title: Cortex.HNTBI4

description:
Drop-Seq; whole cell
DropSeq.Cortex.24hrs.TBI.HN.digital_expression.mtx
DropSeq.Cortex.24hrs.TBI.HN.features.tsv
DropSeq.Cortex.24hrs.TBI.HN.barcodes.tsv
DropSeq.Cortex.24hrs.TBI.HN.metaData.tsv

source_name: cortex HumaninTBI, 24 hours

value: cortex


title: Cortex.HNTBI1

status: Public on Aug 17 2022

type: SRA

city: Los Angeles

first: Xia

last: Yang

state: CA

address: 2000A, 610 Charles E Young Dr S

country: USA

institute: UCLA

library_source: transcriptomic

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  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. Requires the corresponding features (genes) and barcodes (cell names) files. Meta Data files include the cell type labels.

molecule: polyA RNA

organism: Mus musculus

extract_protocol:
The protocol by Brewer et al. was used to suspend cells at a final concentration of 100 cells/μl in 0.01% BSA-PBS by digesting freshly dissected hippocampus and frontal cortex tissue with papain (Worthington, Lakewood, NJ, USA). Briefly, hippocampi from the ipsilateral side of the brain and frontal corticies were rapidly dissected on ice. The hippocampi and cortices were transferred into 4 ml HABG (Fisher Scientific, Hampton, NH, USA) and incubated in water bath at 30 °C for 8 min. The supernatant was discarded and the remaining tissue was incubated with papain (12 mg in 6 ml HA-Ca) at 30 °C for 30 min. After incubation, the papain solution was removed from the tissue and washed with HABG three times. Using a siliconized 9-in Pasteur pipette with a fire-polished tip, the solution was triturated approximately ten times in 45 s. Next, the cell suspension was carefully applied to the top of the prepared OptiPrep density gradient (Sigma Aldrich, St. Louis, MO, USA) and floated on top of the gradient. The gradient was then centrifuged at 800 g for 15 min at 22 °C. We aspirated the top 6 ml containing cellular debris. To dilute the gradient material, we mixed the desired cell fractions with 5 ml HABG. The cell suspension containing the desired cell fractions was centrifuged for 3 min at 22 °C at 200 g, and the supernatant containing the debris was discarded. Finally, the cell pellet was loosened by flicking the tube and the cells were re-suspended in 1 ml 0.01% BSA (in PBS). This final cell suspension solution was passed through a 40-micron strainer (Fisher Scientific, Hampton, NH, USA) to discard debris, followed by cell counting.
Barcoded single cells, or STAMPs (single-cell transcriptomes attached to microparticles), and cDNA libraries were generated following the drop seq protocol from Macosko et al11. and version 3.1 of the online Drop-seq protocol [http://mccarrolllab.com/download/905/]. Briefly, single cell suspensions at 100 cells/μl, EvaGreen droplet generation oil (BIO-RAD, Hercules, CA, USA), and ChemGenes barcoded microparticles (ChemGenes, Wilmington, MA, USA) were co-flowed through a FlowJEM aquapel-treated Drop-seq microfluidic device (FlowJEM, Toronto, Canada) at recommended flow speeds (oil: 15,000 μl/hr, cells: 4000 μl/hr, and beads 4000 μl/hr) to generate STAMPs. The following modifications were made to the online published protocol to obtain enough cDNA as quantified by a high sensitivity BioAnalyzer (Agilent, Santa Clara, CA, USA) to continue the protocol: (1) The number of beads in a single PCR tube was 4000. (2) The number of PCR cycles was 4 + 11 cycles. (3) Multiple PCR tubes were pooled. The libraries were then checked on a BioAnalyzer high sensitivity chip (Agilent, Santa Clara, CA, USA) for library quality, average size, and concentration estimation. The samples were then tagmented using the Nextera DNA Library Preparation kit (Illumina, San Diego, CA, USA) and multiplex indices were added. After another round of PCR, the samples were checked on a BioAnalyzer high sensitivity chip for library quality check before sequencing. A cell doublet rate of 5.6% was obtained by running the microfluidic device without the lysis buffer and counting the percentage of cell doublets through three separate runs.

tag: strain/backgorund

tag: treatment

value: Humanin/TBI

tag: time

value: 24 hours

tag: tissue

tag: age

value: 10 weeks


title: T2Hip

description:
Drop-Seq; whole cell
DropSeq.Hippocampus.7days.24hrs.TBI.Sham.digital_expression.mtx
DropSeq.Hippocampus.7days.24hrs.TBI.Sham.features.tsv
DropSeq.Hippocampus.7days.24hrs.TBI.Sham.barcodes.tsv
DropSeq.Hippocampus.7days.24hrs.TBI.Sham.metaData.tsv

source_name: hippocampus TBI, 7 days

value: TBI

value: 7 days

value: hippocampus


title: T2Cortex

description:
Drop-Seq; whole cell
DropSeq.Cortex.7days.24hrs.TBI.Sham.digital_expression.mtx
DropSeq.Cortex.7days.24hrs.TBI.Sham.features.tsv
DropSeq.Cortex.7days.24hrs.TBI.Sham.barcodes.tsv
DropSeq.Cortex.7days.24hrs.TBI.Sham.metaData.tsv

source_name: cortex TBI, 7 days


title: T1Hip


title: Cortex.HNTBI3


title: T3Cortex


title: T1Blood

description:
Drop-Seq; whole cell
DropSeq.Blood.7days.24hrs.TBI.Sham.digital_expression.mtx
DropSeq.Blood.7days.24hrs.TBI.Sham.features.tsv
DropSeq.Blood.7days.24hrs.TBI.Sham.barcodes.tsv
DropSeq.Blood.7days.24hrs.TBI.Sham.metaData.tsv

source_name: blood TBI, 7 days

value: blood


title: T1Cortex


title: S3Cortex

source_name: cortex Sham, 7 days

value: Sham


title: T2Blood


title: T3Blood


title: S3Blood

source_name: blood Sham, 7 days


title: S2Blood


title: S2Hip

source_name: hippocampus Sham, 7 days


title: S2Cortex


title: Cortex.HNTBI2


title: S3Hip


title: TBIHip3

source_name: hippocampus TBI, 24 hours


title: TBIHip5


title: TBIHip1


title: TBICortex5

source_name: cortex TBI, 24 hours


title: S1Cortex


title: T3Hip


title: S1Blood


title: TBICortex3


title: TBIBlood3

source_name: blood TBI, 24 hours


title: TBIBlood1


title: ShamHip2

source_name: hippocampus Sham, 24 hours


title: ShamHip4


title: TBIBlood5


title: ShamCortex4

source_name: cortex Sham, 24 hours


title: ShamBlood4

source_name: blood Sham, 24 hours


title: ShamBlood6


title: ShamBlood2


title: ShamCortex6


title: S1Hip


title: ShamCortex2


title: TBICortex1


title: SHRWT5

city: Guangzhou

first: guodong

last: he

address: zhongshan road No.102

country: China

institute: Guangdong Provincial People's Hospital

data_processing:
Cutadapt (v2.5) was used to trim adapters and filter for sequences.
The 150 bp paired-end reads were mapped to the reference genome by using hisat2 (v2.1.0).
The reads mapped the genome were calculated using featureCounts (v1.6.3).
Differential gene expression analysis was performed using the DESeq2 R-package
Genome_build: Rnor_6.0
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

molecule: total RNA

organism: Rattus norvegicus

source_name: Visceral white adipose tissue (vWAT)

extract_protocol:
RNA of visceral white adipose tissue was isolated using the TRIzol reagent/chloroform isolation method.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Visceral white adipose tissue (vWAT)

tag: disease state

value: spontaneously hypertensive treated with 1g/L TMAO


title: Atrial fibroblasts, si-NC2

city: Harbin

first: Yue

last: Li

state: Heilongjiang

address: Youzheng Street 23#

institute: The First Affiliated Hospital of Harbin Medical University

data_processing:
Illumina Bcl2FastQ  software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to rn6 whole genome using Hisat2 v2.1.0 with default parameters.
HTSeq v0.12.4 was subsequently employed to convert aligned short reads into read counts for each gene model.
Assembly: rn6
Supplementary files format and content: tab-delimited text files include RPKM/counts for each Sample

source_name: heart (atrial muscle)

growth_protocol: Cell were centrifuged and resuspended in Dulbecco modified Eagle medium (Hyclone) containing 10% fetal bovine serum, 100ug/ml penicillin and 100μg/ml streptomycin under standard culture conditions (37°C, 5% CO2).

extract_protocol:
Atrial fibroblasts were isolated from 1 to 3 days old sprague-dawley (SD) rats. Hearts were minced and placed together in 0.25% trypsin. Atrial fibroblasts were isolated by removal of atrial myocytes through selective adhesion of non-myocytes at a 1.5 h preplating interval.
PolyA-Seq is based on the 3' end of eukaryotic mRNA and part of long non-coding RNA (lncRNA).  It has a polyA tail structure, and the RNA is grabbed by the polyA tail for library construction and sequencing, and then the differential analysis of all genes and transcripts containing polyA structure is performed.  Different expression or structural variation is detected, and molecular markers associated with diseases or traits are screened. PolyA-Seq can generate 6G of Clean bases, which can  Accurate detection of low-abundance gene transcripts can reveal the complexity of the transcriptome, determine gene and transcript structure, alternative splicing, RNA editing, banding  polyA-tailed noncoding RNAs and novel transcripts.vv

treatment_protocol: si-NC and si-GPD1L were transfected into atrial fibroblasts and cultured for 24 hours before sequencing.

tag: strain

value: Sprague-Dawley

value: heart (atrial muscle)

tag: cell type

value: Atrial fibroblasts

tag: genotype

value: si-NC

value: Atrial differentiation


title: SHRWT6


title: Atrial fibroblasts, si-GPD1L2


title: Atrial fibroblasts, si-NC3


title: Atrial fibroblasts, si-NC1


title: Atrial fibroblasts, si-GPD1L3


title: ShamHip6


title: SHRWT3


title: SHRWT4


title: SHRWT1


title: SHRWT2


title: SHRW6

value: spontaneously hypertensive


title: RP-48OVA-LLO190, BOM.IFNg, rep1 (cultured SCLC cells)

city: Seattle

first: Joseph

middle: Brian

last: Hiatt

state: WA

address: 1100 Fairview Ave N

department: Human Biology

institute: Fred Hutchinson Cancer Center

data_processing:
Image analysis and base calling was performed using Illumina's Real Time Analysis software v1.18.66.3 for HiSeq 2500 data and v3.9.25 for NextSeq 2000 data, followed by 'demultiplexing' of indexed reads and generation of FASTQ files, using Illumina's bcl2fastq Conversion Software v2.20. Fastq files were filtered to exclude reads that did not pass Illumina’s base call quality threshold.
STAR v2.7 with 2-pass mapping was used to align reads to mouse genome build mm10 and GENCODE gene annotation M23 (https://www.gencodegenes.org/mouse/).
FastQC 0.11.9 and RSeQC 3.0.0 were used for QC including insert fragment size, read quality, read duplication rates, gene body coverage and read distribution in different genomic regions.
FeatureCounts in Subread 2.0 was used to quantify gene-level expression by unstranded read counting.
Assembly: mm10
Supplementary files format and content: Each processed data file is in plain text format containing gene-level raw counts of each sample. Gene information is based on GENCODE gene annotation M23. The overall exonic length of each gene is included and used for computing normalized expression.

extract_protocol:
RNA was extracted from cell pellets or tumor samples using TRIzol reagent following manufacturers protocol.
RNAseq libraries were generated from 500ng of RNA using the NEBNext® Ultra™ RNA Library Prep Kit for Illumina (New England Biolabs E7530L).

tag: cell line

value: cultured SCLC cells

tag: histology

value: mSCLC

value: BOM, IFNg


title: RP-48OVA-LLO190, DMSO.IFNg, rep3 (cultured SCLC cells)

value: DMSO, IFNg


title: RP-48OVA-LLO190, BOM.IFNg, rep2 (cultured SCLC cells)


title: SHRW5


title: SHRW4


title: RP-48OVA-LLO190, DMSO.IFNg, rep1 (cultured SCLC cells)


title: Atrial fibroblasts, si-GPD1L1


title: RP-48OVA-LLO190, DMSO.IFNg, rep2 (cultured SCLC cells)


title: RP-48OVA-LLO190, BOM, rep2 (cultured SCLC cells)

value: BOM


title: SHRW2


title: SHRW3


title: RP-48OVA-LLO190, DMSO, rep3 (cultured SCLC cells)

value: DMSO


title: WYKW6

value: normotensive controls


title: RP-48OVA-LLO190, DMSO, rep2 (cultured SCLC cells)


title: SHRW1


title: RP-48OVA-LLO190, BOM, rep1 (cultured SCLC cells)


title: YBQ 2

city: Changsha

first: Touming

last: Liu

address: NO.348, western road of xianjia lake

department: Institute of Bast Fiber Crops

data_processing:
cDNA library was carried out a paired-end sequencing using a HiSeq PE Cluster Kit v4 cBot (Illumina, San Diego, CA, USA) on the Illumina sequencing platform, following the manufacturer’s instructions.
After filtering the low-quality reads, the clean reads were aligned with the garlic genome (GenBank accession: GCA_014155895.2) using hisat2 software
Then, gene expression level was quantified by estimating fragments per kilobase per million reads (FPKM)
Supplementary files format and content: the excel file contain the gene name and RPKM value,

organism: Allium sativum

source_name: Yuanjiangyangsuan

growth_protocol: three varieties, Chalingzipisuan, Ershuizao, and Yuanjiangyangsuan, were planted in the farm of Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, China, in Oct. of 2019; and in the Feb. and Mar. of 2020, when the bulbs had not initiated to enlarge and were under enlarging growth, respectively, the parts of bulbs were collected.

extract_protocol:
Total RNAs of each sample were extracted using an E.Z.N.A. Plant RNA Kit (OMEGA Bio-Tek, Norcross, GA, USA) according to the protocol of manufacturer.
these RNAs were individually used for performing the construction of cDNA libraries, with a fragment length of 300 bp, using a NEBNext UltraTM RNA Library Prep Kit for Illumina (New England BioLabs, Ipswich, MA, USA) according to the manufacturer’s instructions.

treatment_protocol: Three individuals were used as three replications. These samples were immediately frozen in liquid nitrogen, and stored at −80 °C until use.

value: leaf

tag: developmental stage

value: bulb without enlargment


title: RP-48OVA-LLO190, DMSO, rep1 (cultured SCLC cells)


title: WYKW5

value: Visceral white adipose tissue (vWAT)


title: WYKW4


title: YBQ 1

institute: Chinese Academy of Agricultural Sciences


title: WYKW1


title: Yba 3

value: bulb under enlarging-growth


title: YBQ 3


title: WYKW3


title: WYKW2


title: APHSpleen_INVEN_Ter119_ATAC_2

status: Public on Aug 18 2022

city: Oxford

first: Mira

middle: Tony

last: Kassouf

state: England

address: John Radcliffe Hospital, Headly way

department: Weatherall Institute of Molecular Medicine

country: United Kingdom

institute: University of Oxford

description: Genome-wide library of transposed elements

library_source: genomic

data_processing:
Trim_galore (to remove sequencing adaptors)
Alignment to the genome Bowtie 1 standard parameters with -m set to 2
Removal of PCR duplicates;
plot density of alignments in a moving 300bp window with an moving increment of 30 bp
Assembly: mm9
Supplementary files format and content: BigWig

molecule: genomic DNA

source_name: mouse derived Erythroid cells

extract_protocol:
Spleen from WT APH-treated mice are disaggregated and cells stained with ter119-PE antibody then incubated with anti-PE MACS beads (Miltenyi) and purified using LS columns (Miltenyi), all following manufacturor's instructions.
To produce CD71+ erythroid cells in vitro from differentiated mESCs (WT or mutant): 24h prior to differentiation, mESCs were induced by passaging into IMDM base media, trypsinised and plated in differentiation media (IMDM suplemented serum and other reagents and growth factors) in either triple vent petri dishes (Thermo Fisher) or flat-bottom 96-well plates (Thermo Fisher) at 3x104 cells in 10 cm dishes or 250 cells per well of a 96-well plate for up to seven days without disruption. EBs were harvested and disaggregated in 0.25% trypsin for 3 minutes at 37°C. CD71-positive cells were isolated by magnetic column separation (LS Column, Miltenyi), according to the manufacturer’s instructions. Briefly, cells (from disaggregated EBs) were labelled with anti-mouse CD71-FITC (eBioscience 11-0711-85; 1:200) in staining buffer (PBS with 10% FCS; 500 ul per 10^7 cells) for 20 minutes at 4°C, washed, then incubated with MACS anti-FITC separation microbeads (Miltenyi; 10 ul  per 10^7 cells, following the manufacturer’s instructions) and bead-labelled cells were retained by LS columns. Cells were then processed for ATAC-Seq as in (Buenrostro et al, 2013).
Assay for transposition of active chromatin sequencing (ATAC-Seq) was performed as previously published (Buenrostro, 2013). 60000-80000 cells were used per biological replicate. Cells were lysed and nuclei were isolated prior to transposition with Tn5 transposase (Nextera, Illumina) for 30 minutes at 37°C. DNA was purified using a MinElute kit (Qiagen). Libraries were amplified and barcoded using the NEBNext 2xMastermix (NEB) and the custom primers as published in Buenrostro et al., 2013. ATAC-Seq libraries profiles were visualized using D1000 tape on the Tapestation (Agilent). Due to the broad range of DNA fragment sizes found in these libraries, quantitation with the Qubit for DNA concentration was found to be highly variable and was omitted. The libraries were quantified using the universal library quantification kit (KAPA Biosystems). Samples were sequenced using 40 bp paired end reads (NextSeq platform).
The strategy was to survey regions of open chromatin in our cell population of interest (primary mouse derived erythroid cells or CD71+ EB-derived cells) as they mark regulatory genomic regions. The modified Tn5 can in one step identify open chromatin fragments, cut, and ligate adaptors. The fragments can then be multiplexed and sequenced

value: Ter119+  erythroid cells purified from the spleen of a WT Phenylhydrazine APH-treated mice, sample 2


title: Yba 2


title: EQB 3

source_name: Ershuizao


title: Yba 1


title: EQB 1


title: EQB 2


title: EbH 3


title: EbH 1


title: Cba 2

source_name: Chalingzipisuan


title: Cba 3


title: WT ChIP Input flag 2

city: Eugene

first: Laura

middle: Emily

last: McKnight

state: Oregon

address: 1318 Franklin Blvd Room 273 Onyx Bridge

department: Institute of Molecular Biology

institute: University of Oregon

data_processing:
Aligned to sacCer3 reference genome using bowtie2.
Bam files were converted to bigwig using deeptools.
Assembly: sacCer3
Supplementary files format and content: fastq- raw data
Supplementary files format and content: bigwig - aligned chip data

organism: Saccharomyces cerevisiae

growth_protocol: Cells were grown in 25 mL YPD at 30 °C until they reached log or stationary phase.

extract_protocol:
Cells were crosslinked in 1% formaldehyde, frozen at -80 degrees and lysed with a bead beater.  Sheared chromatin was made through sonication.
Libraries were constructed using the NuGEN Ovation Ultralow kit.

value: log phase

value: WT


title: Tup1 ChIP Stationary Phase 1

growth_protocol: Cells were grown in 25 mL YPD at 30 °C until they reached diauxic shift or stationary phase.

value: stationary phase


title: Tup1 ChIP Diauxic Shift 1

value: diauxic shift


title: Tup1 ChIP Stationary Phase 2


title: Xbp1 ChIP Log Phase 2


title: Xbp1 ChIP Stationary Phase 1


title: WT ChIP Input flag 1


title: Cba 1


title: CB Q 3


title: WT ChIP Input Myc 1


title: CB Q 1


title: WT ChIP Input Myc 2


title: Xbp1 ChIP Stationary Phase 2


title: Tup1 ChIP Diauxic Shift 2


title: EbH 2


title: Xbp1 ChIP Log Phase 1


title: 1511-U.NK3

city: Hangzhou

first: Li

last: Ruan

state: Zhejiang

address: Meiling South Road No. 9

institute: Tea Research Institute, Chinese Academy of Agricultural Science

data_processing:
Illumina Casava 1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to Camellia sinensis whole genome using hisat2 v2.0.5 with parameters hisat2 [options]* -x <hisat2-idx> {-1 <m1> -2 <m2> | -U <r> | --sra-acc <SRA accession number>} [-S <hit>]
Fragments Per Kilobase of exon per Megabase of library size (FPKM) were calculated using a protocol from Trapnell,Cole et al., Transcript assembly and quantification by RNA-seq reveals unannotated transcripts and isoform switching during cell differentiation. Nat. Biotechnol, 2010. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Supplementary files format and content: tab-delimited text file include FPKM values for every sample
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample

organism: Camellia sinensis

growth_protocol: The composition of other nutrients in the hydroponic solution was as follows: 1 mM K2SO4, 1.0 mM NH4NO3, 0.035 mM CaH4O4P2, 0.67 mM MgSO4, 0.495 mM CaCl2, 0.035 mM Al2 (SO4)3•18H2O, 7.0×10−3 mM H3BO4, 1.0×10−3 mM MnSO4•H2O, 6.7×10−4 mMZnSO4•7H2O, 1.3×10−4 mM CuSO4•5H2O, 4.7×10−5 mM (NH4)6Mo7O24•4H2O and 4.2×10−3 mM EDTA-FeNa. Before the treatments were imposed, the tea plants were first cultured in the K nutrient solution until fresh white roots had well developed; this process took 60 days.

extract_protocol:
The collected root samples were ground with mortar in liquid nitrogen. The total RNA was extracted from roots with a TRIZOL reagent (Cat#15596-018, Life Technologies, Carlsbad, CA), following the operating instructions from the manufacturer. The degradation and contamination of RNA were monitored on 1% agarose gel. The purity of RNA was checked by a NanoPhotometer® spectrophotometer (NP80, IMPLEN, CA). The RNA integrity was evaluated using RNA Nano 6000 Assay Kit of Bioanalyzer 2100 system (Agilent Technologies, Palo Alto, CA).
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Three treatments were included to simulate the heterogeneous and homogeneous K environments as follows: (1) a homogeneous K condition (U.NK: both compartments had a K nutrient solution added), (2) a heterogeneous K condition (Sp.NK/Sp.SK: one compartment had a K nutrient solution added, while the other had a K starvation nutrient solution added), and (3) a homogeneous K starvation condition (U.SK: both compartments had a K starvation nutrient solution added). The K nutrient solution and K starvation nutrient solution contained 1 mM and 0 mM K2SO4, respectively. The composition of other nutrients in the hydroponic solution was as follows: 1.0 mM NH4NO3, 0.035 mM CaH4O4P2, 0.67 mM MgSO4, 0.495 mM CaCl2, 0.035 mM Al2 (SO4)3•18H2O, 7.0×10−3 mM H3BO4, 1.0×10−3 mM MnSO4•H2O, 6.7×10−4 mMZnSO4•7H2O, 1.3×10−4 mM CuSO4•5H2O, 4.7×10−5 mM (NH4)6Mo7O24•4H2O and 4.2×10−3 mM EDTA-FeNa.

value: Root


title: 1511-U.NK1


title: Xbp1 Knockout Staionary Phase Replicate 1

data_processing:
Paired end reads were filtered and aligned to the S. cerevisiae sacSer3 genome using bowtie2.
Differential expression analysis was performed using DESeq2.
Assembly: sacCer3
Supplementary files format and content: fastq - raw data
Supplementary files format and content: csv - differential expression analysis files

extract_protocol:
Cells were frozen at -80 °C and ground with a mortar and pestle in liquid nitrogen. RNA was extracted using hot acid phenol. RNeasy kit from Qiagen was used to purify RNA.
Libraries were prepared using the NuGEN Universal Plus mRNA kit with poly-A selection.

value: Xbp1 knockout


title: Xbp1 Knockout Staionary Phase Replicate 2


title: 1511-U.SK3


title: Isw2 Knockout Staionary Phase Replicate 2

value: Isw2 knockout


title: Isw2 Knockout Staionary Phase Replicate 1


title: Isw2 Knockout Diauxic Shift Replicate 2


title: Isw2 Knockout Diauxic Shift Replicate 1


title: 1511-U.SK2


title: 1511-U.NK2


title: Tup1 ChIP Log Phase 2


title: Sds3 Knockout Staionary Phase Replicate 2

value: Sds3 knockout


title: Sds3 Knockout Diauxic Shift Replicate 2


title: 1511-Sp.SK2


title: 1511-U.SK1


title: 1511-Sp.SK1


title: Sds3 Knockout Staionary Phase Replicate 1


title: CB Q 2


title: 1511-Sp.SK3


title: Tup1 ChIP Log Phase 1


title: 1601-U.NK3


title: Xbp1 Knockout Diauxic Shift Replicate 2


title: 1511-Sp.NK3


title: Sds3 Knockout Diauxic Shift Replicate 1


title: 1511-Sp.NK2


title: Tup1 Knockout Staionary Phase Replicate 2

value: Tup1 knockout


title: 1511-Sp.NK1


title: Xbp1 Knockout Diauxic Shift Replicate 1


title: 1601-U.NK2


title: Tup1 Knockout Staionary Phase Replicate 1


title: Tup1 Knockout Diauxic Shift Replicate 2


title: Tup1 Knockout Diauxic Shift Replicate 1


title: 1601-U.NK1


title: 1601-U.SK3


title: Wild Type Staionary Phase Replicate 2

value: wild type


title: 1601-Sp.SK3


title: 1601-Sp.SK2


title: Wild Type Diauxic Shift Replicate 2


title: 1601-U.SK1


title: 1601-U.SK2


title: Wild Type Diauxic Shift Replicate 1


title: 1601-Sp.NK2


title: Mnase-Seq Isw2 stationary MNase 2

description: Isw2 stationary MNase 2

data_processing:
Aligned to sacCer3 reference genome using bowtie2.
Bam files were converted to bigwig using deeptools.
Bigwig files were visualized in IGV.
Assembly: sacCer3

growth_protocol: Cells were grown in 25 mL YPD at 30 °C until they reached stationary phase.

extract_protocol:
Cells were grown in 25 mL YPD at 30 °C until they reached stationary phase, where they were crosslinked in 1% formaldehyde.  Cells were treated with zymolayse and digested with MNase. Individual nucleosome fragments were purified.
Libraries were constructed using the NuGEN Ovation Ultralow kit.


title: Mnase-Seq Tup1 stationary MNase 2

description: Tup1 stationary MNase 2


title: Mnase-Seq Isw2 stationary MNase 1

description: Isw2 stationary MNase 1


title: 1601-Sp.NK1


title: Mnase-Seq Tup1 stationary MNase 1

description: Tup1 stationary MNase 1


title: Mnase-Seq Wild type stationary MNase 2

description: Wild type stationary MNase 2

value: Wild type


title: plasmid library MPRA

city: Stanford

first: Margaret

last: Guo

address: 269 Campus Dr. CCSR Room 2150

institute: Stanford University

description: plasmid library sequencing and counts

data_processing:
Library strategy: plasmid library sequencing
mRNA from the cells was extracted using the mRNA direct kit (ThermoFisher Catalog # 61012) per manufacturer’s instructions and eluted to 30 ul per replicated. Extracted mRNA was Turbo DNase treated (ThermoFisher, Catalog no. M2238) for 1 hour at 37C and then subsequently purified using Ampure XP beads (Beckman Coulter, Catalog # A63881) at a 1:1.9 sample:Ampure bead ratio. cDNA was generated using SuperScript IV Reverse Transcriptase (ThermoFisher, Catalog no 18090050) in 500 ng RNA reactions using an P5 primer (see supplementary items XX), per manufacturer’s instructions. No RT enzyme conditions were included as a control. Reaction were treated with 1ul of thermolabile exonuclease I (NEB, Catalog no. M0293) and incubated at 37C for 10 minutes then heat inactivated. A second Ampure XP purification step was done, using a 1: 1.1 sample to beads ratio. Test qPCR assays using PrimeStar Max Polymerase,the Illumina P7 primer and 5’-AATGATACGGCGACCACCGAGATCTAC-3’ and were run to determine the optimal number of cycles with a 50C annealing temperature for 15 seconds and a 72C extension temperature for 20 seconds. Samples were removed when qPCR reached a linear phase (typically cycle 20-25). Care was taken to ensure the cycle stopped prior to when the NRT negative control began to rise. qPCR amplification product was gel purified on a 2% agarose gel and the resultant amplicon was 277 bp. Library concentration of the cDNA libraries was determined using Kapa Library Quantification Kit (Roche Diagnostics Corporation, Catalog no. KK4854) and BioAnalyzer prior to pooling for sequencing
cDNA libraries were sequenced using 2x150 bp reads on the Illumina NovaSeq 6000 instrument to an average read depth of 200 million reads per sample.
DNA plasmid library and MPRA library reads were sequenced and analyzed using the same approach. Fastq read files from MPRA sequencing were pre-processed as such: reads were trimmed to only include the 20 bp barcode section in the correct orientation. The UMI from index 2 was processed and joined to the barcode. The barcode+UMI sequences were collapsed to remove PCR duplicates. The 20 bp barcode sequences were saved, and aligned to the MPRA library using bowtie2 (Langmead and Salzberg, 2012). Counts for each barcode were determined and summed across all sequencing lanes performed through Novogene.   RNA counts were normalized to plasmid fractions as done previously (Kim et al.). Briefly, MPRA counts were multiplied by the plasmid fractions, converted to fractions, then multiplied by the total count across the MPRA library for the sample. These processed counts were then run through the regularized log transformation (rlog) from DESeq2 (Love et al., 2014) to get a normalized MPRA signal for each barcode in each cell type. Normalized counts were used in further downstream analysis and visualization
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited files include count values for each barcode per sample

organism: synthetic construct

source_name: Plasmid

extract_protocol:
Cells were harvested and pellets were flash frozen on dry ice. RNA was extracted using the RNeasy Mini Kit (QIAGEN).
MPRA was performed on biological replicates using the Lexogen Quant-seq 3’ mMPRA Library Prep Kit FWD for Illumina protocol (Lexogen, 015.96). Briefly, total RNA was extracted from cells using the RNeasy Mini Kit (QIAGEN). 1 ug of total RNA was hybridized with an oligo-dT primer containing an Illumina-compatible sequence at its 5’ end and reverse transcription is performed. Following first strand cDNA synthesis, RNA is removed. Double-stranded cDNA was synthesized followed by a purification step. qPCR was performed to determine optimal PCR cycle number using the PCR Add-on Kit for Illumina (Lexogen, 020.96). i7 adapters for Illumina sequencing were added during PCR amplification. Following purification, MPRA libraries were quantified using the BioAnalyzer High Sensitivity DNA Kit (Agilent) prior to sequencing using 1x150 bp single-end reads on an Illumina HiSeq 4000 instrument at a depth of 50 million reads per sample.

tag: plamid

value: Plasmid


title: Mnase-Seq Wild type stationary MNase 1

description: Wild type stationary MNase 1


title: ChIP-Seq Xbp1 Knockout Staionary Phase Replicate 1


title: 055_Neutrophil_NLR_Low [NLR_Low_N_6]

city: Cleveland

first: Ernest

middle: R

last: Chan

state: OH

address: 10900 Euclid Ave, Robbins E211

department: PQHS

institute: CWRU

data_processing:
Illumina reads were mapped to reference genome using STAR Aligner program.
The expression levels of genes were determined using Cufflinks and presented as FPKM
Differential expression analysis was done using Cuffdiff
Assembly: hg38
Supplementary files format and content: genematrix.txt (tab delimited file containing FPKM values for each gene/sample)

organism: Homo sapiens

source_name: blood

extract_protocol:
Neutrophil and lymphocyte cells were isolated from whole blood using EasySep Direct Human Cel Isolation Kits (STEMCELL Tech). RNA was extracted from the pelleted cells using QIAGEN’s RNEasy Mini Kit (Qiagen).
RNA-Seq libraries were generated using the Illumina mRNA TruSEQ Directional library kit and sequenced using an Illumina NextSeq 550

value: blood

value: Neutrophil

tag: nl ratio


title: 050_Neutrophil_NLR_Low [NLR_Low_N_5]


title: ChIP-Seq Sds3 Knockout Staionary Phase Replicate 2


title: ChIP-Seq Xbp1 Knockout Staionary Phase Replicate 2


title: 040_Neutrophil_NLR_Low [NLR_Low_N_1]


title: 1601-Sp.NK3


title: ChIP-Seq Tup1 Knockout Staionary Phase Replicate 1


title: 048_Neutrophil_NLR_Low [NLR_Low_N_4]


title: 042_Neutrophil_NLR_Low [NLR_Low_N_2]


title: 1601-Sp.SK1


title: Wild Type Staionary Phase Replicate 1


title: 047_Neutrophil_NLR_High [NLR_High_N_4]


title: 057_Neutrophil_NLR_High [NLR_High_N_6]


title: 052_Neutrophil_NLR_High [NLR_High_N_5]


title: ChIP-Seq Sds3 Knockout Staionary Phase Replicate 1


title: 043_Neutrophil_NLR_Low [NLR_Low_N_3]


title: ChIP-Seq Wild Type Staionary Phase Replicate 1

description: Wild Type Staionary Phase Replicate 1


title: 046_Neutrophil_NLR_High [NLR_High_N_3]


title: 150507D3

city: Chicago

first: Xiaoying

state: IL

address: 240 E Huron St., McGaw M-319

institute: Northwestern University

data_processing: Raw gene counts from htseq

source_name: Liver

extract_protocol: Total RNA was isolated from liver biopsies using the RNeasy micro kit.

value: Liver

tag: phenotype

value: Others


title: 038_Neutrophil_NLR_High [NLR_High_N_2]


title: 150428L1


title: ChIP-Seq Wild Type Staionary Phase Replicate 2

description: Wild Type Staionary Phase Replicate 2


title: 150420L1


title: 150130L1


title: 053_Neutrophil_Control [NLR_Control_N_6]

value: Control


title: 036_Neutrophil_NLR_High [NLR_High_N_1]


title: 039_Neutrophil_Control [NLR_Control_N_5]


title: 140304L3

value: Hyperbilirubinemia


title: ChIP-Seq Tup1 Knockout Staionary Phase Replicate 2


title: 140128L2


title: 031_Neutrophil_Control [NLR_Control_N_2]


title: 130812D1


title: 130308D1


title: 150528L4


title: 034_Neutrophil_Control [NLR_Control_N_4]


title: 028_Neutrophil_Control [NLR_Control_N_1]


title: 055_Lymphocyte_NLR_Low [NLR_Low_L_6]

value: Lymphocyte


title: 130603Z3

value: Acute Rejection


title: 033_Neutrophil_Control [NLR_Control_N_3]


title: 050_Lymphocyte_NLR_Low [NLR_Low_L_5]


title: 048_Lymphocyte_NLR_Low [NLR_Low_L_4]


title: 141226L1


title: 140224L5

value: Normal


title: 043_Lymphocyte_NLR_Low [NLR_Low_L_3]


title: 130313D1


title: 042_Lymphocyte_NLR_Low [NLR_Low_L_2]


title: 130624Z3


title: 130923Z1


title: 052_Lymphocyte_NLR_High [NLR_High_L_5]


title: 040_Lymphocyte_NLR_Low [NLR_Low_L_1]


title: 130408B2


title: 057_Lymphocyte_NLR_High [NLR_High_L_6]


title: 130118D1


title: 047_Lymphocyte_NLR_High [NLR_High_L_4]


title: 130121Z1


title: OC28

city: Beiijing

first: haoling

last: xie

address: 5 Yiheyuan Road Haidian District Beijing

institute: Peking University

data_processing:
splitting raw paired-end sequencing reads for each cell according to the cell-specific barcodes in Read 2
Trim Galore was used to remove adapter contamination and low-quality bases
cleaned reads were mapped to the human reference genome (hg19, UCSC) using TopHat  and only uniquely mapped reads were retained
counted the reads mapped to each gene using HTSeq
filtered out cells with either ≤ 1000 genes or ≤ 10000 transcripts
Genome_build: hg19
Supplementary files format and content: RNA_Count_matrix.csv: Raw counts.
Supplementary files format and content: RNA_meta_data.csv: Cell information.

source_name: Fallopian tube

extract_protocol:
The fresh specimens were washed with cold DPBS (Corning, #R21-031-CV) buffer, blood vessels and adipose tissue were removed. Subsequently, the tissue was chopped into small pieces. Then, these tumor pieces were digested into single-cell suspensions using the MACS Tissue Dissociation Kit (Miltenyi Biotec, #130-095-929). The dissociated cells were filtered through 40 µm cell strainers (Falcon, #352340) to remove cell clumps and treated with human red blood cell (RBC) lysis (TIANDZ, #90309-250) to remove the RBCs. The single cells were picked into a 200 µl-tube containing freshly prepared cell lysis buffer. The mRNA was subjected to reverse transcription following the modified STRT-seq protocol
The mRNA were transferred into Smart-seq2 reverse transcription (RT) mixture, and then were incubated at 25℃ for 5 min, 42℃ for 60 min, 50℃ for 30 min, and 70℃ for 10 min for the synthesis of cDNA. Then, we add 15 µl Smart-seq2 PCR mix to amplify of cDNA. The cDNA of cells with different barcodes were pooled together and the construction of the library were performed using KAPA Hyper Prep Kit (KK8504)

tag: tumor stage

value: IA

value: untreated

value: Fallopian tube


title: 046_Lymphocyte_NLR_High [NLR_High_L_3]


title: 038_Lymphocyte_NLR_High [NLR_High_L_2]


title: OC26


title: OC25

value: IC


title: OC21


title: OC22


title: 150122L7


title: OC20


title: 033_Lymphocyte_Control [NLR_Control_L_3]


title: OC16

source_name: Primary tumor; Omental metastasis;  Peritoneal metastasis; Rectal metastasis

value: IIIC


title: OC14

source_name: Primary tumor; Omental metastasis

value: Primary tumor; Omental metastasis


title: 028_Lymphocyte_Control [NLR_Control_L_1]


title: OC13

source_name: Primary tumor; Lymph node metastasis

value: IVB

value: Primary tumor; Lymph node metastasis


title: OC10

value: IIIB


title: OC09


title: OC08

source_name: Primary tumor

value: Primary tumor


title: OC07

source_name: Primary tumor; Mesenteric metastasis

value: Primary tumor; Mesenteric metastasis


title: 036_Lymphocyte_NLR_High [NLR_High_L_1]

value: blood


title: OC06

value: IVA


title: 039_Lymphocyte_Control [NLR_Control_L_5]

value: Control


title: 053_Lymphocyte_Control [NLR_Control_L_6]

value: Lymphocyte


title: 034_Lymphocyte_Control [NLR_Control_L_4]


title: OC05

source_name: Primary tumor; Ascites; Peritoneal metastasis


title: OC03

source_name: Primary tumor; Ascites; Round ligament metastasis


title: 031_Lymphocyte_Control [NLR_Control_L_2]


title: OC04


title: OC02

source_name: Primary tumor; Ascites

value: Primary tumor; Ascites


title: OC01


title: OC11

value: IV


title: OA4_IL-4β+TNF-α

first: tang

last: su'an

state: Guangdong

address: 107# Yan Jiang Road West

department: Department of Orthopedics

institute: Sun Yat-sen Memorial Hospital

data_processing:
Reads filtering under criteria removing reads with 20% of the base quality lower than 13
HISAT2.1.0 mapping to reference genome
count counting
Genome_build: GRCh38
Supplementary_files_format_and_content: TXT file contain counts for each sample

source_name: human primary chondrocytes

extract_protocol:
Chondrocytes treated with inflammatory cytokines was harvested for RNA using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Inflammtory cytokines (10 ng/mL IL-1β and 10 ng/mL TNF-α) were added into medium for 4 hours

value: human primary chondrocytes

value: cartilage

value: treated with 10 ng/mL IL-1β and 10 ng/mL TNF-α for 4 hours


title: Symbionts_liver_rep6

type: RNA

city: Niigata

first: Kazuhisa

last: Yamazaki

address: 2-110-1 Gakkocho-dori, Chu-o-ku

country: Japan

institute: Niigata University

hyb_protocol: Following fragmentation, 1.65 ug of cRNA were hybridized to the Agilent expression microarray according to the protocols provided by the manufacturer

scan_protocol: Arrays were scanned using the Agilent Technologies G4900DA SG12494263

data_processing: Array data export processing and analysis was performed using Agilent Feature Extraction v11.0.1.1

source_name: Liver Symbionts

label_protocol: Total RNA was labeled and hybridized to an Agilent SurePrint G3 Mouse Gene Expression 8 × 60 K mRNA microarray chip.

extract_protocol: Total RNA from the tissue samples was extracted using TRIzol reagent (Molecular Research Center).

tag: gender

value: Male


title: Symbionts_liver_rep3


title: Symbionts_liver_rep2


title: Symbionts_liver_rep5


title: Pathobionts_liver_rep5

source_name: Liver Pathobionts


title: A431 MPRA rep 2

data_processing:
Library strategy: MPRA
mRNA from the cells was extracted using the mRNA direct kit (ThermoFisher Catalog # 61012) per manufacturer’s instructions and eluted to 30 ul per replicated. Extracted mRNA was Turbo DNase treated (ThermoFisher, Catalog no. M2238) for 1 hour at 37C and then subsequently purified using Ampure XP beads (Beckman Coulter, Catalog # A63881) at a 1:1.9 sample:Ampure bead ratio. cDNA was generated using SuperScript IV Reverse Transcriptase (ThermoFisher, Catalog no 18090050) in 500 ng RNA reactions using an P5 primer (see supplementary items XX), per manufacturer’s instructions. No RT enzyme conditions were included as a control. Reaction were treated with 1ul of thermolabile exonuclease I (NEB, Catalog no. M0293) and incubated at 37C for 10 minutes then heat inactivated. A second Ampure XP purification step was done, using a 1: 1.1 sample to beads ratio. Test qPCR assays using PrimeStar Max Polymerase,the Illumina P7 primer and 5’-AATGATACGGCGACCACCGAGATCTAC-3’ and were run to determine the optimal number of cycles with a 50C annealing temperature for 15 seconds and a 72C extension temperature for 20 seconds. Samples were removed when qPCR reached a linear phase (typically cycle 20-25). Care was taken to ensure the cycle stopped prior to when the NRT negative control began to rise. qPCR amplification product was gel purified on a 2% agarose gel and the resultant amplicon was 277 bp. Library concentration of the cDNA libraries was determined using Kapa Library Quantification Kit (Roche Diagnostics Corporation, Catalog no. KK4854) and BioAnalyzer prior to pooling for sequencing
cDNA libraries were sequenced using 2x150 bp reads on the Illumina NovaSeq 6000 instrument to an average read depth of 200 million reads per sample.
DNA plasmid library and MPRA library reads were sequenced and analyzed using the same approach. Fastq read files from MPRA sequencing were pre-processed as such: reads were trimmed to only include the 20 bp barcode section in the correct orientation. The UMI from index 2 was processed and joined to the barcode. The barcode+UMI sequences were collapsed to remove PCR duplicates. The 20 bp barcode sequences were saved, and aligned to the MPRA library using bowtie2 (Langmead and Salzberg, 2012). Counts for each barcode were determined and summed across all sequencing lanes performed through Novogene.   RNA counts were normalized to plasmid fractions as done previously (Kim et al.). Briefly, MPRA counts were multiplied by the plasmid fractions, converted to fractions, then multiplied by the total count across the MPRA library for the sample. These processed counts were then run through the regularized log transformation (rlog) from DESeq2 (Love et al., 2014) to get a normalized MPRA signal for each barcode in each cell type. Normalized counts were used in further downstream analysis and visualization
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited files include count values for each barcode per sample

source_name: Human Squamous Cell Carcinoma

growth_protocol: A-431 human epidermoid carcinoma cell line was obtained from ATCC (CRL-1555) and grown in DMEM (ThermoFisher, 11995-065) supplemented with 10% FBS.

value: untreated


title: Pathobionts_liver_rep6


title: OA3_IL-3β+TNF-α


title: A431 MPRA rep 3


title: A431 MPRA rep 1


title: Pathobionts_liver_rep2


title: Pathobionts_liver_rep4


title: COLO 829 MPRA rep 3

source_name: Human Melanoma Cell Line

growth_protocol: COLO 829 human melanoma cell line was obtained from ATCC (CRL-1974) and grown in RPMI 1640 Media (ThermoFisher, A1049101) supplemented with 10% FBS. Cells were grown in T-75 flasks.

value: 2 uM DMSO

tag: time point

value: 24 hours

value: COLO 829


title: OA1_IL-1β+TNF-α

tag: treatment


title: OA4_NC

value: PBS


title: OA2_IL-2β+TNF-α


title: OA3_NC


title: Pathobionts_liver_rep3


title: COLO 829 MPRA rep 1

value: 1 uM DMSO


title: COLO 829 MPRA rep 2


title: OA2_NC


title: Symbionts_liver_rep1


title: Symbionts_liver_rep4


title: Pathobionts_liver_rep1


title: OA1_NC


title: PD-L2 KO 2

first: Benjamin

middle: Pierre

last: Hurrell

address: 1450 Biggy Street

department: MMI

institute: University of Southern California

data_processing:
Image analysis and base calling was carried out using RTA 1.13.48.0.  Final file formatting, demultiplexing and fastq generation were carried out using CASAVA v 1.8.2.
Raw sequencing reads were first trimmed from both ends with Quality Score method (bases with quality score Phred less than 20 were trimmed from both ends, and trimmed reads shorter than 25 nt were excluded from downstream analyses)
Trimmed reads were then mapped to the mouse genome mm10 using STAR (v3.5.3) with default parameter settings
Gencode M20 annotation was used to quantify the aligned reads to genes/transcripts using Partek E/M method.
read counts per gene/transcript in all samples were normalized using Upper Quartile normalization and analyzed for differential expression using Partek Gene Specific Analysis method (genes/transcripts with less than 10 reads in any sample among a data set were excluded).
Assembly: mm10
Supplementary files format and content: .txt file with normalized gene counts

source_name: sorted ILC2s

extract_protocol:
Total RNA was isolated using MicroRNAeasy (Qiagen, Valencia, California). 10ng of input RNA was used to produce cDNA for downstream library preparation.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Freshly isolated splenic pTregs were isolated and cultured overnight with 1:1 dynabeads, IL-2 and TGF-b

value: BALB/c PD-L2 KO Foxp3GFP

value: lung

value: 6 weeks


title: Human Melanocytes MPRA rep 2

source_name: Primary Human Melanocyte Cells

growth_protocol: Primary human melanocytes were isolated and cultured from fresh, surgically discarded neonatal foreskin. All human cells were collected and analyzed by protocols approved by the Stanford Human Subjects Institutional Review Board and in accordance with the NIH genomic data sharing policy. Melanocytes were maintained in Medium 254 (ThermoFisher, m-254-500) and supplemented with HMGS supplement (ThermoFisher, s-002-5) and 1% anti-mycoplasma and 1% pen/strep.

value: Primary Human Melanocyte Cells


title: Human Keratinocytes MPRA rep 3

source_name: Primary Human Keratinocyte Cells

growth_protocol: Primary human keratinocytes were isolated and cultured from fresh, surgically discarded neonatal foreskin. All human cells were collected and analyzed by protocols approved by the Stanford Human Subjects Institutional Review Board and in accordance with the NIH genomic data sharing policy. Keratinocytes were maintained in a 1:1 mixture of Keratinocyte-SFM (ThermoFisher, 17005042) and Medium 154 (ThermoFisher, M-154-500) supplemented with HKGS (ThermoFisher, S-001-5). Keratinocyte differentiation was induced by the addition of 1.2 mM calcium for 6 days at full confluence.

value: 1.2 mM calcium

value: 6 days

value: Primary Human Keratinocyte Cells


title: Human Melanocytes MPRA rep 3


title: Human Melanocytes MPRA rep 1


title: PD-L2 KO 1


title: WT 1

value: BALB/c Foxp3GFP


title: Human Keratinocytes MPRA rep 1


title: WT 2


title: Human Keratinocytes MPRA rep 2


title: GM12878 Cells MPRA rep 3

source_name: GM12878 Cell Line

growth_protocol: GM12878 were obtained from Coriel (Catalog # GM12878) and grown in RPMI-1640 supplemented with 2mM L-glutamine (Thermo Fisher 25030149), 15% FBS (XXX, non-heat-inactivated) and 1% pen/strep. Cells were grown in T-25 or T-75 flasks in accordance with ENCODE guidelines.


title: GM12878 Cells MPRA rep 2


title: Vehicle.5days.rep3

city: Melbourne

first: Emily

last: Gruber

state: VIC

address: 305 Grattan St

country: Australia

institute: Peter MacCallum Cancer Centre

data_processing:
Sequencing reads were demultiplexed using bcl2fastq (v 2.17.1.14), low quality (Q < 30) reads removed, and trimmed at the 5’ and 3’ ends using cutadapt (v 1.14) to remove adapter sequences and poly-A-tail derived reads respectively
Sequencing reads were mapped to the mouse reference genome (mm10) using HISAT2 (v 2.1.0) and counted using the featureCounts command of the Subread package (v 1.6.3)
Read normalisation and differential gene expression analysis was performed in R (v 3.6.2) using R packages limma (v 3.42.2) and EdgeR (v 3.28.1)
Assembly: mm10
Supplementary files format and content: tab-delimited raw counts
Supplementary files format and content: Differential gene expression tables

source_name: I1DN leukemic progenitor cells (cKit+/Cd11b-)

extract_protocol:
1 – 5 x 10^5 I1DN progenitor cells (cKit+CD11b-) per mouse were isolated by FACS, washed with PBS and pelleted by centrifugation (450 x g, 10 min, 4 oC) prior to being stored at -80 °C in TRIzol Reagent (Invitrogen). RNA was extracted with the Direct-zol RNA Microprep kit as per manufacturer’s instructions (Zymo Research). Purified RNA was quantified using the TapeStation 2200 system (Aligent) with RNA HS screentape (Aligent) according to the manufacturer’s instructions.
The Molecular Genomics Core of the Peter MacCallum Cancer Centre used the QuantSeq 3´ mRNA-seq Library Prep Kit for Illumina (Lexogen), according to the manufacturer’s instructions

treatment_protocol: Mice transplanted with I1DN leukemic cells were treated for 5 or 14 days with vehicle or AG120. In addition, a cohort of mice were treated with the inhibitor for the full treatment duration (28 days) and monitored for disease relapse

value: Vehicle

tag: time

value: Day 5


title: Vehicle.5days.rep2

value: I1DN leukemic progenitor cells (cKit+/Cd11b-)


title: Vehicle.14days.rep2

value: Day 14


title: Colon Epithelial Cells MPRA rep 3

source_name: Human Primary Colonic Epithelial Cells

growth_protocol: Human Primary Colonic Epithelial Cells (Colon) were obtained from CellBiologics (H-6047) and grown in Complete Human Epithelial Cell Medium supplemented with Human Epithelial Cell Medium Supplement Kit (CellBiologics, H6621). Cells were grown in 15 cm dishes.

value: untreated

value: Human Primary Colonic Epithelial Cells


title: AG120.5days.rep3


title: AG120.28days_and_relapsed.rep4

value: 28days treatment then later relapsed


title: Vehicle.14days.rep1


title: Colon Epithelial Cells MPRA rep 1


title: Human Keratinocytes HiChIP

data_processing:
Library strategy: HiChIP-Seq
Raw reads were mapped to hg19 and counts were obtained using STAR with the following settings (--runThreadN 16 --outSJfilterReads Unique --outFilterType BySJout --outSAMunmapped Within --outSAMattributes NH HI AS NM MD --outFilterMultimapNmax 20 --outFilterMismatchNmax 999 --alignIntronMin 20 --outFilterMismatchNoverReadLmax 0.04 --alignIntronMax 1000000 --alignSJoverhangMin 8 --alignSJDBoverhangMin 1 --sjdbScore 1 --outSAMtype BAM SortedByCoordinate --outBAMcompression 10 --limitBAMsortRAM 60000000000 --quantMode TranscriptomeSAM GeneCounts --quantTranscriptomeBAMcompression 10 –outSAMstrandField intronMotif)37.
HiChIP paired-end reads were aligned to the hg19 genome using the HiC-Pro pipeline. Default settings were used to remove duplicate reads, assign reads to MboI restriction fragments, filter for valid interactions, and generate binned interaction matrices. HiC-Pro filtered reads were then processed using hichipper using the {EACH, ALL}  settings to call HiChIP peaks to MboI restriction fragments. HiC-Pro valid interaction pairs and hichipper HiChIP peaks were then processed using FitHiChIP to call significant chromatin contacts using the default settings except for the following: MappSize=500, IntType=3, BINSIZE=5000, QVALUE=0.01, UseP2PBackgrnd=0, Draw=1, TimeProf=1. We note that N-D28 samples were removed from subsequent analysis because of poor QC metrics.
Differential analysis was performed using diffloop and limma with default settings.
Genome_build: hg19
Supplementary_files_format_and_content: looped regions outputed plus the count frequencies of the loop

extract_protocol:
The HiChIP protocol was performed for Astrocytes, ESC cells, N-D2, N-D4, N-D10, and N-D28 as previously described (Mumbach 2016) using antibody H3K27ac (Abcam, ab4729) with the following modifications. Samples were sheared using a Covaris E220 using the following parameters: Fill Level = 10, Duty Cycle = 5, PIP = 140, Cycles/Burst = 200, Time = 4 minutes and then clarified by centrifugation for 15 minutes at 16100 rcf at 4° C.  We used 4 ug of antibody to H3K27ac and captured the chromatin-antibody complex with 34 uL Protein A beads (Thermo Fisher). Qubit quantification following ChIP ranged from 125-150 ng. The amount of Tn5 used and number of PCR cycles performed were based on the post-ChIP Qubit amounts.
HiChIP samples were size selected by PAGE purification (300-700 bp) for effective paired-end tag mapping and where therefore removed of all primer contamination. All libraries were sequenced on the Illumina NovaSeq 6000 instrument to an average read depth of 300 million total reads.


title: Vehicle.5days.rep1


title: WM-266-4 ATAC-seq

data_processing:
Raw reads were mapped to hg19 and counts were obtained using STAR with the following settings (--runThreadN 16 --outSJfilterReads Unique --outFilterType BySJout --outSAMunmapped Within --outSAMattributes NH HI AS NM MD --outFilterMultimapNmax 20 --outFilterMismatchNmax 999 --alignIntronMin 20 --outFilterMismatchNoverReadLmax 0.04 --alignIntronMax 1000000 --alignSJoverhangMin 8 --alignSJDBoverhangMin 1 --sjdbScore 1 --outSAMtype BAM SortedByCoordinate --outBAMcompression 10 --limitBAMsortRAM 60000000000 --quantMode TranscriptomeSAM GeneCounts --quantTranscriptomeBAMcompression 10 –outSAMstrandField intronMotif)37.
ATAC-seq read alignment, quality filtering, duplicate removal, transposase shifting, peak calling, and signal generation were all performed through the ENCODE ATAC-seq pipeline (https://github.com/ENCODE-DCC/atac-seq-pipeline). Briefly, adapter sequences were trimmed, sequences were mapped to the hg19 reference genome using Bowtie2 (-X2000), poor quality reads were removed, PCR duplicates were removed (Picard Tools MarkDuplicates), chrM reads were removed, and read ends were shifted +4 on the positive strand or -5 on the negative strand to produce a set of filtered high-quality reads. These reads were put through MACS2 to get peak calls and signal files. Finally, IDR analysis was run on the two replicate peak files to produce an IDR peak file that is the reproducible set of peaks across both replicates. The full pipeline can be found on the ENCODE portal.
Differential analysis was performed using DESeq2 with default settings.
Genome_build: hg19
Supplementary_files_format_and_content: peak files of significantly called peak

growth_protocol: WM-266-4 human malignant melanoma cell line was obtained from ATCC (CRL-1676) and grown in DMEM (ThermoFisher, 11995-065) supplemented with 10% FBS.  Cells were grown in T-75 flasks.

extract_protocol:
Fast-ATAC sequencing on biological replicates was performed as previously described (Corces et al., 2016). Briefly, 55,000 viable cells were pelleted and resuspended in 50 uL of ATAC resuspension buffer (RSB) with 0.1% Igepal CA-630 (NP-40), 0.1% Tween-20, and 0.01% digitonin (Promega, G9441). After 3 minutes on ice, 1 mL of ATAC RSB with 0.1% Tween-20 was added, tubes were inverted, and nuclei pelleted by centrifugation at 500 RCF for 10 minutes at 4C. Supernatant was carefully removed and the nuclei pellet was resuspended in 50 uL of transposition mixture (25 uL TD buffer, 2.5 uL of TDE1 (Illumina, 20034197), 16.5 uL PBS, 0.5 uL 1% digitonin,  0.5 uL 10% Tween-20, 5 uL nuclease-free water).
Transposition reactions were incubated at 37°C for 30 minutes in an Eppendorf ThermoMixer with agitation at 1000 RPM. Transposed DNA was purified using a Zymo DNA Clean and Concentrator-5 Kit (Zymo, D4014) and purified DNA was eluted in 20 ul elution buffer (10 mM Tris-HCl, pH 8).

value: 6 uM DMSO

value: 24 hours


title: Colon Epithelial Cells MPRA rep 2


title: AG120.5days.rep2


title: AG120.5days.rep1


title: Human Melanocytes HiChIP


title: SK-MEL-5 ATAC-seq

growth_protocol: SK-MEL-5 human malignant melanoma cell line was obtained from ATCC (HTB-70) and grown in in DMEM (ThermoFisher, 11995-065) supplemented with 10% FBS and 1% Pen/Strep. Cells were grown in T-75 flasks.

value: 4 uM DMSO


title: AG120.28days_and_relapsed.rep3


title: Human Keratinocytes ATAC-seq


title: AG120.28days_and_relapsed.rep1


title: AG120.28days_and_relapsed.rep2


title: Human Melanocytes ATAC-seq


title: GM12878 Cells MPRA rep 1


title: AG120.14days.rep2


title: AG120_AZA.rep2

data_processing:
Sequencing reads were demultiplexed using bcl2fastq (v 2.17.1.14), low quality (Q < 30) reads removed, and trimmed at the 5’ and 3’ ends using cutadapt (v 1.14) to remove adapter sequences and poly-A-tail derived reads respectively
Sequencing reads were mapped to the mouse reference genome (mm10) using HISAT2 (v 2.1.0) and counted using the featureCounts command of the Subread package (v 1.6.3)
Read normalisation and differential gene expression analysis was performed in R (v 3.6.2) using R packages limma (v 3.42.2) and EdgeR (v 3.28.1)
Assembly: mm10
Supplementary files format and content: tab-delimited voom normalized counts

treatment_protocol: Mice transplanted with I1DN leukemic cells were treated for 5 vehicle, AG120, AZA or the combination

value: AG120 + AZA

value: 5 Days


title: Renal Epithelial Cells ATAC-seq

growth_protocol: Human Primary Proximal Tubular Epithelial Cells (Renal) were obtained from CellBiologics (H-6015) and grown in Complete Human Epithelial Cell Medium supplemented with Human Epithelial Cell Medium Supplement Kit (CellBiologics, H6621). Cells were grown in 15 cm dishes.


title: Thyroid Epithelial Cells ATAC-seq

source_name: Human Primary Thyroid Epithelial Cells

growth_protocol: Human Primary Thyroid Epithelial Cells (Thyroid) were obtained from CellBiologics (H-6040) and grown in Complete Human Epithelial Cell Medium supplemented with Human Epithelial Cell Medium Supplement Kit (CellBiologics, H6621). Cells were grown in 15 cm dishes.


title: GM12878 Cells ATAC-seq


title: Uterine Epithelial Cells ATAC-seq

source_name: Endometrial Epithelial Cells

growth_protocol: Endometrial (Uterine) Epithelial Cells were obtained from Lifeline Cell Technology (FC-0078) and grown in ReproLife™ Reproductive Medium Complete Kit (Lifeline Cell Technology, LL-0068). Cells were grown in 15 cm dishes.


title: AG120_AZA.rep1


title: AZA.rep2

value: AZA


title: AG120.rep2


title: Prostate Epithelial Cells ATAC-seq

source_name: Human Prostate Epithelial Cells

growth_protocol: Human Prostate Epithelial Cells (Prostate) were obtained from Lonza (CC-2555) and grown in Prostate epithelial basal medium (Lonza, CC-3165) and supplemented with PrEGM Prostate Epithelial Cell Growth Medium SingleQuots Supplements and Growth Factors (Lonza, CC-4177)


title: Ovarian Epithelial Cells ATAC-seq

source_name: Human Primary Ovarian Epithelial Cells

growth_protocol: Human Primary Ovarian Epithelial Cells (Ovarian) were obtained from CellBiologics (H-6036) and grown in grown in Complete Human Epithelial Cell Medium supplemented with Human Epithelial Cell Medium Supplement Kit (CellBiologics, H6621). Cells were grown in 15 cm dishes.


title: AG120.rep1


title: Esophageal Epithelial Cells ATAC-seq

growth_protocol: Human Primary Esophageal Epithelial Cells (Esophageal) were obtained from CellBiologics (H-6046) and grown in Complete Human Epithelial Cell Medium supplemented with Human Epithelial Cell Medium Supplement Kit (CellBiologics H6621). Cells were grown in 15 cm dishes.


title: Pancreas Epithelial Cells ATAC-seq

growth_protocol: Human Primary Pancreatic Epithelial Cells (Pancreas) were obtained from CellBiologics ( H-6037) and grown in Complete Human Epithelial Cell Medium supplemented with Human Epithelial Cell Medium Supplement Kit (CellBiologics, H6621). Cells were grown in 15 cm dishes.


title: Human Mammary Epithelial Cells ATAC-seq

source_name: Human Mammary Epithelial Cells

growth_protocol: Human Mammary Epithelial Cells (HMECs) were obtained from Lonza (CC-2551) and grown in MEGM Mammary Epithelial Cell Growth Medium BulletKit (Lonza, CC-3150). Cells were grown in 15 cm dishes.


title: Colon Epithelial Cells ATAC-seq


title: Vehicle.rep1


title: Vehicle.rep2


title: SK-MEL-5 RNA-seq rep 2

data_processing:
Raw reads were mapped to hg19 and counts were obtained using STAR aligner (version 2.5.4b) with the following settings (--runThreadN 16 --outSJfilterReads Unique --outFilterType BySJout --outSAMunmapped Within --outSAMattributes NH HI AS NM MD --outFilterMultimapNmax 20 --outFilterMismatchNmax 999 --alignIntronMin 20 --outFilterMismatchNoverReadLmax 0.04 --alignIntronMax 1000000 --alignSJoverhangMin 8 --alignSJDBoverhangMin 1 --sjdbScore 1 --outSAMtype BAM SortedByCoordinate --outBAMcompression 10 --limitBAMsortRAM 60000000000 --quantMode TranscriptomeSAM GeneCounts --quantTranscriptomeBAMcompression 10 –outSAMstrandField intronMotif)37.
TPM were obtained from the mapped by using RSEM (version 1.3.0) with the following settings (--paired-end --seed-length 21 --no-bam-output --calc-pme --calc-ci –alignments).
Differential analysis was performed using limma with default settings.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited files include TPM values for each sample

extract_protocol:
Cells were harvested and pellets were flash frozen on dry ice. RNA was extracted using the RNeasy Mini Kit (QIAGEN).
RNA-seq was performed on biological replicates using the Lexogen Quant-seq 3’ mRNA-seq Library Prep Kit FWD for Illumina protocol (Lexogen, 015.96). Briefly, total RNA was extracted from cells using the RNeasy Mini Kit (QIAGEN). 1 ug of total RNA was hybridized with an oligo-dT primer containing an Illumina-compatible sequence at its 5’ end and reverse transcription is performed. Following first strand cDNA synthesis, RNA is removed. Double-stranded cDNA was synthesized followed by a purification step. qPCR was performed to determine optimal PCR cycle number using the PCR Add-on Kit for Illumina (Lexogen, 020.96). i7 adapters for Illumina sequencing were added during PCR amplification. Following purification, RNA-seq libraries were quantified using the BioAnalyzer High Sensitivity DNA Kit (Agilent) prior to sequencing using 1x150 bp single-end reads on an Illumina HiSeq 4000 instrument at a depth of 50 million reads per sample.

value: 1 uM DMSO for 24 hours


title: Bladder Epithelial Cells ATAC-seq

source_name: Primary Human Bladder Epithelial Cells

growth_protocol: Primary Human Bladder Epithelial Cells (A/T/N) (Bladder) were obtained from ATCC (PCS-420-010) and grown in Bladder Epithelial Cell Basal Medium ((ATCC PCS-420-032) supplemented with Bladder Epithelial Cell Growth Kit (ATCC PCS-420-042) . Cells were grown in 15 cm dishes.


title: Human Astrocytes ATAC-seq

source_name: Human Astrocyte Cells

growth_protocol: Human Astrocytes (Astrocytes) were obtained from Lonza (N7805-100) and grown in Gibco Astrocyte Medium (ThermoFisher, A1261301). Cells were grown in 15 cm dishes.


title: WM-266-4 RNA-seq rep 1


title: COLO 829 RNA-seq rep 2

growth_protocol: COLO 829 human melanoma cell line was obtained from ATCC (CRL-1974) and grown in RPMI 1640 Media (ThermoFisher, A1049101) supplemented with 10% FBS. Cells were grown in T-75 flasks.

value: COLO 829


title: AG120.14days.rep1


title: WM-266-4 RNA-seq rep 2


title: SK-MEL-5 RNA-seq rep 1


title: AZA.rep1


title: Human Melanocytes RNA-seq rep 2

growth_protocol: Primary human melanocytes were isolated and cultured from fresh, surgically discarded neonatal foreskin. All human cells were collected and analyzed by protocols approved by the Stanford Human Subjects Institutional Review Board and in accordance with the NIH genomic data sharing policy. Melanocytes were maintained in Medium 254 (ThermoFisher, m-254-500) and supplemented with HMGS supplement (ThermoFisher, s-002-5) and 1% anti-mycoplasma and 1% pen/strep.

value: Primary Human Melanocyte Cells


title: WT_Tpex2

city: Clayton

first: Wei

last: Shi

state: Victoria

address: 15 Innovation Walk

department: Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute

institute: Monash University

data_processing:
The libraries were aligned to the GRCm38/mm10 genome using Rsubread_2.2.6; only uniquely mapped read-pairs were allowed. The mapped read-pairs in each library were assigned to the NCBI RefSeq gene annotation for mm10 (build 38.1) by using featureCounts.
Genes were excluded from downstream analysis if they failed to achieve a CPM (counts per million mapped reads) value of at least 0.5 in at least 2 libraries. Counts were quantile normalized, precision weighted with the “voom” function of the limma package and converted to log2 counts per kilobase per million(log2 FKPM).
A linear model was fitted to each gene, and empirical Bayes moderated t-statistics were used to assess differences in expression. Genes were called differentially expressed if they achieved a false discovery rate of 10% or less.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include normalized log2-FPKM values for each library. The supplementary file, Supp_Raw_Counts.txt, includes raw read counts for genes in all the libraries.

extract_protocol:
RNA extraction from sorted P14 T cells was performed following the manufacturer’s protocol using the RNAeasy Plus Mini Kit (Qiagen)
Libraries were generated following the manufacturer's protocol using the TruSeq RNA Library Preparation Kit (Illumina, San Diego, USA)

value: wildtype

tag: tissue

value: splenocytes

tag: cell population

value: TPEX (Ly108+TIM3-) P14 T cells

tag: timepoint

value: 7 days after infection with LCMV docile


title: COLO 829 RNA-seq rep 1


title: Human Melanocytes RNA-seq rep 1


title: WT_Tex2

value: TEX (Ly108-TIM3+) P14 T cells


title: WT_Tex1


title: Myb_KO_Tpex2

value: Myb-KO


title: Human Keratinocytes RNA-seq rep 2

growth_protocol: Primary human keratinocytes were isolated and cultured from fresh, surgically discarded neonatal foreskin. All human cells were collected and analyzed by protocols approved by the Stanford Human Subjects Institutional Review Board and in accordance with the NIH genomic data sharing policy. Keratinocytes were maintained in a 1:1 mixture of Keratinocyte-SFM (ThermoFisher, 17005042) and Medium 154 (ThermoFisher, M-154-500) supplemented with HKGS (ThermoFisher, S-001-5). Keratinocyte differentiation was induced by the addition of 1.2 mM calcium for 6 days at full confluence.

value: 1.2 mM calcium for 6 days

value: Primary Human Keratinocyte Cells


title: Myb_KO_Tex1


title: GM12878 Cells RNA-seq rep 2

growth_protocol: GM12878 were obtained from Coriel (Catalog # GM12878) and grown in RPMI-1640 supplemented with 2mM L-glutamine (Thermo Fisher 25030149), 15% FBS (XXX, non-heat-inactivated) and 1% pen/strep. Cells were grown in T-25 or T-75 flasks in accordance with ENCODE guidelines.

value: untreated

value: GM12878 Cell Line


title: Uterine Epithelial Cells RNA-seq rep 2

value: Endometrial Epithelial Cells


title: GM12878 Cells RNA-seq rep 1


title: Human Keratinocytes RNA-seq rep 1


title: Myb_KO_Tpex1


title: High-fiber sample 2

city: New York

first: Gregory

last: Putzel

state: NY

address: 430 East 29th Street

department: Microbiology

institute: NYU Langone Health

data_processing:
Alignment was performed using Space Ranger version 1.1.0
Space Ranger output was imported into R using the Seurat Load10X_Spatial function. Spots that were not aligned with tissue slices were removed from the analysis. Each tissue sample was separately normalized using the Seurat SCTransform function. For the purposes of clustering spots across all samples, one of the samples (Ctrl1) was selected as a reference dataset.
The k-means clusters (with k=4) generated by Space Ranger for the reference sample were then used to predict cluster identities for the other samples using the FindTransferAnchors and TransferData functions of Seurat. All samples (2 control and 2 high-fiber) were then merged into a single Seurat object used in all further analysis.
Genome_build: mm10
Supplementary_files_format_and_content: HDF5 (.h5) files generated by SpaceRanger 1.1.0
Supplementary_files_format_and_content: Serialized R object (.rds) generated by Seurat R package version 3.2.1 in R version 3.6.3

source_name: Colon

extract_protocol:
Visium Spatial Tissue Optimization Reagent Kit (PN-1000192)
Visium Library Construction Kit (PN-1000190)
Spatial transcriptomics

tag: strain

tag: diet

value: High fiber


title: Myb_KO_Tex2

tag: genotype


title: Airway Epithelial Cells ATAC-seq

source_name: Bronchial/Tracheal Epithelial Cells

growth_protocol: Bronchial/Tracheal Epithelial Cells (Airway) were obtained from ATCC (PCS-300-010) and grown in Airway Epithelial Cell Basal Medium (ATCC, PCS-300-030) supplemented with Bronchial Epithelial Cell Growth Kit (ATCC, PCS-300-040). Cells were grown in 15 cm dishes.


title: Control sample 2

value: Control


title: Thyroid Epithelial Cells RNA-seq rep 2

tag: cell type

value: Human Primary Thyroid Epithelial Cells


title: WT_Tpex1


title: SICd4m2s1_4

city: Baltimore

first: Immunometabolism

last: Department

state: Maryland

address: 1650 Orleans Street

department: Immunometabolism

institute: Johns Hopkins University

description: library of 96 CD45+ TCRb+ CD4+ SI T cells from primary H. polygyrus - biological replica 2

data_processing:
For image aquisition, intensity extraction and basecalling HiSeq Control Software  2.0.2, RTA 2.4.11 / Recipe Fragment 2.0.0.2(Hiseq2500) or Control Software HD 3.4.0.38 / RTA2.7.7 / Recipe Fragment HD 3.5.0.4(Hiseq3000) was used. Conversion of bcl2fastq files was performed using bcl2fastq 2.17.1.14
Paired end reads were aligned to the transcriptome using bwa (version 0.6.2-r126) with default parameters (Li and Durbin, 2010). The transcriptome contained all gene models based on the mouse ENCODE VM9 release downloaded from the UCSC genome browser comprising 57,207 isoforms with 57,114 isoforms mapping to fully annotated chromosomes (1 to 19, X, Y, M). All isoforms of the same gene were merged to a single gene locus. Furthermore, gene loci overlapped by >75% were merged to larger gene groups. This procedure resulted in 34,111 gene groups.
The right mate of each read pair was mapped to the ensemble of all gene loci and to the set of 92 ERCC spike-ins in sense direction. Reads mapping to multiple loci were discarded. The left read contains the barcode information: the first six bases correspond to the unique molecular identifier (UMI) followed by six bases representing the cell specific barcode. The remainder of the left read contains a poly(T) stretch. The left read was not used for quantification. For each cell barcode, the number of UMIs per transcript was counted and aggregated across all transcripts derived from the same gene locus.
Based on binomial statistics, the number of observed UMIs was converted into transcript counts, representing processed data files (Grun et al., 2014)
Genome_build: ENCODE VM9
Supplementary_files_format_and_content: CSV files, columns represent each cell barcode (total barcodes used = 192), rows represent the geneid and the values in the file are the quantified number of transcripts.

source_name: small intestine lamina propria - primary infection H. polygyrus

growth_protocol: C57BL/6J mice (RRID: IMSR_JAX:000664) were purchased from the Jackson Laboratory. All mice were maintained in specific-pathogen-free conditions in the animal facility of the Max Planck Institute for Immunobiology and Epigenetics (Freiburg, Germany)

extract_protocol:
Isolation of cells from mFAT and SI LP: For isolation of cells from mFAT mice were euthanised and transcardially perfused with 10ml of ice-cold PBS. mFAT was separated from mLN, intestine and omentum, minced and digested in 3ml of low glucose DMEM containing 25mM HEPES, 1% low fatty acid BSA, 2mM L-glutamine (L-glut), 100U/ml Penicillin/Streptomycin (P/S), with the addition of Liberase TL (0.2mg/ml, Roche) and DNase I (0.25mg/ml, Roche) for 30-40min in 37°C rotating. After digestion 2ml DMEM containing 2mM EDTA was added and the suspension filtered through 70um strainer. Cells in SVF were then separated from the adipocyte layer by centrifugation. For isolation of cells from SI LP small intestines were open longitudinally, cleaned, cut into 2cm pieces and placed in RPMI medium containing 3% FBS, 25mM HEPES, 2mM L-glut, 100U/ml P/S, 1mM DTT and agitated for 25min, after which samples were washed 3-4 times with RPMI containing 2mM EDTA. Intestines were digested in RPMI medium containing 25mM HEPES, 2mM L-glut, 100U/ml P/S, Liberase TL
As described in CEL-Seq2 protocol (Hashimshony et al. 2016)
Adapted from TruSeq Small RNA Library Preparation Protocol

treatment_protocol: To induce H. polygyrus infection mice were gavage with 200 L3 infectious stage larvae in PBS. For primary infection mice were left for 11-13 days before being sacrificed. For recovery mice were orally treated with anti-helminth pyrantel pamoate (1mg/mouse) and left for 4-5 weeks. For secondary infection mice were gavaged with 200 L3 H. polygyrus at the end of recovery stage and sacrificed at 11-13 days post-secondary infection

value: C57BL/6 - female

value: small intestine lamina propria

tag: age

value: 6-8 weeks + 11-13 days infection


title: Thyroid Epithelial Cells RNA-seq rep 1


title: Control sample 1


title: SICd4m2s1_1


title: SICd4m2s1_2


title: SICd4m1s2_4

description: library of 96 CD45+ TCRb+ CD4+ SI T cells from primary H. polygyrus - biological replica 1


title: Renal Epithelial Cells RNA-seq rep 1

source_name: Human Primary Proximal Tubular Epithelial Cells


title: No364 osteosarcoma CD44-/-

city: Jena

first: Marco

last: Groth

address: Beutenbergstraße 11

department: Core Facility - Next Generation Sequencing

country: Germany

institute: Leibniz Institute on Aging - FLI

description: CD44-/-; Nf2Δ2/+

data_processing:
Reads were extracted in FastQ format using Illumina’s bcl2FastQ v1.8.4
Reads were aligned to the mouse reference genome sequence (ENSEMBL Mus musculus GRCm38.84) using HISAT2 (hisat2-2.0.2-beta). (hisat2-2.0.2-beta).
Read counts were determined by read summarization with feature Counts (subread-2.0.0).
Assembly: GRCm38.84
Supplementary files format and content: raw_counts.csv: read counts per gene per sample

source_name: osteosarcoma

extract_protocol:
Total RNA was isolated from cell lines using RNeasy mini kit (Qiagen) as per manufacturer’s instructions.
Library preparation was done using Illumina’s TruSeq stranded mRNA kit following the manufacturer’s description.

value: osteosarcoma

value: C57BL/6 x 129/Sv x FVB


title: Uterine Epithelial Cells RNA-seq rep 1


title: High-fiber sample 1


title: Prostate Epithelial Cells RNA-seq rep 2

value: Human Prostate Epithelial Cells


title: SICd4m1s2_1


title: Prostate Epithelial Cells RNA-seq rep 1


title: No203 osteosarcoma CD44-/-

description: CD44-/-; Nf2Δ2/+


title: SICd4m1s1_4


title: SICd4m1s1_3


title: Renal Epithelial Cells RNA-seq rep 2

value: Human Primary Proximal Tubular Epithelial Cells


title: No368 osteosarcoma CD44+/+

description: CD44+/+; Nf2Δ2/+


title: SICd4m1s1_2


title: SICd4m1s1_1


title: SICd4m2s1_3


title: mLN2nd_4

description: library of 96 CD45+ TCRb+ CD4+ mLN T cells from secondary H. polygyrus infection

source_name: mesenteric lymph node  - secondary infection H. polygyrus

value: mesenteric lymph node

value: 6-8 weeks + 11-13 days 1st infection + 4-5 weeks recovery + 11-13 2nd infection


title: No279 osteosarcoma CD44-/-

description: CD44-/-; Nf2Δ2/+


title: mLN2nd_2


title: Pancreas Epithelial Cells RNA-seq rep 2

source_name: Human Primary Pancreatic Epithelial Cells


title: Pancreas Epithelial Cells RNA-seq rep 1

value: Human Primary Pancreatic Epithelial Cells


title: No316 osteosarcoma CD44+/+

description: CD44+/+; Nf2Δ2/+


title: SICd4m1s2_2


title: mLN2nd_3


title: mLN1st_4

description: library of 96 CD45+ TCRb+ CD4+ mLN T cells from primary H. polygyrus infection

source_name: mesenteric lymph node - primary infection H. polygyrus


title: Ovarian Epithelial Cells RNA-seq rep 2

value: Human Primary Ovarian Epithelial Cells


title: RP-48OVA-LLO190, BOM-anti.PD1, rep4 (flank tumor)

first: Joseph

address: 1100 Fairview Ave N

institute: Fred Hutchinson Cancer Center

data_processing:
Image analysis and base calling was performed using Illumina's Real Time Analysis software v1.18.66.3 for HiSeq 2500 data and v3.9.25 for NextSeq 2000 data, followed by 'demultiplexing' of indexed reads and generation of FASTQ files, using Illumina's bcl2fastq Conversion Software v2.20. Fastq files were filtered to exclude reads that did not pass Illumina’s base call quality threshold.
STAR v2.7 with 2-pass mapping was used to align reads to mouse genome build mm10 and GENCODE gene annotation M23 (https://www.gencodegenes.org/mouse/).
FastQC 0.11.9 and RSeQC 3.0.0 were used for QC including insert fragment size, read quality, read duplication rates, gene body coverage and read distribution in different genomic regions.
FeatureCounts in Subread 2.0 was used to quantify gene-level expression by unstranded read counting.
Assembly: mm10
Supplementary files format and content: Each processed data file is in plain text format containing gene-level raw counts of each sample. Gene information is based on GENCODE gene annotation M23. The overall exonic length of each gene is included and used for computing normalized expression.

source_name: flank tumor model of SCLC

extract_protocol:
RNA was extracted from cell pellets or tumor samples using TRIzol reagent following manufacturers protocol.
RNAseq libraries were generated from 500ng of RNA using the NEBNext® Ultra™ RNA Library Prep Kit for Illumina (New England Biolabs E7530L).

value: flank tumor model of SCLC

tag: cell line

tag: histology

value: mSCLC

value: BOM, anti-PD1


title: mLN2nd_1


title: Ovarian Epithelial Cells RNA-seq rep 1

value: untreated


title: mLN1st_3


title: mLN1st_2


title: RP-48OVA-LLO190, BOM-anti.PD1, rep3 (flank tumor)


title: mLN1st_1


title: Human Mammary Epithelial Cells RNA-seq rep 2

value: Human Mammary Epithelial Cells


title: RP-48OVA-LLO190, BOM-anti.PD1, rep2 (flank tumor)


title: Human Mammary Epithelial Cells RNA-seq rep 1


title: No244 osteosarcoma CD44+/+

description: CD44+/+; Nf2Δ2/+


title: mFat2nd_2

description: library of 96 CD45+ TCRb+ CD4+ mFAT T cells from secondary H. polygyrus infection

source_name: mesenteric fat - secondary infection H. polygyrus

value: mesenteric fat


title: mFat2nd_3

value: C57BL/6 - female


title: Esophageal Epithelial Cells RNA-seq rep 2

source_name: Human Primary Esophageal Epithelial Cells


title: RP-48OVA-LLO190, anti.PD1, rep5 (flank tumor)


title: RP-48OVA-LLO190, BOM-anti.PD1, rep1 (flank tumor)


title: mFat2nd_1


title: mFat1st_4

description: library of 96 CD45+ TCRb+ CD4+ mFAT T cells from primary H. polygyrus infection

source_name: mesenteric fat - primary infection H. polygyrus


title: RP-48OVA-LLO190, anti.PD1, rep4 (flank tumor)


title: Esophageal Epithelial Cells RNA-seq rep 1

value: Human Primary Esophageal Epithelial Cells


title: Colon Epithelial Cells RNA-seq rep 2

source_name: Human Primary Colonic Epithelial Cells

growth_protocol: Human Primary Colonic Epithelial Cells (Colon) were obtained from CellBiologics (H-6047) and grown in Complete Human Epithelial Cell Medium supplemented with Human Epithelial Cell Medium Supplement Kit (CellBiologics, H6621). Cells were grown in 15 cm dishes.

value: Human Primary Colonic Epithelial Cells


title: mFat1st_2

value: 6-8 weeks + 11-13 days infection


title: RP-48OVA-LLO190, anti.PD1, rep3 (flank tumor)


title: mFat1st_1


title: RP-48OVA-LLO190, anti.PD1, rep2 (flank tumor)


title: mFat2nd_4


title: Bladder Epithelial Cells RNA-seq rep 2

value: Primary Human Bladder Epithelial Cells


title: RP-48OVA-LLO190, anti.PD1, rep1 (flank tumor)


title: mFat1st_3


title: Colon Epithelial Cells RNA-seq rep 1


title: Human Astrocytes RNA-seq rep 2

value: Human Astrocyte Cells


title: RP-48OVA-LLO190, BOM, rep3 (flank tumor)

value: BOM


title: RP-48OVA-LLO190, BOM, rep2 (flank tumor)


title: Airway Epithelial Cells RNA-seq rep 2

value: Bronchial/Tracheal Epithelial Cells


title: Human Astrocytes RNA-seq rep 1


title: RP-48OVA-LLO190, BOM, rep1 (flank tumor)


title: Airway Epithelial Cells RNA-seq rep 1


title: RP-48OVA-LLO190, Vehicle, rep5 (flank tumor)

value: Vehicle


title: Bladder Epithelial Cells RNA-seq rep 1


title: RP-48OVA-LLO190, BOM, rep4 (flank tumor)


title: RP-48OVA-LLO190, Vehicle, rep4 (flank tumor)


title: RP-48OVA-LLO190, Vehicle, rep3 (flank tumor)


title: 22Rv1_GE

first: Bic

last: MSKCC

address: 1275 York Ave.

institute: Memorial SLoan-Kettering Cancer Center

description: Cut&Tag pull down DNA

data_processing:
Library strategy: CUT&Tag
CUT&Tag sequencing reads were trimmed and filtered for quality and adapter content using version 0.4.5 of TrimGalore (https://www.bioinformatics.babraham.ac.uk/projects/trim_galore)
Supplementary_files_format_and_content: bw

growth_protocol: Cell are cultured in standard condition according to ATCC

extract_protocol:
based on the CUT&Tag for bench-top application (PMID: 31036827).
DNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: No treatment

tag: cell  type

value: Human Prostate cancer Cell

tag: source

value: ATCC


title: 22Rv1_AB

description: Cut&Tag pull down DNA


title: 22Rv1_SC

description: Cut&Tag pull down DNA


title: RP-48OVA-LLO190, Vehicle, rep2 (flank tumor)

last: Hiatt

value: flank tumor model of SCLC


title: PC3_SC

description: Cut&Tag pull down DNA


title: PC3_AB

description: Cut&Tag pull down DNA


title: PC3_GE

description: Cut&Tag pull down DNA


title: G8545, BOM, rep1 (cultured SCLC cells)

value: cultured SCLC cells

value: mSCLC


title: RP-48OVA-LLO190, Vehicle, rep1 (flank tumor)


title: RB_CHLA_24

type: genomic

city: Los Angeles

first: Gangning

last: Liang

address: 1441 Biggy street

department: Urology

institute: USC Keck school of medicine

hyb_protocol: Standard Illumina Procotol

scan_protocol: Illumina iScan technology using standard scanner setting

data_processing: R package 'minfi' was used for data processing and background normalization

label: Cy5 and Cy3

source_name: RB primary tumor 24

label_protocol: Standard Illumina Procotol

extract_protocol: QIAamp circulating nucleic acid kit and QIAamp FFPE DNA extraction mini kit

tag: protocol

value: Primary enucleated


title: G8545, DMSO, rep1 (cultured SCLC cells)

value: DMSO


title: RB_CHLA_29

source_name: RB aqueous humor 29


title: RB_CHLA_28

source_name: RB primary tumor 28


title: RB_CHLA_14

source_name: RB primary tumor 14


title: AH_CHLA_13

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation27 Beadchip using standard Illumina protocol

source_name: RB aqueous humor 13

value: Secondary Enucleated


title: AH_CHLA_14

source_name: RB aqueous humor 14


title: AH_CHLA_15

source_name: RB aqueous humor 15


title: AH_CHLA_9

source_name: RB aqueous humor 9

value: Salvaged


title: RB_CHLA_33

source_name: RB aqueous humor 33


title: AH_CHLA_10

source_name: RB aqueous humor 10


title: RB_CHLA_46

source_name: RB aqueous humor 46


title: TDP43-ALS iPSC-derived MN_2

city: Rostock

first: Andreas

last: Hermann

state: Mecklenburg-Western Pomerania

address: Gehlsheimer Str.20

department: Neurology

institute: University Medical Center Rostock

description: TDP43 G294V_BRC2TDP4312

data_processing:
Partek Genomics Suite version 7.0  (PGS 7.0)
Sequence reads were trimmed for adaptor sequence/low-quality sequence using Partek Genomics Suite (parameter- Quality limit: 0.05)
Trimmed sequence reads were mapped to the human reference genome hg38 from Ensembl transcripts release100 using Partek Genomics Suite
Read count extraction and normalization were performed using Partek Genomics Suite
The expression levels of genes in each sample and the corresponding fold changes were estimated by DESeq2 1.16.1 (Partek Genomics Suite). To generate significantly DEGs among different samples, a cutoff of the false discovery rate adjusted P < 0.05 (Benjamini–Hochberg correction) and fold change FC ≥ 1.5 were applied
Assembly: hg38
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

source_name: iPSC-derived spinal motor neurons

growth_protocol: Neurons were cultured in N2B27 medium with 10 ng/µl BDNF, 500 µM dbcAMP and 10 ng/µl GDNF

extract_protocol:
Total RNA was isolated using Qiagen Rneasy mini plus kit including a column DNase digest. 1 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using TrueSeq RNA Library Prep Kit v2 (Illumina) following manufacturer's protocols.

treatment_protocol:
Not applicable
Not applicable

tag: disease status

value: Familial ALS (fALS)

tag: cell line_(ipsc_source)

value: Fibroblast

value: iPSC-derived spinal motor neurons

tag: genotype (donor)

value: fALS patient1 carrying TDP43 mutation

value: not applicable


title: CTH+11 remission

city: Perugia

first: Cristina

last: Mecucci

address: Piazzale Menghini n.9

department: Department of Medicine, Hematology and Bone Marrow Transplantation Unit

country: Italy

institute: University of Perugia

hyb_protocol: DNA was restriction digested, ligated, PCR amplified, fragmented, labeled and hybridized to each array according to the manufacturer's instructions

scan_protocol: The Arrays were then washed using Affymetrix fluidics stations, and scanned using the Gene Chip Scanner 3000 7G

data_processing:
Protocol was supported by Affymetrix GeneChip Command Console (AGCC) software. Analysis was performed through Affymetrix Chromosome Analysis 4.0 (ChAS) software with filters set at 200 Kb for Copy Number Alterations (CNAs) and 10 Mb for copy neutral Loss Of Heterozygosity (cnLOH). Our data refer to NetAffx Build 32.3 (hg19) database
Genotype Call (SNP call): AA, AB, BB, NC, and NoCall; 'Signal' = Summarized signal

label: Biotin

source_name: Unsorted Bone Marrow Cells

label_protocol: As per manufacturer (Affymetrix)

extract_protocol: DNA were extracted from bone marrow cells of patients using All Prep DNA/RNA Mini Kit (Qiagen). DNA quality and quantity was assessed using a Nanodrop Spectrophotometer, Bioanalyzer and/or Tapestation visualization (Agilent 2100 Bioanalyzer) and agarose gel electrophoresis

value: T-ALL

tag: chromothripsis status

value: positive


title: AH_CHLA_7

source_name: RB aqueous humor 7


title: RP-48, DMSO, rep1 (cultured SCLC cells)

city: Seattle

tag: treatment

tag: time


title: CTH+11

tag: subtype

value: immature


title: RB_CHLA_49

source_name: RB aqueous humor 49


title: TDP43-ALS iPSC-derived MN_1

description: TDP43 G294V_BRC15TDP4311


title: AH_CHLA_4

source_name: RB aqueous humor 4


title: AH_CHLA_12

source_name: RB aqueous humor 12


title: RB_CHLA_41

source_name: RB aqueous humor 41


title: COLO 829 ATAC-seq

first: Margaret

address: 269 Campus Dr. CCSR Room 2150

institute: Stanford University

source_name: Human Melanoma Cell Line

value: 2 uM DMSO

tag: time point

value: 24 hours


title: TDP43-ALS iPSC-derived MN_3

description: TDP43 S393L_MCC25TDP4321

value: fALS patient2 carrying TDP43 mutation


title: CTH+10 fibroblasts

source_name: Bone Marrow Fibroblasts


title: CTH+10


title: SOD1-ALS iPSC-derived MN_2

description: SOD1 D90A_MM41

value: fALS patient2 carrying SOD1 mutation


title: CTH+8


title: CTH+9


title: RP-116, DMSO, rep1 (cultured SCLC cells)

value: cultured SCLC cells

value: mSCLC


title: AH_CHLA_11

source_name: RB aqueous humor 11


title: CTH+12


title: AH_CHLA_2

source_name: RB aqueous humor 2

value: Primary enucleated


title: RP-48, BOM, rep1 (cultured SCLC cells)

value: BOM


title: RB_CHLA_4

source_name: RB primary tumor 4


title: CTH+7


title: SOD1-ALS iPSC-derived MN_1

description: SOD1 R115G_D8.9

value: fALS patient1 carrying SOD1 mutation


title: CTH+6 remission


title: mNFA_M3

city: Halle

first: Bayram

last: Edemir

address: Ernst-Grube-Str. 20

institute: University Hospital Halle (Saale)

data_processing:
Raw data (raw reads) of FASTQ format were firstly processed through in-house scripts. In this step, clean data (clean reads) were obtained by removing reads containing adapter and poly-N sequences and reads with low quality from raw data. At the same time, Q20, Q30 and GC content of the clean data were calculated. All the downstream analyses were based on the clean data with high quality
Reference genome and gene model annotation files were downloaded from genome website browser (NCBI/UCSC/Ensembl) directly. Paired-end clean reads were mapped to the reference genome using HISAT2 software. HISAT2 uses a large set of small GFM indexes that collectively cover the whole genome. These small indexes (called local indexes), combined with several alignment strategies, enable rapid and accurate alignment of sequencing reads
HTSeq was used to count the read numbers mapped of each gene, including known and novel genes. And then RPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene. RPKM, Reads Per Kilobase of exon model per Million mapped reads, considers the effect of sequencing depth and gene length for the reads count at the same time, and is currently the most commonly used method for estimating gene expression levels
Genome_build: mm9
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

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

value: Kidney

tag: gender

value: male

tag: tissue

value: renal medulla


title: mNFA_M2

tag: cell type


title: Healthy control iPSC-derived MN_3

value: Healthy

value: Fibroblast

value: iPSC-derived spinal motor neurons

value: Healthy donor 3-clone 1


title: RB_CHLA_31

source_name: RB aqueous humor 31


title: CTH+5

value: T-ALL

value: positive

value: immature

tag: age


title: Healthy control iPSC-derived MN_2

value: Healthy donor2-clone 1

value: not applicable


title: AH_CHLA_1

source_name: RB aqueous humor 1


title: CTH+6


title: CTH+4


title: AH_CHLA_6

source_name: RB aqueous humor 6

value: Salvaged


title: RB_CHLA_20

source_name: RB primary tumor 20


title: AH_CHLA_5

source_name: RB aqueous humor 5


title: mNFA_M1


title: CTH+2


title: CTH+3


title: CTH+1


title: mNFA_C2

value: renal cortex


title: ChiwiControl_NeuralFolds2

city: Pasadena

first: Riley

last: Galton

address: 1200 E California Blvd

department: BBE

institute: Caltech

data_processing:
Reads were trimmed to remove adapter sequences and mapped to galGal6 genome using Bowtie2
Reads mapping to genes and repetitive elements were counted using featurecounts
Differential expression analysis was performed with DEseq2
Genome_build: galGal6
Supplementary_files_format_and_content: raw count files for genes and repetitive elements

organism: Gallus gallus

source_name: HH9- cranial neural folds

growth_protocol: Chick embryos were grown at 37C for ~18 hours to reach HH4, then electroporated and subsequently grown ~14 hours to reach HH9-

extract_protocol:
Cranial neural folds were dissected and total RNA extracted
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: HH4 embryos were electroporated with a Cas9 expression construct and either Chiwi or control guide constructs and grown until HH9-

tag: Stage

value: Cranial neural folds

value: CRISPR control


title: AH_CHLA_3

source_name: RB aqueous humor 3

value: Primary enucleated


title: ChiwiKO_NeuralFolds2

value: Chiwi CRISPR knockout


title: MPNST-40

city: NEW YORK

first: Ping

last: Chi

address: 1275 YORK AVENUE

institute: MEMORIAL SLOAN KETTERING CANCER CTR

data_processing:
The sequence data were processed and mapped to the human reference genome (hg20) using STAR v2.3 (Dobin et al., 2013)
Gene expression was quantified to transcripts-per-million (TPM) using the STAR (Trapnell et al., 2010) and Log 2 transformed.
Assembly: hg20
Supplementary files format and content: tab-delimited text file includes raw gene counts for every gene and every sample

source_name: MPNST tumor

extract_protocol:
Total RNA were isolated from tumor tissues using Trizol (Thermo Fisher #15596026).
RNA libraries were prepared for sequencing using standard Illumina protocols
RNA-Seq by poly (A) capture

value: MPNST tumor

tag: genotype

value: PRC2 loss of function


title: MPNST-41


title: MPNST-39


title: mICRE_M6

value: Kidney

value: male

value: renal medulla


title: mNFA_C3


title: RB_CHLA_2

source_name: RB primary tumor 2


title: mNFA_C1


title: ChiwiKO_NeuralFolds1


title: Primary microglia, Aβ40_03

city: Kingston

first: Willam

middle: Van

last: Nostrand

state: Rhode Island

address: 7 Greenhouse Rd

department: College of Pharmacy

institute: University of Rhode Island

data_processing:
Basespace RNA-Seq Alignment APP     - Read mapping using the STAR aligner; Quantification of reference genes and transcripts using salmon; Rattus norvegicus UCSC rn5 (RefSeq gene annotation)  - SNVs and INDELs called by Strelka Variant caller  - Gene fusions detected by Manta     https://support.illumina.com/help/BS_App_RNASeq_Alignment_v2_OLH_1000000006112/Content/Source/Informatics/Apps/WkflDescr_swBS_appRNASeq.htm
Read mapping using the STAR aligner; Quantification of reference genes and transcripts using salmon; Rattus norvegicus UCSC rn5 (RefSeq gene annotation)
SNVs and INDELs called by Strelka Variant caller
Gene fusions detected by Manta
Basespace DESeq2 APP -  produces gene counts, gene FPKMs
Assembly: Rattus norvegicus UCSC rn5 (RefSeq gene annotation)
Supplementary files format and content: tab-delimited text files include  gene FPKMs  values for each Sample

source_name: brain

extract_protocol:
E.Z.N.A.® Total RNA Kit II - https://www.omegabiotek.com/product/e-z-n-a-total-rna-kit-ii/
RNA sequencing libraries were prepared using TruSeq Stranded mRNA Library Prep Kit (Illumina, Inc., San Diego, CA, USA) according to the manufacturer`s protocol by Omega Bioservice Company.

value: brain

value: Primary microglia cells

value: WT


title: mICRE_M1


title: RB_CHLA_3

source_name: RB primary tumor 3


title: Primary microglia, Aβ40_01


title: Primary microglia, Aβ42_03


title: MPNST-38


title: Healthy control iPSC-derived MN_1

source_name: iPSC-derived spinal motor neurons

value: Healthy

value: Fibroblast

value: iPSC-derived spinal motor neurons

value: Healthy donor1-clone 1


title: Primary microglia, Aβ42_02


title: MPNST-37


title: mICRE_C1

value: renal cortex


title: Primary microglia, control_03

value: control


title: mICRE_C6


title: Primary microglia, control_01


title: Primary astrocyte, Aβ40_03

value: Primary astrocyte cells


title: f_NFA_M6

value: female


title: MPNST-35


title: Primary microglia, control_02


title: Primary microglia, Aβ40_02


title: ChiwiControl_NeuralFolds1

value: Cranial neural folds

value: CRISPR control


title: MPNST-34

value: MPNST tumor

value: PRC2 loss of function


title: fNFA_M5

value: Kidney


title: Primary astrocyte, Aβ40_02


title: AH_CHLA_8

source_name: RB aqueous humor 8

value: Salvaged


title: Primary astrocyte, Aβ40_01

value: brain


title: MPNST-33


title: RB_CHLA_1

source_name: RB primary tumor 1

value: Primary enucleated


title: Primary astrocyte, Aβ42_03

value: WT


title: Primary astrocyte, Aβ42_02


title: fNFA_M4

value: renal medulla


title: Primary astrocyte, Aβ42_01


title: Primary astrocyte, control_03


title: fNFA_C6


title: Primary astrocyte, control_02


title: Primary microglia, Aβ42_01

value: Primary microglia cells


title: MPNST-36


title: MPNST-31