title: PA-biofilm-ΔΔ, replicate 2, scRNA-seq

first: Xiaodan

last: Yan

state: Hubei Province

address: Donghu Road, No. 115, Wuchang District,

department: Medical Research Institute

description:
RiboD-mSPLiT
0122-H
PAO1 rRNA and mRNA reads.txt

data_processing:
The demultiplexing, barcodes processing, gene counting and aggregation of scRNA-seq data were made by scripts compiled in Python 2.7.15 as previously described with some modifications. [lattman, W. Jiang, P. Oikonomou, S. Tavazoie, Prokaryotic single-cell RNA sequencing by in situ combinatorial indexing. Nature microbiology 5, 1192 (Oct, 2020).]. Downstream analysis of single cell data was performed using pipelines detailed in Seurat v4.3.0.
For corralation analysis of bulk RNA-Seq and scRNA-seq data, scRNA-seq data was combined with the UMI sums of all cells. Single-cell and bulk transcriptomes of E.coli were compared by computing the Pearson correlation of log2 transcripts reads of each gene between the two measurements.
For scRNA-seq data mRNA / total RNA ratio analysis, we removed the barcodes sequence contained in the front, and the interference of the last ten bases, and kept only 20 bases for mapping. Then we mapped the data from the different species to the corresponding reference genomes.
(Detailed codes were saved in "Detailed Computational Pipeline.docx" and "scripts" compressed package .)
Assembly: E.coli MG1655 K12
Supplementary files format and content: matrix files
Supplementary files format and content: xlsx file include raw counts for RNA-seq and UMI sums of scRNA-seq data
Supplementary files format and content: tab-delimited files includes raw counts for samples of the same species

organism: Pseudomonas aeruginosa PAO1

source_name: bacterial cell

extract_protocol:
For RiboD-mSPLiT, all  cells were from pure culture in vitro. Cells were harvested by centrifuge;
For RiboD-mSPLiT, library was performed accarding to the Materials and Methods section;

value: WT

value: 24 h static biofilm


title: BM-cDC1 anti-CD40 rep2

status: Public on Feb 20 2024

type: SRA

city: Parkville

first: Jan

last: Schroeder

state: Victoria

address: Peter Doherty Institute Melbourne

department: DMI

country: Australia

institute: University of Melbourne

library_source: genomic

data_processing:
Reads were aligned to the GRCm39 reference genome using bwa mem (version 0.7.17)
BAM files were coordinate sorted using samtools (version 1.16.1)
Duplicates were removed using Picard Tools' MarkDuplciates (version 2.25.0)
Peaks were called using MACS2 (version 2.2.7.1)
Peaks were annotated using homer
Assembly: Ensemblgene GRCm39 build 105
Supplementary files format and content: Tab separated peak files (annotated)
Library strategy: CUT&Tag

molecule: genomic DNA

organism: Mus musculus

source_name: BM-derived cDC1

growth_protocol: BM-cDC1 were sorted from BM-derived DCs that were generated from bone marrow precursors cutlured for 8 days with Flt3L (150 ng/mL).

extract_protocol:
Isolated nuclei bound to activated Concanavalin A-coated magnetic beads before immunoprecipitation with 0.5ug of primary Ab (anti-IRF1 or rabbit anti-mous IgG control)
CUT&Tag libraries were prepared using hyperactive in situ ChIP Library Prep Kit purchased from Epicypher (CUTANA™ CUT&Tag Assays) following manufacturer's protocols.

treatment_protocol: Following sort, BM-cDC1 were washed and were stimulated with IFNaA (1000 U/mL) and/or anti-CD40 (10 ug/mL) for 4h. Following stimulation, samples were washed and frozen down.

tag: cell type

value: BM-derived cDC1

tag: treatment

value: anti-CD40 for 4h


title: BM-cDC1 IFNaA+anti-CD40 rep1

value: IFNaA + anti-CD40 for 4h


title: MG1655 30min -1

city: Giessen

first: Bork

middle: A.

last: Berghoff

address: Heinrich-Buff-Ring 26-32

country: Germany

institute: University of Giessen

library_source: transcriptomic

data_processing:
Quality and adapter trimming was performed with Trim Galore (Version 0.6.5) with Cutadapt Version 2.7 using the parameters ‘--quality 20 --length 20’ and default adapter detection and trimming.
MultiQC (Version 1.8) and FastQC (Version 0.11.8) were used for quality control.
The preprocessed reads were aligned with Bowtie2 (Version 2.3.5)  using the ‘--mm’ and ‘--very-sensitive’ settings and GCF_000005845.2 (NCBI; downloaded 25.11.2019) as a reference genome.
For postprocessing of the alignments, gene counting and data analysis, Samtools (Version 1.9), featureCounts (Version 1.6.4) and DESeq2 (Version 1.26) were applied, respectively.
All bioinformatic calculations were performed using Curare (Version 0.1.1)  and R statistical language.
Assembly: GCF_000005845.2
Supplementary files format and content: Excel file containing normalized read counts of each sample and DESeq2 comparison between conditions.

molecule: total RNA

organism: Escherichia coli

growth_protocol: Cells were grown in LB medium at 37°C and shaking at 180 rpm.

extract_protocol:
RNA was isolated according to the hot acid-penol method. DNA was removed with TURBO DNA-freeTM kit (Invitrogen) according to "rigorous treatment" instructions. The final clean-up was performed using phenol/chloroform/isoamyl alcohol (25:24:1) mixed with the sample in a 1:1 ratio, followed by chloroform treatment and precipitation.
For cDNA synthesis, all RNA samples were first fragmented using ultrasound (4 pulses of 30 seconds, each at 4°C). Then, an oligonucleotide adapter was ligated to the 3’ end of the RNA molecules. First-strand cDNA synthesis was performed using M-MLV reverse transcriptase and the 3’ adapter as primer. The first-strand cDNA was purified and the 5’ Illumina TruSeq sequencing adapter was ligated to the 3’ end of the antisense cDNA. The resulting cDNA was PCR-amplified to about 10-20 ng/µl using a high-fidelity DNA polymerase for 12 cycles. The TruSeq barcode sequences, which are part of the 5’ and 3’ TruSeq sequencing adapters, were used. The cDNA was purified using the Agencourt AMPure XP kit (Beckman Coulter Genomics) and analyzed by capillary electrophoresis.

treatment_protocol:
tisB was induced with L-arabinose (0.2%) for 30 min.
L-arabinose was removed by washing with 0.9% NaCl and cells were resuspended in LB medium for recovery.

tag: strain

tag: genotype

value: K-12 F-lambda-

value: bacterial cell

tag: treatment 1

value: L-arabinose (0,2%)

tag: treatment 2

tag: time

value: 30 min


title: H1299_si-phf12

city: Shanghai

first: Yiru

last: Kong

state: Shanghai

address: 130 Dong 'an Road, Xuhui District, Shanghai

country: China

institute: Fudan University

data_processing:
The clean reads were obtained after removal of reads containing adapter, poly-N and at low quality from raw  data. HISAT2 was used to align the clean reads to the human reference genome hg38 with default param_x0002_eters. HTSeq was subsequently employed to convert aligned short reads into read counts for each gene  model.
Assembly: human hg38
Supplementary files format and content: txt format for gene expression

organism: Homo sapiens

source_name: lung cancer

extract_protocol:
Total RNA was isolated from cells/tissues using the Magzol Reagent (Magen, China) according to the manufac_x0002_turer's protocol. The quantity and integrity of RNA yield was assessed by using the K5500 (Beijing Kaiao, China), and the Agilent 2200 TapeStation (Agilent Technologies, USA) separately.
Briefly, the mRNA was enriched by oligodT according to instructions of NEBNext® Poly(A) mRNA Magnetic Isolation Module (NEB,USA).  And then fragmented to approximately 200bp.  Subsequently, theRNA fragmentswere subjected to first strand and second strand cDNA synthesis following by adaptor ligation and enrichment with a low-cycleaccording to in_x0002_structions ofNEBNext® Ultra™ RNA Library Prep Kit for Illumina. The purified library products were evaluated using the Agilent 2200 TapeStation and Qubit(Thermo Fisher Scientific, USA). The libraries were sequenced by Illumina (Illumina, USA) with paired-end 150bp at Ribobio Co. Ltd (Ribobio, China).

tag: tissue

value: lung cancer

tag: cell line

value: wild type

value: PHF12 KD


title: PA-biofilm-ΔΔ, replicate 1, scRNA-seq

city: Wuhan

institute: Wuhan University

description:
RiboD-mSPLiT
0122-G
PAO1 rRNA and mRNA reads.txt

library_source: transcriptomic single cell


title: H1299_nc


title: BM-cDC1 IFNaA rep1

value: IFNaA for 4h


title: BM-cDC1 anti-CD40 rep1


title: PA-biofilm, replicate 2, scRNA-seq

description:
mSPLiT
0119-D
PAO1 rRNA and mRNA reads.txt


title: MG1655 0h -3

value: 0 min


title: PA-biofilm, replicate 1, scRNA-seq

description:
mSPLiT
0119-C
PAO1 rRNA and mRNA reads.txt


title: MG1655 0h -2


title: Nc-1-IP

data_processing:
Raw fastq sequences were treated with Trimmomatic tools (v 0.36) using the following options: TRAIL_x0002_ING: 20, SLIDINGWINDOW:4:15 MINLEN:52, to remove trailing sequences below a phred quality score of 20  and to achieve uniform sequence lengths for downstream clustering processes.
Sequencing read quality was inspected using the FastQC software. Adapter removal and read trimming were performed using Trimmomatic. Sequencing reads were trimmed from the end (base quality less than Q20) and filtered by length (less than 52).
Genomic alignment (version from UCSC genome browser) was using bowtie2 (version: 2.4.2) to get uniquely mapping reads.
MACS2 (version 2.2.7) was employed to perform peak calling with the corresponding input sample serving as control.
Assembly: human hg38
Supplementary files format and content: txt format peak file

source_name: Lung

extract_protocol:
The CHIP DNA was assessed by Agilent 2200 TapeStation(Agilent Technologies, USA) and Qubit(Thermo Fisher Scientifc,USA)
The ChIP-Seq libraries were constructed following the Illumina ChIP-Seq library generation protocol. Briefly, chip DNA was fragmented to approximately 200bp , Subsequently, the fragments were  repaired end and added A-tailing following by adaptor ligation. The adaptor-ligated DNA was enrichment with  a low-cycle according to instructions of NEBNext® Ultra™DNA Library Prep Kit for Illumina (NEB, USA). The  DNA library products were assessed using the Agilent 2200 TapeStation(Agilent Technologies, USA) and Qubit  (Thermo Fisher Scientific, USA), the libraries were then sequenced with pair-end 150 bp by Illumina platform  （Illumina,USA）at Ribobio Co. Ltd (Ribobio, China).

value: Lung

tag: chip antibody


title: MG1655 0h -1


title: BM-cDC1 Unstimulated rep1

value: Untreated


title: NL.71, lesional, week 4

status: Public on Feb 19 2024

city: Rochester

first: Tao

last: Ma

state: MN

address: 200 1st ST SW

country: USA

institute: Mayo Clinic

data_processing:
Samples were sequenced using a 2x100bp Paired End (PE) configuration with Illumina HiSeq instrument (4000)
Image analysis and base calling were performed with Illumina BCL2FASTQ v2.19.0
QC was performed on the FASTQ files using RSeQC software (http://rseqc.sourceforge.net/)
The paired end reads were aligned by STAR 2.6.1c
Gene counts were generated using Subread featureCounts (http://subread.sourceforge.net/)
Assembly: HG38
Supplementary files format and content: tab-delimited text files include raw count and RPKM values for each Sample

source_name: Patient skin biopsy

extract_protocol:
RNA was isolated using miRNeasy Mini Kit (Qiagen). 40 ng of Total RNA was used to prepare the sequencing libraries.
RNA libraries for RNA-seq were prepared using the Illumina RNA Access Library Prep Kit following manufacturer's protocols.

value: Patient skin biopsy

tag: disease

value: Necrobiosis Lipoidica

value: week 4


title: NL.65, lesional, week 4


title: NL.41, lesional, week 4


title: NL.53, lesional, week 4


title: NL.59, lesional, week 4


title: NL.35, lesional, week 4


title: NL.29, lesional, week 4


title: NL.23, lesional, week 4


title: NL.11, lesional, week 4


title: NL.5, lesional, week 4


title: NL.67, lesional, week 0

value: Lesional

value: week 0


title: NL.17, lesional, week 4


title: NL.61, lesional, week 0


title: NL.55, lesional, week 0


title: NL.37, lesional, week 0


title: Nc-1-Input


title: NL.31, lesional, week 0

description: removed from differential analysis due to QC


title: NL.13, lesional, week 0


title: NL.7, lesional, week 0


title: NL.69, nonlesional, week 0

value: NonLesional


title: NL.19, lesional, week 0


title: NL.63, nonlesional, week 0


title: NL.57, nonlesional, week 0


title: NL.47, lesional, week 4


title: NL.51, nonlesional, week 0


title: NL.45, nonlesional, week 0


title: NL.33, nonlesional, week 0


title: NL.27, nonlesional, week 0


title: NL.21, nonlesional, week 0


title: NL.15, nonlesional, week 0


title: NL.39, nonlesional, week 0


title: NL.9, nonlesional, week 0


title: NL.3, nonlesional, week 0


title: Radiation_LPS_4

city: Groningen

first: Takuya

last: Oshima

state: Groningen

address: Antonius Deusinglaan 1

department: Department of Biomedical Sciences of Cells & Systems

country: Netherlands

institute: University Medical Center Groningen

data_processing:
Quality control was performed using third-party (FastQC v0.11.9) and in-house (FastQA v3.1.27) QC tools.
Adapter trimming and quality filtering was performed with fastp (v0.23.2.)
Alignment with the Ensembl genome Rattus norvegicus (mRatBN7.2) was performed with STAR2 (v2.7.10)
Transcripts were counted with HTSeq (v2.0.2)
Assembly: Ensembl genome Rattus norvegicus (mRatBN7.2)
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample

organism: Rattus norvegicus

source_name: brain

extract_protocol:
Microglia were isolated using a mechanical tissue dissociation protocol at 4°C as previously described (Galatro et al., 2017). Microglia were sorted by gating the DAPIneg CD11bhigh CD45int cells with FACS. Total RNA was isolated using RNeasy Micro Kit (Qiagen, cat# 74004) according to the manufacturer’s instructions.
Sequencing libraries were generated using the NEBNext Low Input RNA Library Prep Kit for Illumina (New England Biolabs, cat# E6420S/L).
DNA sequencing was performed using a NovaSeq6000 according to the manufacturer's protocols. NovaSeq control software NCS v1.7 was used. Image analysis, base calling, and quality check was performed with the Illumina data analysis pipeline RTA3.4.4 and Bcl2fastq v2.20.

value: Wistar (Hsd/Cpb:WU)

value: brain

tag: Sex

value: male

value: microglia

tag: condition

value: radiation

value: LPS


title: Control_LPS_4

value: sham


title: Radiation_PBS_4

value: PBS


title: NL.43, lesional, week 0


title: Radiation_LPS_3


title: NL.49, lesional, week 0


title: Radiation_PBS_3


title: Control_PBS_4


title: Control_LPS_3


title: Control_PBS_3


title: Radiation_LPS_2


title: NL.1, lesional, week 0


title: Radiation_PBS_2


title: NL.25, lesional, week 0


title: Control_PBS_2


title: Control_LPS_2


title: Radiation_PBS_1


title: Radiation_LPS_1


title: Control_LPS_1


title: Control_PBS_1


title: NCF, MGT+TMP269, bio rep 3

city: ANN ARBOR

first: Liu

last: Liu

state: MICHIGAN

address: 2800 Plymouth Rd,SPC 2800

department: Cardiac Surgery

institute: University of Michigan

description: Sample 6

data_processing:
The libraries were sequenced using Hiseq 4000 by the University of Michigan Sequencing Core. The quantification of RNA expression was estimated by Kallisto 46. The transcript abundance was imported using tximport followed by DESeq2 analysis. The abundance of genes was used to calculate fold change and p values. Differentially expressed genes were identified as a fold change greater than 2 and padj values less than 0.05.
Assembly: mm9
Supplementary files format and content: excel file contain RPKM values for each sample

source_name: neonatal cardiac fibroblasts

growth_protocol: induction medium composed of DMEM/199 (4:1) (Gibco, Thermo Fisher Scientific) containing 10% FBS, 1% penicillin/ streptomycin and 10 μl/ml GlutaMAX (Gibco, Thermo Fisher Scientific). Medium was changed every 2–3 days with or without indicated chemicals for two weeks before cells were examined.

extract_protocol:
Total RNAs from all groups of cells were isolated using TRIzol following the provider’s instructions.
RNA (RIN > 8.5) was used for RNA-seq library preparation by using NEBNext® Ultra™ II Directional RNA Library Prep Kit for Illumina (E7760S)

treatment_protocol: fresh fibroblasts were seeded on tissue culture dishes at a density of 10,000 cells/cm2 before virus infection. Fibroblasts were infected with fresh viral mixture containing 8 μg/ml polybrene (Sigma) 24 hours after seeding.

value: neonatal cardiac fibroblasts

value: WT

value: MGT virus infection+TMP269 treatment


title: NCF, DsRed, bio rep 3

description: Sample 9

value: DSRED virus infection


title: NCF, DsRed, bio rep 1

description: Sample 7


title: NCF, MGT, bio rep 3

description: Sample 3

value: MGT virus infection


title: NCF, DsRed, bio rep 2

description: Sample 8


title: NCF, MGT+TMP269, bio rep 2

description: Sample 5


title: NCF, MGT+TMP269, bio rep 1

description: Sample 4


title: NCF, MGT, bio rep 2

description: Sample 2


title: 10-weeks TCR

city: Pittsburgh

first: Alok

last: Joglekar

state: PA

address: Assembly 3045, 5051 Center Ave

department: Immunology

institute: University of Pittsburgh

description:
AJ39-VDJ
TCR library

data_processing:
Sequence data were downloaded on the Joglekar laboratory server and aligned to the mouse genome (Mm10) using cellranger (10x Genomics Inc). TCR annotation was performed using cellranger vdj using mouse GRCm38 assembly. All three timepoints were sequenced and processed separately. Cellranger and cellranger vdj output files were used as inputs in Seurat
Assembly: Mm10 / GRCm38
Supplementary files format and content: barcodes.tsv, matrix.mtx, and features.tsv files for each run were generated using cellranger count. Filtered.contig.annotations.csv files were generated using cellranger vdj

source_name: Pancreas

extract_protocol:
NOD mice were euthanized by CO2 asphyxiation and immediately dissected for pancreas perfusion and individual islet picking. Pancreas perfusion was performed under a dissecting microscope. The pancreatic duct was clamped using surgical clamps and 3 ml of 600 U/ml Collagenase IV (Gibco) dissolved in HBSS (Gibco) was injected using a 30G needle. Perfused pancreata were harvested and incubated at 37°C for 30 min. After the incubation, HBSS with R10 was added to quench collagenase. After washing twice with HBSS+R10, the tissue was plated on a 10 cm plate, individual islets were picked using a micropipettor. Islets were then incubated in dissociation buffer (Gibco), centrifuged, and resuspended in the staining mix (1:500 dilution of anti-Thy1.2-BV605 + 1:500 dilution of Live/Dead-APC-Cy7, and 1:100 dilution of cell hashing TotalSeq antibodies (Biolegend)). After staining, the cells were resuspended in PBS+0.04% BSA (Millipore Sigma) and sorted on BD FACS Aria III sorter. After sorting the cells, they were counted and processed for scRNAseq.
Cells were processing using 10x 5’ single cell gene expression kit v3 in a Chromium controller according to the manufacturer’s protocols. V(D)J enrichment was done using the single cell 5’ VDJ enrichment kit according to the manufacturer’s protocols. Libraries were sequenced on HiSeq4000 (Novogene Inc) with a 70:20:10 mix for gene expression:VDJ:hashing libraries.
scRNAseq; Individual mice are hash-tagged with TotalSeq antibodies. 3-4 mice from each time point were pooled using cell hashes, and run on a GEM. Each timepoint was processed independently through 10x protocol and through Illumina sequencing.

value: Pancreas

value: T cells

value: NOD/ShiLtJ


title: 10-weeks Gene Expression

description:
AJ39-GEX
Gene expression library


title: 10-weeks Cell hashing

description:
AJ39-HTO
Cell hashing library


title: 8-weeks Gene Expression

description:
AJ31-GEX
Gene expression library


title: 6-weeks Cell hashing

description:
AJ36-HTO
Cell hashing library


title: 8-weeks TCR

description:
AJ31-VDJ
TCR library


title: 6-weeks Gene Expression

description:
AJ36-GEX
Gene expression library


title: 6-weeks TCR

description:
AJ36-VDJ
TCR library


title: 8-weeks Cell hashing

description:
AJ31-HTO
Cell hashing library


title: PNET08

type: RNA

city: Toronto

first: Cynthia

last: Hawkins

state: ON

address: 555 University Ave.

department: Pediatric Laboratory Medicine

country: Canada

institute: The Hospital for Sick Children

description: Sample 569

hyb_protocol: Per manufacturer protocols.

scan_protocol: Scanning was performed on the NanoString nCounter platform per the manufacturer protocols.

data_processing: All data analysis used Bioconductor version 3.14 or 3.16 packages in R version 4.1 or 4.2, respectively, unless otherwise stated. Raw NanoString data (RCC files) was processed using the NanoStringQCPro package (v1.26.0). For quality control, the geometric mean of the housekeeping genes was used as a metric of overall RNA quality and quantity, and samples with a value of < 100 were excluded. The data from all samples was normalized together using housekeeping genes and positive control genes as recommended in the NanoString data analysis guidelines. Briefly, for each sample a normalization was performed sequentially using first the positive controls and then the housekeeping genes. For each sample the geometric mean of the positive controls was calculated (geomeancontrol). The geometric mean of all the geometric means was then calculated (geomeangeomeans) and this was used to calculate a sample specific normalization factor (geomeangeomeans /geomeancontrol), which was multiplied by the gene counts for each sample. The same steps were then taken using the housekeeping genes instead of the positive controls, to provide the final normalized gene counts.

source_name: pediatric brain tumor

label_protocol: Gene quantification was performed on the NanoString nCounter platform per the manufacturer protocols.

extract_protocol: Total RNA was extracted from FFPE and snap frozen tissue using RNAstorm FFPE and fresh frozen kits, respectively, as per the manufacturer's instructions (CellData). RNA concentration was measured (Nanodrop) and RNA integrity assessed using the Agilent 2100 bioanalyzer.

tag: tumor type

value: MMRD HGG

tag: nanostring cartridge


title: PNET13

description: Sample 570

value: HGG


title: NB_12

description: Sample 566

source_name: non-tumor brain control

value: Normal brain


title: PNET04_T1

description: Sample 567


title: NB_11

description: Sample 565


title: PNET04_T2

description: Sample 568


title: NB_10

description: Sample 564


title: NCF, MGT, bio rep 1

description: Sample 1


title: MMRD67_T2

description: Sample 548


title: NB_07

description: Sample 561


title: MMRD70

description: Sample 552


title: NB_08

description: Sample 562


title: NB_05

description: Sample 559


title: NB_02

description: Sample 556


title: MMRD68_T2

description: Sample 550


title: NB_03

description: Sample 557


title: MMRD71

description: Sample 553


title: MMRD66

description: Sample 546


title: MMRD67_T1

description: Sample 547


title: MMRD68_T1

description: Sample 549


title: MMRD69

description: Sample 551


title: NB_04

description: Sample 558


title: NB_09

description: Sample 563


title: NB_06

description: Sample 560


title: PNET19

description: Sample 571


title: MMRD64

description: Sample 544


title: MMRD65

description: Sample 545


title: MMRD62

description: Sample 541


title: MMRD63_T1

description: Sample 542


title: MMRD61_T3

description: Sample 540


title: MMRD61_T1

description: Sample 538


title: MMRD61_T2

description: Sample 539


title: NB_01

description: Sample 555


title: MMRD60

description: Sample 537


title: MMRD72

description: Sample 554


title: MMRD57_T2

description: Sample 536


title: MMRD63_T2

description: Sample 543


title: MMRD56_T2

description: Sample 534


title: MMRD57_T1

description: Sample 535


title: MMRD56_T1

description: Sample 533


title: MMRD55

description: Sample 532


title: MMRD53_T1

description: Sample 529


title: MMRD54

description: Sample 531


title: MMRD52

description: Sample 528


title: MMRD49

description: Sample 526


title: MMRD53_T2

description: Sample 530


title: MMRD48

description: Sample 525


title: MMRD47

description: Sample 524


title: MMRD46

description: Sample 523


title: MMRD51

description: Sample 527


title: MMRD42

description: Sample 519


title: MMRD43_T1

description: Sample 520


title: MMRD41

description: Sample 518


title: MMRD39

description: Sample 517


title: MMRD45

description: Sample 522


title: MMRD43_T2

description: Sample 521


title: MMRD37

description: Sample 515


title: MMRD36

description: Sample 514


title: MMRD38

description: Sample 516


title: MMRD35_T1

description: Sample 512


title: MMRD33

description: Sample 511


title: MMRD32

description: Sample 510


title: MMRD35_T2

description: Sample 513


title: MMRD31_T2

description: Sample 509


title: MMRD31_T1

description: Sample 508


title: B0IP0451

type: genomic

city: Exeter

first: Ailsa

last: MacCalman

address: Barrack Road

country: United Kingdom

institute: University of Exeter

hyb_protocol: Standard Illumina Protocol

scan_protocol: Illumina HiScan

data_processing: WateRmelon

label: Cy5, Cy3

source_name: Adult pancreas

label_protocol: DNA methylation was measured using the Infinium MethylationEPIC BeadChip platform

growth_protocol: Tissue is obtained from the HDBR from elective terminations

extract_protocol: DNA was extracted using Qiagen allPrep Universal kit

tag: age

value: 75 years

value: Female


title: B01P0162

value: 51 years


title: B01P0518

value: 78 years

value: Male


title: B01P0114

value: 49 years


title: B01P0117

value: 54 years


title: B01P0476

value: 64 years


title: B01P0712


title: B01P0091

value: 80 years


title: B01P0113

value: 65 years


title: B0IP0334

value: 34 years


title: B01P0321

value: 60 years


title: B01P0088

value: 35 years


title: B01P0071

value: 70 years


title: B01P0255

value: 48 years


title: MMRD28

description: Sample 507

value: MMRD HGG


title: MMRD27

description: Sample 506


title: B01P0246

value: 56 years


title: 14459

source_name: Fetal pancreas

value: 20 PCW


title: B01P0480

value: 40 years

value: Female


title: B01P0024


title: B01P0125

value: 52 years


title: B01P0094


title: B01P0124

value: 73 years


title: MMRD26_T1

description: Sample 504


title: B01P0011

value: 72 years

value: Male


title: MMRD25

description: Sample 503


title: B01P0031


title: B01P0147

value: 76 years


title: MMRD24

description: Sample 502


title: MMRD20

description: Sample 500


title: MMRD19

description: Sample 499


title: MMRD23

description: Sample 501


title: MMRD18

description: Sample 498


title: MMRD17

description: Sample 497


title: 14756

value: 21 PCW


title: MMRD15

description: Sample 496


title: MMRD14

description: Sample 495


title: MMRD26_T2

description: Sample 505


title: MMRD13

description: Sample 494


title: 12963

value: 19 PCW


title: 14238


title: MMRD12_T5

description: Sample 493


title: 13378


title: MMRD12_T4

description: Sample 492


title: MMRD12_T2

description: Sample 491


title: 14441


title: MMRD11_T2

description: Sample 490


title: MMRD11_T1

description: Sample 489


title: MMRD10

description: Sample 488


title: MMRD09_T3

description: Sample 487


title: MMRD09_T2

description: Sample 486


title: MMRD09_T1

description: Sample 485


title: 14840


title: 13782


title: MMRD08_T2

description: Sample 484


title: MMRD07_T1

description: Sample 481


title: MMRD07_T2

description: Sample 482


title: MMRD08_T1

description: Sample 483


title: MMRD06

description: Sample 480


title: 14259


title: MMRD05_T3

description: Sample 479


title: 13380


title: MMRD05_T2

description: Sample 478


title: 12521


title: 12026

value: 17 PCW


title: 14613


title: MMRD05_T1

description: Sample 477


title: MMRD04

description: Sample 476


title: 12520


title: LGG997

description: Sample 474

value: LGG


title: MMRD02

description: Sample 475


title: 14773


title: 14722


title: 12305


title: 12584


title: 14473


title: LGG995

description: Sample 473


title: 12252


title: 12663

value: 18 PCW


title: LGG986

description: Sample 471


title: 13935


title: 11907

value: 16 PCW


title: LGG981

description: Sample 469


title: 11990


title: 13917


title: LGG984

description: Sample 470


title: 15232


title: LGG969

description: Sample 468


title: LGG959

description: Sample 466


title: LGG962

description: Sample 467


title: 15193

value: 15 PCW


title: LGG991

description: Sample 472


title: LGG955

description: Sample 464


title: 14738


title: 12773


title: LGG952

description: Sample 462


title: LGG954

description: Sample 463


title: 15216


title: LGG956

description: Sample 465


title: 14397


title: 14611


title: LGG950

description: Sample 461


title: 15191


title: 14022


title: LGG948

description: Sample 460


title: LGG946

description: Sample 459


title: 15208

value: 14 PCW


title: 14633


title: LGG944

description: Sample 458


title: LGG943

description: Sample 457


title: 14604


title: LGG941

description: Sample 456


title: LGG940

description: Sample 455


title: 14408


title: 13334


title: LGG938

description: Sample 454


title: LGG937

description: Sample 453


title: 14749

value: 13 PCW


title: 15212


title: LGG933

description: Sample 452


title: LGG931

description: Sample 451


title: LGG930

description: Sample 450


title: LGG924

description: Sample 448


title: 15205


title: 15237


title: 14667


title: LGG922

description: Sample 447


title: 14428


title: LGG929

description: Sample 449


title: 15210

value: 12 PCW


title: LGG921

description: Sample 446


title: LGG919

description: Sample 445


title: 14586


title: LGG917

description: Sample 444


title: 14797


title: 15177

value: 11 PCW


title: 12352

value: Female


title: LGG911

description: Sample 440


title: LGG914

description: Sample 442


title: LGG913

description: Sample 441


title: 14577


title: LGG916

description: Sample 443


title: 14727


title: 14651

value: 10 PCW


title: LGG908

description: Sample 438


title: 14511


title: 11942


title: LGG903_T1

description: Sample 436


title: 14652


title: 11762


title: 14632

value: 9 PCW


title: LGG902

description: Sample 435


title: 14451


title: 14201


title: LGG900

description: Sample 433


title: 14900


title: LGG897

description: Sample 432


title: LGG903_T2

description: Sample 437


title: 12345


title: 15394


title: 14777


title: 14453


title: 12424


title: LGG910

description: Sample 439


title: LGG896

description: Sample 431


title: LGG894

description: Sample 430


title: 14107


title: LGG889

description: Sample 427


title: LGG901

description: Sample 434


title: LGG890

description: Sample 428


title: LGG888

description: Sample 426


title: 15220

value: 8 PCW


title: 15378


title: LGG893

description: Sample 429


title: LGG886

description: Sample 424


title: LGG885

description: Sample 423


title: LGG887

description: Sample 425


title: LGG882

description: Sample 422


title: 14922

value: Male


title: 15190


title: LGG881

description: Sample 421


title: 15146


title: LGG875

description: Sample 419


title: LGG880

description: Sample 420


title: LGG873

description: Sample 418


title: 14866


title: 14690


title: 14817


title: LGG871

description: Sample 417


title: 14832


title: LGG868

description: Sample 416


title: LGG865_T3

description: Sample 415


title: curly hair follicle, biological repl.6

city: Braga

first: Artur

last: Cavaco-Paulo

address: Campus de Gualtar

department: CEB

country: Portugal

institute: University of Minho

description:
Gene Expression from hair curvature classification: class V-VIII
Af18

hyb_protocol: 5 µg of end-labeled, fragmented cDNA was used in a 100-µl hybridization cocktail containing added hybridization controls. 80 µl of mixture was hybridized on arrays for 17 h at 45°C. Standard post hybridization wash and double-stain protocols (FS450_0007; GeneChip HWS kit, Affymetrix) were used on an Affymetrix GeneChip Fluidics Station 450.

scan_protocol: Arrays were scanned on an Affymetrix GeneChip scanner 3000 7G.

data_processing: The 11 arrays were analyzed using Chipster 2.2 (Kallio et al., 2011) using custom cdf file HuGene10stv1_Hs_ENTREZG as available from Brainarray database version 14 (Sandberg & Larsson, 2007). Following RMA normalization and biomaRt annotation, differential expression was determined by empirical Bayes two-group test (Smyth, 2004) with Benjamini-Hochberg multiple testing correction and a p-value cut-off of 0.05.

label: biotin

source_name: anagen hair follicle, very curly hair phenotype

label_protocol: Total RNA was processed for use on Affymetrix (Santa Clara, CA, USA) GeneChip HuGene 1.0 ST Arrays, according to the manufacturer’s Whole Transcript Sense Target Labeling Assay. Briefly, 100 ng of total RNA containing spiked in Poly-A RNA controls (GeneChip Expression GeneChip Eukaryotic Poly-A RNA Control Kit; Affymetrix) was used in a reverse transcription reaction (GeneChip® WT cDNA Synthesis Kit; Affymetrix) to generate first-strand cDNA. After second-strand synthesis, double-stranded cDNA was used in an in vitro transcription (IVT) reaction to generate cRNA (GeneChip® WT cDNA Amplification Kit; Affymetrix). 15 ug of this cRNA was used for a second cycle of first-strand cDNA synthesis (GeneChip® WT cDNA Synthesis Kit; Affymetrix). 5.5 ug of single stranded cDNA was fragmented and end-labeled (GeneChip® WT Terminal Labeling Kit; Affymetrix). Size distribution of the fragmented and end-labeled cDNA, respectively, was assessed using an Agilent 2100 Bioanalyzer with a RNA 6000 Nano Assay.

extract_protocol:
sample collection protocol: The collection procedure consisted first in the isolation of one hair with fingers protected by gloves and then pulling it close to the root with tweezers. After visually checking the integrity and the anagen stage, the follicle was immersed into a preservation solution (RNAlater, Ambion, Applied Biosystems, Foster City, Califórnia, EUA). Then, the excess of hair fiber was cut-off with scissors. The process was repeated until 50 follicles were collected from the entire scalp. The microtube was stored as soon as possible at 4°C and later transferred to -80°C.
Samples were defrost on ice and the RNAlater was removed. Total RNA was extracted using the SV Total RNA Isolation system (Promega Corporation, Madison, Wisconsin USA) according to the protocol of the kit. RNA elution volume was 50 microliters/ 50 hair follicles sample. Concentration and purity was determined by spectrophotometry (NanoDrop ND-1000 UV/VIS, ThermoFisher Scientific,Waltham, Massachusetts, EUA) and integrity was confirmed using an Agilent 2100 Bioanalyzer with a RNA 6000 Nano Assay (Agilent Technologies, Palo Alto, CA).

value: plucked anagen hair follicles

tag: gender

value: male

value: 19 years old

tag: etenic hair group

value: african


title: LGG865_T1

description: Sample 414

value: LGG


title: 14834


title: 15058


title: 14868


title: curly hair follicle, biological repl.5

description:
Gene Expression from hair curvature classification: class V-VIII
Af15

value: 27 years old


title: LGG864

description: Sample 413


title: 14783


title: LGG860

description: Sample 412


title: TCREG9.1 CLONE 4.5 +DOX 3

city: Edinburgh

first: Alasdair

last: Ivens

address: Kings Buildings

institute: Centre for Immunity, Infection and Evolution

data_processing:
Raw data were assesed for quality using FastQC
Read paiirs aligned to the reference genome using bowtie2 with parameters -very-sensitive -p 20 -x $db --no-discordant --no-unal.
Bam files were sorted and indexed using samtools
Raw counts extracted using bedtools multicov from the bam files
Subsequent analyses performed in R using DESeq2 and other Bioconductor packages.
Assembly: Release 46 from https://tritrypdb.org/tritrypdb/app/downloads
Supplementary files format and content: Raw counts in tab-delimited format

organism: Trypanosoma congolense

source_name: whole cell

growth_protocol: T. congolense bloodstream forms were cultured in TcBSF3 supplemented with 20%goat serum and 1% Penicillin/ Streptomycin at 34°C with 5% CO2. T. congolense parasites were cultured up to a density of 1x107 cells/ml, and were generally not maintained at a density lower than 5x104 cells/ml

extract_protocol:
QIAgen RNA preparation kit according to the manufacturer’s instructions
RNAseq libraries were constructed by BGI Hong Kong

treatment_protocol: RNA samples were isolated from TcREG9.1 clones 3.1 and 4.5 induced with doxycycline or not for 3 days

value: whole cell

value: TcREG9.1 RNAi clone 4.5.

tag: treatment

value: DOX positive


title: LGG858

description: Sample 411


title: curly hair follicle, biological repl.4

description:
Gene Expression from hair curvature classification: class V-VIII
Af14

value: 30 years old


title: LGG857

description: Sample 410


title: 14088


title: 14666


title: LGG853

description: Sample 407


title: 15086

value: 7 PCW


title: curly hair follicle, biological repl.2

description:
Gene Expression from hair curvature classification: class V-VIII
Af1

value: 40 years old


title: TCREG9.1 CLONE 4.5 +DOX 2


title: 14059

value: Female


title: 14452


title: TCREG9.1 CLONE 4.5 -DOX 3

value: DOX negative


title: 12361


title: 14798


title: LGG855

description: Sample 408


title: LGG842

description: Sample 405


title: curly hair follicle, biological repl.1

description:
Gene Expression from hair curvature classification: class V-VIII
Black2P

value: 33 years old


title: LGG846

description: Sample 406


title: 15395


title: curly hair follicle, biological repl.3

description:
Gene Expression from hair curvature classification: class V-VIII
Af13


title: LGG841

description: Sample 404


title: 11884

value: 8 PCW


title: TCREG9.1 CLONE 4.5 -DOX 1


title: LGG856

description: Sample 409


title: LGG832

description: Sample 401


title: LGG834

description: Sample 402


title: LGG836

description: Sample 403


title: TCREG9.1 CLONE 4.5 +DOX 1


title: 15214

value: Male


title: straight hair follicle, biological repl.4

description:
Gene Expression from hair curvature classification: class I
Cauc2P

source_name: anagen hair follicle, straight hair phenotype

value: plucked anagen hair follicles

value: 35 years old

value: caucasian


title: LGG830

description: Sample 400


title: LGG828

description: Sample 399


title: straight hair follicle, biological repl.3

description:
Gene Expression from hair curvature classification: class II
Cauc1P

value: male


title: TCREG9.1 CLONE 4.5 -DOX 2


title: TCREG9.1 CLONE 3.3 +DOX 2

value: TcREG9.1 RNAi clone 3.3.


title: LGG827

description: Sample 398

value: LGG


title: 12183


title: straight hair follicle, biological repl.2

description:
Gene Expression from hair curvature classification: class I
3P


title: LGG825

description: Sample 397


title: 14889


title: TCREG9.1 CLONE 3.3 +DOX 1

value: whole cell


title: 14691


title: Human pulmonary arterial endothelial cells 3

city: Bonn

first: Muhammad Ahmer

last: Jamil

state: NRW

address: Sigmund-Freud Str. 25

department: Institute of experimental haematology and transfusion medicine

institute: University Clinic Bonn

description:
HPAEC_3
processed_file_ECs_Only.txt

data_processing:
Reads quality were checked using fastqc and adapter were trimmed using cutadapt
Data was analyzed using miARMa-seq pipeline and count data was converted to expression data using FPKM normalization for liver cells only using Qlucore Omics Explorer 3.6
Data was analyzed using miARMa-seq pipeline and count data was converted to expression data using TMM normalization for ECs cells only using Qlucore Omics Explorer 3.6
Assembly: GRChg38
Supplementary files format and content: Text files. Liver files contains microRNAs Ids and microRNA expression of 3 hepatocytes and 3 liver sinusoidal endothelial cells
Supplementary files format and content: Text files. Ecs files contains microRNAs Ids and microRNA expression of 3 liver sinusoidal endothelial cells, 3 human cardiac microvascular endothelial cells, 3 human pulmonary microvascular endothelial cells, and 3 human pulmonary arterial endothelial cells

source_name: Pulmonary

extract_protocol:
All molecular materials (cells, RNA and DNA) were isolated at passage one as stated by the manufacturing certificate. Sciencell provide ethical statement, on isolation of the samples, on their website that can be accessed at:  https://www.sciencellonline.com/ethical-statement
TruSeq Small RNA Library Preparation Kits | Sequence micro and small RNAs” from Illumina (Prep Kit Code: RS-200-0012)

value: Pulmonary

value: HPAEC

tag: cell type

value: WT

value: primary cells


title: Human pulmonary arterial endothelial cells 2

description:
HPAEC_2
processed_file_ECs_Only.txt

tag: genotype


title: 11878

value: 7 PCW


title: 11865


title: TCREG9.1 CLONE 3.3 -DOX 2


title: TCREG9.1 CLONE 3.3 -DOX 3


title: straight hair follicle, biological repl.1

description:
Gene Expression from hair curvature classification: class I
1P

value: 21 years old


title: LGG817

description: Sample 394


title: Human pulmonary arterial endothelial cells 1

description:
HPAEC_1
processed_file_ECs_Only.txt


title: LGG821

description: Sample 395


title: LGG824

description: Sample 396


title: TCREG9.1 CLONE 3.3 -DOX 1

value: DOX negative


title: LGG812

description: Sample 391


title: LGG810

description: Sample 390


title: 15049

value: Female


title: LGG813

description: Sample 392


title: Human pulmonary microvascular endothelial cells 3

description:
HPMEC_3
processed_file_ECs_Only.txt

value: HPMEC


title: LGG809

description: Sample 389


title: TCREG9.1 CLONE 3.3 +DOX 3

value: DOX positive


title: LCAT-4

first: Wenzhi

last: He

state: None Selected

address: No. 299 Bayi Road

data_processing:
The raw sequencing data were initially subjected to quality control and filtering using tools such as FastQC, followed by alignment using the HISAT2 tool.
Samtools processes aligned sequencing data, converting formats, sorting, indexing, and providing tools for manipulation and statistical analysis.
StringTie assembles and quantifies transcript expression levels from aligned RNA-seq reads, providing the normalized expression matrix.
Assembly: mm10
Supplementary files format and content: xls file includes RPKM values for all Samples

molecule: polyA RNA

source_name: liver

extract_protocol:
The total RNA was extracted using TRIzol reagent, and 200 ng RNA for library construction
RNA libraries for RNA-seq were prepared following BGI manufacturer's protocols

value: liver

value: LCAT-overexpression


title: Human pulmonary microvascular endothelial cells 2

description:
HPMEC_2
processed_file_ECs_Only.txt


title: 14607

value: 6 PCW

value: Male


title: LCAT-3


title: Human pulmonary microvascular endothelial cells 1

description:
HPMEC_1
processed_file_ECs_Only.txt


title: Human cardiac microvascular endothelial cells 3

description:
HCMEC_3
processed_file_ECs_Only.txt

source_name: Cardiac

value: Cardiac

value: HCMEC


title: LGG792

description: Sample 385

value: LGG


title: LCAT-1


title: LCAT-2


title: LGG796

description: Sample 386


title: LGG803

description: Sample 387


title: Human cardiac microvascular endothelial cells 2

description:
HCMEC_2
processed_file_ECs_Only.txt


title: LGG804

description: Sample 388


title: 15242


title: Vec-4

value: empty-vector


title: LGG788

description: Sample 384


title: LGG816

description: Sample 393


title: LGG785

description: Sample 383


title: LGG769

description: Sample 381


title: LGG768

description: Sample 380


title: LGG781

description: Sample 382


title: Vec-3


title: Hepatocytes 3

description:
HH_3
processed_file_liver_Only.txt

source_name: Liver

value: Liver

value: HH

value: Hepatocytes


title: LGG751_T1

description: Sample 377


title: LGG751_T2

description: Sample 378


title: 14933

value: 7 PCW


title: Vec-2

value: WT


title: LGG747

description: Sample 376


title: Hepatocytes 2

description:
HH_2
processed_file_liver_Only.txt

value: primary cells


title: LGG731

description: Sample 375


title: Hepatocytes 1

description:
HH_1
processed_file_liver_Only.txt


title: Human cardiac microvascular endothelial cells 1

description:
HCMEC_1
processed_file_ECs_Only.txt


title: OVX-4

value: Ovariectomy


title: Liver sinusoidal endothelial cells 3

description:
LSEC_3
processed_file_liver_Only.txt
processed_file_ECs_Only.txt

value: LSEC

value: Liver sinusoidal endothelial cells


title: LGG714_T1

description: Sample 373


title: Vec-1

value: liver


title: LGG767

description: Sample 379


title: Liver sinusoidal endothelial cells 2

description:
LSEC_2
processed_file_liver_Only.txt
processed_file_ECs_Only.txt


title: OVX-2


title: LGG672

description: Sample 372


title: OVX-1


title: Liver sinusoidal endothelial cells 1

description:
LSEC_1
processed_file_liver_Only.txt
processed_file_ECs_Only.txt


title: OVX-3


title: LGG629

description: Sample 369


title: LGG534

description: Sample 368


title: LGG516

description: Sample 367


title: straight hair follicle, biological repl.5

description:
Gene Expression from hair curvature classification: class I
Liso1

value: plucked anagen hair follicles

value: male

value: caucasian


title: LGG663

description: Sample 371


title: nG1_4

city: Freiburg

first: Nina

last: Peltokangas

address: Stübeweg 51

institute: Max Planck Institute of Immunobiology and Epigenetics

description: control

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

source_name: ileum

growth_protocol: C57BL/6N mice were bred in-house at the animal facility of the University Medical Center Freiburg or acquired from Janvier (France). Female mice between seven and ten weeks of age were used. BALB/c mice were acquired from Janvier (France) and used between seven and nine weeks of age.

extract_protocol:
Intestinal leukocytes were isolated by dissecting 4 cm intestinal segments and removal of Peyer’s patches. The segments were opened longitudinally and rinsed in PBS to remove the remaining feces. Epithelial cells were separated from the lamina propria using cell dissociation (CD) buffer (HBSS without Mg2+, Ca2+, 5 mM EDTA, 10 mM HEPES). The remaining tissue was digested with digestion buffer (HBSS with Mg2+, Ca2+, collagenase D 0.5 mg/ml, DNAse 0.5 mg/ml) to obtain single-cell suspensions.
As described in CEL-Seq2 protocol (Hashimshony et al. 2016) and its modified version (Herman et al., 2018).
Adapted from TruSeq Small RNA Library Preparation Protocol

treatment_protocol: BALB/c recipient mice were irradiated with a lethal dose split into two single doses of 5 Gy each that were at least 4 h apart. The same day, recipients were injected intravenously with 5 x 10ˆ6 donor bone marrow cells and 4 x 10ˆ5 donor T cells (acute GVHD) or no T cells (control) from C57BL/6 mice.

value: ileum

value: allo-HCT with BM cells


title: LGG486_T3

description: Sample 366

value: LGG


title: Sham-4

value: Sham


title: LGG486_T1

description: Sample 364


title: LGG409

description: Sample 363


title: LGG486_T2

description: Sample 365


title: LGG714_T2

description: Sample 374


title: nG1_3

description: control


title: Sham-3


title: LGG390

description: Sample 362


title: nG1_2

description: control


title: LGG661

description: Sample 370


title: LGG365

description: Sample 361


title: Sham-2


title: LGG318

description: Sample 360


title: Sham-1


title: GVHD-081018-N8

description: aGVHD

value: allo-HCT with BM and T cells


title: nG1_1

description: control


title: LGG143

description: Sample 357


title: LGG195

description: Sample 358


title: LGG294

description: Sample 359


title: GVHD-081018-N7

description: aGVHD


title: LGG1395

description: Sample 354


title: GVHD-081018-N6

description: aGVHD


title: B16F10 cells, shMi-2β-2

city: kaifeng

first: Zhixiang

last: Xu

address: Jin Ming Avenue north section

institute: 河南大学

data_processing:
Samples were performed in replicates and sequenced on an Illumina PE150 (Illumina) platform. Reads were mapped to the mm10 reference genome. Peaks with log2 (fold change) ≥ 0.5 and a P value ≤ 0.05 in comparisons were termed significant. Genome coverage (bedgraph) files were generated by the makeTagdirectory with checkGC parameter, and were used for visualization with IGV2. Read distribution (RD) plots were visualized by the Java TreeView, and histograms were visualized by the GraphPad Prism 5 software (GraphPad Software Inc., San Diego, CA).
Assembly: mm10
Supplementary files format and content: narrow peak

growth_protocol: B16F10 cells and primary mouse melanoma cells (extracted and saved by our laboratory) cell were cultured in complete DMEM media (10% FBS and 100U/ml of Penicillin-Streptomycin).

extract_protocol:
5 × 104 cells were resuspended in ice-cold nucleus lysis buffer (10 mM Tris pH 7.4, 10 mM NaCl, 3 mM MgCl2, and 0.1% IGEPAL CA-630) and centrifuged at 500 × g for 10 min at 4 °C. The supernatant was discarded, and the transposition reaction was performed using the Tn5 transposase at 37 °C for 30 min.
DNA was purified using a MinElute PCR Purification Kit (Qiagen, Redwood, CA, USA), and the resulting DNA was PCR amplified. The selection of size and purification of DNA fragments were done using the AMPure beads. Size distribution and molarity of the sequencing library were determined by Qubit (Thermo Fisher Scientific, Beverly, MA). Samples were performed in replicates and sequenced on an Illumina PE150 (Illumina) platform. Reads were mapped to the mm10 reference genome

value: Mouse melanoma cells

value: Mi-2beta  knock down


title: B16F10 cells, shMi-2β-1


title: LGG1425

description: Sample 356


title: LGG1390

description: Sample 353


title: B16F10 cells, shNC-2

value: control


title: LGG1380

description: Sample 352


title: LGG1414

description: Sample 355


title: LGG1361

description: Sample 351


title: LGG1358

description: Sample 350


title: B16F10 cells, shNC-1


title: GVHD-081018-N4

description: aGVHD


title: GVHD-081018-N5

description: aGVHD


title: GVHD-081018-N2

description: aGVHD


title: GVHD-081018-N3

description: aGVHD


title: KO_CD4

city: Portland

first: Amy

middle: E

last: Moran

state: Oregon

address: 3181 SW Sam Jackson Park Rd, Mail code KR-CDCB

department: Department of Cell, Developmental & Cancer Biology

institute: Oregon Health & Science University

description:
10X Genomics
SCL211022AM_KO_CD4

data_processing:
barcoded processing, gene counting, and aggregation were performed with CellRanger v6.2.1
Assembly: mm10
Supplementary files format and content: Tab-separated values and matrix files

source_name: Thymus

extract_protocol:
Thymi from 4 WT or PD-1 knockout animals were harvested and pooled. Thymi were disrupted with a 1-cc syringe plunger through a 70 um nylon cell strainer and filtered to obtain single-cell suspensions using FACS Buffer (PBS containing 2% FBS and 0.01% sodium azide). CD8+ cells were depleted using CD8a-biotin and rapid spheres followed by a second depletion with CD8b-biotin and rapid spheres, which resulted in enrichment of CD4+ thymocytes. Cells were stained with LIVE/DEAD fixable Aqua followed by extracellular staining with HSA, CD25, CD74, CD4, and CD8a. Cells were resuspended for sorting in FACS buffer and sorted on an Aria (BD Biosciences) using an 85-micron nozzle. Live cells were identified and then the following two populations were sorted: CD4+ HSA+ CD73- CD25- (CD4 single positive thymocytes) and CD4+ HSA+ CD73- CD25+ (regulatory T cells and CD25+ regulatory T cell progenitors) for RNA extraction.
Library preparation was performed according to manufacturer's protocol (Next GEM Single Cell 5' Reagent Kit v2).

value: Thymus

value: thymocyte

value: PD-1 knockout

tag: strain

value: 3 wks


title: WT_TregP

description:
10X Genomics
SCL211022AM_WT_TregP

value: WT


title: WT_CD4

description:
10X Genomics
SCL211022AM_WT_CD4


title: LGG1353

description: Sample 348


title: LGG1352

description: Sample 347


title: LGG1349

description: Sample 346


title: G1_16

description: aGVHD


title: GVHD-081018-N1

description: aGVHD


title: LGG1330

description: Sample 345


title: LGG1321

description: Sample 343


title: LGG1323

description: Sample 344


title: LGG1317

description: Sample 342


title: G1_13

description: aGVHD


title: LGG1357

description: Sample 349


title: G1_14

description: aGVHD


title: KO_TregP

description:
10X Genomics
SCL211022AM_KO_TregP


title: LGG1284

description: Sample 339


title: LGG1314

description: Sample 341


title: LGG1308

description: Sample 340


title: CS1

city: jinan

first: Shuaiwen

last: Teng

address: wenhuaxi road 44

institute: Shandoong University

data_processing:
Raw sequencing data was first filtered by Trimmomatic (version 0.36), low-quality reads were discarded and the reads contaminated with adaptor sequences were trimmed.
In brief, clean reads were first clustered according to the UMI sequences, in which reads with the same UMI sequence were grouped into the same cluster.
Deduplicated Reads were mapped to the reference genome of Mus_musculus from GRCm38 using STRA software (version 2.5.3a) with default parameters.
Reads mapped to the exon regions of each gene were counted by featureCounts (Subread-1.5.1; Bioconductor) and then RPKM was calculated.
Assembly: mm10
Supplementary files format and content: All_samples_rpkm.xls，All samples rpkm

source_name: vBNST

extract_protocol:
RNA was eluted from all samples using an RNeasy Mini kit (Qiagen, Venlo, The Netherlands).2 μg of total RNA was used for the construction of sequencing libraries.
2 μg total RNAs were used for stranded RNA sequencing library preparation using Ribo-off rRNA Depletion Kit (Human/Mouse/Rat) (Catalog NO. MRZG12324, Illumina) and KC-DigitalTM Stranded mRNA Library Prep Kit for Illumina® (Catalog NO. DR08502, Wuhan Seqhealth Co., Ltd. China) following the manufacturer’s instruction.

value: vBNST

tag: group

value: CS

tag: antibody

value: Invitrogen Cat# 44-929G;


title: CS3

tag: tissue

value: Invitrogen Cat# 44-933G;


title: Con3

value: Con

value: Invitrogen Cat# 44-927G;


title: LGG1272

description: Sample 338

value: LGG


title: LGG1263

description: Sample 336


title: LGG1268

description: Sample 337


title: CS2

value: Invitrogen Cat# 44-931G;


title: LGG1262

description: Sample 335


title: LGG1260

description: Sample 334


title: LGG1259

description: Sample 333


title: BM-081018-N6

description: control

value: ileum

value: allo-HCT with BM cells


title: Con2

value: Invitrogen Cat# 44-925G;


title: G1_15

description: aGVHD

value: allo-HCT with BM and T cells


title: Con1

value: Invitrogen Cat# 44-923G;


title: LGG1247

description: Sample 332


title: BM-081018-N5

description: control


title: LGG1243

description: Sample 330


title: LGG1245

description: Sample 331


title: BM-081018-N4

description: control


title: Sample32_BMDM cells, Glucocorticoid+LPS stimulated, 24h, Acod1 KO, replicate #4

city: Berlin

last: Wilhelm

address: Virchowweg 11

department: Rheumatology and clinical immunology

institute: Charite Berlin

data_processing:
Sequence reads were mapped to GrCM38/mm10 reference genome using the STAR aligner
Read count extraction were performed using featureCounts
Assembly: mm10
Supplementary files format and content: tab delimited text file containing raw read counts for each sample

source_name: Bone marrow derived macrophages

growth_protocol: Bone marrow was isolated from the femurs and tibias of 8- to 12-week old C57BL/6J mice (Janvier Labs) or Irg1+/+ or Irg1-/- mice (Jackson Research Laboratory). Following erythrocyte lysis, cells were incubated at 37°C with 5% CO2 in bone marrow-derived macrophage (BMDM)- medium constituting of DMEM (GIBCO) supplemented with 10% fetal calf serum (Biochrom), 1% penicillin/streptomycin (GIBCO) and 10% M-CSF-containing L929-supernatant

extract_protocol:
RNA was extracted using the Rneasy Kit from QIAgen
Novogene NGS RNA Library Prep Set (PT042)

treatment_protocol: Cells were treated with 100nM dexamethasone and/or 100ng LPS for 24 hours

value: Bone marrow derived macrophages

tag: strain background

value: Macrophages

value: Acod1 KO

value: Glucocorticoids + LPS


title: LGG1241

description: Sample 329


title: LGG1239

description: Sample 328


title: LGG1235

description: Sample 327


title: BM-081018-N3

description: control


title: Sample29_BMDM cells, Glucocorticoid+LPS stimulated, 24h, Acod1 KO, replicate #1


title: LGG1232

description: Sample 326


title: BM-081018-N1

description: control


title: BM-081018-N2

description: control


title: LGG1228

description: Sample 325


title: Sample28_BMDM cells, LPS stimulated, 24h, Acod1 KO, replicate #4

value: LPS


title: Sample30_BMDM cells, Glucocorticoid+LPS stimulated, 24h, Acod1 KO, replicate #2


title: LGG1227

description: Sample 324


title: LGG1224

description: Sample 323


title: LGG1222_T1

description: Sample 321


title: LGG1222_T2

description: Sample 322


title: Sample27_BMDM cells, LPS stimulated, 24h, Acod1 KO, replicate #3


title: LGG1219

description: Sample 319


title: Sample26_BMDM cells, LPS stimulated, 24h, Acod1 KO, replicate #2


title: LGG1221

description: Sample 320


title: LGG1218

description: Sample 318


title: LGG1150

description: Sample 317


title: LGG1149

description: Sample 316


title: Sample24_BMDM cells, Glucocorticoid stimulated, 24h, Acod1 KO, replicate #4

value: Glucocorticoids


title: LGG1134

description: Sample 315


title: Sample31_BMDM cells, Glucocorticoid+LPS stimulated, 24h, Acod1 KO, replicate #3


title: LGG1131

description: Sample 313


title: LGG1133

description: Sample 314


title: Sample23_BMDM cells, Glucocorticoid stimulated, 24h, Acod1 KO, replicate #3


title: LGG1127

description: Sample 311


title: LGG1121

description: Sample 308


title: LGG1124_T1

description: Sample 309


title: Sample22_BMDM cells, Glucocorticoid stimulated, 24h, Acod1 KO, replicate #2


title: Sample21_BMDM cells, Glucocorticoid stimulated, 24h, Acod1 KO, replicate #1


title: LGG1124_T2

description: Sample 310


title: Sample20_BMDM cells, Control, 24h, Acod1 KO, replicate #4

value: Control


title: LGG1116

description: Sample 305


title: Microglia, 75mM ethanol, cell line 884

city: Piscataway

first: Ronald

middle: P.

last: Hart

state: NJ

address: 604 Allison Rd Rm B430

department: Cell Biology & Neuroscience

institute: Rutgers University

data_processing:
Raw fastq sequencing files were aligned with human reference genome (hg38) using HISAT2
Raw counts of expressed genes were extracted using featureCounts from the Rsubread package.
The counts table was normalized and fit to a linear model (normalized counts ~ 0 + PRS:Concentration + PRS:CellLine) using limma and voom.
Differential gene expression was determined by limma modeling and empirical-Bayes-based differential analysis.  Significance was defined as those with an FDR-adjusted p-value < 0.05 using empirical Bayes F-test.
Assembly: hg38
Supplementary files format and content: Samples x genes, raw counts

growth_protocol: Microglia were prepared from primitive macrophage progenitors (PMPs), derived from yolk sac embryoid bodies.  Microglial cultures were maintained in DMEM/F12 containing N-2 supplement, IL-34 and GM-CSF.

extract_protocol:
Total RNA was prepared using Qiagen Rneasy kits, followed by poly(A) selection using oligo-dT magnetic beads.
Illumina TruSeq 3' RNA Library kits were used.

treatment_protocol: Cultures treated with ethanol were supplemented with 75 mM ethanol.  Medium was replenished daily since ethanol evaporates under culture conditions.

tag: cell line

value: Microglia

value: HPRS

value: 75 mM ethanol


title: LGG1117

description: Sample 306

value: LGG


title: Sample19_BMDM cells, Control, 24h, Acod1 KO, replicate #3


title: LGG1120

description: Sample 307


title: Sample25_BMDM cells, LPS stimulated, 24h, Acod1 KO, replicate #1


title: LGG1113

description: Sample 303


title: Sample18_BMDM cells, Control, 24h, Acod1 KO, replicate #2


title: LGG1115

description: Sample 304


title: Microglia, 75mM ethanol, cell line 864


title: LGG1128

description: Sample 312


title: LGG1092

description: Sample 300


title: Sample17_BMDM cells, Control, 24h, Acod1 KO, replicate #1


title: Microglia, 75mM ethanol, cell line 528


title: Sample16_BMDM cells, Glucocorticoid+LPS stimulated, 24h, Acod1 WT, replicate #4

value: Acod1 WT


title: LGG1082

description: Sample 298


title: LGG1077

description: Sample 297


title: Microglia, 75mM ethanol, cell line 399

value: LPRS


title: LGG1073

description: Sample 296


title: Sample15_BMDM cells, Glucocorticoid+LPS stimulated, 24h, Acod1 WT, replicate #3


title: Microglia, 75mM ethanol, cell line 206


title: LGG1072

description: Sample 295


title: LGG1069

description: Sample 293


title: LGG1071

description: Sample 294


title: LGG1112

description: Sample 302


title: Microglia, 75mM ethanol, cell line 204


title: Microglia, 75mM ethanol, cell line 838


title: Sample14_BMDM cells, Glucocorticoid+LPS stimulated, 24h, Acod1 WT, replicate #2


title: Microglia, 75mM ethanol, cell line 203


title: Sample12_BMDM cells, LPS stimulated, 24h, Acod1 WT, replicate #4


title: LGG1019

description: Sample 291


title: LGG1018

description: Sample 290


title: LGG1085

description: Sample 299


title: LGG1020

description: Sample 292


title: LGG1106

description: Sample 301


title: Microglia, 75mM ethanol, cell line 92


title: Sample13_BMDM cells, Glucocorticoid+LPS stimulated, 24h, Acod1 WT, replicate #1


title: Microglia, control, cell line 884


title: LGG1017

description: Sample 289


title: LGG1014

description: Sample 287


title: LGG1016

description: Sample 288


title: Microglia, control, cell line 864


title: Sample11_BMDM cells, LPS stimulated, 24h, Acod1 WT, replicate #3


title: LGG1004

description: Sample 284


title: LGG1005

description: Sample 285


title: LGG1003

description: Sample 283


title: LGG1007

description: Sample 286


title: LGG1002

description: Sample 282


title: Sample9_BMDM cells, LPS stimulated, 24h, Acod1 WT, replicate #1


title: Microglia, control, cell line 838


title: LGG1001

description: Sample 281


title: Sample8_BMDM cells, Glucocorticoid stimulated, 24h, Acod1 WT, replicate #4


title: Microglia, control, cell line 399


title: IMM_MB68

description: Sample 280

value: Medulloblastoma


title: Sample6_BMDM cells, Glucocorticoid stimulated, 24h, Acod1 WT, replicate #2


title: IMM_MB67

description: Sample 279


title: Sample10_BMDM cells, LPS stimulated, 24h, Acod1 WT, replicate #2


title: Microglia, control, cell line 206


title: Sample5_BMDM cells, Glucocorticoid stimulated, 24h, Acod1 WT, replicate #1


title: IMM_MB64

description: Sample 276


title: Sample4_BMDM cells, Control, 24h, Acod1 WT, replicate #4


title: IMM_MB63

description: Sample 275


title: Microglia, control, cell line 204


title: Microglia, control, cell line 203


title: IMM_MB66

description: Sample 278


title: IMM_MB65

description: Sample 277


title: IMM_MB61

description: Sample 273


title: IMM_MB62

description: Sample 274


title: IMM_MB60

description: Sample 272


title: IMM_MB59

description: Sample 271


title: Microglia, control, cell line 92


title: Sample2_BMDM cells, Control, 24h, Acod1 WT, replicate #2


title: Sample7_BMDM cells, Glucocorticoid stimulated, 24h, Acod1 WT, replicate #3


title: IMM_MB57

description: Sample 269


title: IMM_MB55

description: Sample 267


title: IMM_MB56

description: Sample 268


title: IMM_MB58

description: Sample 270


title: Microglia, control, cell line 528


title: Sample1_BMDM cells, Control, 24h, Acod1 WT, replicate #1


title: BMDM cells, Glucocorticoid+LPS stimulated, 24h, WT, replicate #3

growth_protocol: Bone marrow was isolated from the femurs and tibias of 8- to 12-week old C57BL/6J mice (Janvier Labs). Following erythrocyte lysis, cells were incubated at 37°C with 5% CO2 in bone marrow-derived macrophage (BMDM)- medium constituting of DMEM (GIBCO) supplemented with 10% fetal calf serum (Biochrom), 1% penicillin/streptomycin (GIBCO) and 10% M-CSF-containing L929-supernatant.

treatment_protocol: Cells were treated with 100nM dexamethasone and/or 100ng LPS for either 4 hours or 24 hours

value: WT


title: IMM_MB50

description: Sample 263


title: IMM_MB52

description: Sample 264


title: BMDM cells, Glucocorticoid+LPS stimulated, 24h, WT, replicate #1


title: BMDM cells, Glucocorticoid+LPS stimulated, 24h, WT, replicate #2


title: Sample3_BMDM cells, Control, 24h, Acod1 WT, replicate #3


title: BMDM cells, Glucocorticoid+LPS stimulated, 4h, WT, replicate #3


title: HaCaT, fPS 25 μg/ml, 24h, rep2

city: seoul

first: sungguan

last: hong

address: 84, Heukseok-ro, Dongjak-gu, Seoul, 104-407

department: Chemistry

country: South Korea

institute: Chung-Ang

data_processing:
Raw sequencing data were processed using Illumina bcl2fastq conversion tool to generate FASTQ files
Sequences were aligned to GRCh38.p14 genome to gene expression count using New Tuxedo Protocol's default settings
Gene expression level of Refseq coding genes were quantified using Ballgown tool which inspect the distribution of abundance estimates.
Assembly: GRCh38.p14
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

source_name: Keratinocyte

growth_protocol: HaCaT cells were cultured in Dulbecco’s modified Eagle’s medium (DMEM; GIBCO®, Invitrogen, Waltham, CA, USA) including 10% Fetal bovine serum (FBS; Invitrogen) with 1% penicillin-streptomycin (Invitrogen) at 37°C in a 5% CO2 incubator.

extract_protocol:
Total RNA was isolated from HaCaT cells using Direct-Zol™ RNA microprep kit (Zymo research, CA, USA) according to the manufacturer’s protocol.
1000 ng of total RNA was processed to mRNA enrichment using NEBNext Poly(A) mRNA magnetic isolation module (New England BioLabs, MA, USA) and followed by fragmentation, cDNA synthesis, and library preparation with unique dual index using NEBNext Ultra II RNA library prep kit (New England BioLabs) according to the manufacturer’s manual.

treatment_protocol: DMEM containing 25,100 μg/ml fPS

value: Keratinocyte

value: HaCaT

value: DMEM cotain 25 μg/mL fPS


title: HaCaT, fPS 25 μg/ml, 24h, rep1


title: HaCaT, fPS 100 μg/ml, 24h, rep3

value: DMEM cotain 100 μg/mL fPS


title: BMDM cells, Glucocorticoid+LPS stimulated, 4h, WT, replicate #2

value: Bone marrow derived macrophages

value: Macrophages


title: HaCaT, fPS 100 μg/ml, 24h, rep1


title: IMM_MB47

description: Sample 260


title: HaCaT, fPS 25 μg/ml, 24h, rep3


title: IMM_MB46

description: Sample 259


title: IMM_MB45

description: Sample 258


title: IMM_MB49

description: Sample 262


title: IMM_MB43

description: Sample 256


title: HaCaT, fPS 100 μg/ml, 24h, rep2


title: BMDM cells, Glucocorticoid+LPS stimulated, 4h, WT, replicate #1

value: Glucocorticoids + LPS


title: IMM_MB44

description: Sample 257


title: IMM_MB42

description: Sample 255


title: HaCaT, DMEM, 24h, rep2

value: DMEM


title: IMM_MB53

description: Sample 265


title: IMM_MB54

description: Sample 266


title: BMDM cells, LPS stimulated, 24h, WT, replicate #3

value: LPS


title: IMM_MB39

description: Sample 253


title: IMM_MB38

description: Sample 252


title: IMM_MB48

description: Sample 261


title: IMM_MB37

description: Sample 251


title: BMDM cells, LPS stimulated, 24h, WT, replicate #2


title: BMDM cells, LPS stimulated, 4h, WT, replicate #3


title: IMM_MB36

description: Sample 250


title: BMDM cells, LPS stimulated, 24h, WT, replicate #1


title: IMM_MB35

description: Sample 249


title: HaCaT, DMEM, 24h, rep3


title: IMM_MB40

description: Sample 254


title: Fibroblasts, 6 week 3D +TGFB, rep3

city: SOUTHAMPTON

first: Joseph

last: Bell

state: Hampshire

address: Tremona Road

department: Medicine

institute: Clinical and Experimental Sciences, Southampton General Hospital

data_processing:
Kallisto v0.46.1
Reads were pseudoaligned using Kallisto (v0.46.1) running in paired-end mode.
Raw counts were read into and processed in R using the tximport package (v4.3)
Assembly: hg38
Supplementary files format and content: tab-delimited text file including raw counts for all samples

extract_protocol:
Total RNA was purified using Monarch Total RNA Prep miniprep kits (NEB) before quantitation on a NanoDrop One spectrophotometer
Messenger RNA was purified from total RNA using poly-T oligo-attached magnetic beads. After fragmentation, the first strand cDNA was synthesized using random hexamer primers followed by the second strand cDNA synthesis. The library was ready after end repair, A-tailing, adapter ligation, size selection, amplification, and purification

value: Primary Lung Fibroblasts

value: 3D +TGFB

tag: time

value: 6 week


title: Fibroblasts, 6 week 3D +TGFB, rep4


title: BMDM cells, LPS stimulated, 4h, WT, replicate #1


title: IMM_MB33

description: Sample 247


title: IMM_MB34

description: Sample 248


title: Fibroblasts, 6 week 3D +TGFB, rep2


title: BMDM cells, LPS stimulated, 4h, WT, replicate #2


title: Fibroblasts, 6 week 3D +TGFB, rep1


title: Fibroblasts, 6 week 3D No TGFB, rep4

value: 3D No TGFB


title: HaCaT, DMEM, 24h, rep1


title: IMM_MB27

description: Sample 241


title: BMDM cells, Glucocorticoid stimulated, 24h, WT, replicate #3

value: Glucocorticoids


title: IMM_MB28

description: Sample 242


title: IMM_MB31

description: Sample 245


title: IMM_MB30

description: Sample 244


title: IMM_MB26

description: Sample 240


title: Fibroblasts, 6 week 3D No TGFB, rep3


title: BMDM cells, Glucocorticoid stimulated, 24h, WT, replicate #2


title: IMM_MB25

description: Sample 239


title: IMM_MB24

description: Sample 238


title: IMM_MB23

description: Sample 237


title: Fibroblasts, 6 week 3D No TGFB, rep2


title: IMM_MB32

description: Sample 246


title: BMDM cells, Glucocorticoid stimulated, 24h, WT, replicate #1


title: Fibroblasts, 6 week 3D No TGFB, rep1


title: IMM_MB29

description: Sample 243


title: IMM_MB21

description: Sample 235


title: IMM_MB22

description: Sample 236


title: BMDM cells, Glucocorticoid stimulated, 4h, WT, replicate #3


title: Fibroblasts, 2 week 3D +TGFB, rep4

value: 2 week


title: IMM_MB20

description: Sample 234

value: Medulloblastoma


title: BMDM cells, Glucocorticoid stimulated, 4h, WT, replicate #2

value: WT


title: Fibroblasts, 2 week 3D +TGFB, rep3


title: BMDM cells, Glucocorticoid stimulated, 4h, WT, replicate #1


title: IMM_MB19

description: Sample 233


title: BMDM cells, Control, 24h,WT, replicate #2

value: Control


title: BMDM cells, Control, 24h,WT, replicate #3


title: IMM_MB17

description: Sample 231


title: IMM_MB18

description: Sample 232


title: Fibroblasts, 2 week 3D No TGFB, rep4


title: IMM_MB11

description: Sample 225


title: IMM_MB13

description: Sample 227


title: IMM_MB12

description: Sample 226


title: BMDM cells, Control, 24h,WT, replicate #1


title: Fibroblasts, 2 week 3D +TGFB, rep1


title: Fibroblasts, 2 week 3D No TGFB, rep3


title: IMM_MB15

description: Sample 229


title: Fibroblasts, 2 week 3D No TGFB, rep2


title: Fibroblasts, 2 week 3D +TGFB, rep2


title: BMDM cells, Control, 4h,WT, replicate #2


title: IMM_MB08

description: Sample 222


title: IMM_MB09

description: Sample 223


title: IMM_MB10

description: Sample 224


title: IMM_MB14

description: Sample 228


title: BMDM cells, Control, 4h,WT, replicate #1


title: IMM_MB07

description: Sample 221


title: Fibroblasts, 2 week 3D No TGFB, rep1


title: Fibroblasts, 2 week Ficoll +TGFB, rep3

value: Ficoll +TGFB


title: Fibroblasts, 2 week Ficoll +TGFB, rep4


title: IMM_MB16

description: Sample 230


title: IMM_MB03

description: Sample 217


title: IMM_MB04

description: Sample 218


title: Microglia, replicate 3, batch 2

city: La Jolla

first: Mridu

last: Kapur

state: CA

address: 9500 Gilman Drive

department: Cellular and Molecular Medicine

institute: University of California San Diego

data_processing:
Reads were trimmed to remove adapter sequences (AGATCGGAAGAG) using cutadapt version 3.5  (Martin, 2011) and then quantified using kallisto version 0.46.2 (Bray et al., 2016)  pseudo-aligning to a Gencode M24 transcript reference.
Assembly: Gencode M24 transcript
Supplementary files format and content: Tab delimited text files include counts and tpm for the sample

source_name: Cortex

growth_protocol: Female B6N.129-Rpl22tm1.1Psam/J mice were crossed to the appropriate Cre driver lines to generate Rpl22 fl/+, CreTg/+ mice. Tissue was harvested from 6-week-old mice

extract_protocol:
Freshly isolated tissue was homogenized on ice using a dounce homogenizer in lysis buffer (50mM Tris-Cl pH 7.5, 100mM KCl, 12mM MgCl2, 1mM DTT, 100μg/ml cycloheximide, 1% (v/v) NP-40, 1mg/ml heparin, 25 units/ml Turbo DNaseI (ThermoFisher Scientific), 20 units/ml Superase-In RNAse inhibitor (ThermoFisher Scientific), cOmplete mini protease inhibitor cocktail (Roche)). Ribosomes were then isolated as previously described, with some minor modifications (Sanz et al., 2009). Briefly, for each sample, 200 ml of Pierce anti-HA magnetic beads (ThermoFisher Scientific) was washed in lysis buffer and then added to the lysate containing tagged ribosomes. The samples were incubated for 4 hours at 4ºC with rotation. Ribosome-bound beads were then washed 3 times for 5 minutes each in 1 ml of high salt wash buffer (50mM Tris pH 7.4, 300mM KCl, 12mM MgCl2, 0.5mM DTT, 100μg/ml cycloheximide, 1 % (v/v) NP-40, 20 units/ml Superase-In RNAse inhibitor, cOmplete mini protease inhibitor cocktail). After the final wash, the ribosome-bound RNA was eluted using buffer RLT (supplemented with b-mercaptoethanol) and isolated using the Qiagen RNeasy mini kit following manufacturer’s instructions. RNA was eluted in 30 μL nuclease-free H2O and the quality and concentration were assessed using high sensitivity RNA ScreenTape on a TapeStation (Agilent) and the Qubit RNA high sensitivity kit on a Qubit 2.0 fluorometer (Life Technologies).
Three mRNA libraries were generated for each genotype using the Kapa Stranded mRNA-Seq Kit (Roche) according to the manufacturer’s protocol.

value: Cortex

value: Cortical microglia

value: Rpl22 Fl/+, Tmem119-cre

tag: Sex

value: Male


title: IMM_MB02

description: Sample 216

source_name: pediatric brain tumor


title: IMM_MB05

description: Sample 219


title: Microglia, replicate 2, batch 2


title: Fibroblasts, 2 week Ficoll +TGFB, rep2


title: IMM_EPN17

description: Sample 214

value: Ependymoma


title: IMM_MB01

description: Sample 215


title: BMDM cells, Control, 4h,WT, replicate #3

value: Bone marrow derived macrophages

value: Macrophages


title: IMM_EPN15

description: Sample 213


title: Fibroblasts, 2 week Ficoll +TGFB, rep1

value: Primary Lung Fibroblasts


title: Astrocytes, replicate 2, batch 2

value: Cortical astrocytes

value: Rpl22 Fl/+, Aldh1-cre


title: IMM_EPN13

description: Sample 211


title: IMM_EPN12

description: Sample 210


title: Fibroblasts, 2 week Ficoll No TGFB, rep4

value: Ficoll No TGFB


title: Astrocytes, replicate 2, batch 1


title: Fibroblasts, 2 week Ficoll No TGFB, rep3


title: IMM_EPN11

description: Sample 209


title: IMM_MB06

description: Sample 220


title: Astrocytes, replicate 3, batch 1


title: IMM_EPN09

description: Sample 207


title: IMM_EPN10

description: Sample 208


title: IMM_EPN08

description: Sample 206


title: Fibroblasts, 2 week Ficoll No TGFB, rep2


title: IMM_EPN07

description: Sample 205


title: Fibroblasts, 2 week Ficoll No TGFB, rep1


title: Fibroblasts, 72hr Ficoll +TGFB, rep4

value: 72 hour


title: IMM_EPN06

description: Sample 204


title: Inhibitory interneurons, replicate 2, batch 2

source_name: Hippocampus (pooled from two mice - male and female)

value: Inhibitory interneurons

value: Rpl22 Fl/+, Dlx6a-Cre

value: pooled male and female


title: IMM_EPN14

description: Sample 212


title: IMM_EPN03

description: Sample 201


title: Fibroblasts, 72hr Ficoll +TGFB, rep3


title: IMM_EPN05

description: Sample 203


title: IMM_EPN02

description: Sample 200


title: IMM_EPN04

description: Sample 202


title: IMM_EPN01

description: Sample 199


title: Inhibitory interneurons, replicate 1, batch 2

value: Hippocampus (pooled from two mice - male and female)


title: Microglia, replicate 1, batch 2

value: Female


title: HGG202

description: Sample 198

value: HGG


title: Fibroblasts, 72hr Ficoll +TGFB, rep2

value: Ficoll +TGFB


title: Cerebellar granule cells, replicate 3, batch 2

source_name: Cerebellum

value: Cerebellum

value: Cerebellar granule cells

value: Rpl22 Fl/+, Gabra6-Cre


title: HGG199

description: Sample 197


title: Cerebellar granule cells, replicate 3, batch 1

value: Male


title: Cerebellar granule cells, replicate 2, batch 1


title: HGG198

description: Sample 196


title: HGG193

description: Sample 195


title: HGG192

description: Sample 194


title: Inhibitory interneurons, replicate 3, batch 2

source_name: Hippocampus (pooled from two male mice)

value: Hippocampus (pooled from two male mice)


title: Fibroblasts, 72hr Ficoll No TGFB, rep2

value: Primary Lung Fibroblasts


title: Fibroblasts, 72hr Ficoll No TGFB, rep3


title: HGG190

description: Sample 192


title: Astrocytes, replicate 1, batch 1

value: Cortex

value: Cortical astrocytes


title: Fibroblasts, 72hr Ficoll No TGFB, rep1

value: Ficoll No TGFB


title: Fibroblasts, 72hr Ficoll No TGFB, rep4

value: 72 hour


title: Layer V cortical neurons, replicate 3, batch 1

value: Layer V pyramidal neurons

value: Rpl22 Fl/+, Rbp4-Cre


title: HGG185

description: Sample 190


title: HGG183

description: Sample 188


title: Layer V cortical neurons, replicate 1, batch 2


title: Fibroblasts, 72hr Ficoll +TGFB, rep1


title: HGG191

description: Sample 193


title: HGG187

description: Sample 191


title: HGG184

description: Sample 189


title: HGG181

description: Sample 186


title: HGG180

description: Sample 185


title: Cerebellar granule cells, replicate 1, batch 1


title: HGG179

description: Sample 184


title: Layer V cortical neurons, replicate 2, batch 1


title: Fibroblasts, 2 week 2D +TGFB, rep3

value: 2D +TGFB

value: 2 week


title: HGG182

description: Sample 187


title: HGG178

description: Sample 183


title: HGG177

description: Sample 182


title: Layer V cortical neurons, replicate 1, batch 1

value: Female


title: Fibroblasts, 2 week 2D +TGFB, rep2


title: Dentate gyrus granule cells, replicate 3, batch 2

source_name: Hippocampus

value: Hippocampus

value: Dentate gyrus granule cells


title: Dentate gyrus granule cells, replicate 3, batch 1


title: Fibroblasts, 2 week 2D +TGFB, rep4


title: HGG174_T2

description: Sample 181

value: HGG


title: Fibroblasts, 2 week 2D No TGFB, rep3

value: 2D No TGFB


title: HGG171

description: Sample 179


title: Dentate gyrus granule cells, replicate 2, batch 1


title: HGG169

description: Sample 177


title: Fibroblasts, 2 week 2D No TGFB, rep4


title: HGG163

description: Sample 175


title: HGG166

description: Sample 176


title: HGG170

description: Sample 178


title: HGA159_T2

description: Sample 174


title: Fibroblasts, 2 week 2D No TGFB, rep2


title: HGG174_T1

description: Sample 180


title: Dentate gyrus granule cells, replicate 1, batch 1


title: HGA159_T1

description: Sample 173


title: BALB mice, stress_(2S,6S)-HNK, Rep3

city: Kyoto

first: Shusaku

last: Uchida

state: Kyoto

address: 53 Kawaharamachi, Sakyo-ku

country: Japan

institute: Kyoto University

data_processing:
Sequencing adaptors, low quality reads, and bases were trimmed with Trimmomatic-0.38 tool.
Trimmed reads are mapped to reference genome (GrCM38/mm10) with HISAT2, splice-aware aligner
The aligned reads were subjected to downstream analyses using StringTie and iDEP.
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes read count for each Sample

source_name: Brain (anterior paraventricular nucleus of thalamus)

extract_protocol:
RNA was extracted using Direct-zol RNA kit (Zymo Research). 100 ng of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using SMARTer Ultra low RNA Kit and TruSeq library construction following manufacturer's protocols.

value: BALB/c

tag: stress

value: smSDS

value: SHNK


title: Fibroblasts, 2 week 2D No TGFB, rep1

value: Primary Lung Fibroblasts


title: HGA158

description: Sample 172

tag: tumor type


title: Fibroblasts, 48hr 2D +TGFB, rep4

value: 48 hour


title: HGA157

description: Sample 171

tag: nanostring cartridge


title: HGA155_T

description: Sample 170


title: Fibroblasts, 2 week 2D +TGFB, rep1


title: BALB mice, stress_(2S,6S)-HNK, Rep1

value: Brain (anterior paraventricular nucleus of thalamus)


title: Fibroblasts, 48hr 2D +TGFB, rep3


title: BALB mice, stress_saline, Rep3

value: Saline


title: HGA152

description: Sample 167


title: HGA149_T2

description: Sample 166


title: Fibroblasts, 48hr 2D +TGFB, rep1


title: HGA153

description: Sample 168


title: BALB mice, stress_saline, Rep2


title: Fibroblasts, 48hr 2D +TGFB, rep2


title: BALB mice, stress_saline, Rep1


title: HepG2, non-treated, nanopore sequencing, biological replicate3

city: Guangzhou

first: Jian-Hua

last: Yang

address: No. 135, Xingang Xi Road

department: School of Life Sciences

institute: Sun Yat-sen University

description: Discover the full-length non-capped RNAs of the mammalian transcriptome

data_processing:
NGS raw data gained from Illumina HiSeqX10 with 150 bp paired end reads, TGS raw data gained from MinION nanopore with single end reads
For Illumina sequencing data, Cutadapt (v2.8) (Martin, 2011) was firstly used to cut the sequencing adapters of the paired-end reads with the following parameters: cutadapt -a AGATCGGAAGAGCACACGTCTG -A AGATCGGAAGAGCGTCGT -m 15 -e 0.15. The NAP-seq specific 5’-adapter (AAGCAGTGGTATCAACGCAGAGT) and 3’-adapter (AGTCGTAGTAAGTCTGTGCTCG) which marked the boundary of the napRNAs were subsequently moved by our programme flClipAdapter with the following parameters: -l 15 -e 0.1 -c 6. Finally, the reads were mapped to the reference genome (hg38 or mm10) with STAR (Dobin et al., 2013) software with the following parameters: --genomeLoad NoSharedMemory --limitBAMsortRAM 60000000000 --alignEndsType EndToEnd --outFilterType BySJout --outFilterMultimapScoreRange 0 --outFilterMultimapNmax 20 --outFilterMismatchNmax 10 --outFilterMismatchNoverLmax 0.05  --outFilterScoreMin 0 --outFilterScoreMinOverLread 0 --outFilterMatchNmin 20  --outFilterMatchNminOverLread 0.8  --seedSearchStartLmax 15 --seedSearchStartLmaxOverLread 1 --alignIntronMin 20 --alignIntronMax 1000000 --alignMatesGapMax 1000000 --alignSJoverhangMin 20 --alignSJDBoverhangMin 10 --outSAMtype BAM Unsorted --outSAMmode Full --outSAMattributes All --outSAMunmapped None --outSAMorder Paired --outSAMprimaryFlag AllBestScore --outSAMreadID Standard --outReadsUnmapped Fastx --limitOutSJcollapsed 5000000 --alignEndsProtrude 150 ConcordantPair --readFilesCommand zcat .   For nanopore sequencing data, Cutadapt (v2.8) was used to cut the NAP-seq specific adapters with the following parameters: -j 16 -g AAGCAGTGGTATCAACGCAGAGT -a AGTCGTAGTAAGTCTGTGCTCG -m 20 -e 0.3 -O 10, and then use Cutadapt again to move any possible adapters with the following parameters: -j 16 -g CGAGCACAGACTTACTACGACT -a ACTCTGCGTTGATACCACTGCTT -m 20 -e 0.3 -O 10, and we just retained the read that contained the NAP-seq specific adapters. Finally, thr reads were mapped to the reference genome (hg38) with minimap2 (Li, 2018) with the following parameters: --junc-bed hg38.gencode.v30.geneAnno.bed -t 16 -k15 -w5 --splice -g2000 -G200k -A2 -B4 -O4,96 -E2,0 -C18 -z400,200 -ub --end-bonus=18 --junc-bonus=18 --splice-flank=yes -ub --sam-hit-only --secondary=no -a
To identify pronounced high-confidence napRNAs, we firstly assembled the continuous reads to the contigs, and then calculated the numbers of start reads containing specific 5’-adapter (startReadNum) and end reads containing specific 3’-adapter (endReadNum). We reasoned that the startReadNum and endReadNum of a candidate napRNA should be significantly higher over the sequence upstream and downstream, while the coverage of the contigs should also be significantly higher over the regions around.  Finally, we developed the computational software napSeeker to calculate the numbers of start reads containing specific 5’-adapter (startReadNum) and end reads containing specific 3’-adapter (endReadNum). We calculated the fold change between startReadNum and numbers of reads containing specific 5’-adapter within 100nt upstream and downstream (startFC), in a similar way, the fold change between endReadNum and the numbers of reads containing specific 3’-adapter upstream and downstream within 100nt (endFC). Next, we calculated the fold change between coverage of the contigs and the regions within 20nt upstream/downstream (up20ntFC/down20ntFC).  A high-confidence napRNA had to meet the following criteria: (1) startReadNum, endReadNum ≥ 7; (2) startFold, endFold ≥ 2. (2) up20ntFold, down20ntFold ≥ 2. (4) length≥100. What’s more, the candidate napRNAs had to express in at least 2 samples of all the human (or mouse) samples. Finally, we only retained the napRNA with the summary counts ≥ 20. These stringent parameters allowed us to identify the highest-confidence candidate napRNAs.
Genome_build: hg38, mm10
Supplementary_files_format_and_content: bigwig files were generated using self-developed software; Scores represent Reads per million mapped reads (RPM).

source_name: Human hepatocellular carcinoma cells

growth_protocol: HepG2 and U-87 MG were cultured in MEM supplemented with 10% FBS, 1% penicillin-streptomycin at 37 °C in a humidified. HEK293T and C2C12 cells were clutured in DMEM supplemented with 10% FBS and 1% penicillin-streptomycin at 37 °C in a humidified atmosphere with 95% air and 5% CO2.

extract_protocol:
RNA was harvested using Trizol reagent. 2ug total RNA was used to prepare the sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina or nanopore protocols

treatment_protocol: HepG2 cells were treated with 500ng/ml ADR or 500μM CoCl2 for 24h before harvesting; 2ug/ml poly (I:C) were transfected into HepG2 with lipo2000 and then the cells were cultured for 12h before harvesting. C2C12 cells grow up to 80% confluence, and then the culture medium was changed to the differentiation medium which is consisted of DMEM with 2% horse serum.

value: non-treated

tag: treatment label

value: wild type

tag: molecule subtype

value: total RNA, remove rRNA


title: BALB mice, non-stress_saline, Rep3

value: Non-stress


title: Fibroblasts, 48hr 2D No TGFB, rep4


title: HGA143_T2

last: Hawkins

address: 555 University Ave.

description: Sample 164

data_processing: All data analysis used Bioconductor version 3.14 or 3.16 packages in R version 4.1 or 4.2, respectively, unless otherwise stated. Raw NanoString data (RCC files) was processed using the NanoStringQCPro package (v1.26.0). For quality control, the geometric mean of the housekeeping genes was used as a metric of overall RNA quality and quantity, and samples with a value of < 100 were excluded. The data from all samples was normalized together using housekeeping genes and positive control genes as recommended in the NanoString data analysis guidelines. Briefly, for each sample a normalization was performed sequentially using first the positive controls and then the housekeeping genes. For each sample the geometric mean of the positive controls was calculated (geomeancontrol). The geometric mean of all the geometric means was then calculated (geomeangeomeans) and this was used to calculate a sample specific normalization factor (geomeangeomeans /geomeancontrol), which was multiplied by the gene counts for each sample. The same steps were then taken using the housekeeping genes instead of the positive controls, to provide the final normalized gene counts.

extract_protocol: Total RNA was extracted from FFPE and snap frozen tissue using RNAstorm FFPE and fresh frozen kits, respectively, as per the manufacturer's instructions (CellData). RNA concentration was measured (Nanodrop) and RNA integrity assessed using the Agilent 2100 bioanalyzer.


title: HepG2, non-treated, nanopore sequencing, biological replicate2


title: Fibroblasts, 48hr 2D No TGFB, rep3


title: HGA149_T1

description: Sample 165


title: HGA143

description: Sample 162

value: MMRD HGG


title: HGA143_T1

description: Sample 163


title: BALB mice, non-stress_saline, Rep2


title: NRF2 ChIP in ZMYND8 KO_Rep2

city: Dallas

first: Maowu

last: Luo

state: TX

address: 5323 Harry Hines Blvd.

institute: UT Southwestern Medical Center

data_processing:
ChIP-seq Fastq files were subjected to quality check using fastqc (version 0.11.2, http://www.bioinformatics.babraham.ac.uk/projects/fastqc), fastq_screen (version 0.4.4, http://www.bioinformatics.babraham.ac.uk/projects/fastq_screen), and mapped to human genome (hg19) using bowtie2 (version 2.2.3), filtering out alignments with mapping quality less than 10. Duplicate alignments were removed using picard-tools (version 1.127, https://broadinstitute.github.io/picard/). The ChIP-seq peaks were called using MACS2 (version 2.0.10), with a q-value threshold of 0.05 and using the input of ChIP samples as controls.
Assembly: hg38
Supplementary files format and content: bed

source_name: ZMYND8 KO spheres

growth_protocol: MammoCult Medium (STEMCELL Technologies) , ultralow attachment dish at 37°C in a 5% CO2/95% air incubator.

extract_protocol:
Cells were cross-linked with 1% formaldehyde and quenched in 125 mM glycine. Chromatin was isolated using a SimpleChIP Enzymatic Chromatin IP kit (Cell Signaling Technology).
ChIP DNA libraries were prepared with the NEBNext Ultra II DNA Library Prep Kit for Illumina and sequenced on the Illumina NextSeq 2K.

value: Human breast cancer

value: ZMYND8 KO

tag: chip antibody


title: HGA155_AUT

city: Toronto

first: Cynthia

institute: The Hospital for Sick Children

description: Sample 169


title: BALB mice, stress_(2S,6S)-HNK, Rep2

tag: treatment


title: NRF2 ChIP in ZMYND8 KO_Rep1

tag: cell type


title: Fibroblasts, 48hr 2D No TGFB, rep2


title: BALB mice, non-stress_saline, Rep1


title: HGA137

description: Sample 161


title: NRF2 ChIP in SC_Rep2

source_name: MDA-MB-231 spheres

tag: genotype

value: Parental


title: Fibroblasts, 48hr 2D No TGFB, rep1


title: ED211124_g

city: Martinsried

first: Christian

last: Mayer

address: Am Klopferspitz 18

institute: Max Planck Institute of Neurobiology.

description: CRISPR RNA

data_processing:
N/A
Assembly: mm10-2.1.0

source_name: Guide dataset of ED211124

extract_protocol:
embryonic tissue was collected in ice-cold Leibowitz medium  and papain dissociation was carried out (Wortington, #LK003150). Postnatal tissue was dissected in ice-cold bubbled ACSF and dissociatedwas carried out with the Miltenyi BioTech Neural Tissue Dissociation Kit (P) (#130-092-628)
Transcriptomic libraries were prepared for sequencing using standard Illumina protocols. Barcode libraries were prepared from PCR cDNA to amplify barcode regions with custom primers with standard Illumina adapters.

value: Forebrain

tag: strain

value: FACSorted for GFP

tag: age


title: PSA34_3

city: Hanover

first: Paula

middle: F.

last: Zamora

state: NH

address: 74 College st

institute: Geisel School of Medicine at Dartmouth

data_processing:
Raw reads quality was first confirmed using FastQC v.0.11.9. Reads were trimmed for adapters and low-quality sequences using Trim Galore! v0.6.6 and aligned to the reference human genome GRCh38/hg38 using STAR v2.6.1d.
Assembly: Reads mapping to exons were assigned using featureCounts v2.0.1. Quality control was tracked using MultiQC v1.9.
Supplementary files format and content: Csv files, raw transcript counts for each treatment

source_name: Bronchial epithelium

growth_protocol: CFBE41o- cells were cultured in Minimal Essential Media supplemented with 10% of heat-inactivated fetal bovine serum, 2 mM L-glutamine, and 5 U/ml penicillin-5 mg/ml streptomycin in adherent cell culture conditions at 37°C with 5% CO2.

extract_protocol:
RNA extraction was conducted using the Quick-RNA Miniprep kit (Zymo Research), followed by RNA clean-up using the RNA Clean & Concentrator-5 kit (Zymo Research).
Library preparation was done using the Zymo-Seq RiboFree Total RNA Library Kit (Zymo Research).
Libraries were sequenced on an Illumina NovaSeq 6000 instrument with a sequencing depth of 30 million read pairs.

treatment_protocol: CFBE41o- cells were apically treated with fluorescently labeled phages OMKO1, LPS-5, PSA04, and PSA34 at a concentration of 1 x 109 PFU/ml in MEM pH-adjusted to 6.5 for 24 h.

value: Bronchial epithelium

value: Bronchial epithelial cells

value: CFTR deltaF508/deltaF508


title: HGA136

description: Sample 160

value: HGG


title: NRF2 ChIP in SC_Rep1


title: ED211111_g

description: CRISPR RNA

source_name: Guide dataset of ED211111


title: HGA127

description: Sample 159


title: PSA34_2


title: mutant

city: PHOENIX

first: Bingqiang

last: Wen

state: AZ

address: 475 N 5th st

department: Child Health

institute: The University of Arizona

description: 10x Genomics

data_processing:
The standard celllranger mkfastq software version 3.0 used for basecalling.
The standard celllranger count software version 3.0 used to produced raw expression matrix.
The matrix were normalized and scaled by Seurat v4.3 in R4.2.1 environment.
Assembly: mm10,rn6
Supplementary files format and content: Tab-separated values files and matrix files

organism: Mus musculus x Rattus norvegicus

source_name: lung

extract_protocol:
The lung samples were harvested from E20.5 mouse-rat chimeric embryo. The samples were dissociated into small pieces and digested into single cell suspension.
The libraries were prepared for sequencing using standard 10X 3'v3 protocols

value: lung

value: C57BL/6, SD


title: HGA119

description: Sample 158


title: ED210415_g

description: CRISPR RNA

source_name: Guide dataset of ED210415


title: ED201013_g

description: CRISPR RNA

source_name: Guide dataset of ED201013


title: PSA04_2


title: control

description: 10x Genomics


title: HGA116

description: Sample 157


title: HGA115

description: Sample 156


title: Cerebellum, Input

city: LA JOLLA

first: Carlos

last: Guzman

address: 9262 REGENTS RD

institute: UCSD

data_processing:
ChIP-seq reads were mapped to the mm10 genome using bowtie2 with the following parameters: “bowtie2 -q –very-sensitive-local -N 1”.
Peaks representing areas of strong polymerase binding were called using HOMER with the following parameters: “-style factor -fragLength 150”.
Bigwigs were created using HOMER's makeMultiWigHub.pl
Assembly: mm10
Supplementary files format and content: bigwig

growth_protocol: Female B6.Polr3a cKI/cKI mice were crossed to the appropriate Cre driver lines to generate Polr3a cKI/+, CreTg/+ mice. Tissue was harvested from 6-week-old mice

extract_protocol:
Extracted tissue was minced and then  fixed with 1% formaldehyde for 10 minutes. Crosslinking was terminated with 1/20th volume of 2.625M glycine. Samples were then washed with PBS containing protease inhibitors and lysed in ChIP RIPA buffer (50mM Tris-HCl, pH 7.5, 150mM NaCl, 1mM EDTA, 1% IPEGAL CA-630, 0.25% Na-Deoxycholate, 0.1% SDS, with cOmplete mini protease inhibitor cocktail (Roche)). The lysate was then sonicated using a Branson Digital Sonifier Probe (12-14x cycles, 40% amplitude, 10s ON, 30s OFF). Samples were centrifuged for 10 minutes at  4ºC. 1% of the lysate was saved as the DNA input control for the sample. For ChIP, 20 l Protein G Dynabeads and 2 g of FLAG antibody (Sigma F1804) were added to cleared lysate and rotated overnight at 4° C. Dynabeads were washed 3 times with Wash Buffer 1 (20 mM Tris-HCl pH 7.4, 150 mM NaCl, 2 mM EDTA, 0.1% SDS, 1% Triton X-100), three times with Wash Buffer 3 (250 mM LiCl, 1 mM EDTA, 1% Triton X-100, 0.7% sodium deoxycholate), three times with TET (10 mM Tris-HCl pH 8, 1 mM EDTA, 0.2% Tween 20), and resuspended in nuclease free water.
ChIP DNA from ChIP input and ChIP samples was used to prepare libraries using the NEBNext Ultra II Library preparation kit (NEB E7645S) and KAPA Single-Indexed Adapters for Illumina (Roche, KR1317) according to manufacturer’s protocol. Libraries were amplified by PCR for 14 cycles, size selected for 150-500bp fragments and sequenced, yielding ~10-40 million reads per sample.

value: Cerebellum

value: Polr3a FLAG/FLAG