -n 1 -s 1111111111,11110111101111,1111011100100001111,1111000011001101111 -o 1001 -Q -E --sam-unaligned --strata
Sequences clipped from a read during mapping should be polyC on the 3' end or polyG on the 5' end. If clipped bases were not polyC or polyG the alignment score was corrected by deducting the mismatch score for each non-C,G base in the clipped sequence.
Genome_build: Maps of 5' ends of sequence reads were compiled and analyzed in R (RStudio version 0.98.1091, R version 3.0.1)
Supplementary_files_format_and_content: wig files include RPM (reads per million mapped) for each sample at each non-zero base position in the genome

organism: Saccharomyces cerevisiae

source_name: meiotic culture

extract_protocol:
Based on Pan et al. 2011 Cell 144:719-731. Whole cell extracts were prepared by grinding frozen cells in a bead mill and resuspending powder in 10%TCA. Pellets were then extracted with SDS and soluble protein was subjected to affinity purification of Spo11-Flag fusion with Protein-G Dynabeads. Protein was digested with proteinase K and Spo11-associated oligonucleotides were recovered by ethanol precipitation.
Based on Pan et al. 2011 Cell 144:719-731. Oligonucleotides were tailed with ribo-G using rGTP and terminal transferase, then ligated to duplex DNA adaptors with a dC overhang using T4 RNA ligase 2. Complementary strands were synthesized with Klenow, then purified by denaturing polyacrylamide electrophoresis. Purified complementary strands were subjected to 3' tailing with ribo-G using rGTP and terminal transferase, then another duplex adaptor was ligated using T4 RNA ligase 2. Ligated material was amplified with 16 cycles of PCR to add Illumina HiSeq adaptors

tag: epitope tag

tag: meiotic time-point

value: 5 hr in meiosis


title: mlh3_1

description:
Spo11-associated DNA oligonucleotides
AS_5h_1_IGO_09181_1_S1


title: HK2_10_OTA10

description: processed data file: HK2_rawCounts.txt

value: 10 nM OTA


title: HK2_8_Ctrl

description: processed data file: HK2_rawCounts.txt


title: Patient 28

tag: gender

value: Mild


title: Methylation data from TCGA AML tissue 15

description:
AML_15
TCGA-AB-2992
Bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation450 BeadChip using standard Illumina protocol.

value: IDH Mutant


title: Patient 26

tag: bpd


title: Methylation data from Astrocytoma tissue 8

description:
Astrocytoma_8
RD-15-269
Bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation450 BeadChip using standard Illumina protocol.

value: Astrocytoma

value: Astrocytoma tissue


title: Patient 27

value: Severe


title: Methylation data from TCGA AML tissue 14

description:
AML_14
TCGA-AB-2984
Bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation450 BeadChip using standard Illumina protocol.


title: HK2_7_Ctrl

description: processed data file: HK2_rawCounts.txt


title: 12yGuSCB

city: Urbana

first: Ann

middle: Marie

last: Kemper

state: IL

address: 1008 W Hazelwood Dr

institute: University of Illinois

description: gelded male

data_processing:
Quality control on all 56 samples (112 paired-end files) was performed using fastp (version 0.19.5) and summarized using MultiQC (version 1.6)
All fastq files were trimmed using Trimmomatic(version 0.38) in paired end mode to trim any remaining adaptors, then trim leading or trailing bases with quality scores below 28, then discarding a read pair if either read was shorter than 30 bases
Salmon (version 0.11.3) was used to quasi-map reads in paired-end mode to quantify transcript abundance (with additional arguments –seqBias --gcBias –numBootstraps=30) to the EquCab3.0 genome assembly utilizing NCBI Annotation Release 103
R package tximport was used to estimate gene-level counts from transcript-level quantification.   For the articular cartilage tissue (AC0), two individual horses had two samples taken at slightly different locations (ACD vs. ACS) in the stifle joint.  Gene-level counts for the ACD and ACS samples from the same horse were added together at the gene-level as they looked extremely similar to each other.
Reads were filtered and normalized (TMM) using edgeR, surrogate variables were calculated and counts were corrected using sva, and DE analysis performed using limma-trend
Genome_build: EquCab3.0
Supplementary_files_format_and_content: tab-delimited files with normalized log2(cpm) values for 54 of 56 samples

organism: Equus caballus

source_name: subcondral bone

extract_protocol:
Samples were collected immediately following euthanasia and were flash frozen in liquid nitrogen or placed in RNAlater (Qiagen, Valencia, CA) at 4°C for 24-48 hours prior to storage at -80°C. Frozen samples were pulverized and placed in TRIzol reagent (Invitrogen, Carlsbad, CA) prior to mechanical homogenization. RNA extraction was performed on spin columns using the RNeasy Micro Kit (Qiagen, Valencia, CA) per manufacturer instructions.
Standard library preparation and sequencing (100 base-pair, paired-end) on an Illumina Hi-Seq sequencer (90 samples on a Hi-Seq 2500, 22 samples on a Hi-Seq 4000)

value: 12 years

tag: Sex

value: neuter

value: subcondral bone

tag: location

value: pooled

tag: individual


title: 10yMuSCB

tag: age

value: 10 years

value: female


title: Patient 25

value: Plasma

value: Female


title: HK2_6_OTA100

description: processed data file: HK2_rawCounts.txt

value: Kidney

value: Proximal tubule epithelial cell line


title: 12yGuAC0

description: gelded male

source_name: articular cartilage

value: articular cartilage


title: Methylation data from Astrocytoma tissue 4

description:
Astrocytoma_4
RD-15-143
Bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation450 BeadChip using standard Illumina protocol.


title: 10yMuAC0


title: HK2_5_OTA100

description: processed data file: HK2_rawCounts.txt

value: 100 nM OTA


title: HK2_4_OTA10

description: processed data file: HK2_rawCounts.txt

value: 10 nM OTA


title: Patient 24

value: Mild


title: Methylation data from TCGA AML tissue 12

description:
AML_12
TCGA-AB-2948
Bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation450 BeadChip using standard Illumina protocol.

value: AML

value: IDH Mutant

value: AML tissue


title: 10yGuAC0

description: gelded male


title: HK2_3_OTA10

description: processed data file: HK2_rawCounts.txt


title: Methylation data from TCGA AML tissue 16

description:
AML_16
TCGA-AB-2821
Bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation450 BeadChip using standard Illumina protocol.


title: HK2_2_Ctrl

description: processed data file: HK2_rawCounts.txt

source_name: HK-2 _0 nM OTA

value: 0 nM OTA


title: 09yFuSCB

value: 9 years


title: 09yFuAC0


title: Patient 23

value: Severe


title: 10yGuSCB

description: gelded male

value: neuter

value: subcondral bone

value: pooled


title: Patient 21

value: Plasma

value: Moderate


title: HK2_1_Ctrl

description: processed data file: HK2_rawCounts.txt

value: Kidney


title: Methylation data from Astrocytoma tissue 9

description:
Astrocytoma_9
RD-15-287
Bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation450 BeadChip using standard Illumina protocol.

value: Astrocytoma

value: Astrocytoma tissue


title: Patient 22

value: Female


title: Patient 20


title: HK2_9_OTA10

description: processed data file: HK2_rawCounts.txt

value: Proximal tubule epithelial cell line

value: 10 nM OTA


title: HF_T

city: Hohhot

first: Feng

last: Yang

state: Inner Mongolia

address: 306 Zhaowuda Road

country: China

institute: Inner Mongolia Agricultural University

description: The group information is prefixed with HF-T in column of processed data file

data_processing:
We used CellRanger count pipeline 2.2.0 to analyze the sequencing data and generated the single cell information. To generate same number of total cells for downstream analysis, we used augments ‘--force-cells=7000 \’.
Genome_build: ARS1
Supplementary_files_format_and_content: tab-delimited text files stores normalized and log-transformed single cell expression value

organism: Capra hircus

source_name: telogen skin

extract_protocol:
For each group skin tissues were obtained from at least 3 independent female, prior to digestion. To prepare dorsal skin single cell suspension for single-cell RNA sequencing, the back skin tissues were isolated via microdissection and 0.25 % trypsin/EDTA solution was used to digest dorsal skin tissues at 37 °C for 30 min，mechanically dissociate the tissue once every 10 min. 1 mg/ml collagenase IV (Sigma, St Louis, MO, USA) was used to digest the tissue which digested by trypsin at 37 °C for 30 min. the skin tissues were mechanically dissociated into single cell suspension by pipetting, the cell suspensions were then filtered through a 30 μm nylon cell strainer, to remove villus debris(BD Falcon, BD Biosciences, San Jose, CA, USA) prior to single cell library construction.
Single-cell RNA-seq libraries were prepared using Single Cell 3’ Library Gel Bead Kit V2 (10x Genomics Inc., Pleasanton, CA, USA, Cat#120237) following the manufacture’s introduction.

value: skin

tag: strain

value: Albas White Cashmere Goat

tag: developental stage

value: telogen

value: female


title: HF_C

description: The group information is prefixed with HF-C in column of processed data file

source_name: catagen skin

value: catagen


title: Patient 18

value: Male

value: Mild


title: HF_A

description: The group information is prefixed with HF-A in column of processed data file

source_name: anagen skin

value: anagen


title: 1k_CART_cells

city: Philadelphia

first: Wenliang

last: Wang

state: PENNSYLVANIA

address: 421 Curie Boulevard

institute: University of Pennsylvania

data_processing:
make fastq files with mkfastq from Cell Ranger ATAC pipeline version 1.1.0
analysis with count from Cell Ranger ATAC pipeline version 1.1.0
integration site analysis with epiVIA
Genome_build: hg38

source_name: Bulk human T cells from peripheral blood.

growth_protocol: Bulk human T cells were activated with anti-CD3 and anti-CD28 monoclonal-antibody-coated polystyrene beads for 24 hours and subsequently transduced with a lentiviral vector encoding a  CD19-specific CAR with 4-1BB/CD3ζ domains. T cell expansion was carried out for 9 days as previously described , followed by cryopreservation.

extract_protocol:
T cells were thawed and checked for purity based on cell-surface expression of CD3, CD4, CD8 and CAR via flow cytometry. For scATAC-seq experiments, the first experiment on ~5000 CD8+CAR+ T cells  were isolated using bead-based positive selection, according to the manufacturer’s instructions (Miltenyi Biotech), while in the second experiment on ~1000 cells, they were FACS sorted with CD8 and CAR.
scATAC-seq was carried out using the Chromium platform and following the standard protocols provided by 10X Genomics: 1) “Chromium Single Cell ATAC Reagent Kits” and 2) “Nuclei Isolation for Single Cell ATAC Sequencing.” Libraries were paired-end sequenced (50 bp + 50 bp) on a NextSeq 550 (Illumina).
scATAC-seq

tag: cell type

value: PBMC


title: clone 2

data_processing:
ATAC-seq reads were aligned to the hg38 genome assembly with BWA Version: 0.7.17-r1188
Alignment results were analyzed with epiVIA to identify the integration sites

growth_protocol: HEK293T clones in which a single integration site has been mapped as described (Sherman, E. et al. 2017) were thawed and maintained for 2 passages in DMEM (ATCC® 30-2002™) supplemented with 10% serum and 1X Penicillin/Streptomycin (Gibco 15140-122) in a humidified incubator at 37°C and 5% CO2.

extract_protocol:
ATAC-seq was performed as previously described with minor modifications (Buenrostro et al., 2013). Fifty thousand cells were pelleted at 550 x g and washed with 1 mL 1x PBS, followed by treatment with 50 mL lysis buffer (10 mM Tris-HCl [pH 7.4], 10 mM NaCl, 3 mM MgCl2, 0.1% IGEPAL CA-630). After pelleting nuclei, the pellets were resuspended in 50 mL transposition reaction with 2.5 mL Tn5 transposase (FC-121-1030; Illumina) to tag and fragment accessible chromatin. The reaction was incubated in a 37C water bath for 45 minutes. Tagmented DNA was purified using a MinElute Reaction Cleanup Kit (QIAGEN) and amplified with 12 cycles of PCR.
Libraries were purified using a QIAQuick PCR Purification Kit (QIAGEN). Libraries were paired-end sequenced (38 bp+37 bp) on a NextSeq 550 (Illumina).

value: embryonic kidney


title: Patient 17

value: Plasma


title: clone 1


title: Patient 16


title: Methylation data from TCGA AML tissue 9

description:
AML_9
TCGA-AB-3011
Bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation450 BeadChip using standard Illumina protocol.

value: AML

value: IDH Mutant

value: AML tissue


title: Methylation data from TCGA AML tissue 11

description:
AML_11
TCGA-AB-2877
Bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation450 BeadChip using standard Illumina protocol.