title: ∆czcD 100 µM zinc treated

city: Melbourne

first: Stephanie

middle: Louise

last: Neville

state: Victoria

address: 792 Elizabeth Street

department: Microbiology and Immunology

country: Australia

institute: University of Melbourne

data_processing:
Reads were aligned to the S. pneumoniae D39 genome (NC_008533) using BOWTIE2 version 2.2.6
Counts for each gene were determined using SAMtools version 1.3 and BEDtools version 2.24.0
Differential gene expression was determined using R (DESeq Library) version 3.2.2
Genome_build: NC_008533 reference sequence was used for alignment
Supplementary_files_format_and_content: countsD39WT_Untreated - Raw counts of sequencing reads for all genes as .txt file
Supplementary_files_format_and_content: CountsD39_WT_100Zn -  Raw counts of sequencing reads for all genes as .txt file
Supplementary_files_format_and_content: countsDczcD_100Zn  -  Raw counts of sequencing reads for all genes as .txt file
Supplementary_files_format_and_content: D39WT_Unt_vs_D39WT_100Zn - Output from DESeq (normalised counts) as .xlsx file
Supplementary_files_format_and_content: D39WT_Unt_vs_D39DczcD_100Zn - Output from DESeq (normalised counts) as .xlsx file

organism: Streptococcus pneumoniae

source_name: Bacteria

growth_protocol: S. pneumoniae taken from overnight growth on horse blood agar and inoculated into C+Y media at a starting OD600= 0.05. Culture were grown to OD600= 0.3 at 37 C + 5% CO2 prior to RNA extraction

extract_protocol:
RNA was extracted using Qiagen RNeasy kit. DNA was depleted using Qiagen RNase-free Dnase. RNA integrity was determined using an Agilent Bioanalyzer.
Performed by Australian Genome Research Facility. RNA was prepared using standard Illuminia Sequening protocols with Ultra Directional RNA kit (New England Biolabs)  to generate barcoded libraries.

treatment_protocol: Untreated samples were grown in C+Y + 1 µM manganese, zinc treated samples were grown in C+Y + 1 µM manganese + 100 µM zinc

tag: genotype

value: czcD deletion

tag: agent

value: 100 microM zinc


title: primary/10Gy

status: Public on Feb 01 2022

type: RNA

city: Philadelphia

first: Anuradha

middle: A

last: Shastri

state: Pennsylvania

address: 233 S 10th Street

country: USA

institute: Thomas Jefferson University

description: total RNA samples

hyb_protocol: Hybridization was performed overnight on a µParaflo microfluidic chip using a micro-circulation pump (Atactic Technologies). On the microfluidic chip, each detection probe consisted of a chemically modified nucleotide coding segment complementary to target microRNA (from miRBase, http://miRBase.org) or other RNA (control or customer defined sequences) and a spacer segment of polyethylene glycol to extend the coding segment away from the substrate. The detection probes were made by in situ synthesis using PGR (photogenerated reagent) chemistry. The hybridization melting temperatures were balanced by chemical modifications of the detection probes. Hybridization used 100 uL 6xSSPE buffer (0.90 M NaCl, 60 mM Na2HPO4, 6 mM EDTA, pH 6.8) containing 25% formamide at 34 °C.

scan_protocol: The hybridization melting temperatures were balanced by chemical modifications of the detection probes. Hybridization used 100 mL 6xSSPE buffer (0.90 M NaCl, 60 mM Na2HPO4, 6 mM EDTA, pH 6.8) containing 25% formamide at 34 °C.  After RNA hybridization, tag-conjugating Alexa Fluor®546 dye was circulated through the microfluidic chip for dye staining.  Fluorescence images were collected using a laser scanner (GenePix 4000B, Molecular Device) and digitized using Array-Pro image analysis software (Media Cybernetics).

data_processing: Data were analyzed by first subtracting the background and then normalizing the signals using a LOWESS filter (Locally-weighted Regression) (2). (2) Bolstad, B. M., Irizarry, R. A., Astrandand, M., Speed, T. P. (2003) A comparison of normalization methods for high density oligonucleotide array data based on variance and bias. Bioinfo. 19, 185-193.

molecule: total RNA

organism: Mus musculus

source_name: Primary tumor

label_protocol: Microarray assay was performed using a service provider (LC Sciences).  Total RNA sample (2 µg) were 3’-extended with a poly(A) tail using poly(A) polymerase.  An oligonucleotide tag was then ligated to the poly(A) tail for later fluorescent dye staining.  Hybridization was performed overnight on a µParaflo microfluidic chip using a micro-circulation pump (Atactic Technologies) (1). On the microfluidic chip, each detection probe consisted of a chemically modified nucleotide coding segment complementary to target microRNA (from miRBase, http://mirbase.org) or other RNA (control or customer defined sequences) and a spacer segment of polyethylene glycol to extend the coding segment away from the substrate.  The detection probes were made by in situ synthesis using PGR (photogenerated reagent) chemistry.  (1) (a) Gao, X., Gulari, E., and Zhou, X. (2004) In situ synthesis of oligonucleotide microarrays. Biopolymers 73, 579-596; (b) Zhu, Q., Hong, A., Sheng, N., Zhang, X., Jun, K.-Y., Srivannavit, O., Gulari, E., Gao, X., and Zhou, X. (2007) Microfluidic biochip for nucleic acid and protein analysis. in Methods Mol. Biol. Ed. Rampal, J. B. 382:287-312.

growth_protocol: 20 Female Balb/s mice were orthotopically injected with 50000 4T1 cells. When the tumor was 1cm3, half the mice were treated with sham radiation and other 10 treated with 10 Gy dose to the primary tumor. This was followed mastectomy of primary tumor and metastatic tumor were allowed to grow till end point.

extract_protocol: Qiagen miRNeasy kit was used for total RNA extraction following manufacturer's protocol.

treatment_protocol: Primary tumor treated with Sham radiation or 10Gy RT

tag: tissue

value: Tumor


title: Untreated

type: SRA

library_source: transcriptomic

tag: strain

value: wild type


title: m151 Pregnant mice at E15.5

city: Changchun

first: Zijiao

last: Zhao

state: Jilin Provience

address: No. 5333 Xi'an Road

country: China

institute: Jilin University

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm8 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Reads Per Kilobase of exon per Megabase of library size (FPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. 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.
Data filtering steps.Prior to assembly, the low quality reads(1,reads containing sequencing adaptors; 2,reads containing sequencing primer;3, nucleotide with q quality score lower than 20 )were removed .software CutAdapter,parameters -o 5 -p 100
Read alignment software,software HISAT ,version 2.0 ,parameters -l fr-firststrand -mi 20 -mx 500000 -p 2 -b dta -q phred33-quals -x 9
perform expression level for mRNAs and lncRNAs by calculating FPKM.stimate the expression levels of all transcripts.software StringTie ,version 1.3.0,parameters -b dta -q phred33-quals.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

organism: Mus

source_name: uterus

extract_protocol:
Total RNA was extracted using Trizol reagent (Invitrogen, CA, USA) following the manufacturer's procedure. The total RNA quantity and purity were analysis of Bioanalyzer 2100 and RNA 6000 Nano LabChip Kit (Agilent, CA, USA) with RIN number >7.0. Approximately 10 ug of total RNA representing a specific adipose type was subjected to isolate Poly (A) mRNA with poly-T oligoattached magnetic beads (Invitrogen). Following purification, the poly(A)- or poly(A)+ RNA fractions is fragmented into small pieces using divalent cations under elevated temperature. Then the cleaved RNA fragments were reverse-transcribed to create the final cDNA library in accordance with the protocol for the mRNA-Seq sample preparation kit (Illumina, San Diego, USA), the average insert size for the paired-end libraries was 300 bp (±50 bp). And then we performed the paired-end sequencing on an Illumina Novaseq™ 6000 at the (lc-bio, China) following the vendor's recommended protocol.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: tag

value: ICR

tag: time point

value: Pregnant mice at E15.5


title: mets/10Gy

description: total RNA samples

source_name: Metastases

value: Metastases


title: ERF096-RNAi cold stress rep3

city: Da qing

first: Yang

last: shen

state: Heilongjiang Province

address: No. 5 Xinfeng Road, Longfeng District

institute: Heilongjiang Bayi Agricultural University

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to  Rice Annotation Project Database whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. 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.
Genome_build: Rice Annotation Project Database
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample ...

organism: Oryza sativa Japonica Group

growth_protocol: Wild-type, OsERF096-OX and OsERF096-RNAi transgenic rice were grown in a culture room (14h day 10h night) to the three-leaf stage.

extract_protocol:
Frozen on dry ice, and RNA was harvested 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: The leaves of rice under normal growth conditions and those treated at 4°C for 12 h were quick-frozen in liquid nitrogen.

tag: developmental stage

value: three leaf

value: leaf


title: ERF096-RNAi cold stress rep2


title: E0452 Pregnant mice at E4.5

value: Pregnant mice at E4.5


title: ERF096-OX cold stress rep1


title: m152 Pregnant mice at E15.5


title: ERF096-OX CK rep2


title: ERF096-OX CK rep1


title: 100 µM zinc treated


title: WT CK rep3

source_name: wild type


title: E0451 Pregnant mice at E4.5


title: Bone marrow derived macrophages - WT_KO_rep2

city: West Haven

first: Francesc

last: Lopez

state: CT

department: Department of Genetics

institute: Yale University

data_processing:
Basecalls performed using CASAVA version 1.8.2
For each read, the first 6 and the last nucleotides were trimmed to the point where the Phred score of an examined base fell below 20 using in-house scripts. If, after trimming, the read was shorter than 45 bp, the whole read was discarded.
Trimmed reads were mapped to the Mus musculus reference genome (mm10) with Tophat v2.1.1 using the very-sensitive preset, first-strand library type and providing the corresponding gene model annotation. Alignments with quality score below 20 were excluded from further analysis.
The program Cufflinks v2.2.1 was used to convert aligned reads generated from Tophat into relative expression values for each gene represented as FPKM (fragments per kilobase of exon per million mapped reads). Cuffdiff was used to obtain differential gene expression between the experimental groups using first-strand library type, providing gene model annotation and the genome sequence file for detection and correction of sequence-specific bias
Genome_build: mm10
Supplementary_files_format_and_content: tsv files with the output from cuffdiff (including normalized abundance measurements per sample) and differential expression analysis results

source_name: Primary bone marrow

growth_protocol: Femurs and tibias from the indicated mouse lines mice were dissected, cleaned, disinfected in 70% ethanol, and washed with fully supplemented RPMI 1640 medium. Red blood cells were removed by ammonium-chloride potassium lysis buffer and subsequent centrifugation. Remaining bone marrow cells were then cultured at a density of 3.5 × 10^6 cells/10cm Petri dish in fully supplemented RPMI with 30% (vol/vol) L929 cell-conditioned medium. Cells were matured to phenotypic macrophages over 6 days as confirmed by >98% expression of F4/80 and CD68.

extract_protocol:
Total RNA from polarized BMDMs was extracted with the RNeasy kit (QIAGEN; cat.74106).
Poly-A, strand-specific RNA library construction was performed by the Yale Center for Genomic Analysis utilizing the TruSeq Library Prep Kit 2.0 per the manufacturers specifications. . Following first-strand synthesis with random primers, second strand synthesis was performed with dUTP for generating strand-specific sequencing libraries.

treatment_protocol: Polarization of BMDMs was carried out by incubation with LPS (100ng/mL; Sigma-Aldrich L2630) and IFN-g (50ng/mL; BioLegend 575304) or with IL-4 (10ng/mL; BioLegend 574304) and IL-13 (10ng/mL; BioLegend cat.575904) for 24 hours.

tag: cell type

value: Bone marrow derived macrophages

tag: mouse strain

value: CSF1Rcre Dicer1fl/fl C57BL6/J

tag: treatment


title: Bone marrow derived macrophages - KO_M2_rep1

value: IL-4 (10ng/mL; BioLegend 574304) and IL-13 (10ng/mL; BioLegend cat.575904) for 24 hours


title: Bone marrow derived macrophages - KO_M1_rep1

value: LPS (100ng/mL; Sigma-Aldrich L2630) and IFN-g (50ng/mL; BioLegend 575304) for 24 hours


title: primary/no rad

description: total RNA samples


title: m181 Pregnant mice at E18.5

value: Pregnant mice at E18.5


title: E0052 Pregnant mice at E0.5

value: Pregnant mice at E0.5


title: WBCs, 4127DS

type: genomic

city: Lebanon

first: Ji-Qing

last: Chen

state: New Hampshire

address: 1 Medical Center Drive, Williamson level 6

department: Epidemiology

institute: Dartmouth College

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

scan_protocol: Arrays were imaged using BeadArray Reader using standard recommended Illumina scanner setting

data_processing:
R studio
Matrix_Processed.csv  represents SeSAMe Processed Average Beta values.

label: Cy5 and Cy3

molecule: genomic DNA

organism: Homo sapiens

source_name: White blood cell

label_protocol: Standard Illumina Protocol

extract_protocol: genomic DNA was extracted and purified from samples using Qiagen DNeasy Kit according to standard instructions

tag: disease state

value: non-muscle-invasive bladder cancer (NMIBC)

tag: gender

value: male

tag: age

tag: ten year-recurrence or death

value: Yes

value: White blood cell


title: ERF096-RNAi cold stress rep1


title: Bone marrow derived macrophages - WT_M1_rep2

value: Dicer1fl/fl C57BL6/J


title: Bone marrow derived macrophages - WT_M1_rep1


title: E0051 Pregnant mice at E0.5

value: ICR


title: ERF096-OX cold stress rep3


title: WT cold stress rep3

value: wild type


title: WT cold stress rep2


title: ERF096-RNAi CK rep1


title: WT cold stress rep1


title: mets/no rad

description: total RNA samples

value: Metastases


title: MUSCs_WO_2

city: La Jolla

first: Pier Lorenzo

last: Puri

state: CA

address: 10901 N Torrey Pines Rd

institute: Sanford Burnham Prebys

data_processing:
RNAseq Mapping was performed with TopHat 2.0.9
RNAseq read counts were generated using HTSeq-0.6.1p1
RNAseq differential analysis was performed using Deseq2
Genome_build: GRCm38.78
Supplementary_files_format_and_content: FPKM

source_name: Muscular Adult Stem Cells

extract_protocol:
Muscle-derived cells were isolated by FACS and immediatly processed to isolate histone-DNA complexes with H3K9/14ac and H3K27ac antibodies from sonicated nuclei (ChIP-seq) and to harvest RNA using Trizol reagent (RNA-seq).
DNA and RNA libraries were prepared for sequencing using standard Illumina protocols and sequenced on Illumina Hiseq2500 platform.

treatment_protocol: C57Bl6 mdx mice at 1.5 and 12 months of age were treated before FAPs isolation for 15 days with daily intra peritoneal injections of Trichostatin A, TSA (0.6 mg/kg/day), dissolved in saline solution or in saline alone as vehicle control (CTR).

value: Muscular Adult Stem Cells

tag: background strain

value: Old

value: Wild Type


title: MAC_YC_2

source_name: Macrophages

value: Macrophages

value: Young

value: MDX

value: CTR


title: MAC_OC_1


title: MUSCs_WO_1


title: ERF096-OX cold stress rep2

value: three leaf

value: leaf


title: MUSCs_OC_1


title: ERF096-OX CK rep3


title: WT CK rep2


title: WT CK rep1


title: ERF096-RNAi CK rep2


title: ERF096-RNAi CK rep3


title: FAPs_WO_2

source_name: Fibro Adipogenic Progenitors

value: Fibro Adipogenic Progenitors


title: Bone marrow derived macrophages - WT_M2_rep1

value: Bone marrow derived macrophages

value: IL-4 (10ng/mL; BioLegend 574304) and IL-13 (10ng/mL; BioLegend cat.575904) for 24 hours


title: Bone marrow derived macrophages - KO_M1_rep2

value: CSF1Rcre Dicer1fl/fl C57BL6/J

value: LPS (100ng/mL; Sigma-Aldrich L2630) and IFN-g (50ng/mL; BioLegend 575304) for 24 hours


title: FAPs_WY_2


title: MAC_YC_1


title: MUSCs_WY_1


title: FAPs_OC_1


title: FAPs_OT_1

value: TSA


title: Bone marrow derived macrophages - WT_M2_rep2

value: Dicer1fl/fl C57BL6/J


title: MAC_OC_2


title: FAPs_YC_1


title: MUSCs_OC_2


title: MUSCs_YC_2


title: FAPs_YT_1


title: H3k9/14ac_FAPs_OC

description: Immuno-precipitated DNA

library_source: genomic

data_processing:
RNAseq Mapping was performed with TopHat 2.0.9
RNAseq read counts were generated using HTSeq-0.6.1p1
RNAseq differential analysis was performed using Deseq2
Chipseq reads were alligned with the murine genome using bowtie-0.12.7
Chipseq duplicated reads were removed using samtools1.3
ChIpseq H3K9/14ac and H3K27ac occupancy were determined using macs2 with a FDR < 0.001 and an ExtSize of 147 against their inputs
ChIPseq significant peaks revealed by macs 2 were further filtered using a threshold of macs_score > 100. . Peaks were then processed with Homer to have more than 80 tags
Genome_build: GRCm38.78


title: H3k27ac_FAPs_OT

description: Immuno-precipitated DNA


title: H3k9/14ac_FAPs_OT

description: Immuno-precipitated DNA


title: MUSCs_WY_2


title: FAPs_OC_2


title: FAPs_WO_1


title: FAPs_YT_2


title: H3k9/14ac_FAPs_YT

description: Immuno-precipitated DNA


title: FAPs_OT_2


title: Control

city: Nanjing

first: Bin

last: Yan

address: 140Hanzhong Road

institute: Nanjing Medical University

data_processing:
Cell Ranger version 3.0.0 (10x Genomics) was used to process the raw sequencing data, gene x cell expression matrices were loaded into the R package Seurat version 3.0.0 for downstream analyses, Cells with low quality were filtered out based on at least 200 genes being detected per 1 000 UMIs and mitochondrial gene content. Only those genes found in more than 3 cells were retained. Differential expression testing was carried out using the Wilcoxon rank sum test in Seurat,
mm10
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every cell

molecule: polyA RNA

source_name: macrophage  extracted from control murine alveolar bone

extract_protocol:
Samples were washed twice in PBS (Life Technologies) plus 0.04% BSA (Sigma‐Aldrich). Each wash was performed with a 5-min centrifugation at 330 g and resuspension in 1 ml PBS plus 0.04% BSA. Sample viability was assessed using trypan blue (Thermo Fisher) and a hemocytometer (Thermo Fisher), and the appropriate volume for each sample was calculated. After droplet generation (the generation of GEMs with RT primers), samples were transferred onto a prechilled 96-well plate (Eppendorf), and reverse transcription was performed. Next, post GEM-RT was recovered using Recovery Agent provided by 10x Genomics followed by DynaBead cleanup
cDNA libraries were prepared as outlined by the Single Cell 3′ Reagent kit v2 user guide with appropriate modifications to the PCR cycles based on the calculated cDNA concentration (as recommended by 10x Genomics).

value: 8 weeks

value: Alveolar Bone

value: alveolar macrophages


title: MUSCs_YC_1

value: Muscular Adult Stem Cells


title: P10.WT.2

city: Bethesda

first: Matthew

middle: J

last: Brooks

state: MD

address: 6 Center Dr Bldg 6, Rm 303

department: NEI

institute: NIH

description: flow-sorted Nrl-GFP positive cells from retina at post natal day P10 wild-type mouse, replicate number 2

data_processing:
Unprocessed fastq files from the sequencer were quality checked, trimmed and aligned to the Mus musculus Ensembl annotation.
Transcript level quantitation was performed using Kallisto v0.42.4 employing a merged transcript cDNA and ncRNA FASTA file downloaded from the Ensembl v84 ftp site.
Gene level quantification was generated by summarization of the transcript level quantitation using tximport v0.99.9 with the option countFromAbundance=lengthScaledTPM. The gene level count values were TMM normalized and converted to count per million (CPM) via edgeR v3.32.1.
Genome_build: Assembly GRCm38.p5, Annotation Ensembl v84
Supplementary_files_format_and_content: Tab-delimited text files containing transcript level counts, gene level counts, or normalized gene level counts-per-million results.

growth_protocol: Mice were housed in 12-hour light-dark housing conditions and were cared for following recommendations of the Guide for the Care and Use of Laboratory Animals, Institute of Laboratory Animal Resources, the Public Health Service Policy on Humane Care and Use of Laboratory Animals. All mouse protocols have been approved by the Animal Care and Use Committee of the National Eye Institute (ASP#650).

extract_protocol:
Isolated cells were lysis with TRIzol LS and the total RNA were isolated.
RNAseq data were generated using TruSeq Stranded mRNA Sample Prep Kit (Illumina).

treatment_protocol: Rod photoreceptors from Pde6brd1/rd1; TgNrlp-GFP (rd1) and TgNrlp-GFP (WT) mice were isolated. Dissected retinas were treated with papain and dissociated singe cells were collected by centrifugation at 800 x g for 5 min at 4oC and resuspended in ice cold PBS. GFP-positive photoreceptor cells were isolated using FACS Aria II with a stringent precision setting which maximize the purity of sorted cells.

tag: post-natal age

value: wild-type

tag: replicate


title: Input_FAPs_OC

description: DNA

value: Old


title: Input_FAPs_YT

description: DNA

value: Young

value: MDX


title: Input_FAPs_OT

description: DNA


title: P8.WT.1

description: flow-sorted Nrl-GFP positive cells from retina at post natal day P8 wild-type mouse, replicate number 1

tag: genotype


title: FAPs_YC_2

value: CTR


title: H3k27ac_FAPs_OC

description: Immuno-precipitated DNA


title: H3k27ac_FAPs_YT

description: Immuno-precipitated DNA


title: P8.rd1.2

description: flow-sorted Nrl-GFP positive cells from retina at post natal day P8 rd1 mouse, replicate number 2


title: P6.WT.3

description: flow-sorted Nrl-GFP positive cells from retina at post natal day P6 wild-type mouse, replicate number 3


title: P10.WT.4

description: flow-sorted Nrl-GFP positive cells from retina at post natal day P10 wild-type mouse, replicate number 4


title: FAPs_WY_1

value: Wild Type


title: H3k9/14ac_FAPs_YC

description: Immuno-precipitated DNA


title: Input_FAPs_YC

description: DNA


title: Case

source_name: macrophage  extracted from case murine alveolar bone


title: P6.rd1.2

description: flow-sorted Nrl-GFP positive cells from retina at post natal day P6 rd1 mouse, replicate number 2


title: H3k27ac_FAPs_YC

description: Immuno-precipitated DNA


title: P10.rd1.2

description: flow-sorted Nrl-GFP positive cells from retina at post natal day P10 rd1 mouse, replicate number 2


title: P4.rd1.2

description: flow-sorted Nrl-GFP positive cells from retina at post natal day P4 rd1 mouse, replicate number 2


title: P10.rd1.1

description: flow-sorted Nrl-GFP positive cells from retina at post natal day P10 rd1 mouse, replicate number 1


title: P2.WT.2

description: flow-sorted Nrl-GFP positive cells from retina at post natal day P2 wild-type mouse, replicate number 2


title: P10.WT.5

description: flow-sorted Nrl-GFP positive cells from retina at post natal day P10 wild-type mouse, replicate number 5


title: P2.WT.1

description: flow-sorted Nrl-GFP positive cells from retina at post natal day P2 wild-type mouse, replicate number 1


title: P8.WT.2

description: flow-sorted Nrl-GFP positive cells from retina at post natal day P8 wild-type mouse, replicate number 2


title: P8.rd1.1

description: flow-sorted Nrl-GFP positive cells from retina at post natal day P8 rd1 mouse, replicate number 1


title: P8.rd1.3

description: flow-sorted Nrl-GFP positive cells from retina at post natal day P8 rd1 mouse, replicate number 3


title: P6.WT.2

description: flow-sorted Nrl-GFP positive cells from retina at post natal day P6 wild-type mouse, replicate number 2


title: P2.rd1.2

description: flow-sorted Nrl-GFP positive cells from retina at post natal day P2 rd1 mouse, replicate number 2


title: P10.WT.3

description: flow-sorted Nrl-GFP positive cells from retina at post natal day P10 wild-type mouse, replicate number 3


title: CD4+ Tn/mem-iPSC derived CD19-CAR T cells replicate #2

city: Duarte

first: wei

last: chen

address: 1500 E Duarte Rd

department: Cancer Biology-BRI

institute: City of Hope National Medical Center

data_processing:
Base calling was done using Illumina RTA and bcl2fastq v2.18.0.12
Sequences were aligned to hg19 using Tophat2 with default settings
Gene expression level of Ensembl GRCh37 coding genes were quantified using HTSeq v0.6.1p1
Genome_build: hg19
Supplementary_files_format_and_content: tab delimited text file gene expression counts

source_name: Tn/mem-iPSC derived T cells

growth_protocol: iPS cells were cultured in mTeSR medium, iPSC CAR T cells were cultured in X-VIVO 15 medium with 10 ng/mL rhIL-7 and 50 U/mL rhIL-2 after 14 days REM expansion, conventional PBMC CAR T cells were cultured in X-VIVO 15 medium with 50 U/mL rhIL-2 and 0.5 ng/mL rhIL15, PBMC derived NK cells were cultured in X-VIVO 15 medium with 100U/mL rhIL-2 with irradiated feeder cells. (Detailed information see the method part of the paper.)

extract_protocol:
RNA was extracted with the Quick-RNA Microprep kit (Zymo Research) and treated with DNase I.
RNA-seq libraries were constructed by using KAPA mRNA HyperPrep kits ( Roche )

value: T lymphocyte

value: differentiated from CD19-CAR+ iPSC and ex vivo expanded for 14 days by REM protocol, sorted cells

tag: Stage

value: lymphocyte lineage


title: P8.rd1.4

description: flow-sorted Nrl-GFP positive cells from retina at post natal day P8 rd1 mouse, replicate number 4


title: P2.rd1.1

description: flow-sorted Nrl-GFP positive cells from retina at post natal day P2 rd1 mouse, replicate number 1


title: P6.WT.1

description: flow-sorted Nrl-GFP positive cells from retina at post natal day P6 wild-type mouse, replicate number 1


title: CD4+ Tn/mem-iPSC derived CD19-CAR T cells replicate #1

value: differentiated from iPSC and ex vivo expanded for 14 days by REM protocol, sorted cells


title: P6.rd1.1

description: flow-sorted Nrl-GFP positive cells from retina at post natal day P6 rd1 mouse, replicate number 1


title: P4.WT.2

description: flow-sorted Nrl-GFP positive cells from retina at post natal day P4 wild-type mouse, replicate number 2


title: P6.rd1.3

description: flow-sorted Nrl-GFP positive cells from retina at post natal day P6 rd1 mouse, replicate number 3


title: P4.WT.3

description: flow-sorted Nrl-GFP positive cells from retina at post natal day P4 wild-type mouse, replicate number 3


title: P4.rd1.1

description: flow-sorted Nrl-GFP positive cells from retina at post natal day P4 rd1 mouse, replicate number 1


title: KB1P spleen 5 [5289_13_KB1P_5_spleen]

city: Amsterdam

first: Roebi

middle: de

last: Bruijn

address: Plesmanlaan 121

country: Netherlands

institute: Netherlands Cancer Institute

data_processing:
library strategy: CNV-seq
A snakemake pipleine (https://github.com/jrderuiter/snakemake-cnvseq) was used to generate the counts using snakemake version 5.19.2 and wrapper version 0.60.0.
The input reads were trimmed to remove adapters and/or poor quality base calls using cutadapt version 2.5
The trimmed reads were aligned to the reference genome using bwa aln version 0.7.17
The alignments were sorted and indexed using samtools version 1.10
Bam files from multiple lanes were merged using samtools version 1.10
Picard MarkDuplicates was used to remove optical/PCR duplicates version 2.22.1
The final alignments are indexed using samtools index version 1.10
QDNAseq version 1.10 was used to generate copy number profiles/calls from the alignments
Genome_build: mm10
Supplementary_files_format_and_content: tab-delemited txt file sym_logratios.txt contains the logratios per gene for every sample
Supplementary_files_format_and_content: tab-delemited txt file sym_segments.txt contains the segmented logratios per gene for every sample
Supplementary_files_format_and_content: tab-delemited txt file sym_copies.txt contains the number of chromosomal copies per gene for every sample

source_name: spleen

extract_protocol:
Genomic DNA of ESCs and tumor samples was extracted by proteinase K lysis and organic extraction with phenol-chloroform.
For DNA sequencing, DNA libraries for Illumina sequencing were prepared by using the KAPA HTP Library Preparation Kit (KAPA Biosystems) according to the manufacturer’s instructions. The amount of dsDNA in the genomic samples was quantified by using the Qubit dsDNA HS Assay Kit (Invitrogen). As much as 250 ng of double-stranded genomic DNA was fragmented by Covaris shearing to obtain fragment sizes of 160–180 bp. Samples are purified using 1.8× Agencourt AMPure XP PCR Purification beads according to the manufacturer’s instructions (Beckman Coulter). The sheared DNA samples were quantified and qualified on the Agilent Technologies 2100 Bioanalyzer instrument by using the HS assay kit (Agilent Technologies). DNA library preparation for Illumina sequencing was performed by using the KAPA HTP Library Preparation Kit (KAPA Biosystems). During library enrichment, 10 PCR cycles were used to obtain enough yield for sequencing. After library preparation the libraries were cleaned up by using 1× AMPure XP beads. All DNA libraries were analyzed on a BioAnalyzer system by using DNA7500 chips (Agilent Technologies) to determine the molarity. As many as 10 uniquely indexed samples were mixed together by equimolar pooling, in a final concentration of 10 nM, and subjected to sequencing on an Illlumina HiSeq2000 machine in one lane of a single-read 50-bp run, according to the manufacturer’s instructions. Reads were aligned to the reference genome (hg19) by using the Burrows-Wheeler Alignment (BWA) backtrack algorithm (32) and counted in 20-kb nonoverlapping bins. These bin counts were corrected for GC bias using a loose fit. The “mappability” value of each bin is precomputed by summarizing the alignment results of all possible 51-mers from the reference sequence. A linear model intercepting 0 was used to fit the loess-corrected count data to the mappability values. The slope of this fit, multiplied with the mappability value for each bin, provides the bin’s reference value that is used to calculate the final log2 copy number ratios. Encyclopedia of DNA Elements (ENCODE) (33) blacklisted regions and bins with a mappability < 0.2 were excluded from the final dataset.

tag: histologic type

value: x

tag: percentage epithelial


title: CD8+ Tn/mem-iPSC derived CD19-CAR T cells replicate #1


title: L1363P spleen 6 [5289_25_L1363P_6_spleen]


title: CD8+ PBMC derived CD19-CAR T cells replicate #2

source_name: PBMC derived T lymphocyte

value: ex vivo expanded for 18 days, sorted cells


title: P4.WT.1

description: flow-sorted Nrl-GFP positive cells from retina at post natal day P4 wild-type mouse, replicate number 1


title: P6.WT.4

description: flow-sorted Nrl-GFP positive cells from retina at post natal day P6 wild-type mouse, replicate number 4


title: CD8+ Tn/mem-iPSC derived CD19-CAR T cells replicate #2


title: KP spleen 5 [5289_1_KP_5_spleen]

value: KP


title: CD4+ PBMC derived CD19-CAR T cells replicate #2


title: CD4+ PBMC derived CD19-CAR T cells replicate #1


title: Tn/mem-iPSC derived CD19-CAR  T cells replicate #2

value: differentiated from CD19-CAR+ iPSC and ex vivo expanded for 14 days by REM protocol


title: KP sample 50 [KP_50]

source_name: mammary tumor

value: sarcomatoid


title: KP sample 60 [KP_60]


title: KP sample 49 [KP_49]


title: Tn/mem-iPSC derived CD19-CAR T cells replicate #1


title: KP sample 57 [KP_57]


title: PBMC derived NK cells replicate #1

source_name: NK cell

value: NK cell

value: CD56+ enriched and ex vivo expanded for 14 days


title: Tn/mem-iPSC derived T cells replicate #2

value: differentiated from iPSC and ex vivo expanded for 14 days by REM protocol


title: PBMC derived NK cells replicate #2


title: KP sample 34 [KP_34]


title: Tn/mem-iPSC derived T cells replicate #1


title: KP sample 64 [KP_64]


title: KP sample 41.2 [KP_41_2]


title: KP sample 16 [KP_16]


title: KP sample 9.2 [KP_9_2]


title: PBMC derived CD19-CAR T cells replicate #1

description: 27383_cF12055-1_HD460_PBMC_derived_CD1928CART_S19

value: ex vivo expanded for 18 days


title: PBMC derived mock T cells replicate #1

description: 27381_cF12053-1_HD460_PBMC_derived_T_S17


title: KB2P sample 8 [KB2P8-N]

value: adenocarcinoma


title: KB2P sample 5 [KB2P5-N]


title: CD8+ PBMC derived CD19-CAR T cells replicate #1


title: iPSC clone B5.1

source_name: T cell derived iPS cells

value: induced pluripotent stem cells (iPSC)

value: non-treated iPSC

value: pluripotent stem cells


title: PBMC derived mock T cells replicate #2

description: 27382_cF12053-2_HD460_PBMC_derived_T_S18

value: T lymphocyte


title: KB2P sample 41 [KB2P41-N]


title: KB2P sample 38 [KB2P38-N]


title: KB2P sample 51 [KB2P51-N]


title: NIHAD9

city: New York

first: Seungyeul

last: Yoo

state: NY

address: 1425 Madison Avenue

department: Genetics and Genomic Sciences

institute: Icahn School of Medicine at Mount Sinai

data_processing:
The RNA sequencing reads were processed through a standard protocol for TopHat and Cufflinks (Trapnell, C., et al. Nat Protoc, 2012).
For reference genome and transcriptome, hg19 reference genome and UCSC refseq gtf files were downloaded (https://genome.ucsc.edu).
Genome_build: hg19 (GRCh37)
Supplementary_files_format_and_content: NIHAD_FPKM_normalized.txt: Tab-delimited text file includes FPKM values (log2) for each sample.

source_name: Lung adenocarcinoma

extract_protocol:
Tumor frozen sections were stained using 1% cresyl violet and were microscope guided needle dissected in an RNase free collection tip under vacuum suction to enrich for tumor >75% for further analysis. RNA quality was assessed by Agilent Bioanalyzer, and tumors with RIN values <7.0 were excluded. Total RNA (approximately 100-300 ng per sample) for each resected tumor sample was poly(A)-selected, fragmented, converted to cDNA and barcoded for multiplex sequencing on the Illumina HiSeq 2500.
RNA libraries were prepared for sequencing using standard Illumina protocols.

tag: Sex

value: Female

tag: tissue

value: Lung adenocarcinoma

tag: histology

value: SOL

tag: subtype

value: Invasive


title: NIHAD83

value: AIS

value: Indolent


title: iPSC clone M3

tag: cell type


title: KB2P sample 34 [KB2P34-N]


title: NIHAD87


title: NIHAD88

value: Male


title: PBMC derived CD19-CAR T cells replicate #2

description: 27384_cF12055-2_HD460_PBMC_derived_CD1928CART_S20

tag: treatment

value: lymphocyte lineage


title: NIHAD85


title: KB2P sample 46 [KB2P46-N]


title: KP sample 35.2 [KP_35_2]

value: KP

value: sarcomatoid


title: KB2P sample 36 [KB2P36-N]


title: NIHAD81


title: NIHAD80


title: KB2P sample 30 [KB2P30-N]


title: NIHAD8


title: KB2P sample 27 [KB2P27-N]


title: KB2P sample 25 [KB2P25-N]


title: KB2P sample 26 [KB2P26-N]


title: NIHAD74

value: LPA


title: NIHAD82


title: NIHAD71


title: NIHAD70


title: NIHAD69


title: KB2P sample 31 [KB2P31-N]


title: KB2P sample 18 [KB2P18-N]


title: KB2P sample 16 [KB2P16-N]


title: KB2P sample 3 [KB2P3-N]


title: NIHAD66


title: NIHAD75


title: NIHAD77


title: NIHAD62

value: AC


title: KB2P sample 2 [KB2P2-N]

value: adenocarcinoma


title: KB2P sample 23 [KB2P23-N]


title: NIHAD63


title: KB2P sample 24 [KB2P24-N]


title: NIHAD58


title: NIHAD67


title: KB2P sample 21 [KB2P21-N]


title: NIHAD53


title: KB1PM sample 7 [KB1PM7-N]


title: NIHAD68

value: PAP


title: KB1PM sample 8 [KB1PM8-N]


title: KB2P sample 13 [KB2P13-N]


title: KB2P sample 17 [KB2P17-N]


title: NIHAD73


title: KB2P sample 33 [KB2P33-N]


title: KB2P sample 10 [KB2P10-N]


title: NIHAD51

value: MP


title: KB1PM sample 3 [KB1PM3-N]


title: NIHAD64


title: KB1PM sample 4 [KB1PM4-N]


title: KB2P sample 12 [KB2P12-N]


title: NIHAD47

value: MIA


title: NIHAD61


title: KB1PM sample 9 [KB1PM9-N]


title: KB1P sample 9 [KB1P9-N]


title: KB1PM sample 2 [KB1PM2-N]


title: NIHAD52


title: KB1P sample 7 [KB1P7-N]


title: KB1P sample 5 [KB1P5-N]


title: NIHAD44


title: NIHAD48


title: KB1PM sample 11 [KB1PM11-N]


title: KB1PM sample 1 [KB1PM1-N1]


title: NIHAD49


title: NIHAD35

value: NX


title: NIHAD40

value: Female

value: indolent


title: KB1P sample 4 [KB1P4-N]


title: KB1PM sample 10 [KB1PM10-N]


title: KB1P sample 3 [KB1P3-N]


title: KB1PM sample 6 [KB1PM6-N]


title: NIHAD37

value: Lung adenocarcinoma


title: NIHAD36


title: NIHAD32


title: NIHAD45


title: NIHAD38


title: KB1P sample 13 [KB1P13-N]


title: NIHAD4

value: SOL

value: Invasive


title: NIHAD31

value: Indolent


title: NIHAD50


title: KB1P sample 1 [KB1P1-N]


title: KB1P sample 12 [KB1P12-N]


title: KB1P sample 11 [KB1P11-N]


title: NIHAD25


title: NIHAD29


title: KP sample 130.10A [5490_7_KP_130_10A]

value: carcinosarcoma


title: NIHAD20

value: Male


title: NIHAD30


title: KB1P sample 2 [KB1P2-N]


title: KB1P sample 6 [KB1P6-N]


title: KP sample 236.1 [5490_9_KP_236_1]

value: KP


title: KP sample 131.03A [5490_8_KP_131_03A]


title: NIHAD18


title: NIHAD10


title: NIHAD14


title: NIHAD21


title: NIHAD11


title: NIHAD15


title: L1363P sample 9.1 [5289_30_L1363P_9_1]

value: sarcomatoid


title: L1363P sample 53 [5490_2_19_BOU_005_53]


title: L1363P sample 52 [5490_1_19_BOU_004_52]


title: L1363P sample 54.1 [5490_3_19_BOU_006_1_54_1]


title: L1363P sample 7.1 [5289_36_L1363P_7_1]


title: KP sample 90.1 [5490_6_KP_90_1]


title: L1363P sample 54.2 [5490_4_19_BOU_006_2_54_2]


title: NIHAD1


title: NIHAD28

value: LPA


title: KP sample 89 [5490_5_KP_89]


title: U2OS-shARVCF_3+Nutlin

city: Sapporo

first: Masashi

last: Idogawa

country: Japan

institute: Sapporo Medical University

data_processing:
Illumina bcl2fastq v1.8.3 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg38 whole genome using HISAT2 v2.1.0
Each gene expression was quantified by Cuffquant v2.2.1 and normalized by Cuffnorm v2.2.1.

source_name: Osteosarcoma U2OS cells

growth_protocol: U2OS cells were cultured in DMEM with 10% FCS.

extract_protocol:
Total RNA was extracted by RNeasy mini kit (QIAGEN) according to manufacturer's protocol. RNA was quantified using the NanoDrop spectrophotometer and Agilent Bioanalyzer 2100.
RNA libraries were prepared for sequencing using TruSeq Stranded mRNA Sample Prep Kit and standard Illumina protocols.

treatment_protocol: U2OS cells were independently infected with lentiviruses whice express three different shRNAs targeting ARVCF or negative control shRNA, and these cells were cultured in media containing puromycin (1 ug/ml), and resistant cells were selected. Each single clone was treated with 10uM nutlin-3a for 24h.

tag: genotype/variation

value: U2OS cells stably expressing shRNA(3) targeting ARVCF

value: treated with 10uM nutlin-3a

tag: cell line


title: L1363P sample 6 [5289_6_L1363P_6]


title: L1363P sample 7.2 [5289_18_L1363P_7_2]

value: adenocarcinoma


title: U2OS-shCont+Nutlin_replicate2

value: U2OS cells stably expressing negative control shRNA


title: U2OS-shCont+Nutlin_replicate3


title: L1363P sample 43 [5289_32_L1363P_43]


title: U2OS-shARVCF_1+Nutlin

value: U2OS cells stably expressing shRNA(1) targeting ARVCF


title: L1363P sample 51 [5289_35_L1363P_51]


title: U2OS-shARVCF_2+Nutlin

value: U2OS cells stably expressing shRNA(2) targeting ARVCF


title: U2OS-shARVCF_3_no_treat

value: untreated


title: U2OS-shCont+Nutlin


title: L1363P sample 45 [5289_33_L1363P_45]


title: L1363P sample 41 [5289_24_L1363P_41]


title: L1363P sample 40.1 [5289_19_L1363P_40_1]


title: U2OS-shCont_no_treat


title: L1363P sample 29 [5289_12_L1363P_29]


title: L1363P sample 4 [5289_31_L1363P_4]


title: L1363P sample 37 [5289_23_L1363P_37]


title: U2OS-shARVCF_1_no_treat


title: L1363P sample 26.2 [5289_21_L1363P_26_2]


title: L1363P sample 26.1 [5289_20_L1363P_26_1]


title: L1363P sample 21.1 [5289_7_L1363P_21_1]


title: U2OS-shARVCF_2_no_treat


title: L1363P sample 20 [5289_11_L1363P_20]


title: L1363P sample 18 [5289_10_L1363P_18]


title: L1363P sample 17 [5289_9_L1363P_17]


title: L1363P sample 32 [5289_22_L1363P_32]


title: KP sample 40 [5289_26_KP_40]


title: KP sample 39 [5289_14_KP_39]


title: KB1P sample 5 [5289_4_KB1P_5]


title: S310

city: Houston

first: Shervin

last: Assassi

state: TX

address: 6431 Fannin

department: Division of Rheumatology

institute: The University of Texas Health Science Center at Houston

hyb_protocol: Fragmented Cy3-labeled cRNA was hybridized onto Agilent Human GE 44K V2 Microarray (Cat# G4845A, 4x44K) for 17 hrs at 65C with constant rotation (10 rpm).

scan_protocol: The slides were scanned using an Agilent microarray scanner.

data_processing: Data were examined for probes that were flagged by Agilent as non-uniform outliers.  Samples were excluded if >1% of probes for that sample were flagged.  Data were imported into BRB Array Tools (National Cancer Institute) as processed signal values, as recommended by Agilent.  Values were excluded if the mean signal was not significantly greater than background.  For genes with replicate probes, the average value of the replicates was used.  Values were then log2 transformed followed by quantile normalization.  Genes with >20% missing values across arrays were filtered out.

source_name: skin

label_protocol: Total RNA (100-200 ng) from each sample was reverse transcribed with Agilent spike RNA and amplification carried out using the one color Microarray-Based Gene Expression Analysis low RNA input quick amplification kit (Agilent).

growth_protocol: One 3-millimeter punch biopsy was obtained from the forearm skin.

extract_protocol: RNA was extracted using miRNeasy Mini kits (Qiagen) according to manufacturer’s instructions.

treatment_protocol: Sample was immersed in RNAlater solution (Qiagen).

tag: condition

value: systemic sclerosis patient

tag: subject

tag: sample number within subject

tag: age

tag: gender

value: Female

tag: race

value: White

tag: mrss at baseline sample

tag: diffuse at baseline sample

value: Limited

tag: disease duration

tag: anti-topoisomerase i

value: Negative

tag: anti-rna polymerase iii

tag: anti-centromere

value: Positive


title: S090

value: Hispanic

value: Diffuse


title: S330


title: S077


title: S249


title: S247


title: L1363P sample 10 [5289_8_L1363P_10]

tag: genotype

tag: histologic type

value: sarcomatoid

tag: percentage epithelial


title: S329


title: KB1P sample 47 [5289_34_KB1P_47]


title: KB1P sample 46.1 [5289_28_KB1P_46_1]


title: KP sample 5 [5289_2_KP_5]

value: KP

value: carcinosarcoma


title: KB1P sample 36.1 [5289_17_KB1P_36_1]


title: S308


title: S091


title: S309


title: S248


title: KB1P sample 30 [5289_16_KB1P_30]


title: S089


title: KB1P sample 19.1 [5289_27_KB1P_19_1]


title: S208


title: S209


title: S088


title: KB1P sample 49.1 [5289_29_KB1P_49_1]


title: KB1P sample 12 [5289_5_KB1P_12]


title: S130


title: KB1P sample 11.1 [5289_15_KB1P_11_1]


title: S128


title: S137


title: KB2P sample 8 RNA-seq [KB2P8-N]

data_processing:
A snakemake pipleine (https://github.com/jrderuiter/snakemake-rnaseq) was used to generate the counts using snakemake version 5.19.2 and wrapper version 0.63.0.
Cutadapt version 2.10 was used to trim the input reads for adapters and/or poor-quality base calls.
The trimmed reads were aligned to the reference genome using STAR version 2.7.3a.
The resulting alignments were sorted and indexed using sambamba version 0.6.6.
featureCounts version 2.0.0 was used to generate gene expression counts.
The merged counts were normalized for differences in sequencing depth (using DESeq's median-of-ratios approach) and log-transformed.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited txt-file named rnaseq.txt contains the raw read counts (samples by gene symbol)
Supplementary_files_format_and_content: tab-delimited txt-file named log2_norm_counts.txt contains the normalized and log-transformed counts (samples by gene symbol)

extract_protocol:
Total RNA was extracted using TRIzol reagent (Ambion Life Technologies) according to the manufacturer’s instructions.
For RNA sequencing, strand-specific sequencing libraries were generated by using the TruSeq Stranded mRNA sample preparation guide (Illumina) according to the manufacturer’s protocol. Strand-specific sequencing libraries were generated by using the TruSeq Stranded mRNA sample preparation guide (Illumina) according to the manufacturer’s instructions. Briefly, polyadenylated RNA from intact total RNA was purified by using oligo-dT beads. Following purification, the RNA was fragmented, random primed, and reverse transcribed by using SuperScript II Reverse Transcriptase (Invitrogen) with the addition of actinomycin D. Second-strand synthesis was performed by using polymerase I and RNaseH with replacement of dTTP for dUTP. The generated cDNA fragments were 3′-end adenylated and ligated to Illumina paired-end sequencing adapters and subsequently amplified by 12 cycles of PCR. The libraries were analyzed on a 2100 Bioanalyzer (Agilent) using a 7500 chip (Agilent) and diluted to 10 nM. The 10-nM RNAseq libraries were denatured and diluted in hybridization buffer (Illumina) to 7 pM concentrations and spiked (0.5%) with a standard PhiX library. Cluster generation was achieved in a c-Bot instrument (Illumina), and deep sequencing was done with a HiSeq2500 machine (Illumina).


title: KB2P sample 51 RNA-seq [KB2P51-N]


title: S136


title: KB2P sample 5 RNA-seq [KB2P5-N]


title: KB2P sample 46 RNA-seq [KB2P46-N]


title: KB1P sample 1 [5289_3_KB1P_1]


title: KB2P sample 34 RNA-seq [KB2P34-N]


title: KB2P sample 36 RNA-seq [KB2P36-N]


title: KB2P sample 38 RNA-seq [KB2P38-N]


title: KB2P sample 31 RNA-seq [KB2P31-N]


title: KB2P sample 3 RNA-seq [KB2P3-N]


title: KB2P sample 30 RNA-seq [KB2P30-N]


title: KB2P sample 27 RNA-seq [KB2P27-N]


title: KB2P sample 26 RNA-seq [KB2P26-N]


title: S235


title: S240


title: S241


title: S067

value: Male


title: S068


title: S069


title: S083


title: S058


title: S057


title: S059


title: S234


title: S081


title: S082


title: KB2P sample 23 RNA-seq [KB2P23-N]

value: adenocarcinoma


title: KB2P sample 21 RNA-seq [KB2P21-N]


title: KB2P sample 18 RNA-seq [KB2P18-N]


title: KB2P sample 41 RNA-seq [KB2P41-N]


title: S236


title: KB2P sample 17 RNA-seq [KB2P17-N]


title: KB2P sample 24 RNA-seq [KB2P24-N]


title: S267


title: KB2P sample 16 RNA-seq [KB2P16-N]


title: S266


title: KB2P sample 2 RNA-seq [KB2P2-N]


title: S017

value: Black


title: KB2P sample 12 RNA-seq [KB2P12-N]


title: KB2P sample 13 RNA-seq [KB2P13-N]


title: S268


title: S015


title: KB1PM sample 8 RNA-seq [KB1PM8-N]


title: S025


title: KB1PM sample 3 RNA-seq [KB1PM3-N]


title: S065


title: KB1PM sample 6 RNA-seq [KB1PM6-N]


title: KB2P sample 10 RNA-seq [KB2P10-N]


title: KB1PM sample 11 RNA-seq [KB1PM11-N]


title: S198


title: KB1PM sample 10 RNA-seq [KB1PM10-N]


title: KB1PM sample 9 RNA-seq [KB1PM9-N]


title: WBCs, BDB1P04082

tag: disease state

value: non-muscle-invasive bladder cancer (NMIBC)

value: male

tag: ten year-recurrence or death

value: Yes

tag: cell type

value: White blood cell


title: KB1PM sample 1 RNA-seq [KB1PM1-N]


title: S172

tag: condition

value: systemic sclerosis patient

tag: subject

value: Female


title: S24-

tag: sample number within subject

tag: age


title: S033

tag: gender

tag: race

value: White


title: S064

tag: mrss at baseline sample

tag: diffuse at baseline sample

value: Limited

value: Negative


title: S032

tag: disease duration

tag: anti-topoisomerase i


title: S229

tag: anti-rna polymerase iii

tag: anti-centromere


title: S182

value: Hispanic

value: Positive


title: S170


title: S066


title: KB1PM sample 2 RNA-seq [KB1PM2-N]

tag: genotype

tag: histologic type


title: KB1P sample 7 RNA-seq [KB1P7-N]

tag: percentage epithelial


title: KB1P sample 6 RNA-seq [KB1P6-N]


title: KB1P sample 4 RNA-seq [KB1P4-N]


title: KB1P sample 5 RNA-seq [KB1P5-N]


title: KB1PM sample 7 RNA-seq [KB1PM7-N]


title: KB1P sample 3 RNA-seq [KB1P3-N]


title: KB1P sample 9 RNA-seq [KB1P9-N]


title: KB1PM sample 4 RNA-seq [KB1PM4-N]


title: KB1P sample 11 RNA-seq [KB1P11-N]


title: S227


title: S228


title: S147


title: S146


title: S181

value: Diffuse


title: S171


title: KB1P sample 1 RNA-seq [KB1P1-N]


title: KB1P sample 2 RNA-seq [KB1P2-N]


title: L1363P sample 9.1 RNA-seq [5625_26_L1363P_9_1]

value: sarcomatoid


title: S337


title: S016


title: S099


title: S056


title: KB1P sample 12 RNA-seq [KB1P12-N]


title: KB1P sample 13 RNA-seq [KB1P13-N]


title: KP sample 130.10A RNA-seq [5625_21_KP_16-KDV-130-10A]

value: KP

value: carcinosarcoma


title: L1363P sample 21.1 RNA-seq [5625_22_L1363P_21_1]


title: KP sample 40 RNA-seq [5625_29_KP_16_BUR_040]

value: adenocarcinoma


title: S054

value: Male


title: S180


title: KP sample 5 RNA-seq [5625_27_KP_16_BUR_005]


title: S336


title: S145


title: S158


title: S169


title: S258

value: Asian


title: S100


title: S335


title: S101


title: KP sample 39 RNA-seq [5625_28_KP_16_BUR_039]


title: L1363P sample 40.1 RNA-seq [5625_25_L1363P_40_1]


title: L1363P sample 37 RNA-seq [5625_17_L1363P_37]


title: L1363P sample 18 RNA-seq [5625_23_L1363P_18]


title: L1363P sample 4 RNA-seq [5625_24_L1363P_4]


title: L1363P sample 43 RNA-seq [5625_19_L1363P_43]


title: L1363P sample 32 RNA-seq [5625_16_L1363P_32]


title: L1363P sample 29 RNA-seq [5625_15_L1363P_29]


title: L1363P sample 20 RNA-seq [5625_14_L1363P_20]


title: KP sample 26.02A RNA-seq [5625_20_KP_17-KDV-026-02A]


title: L1363P sample 10 RNA-seq [5625_12_L1363P_10]


title: L1363P sample 41 RNA-seq [5625_18_L1363P_41]


title: S257


title: S302


title: S020


title: L1363P sample 17 RNA-seq [5625_13_L1363P_17]


title: L1363P sample 54.1 RNA-seq [5625_9_L1363P_54_1_19-6]


title: S055


title: S256


title: S021


title: S167


title: L1363P sample 54.2 RNA-seq [5625_10_L1363P_54_2_19-6_2]


title: S225


title: S021-2


title: L1363P sample 45 RNA-seq [5625_6_L1363P_45]


title: S226


title: S168


title: KP sample 131.03A RNA-seq [5625_11_KP_16-KDV-131-03A]


title: S300


title: S301


title: S224


title: KP sample 89.01A RNA-seq [5625_3_KP_17-KDV-089-01A]


title: L1363P sample 53 RNA-seq [5625_8_L1363P_53_19-5]


title: L1363P sample 7.2 RNA-seq [5625_2_L1363P_7_2]


title: S201


title: L1363P sample 6 RNA-seq [5625_1_L1363P_6]


title: S112

value: Black


title: S327


title: Inguinal white adipose tissue Raptor WT + rosiglitazone Replicate 3

city: Boston

first: NORC

last: Boston

state: MA

address: 3 Blackfan Circle, CLS0733

institute: Beth Israel Deaconess Medical Center

data_processing:
Transcripts from the GCRm38/mm10 mouse transcriptome were quantified by quasi-mapping sequencing reads using Salmon
Transcript counts were merged into gene counts using the tximport library
Normalization and analysis of variance (ANOVA) were performed using EdgeR
Gene set enrichment analysis was performed using ShinyGO
Genes were considered significant if they passed a false discovery rate (FDR) cutoff of FDR < 0.05.
Genome_build: GRCm38/mm10 mouse transcriptome
Supplementary_files_format_and_content: Raw quants tsv files

source_name: Inguinal white adipose tissue

extract_protocol:
Inguinal white adipose tissue were removed, flash frozen on dry ice, and RNA was harvested using Trizol reagent. Illumina Nextera XT DNA Library Preparation Kit (FC-131-1096) was used for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: 8 weeks old Raptor floxed (WT) or Raptor KO were fed a high fat diet supplemented or not with rosiglitazone (30mg/kg/day) during 8 weeks

tag: strain

tag: tissue

value: Inguinal white adipose tissue

value: 16 weeks

value: Raptor floxed

tag: treatment

value: high fat diet


title: S326

tag: condition

value: systemic sclerosis patient

tag: subject

value: Female


title: S328

tag: sample number within subject

tag: age

value: Negative


title: KP sample 90.01A RNA-seq [5625_4_KP_17-KDV-090-01A]


title: S200

tag: gender

tag: race

value: White


title: S179

value: Hispanic

tag: mrss at baseline sample

tag: diffuse at baseline sample

value: Positive


title: S110

value: Diffuse

tag: disease duration

tag: anti-topoisomerase i


title: Inguinal white adipose tissue Raptor WT + rosiglitazone Replicate 1


title: Inguinal white adipose tissue Raptor WT + rosiglitazone Replicate 2


title: S202

tag: anti-rna polymerase iii

tag: anti-centromere


title: L1363P sample 52 RNA-seq [5625_7_L1363P_52_19-4]

tag: genotype

tag: histologic type


title: L1363P sample 26.2 RNA-seq [5625_5_L1363P_26_2]

tag: percentage epithelial


title: Inguinal white adipose tissue Raptor WT Replicate 1

tag: strain

tag: tissue

value: high fat diet + rosiglitazone


title: Inguinal white adipose tissue Raptor WT Replicate 3

tag: treatment


title: S177

tag: condition

tag: subject


title: Inguinal white adipose tissue Raptor WT Replicate 2

tag: age


title: S255

tag: sample number within subject

tag: gender

value: Limited


title: S274

tag: race

tag: mrss at baseline sample


title: Inguinal white adipose tissue Raptor KO + rosiglitazone Replicate 3

value: Raptor floxed adiponectin Cre positive


title: S111

tag: diffuse at baseline sample

tag: disease duration


title: S275

tag: anti-topoisomerase i

tag: anti-rna polymerase iii


title: S273

tag: anti-centromere


title: Inguinal white adipose tissue Raptor KO + rosiglitazone Replicate 2

tag: genotype


title: S178


title: S254


title: Inguinal white adipose tissue Raptor KO Replicate 2


title: S253


title: Inguinal white adipose tissue Raptor KO + rosiglitazone Replicate 1


title: wt_7

city: Kansas City

first: Chris

middle: W

last: Seidel

state: MO

department: Genomics

institute: Stowers Institute

data_processing:
Following sequencing, Illumina RTA 1.18.61.0 and CASAVA-1.8.2 were used to generate FASTQ files.
FASTQ files were aligned to mm10 using STAR under default parameters and --quantMode with gene models from Ensembl 98 to generate gene counts.
Genome_build: mm10
Supplementary_files_format_and_content: text file with Transcripts Per Million (TPM)

source_name: vagal region of E9.5 embryo

extract_protocol:
Total RNA was extracted using a Qiagen RNEasy kit according to the manufacturer’s protocol, and analyzed on the Agilent 2100 BioAnalyzer.
Poly-A stranded RNA-Seq libraries were created using the TruSeq Stranded mRNA Library Preparation Kit Set A from Illumina (Catalog #RS-122-2101).

treatment_protocol: The vagal (somite 1-7) region was extracted from stage E9.5 mouse embryos.

value: wt

tag: replicate

value: vagal region of embryo

tag: developmental stage


title: wt_8

tag: tissue


title: Inguinal white adipose tissue Raptor KO Replicate 1

tag: strain

tag: treatment


title: trex_4

value: Rdh10(trex/trex) mutant


title: wt_6


title: wt_5


title: trex_3


title: S098

tag: condition

tag: subject


title: trex_2


title: S97-

tag: sample number within subject

tag: age


title: S096

tag: gender

tag: race


title: trex_1


title: S215

value: Black

tag: mrss at baseline sample

tag: diffuse at baseline sample


title: S216

tag: disease duration

tag: anti-topoisomerase i


title: S127

tag: anti-rna polymerase iii

tag: anti-centromere


title: S125


title: S124


title: S126


title: KOChalle_2

city: London

first: Miguel

last: Muñoz-Ruiz

address: 1 Midland Rd, Somers Town

country: United Kingdom

institute: The Francis Crick institute

data_processing:
Adaptor removal and quality trimming done with Trimmomatic v 0.36
Read alingment and gene counts was performed with RSEM v 1.2.31 and STAR v 2.5.2a
Differential expression analysis was carried out with DESeq2 package ( version 1.20.0 ) with R version 3.5.1
Genome_build: Ensembl GRCm38 release 86
Supplementary_files_format_and_content: Tab-delimited text include normalized counts per gene and per sample (generated by DESeq2).

source_name: γδT cell

extract_protocol:
To analyze epidermal T cell populations, separate epidermal cell suspensions were prepared as described(Mallick-Wood et al., 1998) from ears or back skin of individual animals.
 libraries were prepared using the NEBNext Single Cell / Low Input RNA Library Prep kit.  RNA was quantified using the Agilent TapeStation High Sensitivity Screen Tape and Promega Glomax.  RNA was normalized to 5 ng and prepared into libraries according to manufacturer’s instructions.

treatment_protocol: To induce allergic contact dermatitis (ACD), mice were sensitized on day 0 by epicutaneous application to razor-shaved abdominal skin of 40 μl of 0.5% DNFB in a mixture of acetone:olive oil (3:1). On day 6, mice were challenged (1st Challenge) by applying 20 μl of 0.25% DNFB in acetone:olive oil at the back skin of ear.

tag: cell type

value: Epidermal gamma delta T cells

tag: background strain

tag: genotype

value: IFNg RI -/-

value: treated


title: WTChalle_3

value: WT


title: KOChalle_3


title: KOChalle_1


title: WTChalle_2


title: KOcontrol_3

value: untreated


title: S151

value: systemic sclerosis patient

value: Female

value: Negative


title: WTChalle_1


title: S334

value: White

value: Positive


title: S152

value: Diffuse


title: S153


title: S333

value: Limited


title: KOcontrol_1


title: S332


title: S190


title: WTcontrol_3


title: S085

value: Hispanic


title: S087


title: S189


title: WTcontrol_2


title: S197


title: KOcontrol_2


title: Casz1_cKO_ChIPseq_H3K27me3

city: Ottawa

first: Pierre

last: Mattar

state: ON

address: CCW6109, Box 511, 501 Smyth Rd.

country: Canada

institute: OHRI

description: ChIP-seq

data_processing:
Fastq groomer (Galaxy)
Bowtie2 (Galaxy)
bamCoverage (Deeptools; Galaxy)
MACS2 (Galaxy)
Interval to Bed (Galaxy)
Genome_build: mm10
Supplementary_files_format_and_content: BAM, bedGraph, bed

source_name: Microdissected retina tissue

growth_protocol: For Chip-seq, Casz1 cKO tissue was isolated from peripheral retinas using epifluorescence. For ATAC-seq, retinal explants were transfected with expression plasmids encoding GFP alone, or GFP with Cre. After 2 days ex vivo, retinal explants were dissociated, and 50 000 cells per replicate were sorted by flow cytometery using EGFP epifluorescence. Propidium iodide staining was used to exclude non-viable cells. Two experiments were run independently on different days.

extract_protocol:
For ChIP-seq, tissue samples were fixed in 1% formaldehyde for 10 minutes, nuclei were extracted and lysed, and chromatin was sheared to ~300 bp average length. Immunoprecipitations were performed using antibodies to H3K27ac (Abcam AB4729) or H3K27me3 (Millipore 07-449), coupled to Dynal Protein A dynabeads (Invitrogen). For ATAC-seq, tagmentation was performed using the Nextera DNA Libarary Preparation kit (Illumina). 12.5 microlitres of Tn5 enzyme was incubated with the cells for 30 minutes at 37 degrees.
Libraries were prepared according to the Illumina protocol.
Illumina HiSeq 2500 (paired ends)

tag: strain

tag: tissue

value: retina

value: Casz1 cKO


title: control_ChIPseq_H3K27me3

description: ChIP-seq

value: wild type


title: Casz1_cKO_ChIPseq_H3K27ac

description: ChIP-seq


title: S196

tag: condition

value: Black


title: S044

tag: subject

value: Male


title: WTcontrol_1

value: Epidermal gamma delta T cells

tag: treatment


title: S042

tag: sample number within subject

tag: age


title: S086

tag: gender

tag: race


title: control_ChIPseq_H3K27ac

description: ChIP-seq


title: S043

tag: mrss at baseline sample

tag: diffuse at baseline sample


title: S195

tag: disease duration

tag: anti-topoisomerase i


title: Casz1_cKO_ChIPseq_Input

description: Input chromatin


title: Total RNA from DBTRG-05MG cell line, after interferon treatment, rep 3

city: Moscow

first: Anastasia

last: Nikitina

address: Malaya Pirogovskaya

department: Department of Molecular Biology and Genetics

country: Russia

institute: Federal Research and Clinical Center of Physical-Chemical Medicine of FMBA of Russia

data_processing:
RNA-Seq reads were mapped to human genome (version hg19) using STAR with option “--outFilterIntronMotifs RemoveNoncanonical” to remove the non-canonical splice junctions.
Option “--quantMode GeneCounts” was used to count the number of reads overlapping annotated regions. The human genome annotation was obtained from GENCODE (Release 19, GRCh37.p13).
Bioconductor package edgeR was used to normalize gene counts to library size to obtain count per million reads (CPMs).
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include raw counts  for each sample
Supplementary_files_format_and_content: matrix table with CPM values for every gene expressed in dataset and every sample

source_name: glioblastoma cell line

growth_protocol: Cells were grown in DMEM medium (PanEco, Moscow, Russia) supplemented with 10% fetal bovine serum (Gibco, Thermo Fisher Scientific, Waltham, MA, USA).

extract_protocol:
Total RNA was extracted from 1.5 million cells ffor each sample using an RNeasy mini kit (Qiagen, Germany).
PolyA transcriptomic libraries were constructed from mRNA isolated using oligo(dT)-attached magnetic beads.

treatment_protocol: 6 samples were treated with IFN α-2b at concentration of 100 units/ml for 24 hours

value: glioblastoma cell line

tag: cell line

value: treated with IFN alpha-2b at concentration of 100 units/ml for 24 hours


title: S008

tag: anti-rna polymerase iii

tag: anti-centromere


title: control_ChIPseq_Input

description: Input chromatin

tag: genotype


title: Total RNA from DBTRG-05MG cell line, after interferon treatment, rep 2


title: S007


title: S006


title: Total RNA from DBTRG-05MG cell line, after interferon treatment, rep 1


title: Casz1_cKO_ATACseq_rep2

description: ATAC-seq

source_name: Flow sorted GFP+ retinal cells

tag: strain

value: post natal day 2


title: Total RNA from DBTRG-05MG cell line, no treatment, rep 1

tag: tissue

value: no


title: Total RNA from DBTRG-05MG cell line, no treatment, rep 2


title: Total RNA from HOS cell line, after interferon treatment, rep 3

source_name: osteosarcoma cell line

value: osteosarcoma cell line

value: HOS


title: Total RNA from DBTRG-05MG cell line, no treatment, rep 3


title: Total RNA from HOS cell line, after interferon treatment, rep 2


title: Casz1_cKO_ATACseq_rep1

description: ATAC-seq


title: S144

tag: condition

value: systemic sclerosis patient

value: Female

value: White

value: Negative


title: Total RNA from HOS cell line, after interferon treatment, rep 1


title: S142

tag: subject

value: Limited

value: Positive


title: control_ATACseq_rep2

description: ATAC-seq

value: retina


title: S063

value: Hispanic


title: Total RNA from HOS cell line, no treatment, rep 3

tag: treatment


title: control_ATACseq_rep1

description: ATAC-seq

value: wild type


title: Lactate_IgG

city: Wuhan

first: Li-quan

last: Zhou

state: Hubei

address: 13 Hangkong road

department: Tongji Medical College

institute: Huazhong University of Science and Technology

data_processing:
Library strategy: CUT&TAG
Raw reads were processed with cutadapt v1.8.1 to remove adapters and perform quality trimming.
Trimmed reads were mapped to the UCSC mm10 assembly using Bowtie2 with default parameters.
Genome_build: mm10
Supplementary_files_format_and_content: Bigwig files were generated for data visualization.

source_name: embryonic stem cell

growth_protocol: The mouse ESC line AB2.2 was cultured on mouse embryonic fibroblast (MEF) feeder cells with ES cell medium supplemented with 15% fetal bovine serum, 1000 U/ml leukemia inhibitory factor, 3 μM CHIR99021 and 1 μM PD0325901.

extract_protocol:
We used Hyperactive In-Situ ChIP Library Prep Kit for library preparation.
Libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: 50mM lactate was added and maintained for 24h before experimental procedures.

tag: cell type

value: embryonic stem cell AB2.2

value: Lactate treatment

tag: antibody

value: IgG, ab6702, Abcam


title: Total RNA from HOS cell line, no treatment, rep 2


title: S143

tag: sample number within subject

tag: age

tag: gender


title: Total RNA from HOS cell line, no treatment, rep 1


title: AB22_IgG

value: Control


title: In Vitro Pax7GFP MPCs-rep2

city: Suwon

first: Su Bin

last: Lim

state: Gyeonggi-do

address: Worldcup-Ro 164, Yeongtong-Gu

country: South Korea

institute: Ajou University School of Medicine

description: Myogenic progenitors derived from PAX7::GFP hESC

data_processing:
bcl2fastq v2.20.0.422
Raw data (FASTQ files) were imported into Altanalyze v2.1.4 software, which uses the embedded software Kallisto and Ensembl 72 annotations
Genome_build: hg19
Supplementary_files_format_and_content: processed_data.txt (Processed read counts generated by Altanalyze v2.1.4 software)

source_name: In Vitro Pax7GFP MPCs

growth_protocol: PAX7::GFP MPCs were derived from PAX7::GFP hESC and maintained in N2 medium supplemented with 10%FBS,  FGF2 and FGF8.

extract_protocol:
Trizol/chloroform aqueous layer combined with 1.5X 100% EtOH and transferred to Qiagen Rneasy Mini column.  Followed manufacturer's recommendations for Qiagen Rneasy extraction.
Takara SMARTseq v4 Ultra Low Input RNA

treatment_protocol: PAX7::GFP MPCs were transplanted into TA muscle of NSG mice and isolated via FACS after 1 month with GFP signal. The PAX7::GFP MPCs were cultured for 4 more days before seqencing.

value: In Vitro Pax7GFP MPCs


title: S061

value: Male

tag: race

tag: mrss at baseline sample

tag: diffuse at baseline sample


title: Lactate_PolII rep2

value: RNA polII, 39097, Active Motif


title: In Vivo Pax7GFP MPCs-rep2

source_name: In Vivo Pax7GFP MPCs

value: In Vivo Pax7GFP MPCs


title: Lactate_PolII rep1


title: AB22_PolII rep1


title: Lactate_H3K4me3 rep2


title: S062

value: systemic sclerosis patient

tag: disease duration

tag: anti-topoisomerase i


title: 204900610024_R04C01

city: Lund

first: Petter

last: Storm

address: Sölvegatan 19, BMC A11

department: Developmental and Regenerative Neurobiology

country: Sweden

institute: Lund University

hyb_protocol: According to the manufacturers instructions

data_processing: Illumina Beadstudio and R/minfi

label: Cy3, Cy5

source_name: genomic DNA from HD2

label_protocol: Bisulfite conversion was performed using the EZ DNA MethylationTM Kit from Zymo Research. Product No: D5004 with 250 ng of DNA per sample. The bisulfite converted DNA was eluted in 15μl according to the manufacturer´s protocol, evaporated to a volume of <4μl, and used for methylation analysis using the Illumina Methylation EPIC array.

growth_protocol: All cell culture work on fibroblasts cells and direct neuronal conversion was perfomed as described before (Drouin-Ouellet J, Lau S, Brattås PL, Rylander Ottosson D, Pircs K, Grassi DA, et al. REST suppression mediates neural conversion of adult human fibroblasts via microRNA-dependent and -independent pathways. EMBO Mol Med. 2017;9(8):1117-31.)

extract_protocol: Total DNA was extracted from all samples with DNeasy Blood & Tissue Kits Print (Qiagen) according to manufacturer’s protocol.

treatment_protocol: Induced neurons collected after 28 days of conversion.

tag: disease status

value: Huntington’s disease

value: M


title: In Vitro Pax7GFP MPCs-rep1


title: S188

value: Female

value: White

value: Diffuse

value: Negative

tag: anti-rna polymerase iii

tag: anti-centromere


title: In Vivo Pax7GFP MPCs-rep1


title: Lactate_H3K4me3 rep1


title: 6000_rep2

city: San Francisco

first: Fiorella

middle: Carla

last: Grandi

address: 1650 Owens Street

institute: Gladstone

description: processed TSS metric in Sup. Fig.  4

data_processing:
Pepatac
Custom peak merging script found here: https://github.com/corceslab/ATAC_IterativeOverlapPeakMerging
TSS enrichment was calculated using PEPATAC and used to determine library quality.
Genome_build: hg38
Supplementary_files_format_and_content: bigwig files were generated from bam files using a custom script

growth_protocol: cells were grown in RPMI media with 10% FBS and 1/ P/S according to guidelines from ATCC

extract_protocol:
Cells were lyzed in ATAC-seq lysis buffer and processed as detailed in the corresponding protocol paper and described in Corces 2017.
Libraries were constructed as detailed in the corresponding protocol paper

tag: cell line

value: b-lymphocyte

tag: input cell no.


title: S186

tag: condition

tag: subject


title: 204900610024_R08C01

scan_protocol: According to the manufacturers instructions

source_name: genomic DNA from HD5


title: 204894630096_R02C01

source_name: genomic DNA from HD7


title: 204894630096_R01C01

source_name: genomic DNA from HD6


title: Lactate_H3K18la rep1

tag: cell type

tag: treatment

value: Anti-H3K18 Lactylation, PTM-1406RM, PTM BIO


title: AB22_H3K4me3 rep1

value: embryonic stem cell AB2.2

tag: antibody


title: 500000_rep2

description: processed TSS metric in Sup. Fig.  4


title: 204894630096_R06C01

source_name: genomic DNA from HD10

tag: age


title: 500000_rep1

description: processed TSS metric in Sup. Fig.  4


title: 204894630096_R03C01

source_name: genomic DNA from HD8

tag: gender

value: F


title: 204425700045_R07C01

source_name: genomic DNA from C9

value: Healthy


title: 204425700080_R06C01

source_name: genomic DNA from C6


title: 204900610024_R05C01

source_name: genomic DNA from HD3


title: AB22_H3K18la rep1

value: Control


title: 6000_rep1

description: processed TSS metric in Sup. Fig.  4


title: Lactate_H3K18la rep2

value: Lactate treatment


title: AB22_H3K4me3 rep2


title: 50000_rep5

description: processed TSS metric in Sup. Fig.  4


title: lactate treatment rep1

data_processing:
Raw reads were processed with Cutadapt v1.16. Trimmed reads were mapped to mouse genome using STAR with default settings.
RSEM was used to calculate FPKM values.
Genome_build: mm10
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

extract_protocol:
Total RNA of mouse ESCs was harvested using Trizol reagent, and Illumina TruSeq RNA Sample Prep Kit was used for construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols


title: AB22_H3K18la rep2


title: AB22_PolII rep2


title: 50000_rep6

description: processed TSS metric in Sup. Fig.  4


title: lactate treatment rep2


title: AB22 rep2


title: AB22 rep1


title: 50000_rep4

description: processed TSS metric in Sup. Fig.  4


title: 50000_rep2

description: processed TSS metric in Sup. Fig.  4


title: 50000_rep1

description: processed TSS metric in Sup. Fig.  4


title: 204900610024_R02C01

source_name: genomic DNA from HD1


title: D30-3

city: Tai’an

first: Chao

last: Tianle

state: Shandong

address: Daizong street, no. 61, 6/5000 Shandong Agricultural University

institute: 6/5000 Shandong Agricultural University

data_processing:
Paired-end RNA-seq sequencing library was sequenced with the Illumina Hiseq 4000.
The raw paired-end reads were trimmed and quality controlled by fastp (version 0.18.0)
Clean reads were separately aligned to the Apis mellifera genome Amel_HAv3.1 with orientation mode using HISAT2 (version 2.1.0) software. The mapped reads of each sample were assembled by StringTie (https://ccb.jhu.edu/software/stringtie/index.shtml?t=example) in a reference-based approach.
The expression level of each genes was calculated according to fragments per kilobases per million reads (FPKM) method.
Genome_build: Amel_HAv3.1
Supplementary_files_format_and_content: Tab-delimited text files include gene FPKM values for each Sample

organism: Apis mellifera ligustica

source_name: A.mellifera ligustica brain

extract_protocol:
The royal jelly glands and pigments were removed from the brain, and the brain tissue was immediately stored in RNA preservation solution.Total RNA of each sample were extracted with Trizol.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: A.mellifera ligustica with similar group potential and randomly divided them into two sets (3 replicates in each group). One set as control groups, and the other set as test groups. The test groups were exposed to fluvalinate at a normal dosage for administration to honeybees (according to the instructions for use of the medicine, mite treatment was added every 7 days). The sequencing is performed by the Illumina HiSeq TM 2500.

tag: tissue

value: brain

tag: timepoint

value: 30 days after fluvalinate exposure


title: Islet_GFP_2

first: Youngjae

last: Bahn

state: Maryland

address: 10 Center Dr.

data_processing:
Raw data (raw reads) of FASTQ format were firstly processed through fastp.
Single-end clean reads were aligned to the reference genome using the Spliced Transcripts Alignment to a Reference (STAR) software.
FeatureCounts was used to count the read numbers mapped of each gene. RPKM (Reads Per Kilobase Million) of each gene was calculated based on the length of the gene and the reads count mapped to that gene.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each gene and differential gene expression (DESeq2)

source_name: Islet

extract_protocol:
Total RNA was extracted from isolated mouse pancreatic islet cells, using RNAqueous Micro Total RNA isolation Kit (ThermoFisher). RNA integrity and quantitation were assessed using the RNA Nano 6000 Assay Kit and a Bioanalyzer 2100 system (Agilent Technologies, CA, USA).
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: PVNOXT:TeNT and PVNOXT:GFP mice were fasted for 24 hours (2 p.m. to 2 p.m.)

value: Pancreas (islet)

tag: strain

tag: animal

value: PVNOXT:GFP mice


title: Islet_TeNT_2

value: PVNOXT:TeNT mice


title: Islet_GFP_3


title: Islet_TeNT_3


title: 50000_rep3

description: processed TSS metric in Sup. Fig.  4


title: Islet_GFP_1


title: 250000_rep2

description: processed TSS metric in Sup. Fig.  4


title: S050

source_name: skin

value: systemic sclerosis patient

tag: sample number within subject

value: Male

tag: race

tag: mrss at baseline sample

tag: diffuse at baseline sample

value: Limited

tag: disease duration

tag: anti-topoisomerase i


title: S338

tag: condition

value: Female

value: White

value: Diffuse

tag: anti-rna polymerase iii

tag: anti-centromere

value: Positive


title: Islet_GFP_4


title: Islet_TeNT_1


title: 204900610024_R07C01

source_name: genomic DNA from HD4

tag: disease status

value: Huntington’s disease


title: S051

tag: subject

value: Negative


title: S231

tag: age

value: Hispanic


title: Islet_TeNT_4


title: D10-3

value: 10 days after fluvalinate exposure


title: S232

tag: gender


title: 204425700045_R08C01

source_name: genomic DNA from C5

value: Healthy

value: F


title: S339


title: 25000_rep4

description: processed TSS metric in Sup. Fig.  4

tag: cell line

tag: cell type

value: b-lymphocyte

tag: input cell no.


title: 204425700080_R03C01

source_name: genomic DNA from C3


title: S187


title: S340


title: D10-2

tag: tissue

value: brain

tag: timepoint


title: D20-1

value: 20 days after fluvalinate exposure


title: S149

tag: sample number within subject

tag: race

value: Black


title: CK3

value: 1 day before fluvalinate exposure


title: CK1


title: CK2


title: 204425700080_R05C01

source_name: genomic DNA from C1

value: M


title: D30-1

value: 30 days after fluvalinate exposure


title: D30-2


title: 250000_rep1

description: processed TSS metric in Sup. Fig.  4


title: D20-3


title: 25000_rep1

description: processed TSS metric in Sup. Fig.  4


title: S325

value: systemic sclerosis patient

value: Female

tag: mrss at baseline sample

tag: diffuse at baseline sample

value: Limited


title: S150

value: Diffuse

tag: disease duration

tag: anti-topoisomerase i

value: Positive


title: S299

tag: condition

value: White

value: Negative

tag: anti-rna polymerase iii


title: S148

tag: anti-centromere


title: 204425700080_R07C01

source_name: genomic DNA from C2

tag: disease status


title: HD-corrected_iBMEC_2

city: BALTIMORE

first: Peter

middle: C

last: Searson

address: 3400 North Charles Street

institute: Johns Hopkins University

data_processing:
Alignment and quantification to reference genome (GRCh38) was performed using Rsubread (v2.0.1)
Fragments Per Kilobase of transcript per Million fragments mapped (FPKM) values were computed according to Trapnell et al., Nature Biotechnology, 2010. For every gene, one meta-transcript was created by merging the exons from all isoforms of that gene. Next, for each sample, the total number of unique paired-end reads mapped to each meta-transcript was tallied and normalized by the size of the meta-transcript, as well as by the size of the library.
Normalization, visualization, and differential analysis was performed using DESeq2 (v1.28.1)

source_name: HD-corrected iBMEC

growth_protocol: Cell culture was conducted at 5% CO2 and 37 °C. iPSC samples were passed onto Matrigel-coated plates at 10,000 cells/cm^2 and grown for three days in mTESR1 with daily media switches.  iBMECs were differentiated using sequential treatment of day 3 iPSC colonies with unconditioned media without bFGF (for six days) and endothelial media (for two days).  Unconditioned media without bFGF: DMEM/F12 supplemented with 20% knockout serum replacement, 1% non-essential amino acids, 0.5% GlutaMAX, and 0.836 μM beta-mercaptoethanol. Endothelial media: human endothelial cell serum-free medium supplemented with 1% human platelet poor derived serum, 2 ng/mL bFGF, and 10 μM all-trans retinoic acid.

extract_protocol:
iBMECs were subcultured at the end of the differentiaiton on six-well plates coated with 50 μg/mL human placental collagen IV and 25 μg/mL fibronectin from human plasma in endothelial media supplemented with 1% penicillin-streptomycin and 10 μM ROCK inhibitor Y27632.  After one hour, media was switched for an additional 24 hours in the same media, before switching to human endothelial serum free media supplemented with 1% penicillin-streptomycin and 10 mM ROCK inhibitor after another 24 hours. At day 2 of subculture (for iBMECs) or day 3 of culture for iPSCs, cells were washed with 1x PBS and lysed using RLT buffer supplemented with β-mercaptoethanol, before isolating RNA using a RNeasy Mini Kit (Qiagen) with DNase I digestion (Qiagen).
RNA libraries were prepared for sequencing using standard Illumina protocols conducted by Novogene.

value: iBMEC

tag: cag length


title: S324

tag: subject

tag: age

tag: gender


title: HD-corrected_iBMEC_1

tag: cell type


title: D20-2

tag: tissue


title: 25000_rep3

description: processed TSS metric in Sup. Fig.  4

tag: cell line

tag: input cell no.


title: 25000_rep2

description: processed TSS metric in Sup. Fig.  4


title: 12000_rep1

description: processed TSS metric in Sup. Fig.  4


title: A255

first: Daylon

last: James

address: 515 East 71st

institute: Weill Cornell Medicine

data_processing:
fastq files were processed using CellRangr count and individual libraries were aggregated using CellRangr aggr
Resultant features/barcodes file was imported into R Studio and used to generate a Seurat Object in Seurat
Genome_build: GRCh38
Supplementary_files_format_and_content: filtered feature matrix and barcodes

source_name: human antral follicle derived cells

growth_protocol: cells were isolated from xenograft derived antral ovarian follicles

extract_protocol:
cells were enzymatically separated and sorted by fluorescence activated cell sorting
RNA libraries were prepared for sequencing using version 3 10x Chromium library preparation kits

treatment_protocol: Ovarian tissue from which antral follicles were derived were co-transplanted with either control or AMH-expressing endothelial cells

value: stroma cells

tag: source

value: AMH EC Follicle


title: HD180_iPSC_1

source_name: HD180 iPSC

value: iPSC


title: HD180_iBMEC_1

source_name: HD180 iBMEC


title: 100000_rep2

description: processed TSS metric in Sup. Fig.  4

value: b-lymphocyte


title: HD-corrected_iPSC_2

source_name: HD-corrected iPSC


title: C339

value: Control EC Follicle


title: 12000_rep3

description: processed TSS metric in Sup. Fig.  4


title: C6

value: granulosa and stroma cells


title: A4


title: HD-corrected_iPSC_1


title: HD180_iPSC_2


title: 100000_rep1

description: processed TSS metric in Sup. Fig.  4


title: INPUT: LNCaP Input

city: Bedford Park

first: Luke

last: Selth

state: SA

address: Flinders Drive

department: College of Medicine and Public Health

institute: Flinders University

data_processing:
Basecalls performed in BaseSpace
ChIP-seq reads were aligned to the hg19 genome assembly using Bowtie2, with default parameters.
Reads were filtered using minimum MAPQ quality score of 15.
Peaks were called using MACS2 with default parameters.
Genome_build: hg19
Supplementary_files_format_and_content: Bigwig files were generated using Deeptools

source_name: LNCaP

extract_protocol:
After 4h hours, cells were fixed with formaldehyde. Nuclear pellets were sonicated on ice for 10 cycles (30 sec on, 30 sec off) using a Diagenode Bioruptor. Lysates were immunoprecipitated with 4 ug AR antibody which had been pre-coupled to Protein G Dynabeads (Life Technologies, 10004D). DNA was purified using a PCR purification kit (Qiagen) and eluted in 100 µl.
Libraries were prepared according to Illumina's instructions accompanying the TruSeq ChIP Library Prep Kit

treatment_protocol: LNCaP cells were grown in baseline conditions (media supplemented with 10% DCC-FBS). Cells were treated with MeT and/or DHT for 4h.

value: LNCaP

tag: treatment

value: Input


title: A1GCNecLo

value: granulosa cells


title: HD180_iBMEC_2


title: M2: LNCaP MeT 1nM Rep2

growth_protocol: LNCaP cells were grown in baseline conditions (media supplemented with 10% DCC-FBS).

value: MeT 1nM


title: A2GC


title: A155


title: A1GC


title: S323

data_processing: Data were examined for probes that were flagged by Agilent as non-uniform outliers.  Samples were excluded if >1% of probes for that sample were flagged.  Data were imported into BRB Array Tools (National Cancer Institute) as processed signal values, as recommended by Agilent.  Values were excluded if the mean signal was not significantly greater than background.  For genes with replicate probes, the average value of the replicates was used.  Values were then log2 transformed followed by quantile normalization.  Genes with >20% missing values across arrays were filtered out.

extract_protocol: RNA was extracted using miRNeasy Mini kits (Qiagen) according to manufacturer’s instructions.

value: systemic sclerosis patient

tag: sample number within subject

value: Female

tag: race

tag: mrss at baseline sample

tag: diffuse at baseline sample


title: S246

tag: condition

value: Limited

tag: disease duration

tag: anti-topoisomerase i

tag: anti-rna polymerase iii


title: S298

tag: subject

value: Diffuse

value: Positive

tag: anti-centromere


title: S244

tag: age

tag: gender

value: White

value: Negative


title: C5GC

tag: cell type


title: S093

value: Asian


title: S095


title: 12000_rep2

description: processed TSS metric in Sup. Fig.  4

tag: cell line


title: C239

value: stroma cells


title: M1: LNCaP MeT 1nM Rep1


title: S306


title: S297


title: D2: LNCaP DHT 1nM Rep2

value: DHT 1nM


title: V1: LNCaP Vehicle Rep1

value: Ethanol 0.1% (vehicle)


title: A3

value: AMH EC Follicle


title: C1GC

value: Control EC Follicle


title: S031

value: Male


title: A10

value: granulosa and stroma cells


title: Vehicle_2

description: Vehicle Rep2

data_processing:
The quality of raw data was initially assessed using FastQC (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/). Raw FASTQ files were then filtered for short sequences using Cutadapt v1.16.6  with the following settings: minimum overlap length in Adaptor options: 3, Minimum length in filter options: 20, maximum error rate: 0.1, quality cut-off: 20.
To evaluate expression of protein-coding genes, reads were mapped against the human reference genome (hg19) using STAR version 2.6.0b-2 with default parameters. FeatureCounts was used to count and assign the mapped reads to genomic features . Count tables generated by featureCounts were used for differential expression analysis using R version 3.2.3 and edgeR version 3.3 as described previously.
Genome_build: GRCh37
Supplementary_files_format_and_content: CSV file containing counts per million (CPM) data for genes

extract_protocol:
Total RNA was extracted using Trizol and phenol-chloroform extraction method.
Libraries were generated using 300 ng of RNA and NEXTflex Rapid Illumina Directional RNA-Seq Library Prep Kits
RNA-Seq; Illumina NextSeq 500 (High Output v2) single-end 75 bp reads.

treatment_protocol: LNCaP cells were grown in baseline conditions (media supplemented with 10% FBS). Cells were treated with MeT and/or DHT for 6h and 24h.

value: LNCaP


title: S245


title: Vehicle_1

description: Vehicle Rep1

growth_protocol: LNCaP cells were grown in baseline conditions (media supplemented with 10% FBS).


title: D1: LNCaP DHT 1nM Rep1


title: S117


title: S094


title: A1GCNecHi

value: granulosa cells


title: C4GCNecHi


title: LSC-EP300 rep1

city: Bengbu

first: Mingsen

last: Li

state: Anhui

address: No. 2600, Donghai Avenue, Bengbu City, Anhui Province

department: Interdisciplinary Eye Research Institute (EYE-X Institute)

institute: Bengbu Medical University

data_processing:
For ChIP-Seq data, reads were trimmed by trimmomatic tool and then aligned to human hg19 reference genome using BWA software (version 0.7.17). For Hi-C data, the clean Hi-C reads were iteratively mapped to the human genome by the ICE software package.
For ChIP-Seq data, duplicated reads were removed by Picard Markduplicates (version 2.18.16) and only uniquely mapping reads were retained for further analysis. For Hi-C data, we pooled the valid pairs of the two replicates together for further analysis.
For ChIP-Seq data, MACS2 (version 2.1.1) was used to call peak. For sharp peaks, we used the following parameters: -f BAMPE -B --SPMR -q 0.001 --call-summits --fix-bimodal --seed 11521 --extsize 200. For broad peaks (H3K27me3 and H3K9me2), the following parameters were used: -f BAMPE -B --SPMR --fix-bimodal --extsize 500 --broad --broad-cutoff 0.01 --seed 11521 -c input file.
For Hi-C data, principal component analysis of the normalized Hi-C matrices at 100-kb resolution was used for identification of chromatin A/B compartments. We determined the location and number of TADs and identified the locations of TAD borders using an insulation score algorithm based on normalized contact matrices at 40-kb resolution. The intra-chromosome interactions at 10-kb resolution were determined by Ay’s Fit-Hi-C software. The interactions with P value < 0.01, FDR < 0.01 and contact count > 2 were considered to be significant.
Genome_build: hg19
Supplementary_files_format_and_content: ChIP-Seq peak files containing the enriched genomic site. A EXCEL file containing chromosome compartments, TADs and chromatin cis-interactions.

source_name: limbal stem cells

growth_protocol: LSCs  were grown in DMEM/F-12 (1:1) medium containing  1% penicillin/streptomycin, 10% fetal bovine serum, 10 ng/ml EGF, 5 μg/ml insulin, 0.4 μg/ml hydrocortisone, 0.1 nM cholera toxin and 2 nM 3,3',5-triiodo-L-thyronine.

extract_protocol:
For ChIP-seq, chromatin was fixed with 1% formaldehyde for 10 min and sheared in a sonification buffer. Fragmented DNA was incubated with primary antibodies overnight at 4℃ and then with Protein A/G Dynabeads  for 1 h. The beads were collected and washed sequentially with the following solutions: high-salt buffer, low-salt wash buffer, and TE buffer.  Elution of the immunoprecipitated protein/DNA complexes was performed using elution buffer at 65℃ for 4 h. Next, the protein/DNA complexes were incubated with proteinase K (Invitrogen) and RNase A (Invitrogen) for 1 h. De-crosslinked DNA was purified using the PCR Purification Kit (Qiagen). For Hi-C, Following cellular cross-linking with 1% formaldehyde and nuclei extraction in hypotonic solution, the genomic DNA was digested with restriction enzyme MboI (NEB) at 37 °C overnight and labelled with biotinylated nucleotides when the cohesive ends were filled. Then, blunt-end proximity ligation was performed with T4 DNA ligase (NEB) at 16 °C for 4 h. After decrosslinking with proteinase K (Thermo) at 65°C overnight, ligated DNA was purified by QIAamp DNA Mini Kit (Qiagen) and sheared to ~400 bp. Next, Dynabeads™ MyOne™ Streptavidin C1 (Invitrogen) was used to pull down the biotin-marked ligation junctions.
Purified DNA was used to prepare ChIP-seq DNA libraries for Illumina sequencing by KAPA Hyper Prep Kit (KAPABIOSYSTEMS) according to the manufacturer’s instructions. The Hi-C library was generated using NEBNext Ultra™ II DNA library Prep Kit (NEB) according to the manufacturer’s instructions.
ChIP-seq, Hi-C

value: primary limbal stem cells

value: untreated


title: A8


title: LSC-p63 rep1


title: C4GCNecLo


title: S036

value: systemic sclerosis patient

value: Black


title: C4GC


title: C2GC


title: LSC-SMC1 rep2


title: C3GC


title: V2: LNCaP Vehicle Rep2


title: S318

value: Female

value: Diffuse

value: Positive


title: S030

value: White

value: Limited

value: Negative


title: C7


title: A7


title: Vehicle_3

description: Vehicle Rep3

value: Ethanol 0.1% (vehicle)


title: S207

value: Asian


title: A9

value: AMH EC Follicle


title: A5


title: LSC-H3K9me2 rep2


title: LSC-H3K9me2 rep1


title: A6


title: DHT_1

description: DHT 1nM Rep1

value: DHT 1nM


title: S317


title: S205


title: S118


title: S119


title: S213


title: GEX_Day 3 post vaccination 1 (visit 8)

city: Seattle

first: Raphael

last: Gottardo

state: WA

address: 1100 Fairview Ave N

department: VIDD

institute: Fred Hutch

data_processing:
Raw count data was filtered to remove cells where 1) a mitochondrial RNA fraction greater than 7.5% of total RNA counts per cell, and 2) less than 200 or greater than 2500 genes were detected. The resultant count matrix was used to create a Seurat (v4.0.1) object.
Filtered read counts were normalized, scaled, and corrected for mitochondrial and rRNA read percentages with the SCTransform function. The FB matrix was normalized per feature using center log normalization.
Cell types in each sample were annotated by mapping to the annotated reference PBMC dataset provided in the Seurat v4 Azimuth workflow. Briefly, anchors between the query and reference datasets were identified using a precomputed supervised PCA on the reference dataset.
Next, cell type labels from the reference dataset, as well as imputations of all measured protein markers, were transferred to each cell of the query datasets through the previously identified anchors. The query datasets were then merged and projected onto the UMAP structure of the reference.
The genes expressed in each specific cell cluster were identified using the function FindAllMarkers() from the Seurat4 package, and filtered based on average logarithm of fold changes larger than 1 and FDR < 0.05.
Genome_build: GRCh38
Supplementary_files_format_and_content: Output from CellRanger (10X Genomics) which includes three files: barcodes.tsv, features.tsv, and matrix.mtx

source_name: PBMC

growth_protocol: PBMCs were isolated, cryopreserved, and thawed using standard protocols.

extract_protocol:
Live frozen PBMCs were obtained from a single vaccinated individual in cohort 1 of the IMRAS trial at day 0, and three- and 14-days post first vaccination. Cells were thawed and washed with RPMI supplemented with 10% FBS and benzonase nuclease (Millipore EMD 0.05 U/ml). PBMCs were resuspended in 100 µl of PBS supplemented with 2% w/v Fetal Bovine Serum (FBS) and incubated with Fixable Viability Stain 510  and Human BD Fc Block for 30 minutes at room temperature. Cells were washed with 2% FBS PBS before incubating with a panel of previously titrated 14 barcoded oligo-conjugated antibodies (BioLegend TotalSeq-C), including  FITC-anti-CD45. Stained PBMC samples were then sorted by fluorescence activated cell sorting (FACS) on a BD FACSMelody to enrich for live, hematopoietic cells. A standard viable CD45+ cell gating scheme was employed; FSC-A v SSCA (to exclude sub-cellular debris), two FSC-A doublet exclusion gates (FSC-W followed by FSC-H), dead cell exclusion gate (BV510 LIVE/DEAD negative) followed by CD45+ inclusion gate.
Sorted cells were resuspended in PBS supplemented with 1% BSA. Cells were loaded onto the 10X Chromium system, where we aimed for recovery of ~5000 cells per sample, and subject to partitioning with barcoded 5’ V1.1 chemistry gel-beads (10X Genomics) to generate the Gel-Bead in Emulsions (GEMs). The RT reaction was conducted in the GEMs, barcoded cDNA extracted by post-GEM RT-cleanup, and cDNA and antibody barcodes amplified for 14 cycles. Amplified cDNA was subjected to SPRI bead cleanup at 0.6X. Amplified antibody barcodes were recovered from the supernatant and were processed to generate TotalSeq-C libraries as instructed by the manufacturers (10X Genomics and BioLegend, TotalSeq-C with 10x Feature Barcoding Protocol). The remaining amplified cDNA was subjected to enzymatic fragmentation, end-repair, A-tailing, adapter ligation and 10X specific sample indexing as per manufacturer’s protocol. Libraries were quantified using Bioanalyzer (Agilent) analysis. 10x Genomics scRNA-Seq and TotalSeq-C libraries were pooled and sequenced on an Illumina NovaSeq Sp100 flow cell using the recommended sequencing read lengths of 26 bp (Read 1), 8 bp (i7 Index Read), and 91 bp (Read 2), and depths of 50,000 and 5000 read pairs per cell for the 5’ Gene Expression and TotalSeq-C libraries respectively. Cell Ranger v3.1.0 (10x Genomics) was used to demultiplex raw sequencing data and quantitate transcript levels against the 10x Genomics GRCh38 reference.

treatment_protocol: PBMCs were stained with a panel of 14 barcoded, oligo-conjugated antibodies, and viable cells (CD45+) enriched by FACS.

tag: day

value: Day 3

tag: immune status

value: post vaccination 1

tag: visit

value: visit 8


title: GEX_Day 14 post vaccination 1 (visit 10)

value: Day 14

value: visit 10


title: MeT_3

description: MeT 1nM Rep3

value: LNCaP

tag: treatment

value: MeT 1nM


title: GEX_Day 0 pre-immune (visit 4)

value: Day 0

value: pre-immune

value: visit 4


title: LSC-EP300 rep2

value: primary limbal stem cells

value: untreated


title: HEK293T cells, LRNP_rep1, CLIP-seq

city: beijing

first: Sun

last: Xianhui

state: 北京

address: No 15 Datun Road, Chaoyang District, Beijing

institute: institute of biophysics,chinese academy of sciences

data_processing:
Adapters and index sequences were removed with cutadapt2.7 using –u 4 and –a TGGAATTCTCGGGTGCCAAGGAACTCCAGTCA.
Quality check were done by fastqc
Reads were mapped to h38 human genome using STAR-2.5.2a.
Read counts were done by a custom python script
Genome_build: hg38
Supplementary_files_format_and_content: raw counts

molecule: cytoplasmic RNA

growth_protocol: HEK293T cells were grown in Dulbecco’s modified eagle medium (DMEM, Gibco) with 4.5 g/L D-glucose, 4 mM L-glutamine, 110 mg/L sodium pyruvate supplemented with 10% FBS.

extract_protocol:
Cell lysates were centrifugated at 36,000 r.p.m. for 2.5 hours in 10%-50% sucrose gradient and Ago2-RNA complexes were isolated with antibody
Ago2-RNA complexes were digested by micrococcal nuclease and treated with FastAP phosphatase. Preadenylylated 3'inker were ligated to Ago2-bound RNAs using truncated T4 RNA ligase 2. After purification by SDS-APGE, Ago2-bound RNAs were extracted, ligated by 5'inker, reverse transcription and PCR amplified with Illumina primers for 20 cycles.
CLIP-seq

treatment_protocol: Cells were treated with 100 ug/mL cycloheximide for 10 min at 37C and UV irradiated at 120 mJ/cm2

value: Human embryonic kidney cells

tag: clip antibody

tag: fraction

value: light ribonucleoprotein


title: LSC-p63 rep2


title: S212

first: Shervin

last: Assassi

address: 6431 Fannin

institute: The University of Texas Health Science Center at Houston

value: systemic sclerosis patient

tag: sample number within subject

value: Female

tag: race

value: Black

tag: mrss at baseline sample

tag: diffuse at baseline sample

value: Diffuse

value: Positive

value: Negative


title: FB_Day 14 post vaccination 1 (visit 10)

value: Day 14

value: post vaccination 1