title: MM02EM_27

description:
Single-cell RNA-seq
MM02P_27_CTCTCTAC-CTAAGCCT
MM02EM_27

tag: cell type

value: Multiple myeloma


title: TH 421

status: Public on Oct 17 2019

type: RNA

city: Homburg Saar

first: Masood

last: Abu-Halima

address: Kirrberger St 60

department: Human Genetics

country: Germany

institute: Univeristy of Saarland

description: univentricular heart (UVH)

hyb_protocol: The expression profile of 2549 human miRNAs was determined using SurePrint G3 8x60k miRNA microarrays (Agilent) according to the manufacturers recommendations

scan_protocol: Array´s were scanned with the Agilent Scanner with default settings.

data_processing: Raw expression values were extracted using the Feature Extraction Software of Agilent. Raw signal intensities were quantil-normalized

label: using miRNA Complete Labeling and Hyb Kit (Agilent, Cat. No 5190-0456),  Cyanine 3-pcp

molecule: total RNA

organism: Homo sapiens

source_name: Blood

extract_protocol: Total RNA including miRNAs was isolated using the Qiagen PAXgene™ Blood miRNA  according to manufacturers recommendations.

tag: disease state

value: healthy control

tag: tissue

value: blood


title: WT Sham 1-3 female

city: Pittsburgh

first: Anne

last: Barbosa Diniz

state: PA

address: 3501 Terrace St

department: Pharmaceutical Sciences

country: USA

institute: University of Pittsburgh

description: 100mg of frozen livers from 3 different mice in the same group were pooled together

hyb_protocol: Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Mus musculus Genome Array. GeneChips were washed and stained in the Affymetrix Gene Scanner 7G.

scan_protocol: GeneChips were scanned using the Affymetrix Gcos/Genechip operating software.

data_processing: GeneChips were processed using the Affymetrix Gcos/Genechip operating software.

label: biotin

organism: Mus musculus

source_name: Hepatic tissue

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 8 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

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

treatment_protocol: 8 weeks old C57BL/6 (WT) mice underwent a sham or 30 minutes of warm bilateral renal ischemia-reperfusion injury (IRI). These mice were sacrificed 24 hours later and their livers were harvested and frozen at -80C. 100mg of frozen livers from 3 different mice in the AKI group were pooled together in the same tube. 100mg of frozen livers from 3 different mice in the Sham group were pooled together in the same tube.

value: liver

tag: strain

tag: gender

value: female

tag: treatment

value: sham

tag: genotype

value: wt


title: B6_pGSN_D9_R3

type: SRA

city: Boston

first: Lester

last: Kobzik

state: MA

address: 665 Huntington Ave

department: Environmental Health

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

library_source: transcriptomic

data_processing:
FASTQ files with basecalls were generated using Illumina bcl2fastq software with the arguments --create-fastq-for-index-reads --ignore-missing-bcls --minimum-trimmed-read-length 0 --mask-short-adapter-reads 0
DriverMap read counts were determined using Cellecta DriverMap Data Alignment Software, as detailed in https://manuals.cellecta.com/drivermap-targeted-expression-profiling-kits/v1/en/topic/run-data-extraction
The resulting data matrix of counts for genes analyzed (columns B & C) shows counts for each sample as a column (see raw data file, DriverMapDay9LungRawDataMatrix.txt)
Read counts were normalized using total counts per column (sample) to calculate scaling factors used to multiply all column values to result in identical total counts per column for all columns (samples), see processed data file DriverMapDay9LungProcessedData.txt
Supplementary_files_format_and_content: tab-delimited text file

source_name: Lung

extract_protocol:
Lung tissue RNA was isolated using the QIAGEN RNeasy mini kit (Cat. # 74104).
RNA Samples were processed using the DriverMap targeted sequencing platform and protocol developed by Cellecta, Inc (https://www.cellecta.com/products-3/drivermap-targeted-rna-sequencing/). The DriverMap platform combines multiplex PCR for ~4700 gene coding regions and quantitation by next generation sequencing.

treatment_protocol: Mice were treated by intraperitoneal injection with rhu-pGSN (2 mg/day days 3-6, then 5 mg per day days 7-9 after influenza infection) or vehicle

tag: Sex

value: Male

tag: age

value: 6-8 weeks old

tag: infection

value: influenza

value: pGSN

tag: day of lung harvest


title: MM02EM_26

city: Seoul

first: Daeun

last: Ryu

address: 81, Irwon-ro

country: South Korea

institute: Samsung Genome Institute

description:
Single-cell RNA-seq
MM02P_26_CTCTCTAC-AGAGTAGA
MM02EM_26

data_processing:
A modified reference was generated by merging the three array control RNA spike-ins (ThermoFisher), 92 ERCC spike-ins and the human genome reference (hg19) with the GENCODE 19 annotations.
Paired-end 100bp reads were aligned to STAR_2.4.0b with default parameters.
Transcripts Per Million (TPM) values were estimated using RSEM v1.2.17 with default parameters.
hg19
Supplementary_files_format_and_content: A processed file is tab-delimited and contains the raw TPM values for 477 single cells and 11 CD138 negative bulk samples.

extract_protocol:
Plasma cells were purified using EasySep(®) CD138 Positive Selection kit before loading to integrated fluidic circuit (IFC) chip. Each suspension was loaded to 5-10um IFC for mRNA sequencing chip then cDNA synthesis and amplification were performed with SMARTer Ultra Low RNA Kit (Clontech) in the C1TM Single-Cell Auto Prep System (Fluidigm). Two types of external sequence, 1,4,7 ArrayControl TM RNA Spikes and ERCC RNA Spike-In Control Mix (ThermoFisher) were added to the lysis mix for validation of array and batch effect. All of amplified cDNAs were quantified and qualified by the Qubit® 2.0 Fluorometer (Life Technologies) and 2100 Bioanalyzer (Agilent Technologies).
We analyzed single cell RNA sequencing(scRNA-seq) data after applied filtering criteria to remove cells with low sequencing quality. Also eleven CD138-negative bulk samples analyzed by the scRNA-seq pipeline.

tag: patient id

value: male

tag: death(alive=0; death=1)

tag: prep-site

value: Pleural effusion

tag: facs sorting

value: CD138 positive


title: WT AKI 1-3

description: A total of 180mg of frozen renal tissues from 3 different mice in the same group were pooled together

source_name: Renal tissue

treatment_protocol: 8 weeks old C57BL/6 (WT) mice underwent a sham or 30 minutes of warm bilateral renal ischemia-reperfusion injury (IRI). These mice were sacrificed 24 hours later and their kidneys were harvested and frozen at -80C. 180mg of frozen kidneys from 3 different mice in the WT AKI group were pooled together in the same tube. 124mg of frozen livers from 6 different mice in the EST KO AKI group were pooled together in the same tube.

value: kidney

value: acute kidney injury


title: WT IRI 1-3

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).


title: WT Sham 1-3


title: Recurrent Hypoglycemia replicate 6

city: Salt Lake City

first: Rahul

last: Agrawal

state: UTAH

institute: University of Utah

description:
2_RH5
Laboratory Rat
processed data file: counts.txt

data_processing:
Reads were aligned with Novocraft Novoalign (version 2.8) to a genome index containing all known splice junctions based on Ensembl release 83. Up to 50 alignments were allowed per read, and adapter sequence provided for trimming. Known transcript junctions were built using USeq MakeTranscriptome (version 8.8.8) with a radius of 46 bp.
Alignments to splice junctions were converted to genomic coordinates using USeq SamTranscriptomeParser (version 8.8.8) allowing for only one random alignment.
Alignments were counted against known miRNA genes using USeq DefinedRegionsDifferentialSeq (version 8.8.8). The miRNA genes were extracted from mirBase for Rn5 and lifted over to Rn6 coordinates.
Genome_build: Rn6 (Rnor_6.0)
Supplementary_files_format_and_content: counts.txt: Tab-delimited text file of counts for each miRNA gene.

organism: Rattus norvegicus

source_name: Ventromedial Hypothalamus

extract_protocol:
Brains were removed and flash frozen on dry ice and sectioned in cryostat. Ventromedial Hypothalamic tissues were dissected out from frozen brain sections using punch biopsies. Total RNA was extracted and purified from VMH using Qiagen miRNeasy Mini Kit and the quality of the RNA was determined by Agilent 2200 TapeStation.
Small RNA sequencing libraries were prepared as described from 100-500 ng of total RNA using the NEBNext Multiplex Small RNA Library Prep Set for Illumina (NEB #E7300). Following PCR amplification, the library was size selected to enrich for adapter-ligated molecules encoding small RNA species. Size selection was performed on a Sage Science 3%25 agarose, dye free, Pippin Prep Gel Cassette with internal markers (CDF3010) using the following parameters: BP Start=105 bp, BP End=155 bp. Size selected libraries were qualified on an Agilent Technologies 2200 TapeStation High Sensitivity D1000 ScreenTape assay (5067-5584 and 5067-5585) and the molarity of adapter-modified molecules was defined by quantitative PCR using the Kapa Biosystems Kapa Library Quant Kit (cat#KK4824). The molarity of individual libraries were normalized to 5 nM and equal volumes were pooled in preparation for Illumina sequence analysis.

treatment_protocol: Rats were subjected with 3 days treatment of either saline or insulin for recurrent saline or recurrent hypoglycemia, respectively.

value: Sprague-Dawley

value: Ventromedial Hypothalamus

value: 9 weeks

value: Insulin


title: Recurrent Hypoglycemia replicate 5

description:
2_RH4
Laboratory Rat
processed data file: counts.txt


title: Recurrent Hypoglycemia replicate 4

description:
2_RH3
Laboratory Rat
processed data file: counts.txt


title: B5_pGSN_D9_R2


title: MM02EM_25

description:
Single-cell RNA-seq
MM02P_25_CTCTCTAC-TAGATCGC
MM02EM_25

value: Multiple myeloma


title: Recurrent Hypoglycemia replicate 3

description:
2_RH2
Laboratory Rat
processed data file: counts.txt


title: Sorted CD45RO+ TMEM cell subset from healthy donor 8

city: Rozzano, Milan

first: Emilia Maria Cristina

last: Mazza

address: Via Alessandro Manzoni, 56

country: Italy

institute: Humanitas Clinical and Research Center

hyb_protocol: Samples were hybridized to GeneChip Human Transcriptome Arrays 2.0 (Thermo Scientific) following the Encore Biotin Module user guide (NuGen Technlogies) and Affymetrix's Hybridization procedures

scan_protocol: Arrays were scanned following the GCS 3000 7G User guide (Thermo Scientific)

data_processing: RMA of .CEL files using affy Bioconductor library and Brainarray: hta20hsentrezgcdf v21.0.0 custom CDF. In RMA, PM values have been background adjusted, normalized using quantile normalization, and expression measure calculated using median polish summarization

source_name: sorted CD8+ T cell subset from human PBMCs

label_protocol: Samples were amplified an labeled according to Ovation Pico WTA System V2 and Encore Biotin Module user guides (NuGen Technlogies)

extract_protocol: Toral RNAs were isolated following the microRNeasy kit guidelines (Qiagen)

value: Sorted CD45RO+ TMEM cell subset


title: TH 420

description: univentricular heart (UVH)

label_protocol: The expression profile of 2549 human miRNAs was determined using SurePrint G3 8x60k miRNA microarrays (Agilent) according to the manufacturers recommendations

value: healthy control

value: blood


title: Recurrent Hypoglycemia replicate 2

description:
2_RH1
Laboratory Rat
processed data file: counts.txt


title: B3_Veh_D9_R5

value: Male

value: vehicle


title: B4_pGSN_D9_R1

value: 6-8 weeks old

value: influenza


title: Sorted TNR3+ cell subset from healthy donor 4

value: Sorted TNR3+ cell subset


title: MM02EM_23

description:
Single-cell RNA-seq
MM02P_23_GGACTCCT-AAGGAGTA
MM02EM_23

value: male

value: Pleural effusion


title: MM02EM_24

description:
Single-cell RNA-seq
MM02P_24_TAGGCATG-TAGATCGC
MM02EM_24

value: CD138 positive


title: TH 844

description: univentricular heart (UVH)


title: TH 419

description: univentricular heart (UVH)


title: TH 842

description: univentricular heart (UVH)


title: B1_Veh_D9_R3


title: MM02EM_20

description:
Single-cell RNA-seq
MM02P_20_GGACTCCT-ACTGCATA
MM02EM_20


title: Recurrent Saline replicate 6

description:
1_SAL5
Laboratory Rat
processed data file: counts.txt

value: Saline


title: MM02EM_19

description:
Single-cell RNA-seq
MM02P_19_AGGCAGAA-CTCTCTAT
MM02EM_19


title: Recurrent Saline replicate 4

description:
1_SAL3
Laboratory Rat
processed data file: counts.txt

value: Sprague-Dawley


title: MM02EM_21

description:
Single-cell RNA-seq
MM02P_21_TCCTGAGC-CTAAGCCT
MM02EM_21


title: A12_Veh_D9_R2


title: MM02EM_18

description:
Single-cell RNA-seq
MM02P_18_CTCTCTAC-AAGGAGTA
MM02EM_18


title: TH 839

description: univentricular heart (UVH)


title: A11_Veh_D9_R1


title: Recurrent Saline replicate 3

description:
1_SAL2
Laboratory Rat
processed data file: counts.txt

value: Ventromedial Hypothalamus


title: Sorted TNR3+ cell subset from healthy donor 1


title: Recurrent Saline replicate 2

description:
1_SAL1
Laboratory Rat
processed data file: counts.txt

value: 9 weeks


title: A10_pGSN_D7_R5

value: pGSN


title: Recurrent Hypoglycemia replicate 1

description:
2_RH0
Laboratory Rat
processed data file: counts.txt

value: Insulin


title: B2_Veh_D9_R4


title: TH 837

description: univentricular heart (UVH)


title: MM02EM_17

description:
Single-cell RNA-seq
MM02P_17_CTCTCTAC-GTAAGGAG
MM02EM_17

value: Multiple myeloma


title: TH 833

description: univentricular heart (UVH)

value: healthy control


title: TH 841

description: univentricular heart (UVH)

value: blood


title: TH 831

description: univentricular heart (UVH)


title: Recurrent Saline replicate 1

description:
1_SAL0
Laboratory Rat
processed data file: counts.txt


title: TH 832

description: univentricular heart (UVH)


title: Recurrent Saline replicate 5

description:
1_SAL4
Laboratory Rat
processed data file: counts.txt


title: A9_pGSN_D7_R4

value: Male


title: A8_pGSN_D7_R3


title: A7_pGSN_D7_R2


title: MM02EM_11

description:
Single-cell RNA-seq
MM02P_11_CAGAGAGG-TATCCTCT
MM02EM_11


title: TH 827

description: univentricular heart (UVH)


title: TH 824

description: univentricular heart (UVH)


title: MM02EM_9

description:
Single-cell RNA-seq
MM02P_09_CAGAGAGG-TAGATCGC
MM02EM_09


title: MM02EM_10

description:
Single-cell RNA-seq
MM02P_10_TAGGCATG-GTAAGGAG
MM02EM_10


title: A5_Veh_D7_R5

value: vehicle


title: A6_pGSN_D7_R1

value: 6-8 weeks old


title: TH 823

description: univentricular heart (UVH)


title: Stimulation CTL, chick ID 107, time point D6

city: Pierre Bénite

first: Jeremie

middle: FC

last: Becker

address: Centre Hospitalier Lyon Sud, Bâtiment 3F

department: Medical diagnostic Discovery department

country: France

institute: bioMérieux

hyb_protocol: WT PLUS hybridization protocol

scan_protocol: Affymetrix Gene ChIP Scanner 3000 7G

data_processing:
RMA
probe group file: ChiGene-1_0-st.pgf
meta-probeset file: ChiGene-1_0-st.ps

organism: Gallus gallus

source_name: CTL_D6_whole blood

label_protocol: WT PLUS labelling protocol

extract_protocol: PAXgene tube (Ozyme # BD762165) and HT simply RNA Kit (Promega # AX2420) followed by a DNase step (RNA clean-up Nucleospin, Macherey-Nagel # 740948)

tag: stimulation

value: CTL

tag: time point

value: whole-blood


title: Stimulation CTL, chick ID 109, time point D6


title: MM02EM_6

description:
Single-cell RNA-seq
MM02P_06_TAGGCATG-CTCTCTAT
MM02EM_06

value: male

tag: cell type


title: MM02EM_15

description:
Single-cell RNA-seq
MM02P_15_TCCTGAGC-TATCCTCT
MM02EM_15

value: Pleural effusion


title: MM02EM_8

description:
Single-cell RNA-seq
MM02P_08_CGTACTAG-AGAGTAGA
MM02EM_08

value: CD138 positive


title: A4_Veh_D7_R4

value: influenza


title: Stimulation CTL, chick ID 106, time point D6


title: Stimulation CTL, chick ID 108, time point D6


title: Stimulation CTL, chick ID 105, time point D6


title: MM02EM_5

description:
Single-cell RNA-seq
MM02P_05_CAGAGAGG-AGAGTAGA
MM02EM_05


title: TH 822

description: univentricular heart (UVH)

tag: disease state


title: TH 817

description: univentricular heart (UVH)

tag: tissue


title: TH 818

description: univentricular heart (UVH)


title: A2_Veh_D7_R2

tag: strain


title: MM02EM_4

description:
Single-cell RNA-seq
MM02P_04_AGGCAGAA-ACTGCATA
MM02EM_04

tag: gender


title: Stimulation CTL, chick ID 103, time point D6


title: A1_Veh_D7_R1

tag: treatment


title: TH 816

description: univentricular heart (UVH)


title: TH 815

description: univentricular heart (UVH)


title: MM02EM_2

description:
Single-cell RNA-seq
MM02P_02_TAAGGCGA-AAGGAGTA
MM02EM_02


title: Stimulation CTL, chick ID 102, time point D6


title: MM02EM_1

description:
Single-cell RNA-seq
MM02P_01_AGGCAGAA-TATCCTCT
MM02EM_01


title: A3_Veh_D7_R3


title: Stimulation CTL, chick ID 101, time point D6


title: Lib_20_CD5_hi

data_processing:
Basecalls performed using RTA v2 version 2.4.11
RNA-seq reads were aligned to the GRCm38 genome assembly using STAR version 2.5.1b
Differential Gene Expression analysis was performed using EdgeR 3.20.9 R version 3.4.4
Genome_build: GRCm38

source_name: Sorted CD5hi TN cell subset

growth_protocol: Spleens from C57BL/6 male mice were collected at 12 weeks of age and mechanically smashed by plunger of a 2ml syringe with a 40 μm cell strainer. Splenocytes were enriched for CD8+ T cells with the MojoSort mouse CD8+ naïve T cell isolation kit and stained for FACS sorting. FACS-sorted cells were lysed with 50 mL RLT buffer, with the addition of 1 mL RNAse inhibitor

extract_protocol:
RNA extraction was performed with RNeasy Micro Kit, according to manufacturer instructions
Libraries were prepared using SMART-Seq v4 Ultra Low Input RNA Kit, according to manufacturer instructions

value: Sorted CD5hi TN cell subset

value: spleen


title: TH 814

description: univentricular heart (UVH)


title: Blastocysts

city: La Jolla

first: Ronghui

last: Li

state: CA

address: 10010 North Torrey Pines Road

department: Gene Expression Lab

institute: Salk Institute for Biological Studies

data_processing:
I1 read: contains the sample index.
R1 read: contains the cell barcode (first 16 nt) and UMI (next 10 nt).
R2 read: contains the RNA sequence.
We use STAR v2.5.1b1 to align reads to the 10x Genomics pre-built mm10 reference genome and utilized CellRanger v3.0.2 software for blastocysts (288 cells) and EPS- blastoids (3528 cells) datasets with default setting for de-multiplexing to generate feature-barcode matrix.
The R package Seurat v3.0.12 was used to read and analyze feature-barcode matrix following the steps: First, we filtered the cells that have unique feature counts over 5000 according to quality control matrix plots (184 and 2518 cells in the blastocysts and EPS-blastoids group passed the filter, respectively);
Then UMI counts were normalized with NormalizeData function using defalult settings. Seurat’s RunUMAP function was used to do non-linear dimension reduction and cluster with resolution setting as 0.2.
Differentially expressed genes in the clusters between blastocysts and EPS-blastoids were determined by the FindMarkers function using a bimodal likelihood ratio test. For the differentially expressed genes, we tested weather each had enriched GO terms in biological process and molecular functions using the ToppGene Suite3. Unsupervised clustering analysis (UCA) was performed using the R package ComplexHeatmap v2.1.0.
Genome_build: mm10
Supplementary_files_format_and_content: processed tsv files contain information on barcodes and gene annotations; the processed mtx files contain gene umi counts

source_name: Blastocysts

growth_protocol: EPS colonies were dissociated into single cells by incubation with TrypLE (Gibco). To remove irradiated MEF cells, cell resuspension was transferred into a 0.1% gelatin-coated plate and incubated at 37°C for 30 min. EPS cells were collected, filtered through a 40 μm cell strainer, and counted. AggreWell 400 (STEMCELL Technology) were prepared following the manufacturer’s instructions. The basal medium for the EPS-blastoid induction medium is composed of 25% TSC basal medium, 25% N2B27 basal medium, and 50% KSOM (homemade or Millipore, MR020P5D). Approximately 6,000 cells (five cells per microwell for 1200 microwells) were resuspended in basal medium supplemented with 2μM ROCK inhibitor Y-27632 (Reagents Direct, 53-B80-50), 12.5ng/ml rhFGF4 (R&D, 235F4025), 12.5ng/ml Heparin (Sigma, H3149), 3μM GSK3 inhibitor CHIR99021 (Axon Medchem, 27-H76), 5ng/ml BMP4 (Proteintech, HZ-1040), and 0.5μM A83-01 (Axon Medchem, 1421) and seeded into the AggreWell 400. The plate was centrifuged at 300g for one minute and transferred into a incubator. The next day, the medium was removed and replaced with fresh induction medium without Y- 27632. Blastoids were manually picked up under a stereomicroscope for downstream experiments or analysis. For blastocysts preparation, ICR female mice were superovulated by intraperitoneal (i.p.) injection of 7.5 Unit of pregnant mares' serum gonadotrophin (PMSG) and 46–48 h later by 7.5 Unit of human chorionic gonadotrophin (HCG), and then mated with ICR male mice immediately. The blastocysts were flushed from female mice 3.5 days after detection of the vaginal plug, and cultured in KSOM under 37°C with an atmosphere of 5% CO2 in the air.

extract_protocol:
EPS-blastoids were manually picked up using mouthpipette and washed three times. ~500 EPS-blastoids were harvested and dissciated with a homemade enzyme mix composed of 0.5X versene (Lonza, 17711E), 0.5X Acumax (Innovative Cell Tech, AM105), and 0.05X Dnase (STEMCELL Tech, 07900) at 37°C for 30min with agitation. Dissociated cells were spinned down and wash with PBS + 0.04%BSA for three times and resupended in the same buffer. Cell density was determined by a TC10 cell counter (Biorad, 1450001). Blastocysts were dissociated using the same protocol.
Dissociated cells (~4800 cells for EPS-blastoids and ~1000 cells for blastocysts) were loaded into the Chromium single cell controller (10xGenomics) to generate single-cell gel beads in the emulsion according to the manufacturer’s protocol. The library was generated using the Chromium Single Cell 3' Reagent Kits according to the manufacturer’s manual. The two libraries were pooled and sequenced using Nextseq 500 (150 cycles, high output).

tag: sample type

value: embryos

tag: sample source

value: Blastocysts

value: pooled male and female


title: Lib_19_mem

source_name: Sorted CD44hi conventional TMEM cell subset


title: EPS-blastoids

source_name: Blastoids generated from EPS cells

value: synthetic embryos

value: EPS-blastoids

tag: Sex


title: Mouse Adipose Nuclei N CL

city: Los Angeles

first: Douglas

last: Arneson

address: 2000 Terasaki Life Sciences Bldg 610 Charles E Young Drive East

department: Integrative Biology and Physiology

institute: UCLA

description: 10X Genomics Single Cell; nuclei

data_processing:
Base calls performed with bcl2fastq2.15.
Read 2 was aligned with Star v2.5.0c.
Each aligned read was tagged with its mate-pair UMI and cell barcode.
Each aligned exonic read was tagged with a gene name.
A digital gene expression matrix was built by counting the number of unique UMIs per gene within each cell; columns are cells, and rows are genes.
Drop-seq samples were processed using Drop-seq Tools and 10X Genomics samples were processed using cell ranger.
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: Digital gene expression matrices (genes x cells) in sparse matrix format. Compressed, flat text files with tab delimiters. Same format as generated by 10X Genomics Cell Ranger -- compatible with the R package Seurat. Requires the corresponding features (genes) and barcodes (cell names) files. Meta Data files include the cell type labels.

source_name: Mus musculus mature adipose nuclei, Il10rαF/F, catecholamine treatment

extract_protocol:
Single-cell suspensions were processed through Drop-Seq or 10X Genomics Chromium to generate single-cell cDNA libraries. Microbeads were counted, and amplified by PCR, and the 3' end of the cDNA prepared for sequencing.
Mouse iWAT was dissected and separated in SVF and mature adipocytes and then dissociated into single-cell suspension, followed by drop-seq or 10X genomics single cell library preparation. Libraries were prepared following the latest drop-seq and 10X genomics protocol..

tag: strain/backgorund

value: C57BL/6 Il10rαF/F

value: CL; 1mg/kg/day for 4 days

value: Mature Adipocyte Nuclei

tag: age

value: 10 weeks


title: Stimulation CTL, chick ID 100, time point D6

value: CTL


title: Mouse Adipose Nuclei P CL

description: 10X Genomics Single Cell; nuclei

source_name: Mus musculus mature adipose nuclei, AdIL10RαKO, catecholamine treatment

value: C57BL/6 AdIL10RαKO


title: TH 810

description: univentricular heart (UVH)

value: healthy control

value: blood


title: TH 811

description: univentricular heart (UVH)


title: TH 809

description: univentricular heart (UVH)


title: Mouse Adipose Nuclei P 4days

description: 10X Genomics Single Cell; nuclei

source_name: Mus musculus mature adipose nuclei, AdIL10RαKO, 4days @ 4 °C

value: 4days at 4 °C


title: Lib_18_CD5_low

source_name: Sorted CD5lo TN cell subset

value: Sorted CD5lo TN cell subset

value: male


title: Stimulation CTL, chick ID 98, time point D6

value: whole-blood


title: Lib_17_CXCR3_p

source_name: Sorted TNR3+ cell subset

value: Sorted TNR3+ cell subset

value: spleen


title: Stimulation CTL, chick ID 97, time point D6


title: Mouse Adipose Nuclei N 4days

description: 10X Genomics Single Cell; nuclei

source_name: Mus musculus mature adipose nuclei, Il10rαF/F, 4days @ 4 °C


title: Mouse Adipose Nuclei P 48hr

description: 10X Genomics Single Cell; nuclei

source_name: Mus musculus mature adipose nuclei, AdIL10RαKO, 48hrs @ 4 °C

value: 48hrs at 4 °C


title: TH 808

description: univentricular heart (UVH)

source_name: Blood


title: Stimulation CTL, chick ID 91, time point D3

source_name: CTL_D3_whole blood


title: TH 806

description: univentricular heart (UVH)


title: Stimulation CTL, chick ID 92, time point D3


title: Mouse Adipose Nuclei N 48hr

description: 10X Genomics Single Cell; nuclei

source_name: Mus musculus mature adipose nuclei, Il10rαF/F, 48hrs @ 4 °C


title: Lib_15_mem

value: Sorted CD44hi conventional TMEM cell subset


title: Stimulation CTL, chick ID 90, time point D3


title: TH 876

description: univentricular heart (UVH)

value: Univentricular Patient


title: Lib_14_CD5_low


title: Mouse Adipose Nuclei P 24hr

description: 10X Genomics Single Cell; nuclei

source_name: Mus musculus mature adipose nuclei, AdIL10RαKO, 24hrs @ 4 °C

value: 24hrs at 4 °C


title: Mouse Adipose Nuclei N 24hr

description: 10X Genomics Single Cell; nuclei

source_name: Mus musculus mature adipose nuclei, Il10rαF/F, 24hrs @ 4 °C

value: C57BL/6 Il10rαF/F


title: Lib_13_CXCR3_p


title: Mouse Adipose Nuclei P RT

description: 10X Genomics Single Cell; nuclei

source_name: Mus musculus mature adipose nuclei, AdIL10RαKO, room temperature

value: Room Temperature

value: Mature Adipocyte Nuclei


title: TH 866

description: univentricular heart (UVH)


title: Stimulation CTL, chick ID 89, time point D3

value: CTL


title: Lib_12_CD5_hi

source_name: Sorted CD5hi TN cell subset

value: Sorted CD5hi TN cell subset


title: Stimulation CTL, chick ID 99, time point D6

source_name: CTL_D6_whole blood


title: TH 521

description: univentricular heart (UVH)


title: TH 863

description: univentricular heart (UVH)


title: TH 864

description: univentricular heart (UVH)


title: Lib_09_CXCR3_p


title: Lib_10_CD5_low


title: Lib_16_CD5_hi


title: TH 634

description: univentricular heart (UVH)


title: Stimulation CTL, chick ID 85, time point D3


title: Lib_08_CD5_hi


title: Mouse Adipose Nuclei N RT

description: 10X Genomics Single Cell; nuclei

source_name: Mus musculus mature adipose nuclei, Il10rαF/F, room temperature

value: 10 weeks


title: Stimulation CTL, chick ID 87, time point D3


title: Mouse SVF CL2

description: Drop-Seq; whole cell

source_name: Mus musculus SVF catecholamine treatment, 10 weeks

value: CL; 1mg/kg/day for 4 days

value: stromal vascular fraction (SVF)


title: Stimulation CTL, chick ID 86, time point D3


title: Stimulation CTL, chick ID 88, time point D3


title: Stimulation CTL, chick ID 82, time point D0+3h

source_name: CTL_D0+3h_whole blood


title: TH 488

description: univentricular heart (UVH)

value: blood


title: TH 508

description: univentricular heart (UVH)


title: Lib_07_mem

source_name: Sorted CD44hi conventional TMEM cell subset

value: male


title: Mouse SVF Saline3

description: Drop-Seq; whole cell

source_name: Mus musculus SVF saline treatment, 10 weeks

value: Saline


title: TH 457

description: univentricular heart (UVH)


title: TH 450

description: univentricular heart (UVH)


title: Mouse SVF Saline2

description: Drop-Seq; whole cell


title: Lib_05_CXCR3_p

value: Sorted TNR3+ cell subset


title: Stimulation CTL, chick ID 80, time point D0+3h

value: whole-blood


title: Mouse SVF CL3

description: Drop-Seq; whole cell


title: Stimulation CTL, chick ID 79, time point D0+3h


title: Mouse SVF Saline1

description: Drop-Seq; whole cell


title: Lib_04_CD5_hi

value: spleen


title: Lib_02_CD5_low

source_name: Sorted CD5lo TN cell subset

value: Sorted CD5lo TN cell subset


title: Mouse SVF CL1

description: Drop-Seq; whole cell


title: WT_3D7-G7_S_TRIBE

city: shanghai

first: meng

last: liu

address: 1239,SiPing Road

country: China

institute: TongJi University

data_processing:
Library strategy: TRIBE
Illumina Casava1.8 software used for basecalling.
pair end sequencing reads were trimmed with cutadapt (v11) by 10bp at each end, reads with average quality score >= 20 and length >=50bp were kept. Genomic DNA reads were aligned using bowtie2 (v2.2.5) (parameters: --sensitive) to the P.falciparum genome (plasmoDB.org, v3 release 32)[29]. Strand specific RNA sequencing reads were aligned using Tophat2 (v2.1.1) (parameters: -m 1 –g 2 -I 50000 --microexon-search --no-coverage-search --library-type fr-firststrand). PCR duplicates were removed for editing analysis.
Only events with minimum 10 and 5% editing were considered to be valid editing events. gDNA coverage>=30 and uniformity of nucleotide were also required to avoid single nucleotide polymorphisms (SNP). As biological replicates of the same treatment and developmental stage were highly correlated based on percentage editing, we combined them for the downstream analysis. RNA editing data is converted to bedgraph file format for display using R (v3.5.1).
Genome_build: PF3D7_32
Supplementary_files_format_and_content: bedgraph files indicating the editing sites of  Pfdis3-ADAR

organism: Plasmodium falciparum

source_name: malaria at schizont

extract_protocol:
Red blood cells infected by highly synchronous parasites were collected by centrifugation and resuspended in trizol that could be stored in -80℃ for a long time. After centrifugation, the supernatant was saved and then RNA was extracted according to reagent specification of Direct-zol™ RNA MiniPrep (R2052). The integrality of RNA was validated by 2% agarose gel.
Construction library was performed based on KAPA Stranded mRNA-Seq Kit (KK8421).

tag: developmental stage

value: Schizont

tag: genotype


title: WT_3D7-G7_R_TRIBE

source_name: malaria at Ring

value: Ring


title: Lib_01_CXCR3_p

source_name: Sorted TNR3+ cell subset


title: TH 413

description: univentricular heart (UVH)

source_name: Blood

value: Univentricular Patient


title: TH 409

description: univentricular heart (UVH)


title: TH 403

description: univentricular heart (UVH)


title: Lib_06_CD5_low


title: Stimulation CTL, chick ID 78, time point D0+3h


title: sh NPM n3

city: Montréal

first: Eric

last: Milot

state: Québec

address: 5415 boul. l'Assomption

department: Medicine

country: Canada

institute: HMR research center/Université de Montréal

data_processing:
Torrent Suite 4.4.2
ampliSeqRNA plugins was use to generate normalyzed read counts (RPM)
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include RPM values for each Sample

source_name: K562 cell line

growth_protocol: K562 were cultured in RPMI-1640 medium supplemented with 10 % fetal bovine serum at 37°C and selected with 2µg/mL puromycine.

extract_protocol:
RNA was extracted with TRIzol (Invitrogen) according to the manusfacturer's protocol.
Librairies were prepared using Ion AmpliSeq Transcriptome Human Gene Expression

value: K562 were infected with sh NPM1


title: Stimulation CTL, chick ID 75, time point D0+3h


title: PfDis3-ADAR_S_rep2_TRIBE

value: transgenic Pfdis3-ADAR


title: Stimulation CTL, chick ID 77, time point D0+3h

value: CTL


title: TH 391

description: univentricular heart (UVH)


title: Stimulation CTL, chick ID 74, time point D0+3h


title: sh NPM n2


title: Stimulation CTL, chick ID 76, time point D0+3h


title: PfDis3-ADAR_T_rep2_TRIBE

source_name: malaria at Trophozoite

value: Trophozoite


title: TH 390

description: univentricular heart (UVH)


title: sh NPM n1


title: PfDis3-ADAR_R_rep2_TRIBE


title: TH 385

description: univentricular heart (UVH)


title: sh Scramble n3

value: K562 were infected with sh Scarmble


title: WT_3D7-G7_T_TRIBE


title: PfDis3-ADAR_S_rep1_TRIBE


title: TH 829

description: univentricular heart (UVH)


title: sh Scramble n2


title: TH 820

description: univentricular heart (UVH)


title: Stimulation CpG, chick ID 35, time point D6

source_name: CpG_D6_whole blood

value: CpG


title: PfDis3-ADAR_T_rep1_TRIBE


title: sh Scramble n1


title: TH 805

description: univentricular heart (UVH)


title: TH 798

description: univentricular heart (UVH)


title: gDNA

library_source: genomic

molecule: genomic DNA

source_name: Genomic DNA

extract_protocol: Highly synchronous parasites were collected during the IDC at ring, trophozoite and schizont stages and genome DNA was extracted using QIAamp DNA FFPE Tissue Kit (QIAGEN, 56404).


title: TH 795

description: univentricular heart (UVH)


title: PfDis3-ADAR_R_rep1_TRIBE


title: TOT_STRESSED_2

city: Boulder

first: Roy

middle: Robert

last: Parker

state: CO

address: 3415 Colorado Ave

department: Chemistry and Biochemistry

institute: University of Colorado at Boulder

data_processing:
Illumina adaptors were trimmed using Trimmomatic 0.32 in paired end (PE) mode.
Reads were aligned using Tophat2.
Differential expression analysis was perfomed using Cuffdiff
Genome_build: GENCODE release 19 GRCh37
Supplementary_files_format_and_content: cuffdiff

source_name: WT U-2 OS cells

growth_protocol: U-2 OS cells were maintained in DMEM with high glucose, 10% FBS and 1% penicillin-streptomycin at 37 degrees C and 5% CO2.

extract_protocol:
Trizol was used to isolate Total RNA.
RNA libraries were prepared for sequencing using KAPA RNA hyperprep kit with riboerase by the CU-Boulder BioFrontiers sequencing facility.

treatment_protocol: Cells were either treated with .5mM sodium arsenite or were left untreated

value: cytoplasmic RNA

value: arsenite treated


title: TOT_STRESSED_3


title: GFP_S_RIP-seq

data_processing:
Low-quality and adaptor sequences were trimmed from the reads using cutadapt (v1.16) with parameters: -a AGATCGGAAGAGC -A AGATCGGAAGAGC --trim-n -m 50 -q 20,20.
Then, the reads were mapped to the Plasmodium falciparum 3D7 genome (Pf 3D7 v32, obtained from PlasmoDB) using Hisat2 strand-specific mode (v2.1.0) with parameters: --rna-strandness RF --dta --no-discordant --no-mixed --no-unal.
The Samtools (v1.9) was used to transfer the mapping results from sam format to position sorted bam format.
Mapped reads were subsequently assembled into transcripts guided by the PlasmoDB gff annotation files (Pf 3D7 v32) using featureCounts (v1.6.1) with parameters: -M -p -B -C for all; -s 2 for sense transcripts; -s 1 for antisense transcripts.
Genome_build: Pf 3D7 v32
Supplementary_files_format_and_content: The raw counts were calculated by featureCounts as described above.

source_name: GFP RIP

extract_protocol: Infected red blood cells (iRBCs) were collected by centrifugation and resuspended in cold PBS(10 volume of iRBC) . Parasites were extracted with 0.15% saponin and washed with cold PBS until the supernatant was clear. Lysis buffer(50 mM Tris-Cl pH7.4, 150mM NaCl, 1mM EDTA, 1mM EGTA, 1% Triton X-100/ NP-40)with protease inhibitors and RNase inhibitors was added to the parasite pellet[1.5ml/ (1×109 parasites)] and incubated with rotation for 1h at 4℃. Cell debris were spinned out at 13000rpm for 15min at 4℃ and supernatant was incubated with 10ug of anti-Ty1 antibodies at 4℃ for 3h with rotation. For preparation of equilibrated protein-G magnetic beads, 50 ul protein-G magnetic beads were washed once with Wash Buffer(10mM Tris-Cl pH 7.5, 150mM MgCl2, 150mM KCl, 0.1% Triton X-100), then washed once with Elution Buffer, and washed twice with Wash Buffer. Protein-G magnetic beads were mixed with supernatant with protease inhibitors and RNase inhibitors at 4℃ overnight with rotation. Beads were washed twice with 500 ul Wash Buffer and once with PBS and then resuspended in 700ul TRIZOL at 4℃ for 10 min. After removed the beads, 140ul chloroform was added to trizol at room temperature for 5 min and mixture was centrifuged at 13800rpm for 30 min at 4℃. Supernatant was added to a new 1.5ml centrifuge tube and centrifuged at 13800rpm for 2 min at 4℃. Supernatant was mixed with 1ul glycogene and equal volume of isopropanol on ice for 2h. Tube was centrifuged at 13800rpm for 30 min at 4℃. Pellet was washed twice with 1 ml of 75% (vol/vol) ethanol, then air-dried and resuspended in 20µl of RNase-free water[3]. DNase I was used to digest DNA for 15min at room temperature. RNase-free water was added up to 100μl, mixed with equal volume of chloroform/isoamyl alcohol pH<5.0 (24:1), and then mixture was centrifuged at 13500rpm for 5 min. Supernatant was mixed with phenol/chloroform/isoamyl alcohol (24:1), and centrifuged at 13500rpm for 5 min. Supernatant was transferred to a new 1.5ml centrifuge tube   with 1ul glycogene, one-tenth volumes of 3 M sodium acetate(pH 5.2), and 2.5 volumes of 100% ethanol and incubated at −80 °C for 20min. Samples were centrifuged at 13500rpm for 15 min and pellet was washed twice with 1 ml of 75% (vol/vol) ethanol, then air-dried and resuspended in 11µl of RNase-free water.

tag: development stage

tag: host

value: Homo sapiens

tag: rip antibody

value: mouse anti-Ty1,Sigma SAB4800032-50 ug

value: wildtype

tag: rip

value: GFP RIP


title: Stimulation CTL, chick ID 73, time point D0+3h

tag: stimulation

tag: time point

value: whole-blood


title: Stimulation CpG, chick ID 32, time point D6

tag: tissue


title: GFP_T_RIP-seq

tag: strain


title: Stimulation CpG, chick ID 33, time point D6


title: TH 790

description: univentricular heart (UVH)

tag: disease state

value: blood


title: TH 779

description: univentricular heart (UVH)


title: TOT_UNSTRESSED_3

tag: treatment

value: unstressed


title: Stimulation CpG, chick ID 28, time point D6


title: Stimulation CpG, chick ID 29, time point D6


title: GFP_R_RIP-seq

value: Ring


title: TOT_UNSTRESSED_2

tag: sample type


title: Stimulation CpG, chick ID 34, time point D6


title: Stimulation CpG, chick ID 27, time point D6


title: TH 701

description: univentricular heart (UVH)

value: Univentricular Patient


title: TH 673

description: univentricular heart (UVH)


title: TOT_UNSTRESSED_1


title: GFP-input_T_RIP-seq

source_name: GFP RIP input

value: GFP RIP input


title: TH 664

description: univentricular heart (UVH)


title: GFP-input_S_RIP-seq

value: Schizont


title: TOT_STRESSED_1


title: Stimulation CpG, chick ID 26, time point D6


title: Stimulation CpG, chick ID 31, time point D6


title: PELLET_STRESSED_3

value: pellet RNA


title: PELLET_STRESSED_2


title: GFP-input_R_RIP-seq


title: Stimulation CpG, chick ID 20, time point D3

source_name: CpG_D3_whole blood


title: PfDis3-input_S_RIP-seq

source_name: Pfdis3 RIP input

value: Pfdis3 RIP input


title: TH 661

description: univentricular heart (UVH)


title: PfDis3-input_T_RIP-seq

value: Trophozoite


title: Stimulation CpG, chick ID 25, time point D6

value: CpG


title: TH 645

description: univentricular heart (UVH)


title: TH 564

description: univentricular heart (UVH)


title: PELLET_STRESSED_1


title: TH 561

description: univentricular heart (UVH)


title: PELLET_UNSTRESSED_3


title: PfDis3-input_R_RIP-seq


title: PELLET_UNSTRESSED_2


title: Stimulation CpG, chick ID 18, time point D3


title: TH 538

description: univentricular heart (UVH)


title: PfDis3_S_rep2_RIP-seq

source_name: Pfdis3 RIP

value: Pfdis3 RIP


title: Stimulation CpG, chick ID 19, time point D3


title: Stimulation CTL, chick ID 81, time point D0+3h

source_name: CTL_D0+3h_whole blood

value: CTL


title: PfDis3_T_rep2_RIP-seq

value: Homo sapiens


title: G3BPKO_TOT_3

source_name: G3BPKO U-2 OS cells

value: cytoplasmic RNA

value: arsenite treated


title: TH 506

description: univentricular heart (UVH)


title: PfDis3_R_rep2_RIP-seq

value: mouse anti-Ty1,Sigma SAB4800032-50 ug

value: wildtype


title: Stimulation CpG, chick ID 16, time point D3

value: whole-blood


title: G3BPKO_TOT_2


title: G3BPKO_TOT_1


title: TH 502

description: univentricular heart (UVH)

value: blood


title: TH 501

description: univentricular heart (UVH)


title: TH 498

description: univentricular heart (UVH)


title: Stimulation CpG, chick ID 17, time point D3


title: Stimulation CpG, chick ID 13, time point D3


title: PfDis3_T_rep1_RIP-seq


title: WT_TOT_2


title: WT_TOT_3


title: PELLET_UNSTRESSED_1

value: unstressed


title: TH 486

description: univentricular heart (UVH)

value: Univentricular Patient


title: Stimulation CpG, chick ID 15, time point D3


title: WT_TOT_1


title: TH 495

description: univentricular heart (UVH)


title: PfDis3_S_rep1_RIP-seq


title: WT_3D7-G7_S_RNA-seq

data_processing:
Low-quality and adaptor sequences were trimmed from the reads using cutadapt (v1.16) with parameters: -a AGATCGGAAGAGC -A AGATCGGAAGAGC --trim-n -m 75 -q 20,20.
Then, the reads were mapped to the Plasmodium falciparum 3D7 genome (Pf 3D7 v32, obtained from PlasmoDB) using Hisat2 strand-specific mode (v2.1.0) with parameters: --rna-strandness RF --dta --no-discordant --no-mixed --no-unal.
The Samtools (v1.9) was used to transfer the mapping results from sam format to position sorted bam format.
Mapped reads were subsequently assembled into transcripts guided by the PlasmoDB gff annotation files (Pf 3D7 v32) using featureCounts (v1.6.1) with parameters: -M -p -B -C for all; -s 2 for sense transcripts; -s 1 for antisense transcripts.
Genome_build: Pf 3D7 v32
Supplementary_files_format_and_content: The raw counts were calculated by featureCounts as described above.

molecule: polyA RNA

value: schizont

tag: genotype/variation

value: wild type


title: G3BPKO_PB_3

value: P-Body RNA


title: TH 482

description: univentricular heart (UVH)


title: WT_3D7-G7-GlcN+_T_RNA-seq

value: wild type-GlcN+


title: Stimulation CpG, chick ID 9, time point D0+3h

source_name: CpG_D0+3h_whole blood


title: Stimulation CpG, chick ID 7, time point D0+3h


title: PfDis3_R_rep1_RIP-seq

value: Ring


title: TH 474

description: univentricular heart (UVH)


title: G3BPKO_PB_1


title: Stimulation CpG, chick ID 10, time point D0+3h

value: CpG


title: TH 458

description: univentricular heart (UVH)


title: WT_3D7-G7_T_RNA-seq

value: Trophozoite


title: WT_3D7-G7-GlcN+_S_RNA-seq

source_name: malaria at schizont


title: Stimulation CpG, chick ID 6, time point D0+3h


title: Stimulation CpG, chick ID 5, time point D0+3h


title: WT_PB_3


title: WT_3D7-G7_R_RNA-seq

source_name: malaria at Ring


title: WT_PB_2


title: TH 448

description: univentricular heart (UVH)


title: TH 483

description: univentricular heart (UVH)


title: Stimulation CpG, chick ID 4, time point D0+3h


title: PfDis3-DD-GlcN+_S_rep1_RNA-seq


title: WT_PB_1


title: TH 444

description: univentricular heart (UVH)


title: G3BPKO_PB_2


title: PfDis3-DD_S_rep1_RNA-seq


title: TH 434

description: univentricular heart (UVH)


title: Stimulation CpG, chick ID 1, time point D0+3h


title: HUVECs, FC (CHIR99021+FGF1)

city: Birmingham

first: Chengming

last: Fan

state: ALABAMA

address: 1670 University Blvd

department: Department of Biomedical Engineering

institute: University of Alabama at Birmingham

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence
exons from all isoforms of a gene were merged to create one meta-transcript.
Supplementary_files_format_and_content: Excel files include abundance measurements, p values for each Sample

source_name: HUVECs

growth_protocol: Human umbilical vein endothelial cells (HUVECs) were purchased from Lonza (Walkersville, MD) and were expanded and subcultured according to the manufacturer’s recommendations. Briefly, cells were thawed, seeded onto a fibronectin-precoated T75 flask (1µg/cm2 or 0.5 µg/mL) and expanded using a complete endothelial cell growth medium supplemented with 5% fetal bovine serum (FBS), human fibroblast growth factor (hFGF), human epidermal growth factor (hEGF), vascular endothelial growth factor (VEGF), R3-insulin-like growth factor-1 (RE3-IGF-1), hydrocortisone, ascorbic acid, gentamicin, and amphotericin-B (GA1000) (Clonetics™, EGM™-2MV BulletKit™; Lonza).

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

treatment_protocol: HUVECs were plated onto a T75 flask and expanded to 70 to 80%, using appropriate culture media. Then, the cells were rinsed twice with DPBS (pH 7.4) and incubated with appropriate serum-free culture medium for 24 hours. After 24 hours, they were exposed to CHIR+FGF1 for 24 hours and cultured in appropriate complete medium. Another one without CHIR+FGF1 as control.

tag: cell type

value: HUVECs

tag: passages

value: three to five

value: FC (CHIR99021+FGF1)


title: WT_3D7-G7-GlcN+_R_RNA-seq

value: Homo sapiens


title: Input-gPTENL_FRRC190665537-1a

first: ge

last: mengkai

state: State...

address: shanghai

institute: Shanghai Jiao Tong University School of Medicine (SJTU-SM)

description: processed data file: gPTENL-CHIP_vs_INPUT.bw

data_processing:
ChIP-seq reads were mapped to the human reference genome (UCSC hg38) using Bowtie2 version 2.3.5 with parameters very-sensitive-local.
Duplicate reads were removed by picard version 2.18.4.
Peaks were called with the MACS version 2.1.1.20160309. Metaplots and heat maps were generated using deeptools version 3.1.0.
Genome_build: hg38
Supplementary_files_format_and_content: bigWig files

source_name: hepatocellular

growth_protocol: Cell lines were maintained in Dulbecco's modified Eagle's medium (DMEM) supplemented with 10% FBS.

extract_protocol:
Lysates were clarified from sonicated nuclei and isolated with antibody.
Libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: Cell lines were infected by lentivirus containing gRNA and CAS9.

tag: cell line

value: hepatocellular carcinoma cell line

value: PTENa/b depletion

tag: chip antibody


title: TH 414

description: univentricular heart (UVH)

data_processing: Raw expression values were extracted using the Feature Extraction Software of Agilent. Raw signal intensities were quantil-normalized

source_name: Blood

extract_protocol: Total RNA including miRNAs was isolated using the Qiagen PAXgene™ Blood miRNA  according to manufacturers recommendations.


title: HUVECs, NC (Negative Control)

value: NC (Negative Control)


title: PfDis3-DD-GlcN+_T_rep1_RNA-seq

source_name: malaria at Trophozoite

tag: developmental stage


title: Input-gNS_FRRC190665536-1a

description: processed data file: gNS-CHIP_vs_INPUT.bw

value: No PTENa/b depletion


title: PfDis3-DD_T_rep1_RNA-seq


title: TH 407

description: univentricular heart (UVH)

value: blood


title: ChIP-gPTENL_FRRC190665539-1a

value: H3K4me3 (Millipore, cat#04-745)


title: PfDis3-DD_S_rep2_RNA-seq

value: schizont


title: PfDis3-DD-GlcN+_S_rep2_RNA-seq


title: P2_gWDR5

data_processing:
Reads were mapped to Human Genome Assembly GRC38 by STAR v2.5. Gene and isoform expression quantification were called by RSEM v1.2 with default parameters on GENCODE human v28 gene annotation file.
Differential expression analysis was preformed by Bioconductor package edgeR v3.18.1.
Significant differentially expressed genes were chosen according to two criteria: 1) significance level FDR < 0.05; 2) expression level average FPKM values bigger than 1 in either treatment or control groups.
Genome_build: hg19 (GRCh37)
Supplementary_files_format_and_content: *.txt: Tab-delimited text files include FPKM values for each Sample.

extract_protocol:
RNA was harvested using Trizol reagent. 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols.

value: WDR5 depletion


title: PfDis3-DD_R_rep1_RNA-seq


title: Stimulation CpG, chick ID 2, time point D0+3h

value: whole-blood


title: Stimulation CpG, chick ID 3, time point D0+3h


title: Kp29

city: Pretoria

first: John

last: Osei Sekyere

state: Gauteng

address: 05 Bopheloweg Off Dr. Savage Road

department: Department of Medical Microbiology

country: South Africa

institute: University of Pretoria

data_processing:
Library strategy: DNA-seq
Automatic minimum seed read length calculation HGAP 2.0
Allow partial alignments
Trimming FASTQ output using HGAP 2.0
Determining genome size using SMRT Analysis v2.0
Supplementary_files_format_and_content: gff files were generated

organism: Klebsiella pneumoniae

source_name: Swab

growth_protocol: 37°C overnignt

extract_protocol:
Genomic DNA was extracted from cells grown overnight in Brain heart infusion broth using the bacterial/fungal ZymoResearch extraction kit.
Libraries were prepared according to the PacBio Technical note (Library Prep)

tag: sequence type

tag: capsule type


title: Kp32

source_name: Urine

tag: host


title: TH 397

description: univentricular heart (UVH)

value: Univentricular Patient


title: TH 375

description: univentricular heart (UVH)


title: PfDis3-DD-GlcN+_T_rep2_RNA-seq


title: PfDis3-DD-GlcN+_R_rep1_RNA-seq

value: Ring


title: PfDis3-DD_T_rep2_RNA-seq


title: P1_gWDR5


title: Kp15

source_name: Catheter tip


title: Kp10


title: PfDis3-DD_R_rep2_RNA-seq


title: P1_gNS

value: No WDR5 depletion


title: ChIP-gNS_FRRC190665538-1a


title: shADAR2 OL cells biological rep1

city: Kyoto

first: Mako

last: Yanai

state: Kyoto

address: 53 Kawahara-cho, Shogoin, Sakyo-ku

department: Institute for Frontier Life and Medical Sciences

country: Japan

institute: Kyoto university

hyb_protocol: The fragmented and labeled ss-cDNAs were hybridized for 16 hours at 45C on Human Clariom S microarrays folowing the Affymetrix protocol.

scan_protocol: The arrays were washed using GeneChip Fluidics Station 450, and then scanned by GeneChip Scanner 3000 according to the Affymetrix protocol.

data_processing: The data were analyzed by Transcriptome Analysis Console with Gene level SST-RMA with default settings.

label: Biotin

source_name: Oligodendroglia cells, shRNA for ADAR2

label_protocol: The fragmented ss-cDNAs were labeled with biotin according to the Affymetrix protocol.

growth_protocol: Oligodendroglia cells were cultured in Dulbecco’s modified Eagle’s minimal essential medium supplemented with 5% fetal calf serum.

extract_protocol: Total RNA was extracted using Trizol according to the manufacturer's instructions.

tag: shRNA


title: shCtrl OL cells biological rep2

source_name: Oligodendroglia cells, shRNA for non-targeting

value: shCtrl


title: GPC16_DSF_3

status: Public on Oct 16 2019

city: London

first: David

last: Michod

address: Gower St, Bloomsbury

country: United Kingdom

institute: UCL

data_processing:
Sequencing was performed on Illumina NextSeq 500 instrument
Illumina’s bcl2fastq Conversion Software v2.19 was used to demultiplex and convert the run data to fastq files
The reads were aligned to the human genome UCSC hg38 using RNA-STAR 2.5.2b and deduplicated using Picard Tools 1.79
FeatureCounts was used to count the reads per transcript
Counts were normalized with DESeq2
Genome_build: hg38
Supplementary_files_format_and_content: normalized counts in tab-delimited text files

source_name: Pediatric high grade glioma

growth_protocol:
The media was supplemented with penicillin (100 units/ml), streptomycin (100 μg/ml).
NeuroCult NS-A Basal medium supplemented with EGF, FGF, PDGF (20 ng/ml each) and NeuroCult NS-A Proliferation Supplement. The flasks were laminin coated.

extract_protocol:
Total RNA was extracted from collected cells using the RNeasy Plus Mini Kit
200 ng total RNA were processed using the NEBNext RNA Ultra II kit with Poly A+ selection

treatment_protocol: Disulfiram (DSF) was dissolved in DMSO. The cells were treated with DSF for 16 h. The same amount of DMSO (without drug) was added to the control cells. CuCl2 (1 μM) was added to all samples.

tag: cell line/source

tag: tumor grade

value: IV

value: Primary patient-derived stem cells

value: Pediatric high grade glioma

value: Disulfiram treated (0.32 microM)


title: GPC16_DSF_2


title: shADAR2 OL cells biological rep2


title: GPC16_Control_1

value: Control


title: shCtrl OL cells biological rep1


title: P2_gNS

value: hepatocellular carcinoma cell line


title: GPC16_Control_2


title: SF188_Control_3

growth_protocol:
The media was supplemented with penicillin (100 units/ml), streptomycin (100 μg/ml).
DMEM/F-12 supplemented with FBS(10%)

value: cell line


title: SF188_Control_2


title: SF188_DSF_3

value: Disulfiram treated (1 microM)


title: GPC16_Control_3


title: GPC16_DSF_1


title: PfDis3-DD-GlcN+_R_rep2_RNA-seq

value: Homo sapiens


title: SF188_DSF_2


title: SF188_DSF_1


title: Kp8

source_name: Pus swab


title: GFP_6h.2 (GFP 6h rep 3)

city: Stockholm

first: Kristian

last: Dreij

address: Nobels väg 13

department: Environmental Medicine

country: Sweden

institute: Karolinska Institutet

data_processing:
The RNA-seq reads were aligned to human reference genome hg38 with STAR v2.5.3a
The counts of reads mapped to genome annotations in GENCODE v27 were calculated using featureCounts program in Subread v1.5.2
The gene counts were further imported to DESeq2 v1.20 for differential expression analysis using Wald significance tests with interaction of time and vector condition.
Genome_build: hg38

source_name: Lung cells

extract_protocol:
Qiagen RNeasy mini kit according to protocol
Illumina TruSeq Standard Total RNA library prep kit according to protocol

treatment_protocol: Transfected cells were sorted based on the co-expressed GFP reporter using BD FACSAria

tag: tissue

value: Lung cells

value: H1299 from ATCC

tag: passage number

value: between 7 and 12

value: pGFP


title: O6_meG_6h.2 (O6meG 6h rep 3)


title: RW_6h.2 (RW 6h rep 3)


title: O6_meG_BnG_6h.2 (O6meG+O6bzG 6h rep 3)

value: p53-O6meG + O6bzG (10 uM)


title: WT_6h.2 (WT 6h rep 3)


title: O6_meG_BnG_6h.1 (O6meG 6h rep 2)


title: RW_6h.1 (RW 6h rep 2)


title: O6_meG_6h.1 (O6meG+O6bzG 6h rep 2)


title: WT_6h.1 (WT 6h rep 2)


title: GFP_6h.1 (GFP 6h rep 2)


title: SF188_Control_1

tag: disease state


title: WT_6h (WT 6h rep 1)


title: O6_meG_24h.2 (O6meG 24h rep 3)


title: O6_meG_6h (O6meG 6h rep 1)


title: RW_24h.2 (RW 24h rep 3)


title: O6_meG_BnG_24h.2 (O6meG+O6bzG 24h rep 3)


title: WT_24h.2 (WT 24h rep 3)


title: GFP_6h (GFP 6h rep 1)


title: GFP_24h.2 (GFP 24h rep 3)


title: GFP_24h.1 (GFP 24h rep 2)


title: WT_24h.1 (WT 24h rep 2)


title: RW_24h.1 (RW 24h rep 2)


title: O6_meG_BnG_24h (O6meG+O6bzG 24h rep 1)


title: O6_meG_24h.1 (O6meG 24h rep 2)


title: O6_meG_24h (O6meG 24h rep 1)


title: O6_meG_BnG_6h (O6meG+O6bzG 6h rep 1)


title: Human Entorhinal Cortex of aged Healthy individuals Ct7-Ct8

city: Singapore

first: Gabriel

last: Chew

address: 8 College Road

country: Singapore

institute: Duke-NUS Medical School

data_processing:
I1 read: contains the sample index.
R1 read: contains the cell barcode (first 16 nt) and UMI (next 10 nt).
R2 read: contains the RNA sequence.
Using the Grch38 (1.2.0) reference from 10x Genomics, we made a pre-mrna reference according to the steps detailed by 10x Genomics (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/advanced/references). Cellranger count was used to obtain raw counts. Our single nuclei data initially comprised 8 10x runs consisting of 4 AD runs and 4 control runs. Each run had 2 individuals (Supplementary Table 1). 2 runs (1 AD run [AD7_AD8] and 1 control run [Ct7_Ct8]) were discarded because of high neuronal enrichment (see Extended data Fig. 2a) possibly indicating neuronal contamination or technical artefacts. In all, this resulted in a final dataset of 6 10x runs consisting of 3 AD runs and 3 control runs.
Genome_build: hg38 pre-mRNA
Supplementary_files_format_and_content: count matrix for final 6 libraries analyzed
covariate data table for count matrix

extract_protocol:
Entorhinal cortex tissue from post-mortem Alzheimer’s disease and non-disease aged matched individuals was obtained from the Victorian Brain Bank (Ethics Approval for patient tissue banking and consent: University of Melbourne HREC Approval No.: 1545740; approval for transcriptomic analysis using banked tissue Monash University MUHREC 2016-0554; patient demographics in Supplementary Table 1). Nuclei isolation was carried out using the Nuclei Isolation Kit: Nuclei EZ Prep (Sigma, #NUC101) as described in 9. Briefly, tissue samples were homogenized using a glass dounce grinder in 2 ml of ice-cold EZ PREP and incubated on ice for 5 min. Centrifuged nuclei (500 × g, 5 min and 4 °C) were washed in ice-cold EZ PREP buffer, and Nuclei Suspension Buffer (NSB; consisting of 1× PBS, 1% (w/v) BSA and 0.2 U/μl RNase inhibitor (Clontech, #2313A). Isolated nuclei were resuspended in NSB to 106 nuclei per 400 μl), filtered through a 40 μm cell strainer and counted with Trypan blue.  Nuclei enriched in Nuclei Suspension Buffer were stained with DAPI (1:1000) for nuclei isolation using the Influx cell sorter (BD Biosciences, Franklin Lakes, NJ; 70 μm nozzle, 21-22 psi). Nuclei were defined as DAPI+ singlets. Sorted nuclei were counted twice prior to loading onto the 10X Chromium (10X Genomics).
Library construction was performed using the Chromium Single Cell 3′ Library & Gel Bead Kit v2 (10X Genomics, #PN-120237) with 18 cDNA pre-amplification cycles and sequencing on one high-output lane of the NextSeq 500 (Illumina). Our sequencing saturation was high, ranging from 83.2% to 97.4%.
10x Genomics Single Nuclei RNA Sequencing

value: Entorhinal Cortex

value: Single Nuclei

tag: individuals

value: control


title: Human Entorhinal Cortex of aged Healthy individuals Ct1-Ct2

tag: sample type


title: GFP_24h (GFP 24h rep 1)

tag: genotype/variation


title: Human Entorhinal Cortex of aged AD individuals AD1-AD2

value: AD


title: RW_6h (RW 6h rep 1 )


title: Human Entorhinal Cortex of aged Healthy individuals Ct5-Ct6


title: Human Entorhinal Cortex of aged Healthy individuals Ct3-Ct4


title: Human Entorhinal Cortex of aged AD individuals AD3-AD4


title: RW_24h (RW 24h rep 1 )


title: Human Entorhinal Cortex of aged AD individuals AD5-AD6


title: Human Entorhinal Cortex of aged AD individuals AD7-AD8


title: S1 xenograft WGBS

city: Jerusalem

first: Yotam

last: Drier

state: Israel

address: Faculty of Medicine, The Hebrew University, Ein Kerem

department: Immunology and Cancer Research

country: Israel

institute: The Hebrew University of Jerusalem

data_processing:
ChIP-seq data were aligned to hg38 using BWA aln 0.7.4, requiring minimal mapping quality of 10. HSBS data were aligned to hg38 by methylCtools 0.9.4 (Volker Hovestadt et al. Nature 2014), utilizing BWA mem 0.7.12, removing reads of mapping qualty 0. HiC and HiChIP were aligned to hg38 using HiC-Pro. RNA-seq reads were aligned using STAR 2.5.3 to the hg19 human reference.
PCR duplicates were removed with picard tools 2.9.2 for all data except CTCF ChIP-seq and RNA-seq
ChIP-Seq density tracks were generated by ‘igvtools count --includeDuplicates --minMapQuality 10' and than converted to BigWig format by igvtools tdftobedgraph and bedGraphToBigWig.
HSBS methylation data were called with methylCtools 0.9.4 (Volker Hovestadt et al. Nature 2014)
Gene expression was estimated by featureCounts 1.6.2. TPM values were calculated as described in (Wagner GP, Kin K, Lynch VJ, Theory Biosci. 2012)
Genome_build: hg38
Supplementary_files_format_and_content: Methylation at CpGs was called by methylCtools 0.9.4. Column 5 represent counts supporting methylated (i.e. not converted) DNA, column 6 represent unmethylated (i.e. converted) DNA at any given loci.

source_name: GIST S1 xeno

growth_protocol: GIST-T1 cell line was obtained from Cosmo Biosciences.  Cells were passaged in DMEM with 10% serum, 1X antibiotics and 1X Glutamax (Life Technologies).

extract_protocol:
For ChIP-seq, cultured cells or minced tissue was fixed in 1% formaldehyde and snap frozen in liquid nitrogen and stored at -80ºC for at least overnight. Sonication of tumor specimens and cultured cells was calibrated such that DNA was sheared to between 400bp and 2000bp. CTCF was immunoprecipitated with a monoclonal rabbit CTCF antibody, clone D31H2 (Cell Signaling 3418).  H3K27ac was immunoprecipitated with an antibody from Active Motif (cat 39133); For hybrid-selection bisulfite-sequencing, total genomic DNA was isolated using the DNAeasy Blood & Tissue Kit (Qiagen) and sheared using the Covaris LE220. Ampure XP beads (Agencourt) were then used to size select gDNA fragments within 150-320bp and sheared distribution was verified via BioAnalyzer (Agilient) prior to continuation. 1 microgram of gDNA was then generated into a sequencing library via end repair, 3’ A base tailing (KAPA Hyper Prep Kit #KK8502) and sequencing adapter ligation (Roche SeqCap Epi Enrichment System). Post-ligation clean-up was performed using Ampure XP beads. Following bead clean-up, DNA library was then bisulfite converted using the EZ DNA Methylation-Lightning Kit (Zymo Research) and amplified via PCR using KAPA HiFi U+ HotStart ReadyMix (KAPA #KK2800). Equal concentration of each bisulfite-converted library was then combined in sets of either three or four libraries/per pool along with SeqCap Epi universal & indexing oligos and bisulfite capture enhancer (SeqCap Epi Accessory Kit). Each pool was subsequently lyophilized using TOMY Micro-Vac (MV100) and resuspended in hybridization buffer (SeqCap Epi Hybridization and Wash Kit) prior to being hybridized to SeqCap Epi Probe Pool (Roche) for 72 hours at 47C in a thermocycler with a heated lid at 57C. Following the 72-hour incubation, captured bisulfite-converted libraries were recovered (SeqCap Pure Capture Bead Kit) at 47C in a thermocycler for 45 minutes, with intermediate vortexing every 15 minutes.  Capture beads were then washed (SeqCap Hybridization and Wash Kit) in a 47C water bath and room temperature, respectively; In-situ HiC was performed following [PMID: 25497547], CTCF HiChIP was performed following [PMID: 27643841]. In brief, 3 tubes of ~5 million GIST-T1 cells were crosslinked in 1% formaldehyde (2 replicates for HiChIP, 1 for HiC). Cells were lysed using Hi-C lysis buffer as described. Chromatin was digested with MboI restriction enzyme (NEB, R0147). After heat inactivation of restriction enzyme, DNA was ligated using T4 buffer (NEB, B0202). HiC DNA was sheered by Covaris E220, while HiChIP DNA was sheerd by Covaris LE220. For HiChIP we used 30 μL monoclonal rabbit CTCF antibody, clone D31H2 (Cell Signaling #3418) per replicate, and incubated with Protein G beads overnight. After washes we incubated in DNA Elution Buffer, added Proteinase K and Zymo purified the samples. Post-ChIP DNA was fragmented with Tn5. For both HiC and HiChIP Biotin Pull-Down was done with M280 Streptavidin beads, and size selection with Ampure XP SPRI beads;  RNA was isolated using an RNeasy Plus Kit (Qiagen). RNA concentration was measured by NanoDrop (Thermo Scientific) and quality was determined by Bioanalyzer (Agilent).
ChIP DNA was used to generate sequencing libraries by end repair (End-It DNA repair kit, Epicentre), 3’ A base overhang addition via Klenow fragment (NEB), and ligation of barcoded sequencing adapters.

value: Metastatic GIST

tag: sdh status

value: Deficient


title: S1 primary WGBS

source_name: GIST S1


title: GEN1C_sgDDX6_H3K4me3

city: Cambridge

first: Jocelyn

last: Charlton

address: 7 Divinity Avenue

department: Stem Cell and Regenerative Biology

institute: Harvard University

data_processing:
Reads were trimmed using cutadapt and aligned to the hg19 genome using BWA. Duplicate reads were marked using picard tools, and reads were filtered for a mapq score > 15.
Macs2 callpeak was used to call peaks, with --broad used for H3K9me3.
To generate peak sets, macs2 called peaks were extended by 500bp then only kept if present and overlapping in both biological replicates.
Genome_build: hg19
Supplementary_files_format_and_content: Processed peak files are in bed format: chr, start, end.

source_name: human induced pluripotent stem cells

growth_protocol: iPSCs (GEN1C) were maintained on Matrigel (Corning) coated dishes in mTeSR edium (Stem Cell Technologies) and passaged using gentle cell dissociation reagent (Stem Cell Technologies). For maintenance, cells were passaged every 4-5 days.

extract_protocol: 1 million cells were washed once with PBS and fixed in 1% formaldehyde

treatment_protocol: Cells were trypsinized

tag: cell type

value: primed hiPSCs


title: S1 xenograft CTCF

data_processing:
ChIP-seq data were aligned to hg38 using BWA aln 0.7.4, requiring minimal mapping quality of 10. HSBS data were aligned to hg38 by methylCtools 0.9.4 (Volker Hovestadt et al. Nature 2014), utilizing BWA mem 0.7.12, removing reads of mapping qualty 0. HiC and HiChIP were aligned to hg38 using HiC-Pro. RNA-seq reads were aligned using STAR 2.5.3 to the hg19 human reference.
PCR dupliactes were removed with picard tools 2.9.2 for all data except CTCF ChIP-seq and RNA-seq
ChIP-Seq density tracks were generated by ‘igvtools count --includeDuplicates --minMapQuality 10' and than converted to BigWig format by igvtools tdftobedgraph and bedGraphToBigWig.
HSBS methylation data were called with methylCtools 0.9.4 (Volker Hovestadt et al. Nature 2014)
Gene expression was estimated by featureCounts 1.6.2. TPM values were calculated as described in (Wagner GP, Kin K, Lynch VJ, Theory Biosci. 2012)
Genome_build: hg38
Supplementary_files_format_and_content: Methylation at CpGs was called by methylCtools 0.9.4. Column 5 represent counts supporting methylated (i.e. not converted) DNA, column 6 represent unmethylated (i.e. converted) DNA at any given loci

tag: material type

value: CTCF (D31H2, Cell Signaling #3418)


title: GEN1C_sgDDX6_H3K27ac


title: S1 xenograft H3K27ac

tag: chip antibody

value: H3K27ac (Active Motif #39133)


title: GEN1C_sgDDX6_H3K9me3


title: GEN1C_sgCTRL_H3K4me3


title: GEN1C_sgCTRL_H3K27ac


title: S4 Input

data_processing:
ChIP-seq data were aligned to hg38 using BWA aln 0.7.4, requiring minimal mapping quality of 10. HSBS data were aligned to hg38 by methylCtools 0.9.4 (Volker Hovestadt et al. Nature 2014), utilizing BWA mem 0.7.12, removing reads of mapping qualty 0. HiC and HiChIP were aligned to hg38 using HiC-Pro. RNA-seq reads were aligned using STAR 2.5.3 to the hg19 human reference.
PCR duplicates were removed with picard tools 2.9.2 for all data except CTCF ChIP-seq and RNA-seq
ChIP-Seq density tracks were generated by ‘igvtools count --includeDuplicates --minMapQuality 10' and than converted to BigWig format by igvtools tdftobedgraph and bedGraphToBigWig.
HSBS methylation data were called with methylCtools 0.9.4 (Volker Hovestadt et al. Nature 2014)
Gene expression was estimated by featureCounts 1.6.2. TPM values were calculated as described in (Wagner GP, Kin K, Lynch VJ, Theory Biosci. 2012)
Genome_build: hg38
Supplementary_files_format_and_content: ChIP-seq: bigwigs
Supplementary_files_format_and_content: Methylation at CpGs was called by methylCtools 0.9.4. Column 5 represent counts supporting methylated (i.e. not converted) DNA, column 6 represent unmethylated (i.e. converted) DNA at any given loci
Supplementary_files_format_and_content: RNA-seq: TPM values are in a file on the series record, sdhd_tumors_tpm.csv
Supplementary_files_format_and_content: HiC: .hic files and text file with all valid pairs.

source_name: GIST S4

extract_protocol:
For ChIP-seq, cultured cells or minced tissue was fixed in 1% formaldehyde and snap frozen in liquid nitrogen and stored at -80ºC for at least overnight. Sonication of tumor specimens and cultured cells was calibrated such that DNA was sheared to between 400bp and 2000bp. CTCF was immunoprecipitated with a monoclonal rabbit CTCF antibody, clone D31H2 (Cell Signaling 3418).  H3K27ac was immunoprecipitated with an antibody from Active Motif (cat 39133);
ChIP DNA was used to generate sequencing libraries by end repair (End-It DNA repair kit, Epicentre), 3’ A base overhang addition via Klenow fragment (NEB), and ligation of barcoded sequencing adapters.

value: Localized GIST


title: GEN1C_sgCTRL_H3K9me3


title: S4 CTCF


title: WT_24h (WT 24h rep 1)

tag: cell line


title: S3 Input

source_name: GIST S3


title: S4 H3K27ac


title: S3 H3K27ac


title: S3 CTCF


title: S2 CTCF

source_name: GIST S2


title: S2 H3K27ac


title: S1 Input


title: S1 H3K27ac


title: S1 CTCF


title: S2 Input


title: S8 RNA-seq

source_name: GIST S8

extract_protocol: RNA was isolated using an RNeasy Plus Kit (Qiagen). RNA concentration was measured by NanoDrop (Thermo Scientific) and quality was determined by Bioanalyzer (Agilent).


title: S2 RNA-seq


title: S6 RNA-seq

source_name: GIST S6


title: S6 CTCF


title: S6 H3K27ac


title: S5 Input

source_name: GIST S5


title: S5 RNA-seq


title: S3 RNA-seq


title: S5 CTCF


title: S6 Input


title: S5 H3K27ac


title: S1 RNA-seq


title: PDGFRA2 CTCF

source_name: GIST PDGFRA2

value: Intact


title: PDGFRA2 Input


title: S4 RNA-seq


title: PDGFRA2 H3K27ac


title: PDGFRA1 Input

source_name: GIST PDGFRA1


title: O6_meG_BnG_24h.1 (O6meG+O6bzG 24h rep 2)


title: PDGFRA1 H3K27ac


title: S7 RNA-seq

source_name: GIST S7


title: NSM4 Input

value: Normal stomach muscle


title: NSM3 Input


title: PDGFRA1 CTCF


title: NSM3 CTCF


title: NSM4 CTCF


title: NSM2 Input


title: Stimulation CpG, chick ID 8, time point D0+3h

data_processing:
RMA
probe group file: ChiGene-1_0-st.pgf
meta-probeset file: ChiGene-1_0-st.ps

source_name: CpG_D0+3h_whole blood

extract_protocol: PAXgene tube (Ozyme # BD762165) and HT simply RNA Kit (Promega # AX2420) followed by a DNase step (RNA clean-up Nucleospin, Macherey-Nagel # 740948)

tag: stimulation

value: CpG

tag: time point

value: whole-blood


title: NSM2 CTCF


title: NSM1 Input


title: NSM1 H3K27ac


title: KIT11 Input

source_name: GIST KIT11


title: Stimulation CpG, chick ID 14, time point D3

source_name: CpG_D3_whole blood


title: NSM1 CTCF


title: KIT9 H3K27ac

source_name: GIST KIT9


title: KIT10 CTCF

source_name: GIST KIT10


title: KIT9 CTCF


title: KIT11 CTCF


title: KIT9 Input


title: KIT8 Input

source_name: GIST KIT8


title: KIT10 Input


title: KIT7 Input

source_name: GIST KIT7


title: KIT8 CTCF


title: KIT6 Input

source_name: GIST KIT6


title: KIT7 H3K27ac


title: KIT7 CTCF


title: KIT6 CTCF


title: KIT5 H3K27ac

source_name: GIST KIT5


title: KIT3 Input

source_name: GIST KIT3


title: KIT11 H3K27ac


title: KIT3 CTCF


title: KIT8 H3K27ac


title: KIT2 Input

source_name: GIST KIT2


title: KIT4 CTCF

source_name: GIST KIT4


title: KIT4 Input


title: KIT5 CTCF


title: KIT1 H3K27ac

source_name: GIST KIT1


title: KIT4 H3K27ac


title: GIST-T1 Input

source_name: GIST-T1 cell line

value: cell line established from a metastatic GIST


title: GIST-T1 HiChIP, rep 1

description: This sample includes the merged processed data files that represent both GSM3376523 and GSM3376524.

data_processing:
Library strategy: HiChIP
ChIP-seq data were aligned to hg38 using BWA aln 0.7.4, requiring minimal mapping quality of 10. HSBS data were aligned to hg38 by methylCtools 0.9.4 (Volker Hovestadt et al. Nature 2014), utilizing BWA mem 0.7.12, removing reads of mapping qualty 0. HiC and HiChIP were aligned to hg38 using HiC-Pro. RNA-seq reads were aligned using STAR 2.5.3 to the hg19 human reference.
PCR duplicates were removed with picard tools 2.9.2 for all data except CTCF ChIP-seq and RNA-seq
ChIP-Seq density tracks were generated by ‘igvtools count --includeDuplicates --minMapQuality 10' and than converted to BigWig format by igvtools tdftobedgraph and bedGraphToBigWig.
HSBS methylation data were called with methylCtools 0.9.4 (Volker Hovestadt et al. Nature 2014)
Gene expression was estimated by featureCounts 1.6.2. TPM values were calculated as described in (Wagner GP, Kin K, Lynch VJ, Theory Biosci. 2012)
Genome_build: hg38
Supplementary_files_format_and_content: ChIP-seq: bigwigs
Supplementary_files_format_and_content: Methylation at CpGs was called by methylCtools 0.9.4. Column 5 represent counts supporting methylated (i.e. not converted) DNA, column 6 represent unmethylated (i.e. converted) DNA at any given loci
Supplementary_files_format_and_content: RNA-seq: TPM values are in a file on the series record, sdhd_tumors_tpm.csv
Supplementary_files_format_and_content: HiC: .hic files and text file with all valid pairs.

extract_protocol: CTCF HiChIP was performed following [PMID: 27643841]. In brief, 3 tubes of ~5 million GIST-T1 cells were crosslinked in 1% formaldehyde (2 replicates for HiChIP, 1 for HiC). Cells were lysed using Hi-C lysis buffer as described. Chromatin was digested with MboI restriction enzyme (NEB, R0147). After heat inactivation of restriction enzyme, DNA was ligated using T4 buffer (NEB, B0202). HiC DNA was sheered by Covaris E220, while HiChIP DNA was sheerd by Covaris LE220. For HiChIP we used 30 μL monoclonal rabbit CTCF antibody, clone D31H2 (Cell Signaling #3418) per replicate, and incubated with Protein G beads overnight. After washes we incubated in DNA Elution Buffer, added Proteinase K and Zymo purified the samples. Post-ChIP DNA was fragmented with Tn5. For both HiC and HiChIP Biotin Pull-Down was done with M280 Streptavidin beads, and size selection with Ampure XP SPRI beads.


title: KIT3 H3K27ac


title: KIT1 Input


title: KIT2 CTCF


title: Dock2_memory_CD8_4

first: Vinay

middle: S

last: Mahajan

address: 65 Landsdowne Street

institute: Brigham and Women's Hospital

data_processing:
Bcl2fastq - demultiplexing
fastqc
RSEM - alignment to mm10 genome, ENSEMBL transcriptome annotation
Genome_build: mm10
Supplementary_files_format_and_content: count matrix; tab-delimited text file of expected counts

source_name: Memory CD8 T cells

extract_protocol:
Qiagen RNAeasy kit
Smartseq2

tag: strain

tag: genotype

value: Dock2-Hsd/Hsd (Dock2-/-)


title: GIST-T1 HiChIP, rep 2

description: The merged processed data files that represent both GSM3376523 and GSM3376524 are available on GSM3376523.


title: GIST-T1 HiC

extract_protocol: In-situ HiC was performed following [PMID: 25497547].


title: WT-k3c

city: New York

first: Theodoros

last: Sakellaropoulos

address: 550 1st Ave

institute: NYU Langone

data_processing:
BCL2FASTQ
Reads were aligned using STAR (version 2.4.2a) aligner with the following parameters: --runThreadN 5 --genomeLoad NoSharedMemory --outFilterType BySJout --outSAMstrandField intronMotif --outSAMattributes NH HI AS nM NM MD XS --twopassMode Basic --readFilesIn LN-KO-k4d_L001_R1.fastq.gz LN-KO-k4d_L001_R2.fastq.gz --quantMode GeneCounts --outStd Log --outFilterIntronMotifs RemoveNoncanonical --readFilesCommand zcat --outReadsUnmapped Fastx --outSAMtype BAM SortedByCoordinate --outFilterMultimapNmax 20 --outFilterMismatchNmax 10 --outFilterMultimapScoreRange 1 --sjdbScore 2 --sjdbOverhang 100 --outFilterMatchNminOverLread 0.33 --outFilterScoreMinOverLread 0.33 --alignSJDBoverhangMin 1 --alignMatesGapMax 1000000 --alignIntronMax 500000  --sjdbGTFfile Mus_musculus.GRCm38.69.gtf
Duplicates were removed using piccard with the following parameters: MarkDuplicates VERBOSITY=WARNING QUIET=true VALIDATION_STRINGENCY=LENIENT MAX_RECORDS_IN_RAM=2500000 ASSUME_SORTED=false CREATE_INDEX=gtrue REMOVE_DUPLICATES=true
Counts were normalized using DESeq2's estimateSizeFactors with default parameters.
Genome_build: GRCm38.69
Supplementary_files_format_and_content: tab-delimited text files quantifying abundance of genes (rows) in samples (columns)

source_name: tumour-draining lymph nodes

extract_protocol:
14 days upon tumour inoculation tumour-draining lymph nodes were isolated and Tregs were sorted (CD4+CD25+GITR+). RNA was isolated with RNA XS kit (Macherey Nagel)
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Mice were inoculateds.c. with 300000 B16.F10 cells

value: tumour-draining lymph nodes

tag: tumour

value: B16.F10 melanoma day 14

value: CD4+CD25+GITR+Foxp3+ T regulatory cells

tag: strain/genotype


title: WT-k2b

tag: tissue


title: KO-k5e

value: il33-/- in C57BL6 background


title: KO-k6f


title: GIST-T1 CTCF


title: KIT2 H3K27ac


title: KO-k4d


title: KIT5 Input


title: Dock2_memory_CD8_2


title: WT-k1a


title: Dock2_memory_CD8_5


title: KIT1 CTCF


title: Dock2_naive_CD8_5

source_name: Naïve CD8 T cells


title: Dock2_memory_CD8_3


title: Dock2_memory_CD8_1


title: Dock2_naive_CD8_4


title: Dock2_naive_CD8_3


title: Dock2_naive_CD8_2


title: WT_memory_CD8_2

value: wild-type


title: WT_memory_CD8_4


title: WT_memory_CD8_3


title: Dock2_naive_CD8_1


title: WT_naive_CD8_4


title: WT_naive_CD8_3


title: WT_naive_CD8_1


title: WT_naive_CD8_2


title: Meta4+Selumetinib

city: Nashville

first: Ken

last: Lau

state: TN

address: 2215 Garland Ave. MRBIV10475

department: Cell and Developmental Biology

institute: Vanderbilt University

data_processing:
After sequencing, reads were filtered, sorted by their barcode of origin and aligned to the reference transcriptome using inDrops pipeline (https://github.com/indrops/indrops). Mapped reads were quantified into UMI-filtered counts per gene, and barcodes that correspond to cells were retrieved based on previously established methods
Barcodes with number of unique UMIs greater than a threshold (Klein et al., 2015) were selected, resulting in the processed data table.
The code-barcode reference is embedded within the inDrops processing pipeline - https://github.com/indrops/indrops. This site includes a reference file for barcode to id conversion.
Technical read: read2 - UMI/cell barcode - the oligo barcodes are inDrop Version 2 which is positioned exactly as in (Klein et al. 2015)
Biological read: read1 - 3' end
Genome_build: Mouse: GRCm38.85
Supplementary_files_format_and_content: Delimited tables, with cells and genes, as columns and rows

source_name: gastric organoids 4 months after induction_Selumetinib

growth_protocol: organoid growth conditions

extract_protocol:
Mouse epithelial cell suspensions were obtained by standard dissociation (refer to manuscript). Viable cells were enriched with MACS. Cells were encapsulated using the inDrop platform (1CellBio), and RNA was extracted according to the protocol of Klein et al., 2015.
CEL-Seq linear amplification of RNA/cDNA followed by index primer-based amplification; RNA-Seq was performed on NextSeq500 with a 2 x 75 paired-end kit using custom read lengths

value: gastric organoids

value: epithelial


title: Meta4

description: 1 inDrop fraction mapped

source_name: gastroids grown from cells isolated from Mist1-Kras mice 4 months after induction

extract_protocol:
Mouse epithelial cell suspensions were obtained by standard dissociation (refer to manuscript). Viable cells were enriched with MACS. Cells were encapsulated using the inDrop platform (1CellBio), and RNA was extracted according to the protocol of Klein et al., 2015.
CEL-Seq linear amplification of RNA/cDNA followed by index primer-based amplification. RNA-Seq was performed on NextSeq500 with a 2 x 75 paired-end kit using custom read lengths.


title: Meta3

description: 2 inDrop fractions mapped together

source_name: gastroids grown from cells isolated from Mist1-Kras mice 3 months after induction


title: Meta4+DMSO

source_name: gastric organoids_4 months after induction_DMSO


title: GEN1C DDX6_OE_TGFBi_rep2

city: Boston

first: Fei

last: Ji

address: 185 Cambridge St

institute: Massachusetts General Hospital

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to reference genome hg19 using STAR
Transcript abundance was calculated using Htseq
Genome_build: Homo sapiens UCSC hg19
Supplementary_files_format_and_content: tab-delimited text files include raw count for each gene

source_name: GEN1C DDX6 OE TGFBi

growth_protocol:
Conventional hiPSCs (CRISPRi (GEN1C clone)) were maintained on Matrigel (Corning) coated dishes in mTeSR1 medium (Stem Cell Technologies) and passaged using Gentle Cell Dissociation Reagent (Stem Cell Technologies). For maintenance, cells were passaged every 4-5 days. DDX6 overexpression in the GEN1C hiPSCs cells (GEN1C DDX6 OE) was achieved by infection with a lentiviral vector expressing the wt DDX6 cDNA (Vector Builder).
For the TGFβi assay, 40,000 GEN1C hiPSCs were seeded into each well of a Matrigel-coated 24 well plates in mTeSR1 medium (Stem Cell Technologies) supplemented with 10 μM Y-27632 (Axon Medchem). 24 hours after seeding, mTeSR1 medium was replaced with mTeSR1 + 1 µM A8301 (Stemgent). Cells were incubated in differentiation media for 48 hours for the TGFβi condition. Media were then replaced with mTeSR1 and incubated for additional 24 hours before FACS analysis for OCT4-GFP expression.

extract_protocol:
RNA isolation was performed using the miRNeasy mini kit (Qiagen). RNA was eluted from the columns using RNase-free water and quantified using a Nanodrop ND-1000.
RNA sequencing libraries were prepared using the NEBNext Ultra™ Directional RNA Library Prep Kit for Illumina (Cat#: E7420).   The RNA input for library construction was 50 ng total.  Libraries were amplified for 14 cycles.  Post library constructions, the samples were validated using 2200 Tapestation System and High Sensitivity D1000 ScreenTape kit.  Libraries were quantified using the Kapa Biosystems Library Quantification kit (Catalog Number KK4828) and the BioRad CFX96 instrument.

treatment_protocol: Cells were harvested following acutase treatment and processed for total RNA extraction

value: primed human induced pluripotent stem cells (hiPSCs)

tag: genotype/treatment

value: DDX6 OE TGFBi


title: GEN1C DDX6_OE_rep1

source_name: GEN1C DDX6 OE

value: DDX6 OE


title: GEN1C CTRL_TGFBi_rep2

source_name: GEN1C CTRL TGFBi

value: CTRL TGFBi


title: GEN1C CTRL_TGFBi_rep1


title: GEN1C DDX6_OE_rep2


title: GEN1C CTRL_rep2

source_name: GEN1C CTRL

value: CTRL


title: WT_memory_CD8_1


title: Myoblast shDDX6 rep2

description: hMyoblasts shDDX6

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to reference genome hg19 using STAR
Transcript abundance was calculated using Htseq
Genome_build: Homo sapiens UCSC hg19

source_name: human myoblasts

growth_protocol: Human iPSC-derived neural progenitors were obtained from Stem Cell Technologies (cat# 70901) and culture in neural progenitor medium 2 (Stem Cell Technologies, cat# 08560). Differentiation into neurons was achieved using the STEMdiff™ Neuron Differentiation Kit (Stem Cell Technologies, cat# 08500). Primary human skeletal myoblasts were obtained from Thermo Fisher (Gibco, A12555) and cultured in MegaCell DMEM (Sigma) containing 5% FBS (Lonza), 2 mM glutamine (Life Technologies), 0.1mM β-mercaptoethanol (Life Technologies), 1X MEM Non-Essential Amino Acids Solution (Life Technologies), 5 ng/ml bFGF (Peprotech), Penicillin (100 U/mL), Streptomycin (100 μg/mL).

tag: treatment

value: myoblasts


title: Myoblast shCTRL rep2

description: hMyoblasts shCTRL

value: shCTRL


title: Myoblast shCTRL rep1

description: hMyoblasts shCTRL


title: NPC shDDX6 rep2

description: hNPCs shDDX6

source_name: human neural progenitor cells

value: neural progenitor cells


title: NPC shDDX6 rep1

description: hNPCs shDDX6


title: Thoracic aorta Fto +/+ mouse - rep 4

city: Charlottesville

first: Brant

last: Isakson

address: MR4 Building 409 Lane Road

institute: University of Virginia School of Medicine

description: Gene expression in thoracic aorta of Fto -/- mice

hyb_protocol: Labeled cRNA was fragmented and hybridized for 17 h at 65°C to the Agilent SurePrint G3 Mouse GE 8x60K microarray according to manufacturer's instruction (One-Color Microarray-Based Gene Expression Analysis / Low Input Quick Amp Labeling; Agilent Technologies).

scan_protocol: The Microarrays were scanned with the Agilent Microarray Scanner G2505C (protocol: AgilentG3_GX_1color; dye: green; scan region: Agilent HD; scan area: 61x21.6 mm; scan resolution 3µm; tiff file: 20 bit; green PMT gain: 100%). Signal intensities on 20 bit tiff images were calculated by Feature Extraction software (FE, Vers. 11.0.1.1; Agilent Technologies; Grid Template: 028005_D_F_20150604; Protocol: GE1_1100_Jul11; MetricSet: GE1_QCMT_Jul11)

data_processing: Probe signal intensities were quantile normalized over all samples to reduce inter-array variability. Baseline transformation was performed  to the median of all samples. Data analysis was performed using GeneSpring GX software (Vers. 12.5; Agilent Technologies).

source_name: Thoracic aorta

label_protocol: cDNA synthesis and subsequent cRNA labeling were performed according to manufactor's instruction (One-Color Microarray-Based Gene Expression Analysis / Low Input Quick Amp Labeling; Agilent Technologies).

growth_protocol: Mice were kept in conventional cages with 12 h day / 12 h night cycle and had access to food and water ad libitum.

extract_protocol: RNA was isolated from thoracic aortae using the RNeasy Lipid Tissue kit (Qiagen,Cat.-No.: 7480)4 according to manufaturer's instruction and used for array analysis. The labelled cRNA was hybridized to Agilent SurePrint G3 Mouse GE 8x60K Microarrays and scanned as described in the manufacturers' protocol.

value: Fto +/+

value: C57BL6J/NMRI background

tag: gender

value: Male


title: Myoblast shDDX6 rep1

description: hMyoblasts shDDX6


title: GEN1C CTRL_rep1


title: Thoracic aorta Fto +/+ mouse - rep 3


title: Thoracic aorta Fto -/- mouse - rep 4

description: Gene expression in thoracic aorta of Fto +/+ mice

value: Fto -/-


title: Thoracic aorta Fto +/+ mouse - rep 2


title: Thoracic aorta Fto -/- mouse - rep 2


title: Myoblast shCTRL_rep2

description: hMyoblasts shCTRL

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to reference genome hg19 using BWA
peaks were called using HOTSPOT with default parameter
Genome_build: hg19
Supplementary_files_format_and_content: bed files for peak calls

growth_protocol: iPSCs (GEN1C) were maintained on Matrigel (Corning) coated dishes in mTeSR edium (Stem Cell Technologies) and passaged using gentle cell dissociation reagent (Stem Cell Technologies). For maintenance, cells were passaged every 4-5 days. Primary human skeletal myoblasts were obtained from Thermo Fisher (Gibco, A12555) and cultured in MegaCell DMEM (Sigma) containing 5% FBS (Lonza), 2 mM glutamine (Life Technologies), 0.1mM β-mercaptoethanol (Life Technologies), 1X MEM Non-Essential Amino Acids Solution (Life Technologies), 5 ng/ml bFGF (Peprotech), Penicillin (100 U/mL), Streptomycin (100 μg/mL).

extract_protocol:
60.000 cells were washed once with 100µl PBS and resuspended in 50µl lysis buffer (10mM Tris-HCl pH 7.4, 10mM NaCl, 3mM MgCl2, 0.2% IGEPAL CA-630)
The suspension of nuclei was then centrifuged for 10min at 500g at 4°C, followed by the addition of 50µl transposition reaction mix (25µl TD buffer, 2.5µl Tn5 Transposase and 22.5µl Nuclease Free H2O) and incubation at 37°C for 30min. DNA was isolated using MinElute Kit (Qiagen). Libraries were amplified by PCR (13 cycles). After the PCR reaction, the library was selected for fragments between 100 and 1000bp with AmpureXP beads (Beckman Coulter). Libraries were purified with Qiaquick PCR (Qiagen) and integrity checked on a Bioanalyzer before sequencing.

value: sgCTRL

value: human myoblasts


title: Thoracic aorta Fto -/- mouse - rep 3


title: Myoblast shDDX6_rep2

description: hMyoblasts shDDX6


title: Thoracic aorta Fto -/- mouse - rep 1


title: GEN1C DDX6_OE_TGFBi_rep1


title: Myoblast shCTRL_rep1

description: hMyoblasts shCTRL


title: GEN1C sgDDX6_rep2

description: GEN1C sgDDX6

source_name: human induced pluripotent stem cells

value: primed hiPSCs


title: Thoracic aorta Fto +/+ mouse - rep 1


title: Myoblast shDDX6_rep1

description: hMyoblasts shDDX6


title: GEN1C sgDDX6_rep1

description: GEN1C sgDDX6


title: NPC shCTRL rep2

description: hNPCs shCTRL


title: GEN1C sgCTRL_rep1

description: GEN1C sgCTRL


title: GEN1C sgCTRL_rep2

description: GEN1C sgCTRL


title: NPC shCTRL rep1

description: hNPCs shCTRL


title: ESC277

city: Madrid

first: Kevin

last: Troulé

state: Madrid

address: Melchor Fernandez Almagro, 3

country: Spain

institute: SPANISH NATIONAL CANCER CENTER

description:
Genotype2_2
processed data file: Experiment1_genes.fpkm_table.xls

data_processing:
RNA-seq processing:
RNA-seq data was analysed with the nextpresso pipeline (http://bioinfo.cnio.es/nextpresso/) as follows:
Reads are quality-checked with FastQC, and aligned to the mouse genome (mm9) with TopHat-2.0.10 (using Bowtie 1.0.0 and Samtools 0.1.19), allowing 2 mismatches and 20 multihits.
Genome_build: mm9 (MGSCv37)
Supplementary_files_format_and_content: Experiment1_genes.fpkm_table.xls: FPKM values calculated with Cufflinks.

source_name: skin

extract_protocol:
Isolation of poly A+ RNA from total RNA.
Samples of 1µg of total RNA were used as provided by the user. Average sample RNA Integrity Number was 7.75 (range 7-9.2) when assayed on an Agilent 2100 Bioanalyzer. PolyA+ fraction was purified and randomly fragmented, converted to double stranded cDNA and processed through subsequent enzymatic treatments of end-repair, dA-tailing, and ligation to adapters as in Illumina's "TruSeq Stranded mRNA Sample Preparation Part # 15031047 Rev. D" kit (this kit incorporates dUTP during 2nd strand cDNA synthesis, which implies that only the cDNA strand generated during 1st strand synthesis is eventually sequenced). Adapter-ligated library was completed by PCR with Illumina PE primers. The resulting purified cDNA library was applied to an Illumina flow cell for cluster generation and sequenced on an Illumina instrument by following manufacturer's protocols.

value: JunB dep

tag: age

value: 6-7 months

value: Skin


title: ESC273

description:
Genotype1_2
processed data file: Experiment1_genes.fpkm_table.xls

tag: genotype/variation

value: JunB +/+


title: ESC276

description:
Genotype2_1
processed data file: Experiment1_genes.fpkm_table.xls


title: RNA-seq_singleSort_nrlKOPhotoreceptor_3_re-analyzed

city: Saint Louis

first: Daniel

last: Murphy

state: MO

address: 660 S. Euclid

institute: Washington University School of Medicine

description:
sample name in processed data file: sCone_3
RNA-seq_count_table.txt
GSM2199345

data_processing:
Alignment (ATAC-seq): Paired-end reads were aligned to mm10 using Bowtie2 (v2.2.5) with a maximum insert size of 2000 (-X 2000). Alignment (RNA-seq): Single-end RNA-seq reads were aligned to mm10 using STAR (v2.7.0d) (index prepared for mm10 with 50 bp reads and RefSeq gene model included in the iGenomes mm10 Annotations).
Sort (ATAC-seq): alignments were sorted in coordinate order using Picard (v2.19.0) SortSam
Merge (ATAC-seq): alignments for individual libraries run on multiple sequencing lanes were merged using Picard (v2.19.0) MergeSamFiles.
Filter (ATAC-seq): alignments were filtered using SAMtools (v1.3) view to retain only properly paired reads (-f 0x0002) with minimum mapping quality 30 (-q 30) not aligning to unlocalized contigs, unassembled contigs, the mitochondrial genome, or ENCODE blacklist regions (-L <POSITION FILE>).
Remove PCR Duplicates (ATAC-seq): PCR duplicates were marked with Picard (v2.19.0) MarkDuplicates and removed with SAMtools (v1.3) view (-F 0x0400).
Filter for nucleosome-free reads(ATAC-seq): alignments were filtered for fragments with an insert size less than 100 using SAMtools (v1.3) view and awk.
Generate bedGraph (ATAC-seq): bedgraph files were generated using HOMER (v4.8) makeUCSCfile (-style DNase -fsize 5e8). Generate bedGraph (RNA-seq): bedgraph files were generated using HOMER (v4.8) makeUCSCfile (-fragLength given).
Call Peaks (ATAC-seq): consensus peaks for each pair of ATAC-seq biological replicates (filtered nucleosome-free reads) were generated using MACS2 (v2.1.1) callpeak (--nomodel --shift -100 --extsize 200 --keep-dup all --pvalue 1e-2 --call-summits) followed by thresholding using the irreproducible discovery rate (IDR) framework.
Feature Counts (ATAC-seq): 200 bp intervals centered on peak summits were merged across peak call sets from this study as well as identically processed peak call sets from photoreceptors (GSE83312) using bedops (v2.4.14), to produce a reference set of photoreceptor and bipolar cell ATAC-seq peaks. Each of the resulting intervals was then scored for coverage using bedtools (v2.24.0) coverageBed to generate the ATAC-seq count table used for differential accessibility analysis. Feature Counts (RNA-seq): RNA-seq counts overlapping RefSeq genes were generated for each biological replicate from this study, as well as identically processed biological replicates from photoreceptors (GSE83312) using HTSeq (v1.9) htseq-count (-f sam -m union -r pos -i gene_name -a 10 --stranded=no). The resulting RNA-seq count table was used for differential expression analysis.
Genome_build: mm10
Supplementary_files_format_and_content: bedGraph (RNA-seq): files generated from normalized RNA-seq reads per genomic interval (3' bases are dropped from reads flanking exon-intron junctions)
Supplementary_files_format_and_content: bedGraph (ATAC-seq): files generated from filtered, nucleosome-free alignment of normalized ATAC-seq reads per genomic interval.
Supplementary_files_format_and_content: ATAC-seq_count_table.txt: Count table of normalized ATAC-seq reads for each biological replicate from photoreceptors (GSE83312) and bipolar cells (this study).
Supplementary_files_format_and_content: RNA-seq_count_table.txt: Count table of normalized RNA-seq reads for each biological replicate from photoreceptors (GSE83312) and bipolar cells (this study).
Supplementary_files_format_and_content: narrowPeak (ATAC-seq): consensus peaks for each replicate.

source_name: FACs sorted retinal cells

extract_protocol:
Retinas were harvested from 6-8 week-old mice, dissociated with papain and treated with DNAse prior to resuspension  in FACS buffer (2.5 mM EDTA, 25 mM HEPES, 1% BSA in HBSS ). Populations of interest were identified by the intensity of GFP-fluorescence and isolated via FACS. For RNA-seq, RNA was isolated with Trizol reagent. For ATAC-seq, taransposition reactions were carried out using the standard protocol (Buenrostro et al. Nature Methods 2013)
ATAC-seq libraries were prepared using the standard protocol (Buenrostro et al. Nature Methods, 2013). RNA-seq libraries were prepared using the SMARTer Ultra Low RNA kit for Illumina Sequencing-HV (Clonetech).

value: retina

value: blue cone photoreceptors

tag: age (post-natal day)

value: Nrl-eGFP;NrlKO

tag: facs

value: Single Sort


title: ESC230

description:
Genotype2_0
processed data file: Experiment1_genes.fpkm_table.xls


title: RNA-seq_singleSort_nrlKOPhotoreceptor_2_re-analyzed

description:
sample name in processed data file: sCone_2
RNA-seq_count_table.txt
GSM2199344

tag: cell type


title: ESC231

description:
Genotype1_0
processed data file: Experiment1_genes.fpkm_table.xls


title: ESC233

description:
Genotype1_1
processed data file: Experiment1_genes.fpkm_table.xls


title: RNA-seq_singleSort_nrlKOPhotoreceptor_1_re-analyzed

description:
sample name in processed data file: sCone_1
RNA-seq_count_table.txt
GSM2199343


title: RNA-seq_singleSort_rod_1_re-analyzed

description:
RNA-seq_count_table.txt
GSM2199340

value: rod photoreceptors

value: Nrl-eGFP


title: ATAC-seq_singleSort_nrlKOPhotoreceptor_2_re-analyzed

description:
ATAC-seq_count_table.txt
GSM2199339
sample name in processed data file: sCone_r2


title: RNA-seq_singleSort_rod_3_re-analyzed

description:
RNA-seq_count_table.txt
GSM2199342


title: ATAC-seq_doubleSort_greenCone_3_re-analyzed

description:
ATAC-seq_count_table.txt
GSM2199336

value: green cone photoreceptors

value: Double Sort


title: ATAC-seq_doubleSort_greenCone_4_re-analyzed

description:
ATAC-seq_count_table.txt
GSM2199337


title: ATAC-seq_singleSort_nrlKOPhotoreceptor_1_re-analyzed

description:
ATAC-seq_count_table.txt
GSM2199338
sample name in processed data file: sCone_r1


title: ATAC-seq_singleSort_greenCone_2_re-analyzed

description:
ATAC-seq_count_table.txt
GSM2199335
sample name in processed data file: mCone_r2


title: ATAC-seq_singleSort_greenCone_1_re-analyzed

description:
ATAC-seq_count_table.txt
GSM2199334
sample name in processed data file: mCone_r1


title: ATAC-seq_OFF-BC_1

value: bipolar

value: Otx2-GFP+/-; Grm6-YFP+/+


title: ATAC-seq_OFF-BC_2


title: ATAC-seq_singleSort_rod_2_re-analyzed

description:
ATAC-seq_count_table.txt
GSM2199333


title: ATAC-seq_ON-BC_1


title: RNA-seq_singleSort_rod_2_re-analyzed

description:
RNA-seq_count_table.txt
GSM2199341