title: A005_9_Input

city: Helsinki

first: Krista

last: Kokki

address: Viikinkaari 9, Biocenter 1, Institute of Biotechnology P.O.Box. 56

department: Department of Biosciences (Genetics)

country: Finland

institute: University of Helsinki

data_processing:
Basecalls were performed using bcl2fastq v2.17 for Novaseq output.
ChIP-seq reads were aligned to the NCBI GRCm38 genome using BWA version 0.7.17. Reads <5 quality were discarded with max 2 mismatches/seed. Unmapped, nonprimary, duplicate and mapping quality <30 alignments were discarded using samtools (v.1.4) and picard (v.2.18.10)
Fragment sizes were estimated with phantompeaktools and peak q<0.05 were called for primary chromosomes with MACS2 (v.2.1.0)
Peaks in all replicates were defined as expressed and were annotated to the neaarest TSS from middle of the peak using ChIPpeakAnno package.
bigWig files were generated using the genomicRanges R package.
Assembly: GRCm38
Supplementary files format and content: bigWig

source_name: Mouse whole liver

extract_protocol:
Small pieces of frozen liver tissue from two ad libitum-fed male C57Bl/6 mice were pulverized in liquid nitrogen, and cross-linked with 1% formaldehyde for 10 min. After quenching with 2.5 M glycine, nuclear extracts were prepared. Chromatin fragmentation was performed by sonication for 20 cycles of 30 s at the highest level. Proteins were immunoprecipitated using anti-BHLHE40 (Novus Bio NB100-1800) antibody and anti-ChREBP (Novus Bio NB400-135) antibody. Antibodies were precipitated, crosslinked and DNA was isolated using phenol/chloroform/isoamyl alcohol. As control sample input DNA was used.
ChIPseq was performed with an average depth of 20 million reads per sample, 75 bp single end reads (75bp cycle kit), on the Illumina NextSeq500.

value: Mouse whole liver

value: none (input)


title: A004_10_BHLHE40

status: Public on Jun 01 2023

type: SRA

library_source: genomic

molecule: genomic DNA

organism: Mus musculus

tag: strain

tag: tissue

tag: chip antibody

value: Novus Bio NB100-1800


title: PD1 +/- Sham, scRNAseq

city: Dallas

first: Miao

last: Cui

state: Texas

address: UT Southwestern Medical Center Department of Molecular Biology 6000 Harry Hines Blvd.

country: USA

institute: UTSW

description: 10x Genomics

library_source: transcriptomic single cell

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v6.1.1 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
The cDNA reads were aligned to the mm10/GRCm38 premRNA reference genome.
Further analyses for quality filtering was performed using the Seurat R package
For data quality filtering, we removed cells that had more than 6000 or fewer than 200 detected genes or cells that had a percent of mitochondrial genes > 10%.
We then normalized the data by the total expression, multiplied by a scale factor of 10,000 and log-transformed the result. IntegrateData function implemented in Seurat V4 was used to correct batch effects between samples and to merge samples into one Seurat object. Briefly, we performed standard preprocessing (log-normalization), and identified the top 2000 variable features for each individual dataset. We then identified integration anchors using the FindIntegrationAnchors function. We used default parameters and dimension 30 to find anchors. We then passed these anchors to the IntegrateData function to generate an integrated Seurat object
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

molecule: total RNA

source_name: Heart

extract_protocol:
Hearts were harvested with atria removed. The tissue was minced with dissecting scissors and digested at 37°C for 45 minutes in DMEM medium containing collagenase I (450 U/mL), hyaluronidase type I-S (60 U/mL) and DNase-I (60 U/mL). The digested material was then filtered, washed and red blood cells were lysed using RBC lysis buffer. Cells suspensions were blocked with TruStain FcX (anti-mouse CD16/32) antibody and True-Stain Monocyte Blocker and incubated with Zombie Fixable Dyes (all from Biolegend) to label dead cells for 15min at RT in dark. Cells were then stained in FACS buffer with monoclonal CD45 antibodies at 4°C for 20 min. Cd45+ immune cells were isolated using cell sorter BD FACSAria II.
Library was performed according to the manufacter’s instructions (single cell 3’ v3 protocol, 10x Genomics). Briefly, CD45+ immune cells were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead-in-emulsion (GEM). The poly-A RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA, which contains an Ilumina R1 primer sequence, Unique Molecular Identifier (UMI) and the 10x Barcode. The pooled barcoded cDNA was then cleaned up with Silane DynaBeads, amplified by PCR and the apropiated sized fragments were selected with SPRIselect reagent for subsequent library construction. During the library construction Ilumina R2 primer sequence, paired-end constructs with P5 and P7 sequences and a sample index were added.

tag: cell type

value: Immune cells

value: Heart

tag: genotype

value: PD1 Het

tag: treatment

value: Sham

tag: age


title: A003_10_ChREBP

value: Novus Bio NB400-135


title: A006_10_Input


title: ATAC Bach2KO_Th1_Bach2_2

city: Cambridge

first: Pratiksha

middle: I

last: Thakore

state: MA

address: 415 Main St

institute: Broad Institute

data_processing:
Base-calling was performed by RTA v2.4.11, and the BCL files were translated to fastqs using bcl2fastq2 v2.20.0.
ATAC-seq: Reads were aligned to reference mouse annotation mm10 using Bowtie2, and filtered for duplicated and mitochondrial reads. Peak-calling was performed using MACS2. Read counts per peak were computed using bedtools multicov tool for each sample and then column combined into a matrix.
Assembly: mm10
Supplementary files format and content: ATAC-seq: comma-separated values (CSV) files include count values for each gene in each sample.

source_name: Sorted Th1 live cells with ATAC Bach2 KO treatment

growth_protocol: For the in vitro differentiation of naive ATAC CD4+ T cells, naive ATAC CD4+ ATAC CD44- CD62L+ cells were activated with plate-bound anti-CD3 and anti-CD28 antibodies in the presence of cytokines. For the acquisition of ex vivo Th17 cells, mice were immunized subcutaneously into the flanks with an emulsion of the MOG35-55 peptide and M. tuberculosis H37Ra extract in CFA for the induction of ATAC EAE.

extract_protocol:
6,000 viable cells were sorted into PBS/2% FCS and were stored in BambankerTM cell freezing media at -80°C.
For bulk ATAC-seq, cells were thawed at 37°C. Subsequently, cells were lysed and tagmented in 1X TD Buffer, 0.2l TDE1 (Illumina), 0.01% digitonin, and 0.3X PBS at 37°C for 30 min at 300 rpm, as previously described [86]. DNA purification was performed with the MinElute PCR purification kit (QIAGEN). The complete eluate was pre-amplified with 5 PCR cycles using indexed primers with NEBNext High-Fidelity 2X PCR Master Mix (NEB) and the number of additional cycles was determined by SYBR Green quantitative PCR. After DNA purification, library quantification and quality control were performed with the Kapa Library Quantification Kit (Kapa Biosystems) and a Qubit dsDNA HS Assay kit (Invitrogen). Libraries were sequenced on an Illumina NextSeq 550 system with paired-end reads of 37 base pairs in length.

treatment_protocol: For the knockout of ATAC Bach2, we obtained naive T cells from Cas9 knock-in mice and in vitro differentiated them to npTh17 and pTh17 cells while simultaneously transducing them with retroviral vectors encoding a ATAC Bach2-targeting single guide RNA (ATAC Bach2 KO) or empty sgRNA as control. For the overexpression of ATAC Bach2, we polarized naive ATAC CD4+ T cells into pTh17 cells by simultaneous transduction of retroviral vectors with a constitutive ATAC Bach2 cDNA expression cassette (ATAC Bach2 OE) or an empty control.

value: Spleen and lymph nodes


title: ATAC Bach2KO_Th1_Bach2_1


title: ATAC Bach2KO_Th1_141_3

source_name: Sorted Th1 live cells with control virus treatment


title: A001_9_ChREBP


title: ATAC Bach2KO_Th1_141_2


title: A002_9_BHLHE40


title: ATAC Bach2KO_Th1_nv_2

source_name: Sorted Th1 live cells with no virus treatment


title: ATAC Bach2KO_Th1_nv_1


title: ATAC Bach2KO_Th1_Bach2_3


title: d13_Pparg_WT_Sp#2

city: Boston

first: CBDM

last: Lab

address: 77 Avenue Louis Pasteur

department: Microbiology and Immunobiology

institute: Harvard Medical School

library_source: transcriptomic

data_processing:
Reads were mapped to the mouse reference genome (mm10) with STAR 2.7.3a
Non-uniquely mapped reads were discarded.
The uniquely mapped reads were assigned to genes using featureCounts with GENCODE annotation (vM25)
Assembly: mm10
Supplementary files format and content: tab-delimited text files include raw read counts for each Sample

source_name: Spleen

extract_protocol:
1,000 Cells were double-sorted by Aria into 5ul Buffer TCL (Qiagen) with 1% 2-Mercaptoethanol (Sigma).Total RNA was captured and purified on RNAClean XP beads (Beckman Coulter)
Polyadenylated mRNA was selected using an anchored oligo(dT) primer and converted to cDNA via reverse transcription. First-strand cDNA was subjected to limited PCR amplification followed by transposon-based fragmentation using the Nextera XT DNA Library Preparation Kit (Illumina). Samples were then PCR-amplified using barcoded primers such that each sample carried a specific combination of illumine P5 and P7 barcodes, and were pooled prior to sequencing. Sequencing was performed on an illumina NextSeq500 using 2X25bp reads.

value: Spleen

tag: cell line

value: Primary cells from mouse

value: Regulatory T cells

value: Pparg+/+ Foxp3-Cre


title: ATAC Bach2KO_Th1_141_1


title: ATAC Bach2KO_Th1_nv_3


title: d13_Pparg_WT_skin#2

source_name: Skin

value: Skin


title: ATAC Bach2KO_npTh17_Bach2_3

source_name: Sorted npTh17 live cells with ATAC Bach2 KO treatment


title: ATAC Bach2KO_npTh17_Bach2_1


title: ATAC Bach2KO_npTh17_nv_3

source_name: Sorted npTh17 live cells with no virus treatment


title: ATAC Bach2KO_npTh17_141_1

source_name: Sorted npTh17 live cells with control virus treatment


title: ATAC Bach2KO_npTh17_141_3


title: ATAC Bach2KO_npTh17_141_2


title: ATAC Bach2KO_npTh17_Bach2_2


title: ATAC Bach2KO_pTh17_Bach2_3

source_name: Sorted pTh17 live cells with ATAC Bach2 KO treatment


title: ATAC Bach2KO_pTh17_Bach2_2


title: ATAC Bach2KO_npTh17_nv_1


title: ATAC Bach2KO_pTh17_141_3

source_name: Sorted pTh17 live cells with control virus treatment


title: ATAC Bach2KO_pTh17_141_2


title: ATAC Bach2KO_pTh17_141_1


title: ATAC Bach2KO_pTh17_Bach2_1


title: ATAC Bach2KO_pTh17_nv_2

source_name: Sorted pTh17 live cells with no virus treatment


title: ATAC Bach2KO_pTh17_nv_1


title: ATAC Bach2KO_pTh17_nv_3


title: ATAC EAE_dLN_3

source_name: Sorted IL17+ cells harvested from the draining lymph node at the peak of ATAC EAE

value: Draining lymph nodes


title: ATAC EAE_dLN_4


title: ATAC Time_course_npTh17_48hr_2

source_name: Sorted live cells polarized in npTh17 conditions after 48hr


title: ATAC Time_course_npTh17_48hr_1


title: ATAC Time_course_npTh17_48hr_3


title: ATAC EAE_dLN_5


title: ATAC Time_course_pTh17_48hr_1

source_name: Sorted live cells polarized in pTh17  conditions after 48hr


title: ATAC Bach2KO_npTh17_nv_2


title: ATAC Time_course_pTh17_48hr_2


title: ATAC Time_course_Th1_48hr_3

source_name: Sorted live cells polarized in Th1 conditions after 48hr


title: ATAC Time_course_Th1_48hr_2


title: ATAC Time_course_npTh17_20hr_3

source_name: Sorted live cells polarized in npTh17 conditions after 20hr


title: ATAC Time_course_npTh17_20hr_1


title: ATAC Time_course_pTh17_20hr_3

source_name: Sorted live cells polarized in pTh17  conditions after 20hr


title: ATAC Time_course_Th1_48hr_1


title: ATAC Time_course_Th1_20hr_2

source_name: Sorted live cells polarized in Th1 conditions after 20hr


title: ATAC Time_course_pTh17_20hr_1


title: ATAC Time_course_npTh17_12hr_3

source_name: Sorted live cells polarized in npTh17 conditions after 12hr


title: ATAC Time_course_npTh17_12hr_2


title: ATAC EAE_dLN_2


title: ATAC Time_course_npTh17_12hr_1


title: ATAC Time_course_pTh17_12hr_3

source_name: Sorted live cells polarized in pTh17  conditions after 12hr


title: ATAC Time_course_pTh17_48hr_3


title: ATAC EAE_dLN_1


title: ATAC Time_course_pTh17_12hr_2


title: ATAC Time_course_pTh17_12hr_1


title: ATAC Time_course_Th1_12hr_2

source_name: Sorted live cells polarized in Th1 conditions after 12hr


title: ATAC Time_course_Th1_12hr_1


title: ATAC Time_course_npTh17_6hr_1

source_name: Sorted live cells polarized in npTh17 conditions after 6hr


title: ATAC Time_course_npTh17_6hr_2


title: ATAC Time_course_pTh17_6hr_1

source_name: Sorted live cells polarized in pTh17  conditions after 6hr


title: ATAC Time_course_Th1_6hr_3

source_name: Sorted live cells polarized in Th1 conditions after 6hr


title: ATAC Time_course_pTh17_6hr_2


title: ATAC Time_course_Th1_6hr_1


title: ATAC Time_course_Th1_6hr_2


title: ATAC Time_course_Th1_20hr_3


title: ATAC Time_course_npTh17_1hr_3

source_name: Sorted live cells polarized in npTh17 conditions after 1hr


title: ATAC Time_course_Th1_20hr_1


title: ATAC Time_course_pTh17_1hr_3

source_name: Sorted live cells polarized in pTh17  conditions after 1hr


title: ATAC Time_course_npTh17_1hr_1


title: ATAC Time_course_npTh17_1hr_2


title: ATAC Time_course_pTh17_1hr_2


title: ATAC Time_course_Th1_1hr_3

source_name: Sorted live cells polarized in Th1 conditions after 1hr


title: ATAC Time_course_npTh17_6hr_3


title: ATAC Time_course_pTh17_1hr_1


title: ATAC Time_course_Th1_12hr_3


title: ATAC Time_course_pTh17_6hr_3


title: ATAC Time_course_Th1_1hr_1


title: ATAC Time_course_naive_0hr_3

source_name: Sorted live cells polarized in naive conditions after 0hr

value: naive


title: ATAC Time_course_naive_0hr_1


title: ATAC Time_course_naive_0hr_2


title: ATAC CD4diff_pTh17_4

source_name: Sorted live cells polarized in pTh17 conditions for 72 hours


title: ATAC CD4diff_pTh17_3


title: ATAC CD4diff_pTh17_2


title: ATAC CD4diff_npTh17_4

source_name: Sorted live cells polarized in npTh17 conditions for 72 hours


title: ATAC CD4diff_npTh17_2


title: ATAC CD4diff_pTh17_1


title: ATAC CD4diff_npTh17_1


title: ATAC CD4diff_Treg_3

source_name: Sorted live cells polarized in Treg conditions for 72 hours

value: Treg


title: ATAC CD4diff_Treg_1


title: ATAC CD4diff_Treg_2


title: ATAC CD4diff_Treg_4


title: ATAC CD4diff_Th1_4

source_name: Sorted live cells polarized in Th1 conditions for 72 hours


title: ATAC CD4diff_Th1_2


title: ATAC CD4diff_Th1_1


title: ATAC Time_course_Th1_1hr_2


title: ATAC CD4diff_Th0_4

source_name: Sorted live cells polarized in Th0 conditions for 72 hours


title: ATAC CD4diff_Th0_3


title: ATAC CD4diff_Th0_2


title: RNA EAE_dLN_4

data_processing:
Base-calling was performed by RTA v2.4.11, and the BCL files were translated to fastqs using bcl2fastq2 v2.20.0.
RNA-seq: Paired reads were mapped to mouse annotation mm10 using TopHat, and after duplicates were removed, counts tables were generaed using htseq counts. For more details, see Method section of paper, "Bulk RNA-seq pre-processing"
Assembly: mm10
Supplementary files format and content: RNA-seq: comma-separated values (CSV) files include read count values for each gene in each sample.

source_name: Sorted IL17+ cells harvested from the draining lymph node at the peak of EAE

growth_protocol: For the in vitro differentiation of naïve CD4+ T cells, naïve CD4+ CD44- CD62L+ cells were activated with plate-bound anti-CD3 and anti-CD28 antibodies in the presence of cytokines. For the acquisition of ex vivo Th17 cells, mice were immunized subcutaneously into the flanks with an emulsion of the MOG35-55 peptide and M. tuberculosis H37Ra extract in CFA for the induction of EAE.

extract_protocol:
6,000 cells were sorted by FACS from the in vitro culture or draining lymph nodes and central nervous system of EAE mice into 5ul TCL buffer supplemented with 1% 2-mercaptoethanol and stored at -80°C until library preparation.
For bulk RNA-seq, full-length RNA-seq libraries were prepared following a modified SMART-Seq2 protocol as previously described. The cDNA concentration was measured using the Quant-iT PicoGreen dsDNA Assay Kit (Thermo Fisher Scientific) and normalized to 0.25ng/ul. The cDNA libraries were prepared using the Nextera XT DNA Library Preparation kit (Illumina). Final libraries were confirmed to have a size of 500 bp using a Bioanalyzer (Agilent). Prior to sequencing, the uniquely barcoded libraries were pooled, normalized to 2 nM, and denatured using 0.1 N NaOH. Flow cell cluster amplification and sequencing were performed according to the manufacturer’s protocols using the paired-end Illumina sequencing (38bp X 2) with 75 cycle Nextseq 500 high output V2 kit (Illumina).

value: Wildtype


title: ATAC CD4diff_Th0_1


title: RNA EAE_dLN_5


title: RNA EAE_dLN_3


title: RNA EAE_dLN_1


title: RNA EAE_dLN_2


title: ATAC CD4diff_npTh17_3


title: RNA Time_course_npTh17_48hr_2

source_name: Sorted live cells polarized in npTh17 conditions after 48hr


title: RNA Time_course_pTh17 _48hr_3

source_name: Sorted live cells polarized in pTh17  conditions after 48hr


title: ATAC CD4diff_Th1_3


title: RNA Time_course_pTh17 _48hr_1


title: RNA Time_course_pTh17 _48hr_2


title: RNA Time_course_Th1_48hr_1

source_name: Sorted live cells polarized in Th1 conditions after 48hr


title: RNA Time_course_npTh17_20hr_3

source_name: Sorted live cells polarized in npTh17 conditions after 20hr


title: RNA Time_course_npTh17_20hr_2


title: RNA Time_course_Th1_48hr_3


title: RNA Time_course_Th1_48hr_2


title: RNA Time_course_npTh17_20hr_1


title: RNA Time_course_npTh17_48hr_3


title: RNA Time_course_pTh17 _20hr_3

source_name: Sorted live cells polarized in pTh17  conditions after 20hr


title: RNA Time_course_Th1_20hr_3

source_name: Sorted live cells polarized in Th1 conditions after 20hr


title: RNA Time_course_Th1_20hr_2


title: RNA Time_course_pTh17 _20hr_1


title: RNA Time_course_npTh17_48hr_1


title: RNA Time_course_Th1_20hr_1


title: RNA Time_course_npTh17_12hr_3

source_name: Sorted live cells polarized in npTh17 conditions after 12hr


title: RNA Time_course_pTh17 _12hr_3

source_name: Sorted live cells polarized in pTh17  conditions after 12hr


title: RNA Time_course_npTh17_6hr_3

source_name: Sorted live cells polarized in npTh17 conditions after 6hr


title: RNA Time_course_pTh17 _12hr_1


title: RNA Time_course_npTh17_6hr_2


title: RNA Time_course_Th1_12hr_2

source_name: Sorted live cells polarized in Th1 conditions after 12hr


title: RNA Time_course_Th1_12hr_3


title: RNA Time_course_npTh17_6hr_1


title: RNA Time_course_pTh17 _6hr_2

source_name: Sorted live cells polarized in pTh17  conditions after 6hr


title: RNA Time_course_pTh17 _6hr_3


title: RNA Time_course_pTh17 _20hr_2


title: RNA Time_course_Th1_6hr_1

source_name: Sorted live cells polarized in Th1 conditions after 6hr


title: RNA Time_course_pTh17 _6hr_1


title: RNA Time_course_Th1_6hr_3


title: RNA Time_course_npTh17_1hr_1

source_name: Sorted live cells polarized in npTh17 conditions after 1hr


title: RNA Time_course_npTh17_1hr_2


title: RNA Time_course_npTh17_1hr_3


title: RNA Time_course_npTh17_12hr_1


title: RNA Time_course_pTh17 _1hr_2

source_name: Sorted live cells polarized in pTh17  conditions after 1hr


title: RNA Time_course_npTh17_12hr_2


title: RNA Time_course_Th1_1hr_3

source_name: Sorted live cells polarized in Th1 conditions after 1hr


title: RNA Time_course_pTh17 _1hr_1


title: RNA Time_course_pTh17 _12hr_2


title: RNA Time_course_naïve_0hr_3

source_name: Sorted live cells polarized in naïve conditions after 0hr


title: RNA Time_course_naïve_0hr_2


title: RNA CD4diff_pTh17_4

source_name: Sorted live cells polarized in pTh17 conditions for 72 hours


title: RNA Time_course_Th1_1hr_1


title: RNA Time_course_naïve_0hr_1


title: RNA CD4diff_pTh17_2


title: PD1 -/- MI, visium

description:
10x Genomics
PD1KO

data_processing:
The Space Ranger Single-Cell Software Suit was used to perform sample demultiplexing, reads alignment, and to generate feature-spot matrices.
The cDNA reads were aligned to the mm10/GRCm38 mRNA reference genome. The H&E staining image was supplemented to Spatial Ranger for tissue detection, fiducial detection, and alignment of the spatial position of sequenced data points.
Assembly: mm10
Supplementary files format and content: Tab-separated values files, matrix files, and H&E tissue staining images

source_name: Heart, transverse section

extract_protocol:
Hearts at 7-day post the surgery were dissected and immediately embedded in a tissue embedding mold filled with OCT and placed in a bath of isopentane and liquid nitrogen. OCT embedded heart tissue blocks were cryosectioned in a cryostat to generate appropriately sized sections for Visium Spatial slides. 10 um sections at 200 um below the ligation suture were collected and placed on the Visum Spatial slides capture areas.
Heart sections were permeabilized for 18 min followed by RNA reverse transcription. The optimized permeabilization time was determined using the Visum Spatial Tissue Optimization Kit (10xGenomics) according to the manufacturer’s protocol. Second strand cDNA was subsequently synthesized on tissue sections and was transferred to an Eppendorf tube after denaturation. The cDNA from the tissue slide that was spatially barcoded was next amplified via PCR and enzymatically fragmentated. P5, P7, i7 and i5 sample indexes are added via End Repair, A-tailing, Adaptor ligation and PCR to make the final sequencing library.
Visium Spatial Transcriptome RNAseq

treatment_protocol: Myocardial infarction surgery was performed on 2-day-old mice by ligating the  left anterior descending artery

value: all cardiac cells

value: Heart, transverse section

value: PD1 KO

value: myocardial infarction


title: RNA CD4diff_npTh17_3

source_name: Sorted live cells polarized in npTh17 conditions for 72 hours


title: RNA CD4diff_npTh17_4


title: RNA CD4diff_npTh17_2


title: RNA CD4diff_pTh17_1


title: RNA Time_course_Th1_6hr_2


title: RNA CD4diff_npTh17_1


title: RNA CD4diff_Treg_4

source_name: Sorted live cells polarized in Treg conditions for 72 hours


title: RNA CD4diff_pTh17_3


title: RNA CD4diff_Treg_3


title: RNA Time_course_pTh17 _1hr_3


title: RNA Time_course_Th1_1hr_2


title: RNA CD4diff_Th1_3

source_name: Sorted live cells polarized in Th1 conditions for 72 hours


title: RNA CD4diff_Treg_2


title: RNA CD4diff_Th1_1


title: RNA CD4diff_Th1_2


title: RNA Il17eGFP_d3_pTh17_GFP_2

description: RNA_seq_npTh17_pTh17_Il17eGFP_rawcounts.txt

source_name: Sorted GFP+ cells polarized in pTh17 conditions for 72 hours


title: RNA Il17eGFP_d3_pTh17_GFP_3


title: RNA Il17eGFP_d3_pTh17_GFP_1


title: RNA Il17eGFP_d2_pTh17_GFP_3

source_name: Sorted GFP+ cells polarized in pTh17 conditions for 48 hours


title: RNA Il17eGFP_d2_pTh17_GFP_1


title: RNA Il17eGFP_d2_npTh17_all_2

source_name: Sorted live cells polarized in npTh17 conditions for 48 hours


title: RNA Il17eGFP_d2_npTh17_all_1


title: RNA Il17eGFP_d1_pTh17_all_1

source_name: Sorted live cells polarized in pTh17 conditions for 24 hours


title: RNA Il17eGFP_d1_npTh17_all_1

source_name: Sorted live cells polarized in npTh17 conditions for 24 hours


title: RNA Il17eGFP_d1_npTh17_all_2


title: RNA Il17eGFP_d2_npTh17_all_3


title: RNA Il17eGFP_d1_npTh17_all_3


title: RNA Il17eGFP_d1_pTh17_all_2


title: RNA CD4diff_Th1_4


title: RNA Il17eGFP_d1_pTh17_all_3


title: BeclinWT_KI_LPS_6h_3_S9

first: Ramnik

last: Xavier

address: 415 Main Street

institute: Broad Institute of MIT and Harvard

description: Wild-type BMDMs harvested after 6 hours of LPS stimulation

data_processing:
Alignment with Tophat
Counting of transcripts with HTSeq
Downstream analysis with custom R script
Assembly: mm10
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample in txt file format

source_name: BMDMs

growth_protocol: Bone marrow from Beclin1flox/flox-LysM-Cre+ and Beclin1flox/flox-LysM-Cre- mice or Beclin1F121A/F121A and littermate control mice were cultured in DMEM supplemented with 10% fetal bovine serum, 100U/ml penicillin, 100mg/ml streptomycin and 20ng/mL murine M-CSF (PeproTech) for 7 days to generate BMDMs

extract_protocol:
Cells were lyzed in RLT buffer (Qiagen) and samples were frozen at -80 until processing
Libraries were constructed from lysates using the Smart-Seq2 protocol. Briefly, RNA was reverse transcribed with an oligo(DT) primer and template switch oligo, and the resulting cDNA was preamplified and used for tagmentation (Nextera XT) and barcoding
Libraries were sequenced with a 75 cycle NextSeq kit and the following parameters : paired End: Index1 8, Index2 8, Read1 38, Read2 38

treatment_protocol: On day 7, adherent BMDMs were dissociated from the plate and re-plated for experiments. BMDMs were stimulated with 100ng/ml LPS (Sigma) plus 100ng/ml IFN𝛾 (BD Biosciences) for M1 activation for the indicated duration (0h, 6h, or 24h).

value: BMDMs

value: WT

value: Mice:7 weeks, BMDMs:stimulated on day 7


title: BeclinWT_KI_LPS_6h_2_S8


title: BeclinWT_KI_LPS_6h_5_S11


title: BeclinWT_KI_LPS_6h_4_S10


title: BeclinWT_KI_LPS_6h_6_S12


title: BeclinWT_KI_LPS_6h_1_S7

description: Wild-type BMDMs harvested after 24 hours of LPS stimulation


title: BeclinWT_KI_LPS_24h_6_S18


title: BeclinWT_KI_LPS_24h_5_S17


title: BeclinWT_KI_LPS_24h_4_S16


title: BeclinWT_KI_LPS_24h_2_S14


title: BeclinWT_KI_LPS_24h_1_S13


title: BeclinWT_KI_LPS_0h_6_S6

description: Wild-type BMDMs harvested after 0 hours of LPS stimulation


title: BeclinWT_KI_LPS_24h_3_S15


title: RNA Il17eGFP_d2_pTh17_GFP_2

value: Spleen and lymph nodes


title: BeclinWT_KI_LPS_0h_4_S4


title: BeclinWT_KI_LPS_0h_3_S3


title: BeclinWT_KI_LPS_0h_5_S5


title: BeclinF121A_LPS_6h_6_S30

description: Knock in BMDMs harvested after 6 hours of LPS stimulation

value: KI


title: BeclinWT_KI_LPS_0h_1_S1


title: BeclinWT_KI_LPS_0h_2_S2


title: BeclinF121A_LPS_6h_3_S27


title: BeclinF121A_LPS_6h_1_S25


title: BeclinF121A_LPS_6h_4_S28


title: BeclinF121A_LPS_24h_6_S36

description: Knock in BMDMs harvested after 24 hours of LPS stimulation


title: BeclinF121A_LPS_6h_2_S26


title: BeclinF121A_LPS_24h_5_S35


title: BeclinF121A_LPS_24h_4_S34


title: BeclinF121A_LPS_24h_3_S33


title: BeclinF121A_LPS_0h_4_S22

description: Knock in BMDMs harvested after 0 hours of LPS stimulation


title: IRF8KO microglia - mCpG_rep2

city: Bethesda

first: Keita

last: Saeki

state: Maryland

address: 6 Center Drive

institute: NIH/NICHD

description: 2x75 paired-end sequence reads

data_processing:
Based on the Bismark M-bias plot, the adapters, low-quality sequence, and additional 10bp of 5'-end and 2bp of 3'-end were trimmed from the sequencing data using TrimGalore.
The data were first aligned using Bismark with -q --score-min L,0,-0.4 --ignore-quals --no-mixed --no-discordant --dovetail --maxins options, and then unmapped sequences were aligned additionally with single-end mode.
Duplicated sequences were removed before methylation calling.
Two methylation calls from each replicate were merged into a single coverage file.
Differential analyses between WT and IRF8KO were performed using R/DSS package with FDR<0.05 for the differential methylated loci (DMLs)  and p<0.001 for the regions (DMRs).
Assembly: mm10
Supplementary files format and content: A single coverage file (.cov file) consists of each CpG locus, %mCpG, methylated cytosine counts, and unmethylated cytosine counts.
Supplementary files format and content: A list of DMLs with stats; IRF8NaiveDML.txt
Supplementary files format and content: A list of DMRs with stats; IRF8Naive1e-03.txt, generated by R/DSS

source_name: Microglia

growth_protocol: Microglia were non-enzymatically isolated from a 3-month-old WT and IRF8KO brain, and enriched by cell sorting.

extract_protocol:
Genomic DNA was extracted from 40,000 microglia using Quick-DNA Microprep plus kit (Zymo Research) as the manufacturer’s protocol.
50ng DNA was bisulfite-converted and processed to the library using Pico Methyl-Seq Library Prep Kit (Zymo Research) with an 8-cycle PCR amplification

value: FACS-sorted microglia

value: untreated


title: BeclinF121A_LPS_24h_1_S31


title: WT microglia - mCpG_rep2

description: 2x75 paired-end sequence reads


title: BeclinF121A_LPS_24h_2_S32


title: BeclinF121A_LPS_0h_5_S23


title: BeclinF121A_LPS_0h_3_S21


title: BeclinF121A_LPS_0h_6_S24


title: BeclinF121A_LPS_0h_1_S19


title: IRF8KO microglia - mCpG_rep1

description: 2x75 paired-end sequence reads


title: WT microglia - mCpG_rep1

description: 2x75 paired-end sequence reads


title: BeclinF121A_LPS_6h_5_S29


title: BeclinF121A_LPS_0h_2_S20


title: E14, D8, primed, replicate 2, ChIP-seq, Input

city: Houston

first: Junwoo

last: Lee

address: 2120 El Paseo Street, Apt.603

department: Epigenetics and Molecular Carcinogenesis

institute: MD Anderson Cancer Center

description:
D8_Brg1_CDM_merge.subtract.bw
D8_H3K4me1_CDM_merge.bw
D8_H3K4me3_CDM_merge.bw
D8_H3K27ac_CDM_merge.bw

data_processing:
Adaptor trimming and low-quality reads were removed by Cutadapt.
Reads were aligned to mm10 using Bowtie 2 alignment tool using --very-sensitive-local preset parameter.
Data from two biological replicates were first compared to check for concordance (R2 > 0.9), and then merged into a single read file for each cell type for further downstream analysis.
The high confidence peak sets were selected from biological replicates using the intersectBed function from BEDTools with default parameters.
For histone and Brg1 ChIP, peaks were called using MACS2 with the following parameters:  --broad -q 0.05 –nomodel -extsize 500. To compare the signals between IP and input, ‘bdgcmp’ from MACS2 option was used. Peaks were annotated using the annotatePeaks module of HOMER package. All the heatmaps were drawn using ‘plotHeatmap’ from deeptools.
Assembly: mm10, M22
Supplementary files format and content: bw files normalized by input control

growth_protocol: Mouse embryonic stem cells (E14Tg2a, ATCC) were maintained on 1% gelatin-coated plates in the ESGRO complete plus clonal grade medium (Millipore). Embryonic stem cells (ESCs) were cultured on gelatin-coated plates in DMEM (Invitrogen) supplemented with 15% FBS, 1X-Gultamax (Gibco), Na-Pyruvate (Gibco), 10mM 2-mercaptoethanol, 0.1 mM nonessential amino acids (Gibco), 1U/ml of ESGRO mLIF (Millipore), and 2i inhibitors (MEK inhibitor PD0325901, Gsk3b inhibitor (CHIR99021 – Stem Cell technology) in naïve (or +2i) condition. In epiblast stem cells (EpiSCs)  or primed condition, cells were cultured in chemically defined medium (IMDM and F12-Invitrogen) supplemented with 2%-BSA (Sigma), Insulin (Roche), Transferrin (Roche), CD-lipid concentrate (Gibco), FGF2 (R&D), and Activin-A (R&D).

extract_protocol:
After 2 washes with ice cold PBS, cells were incubated in lysis buffer (5 mM PIPES pH 8.0, 85 mM KCl, 0.5 % NP-40 supplemented with protease inhibitor) for 10 min, and nuclei were collected after centrifugation. The nuclear pellet was re-suspended in shearing buffer (12 mM Tris-HCl pH 7.5, 6 mM EDTA pH 8.0, 0.5 % SDS supplemented with protease inhibitor) and chromatin was fragmented using ME220 focused ultra-sonicator (Covaris) to obtain DNA fragments ranging 200-600 bp. The chromatin lysate was collected after centrifugation and incubated overnight at 4°C with SMARCA4 and respective histone antibodies conjugated with Dynabeads Protein G (Invitrogen). Next day, antibody-bound DNA were collected using Dynamag, washed extensively as described in the protocol, treated with RNase and Proteinase K, and reverse crosslinked overnight followed by DNA extraction using Ampure X beads (Beckman Coulter).
Purified ChIP DNA was used for library construction using NEB Ultra II DNA library prep kit (New England Biolabs)

treatment_protocol: Cells were crosslinked in 1% formaldehyde for 10 min at room temperature, before quenching with 125 mM glycine for 5 min.

value: embryonic stem cells

value: dAT

value: FGF2 (R&D), and Activin-A (R&D)

tag: developmental stage

value: primed


title: BeclinxLysMCre_LPS_6h_9_S36

description: Knock out BMDMs harvested after 6 hours of LPS stimulation


title: RNA CD4diff_Treg_1

value: Treg


title: E14, D8, primed, replicate 1, ChIP-seq, Input


title: BeclinxLysMCre_LPS_6h_8_S35


title: E14, D8, naïve, replicate 2, ChIP-seq, Input

description:
D8_Brg1_2i_merge.subtract.bw
D8_H3K4me1_2i_merge.bw
D8_H3K4me3_2i_merge.bw
D8_H3K27ac_2i_merge.bw

value: 2i inhibitors (MEK inhibitor PD0325901, Gsk3b inhibitor (CHIR99021 – Stem Cell technology))

value: naive


title: BeclinxLysMCre_LPS_6h_7_S34


title: E14, D8, naïve, replicate 1, ChIP-seq, Input


title: BeclinxLysMCre_LPS_6h_6_S33


title: E14, A2, primed, replicate 2, ChIP-seq, Input

description:
A2_Brg1_CDM_merge.subtract.bw
A2_H3K4me1_CDM_merge.bw
A2_H3K4me3_CDM_merge.bw
A2_H3K27ac_CDM_merge.bw


title: E14, A2, naïve, replicate 2, ChIP-seq, Input

description:
A2_Brg1_2i_merge.subtract.bw
A2_H3K4me1_2i_merge.bw
A2_H3K4me3_2i_merge.bw
A2_H3K27ac_2i_merge.bw


title: BeclinxLysMCre_LPS_6h_1_S28


title: BeclinxLysMCre_LPS_6h_5_S32


title: E14, A2, primed, replicate 1, ChIP-seq, Input


title: BeclinxLysMCre_LPS_6h_4_S31


title: E14, A2, naïve, replicate 1, ChIP-seq, Input


title: BeclinxLysMCre_LPS_24h_8_S53

description: Knock out BMDMs harvested after 24 hours of LPS stimulation


title: BeclinxLysMCre_LPS_24h_9_S54


title: E14, D8, primed, replicate 2, ChIP-seq, H3K27ac

value: H3K27ac (Abcam, ab4729)


title: E14, WT, naïve, ChIP-seq, Input

description:
WT_Brg1_2i_merge.subtract.bw
WT_H3K4me1_WT_2i_merge.subtract.bw
WT_H3K4me3_2i_merge.subtract.bw
WT_H3K27ac_2i_merge.subtract.bw


title: BeclinxLysMCre_LPS_24h_6_S51


title: E14, D8, naïve, replicate 1, ChIP-seq, H3K27ac


title: BeclinxLysMCre_LPS_24h_4_S49


title: BeclinxLysMCre_LPS_24h_7_S52


title: E14, WT, primed, ChIP-seq, Input

description:
WT_Brg1_CDM_merge.subtract.bw
WT_H3K4me1_WT_CDM_merge.subtract.bw
WT_H3K4me3_CDM_merge.subtract.bw
WT_H3K27ac_CDM_merge.subtract.bw


title: E14, D8, primed, replicate 1, ChIP-seq, H3K27ac


title: BeclinxLysMCre_LPS_24h_2_S47


title: BeclinxLysMCre_LPS_0h_9_S18

description: Knock out BMDMs harvested after 0 hours of LPS stimulation


title: E14, A2, primed, replicate 2, ChIP-seq, H3K27ac


title: E14, A2, naïve, replicate 2, ChIP-seq, H3K27ac


title: BeclinxLysMCre_LPS_24h_1_S46


title: BeclinxLysMCre_LPS_24h_5_S50


title: E14, WT, primed, replicate 2, ChIP-seq, H3K27ac


title: BeclinxLysMCre_LPS_0h_8_S17


title: BeclinxLysMCre_LPS_0h_7_S16


title: BeclinxLysMCre_LPS_6h_2_S29


title: E14, A2, naïve, replicate 1, ChIP-seq, H3K27ac


title: E14, A2, primed, replicate 1, ChIP-seq, H3K27ac


title: E14, WT, primed, replicate 1, ChIP-seq, H3K27ac


title: BeclinxLysMCre_LPS_0h_5_S14


title: E14, D8, naïve, replicate 2, ChIP-seq, H3K27ac


title: E14, WT, naïve, replicate 1, ChIP-seq, H3K27ac


title: E14, D8, primed, replicate 2, ChIP-seq, H3K4me3

value: H3K4me3 (Abcam, ab8580)


title: BeclinxLysMCre_LPS_0h_6_S15


title: BeclinxLysMCre_LPS_0h_4_S13


title: E14, WT, naïve, replicate 2, ChIP-seq, H3K27ac


title: E14, D8, primed, replicate 1, ChIP-seq, H3K4me3


title: E14, D8, naïve, replicate 2, ChIP-seq, H3K4me3


title: BeclinWT_LPS_6h_8_S26


title: BeclinxLysMCre_LPS_0h_2_S11


title: E14, A2, primed, replicate 2, ChIP-seq, H3K4me3


title: BeclinWT_LPS_6h_7_S25


title: BeclinxLysMCre_LPS_0h_1_S10


title: E14, A2, primed, replicate 1, ChIP-seq, H3K4me3


title: BeclinWT_LPS_6h_9_S27


title: E14, A2, naïve, replicate 2, ChIP-seq, H3K4me3


title: E14, D8, naïve, replicate 1, ChIP-seq, H3K4me3


title: E14, A2, naïve, replicate 1, ChIP-seq, H3K4me3


title: BeclinWT_LPS_6h_4_S22


title: E14, WT, primed, replicate 2, ChIP-seq, H3K4me3


title: BeclinWT_LPS_6h_5_S23


title: BeclinWT_LPS_6h_6_S24


title: BeclinWT_LPS_6h_1_S19


title: E14, WT, primed, replicate 1, ChIP-seq, H3K4me3


title: BeclinWT_LPS_6h_2_S20


title: E14, WT, naïve, replicate 2, ChIP-seq, H3K4me3


title: BeclinWT_LPS_24h_9_S45


title: BeclinWT_LPS_24h_8_S44


title: E14, WT, naïve, replicate 1, ChIP-seq, H3K4me3


title: E14, D8, primed, replicate 1, ChIP-seq, H3K4me1

value: H3K4me1 (Abcam, ab8895)


title: E14, D8, naïve, replicate 2, ChIP-seq, H3K4me1


title: BeclinWT_LPS_24h_5_S41

value: BMDMs


title: E14, D8, primed, replicate 2, ChIP-seq, H3K4me1


title: BeclinWT_LPS_24h_4_S40

value: WT


title: BeclinWT_LPS_24h_7_S43

value: Mice:7 weeks, BMDMs:stimulated on day 7


title: E14, A2, primed, replicate 2, ChIP-seq, H3K4me1


title: E14, D8, naïve, replicate 1, ChIP-seq, H3K4me1


title: E14, A2, primed, replicate 1, ChIP-seq, H3K4me1


title: BeclinWT_LPS_24h_2_S38


title: E14, WT, primed, replicate 1, ChIP-seq, H3K4me1


title: E14, A2, naïve, replicate 2, ChIP-seq, H3K4me1


title: BeclinWT_LPS_24h_1_S37


title: E14, WT, primed, replicate 2, ChIP-seq, H3K4me1


title: E14, WT, naïve, replicate 2, ChIP-seq, H3K4me1


title: E14, A2, naïve, replicate 1, ChIP-seq, H3K4me1


title: BeclinWT_LPS_0h_7_S7


title: BeclinWT_LPS_0h_9_S9


title: E14, D8, primed, replicate 2, ChIP-seq, Brg1/SMARCA4

value: Brg1/SMARCA4 (Abcam; ab110641)


title: BeclinWT_LPS_0h_6_S6


title: 32s

city: Balice near Krakow

first: Klaudia

last: Pawlina-Tyszko

address: Krakowska 1

department: Deaprtment of Animal Genomics and Molecular Biology

country: Poland

institute: National Research Institute of Animal Production

data_processing:
demultiplexing: bcl2fastq
quality control: FastQC
trimming off the 3' adapter sequences and length filtering (18-26 nt): Trimmomatic, Flexbar
mapping: the filtered reads were mapped to EcuCab3.0 genome using BWA
miRNA identification: miRDeep2 with default parameters with reference to miRBAse 22.1
differential expression analysis: DESeq2 (a Bioconductor R-project package)
Assembly: EcuCab3.0
Supplementary files format and content: CSV file with normalized abundance measurments for all investigated samples

organism: Equus caballus

source_name: equine heart tissue

extract_protocol:
The quantity and quality of the obtained RNA were checked on a NanoDrop 2000 spectrophotometer (Thermo Scientific; Wilmington, USA) and on a TapeStation 2200 instrument (RNAScreen Tape, Agilent, Perlan Technologies, Poland).
microRNA libraries were prepared with the use of NEBNext Multiplex Small RNA Library Prep Set for Illumina (New England Biolabs; E7300L), according the standard protocol. Briefly, the first step was the 3’ adaptor ligation, followed by hybridization with the Reverse Transcription Primer and ligation with the 5’ adaptor. The RNA-adaptor ligation products were subjected to reverse transcription. Then, PCR amplification with 12 different indexed primers was performed to allow further multiplexing of the samples. The amplified samples were purified and size-selected on a Novex 6% TBE PAGE gel (Invitrogen). After the overnight elution from the gel, the libraries were precipitated and purified with ethanol (POCH). Next, they were subjected to a concentration measurement with a Qubit 2.0 Fluorometer (Thermo Fisher Scientific) and a size assessment with a 2200 TapeStation instrument (Agilent). The libraries were stored at -20°C at 10nM concentration until further use.

treatment_protocol: Immediately after slaughter, tissue samples were put in RNA Later solution (Thermo Fisher Scientific) and stored at -80°C

value: heart tissue

tag: molecule subtype

value: microRNA


title: 34p

source_name: equine lung tissue

value: lung tissue


title: 34s


title: 32w

source_name: equine liver tissue

value: liver tissue


title: 34w


title: E14, D8, primed, replicate 1, ChIP-seq, Brg1/SMARCA4

value: embryonic stem cells

value: dAT


title: E14, D8, naïve, replicate 2, ChIP-seq, Brg1/SMARCA4


title: BeclinWT_LPS_0h_5_S5


title: BeclinWT_LPS_0h_4_S4


title: 32p


title: E14, A2, primed, replicate 1, ChIP-seq, Brg1/SMARCA4

value: FGF2 (R&D), and Activin-A (R&D)

value: primed


title: E14, A2, primed, replicate 2, ChIP-seq, Brg1/SMARCA4


title: E14, D8, naïve, replicate 1, ChIP-seq, Brg1/SMARCA4

value: 2i inhibitors (MEK inhibitor PD0325901, Gsk3b inhibitor (CHIR99021 – Stem Cell technology))


title: 30w


title: BeclinWT_LPS_0h_8_S8


title: E14, A2, naïve, replicate 2, ChIP-seq, Brg1/SMARCA4

value: naive


title: E14, WT, naïve, replicate 1, ChIP-seq, H3K4me1


title: BeclinWT_LPS_0h_2_S2


title: 30s


title: 30p


title: E14, WT, naïve, replicate 2, ChIP-seq, Brg1/SMARCA4


title: E14, A2, naïve, replicate 1, ChIP-seq, Brg1/SMARCA4


title: BeclinWT_LPS_0h_1_S1


title: S38_24HRLPS_3


title: E14, WT, primed, replicate 1, ChIP-seq, Brg1/SMARCA4


title: E14, WT, primed, replicate 2, ChIP-seq, Brg1/SMARCA4


title: 27w


title: S38_24HRLPS_2


title: E14, dAT2, primed, replicate 1, ATAC-seq

data_processing:
Adaptor trimming and low-quality reads were removed by Cutadapt.
The Reads were aligned to mm10 using Bowtie 2 alignment tool using --very-sensitive-local preset parameter.
Data from two biological replicates were first compared (R2 > 0.9), and then merged into a single read file for each time point.
ATAC-seq peaks were then called using MACS2 with the following parameters: -q 0.01–nomodel–shift 75 –extsize 150. To get a union set of peaks from all samples (WT and dAT mutants),  MACS2 peaks from each condition were merged using mergePeaks module from HOMER (default parameters)
For identifying differentially accessible regions, the union set of peaks was annotated by Homer and then divided into promoter (-1 kb to +1 kb), and intronic-intergenic regions. Read counts for all peaks in the union set were obtained using the featureCount module of Subread package and differential analysis was done using edgeR. Heatmaps were created using deeptools (default parameters).
To determine the known motif enrichment findMotifsGenome module of the HOMER package was used. For motif heatmap analysis, differential ATAC-seq peaks between WT and dAT mutants  were used to identify the known motifs using ‘findMotifsGenome.pl’ from Homer. Then, p-value of identified motifs were  transformed into Z-score and plotted as a heatmaps using the R ggplot package. For ATAC footprint analysis, normalized ATAC files were corrected using ‘ATACorrect’ module from TOBIAS. Next, the average ATAC-signals were calculated (around +/- 100bp of the center of the motif enriched peaks) and plotted using plotProfile from deeptools.
Assembly: mm10, M22
Supplementary files format and content: bw files normalized by macs2 internal control

extract_protocol:
Briefly, 50,000 cells were washed with cold PBS, collected by centrifugation then resuspended in resuspension buffer (10 mM Tris-HCl, pH 7.4, 10 mM NaCl, 3 mM MgCl2). After collection, cells were lysed in lysis buffer (10 mM Tris-HCl, pH 7.4, 10 mM NaCl, 3 mM MgCl2, 0.1% NP-40) and collected
The collected cells were incubated in transposition mix containing Tn5 transposase (Illumina). Purified DNA was then ligated with adapters, amplified and size selected for sequencing.


title: S38_24HRLPS_1


title: 27s


title: E14, dAT2, naïve, replicate 2, ATAC-seq


title: E14, dAT2, naïve, replicate 1, ATAC-seq


title: E14, dAT1, primed, replicate 1, ATAC-seq


title: Sample 35: Synthetic_0%_Am_Cm_Gm_Treated_rep2

city: Chicago

first: Li-Sheng

last: Zhang

state: IL

address: 929 E 57th St Rm E313

department: Department of Chemistry

institute: The University of Chicago

data_processing:
All these oligo mixtures were subjected to Nm-Mut-seq and the mutation rate pattern of each sequence context were analyzed, followed by plotting a fitting curve of the observed mutation rate vs. methylation fraction. The observed mutation rate “Y” and Nm fraction “x” can be expressed by the following equation:
Y = [B + (R – A * R -  B) * x]  / (1- A *x)
A is the truncation rate (that represents the fraction of short cDNA that could come from RT truncations), B is the background mutation rate (that means the mutation rate at unmodified A, C or G), and R is the mutagenic efficiency.
Genome_build: hg38
Supplementary_files_format_and_content: xlsx (excel)

organism: synthetic construct

source_name: synthetic RNA oligo

growth_protocol: Three 35-mer RNA probes with -NN(Am)NN-, -NN(Cm)NN- and -NN(Gm)NN- were mixed together in equimolar ratio as “100% Nm” standard. The RNA oligos containing -NNANN-, -NNCNN- and -NNGNN- were pooled as “0% Nm”. Then the “100% Nm” and “0% Nm” standard were mixed and generated five oligo mixtures with different methylation fractions (100% Nm, 75% Nm, 50% Nm, 25% Nm, and 0% Nm).

extract_protocol:
Synthetic RNA oligo probes were used for library construction.
The Illumina sequencing libraries were prepared with an optimized protocol based on NEBNext Small RNA Library Prep Set. 1.0 μg synthetic RNA oligo containing different Nm methylation fractions were subjected to 5’-/3’-end repair by T4 PNK treatment (Thermo Fisher Scientific): 40 μl RNA was mixed with 5 μL 10X T4 PNK buffer (NEB) and 5 μl T4 PNK enzyme, incubated at 37°C for 30 min; then 5 μL 10 mM ATP was added into the mixture for another 30-min incubation at 37°C, followed by Oligo Clean & Concentrator purification (Zymo Research). Starting with the 3’-adaptor ligation, the RNA oligos were incubated with 0.5 μL (12 μM) customized adaptors 5’App-NNNNN ATCACGAGATCGGAAGAGCACACGTCT-3SpC3 (containing five randomized nucleotides sequence (NNNNN) together with a 6-mer in-line barcode) at 70 °C for 2 mins and immediately placed on ice. 10 µL 3´ Ligation Reaction Buffer (2X) (NEB) and 3 µL 3´ Ligation Enzyme Mix (NEB) were added to the RNA-adapter mixture. The reaction was incubated at 25 °C for 2 hrs. Then 1.0 µL SR RT Primer for Illumina (NEB) was added to the mixture, followed by 5 minutes at 75°C, 15 minutes at 37°C, 15 minutes at 25°C, and then on ice. The denatured 0.5 µL 5’-Adaptor (5’-GUUCAGAGUUCUACAGUCCGACGAUCNNNNN-3’) was added into the mixture, together with 1.0 µL 5´ Ligation Reaction Buffer (10X) (NEB) and 2.5 µL 5´ Ligation Enzyme Mix (NEB). The reaction was incubated at 25 °C for 2 hrs followed by 16 °C for 4 hrs, followed by RNA Clean & Concentrator purification.  The purified RNA was eluted with 20 μL RNase-free water and subjected to reverse transcription. Two independent RT reactions (10 μL RNA for each reaction) were conducted with evolved RT 41B4 under two dNTP conditions: one RT reaction (as “input”) incubated with 1.0 mM dNTP without generating mutations on Nm sites; the other RT reaction (as “Nm-Mut-seq”) with 2 μM dNTP + 1 mM dATP would reveal mutations on Am, Cm and Gm sites. The RT reactions were performed at 37°C for 1 hour, followed by 80°C inactivation for 10 min. The libraries were amplified using the SR Primer for Illumina (NEB) and indexed primers (from NEBNext Multiplex Oligos for Illumina).
RNA-Seq. All libraries were sequenced on Illumina NovaSeq 6000 with single-end 100 bp read length.

value: synthetic RNA oligo


title: E14, dAT1, naïve, replicate 1, ATAC-seq


title: 27p


title: S37_24HRLPS_2


title: S37_24HRLPS_3


title: Sample 34: Synthetic_0%_Am_Cm_Gm_Treated_rep1

treatment_protocol: Synthetic RNA oligo probes were used for library construction.


title: E14, WT, primed, replicate 2, ATAC-seq


title: E14, WT, primed, replicate 1, ATAC-seq


title: Sample 33: Synthetic_25%_Am_Cm_Gm_Treated_rep2


title: Sample 32: Synthetic_25%_Am_Cm_Gm_Treated_rep1


title: E14, WT, naïve, replicate 1, ChIP-seq, Brg1/SMARCA4


title: Sample 31: Synthetic_50%_Am_Cm_Gm_Treated_rep2


title: S36_24HRLPS_3


title: S36_24HRLPS_2


title: M3KO_SG_arsenite_2

city: New York

first: Ryan

middle: J

last: Ries

state: NY

address: 1300 York Avenue

institute: Weill Cornell Medical College

description: stress granule-enriched RNA

data_processing:
Fastq files were trimmed  by removing Illumina adapter sequences and quality trimming based on a phred score cutoff of >30.  Reads <12 nts were excluded from subsequent analysis.
All read trimming and adapter removal was performed using FLEXBAR.
Reads were aligned to the tRNA and rRNA reference sequences generated from GRCm38.75/mm10 and discarded.  Alignment was performed with STAR aligner.
Reads were aligned to the transcriptome reference sequence generated from GRCm38.75/mm10 and gene counts were generated.  Alignment was performed with STAR aligner.
For RNA-seq analysis, the R package DESeq2 was used to normalize and process raw sequence counts generated from alignment.
Genome_build: GRCm38.75/mm10
Supplementary_files_format_and_content: Processed data includes the raw gene count tables generated from the alignment.

source_name: mouse embryonic fibroblasts

growth_protocol: Mouse embryonic fibroblasts (MEFs) were grown in Dulbecco’s Modified Eagle Medium (DMEM) containing 10% fetal bovine serum (FBS) with 100 U ml-1 of penicillin and 100 ug mL-1 of streptomycin under standard culturing conditions (37°C with 5.0% CO2).  Cells were passaged as needed.

extract_protocol:
Cells were rapidly washed twice with ice-cold PBS.  Cells were pelleted and snap frozen in liquid nitrogen.  For total mRNAs, RNA was purified using Trizol-chloroform extraction followed by polyA-purification with oligo(dT) beads.  Briefly, stress granules were enriched via centrifugation and the granule-enriched RNA pool was purified using Trizol-chloroform extraction and polyA-purified with oligo(dT) beads.
Library construction and sequencing was performed at Genewiz, LLC (South Plainfield, NJ) using the Illumina HiSeq 3000.

treatment_protocol: Mettl3 knockout protocol was performed by treating cells with 500 nM 4-hydroxytamoxifen (4-OHT) for 48 h to induce activation of Cre recombinase.  After 7 days, the complete loss of Mettl3 was confirmed by western blot, and the complete loss of m6A was confirmed using thin-layer chromatography.  Samples were collected on the following day.  To induce cellular stress, sodium arsenite (500 µM, 30 min) was applied to cells.

tag: origin

value: E13.5 mouse embryo

value: Mettl3 knockout


title: M3KO_SG_arsenite_1

description: stress granule-enriched RNA


title: E14, WT, naïve, replicate 1, ATAC-seq


title: S36_24HRLPS_1

value: BMDMs


title: E14, dAT1, primed, replicate 2, ATAC-seq


title: Zfp352OE,ZFP352

city: HangZhou

first: Zhengyi

last: Li

state: ZheJiang

address: 866 Yuhangtang Rd, Hangzhou

department: Institute of Genetics

country: China

institute: Zhejiang University School of Medicine

data_processing:
Quality control for raw reads was performed by FastQC v0.11.8
Sequence reads were trimmed for adaptor sequence/low-quality sequence using cutadapt v2.9
Trimmed sequence reads were mapped to GRCm38/mm10 using STAR,Reads with maximal 1000 multiple mapped sites and no more than 3 mismatches were retained, and only the best hit was kept (parameters- --outFilterMultimapNmax 1000, --outFilterMismatchNmax 3, --outSAMmultNmax 1).
To create ChIP-seq coverage plots, the locations of the mapped ChIP-seq reads were extended to 150 bp to represent sequenced fragments, renormalized (to reads per kilobase per Million mapped reads, rpkm) and reformatted in the bigWig file format.
Peaks were called uing MACS v2.1.0 with the significance cut-off q-value <=0.01
Assembly: GRCm38(mm10)
Supplementary files format and content: bigWig

source_name: E14 WT

growth_protocol: E14 cells were cultured in DMEM high glucose with 15% FBS,100X NEAA,100X L-Glutamine,1000X β–Mercaptoethanol,homemade LIF on gelatin pre-coated plate.

extract_protocol:
Cells were fixed with 1% formaldehyde for 10 minutes. After quenching and cell lysis, chromatin was sonicated using a E220 focused-ultrasonicator (Covaris).
ChIP-seq libraries were prepared using the KAPA HTP Library Preparation Kit complemented with NEXTflex DNA Barcodes from Bioo Scientific. 10 ng of DNA was used as starting material for input and ip samples. Libraries were amplified using 13 cycles on the thermocycler. Post amplification libraries were size selected at 250-450bp in length using Agencourt AMPure XP beads from Beckman Coulter. Libraries were validated using the illumina DNA sequencing Library Prep Kit

treatment_protocol: ZFP352 was over-expressed in cell for 12h

value: E14 WT

value: embryonic stem cell

value: HA


title: S35_24HRLPS_3

value: Mice:7 weeks, BMDMs:stimulated on day 7

value: WT


title: Zfp352OE,input


title: Ctrl_SG_arsenite_2

description: stress granule-enriched RNA

value: control


title: Ctrl_SG_arsenite_1

description: stress granule-enriched RNA


title: E14, dAT1, naïve, replicate 2, ATAC-seq


title: M3KO_total_noStress_1

description: total RNA


title: Ctrl_total_noStress_2

description: total RNA


title: Sample 29: Synthetic_75%_Am_Cm_Gm_Treated_rep2


title: Sample 28: Synthetic_75%_Am_Cm_Gm_Treated_rep1


title: S37_24HRLPS_1


title: S35_24HRLPS_1


title: E14, WT, naïve, replicate 2, ATAC-seq


title: Sample 27: Synthetic_100%_Am_Cm_Gm_Treated_rep2


title: Ch12 treated with TGFb 24h Input for Samd7

first: Yongbing

last: Zhao

address: 10 Center Drive RooM 13C101A

department: NIAMS

institute: National Institutes of Health

description: library: ChIPCh12Tgfb24hBioSmad7InputS1R1

data_processing:
Base calling: Illumina CASAVA 1.8.2
ChIP-Seq: Align raw reads to the reference genome with bowtie2 (default parameters).
ChIP-Seq: Remove duplicates with picard.
ChIP-Seq: Keep high-quality reads with MAPQ>=30.
ChIP-Seq: Make bigwig track with bedtools and bedGraphToBigWig.
ChIP-Seq: Call peak with MACS2.
Genome_build: mm10

source_name: Ch12 cell line

growth_protocol: CH12 B lymphoma cells were cultured in RPMI-1640 media supplemented with 10% FBS (Gemini), 1% Penicillin-Streptomycin and 50 µM of b-mercaptoethanol (Thermo Fisher Scientific).

extract_protocol:
ChIP-Seq: Cultured cells were fixed with 1% formaldehyde (Sigma) for 10’ at 37°C. Fixation was quenched by addition of glycine (Sigma) at a final concentration of 125 mM. Twenty million fixed cells were washed with PBS and stored at −80°C until further processing or resuspended in 800 uL of RIPA buffer (10 mM Tris pH 7.6, 1 mM EDTA, 0.1% SDS, 0.1% sodium deoxycholate, 1% Triton X-100, 1 × Complete Mini EDTA free proteinase inhibitor (Roche)). Sonication was performed using Bioruptor sonicator, 30 cycles of 30” sonication and 30” of pause. Five microgram of respective antibody was incubated with 40 μL of Dynabeads Protein A (or G) for 40 min at room temperature. Antibody-bound beads were added to 500 μL of sonicated chromatin, incubated at 4°C overnight, and washed twice with RIPA buffer, twice with RIPA buffer containing 0.3M NaCl, twice with LiCl buffer (0.25 M LiCl, 0.5% Igepal-630, 0.5% sodium deoxycholate), once with TE (pH 8.0) plus 0.2% Triton X-100, and once with TE (pH 8.0). Crosslinking was reversed by incubating the beads at 65°C for 4 hr in the presence of 0.3% SDS and 1 mg/mL Proteinase K. ChIP DNA was purified by ChIP DNA clean and concentrator column (Zymo research).
ChIP-Seq: Library was prepared in Ovation SP Ultralow library system (Nugen). 50 cycles of sequencing data were acquired on Illumina HiSeq 3000.

treatment_protocol: Cultured CH12 B cells were treated with TGFb (5 ng/ml; 240-B R&D systems) for a period of 6 h or 24 h before harvesting.

value: Ch12 cell line

value: treated with TGFb 24h

tag: target

value: Input

tag: experimental type

value: ChIP-Seq


title: S34_24HRLPS_3


title: S34_24HRLPS_2


title: S35_24HRLPS_2


title: Ch12 treated with TGFb 24h Input for Smad3

description: library: ChIPCh12Tgfb24hBioSmad3InputS1R1


title: Ch12 treated with TGFb 24h Samd7

description: library: ChIPCh12Tgfb24hBioSmad7S1R1


title: Ch12 treated with TGFb 24h Smad3

description: library: ChIPCh12Tgfb24hBioSmad3S1R1


title: S33_24HRLPS_3


title: Sample 30: Synthetic_50%_Am_Cm_Gm_Treated_rep1


title: Sample 26: Synthetic_100%_Am_Cm_Gm_Treated_rep1


title: Ch12 treated with TGFb 6h Input for Smad3

description: library: ChIPCh12Tgfb6hBioSmad3InputS1R2

value: treated with TGFb 6h


title: Ch12 treated with TGFb 6h Input for Samd7

description: library: ChIPCh12Tgfb6hBioSmad7InputS1R2


title: M3KO_total_noStress_2

description: total RNA


title: Ch12 treated with TGFb 6h Samd7

description: library: ChIPCh12Tgfb6hBioSmad7S1R2


title: A2780, paclitaxel sensitive

city: Guangzhou

first: Yongli

address: Department of Cell biology and medical genetics, School of Life Sciences and Biopharmaceutics, Guangdong Pharmaceutical University, 280 Wai Huan Dong Road, University City of Guangzhou

institute: Guangdong Pharmaceutical University

data_processing:
The sequencing data was filtered with SOAPnuke (v1.5.2) by (1) Removing reads containing sequencing adapter; (2) Removing reads whose low-quality base ratio (base quality less than or equal to 5) is more than 20%; (3) Removing reads whose unknown base ('N' base) ratio is more than 5%, afterwards clean reads were obtained and stored in FASTQ format.
The clean reads were mapped to the reference genome using HISAT2 (v2.0.4). (GCF_000001405.39_GRCh38.p13)
Bowtie2 (v2.2.5) was applied to align the clean reads to the reference coding gene set.

organism: Homo sapiens

source_name: Ovarian

extract_protocol:
RNA was harvested using Trizol method, mRNA molecules were purified from total RNA using oligo(dT)-attached magnetic beads for the construction of sequencing libraries.
mRNA molecules fragmented and reversed transcription into cDNA. The synthesized cDNA was subjected to end-repair and added 'A' base and Adapter connection, PCR amplification.  Library was validated on the Agilent Technologies 2100 bioanalyzer.PCR products were heat denatured and circularized. The single strand circle DNA  were formatted as the final library.

value: Ovarian

value: epithelioid cells

value: paclitaxel sensitive


title: S34_24HRLPS_1

description: Wild-type BMDMs harvested after 24 hours of LPS stimulation


title: Sample 25: Synthetic_0%_Am_Cm_Gm_Input_rep2

value: synthetic RNA oligo


title: S33_24HRLPS_2


title: A2780-Taxol,paclitaxel resistant

value: paclitaxel resistant


title: Ch12 treated with TGFb 6h Smad3

description: library: ChIPCh12Tgfb6hBioSmad3S1R2


title: Sample 23: Synthetic_25%_Am_Cm_Gm_Input_rep2


title: Sample 24: Synthetic_0%_Am_Cm_Gm_Input_rep1


title: S33_24HRLPS_1

value: BMDMs


title: Sample 22: Synthetic_25%_Am_Cm_Gm_Input_rep1


title: Ctrl_total_noStress_1

description: total RNA

value: E13.5 mouse embryo


title: Sample 21: Synthetic_50%_Am_Cm_Gm_Input_rep2


title: S37_6HRLPS_3


title: Sample 18: Synthetic_75%_Am_Cm_Gm_Input_rep1


title: S38_6HRLPS_3


title: Sample 17: Synthetic_100%_Am_Cm_Gm_Input_rep2


title: E14, dAT2, primed, replicate 2, ATAC-seq

value: embryonic stem cells

value: dAT

value: FGF2 (R&D), and Activin-A (R&D)

value: primed


title: Sample 20: Synthetic_50%_Am_Cm_Gm_Input_rep1


title: Sample 19: Synthetic_75%_Am_Cm_Gm_Input_rep2


title: S38_6HRLPS_1

value: Mice:7 weeks, BMDMs:stimulated on day 7


title: S38_6HRLPS_2


title: S37_6HRLPS_1


title: 35cycle_10X

city: Oxford

first: Adam

last: Cribbs

address: Windmill Road

department: NDORMS

country: United Kingdom

institute: University of Oxford

data_processing:
We performed basecalling on the raw fast5 data using Guppy (v) (guppy_basecaller –compress-fastq -c dna_r104_450bps_hac.cfg -x “cuda:1”) in GPU mode from Oxford Nanopore Technologies running on a A100 graphics card.
Assembly: hg38
Supplementary files format and content: Tab-separated values files and matrix files

source_name: JJN3 and 5TGMG1

extract_protocol:
Samples were processed using either 10X chromium or the Drop-seq DolomiteBio Nadia encapsulator system.
10X library preperation or scCOLOR-seq protocol was used.
For nanopore sequencing, cDNA was amplified with 30 or 35 PCR reactions and sequencing libraries were prepared using the Oxford Nanopore LSK-114 library preperation kit.

value: JJN3 and 5TGMG1

value: Myeloma cell lines (2000 cells)


title: Sample 16: Synthetic_100%_Am_Cm_Gm_Input_rep1


title: 30cycle_10X


title: 269_ib morphea lesional

type: RNA

first: Jane

last: Zhu

address: 5323 Harry Hines Blvd

institute: University of Texas Southwestern Medical Center

description: morphea lesional

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalized using quantile normalization with IlluminaGUI in R

label: biotin

source_name: skin

label_protocol: Biotinylated RNA using Illumina® TotalPrep™ RNA Amplification Kit

extract_protocol: RNA was extracted using the Illumina TotalPrep kit

tag: biopsied region

value: inflammatory border


title: S36_6HRLPS_3


title: S36_6HRLPS_2


title: 213_sc morphea lesional

description: morphea lesional

value: sclerotic


title: S37_6HRLPS_2


title: 269_sc morphea lesional

description: morphea lesional


title: 268_ua unaffected skin

description: unaffected skin

value: unaffected


title: 268_sc morphea lesional

description: morphea lesional


title: S36_6HRLPS_1


title: 35cycle_dropseq

value: Myeloma cell lines (500 cells)


title: 269_ua unaffected skin

description: unaffected skin


title: 213_ua unaffected skin

description: unaffected skin


title: 266_ua unaffected skin

description: unaffected skin


title: 276_ua unaffected skin

description: unaffected skin


title: 267_sc morphea lesional

description: morphea lesional


title: 266_sc_na morphea lesional

description: morphea lesional


title: 276_sc morphea lesional

description: morphea lesional


title: 276_ib morphea lesional

description: morphea lesional


title: 271_ua unaffected skin

description: unaffected skin


title: S35_6HRLPS_3

description: Wild-type BMDMs harvested after 6 hours of LPS stimulation

value: WT


title: 267_ib morphea lesional

description: morphea lesional


title: 174_ib morphea lesional

description: morphea lesional


title: 271_ib morphea lesional

description: morphea lesional


title: 30cycle_dropseq


title: 225_ua unaffected skin

description: unaffected skin


title: 225_sc morphea lesional

description: morphea lesional


title: Trimer-trimer_3

description: ONT PromethION

data_processing:
We performed basecalling on the raw fast5 data using Guppy (v) (guppy_basecaller –compress-fastq -c dna_r104_450bps_hac.cfg -x “cuda:1”) in GPU mode from Oxford Nanopore Technologies running on a RTX 3090 graphics card.
Assembly: hg38
Supplementary files format and content: Tab-separated values files and matrix files

extract_protocol:
Samples were processed using the Drop-seq DolomiteBio Nadia encapsulator system.
ScCOLOR-seq protocol was used.
For nanopore sequencing, cDNA was amplified with 25 SMART PCR reactions and sequencing libraries were prepared using the Oxford Nanopore LSK-109 library preperation kit.

value: Myeloma cell lines (1000 cells)


title: S35_6HRLPS_2


title: 271_sc morphea lesional

description: morphea lesional


title: DMSO2_Noti

data_processing: The data was processed using a custom pipeline 'pipeline_count' written using cgatcore and included within the TallyNNN repository (https://github.com/cribbslab/TallyNNN). Briefly, the polyA associated UMI sequence by searching for the polyA region and reverse complementing the read if it does not appear in the correct orientation. The 30bp UMI is then identified upstream of the SMART primer by pattern matching for GTACTCTGCGTTGATACCACTGCTT. We then corrected for errors or remove the read based the number of UMI errors and then the UMI is added to the read name. Next, the TSO associated UMI is identified using the SMART primer sequence AAGCAGTGGTATCAACGCAGAGTAAT. The 30bp UMI sequence is then corrected for errors or remove the read based the number of UMI errors and then the UMI is added to the read name. Both the TSO and polyA associated UMIs and primer sequences are removed from the read sequence.  For transcrip0t level analysis, the fastq file is then mapped against the transcriptome using minimap2 (v2.22) with the following settings: -ax map-ont -p 0.9 --end-bonus 10 -N 3. The resulting sam file was then sorted and indexed using samtools18. A custom script was then used to add the transcript name to the XT tag of the samfile for downstream counting by homotrimer deduplication, UMI-tools or mclUMI. For gene level analysis, the fastq data was mapped using minimap2 using the following setting: -ax splice -k 14 --sam-hit-only --secondary=no --junc-bed. The resulting sam file was then sorted and indexed followed by feature annotation using featurecounts (v2.0.1) using the following settings to generate an annotated bam file: featureCounts -a (gtf) -o (output) -R BAM. This bam file was then used for downstream counting by UMI-tools or mclUMI. The reference transcriptome and genomes used for the analysis were hg38_ensembl98 and mm10_ensembl88. Downstream differential expression was performed using Deseq2.

growth_protocol: JJN3, 5TGM1 and RM82  cells were cultured in RPMI with 10% FBS and 1% Pen/Strep in a 37oC incubator with 5% CO2.

extract_protocol:
RNA from cells was harvested using Trizol reagent. Libraries were constructed using NEBNext® Ultra RNA Library Prep Kit for Illumina®
RNA libraries were prepared for sequencing using standard NEB protocols

treatment_protocol: RM82 cells were treated with either DMSO control or SGC-CLK1 inhibitor

value: DMSO


title: 282_ib morphea lesional

description: morphea lesional


title: DMSO1_Noti


title: IRF8KO_3m_female  [scRNA-seq]

description: 10xGenomics matrix

data_processing:
Basecalls performed using bcl2fastq without the acceptance of index mismatch
The fastq files were first processed with Cellranger v3.1 pipeline to make gene expression matrices, and the following analyses were performed with Scanpy
Assembly: mm10
Supplementary files format and content: Cellranger filtered matrices

source_name: FACS-sorted microglia

growth_protocol: In vivo microglia from each brain were non-enzymatically isolated.

extract_protocol:
Microglia pooled from 3 mice of each genotype were FACS-sorted and immediately transferred to 10xGenomics.
The libraries were made using SMART-Seq v4 Ultra Low Input RNA Kit followed by Nextera XT library prep kit

tag: gender

value: female


title: DMSO3_Noti


title: S35_6HRLPS_1

value: BMDMs


title: WT_3m_female [scRNA-seq]

description: 10xGenomics matrix


title: MOUSE WT NIH-3T6 Sample 15

city: Bad Nauheim

first: Lei

last: Gu

state: MASSACHUSETTS

address: parkstreet 1

country: Germany

institute: Max Planck Institute for heart and lung research

description: MOUSE.counts.matrix

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm8 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: hg19,mm10, dm6, sacCer1, GRCz11
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: MOUSE

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


title: S34_6HRLPS_3


title: 299_ua unaffected skin

description: unaffected skin


title: 302_aeb morphea lesional

description: morphea lesional


title: CLK2_Noti


title: 302_ua unaffected skin

description: unaffected skin


title: 299_sc morphea lesional

description: morphea lesional


title: 215_ua unaffected skin

description: unaffected skin


title: S34_6HRLPS_1


title: S33_6HRLPS_3


title: 215_ib morphea lesional

description: morphea lesional


title: 302_sc morphea lesional

description: morphea lesional


title: MOUSE WT NIH-3T5 Sample 14

description: MOUSE.counts.matrix


title: 215_sc morphea lesional

description: morphea lesional


title: CLK1_Noti


title: MOUSE KO NIH-3T4 Sample 13

description: MOUSE.counts.matrix

value: KO


title: S33_6HRLPS_2


title: 311_sc morphea lesional

description: morphea lesional


title: S34_6HRLPS_2


title: 25cycles

source_name: JJN3 and 5TGM1 cells

value: JJN3 and 5TGM1 cells


title: MOUSE KO NIH-3T3 Sample 12

description: MOUSE.counts.matrix


title: Class3_Primary_Rep2

first: David

middle: T

last: Scadden

address: 185 Cambridge St

department: Center for Regenerative Medicine

institute: MGH

description: Gene expression data in primary mouse monocytes

data_processing:
Illumina software used for basecalling.
Raw sequences of RNA-seq were mapped to the mouse reference genome mm9 using a Star aligner v2.7.3a
Read counts for individual genes were produced using the un-stranded count feature in HTSeq v.0.6.0
Genome_build: mm9
Supplementary_files_format_and_content: raw count

source_name: Primary mouse monocytes

growth_protocol: ER-HoxB8 cells were maintained in RPMI medium supplemented with 10% FBS, penicillin/streptomycin, and SCF. For primary monocytes, the mouse bone marrow cells were sorted from flow cytometry.

extract_protocol:
For RNA-seq, total RNAs were extracted using RNeasy mini kit (Qiagen).
RNA-sequencing libraries were generated using library prep kits (NEB) according to the manufacturer’s instructions.

value: Primary monocytes


title: 30cycles


title: CLK3_Noti


title: 20cycles


title: Class2_Primary_Rep2


title: Class4_Primary_Rep2


title: Class2_Primary_Rep1


title: S38_NOSTIM_2

data_processing:
Alignment with Tophat
Counting of transcripts with HTSeq
Downstream analysis with custom R script
Assembly: mm10
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample in txt file format

extract_protocol:
Cells were lyzed in RLT buffer (Qiagen) and samples were frozen at -80 until processing
Libraries were constructed from lysates using the Smart-Seq2 protocol. Briefly, RNA was reverse transcribed with an oligo(DT) primer and template switch oligo, and the resulting cDNA was preamplified and used for tagmentation (Nextera XT) and barcoding
Libraries were sequenced with a 75 cycle NextSeq kit and the following parameters : paired End: Index1 8, Index2 8, Read1 38, Read2 38


title: S33_6HRLPS_1


title: 15cycles


title: S38_NOSTIM_1


title: no template control

city: Brisbane

first: Quan

last: Nguyen

state: Queensland

address: 22 Burns Street, Indooroopilly

country: Australia

institute: Institute for Molecular Bioscience

data_processing:
save-interim-files=false
quality-trim-score=20
2color-trimming=True
adapter1=AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC
adapter2=AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT
adapter-trim-match-length=10
adapter-trim-max-mismatch=3
barcode-max-mismatch=1
stitching-max-mismatch=2
dedup-hd=1
threads=4
Assembly: N/A, sequencing of synthetic tags and alignment to whitelist of RTS_IDs (probe barcodes) found in the config.ini output from the GeoMx DSP platform, see attached PKC file (Hs_R_NGS_WTA_COVID19_v1.0.pkc)
Supplementary files format and content: Digital Count Conversion (DCC) file format outputted from GeoMx NGS Pipeline, contains software versions, scan attributes, GeoMx NGS pipeline parameters and output metrics, Q30 scores, and list of deduplicated counts per RTS_ID (probe barcode)
Supplementary files format and content: Values represented in the collapsed target counts tab are the geometric mean of the probes for a given target--in the case that multiple probes were used-- and excludes any targets flagged as outliers. Analyzed counts represent the upper quartile normalized collapsed counts across the study after removing QC flagged segments and features.
Library strategy: GeoMx Seq

organism: unidentified

source_name: control

extract_protocol:
Samples were incubated with DNA-oligo barcoded RNA-ISH probes which were conjugated with a UV-photocleavable linker following standard ISH protocols, along with flourescently labeled antibodies for visualization of morphological structures. Regions of interest within the tissue were illuminated with UV light and oligo barcodes were physically aspirated from the tissue and collected into microtiter plates by the GeoMx® Digital Spatial Profiler (DSP) platform. For more information about DSP protocols please see Merritt et al. Nature Biotech 2020 (doi: 10.1038/s41598-020-63539-x)
Each collection of oligo tags from one well (representing an ROI from the tissue section) was indexed with i7xi5 unique dual indexes using GeoMx SeqCode primers with 18 cycles of PCR.  After PCR, indexed AOIs were pooled and purified in two rounds of AMPure XP PCR purification using 1.2x bead:sample ratio.

value: control

tag: disease

value: SARS-CoV-2 infection

tag: slide id

value: No Template Control


title: S38_NOSTIM_3

source_name: BMDMs

value: Mice:7 weeks, BMDMs:stimulated on day 7


title: Class3_Primary_Rep1


title: Class1_Primary_Rep2


title: Class4_Primary_Rep1


title: Class1_Primary_Rep1


title: bairdii_prairie_late_06

first: Evan

last: Kingsley

data_processing:
Trimmed reads using Cutadapt 1.13
Mapped reads using STAR 2.5.3
Estimated transcript abundance with RSEM 1.3.0
Combined counts into matrix with Trinity 2.4.0 abundance_estimates_to_matrix.pl
Genome_build: GCA_003704035.3
Supplementary_files_format_and_content: Matrix table with abundances for every gene and every sample

molecule: polyA RNA

organism: Peromyscus maniculatus bairdii

source_name: E14.5-15.5 embryonic tail

extract_protocol:
We extracted total RNA using the PicoPure RNA Isolation kit (ThermoFisher Scientific).
We constructed libraries using a PrepX PolyA kit on an Apollo 324 System

tag: Stage

tag: ecotype

value: prairie


title: NonClassical_Rep2


title: S37_NOSTIM_3

tag: tissue


title: S37_NOSTIM_2


title: bairdii_prairie_late_05


title: NonClassical_Rep1

tag: cell type


title: DDT+PB_2827

city: Washington

first: Lu

last: Jin

address: 3970 Reservoir Rd NW

department: Oncology

institute: Georgetown University

data_processing:
Raw data quality was checked using FastQC (v0.11.9), and adapter trimming on raw data were performed using Cutadapt (v3.5). Reads with low quality (quality score < 25, error rate > 10%) or reduced length after trimming (<15 bp) were removed before alignment.
Single end trimmed reads was aligned against mouse reference genome downloaded from Ensembl GRCm38 release 101 using STAR (v2.7.9a).
Small RNA tags were annotated with miRNA and t-RNA sequence fragments (tRFs) obtained from miRBase, GtRNAdb, Ref-seq, GenBank and Rfam databases using featureCounts (v2.0.3).
DESeq2 R package (v1.36.0) was used for group wise statistical analysis.
Assembly: GRCm38 release 101
Supplementary files format and content: tab-delimited text files include DESeq2 normalized count values for each sample

source_name: sperm

growth_protocol: The c57bl/6 strain of mice was used in all experiments. Adult male mice (8 weeks of age) were either treated daily with a DDT solution (1.7 mg/kg) or vehicle-control solution (vegetable oil) via oral gavage for 17 days.

extract_protocol:
5ul of RNA was used as input for those replacements that could not be quantified. After adapter ligation, UMIs were introduced in the reverse transcription step. The cDNA was amplified using PCR (19 cycles) and during the PCR complementary dual indices (CDI) were added. After PCR the samples were purified using QMN beads.
Library preparation was quality controlled using Fragment Analyzer system by Agilent. Based on quality of the inserts and the concentration measurements the libraries were pooled in equimolar ratios. The library pool(s) were quantified using Qubit. The library pool(s) were then sequenced on a NextSeq550(Illumina Inc.) according to the manufacturer instructions (1x75, 1x8)

treatment_protocol: The DDT solution used mimics the formulation of DDT before its ban in the U.S.: 77.2% p,p’-DDT and 22.8% o,p’-DDT. A sub-set of control-vehicle (CO) or DDT exposed male mice (as above) were concomitantly treated with phenobarbital (20 mg/kg of body weight, i.p.) or saline and used for sperm harvesting

tag: strain

tag: Sex

value: male

value: 8 weeks (adult)

value: sperm

value: DDT with PB


title: DDT+PB_2828

tag: age

tag: treatment


title: bairdii_prairie_late_04


title: DDT+PB_2842


title: S37_NOSTIM_1

tag: genotype


title: S36_NOSTIM_3


title: DDT+PB_2841


title: bairdii_prairie_late_03


title: Intermediate_Rep2


title: CO+PB_2847

value: Control with PB


title: bairdii_prairie_late_01


title: Intermediate_Rep1


title: DDT+PB_2840


title: S36_NOSTIM_2


title: S35_NOSTIM_3

description: Wild-type BMDMs harvested after 0 hours of LPS stimulation

value: WT


title: bairdii_prairie_late_02


title: Classical_Rep2


title: CO+PB_2846


title: Classical_Rep1


title: RNA-Seq Clone25_Minus

description: Gene expression data in ER-Hoxb8 cells

source_name: Mouse Bone Marrow ER-Hoxb8 monocytic cells

value: ER-Hoxb8 cells


title: S35_NOSTIM_2


title: S36_NOSTIM_1


title: RNA-Seq Clone24_Minus

description: Gene expression data in ER-Hoxb8 cells


title: CO+PB_2858


title: bairdii_prairie_early_09

source_name: E12.5-13.5 embryonic tail


title: S35_NOSTIM_1


title: CO+PB_2855


title: DDT_2832

value: DDT


title: RNA-Seq Clone22_Minus

description: Gene expression data in ER-Hoxb8 cells


title: bairdii_prairie_early_07


title: CO+PB_2854


title: bairdii_prairie_early_08


title: RNA-Seq Clone23_Minus

description: Gene expression data in ER-Hoxb8 cells


title: DDT_2831


title: S34_NOSTIM_2

value: BMDMs


title: S34_NOSTIM_3


title: S34_NOSTIM_1


title: bairdii_prairie_early_06


title: DDT_2830


title: bairdii_prairie_early_11


title: RNA-Seq Clone21_Minus

description: Gene expression data in ER-Hoxb8 cells


title: DDT_131


title: RNA-Seq Clone19_Minus

description: Gene expression data in ER-Hoxb8 cells


title: bairdii_prairie_early_10


title: RNA-Seq Clone18_Minus

description: Gene expression data in ER-Hoxb8 cells


title: S33_NOSTIM_1


title: RNA-Seq Clone17_Minus

description: Gene expression data in ER-Hoxb8 cells


title: CO_136

value: Control


title: RNA-Seq Clone20_Minus

description: Gene expression data in ER-Hoxb8 cells


title: bairdii_prairie_early_05


title: S33_NOSTIM_2


title: S33_NOSTIM_3


title: bairdii_prairie_early_04


title: RNA-Seq Clone16_Minus

description: Gene expression data in ER-Hoxb8 cells


title: CO_135


title: DDT_129


title: bairdii_prairie_early_01


title: bairdii_prairie_early_03


title: CO_2853


title: RNA-Seq Clone13_Minus

description: Gene expression data in ER-Hoxb8 cells


title: RNA-Seq Clone15_Minus

description: Gene expression data in ER-Hoxb8 cells


title: MLL34KO H3K27ac

first: Ali

last: Shilatifard

address: 320 E Superior St

department: Department of Biochemistry and Molecular Genetics

institute: Northwestern University Feinberg School of Medicine

description: MLL34KO cells

data_processing:
Basecalls were performed using bcl2fastq v2.17 for NextSeq output.
Both ChIP-seq and RNA-seq reads were trimmed from 3' end until the final base had a quality score > 30, using Trimmomatic v0.33, discarding reads left with < 20 bp
ChIP-seq reads were aligned to UCSC mm9 using Bowtie version 0.12.9.  Only uniquely mapping reads with at most two mismatches were retained.
RNA-seq reads were aligned to UCSC mm9 using Tophat version 2.0.9.  Only uniquely mapping reads with at most two mismatches were retained.
To create ChIP-seq coverage plots, the locations of the mapped ChIP-seq reads were extended to 150 bp to represent sequenced fragments, renormalized (to reads per million, rpm) and reformatted in the bigWig file format.
To create RNA-seq coverage plots, the mapped RNA-seq reads were split according to strand, renormalized (to reads per million, rpm) and reformatted in the bigWig file format.
Assembly: mm9
Supplementary files format and content: bigWig files were generated using the genomicRanges R package.  Score represents the normalized coverage of RNA or DNA fragments at a given genomic coordinate.

source_name: mouse embryonic stem cells

growth_protocol: Cells were maintained serum free neurobasal+DMEM/F12 media supplemented with 2i+LIF

extract_protocol:
RNA was extracted using QIAGEN RNeasy kit. DNA after ChIP protocol was isolated using QIAGEN PCR purification kit.
ChIP-sequencing libraries were prepared using the KAPA HTP Library Preparation Kit complemented with NEXTflex DNA Barcodes from Bioo Scientific. 10 ng of DNA was used as starting material for input and ip samples. Libraries were amplified using 13 cycles on the thermocycler. Post amplification libraries were size selected at 250- 450bp in length using Agencourt AMPure XP beads from Beckman Coulter. Libraries were validated using the Agilent High Sensitivity DNA Kit. RNA-sequencing  libraries were prepared using the Illumina TruSeq Stranded Total RNA Preparation Kit with  Ribo-Depletion. Input RNA quality was validated using the Agilent RNA 6000 Nano Kit. 200ng-1 µg  of total RNA was used as starting material. Libraries were validated using the Agilent DNA  1000 Kit

treatment_protocol: Cells were treated with DMSO, LTX, HPX or LTX+HPX for 48 hours; for shRNA knockdown, cells were infected with lentiviruses expressing the shRNA and selected with puromycin.

value: mouse embryonic stem cells

tag: passages

value: Low passages (6-10)

tag: chip antibody

value: anti-H3K27Ac antibody, cell signaling technology


title: MLL34KO H3K27me3

description: MLL34KO cells

value: anti-H3K27me3 antibody, cell signaling technology


title: WT H3K27me3

description: wild type cells

value: wild type


title: nubiterrae_forest_late_11

address: 77 Avenue Louis Pasteur

institute: Harvard Medical School

organism: Peromyscus maniculatus nubiterrae

value: forest


title: nubiterrae_forest_late_10


title: CO_2850


title: nubiterrae_forest_late_09


title: WT H3K27ac

description: wild type cells


title: ATAC Bach2OE_Rep2_Bach2_4

first: Pratiksha

last: Thakore

address: 415 Main St

institute: Broad Institute

data_processing:
Base-calling was performed by RTA v2.4.11, and the BCL files were translated to fastqs using bcl2fastq2 v2.20.0.
ATAC-seq: Reads were aligned to reference mouse annotation mm10 using Bowtie2, and filtered for duplicated and mitochondrial reads. Peak-calling was performed using MACS2. Read counts per peak were computed using bedtools multicov tool for each sample and then column combined into a matrix.
Assembly: mm10
Supplementary files format and content: ATAC-seq: comma-separated values (CSV) files include count values for each gene in each sample.

source_name: Th17 cells treated with virus overexpressing ATAC Bach2 cDNA

extract_protocol:
6,000 viable cells were sorted into PBS/2% FCS and were stored in BambankerTM cell freezing media at -80°C.
For bulk ATAC-seq, cells were thawed at 37°C. Subsequently, cells were lysed and tagmented in 1X TD Buffer, 0.2l TDE1 (Illumina), 0.01% digitonin, and 0.3X PBS at 37°C for 30 min at 300 rpm, as previously described [86]. DNA purification was performed with the MinElute PCR purification kit (QIAGEN). The complete eluate was pre-amplified with 5 PCR cycles using indexed primers with NEBNext High-Fidelity 2X PCR Master Mix (NEB) and the number of additional cycles was determined by SYBR Green quantitative PCR. After DNA purification, library quantification and quality control were performed with the Kapa Library Quantification Kit (Kapa Biosystems) and a Qubit dsDNA HS Assay kit (Invitrogen). Libraries were sequenced on an Illumina NextSeq 550 system with paired-end reads of 37 base pairs in length.

value: CNS


title: RNA-Seq Clone11_Minus

description: Gene expression data in ER-Hoxb8 cells


title: nubiterrae_forest_late_08


title: RNA-Seq Clone10_Minus

description: Gene expression data in ER-Hoxb8 cells


title: RNA-Seq Clone12_Minus

description: Gene expression data in ER-Hoxb8 cells


title: MLL34KO H3K4me1

description: MLL34KO cells

value: anti-H3K4me1 antibody, cell signaling technology


title: bairdii_prairie_early_02

value: prairie


title: ATAC Bach2OE_Rep2_Bach2_3


title: WT H3K4me1

description: wild type cells


title: ATAC Bach2OE_Rep2_Bach2_2


title: MLL34KO input

description: MLL34KO cells

value: input


title: nubiterrae_forest_late_07


title: RNA-Seq Clone9_Minus

description: Gene expression data in ER-Hoxb8 cells


title: CO_2851

value: male

value: 8 weeks (adult)

value: sperm


title: nubiterrae_forest_late_06


title: WT - input

description: wild type cells


title: ATAC Bach2OE_Rep2_Bach2_1


title: nubiterrae_forest_late_05


title: Wild Type 4

city: Louisville

first: Eric

middle: Christian

last: Rouchka

state: Kentucky

address: 522 East Gray Street

department: Biochemistry and Molecular Genetics

institute: University of Louisville

description:
MH-08-WT-M2-04_S8
PolyA RNA
processed data file: GeneMatrix_RawCounts.txt

data_processing:
Illumina BaseSpace FastQ v1.0.0 used for basecalling.
Raw sequences were checked for quality values using fastQC v0.10.1. Quality trimming was not deemed necessary.
The sequences were directly aligned to the Mus musculus reference genome assembly (mm10) using Star version 2.6.
Read counts for gene regions were obtained with HTSeq v.0.10.0 using Ensembl annotations (GRCm38.93).
The annotation file was parsed to exclude mitochondria and ribosomal protein genes in an effort to reduce non-relevant variation in subsequent steps of the analysis. The resulting annotation file tested 17,207 gene locations.
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: GeneMatrix_RawCounts.txt

source_name: epicenter spinal cord injury site

growth_protocol: Bmal1-/- (B6.129-Arntltm1Bra/J C57BL/6, JaxLab stock 009100) and C57BL/6 WT mice.

extract_protocol:
Tissue: spinal cord, 5mm epicenter of the injury. Total RNA was purified with RNeasy Lipid Tissue Mini Kit (Qiagen Cat# 74804).
Libraries were prepared using the TruSeq Stranded mRNA Library Prep Kit (Cat# 20020594) along with TruSeq RNA Index Set A (Cat# 20020492) with poly-A enrichment.

treatment_protocol: Moderate spinal cord contusion injury (50 kdyn force/400–600 μm displacement) for 72h.

tag: genotype/variation

value: Wild type

tag: injury type

value: T9 Contusion

tag: weeks after injury

value: 3 days

value: Epicenter spinal cord injury site


title: ATAC Bach2OE_Rep2_CTL_4

source_name: Th17 cells treated with control virus


title: RNA-Seq Clone8_Minus

description: Gene expression data in ER-Hoxb8 cells

value: ER-Hoxb8 cells


title: ATAC Bach2OE_Rep2_CTL_3


title: Wild Type 3

description:
MH-07-WT-M1-03_S7
PolyA RNA
processed data file: GeneMatrix_RawCounts.txt


title: RNA-Seq Clone6_Minus

description: Gene expression data in ER-Hoxb8 cells


title: RNA-Seq Clone7_Minus

description: Gene expression data in ER-Hoxb8 cells


title: nubiterrae_forest_late_03


title: RNA-Seq Clone5_Minus

description: Gene expression data in ER-Hoxb8 cells


title: Wild Type 1

description:
MH-05-WT-F1-01_S5
PolyA RNA
processed data file: GeneMatrix_RawCounts.txt


title: Wild Type 2

description:
MH-06-WT-F2-02_S6
PolyA RNA
processed data file: GeneMatrix_RawCounts.txt


title: ATAC Bach2OE_Rep2_CTL_2


title: nubiterrae_forest_late_02


title: ATAC Bach2OE_Rep1_Bach2_4


title: RNA-Seq Clone4_Minus

description: Gene expression data in ER-Hoxb8 cells


title: ATAC Bach2OE_Rep2_CTL_1


title: RNA-Seq Clone3_Minus

description: Gene expression data in ER-Hoxb8 cells


title: nubiterrae_forest_late_01


title: ATAC Bach2OE_Rep1_Bach2_3


title: Arntl Knockout 3

description:
MH-03-ArntlKO-M1-03_S3
PolyA RNA
processed data file: GeneMatrix_RawCounts.txt

value: Arntl knockout


title: nubiterrae_forest_early_07


title: RNA-Seq Clone2_Minus

description: Gene expression data in ER-Hoxb8 cells


title: Arntl Knockout 2

description:
MH-02-ArntlKO-F2-02_S2
PolyA RNA
processed data file: GeneMatrix_RawCounts.txt


title: nubiterrae_forest_early_06


title: ATAC Bach2OE_Rep1_Bach2_2


title: RNA-Seq Clone1_Minus

description: Gene expression data in ER-Hoxb8 cells


title: RNA-Seq Clone25_Plus

description: Gene expression data in ER-Hoxb8 cells

source_name: Mouse Bone Marrow ER-Hoxb8 GMP cells


title: nubiterrae_forest_early_05


title: nubiterrae_forest_late_04


title: hepCLiP_3D_1

city: Philadelphia

first: Takeshi

last: Katsuda

state: PA

address: 421 Curie Blvd, BRB II/III Rm531

department: Perelman School of Medicine

institute: University of Pennsylvania

data_processing:
Reads were mapped to GRCm39 mouse genome using the STAR aligner (version 2.7.10b).
Read counts were obtained using the featureCounts package (v2.0.1)
Read counts were imported to DESeq2, and normalization was performed using the "median of ratios normalization" method.
Assembly: GRCm39
Supplementary files format and content: Tab-delimited normalized data including all the samples.

source_name: Liver

growth_protocol: hepCLiP_2D and bilCLiP_2D were maintained on collagen-coated plates using small hepatocyte medium (SHM) in the presence of 10% FBS and YAC (Y-27632, A83-01 and CHIR99021) (Katsuda et al. Cell Stem Cell 2017).

extract_protocol:
RNA was isolated with Nucleospin RNA kit (Takara)
Library was prepared by Novogene (Sacramento, CA)

treatment_protocol: For hepatic induction, spheroids were generated from hepCLiP_2D and bilCLiP_2D using an Aggrewell400 plate for 3 days in SHM+YAC medium in the absence of FBS. Then, the spheroids were transferred to an ultra-low attachable suspension culture plate, and cultured for 6-8 days in SHM+YAC with 10 ng/ml oncostatin M.

value: Liver

tag: cell line

value: hepCLiP

value: Hepatocyte-derived cells

value: RosaConfetti

value: Hepatic induction under 3D culture


title: hepCLiP_3D_2

value: RosaYFP


title: ATAC Bach2OE_Rep1_CTL_4

value: CNS


title: hepCLiP_2D_2

value: Maintained under 2D culture


title: RNA-Seq Clone24_Plus

description: Gene expression data in ER-Hoxb8 cells


title: nubiterrae_forest_early_04

value: forest


title: nubiterrae_forest_early_03


title: hepCLiP_2D_1


title: nubiterrae_forest_early_02


title: ATAC Bach2OE_Rep1_CTL_3


title: RNA-Seq Clone23_Plus

description: Gene expression data in ER-Hoxb8 cells


title: ATAC Bach2OE_Rep1_CTL_2


title: ATAC Bach2OE_Rep1_CTL_1


title: Liver, GDC-0941, rep 4

first: Alexander

last: Tyshkovskiy

state: Massachusetts

institute: Brigham & Women's Hospital, Harvard Medical School

data_processing:
HiSeq Control Software v2.2 was used for system control and base calling through an integrated primary analysis software RTA (Real Time Analysis. v1.18). The BCL (base calls) binary was converted into FASTQ utilizing illumina package bcl2fastq (v1.8.4).
Quality filtering and adapter removal were performed using Trimmomatic version 0.32.
Reads were mapped to mm10 mouse genome using STAR (version 2.5.2b). Genes were counted via featureCounts (version 1.5).
Assembly: mm10
Supplementary files format and content: comma-separated values file includes gene counts for each sample

extract_protocol:
After sacrifice, liver and kidney were removed and frozen on dry ice. RNA was extracted from tissues with PureLink RNA Mini Kit and passed to CEL-seq.
Sequencing libraries were prepared as described in (Hashimshony et al., 2016).
CEL-seq

treatment_protocol: 3-month old male mice were kept on control diet (Purina 5LG6) or the same diet supplied with AS-703026, ascorbyl-palmitate, AZD8055, enzastaurin, GDC-0941 and KU0063794 for 1 month.

value: Male

tag: dose

value: 50 ppm

value: 4 months


title: RNA-Seq Clone22_Plus

description: Gene expression data in ER-Hoxb8 cells


title: ATAC EAE_CNS_5

source_name: Sorted IL17+ cells harvested from the central nervous system at the peak of ATAC EAE


title: Liver, white-footed mouse, rep 1

data_processing:
To generate reference sequences and identify species-specific ortholog gene sets, pipeline from (Ma et al., 2016) was utilized. Published annotated genomes in Ensembl or NCBI were used if available. Otherwise, de novo transcriptomes were assembled with Trinity.
Reads were mapped to the species-specific ortholog sets using STAR (Dobin et al., 2013).Read counting was performed by featureCounts (Liao et al., 2014).
Supplementary files format and content: comma-separated values file includes gene counts for each sample

organism: Peromyscus leucopus

extract_protocol:
After sacrifice, organs were removed and frozen on dry ice. RNA was extracted from tissues with PureLink RNA Mini Kit and passed to sequencing.
Sequencing libraries were prepared as described in (Fushan et al., 2015)

treatment_protocol: The 39 organ samples for young adults of baboon (Papio anubis), beaver (Castor canadensis), and long-tailed macaque (Macaca fascicularis) were collected from the Southwest National Primate Research Center (SNPRC). The 9 organ samples for young adults of chipmunk (Tamias sibiricus), American black bear (Ursus americanus), sugar glider (Petaurus breviceps), tube-nosed bat (Murina leucogaster), and white-footed mouse (Peromyscus leucopus) were collected as previously described (Fushan et al., 2015).

value: male

value: adult

value: wild type


title: Liver, GDC-0941, rep 3


title: ATAC Bach2OE_Rep1_Bach2_1


title: RNA-Seq Clone20_Plus

description: Gene expression data in ER-Hoxb8 cells

value: ER-Hoxb8 cells


title: nubiterrae_forest_early_01


title: RNA-Seq Clone21_Plus

description: Gene expression data in ER-Hoxb8 cells


title: Liver, GDC-0941, rep 2


title: Brain, white-footed mouse, rep 1

source_name: Brain

value: Brain


title: ATAC EAE_CNS_4


title: Liver, enzastaurin, rep 3

value: Liver

value: Enzastaurin

value: 75 ppm


title: Liver, enzastaurin, rep 4


title: ATAC EAE_CNS_2


title: Arntl Knockout 1

description:
MH-01-ArntlKO-F1-01_S1
PolyA RNA
processed data file: GeneMatrix_RawCounts.txt

value: Arntl knockout

value: T9 Contusion

value: 3 days

value: Epicenter spinal cord injury site


title: Liver, GDC-0941, rep 1


title: ATAC EAE_CNS_1

value: CNS


title: ATAC EAE_CNS_3


title: RNA-Seq Clone19_Plus

description: Gene expression data in ER-Hoxb8 cells


title: RNA-Seq Clone18_Plus

description: Gene expression data in ER-Hoxb8 cells


title: HDLEC, si, rep2

first: lei

last: zeng

address: No. 74, Zhongshan 2nd Road, Yuexiu District

institute: SUN YAT-SEN UNIVERSITY

data_processing:
Sequencing was performed on the DNBSEQ platform.
Raw reads were aligned to the human genome using hierarchical indexing for spliced alignment of transcripts 2 (HISAT2) and Bowtie2.
Assembly: hg38
Supplementary files format and content: tab-delimited text files include count matrix for all replicates.

source_name: human dermal lymphatic endothelial cells

growth_protocol: Human dermal lymphatic endothelial cells were maintained in DMEM supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C.

extract_protocol:
Total RNA was extracted using the Qiagen RNeasy Plus Kit. To obtain sufficient quantitation of RNA, and a total of four relicate experiments were performed.
RNA quality was evaluated via Agilent 2100 Bioanalyzer. One microgram of qualified RNA was used to construct mRNA sequencing libraries.

treatment_protocol: Cells were transfected with 20 pmol control or ITGB3 siRNA per well one day after plating on 6-well plates. Two days afterwards, cells were detached, rinsed, suspended in 0.1% heat inactivated (HI) BSA/serum-free media and seeded at into 24-well plates that were pre-coated with 10 mg/ml vitronectin overnight. Following a 2-hr incubation at 37ºC, non-adherent cells were removed by one gentle wash with warm EBM2 media.

tag: sirna

value: ITGB3 siRNA


title: HDLEC, si, rep4

value: human dermal lymphatic endothelial cells


title: HDLEC, si, rep1


title: RNA-Seq Clone17_Plus

description: Gene expression data in ER-Hoxb8 cells


title: RNA-Seq Clone16_Plus

description: Gene expression data in ER-Hoxb8 cells


title: HDLEC, ctrl, rep3

value: control


title: RNA-Seq Clone13_Plus

description: Gene expression data in ER-Hoxb8 cells


title: HDLEC, ctrl, rep2


title: ATAC Il17eGFP_d3_pTh17_GFP_3

source_name: Sorted GFP+ cells polarized in pTh17 conditions for 72 hours

growth_protocol: For the in vitro differentiation of naive ATAC CD4+ T cells, naive ATAC CD4+ ATAC CD44- CD62L+ cells were activated with plate-bound anti-CD3 and anti-CD28 antibodies in the presence of cytokines. For the acquisition of ex vivo Th17 cells, mice were immunized subcutaneously into the flanks with an emulsion of the MOG35-55 peptide and M. tuberculosis H37Ra extract in CFA for the induction of ATAC EAE.

treatment_protocol: For the knockout of ATAC Bach2, we obtained naive T cells from Cas9 knock-in mice and in vitro differentiated them to npTh17 and pTh17 cells while simultaneously transducing them with retroviral vectors encoding a ATAC Bach2-targeting single guide RNA (ATAC Bach2 KO) or empty sgRNA as control. For the overexpression of ATAC Bach2, we polarized naive ATAC CD4+ T cells into pTh17 cells by simultaneous transduction of retroviral vectors with a constitutive ATAC Bach2 cDNA expression cassette (ATAC Bach2 OE) or an empty control.

value: Spleen and lymph nodes


title: Liver, AS-703026, rep 3

value: Male

value: 30 ppm

value: 4 months


title: ATAC Il17eGFP_d3_pTh17_all_3

source_name: Sorted live cells polarized in pTh17 conditions for 72 hours


title: HDLEC, ctrl, rep4


title: Liver, enzastaurin, rep 1


title: Liver, AS-703026, rep 4


title: ATAC Il17eGFP_d3_pTh17_GFP_1


title: RNA-Seq Clone12_Plus

description: Gene expression data in ER-Hoxb8 cells

value: ER-Hoxb8 cells


title: Liver, enzastaurin, rep 2


title: HDLEC, si, rep3


title: HDLEC, ctrl, rep1


title: ATAC Il17eGFP_d3_pTh17_GFP_2


title: Liver, AS-703026, rep 2


title: RNA-Seq Clone11_Plus

description: Gene expression data in ER-Hoxb8 cells


title: RNA-Seq Clone10_Plus

description: Gene expression data in ER-Hoxb8 cells


title: ATAC Il17eGFP_d3_pTh17_all_1


title: RNA-Seq Clone9_Plus

description: Gene expression data in ER-Hoxb8 cells


title: Kidney, KU0063794, rep 4

source_name: Kidney

value: Kidney

value: 10 ppm


title: ATAC Il17eGFP_d3_npTh17_GFP_3

source_name: Sorted GFP+ cells polarized in npTh17 conditions for 72 hours


title: RNA-Seq Clone8_Plus

description: Gene expression data in ER-Hoxb8 cells


title: RNA-Seq Clone15_Plus

description: Gene expression data in ER-Hoxb8 cells


title: Kidney, KU0063794, rep 3