title: Mus musculus,ZEA exposure group_IP RNA (Biological Repetition 3)

description: Library name: ZEA40_3_IP

data_processing:
Base calling software: BCL convert
Data filter: fastp(0.19.4)，remove adapters, repeat sequences and low quality sequences
reads alignment : HISAT2(2.0.4)
Peak calling diffpeak : R package: exomePeak (1.5.0)
Peak annotation : ANNOVAR
Transcript assembly and quantification : StringTie (2.1.2)
Differential Expression Analysis :R package: edgeR(4.1)
Motif: HOMER(4.10)
Assembly: GRCm39
Supplementary files format and content: Control_IPVSControl_input_peak.xlsx,ZEA40_IPVSZEA40_input_peak.xlsx,which contained methylation site information of m6A
Supplementary files format and content: ControlVSZEA40_diffPeak_result.xlsx, which contained the result  of differential methylation sites
Supplementary files format and content: 4_genes_fpkm_expression.xlsx,which  contained the expression information of various genes in various samples (Expression profile)
Supplementary files format and content: Control_inputVSZEA40_input_Gene_differential_expression.xlsx, which contains the list of differentially expressed genes between control_input and ZEA40_input samples.
Supplementary files format and content: ControlVSZEA40_diffPeak_Gene_differential_expression.xlsx, which contains the integrated analysis of differentially methylated m6A peaks and differentially expressed genes between the Control and ZEA40 groups (genes showing both differential m6A peaks and differential expression).
Library strategy: MeRIP-Seq


title: PAD282

status: Public on Jan 30 2026

type: SRA

city: Gainesville

first: Terence

last: Ryan

address: 1864 Stadium Rd

country: USA

institute: University of Florida

description: Library name: PAD282

library_source: transcriptomic

data_processing:
Sequence reads were trimmed to remove possible adapter sequences and nucleotides with poor quality using Trimmomatic v.0.36. The trimmed reads were mapped to the Homo sapiens GRCh38 reference genome available on ENSEMBL using the STAR aligner v.2.5.2b. The STAR aligner is a splice aligner that detects splice junctions and incorporates them to help align the entire read sequences.
Assembly: Homo sapiens GRCh38 reference genome
Supplementary files format and content: TPM counts file

molecule: polyA RNA

organism: Homo sapiens

source_name: gastrocnemius muscle

extract_protocol:
total RNA isolated using Zymo Direct-Zol RNA isolation kit
Illumina library preparation performed by Azenta Life Sciences

tag: tissue

value: gastrocnemius muscle

tag: disease state

value: PAD


title: Patient HNC0034, PDX sample

city: Derry

first: Mary-Kate

last: Riley

address: 26 Knightsbridge

country: United Kingdom

institute: Queen's University Belfast

description: Library name: HNC0034PRX0A

data_processing:
Sequencing quality was initially assessed using FastQC (v0.11.8) and adapter trimming and quality filtering were performed with Trim Galore (v0.6.10, paired-end mode).
Reads were aligned using STAR (v2.7.3a)
For PDX samples, reads were independently aligned to the mouse and human reference genome, whereas samples derived exclusively from patient material were aligned only to the human reference genome.
Following alignment, XenofilteR (v1.6) (PMID: 30286710) was applied to the resulting BAM files to computationally separate human- and mouse-derived reads in PDX samples.
Gene-level read counts were generated using HTSeq-count
Post-alignment quality control metrics were aggregated and summarized using MultiQC (v1.7)
Assembly: Alignments were performed against the human reference genome GRCh38 with GENCODE v33 annotation and the mouse reference genome GRCm38 with GENCODE vM15 annotation.
Supplementary files format and content: csv files for raw HTSeq counts, normalised DESeq2 counts, and normalised TPM counts. Samples in columns and genes in rows.

molecule: total RNA

source_name: Larynx

extract_protocol:
total RNA was extracted using the miRNeasy Mini Kit (Qiagen) according to the manufacturer’s protocol. RNA quantity and integrity were assessed using an Agilent 2100 Bioanalyzer with the RNA 6000 Nano Kit (Agilent).
total RNA was processed using the Kapa Hyper Plus with ribo-erase RNA Library Prep Kit (Roche) by the Health and Life Sciences Genomics Core Technology Unit at Queen’s University Belfast and sequenced on a HiSeq-X instrument (Illumina) by BGI Genomics using 150-bp paired-end reads, aiming for 30M+ reads per sample.

value: Larynx

tag: cell type

value: Head and Neck Squamous Cell Carcinoma


title: Cerebral cortex, E15, Mock Infection, Mouse Litter 1, Replicate 1

city: New Haven

first: Matthew

last: Yuen

state: Connecticut

address: 100 College

department: Neuroscience

institute: Yale School of Medicine

description:
Library name: Sample_L1_1_380_197
Cerebral cortex of a single offspring, Embryonic Day 15

data_processing:
Quality control on FASTQ reads was performed using FastQC (version 0.11.9) and a threshold set for 95% of bases meeting Q30 within a given read to ensure high sequencing quality. Paired-end reads were trimmed using Fastp (version 0.23.2) with default arguments. Pseudoalignment to mm39 mouse genome (reference provided by the Yale Center for Genome Analysis) and quantification was performed using Salmon (version 1.4.0) with selective alignment enabled.
Assembly: mm39
Supplementary files format and content: *_quant.sf (Salmon quantification file) A tab-separated text file produced by Salmon that contains transcript-level quantification results. Each row corresponds to one transcript (or gene, if Salmon was run in gene mode). Typical columns include: Name (transcript ID), Length (transcript length in bp), EffectiveLength (bias-corrected length used for quantification), TPM (Transcripts Per Million, normalized expression value), and NumReads (estimated number of reads/fragments assigned to the transcript). This file is the main output used for downstream differential expression and expression profiling analyses.

organism: Mus musculus

source_name: Cerebral cortex

extract_protocol:
For bulk RNA-sequencing of the brain and placenta, pregnant dams were euthanized via cervical dislocation. Embryos were harvested from the dams and stored in ice-cold HBSS over ice as the placentas and embryonic brains were dissected in ice-cold HBSS. The placentas and dorsal cortex of offspring were dissected, placed in RNAProtect overnight, and  transferred to -20°C for later archival storage. To extract the RNA from placenta and dorsal cortices, tissue were homogenized using Lysis Matrix D ceramic beads. After centrifugation of the homogenate, the supernatant was extracted and total RNA was purified via the Qiagen RNeasy Mini kit. RNA samples were submitted to Yale’s Center for Genome Analysis for cDNA library preparation (Kapa mRNA HyperPrep) and sequenced (NovaSeq6000) at 100 million reads per sample.
RNA Seq Library Prep: mRNA is purified from a normalized input between 50-1000ng of total RNA with oligo-dT beads and sheared by incubation at 94C in the presence of Mg (Kapa mRNA Hyper Prep). Following first-strand synthesis with random primers, second strand synthesis and A-tailing are performed with dUTP for generating strand-specific sequencing libraries. Adapter ligation with 3’ dTMP overhangs are ligated to library insert fragments. Library amplification amplifies fragments carrying the appropriate adapter sequences at both ends. Strands marked with dUTP are not amplified. Indexed libraries that meet appropriate cut-offs for both are quantified by qRT-PCR using a commercially available kit (KAPA Biosystems) and insert size distribution determined with the LabChip GX or Agilent TapeStation. Samples with a yield of ≥0.5 ng/ul are used for sequencing.

treatment_protocol: Mock Infection (50 uL of 1x PBS) or SARS-CoV-2 Infection (50μl of SARS-CoV-2 [3 × 107 PFU/ml]) of pregnant dams at embryonic day 11.

value: Cerebral cortex

value: Neurons + Glia

tag: genotype

value: Wildtype

tag: treatment

value: Mock Infection (50 uL of 1x PBS)

tag: batch


title: Tonsil_PPP/PAO, No24

type: RNA

city: Shinjuku

first: Satomi

last: Kobayashi

state: Tokyo

address: 2-5-1 Nakaochiai

country: Japan

institute: Seibo International Catholic Hospital

description: Gene expression in tonsil from patient with PPP/PAO

hyb_protocol: 600 ng of Cy3-labelled cRNA (specific activity >6 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 25 ul containing 25x Agilent fragmentation buffer and 10x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 25 ul of 2x Agilent GE hybridization buffer HI-RPM was added to the fragmentation mixture and hybridized to SurePrint G3 Human GE 8x60K Ver.3.0 Microarray (Agilent, G4851C) for 17 hours at 65°C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent).

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2600D) using one color scan setting for 8x60k array slides (Scan Area 61×21.6 mm, Scan resolution 3um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 12.0.3.1 (Agilent) using default parameters (protocol GE1_1200_Jun14 and Grid 072363_D_F_20200924) to obtain background subtracted and spatially detrended Processed Signal intensities. The 75th percentile shift normalization was performed using Agilent GeneSpring GX 14.9.1.

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 50 ng Total RNA using Low Input Quick Amp Labeling Kit (Agilent) according to the manufacturer’s instructions, followed by RNAeasy column purification (QIAGEN). Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

extract_protocol: Tonsillar crypt samples were lysed using QIAzol Lysis Reagent (QIAGEN; Hilden, Germany) and homogenized with a TissueRupter (QIAGEN). RNA was extracted using an RNeasy Plus Universal Kit (QIAGEN) according to the manufacturer’s protocol. RNA concentrations and quality were assessed using a NanoDropTM 1000 (Thermo Fisher Scientific) and an Agilent 2100 Bioanalyzer (Agilent Technologies, Inc., Santa Clara, CA, USA). RNA quality was confirmed if A260/A280 was ≥1.8, A260/A230 was ≥2.0, and the RNA Integrity Number was ≥7.0.

value: Tonsil


title: Mus musculus,ZEA exposure group_IP RNA (Biological Repetition 2)

city: Harbin

first: Lige

last: Bao

state: Heilongjiang

address: 600 Changjiang Road, Xiangfang District, Harbin 150030, P. R. China

country: China

institute: Northeast Agricultural University

description: Library name: ZEA40_2_IP

source_name: testis

extract_protocol:
Total RNA was isolated and purified using TRIzol reagent (Invitrogen, Carlsbad, CA, USA) following the manufacturer's procedure. The RNA amount and purity of each sample was quantified using NanoDrop ND-1000 (NanoDrop, Wilmington, DE, USA), and the RNA integrity was assessed by Bioanalyzer 2100 (Agilent, CA, USA). Poly (A) RNA was purified from 50μg total RNA using Dynabeads Oligo (dT)25-61005 (Thermo Fisher, CA, USA) by two rounds of purification.
the poly(A) RNA was fragmented into small pieces using Magnesium RNA Fragmentation Module (NEB, cat.e6150, USA) under 86℃ 7min. The cleaved RNA fragments were incubated for 2h at 4℃ with m6A-specific antibody (No. 202003, Synaptic Systems, Germany) in IP buffer (50 mM Tris-HCl, 750 mM NaCl and 0.5% Igepal CA-630). The IP RNA was reverse-transcribed to cDNA by SuperScript™ II Reverse Transcriptase (Invitrogen, cat. 1896649, USA), which was next used to synthesise U-labeled second-stranded DNAs with E. coli DNA polymerase I (NEB, cat.m0209, USA), RNase H (NEB, cat.m0297, USA) and dUTP Solution (Thermo Fisher, cat.R0133, USA）. An A-base was added to the blunt ends of each strand, preparing for ligation to the indexed adapters. Dual-index adapters were ligated to the fragments, and size selection was performed with AMPureXP beads. After the heat-labile UDG enzyme (NEB, cat.m0280, USA) treatment of the U-labeled second-stranded DNAs, the ligated products were amplified with PCR by the following conditions: initial denaturation at 95℃ for 3 min; 8 cycles of denaturation at 98℃ for 15 sec, annealing at 60℃ for 15 sec, and extension at 72℃ for 30 sec; and then final extension at 72℃ for 5 min. At last, we performed paired-end sequencing (PE150) on an Illumina Novaseq™ 6000 platform(LC-Bio Technology CO., Ltd., Hangzhou, China) following the vendor's recommended protocol

value: testis

tag: Sex

value: male


title: Patient HNC0070, PDX sample, Biological Replicate B

description: Library name: HNC0070PRX0B

source_name: Oropharynx

value: Oropharynx


title: Tonsil_PPP, No31

description: Gene expression in tonsil from patient with PPP


title: Tonsil_PPP/PAO, No22


title: Mus musculus,ZEA exposure group_input RNA (Biological Repetition 2)

description: Library name: ZEA40_2_input

data_processing:
Base calling software: BCL convert
Data filter: fastp(0.19.4)，remove adapters, repeat sequences and low quality sequences
reads alignment : HISAT2(2.0.4)
Peak calling diffpeak : R package: exomePeak (1.5.0)
Peak annotation : ANNOVAR
Transcript assembly and quantification : StringTie (2.1.2)
Differential Expression Analysis :R package: edgeR(4.1)
Motif: HOMER(4.10)
Assembly: GRCm39
Supplementary files format and content: Control_IPVSControl_input_peak.xlsx,ZEA40_IPVSZEA40_input_peak.xlsx,which contained methylation site information of m6A
Supplementary files format and content: ControlVSZEA40_diffPeak_result.xlsx, which contained the result  of differential methylation sites
Supplementary files format and content: 4_genes_fpkm_expression.xlsx,which  contained the expression information of various genes in various samples (Expression profile)
Supplementary files format and content: Control_inputVSZEA40_input_Gene_differential_expression.xlsx, which contains the list of differentially expressed genes between control_input and ZEA40_input samples.
Supplementary files format and content: ControlVSZEA40_diffPeak_Gene_differential_expression.xlsx, which contains the integrated analysis of differentially methylated m6A peaks and differentially expressed genes between the Control and ZEA40 groups (genes showing both differential m6A peaks and differential expression).


title: Tonsil_RT, No34

description: Gene expression in tonsil from patient with RT


title: Tonsil_PPP/PAO, No25


title: Tonsil_PPP/PAO, No21


title: Tonsil_PPP/PAO, No27


title: Patient HNC0039, PDX sample, Biological Replicate A

description: Library name: HNC0039PRX0A

source_name: Larynx + Oral Cavity

value: Larynx + Oral Cavity


title: PAD272

description: Library name: PAD272


title: Tonsil_RT, No20


title: Patient HNC0039, PDX sample, Biological Replicate B

description: Library name: HNC0039PRX0B


title: PAD273

description: Library name: PAD273


title: Tonsil_PPP/PAO, No26


title: PAD274

description: Library name: PAD274


title: Cerebral cortex, E15, Mock Infection, Mouse Litter 1, Replicate 5

description:
Library name: Sample_L1_5_332_245
Cerebral cortex of a single offspring, Embryonic Day 15


title: Patient HNC0041, PDX sample, Merged Technical Replicate

description: Library name: HNC0041PRX0A

source_name: Oral Cavity

value: Oral Cavity


title: Tonsil_SAS, No19

description: Gene expression in tonsil from patient with SAS


title: Mus musculus,ZEA exposure group_IP RNA (Biological Repetition 1)

description: Library name: ZEA40_1_IP


title: Patient HNC0032, PDX sample, Biological Replicate B

description: Library name: HNC0032PRX0B


title: Patient HNC0027, PDX sample, Biological Replicate B

description: Library name: HNC0027PRX0B


title: Patient HNC0035, PDX sample

description: Library name: HNC0035PRX0B

source_name: Hypopharynx

value: Hypopharynx


title: PAD268

description: Library name: PAD268

value: CKD


title: Mus musculus,Control group_input RNA (Biological Repetition 3)

description: Library name: Control_3_input


title: PAD266

description: Library name: PAD266


title: Tonsil_PPP/PAO, No28


title: Patient HNC0027, PDX sample, Biological Replicate A

description: Library name: HNC0027PRX0A


title: Tonsil_PPP/PAO, No18


title: Tonsil_RT, No16


title: Tonsil_RT, No23


title: PAD269

description: Library name: PAD269


title: Patient HNC0032, PDX sample, Biological Replicate A

description: Library name: HNC0032PRX0A


title: Patient HNC0015, PDX sample, Biological Replicate A

description: Library name: HNC0015PRX0A


title: Patient HNC0028, PDX sample, Merged Technical Replicate

description: Library name: HNC0028PRX0A


title: Mus musculus,Control group_IP RNA (Biological Repetition 3)

description: Library name: Control_3_IP


title: PAD267

description: Library name: PAD267


title: PAD262

description: Library name: PAD262


title: Patient HNC0012, PDX sample, Biological Replicate A

description: Library name: HNC0012PRX0A


title: PAD270

description: Library name: PAD270


title: Patient HNC0015, PDX sample, Biological Replicate B

description: Library name: HNC0015PRX0B


title: Tonsil_PPP/PAO, No14


title: Mus musculus,Control group_input RNA (Biological Repetition 1)

description: Library name: Control_1_input


title: plg_eaca_rnase_3

city: Nashville

first: Danielle

middle: L

last: Michell

state: TN

address: 2220 Pierece Ave

department: Department of Medicine

institute: Vanderbilt Univ. Medical Center

description:
Library name: plg_eaca_rnase_3
plg_eaca_rnase_3

data_processing:
Reads were trimmed to remove adapter sequences using Cutadapt (v4.5)
Quality control on both raw reads and adaptor-trimmed reads was performed using FastQC (v0.12.1)(www.bioinformatics.babraham.ac.uk/projects/fastqc)
Reads were aligned to the Gencode GRCm38.p6 genome using STAR (v2.7.11a). Gencode vM24 gene annotations were provided to STAR to improve the accuracy of mapping. featureCounts (v2.0.6)  was used to count the number of mapped reads to each gene. Heatmap3 was used for cluster analysis and visualization.
Significantly differential expressed genes with absolute fold change >= 2 and FDR adjusted p value <= 0.05 were detected by DESeq2 (v1.40.2)
Assembly: GRCm38.p6
Supplementary files format and content: csv file containing fpkm reads

source_name: bone marrow

growth_protocol: Bone marrow-derived macrophages were differentiated for 7days with GM-CSF (50ng/mL)

extract_protocol:
Total RNA was isolated using the Total RNA Purification kits (Norgen Biotek).
Libraries were generated using the NEBNext Ultra II Directional RNA library prep kit for Illumina with multiplex oligos set 1 (NEB).

treatment_protocol: Macrophages were untreated, treated with PLG exposed to EACA or PLG exposed to EACA+Rnases for 24h

value: bone marrow

value: bone marrow-derived macrophages

value: PLG + EACA + Rnase


title: Mus musculus,ZEA exposure group_input RNA (Biological Repetition 1)

description: Library name: ZEA40_1_input


title: PAD260

description: Library name: PAD260

value: gastrocnemius muscle


title: plg_eaca_rnase_4

description:
Library name: plg_eaca_rnase_4
plg_eaca_rnase_4


title: Tonsil_PPP/PAO, No12


title: Patient HNC0012, PDX sample, Biological Replicate B

description: Library name: HNC0012PRX0B

value: Head and Neck Squamous Cell Carcinoma


title: Mus musculus,Control group_IP RNA (Biological Repetition 1)

description: Library name: Control_1_IP


title: Mus musculus,Control group_IP RNA (Biological Repetition 2)

description: Library name: Control_2_IP


title: Tonsil_PPP/PAO, No10


title: Tonsil_PPP/PAO, No11


title: PAD259

description: Library name: PAD259

value: Control


title: PAD264

description: Library name: PAD264

value: PAD


title: Patient HNC0009, PDX sample, Biological Replicate A

description: Library name: HNC0009PRX0A


title: Patient HNC0009, PDX sample, Biological Replicate B

description: Library name: HNC0009PRX0B


title: plg_eaca_3

description:
Library name: plg_eaca_3
plg_eaca_3

value: PLG + EACA


title: Tonsil_RT, No8


title: Mus musculus,Control group_input RNA (Biological Repetition 2)

description: Library name: Control_2_input


title: Tonsil_PPP, No17


title: PAD263

description: Library name: PAD263

value: PAD+CKD


title: plg_eaca_2

description:
Library name: plg_eaca_2
plg_eaca_2


title: Patient HNC0008, PDX sample, Biological Replicate B

description: Library name: HNC0008PRX0B


title: plg_eaca_rnase_2

description:
Library name: plg_eaca_rnase_2
plg_eaca_rnase_2


title: plg_eaca_rnase_1

description:
Library name: plg_eaca_rnase_1
plg_eaca_rnase_1


title: Tonsil_PPP/PAO, No9

value: Tonsil


title: PAD254

description: Library name: PAD254


title: PAD258

description: Library name: PAD258


title: Patient HNC0007, PDX sample

description: Library name: HNC0007PRX0C


title: unt_4

description:
Library name: unt_4
unt_4

value: Untreated


title: PAD253

description: Library name: PAD253


title: Tonsil_PPP/PAO, No13


title: PAD265

description: Library name: PAD265


title: Patient HNC0005, PDX sample

description: Library name: HNC0005PRX0B

value: Larynx


title: Tonsil_SAS, No6


title: plg_eaca_4

description:
Library name: plg_eaca_4
plg_eaca_4


title: Macrophage_LPS_CGRP_5

city: Gold coast

first: Jiaying

last: Liu

address: G40, parkland drive

country: Australia

institute: Griffith university

description:
Library name: Sample30
Column names in counts_invitro_all_samples.txt:CGRP_23_1 and CGRP_23_2

data_processing:
Cutadapt
Reads of low quality, adapter contamination, and high content of unknown bases (N) were removed using the Cutadapt tool.
After obtaining clean reads, we used STAR to align the clean reads to the reference genome sequence
Assembly: Mus_musculus_mm10/GCF_000001635.20
Supplementary files format and content: TXT file includes count values for all samples listed

growth_protocol: Raw264.7 were cultured in DMEM supplemented with 10% FBS and 1% p/s. Cells were incubated with 5% CO2 at 37℃.

extract_protocol:
RNA was harvest with PureLink RNA extraction kit (Thermofisher). A total of 30μl at concentration above 10ng/μl RNA for each sample was used for the construction of sequencing libraries.
Sequencing libraries were constructed using the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina

treatment_protocol: Raw264.7 were treated with 100ng/ml LPS alone as control, or 100ng/ml LPS and 10nM CGRP as test for 6 hours.

tag: cell line

value: macrophage

value: WT

value: LPS and CGRP stimulation


title: Macrophage_LPS_CGRP_4

description:
Library name: Sample29
Column names in counts_invitro_all_samples.txt:CGRP_22_1 and CGRP_22_2


title: Tonsil_PPP/PAO, No15


title: unt_2

description:
Library name: unt_2
unt_2


title: PAD256

description: Library name: PAD256


title: Tonsil_RT, No4


title: PAD249

description: Library name: PAD249


title: unt_1

description:
Library name: unt_1
unt_1


title: Tonsil_PPP/PAO, No2


title: Macrophage_LPS_CGRP_3

description:
Library name: Sample28
Column names in counts_invitro_all_samples.txt:CGRP_21_1 and CGRP_21_2


title: Patient HNC0002, PDX sample, Biological Replicate B

description: Library name: HNC0002PRX0B

value: Oropharynx


title: PAD246

description: Library name: PAD246


title: PAD257

description: Library name: PAD257


title: Tonsil_RT, No5


title: plg_eaca_1

description:
Library name: plg_eaca_1
plg_eaca_1


title: PAD250

description: Library name: PAD250


title: PAD245

description: Library name: PAD245


title: Mouse_heart_TAC_Sham_5D_CM_NCM

city: Göttingen

first: Laura

last: Zelarayan

address: Robert-Koch-Str 40

country: Germany

institute: University Medical Center Göttingen

description:
Library name: p1162_5D
SMARTseq2

library_source: transcriptomic single cell

data_processing:
Sequence images were transformed to BCL files with BaseCaller Illumina software and demultiplexed to fastq files with bcl2fastq v2.20.0.422. Sequencing quality was determined using FastQC v0.11.5. Sequences were aligned to the reference genome Mus musculus (GRCm38, ENSEMBL version 102) using STAR aligner v2.7.7a, allowing for 2 mismatches within 50 bases. Read counting was performed using featureCounts v2.0.1. Cell quality control, normalization, and clustering were conducted using Seurat v5. Assembly: GRCm38 ENSEMBL 102.
Assembly: Mus musculus ENSEMBL v102 (GRCm38)
Supplementary files format and content: Gene matrix generated with read counts per cell per gene

source_name: heart

growth_protocol: C57BL/6N mice from Charles River Laboratories were housed in temperature/humidity-controlled environment with 12h day/night cycle and fed ad libitum.  All procedures approved by Lower Saxony State Office for Consumer Protection and Food Safety (LAVES, AZ-G 15-1840 and AZ-G 33.9-42502-04-20/3434).

extract_protocol:
Cardiac cells were isolated from whole hearts using a modified Langendorff perfusion protocol. Hearts were perfused with a buffer containing 150 mM NaCl, 5 mM HEPES, 5.4 mM KCl, 10 mM glucose, 2 mM Na-pyruvate, 1.2 mM MgCl2, 10 mM taurine, and 12.38 mM 2,3-butanedione monoxime for 2 min at 37°C, followed by perfusion with the same buffer supplemented with 25 mM CaCl2 and 210 µg/mL Liberase DH (Roche) for 10 min at 37°C. Reactions were stopped with buffer containing 0.5% w/v bovine serum albumin and 200 µM CaCl2. Hearts were minced and homogenized into a single cell suspension.
Samples processed using ICELL8 System (Takara Bio). Cells distributed on 5,184 nanowell ICELL8 250v chips. Single alive cells identified using Hoechst 33342 and propidium iodide staining with CellSelect Software. cDNA synthesis performed by oligo-dT priming in one-step RT-PCR. P5 indexing primers, Terra Polymerase added for library prep. Transposase enzyme (Tn5 mixture) added to each well. P7 indexing primers dispensed. Final libraries amplified, pooled, and purified with AMPureXP beads (Beckman Coulter) with size selection to obtain ~500bp average library size.

treatment_protocol: Wild-type C57BL/6N mice (8-12 weeks old) underwent transverse aortic constriction surgery (TAC) using a 26G blunt cannula or sham surgery (control). Pressure overload by aortic ligation was determined by measuring the ratio between blood flow velocities in right and left carotid arteries. TAC mice with a blood flow gradient <60% were excluded. Echocardiography was performed at baseline and at designated timepoints. Hearts were harvested at 5 days, 8 weeks, and 16 weeks post-surgery.

value: heart

value: Sham/TAC surgery

tag: timepoint

value: 5 days post-surgery


title: Macrophage_LPS_6

description:
Library name: Sample25
Column names in counts_invitro_all_samples.txt: LPS_18_1 and LPS_18_2

value: LPS stimulation


title: PAD244

description: Library name: PAD244

value: gastrocnemius muscle


title: Spinal cord Runx1 ChIP Replicate 1

city: Calgary

first: Jeff

last: Biernaskie

state: Alberta

address: 3330 Hospital Drive NW

department: Comparative Biology and Experimental Medicine

country: Canada

institute: University of Calgary

library_source: genomic

data_processing: The raw data for each sample were trimmed using Trimmomatic v0.38 and quality was assessed via FastQC. Cleaned reads were then aligned to the reference genome GRCm38 using bowtie2. Aligned reads were filtered using samtools 1.9 to keep alignments that (i) had a minimum mapping quality of 30, (ii) were aligned concordantly, and (iii) were the primary-called alignments. PCR or optical duplicates were marked using Picard 2.18.26 and removed. Prior to peak calling, reads mapping to mitochondria (mt) were called and filtered and reads mapping to unplaced contigs were removed. MACS2 2.1.2 was used for peak calling to identify open chromatin regions. If a blacklist of artefactual regions (areas with extremely high or low-mappability) was available for the provided reference genome, called peaks were filtered for these regions to mitigate errors due to mappability.

molecule: genomic DNA

source_name: Spinal cord

extract_protocol:
Spinal cord cells were isolated from male C57BL/6J mice at 8-10 weeks of age. Mice were intracardially perfused with ice-cold PBS and spinal cords were isolated by hydraulic extrusion. Tissue was disaggregated using a dounce homogenizer, and cell debris was removed by density gradient centrifugation with debris removal solution (130-109-398, Miltenyi Biotec). Cells from 5 spinal cords were pooled and resuspended in 1 ml of PBS (with protease inhibitors) and crosslinked with 1% formaldehyde for 10 min at room temperature. Crosslinking was halted by addition of glycine, and cells were washed twice with ice-cold PBS, then processed for chromatin immunoprecipitation (ChIP) using the SimpleChIP Enzymatic Chromatin IP Kit (#9003, Cell Signaling Technology), following the manufacturer’s instructions. Briefly, for each sample containing cells from 5 spinal cords, nuclei were prepared and chromatin was digested by incubation with the provided micrococcal nuclease enzyme, diluted 1/5 relative to the manufacturer’s recommendation. A probe sonicator (VC-40, Sonics & Materials, Inc.) was used to lyse the nuclei, using three 20-sec pulses (output: 30; probe diameter: 3/16”) interspersed with 30 sec incubations on ice. Lysates were centrifuged at 9,400 RCF for 10 min at 4 °C and the supernatant (chromatin) was collected. DNA fragment size of approximately 150-900 bp was verified by gel electrophoresis, and concentration was determined using a NanoDrop spectrophotometer. For each immunoprecipitation, chromatin from 10 spinal cords was pooled, yielding a sample of approximately 10 µg, and incubated with 9 µg of antibody against Runx1 (rabbit polyclonal, ab23980, lot# 1017033-4, Abcam) overnight at 4 °C with rotation. Samples were then incubated with protein G magnetic beads for an additional 2 h at 4 °C with rotation. Beads were pelleted using a magnetic separation rack and washed four times, after which chromatin was eluted from the beads by gentle mixing (1,200 RPM) in elution buffer at 65 °C for 30 min. Crosslinking was reversed by adding proteinase K and incubating at 65 °C for an additional 2 h. ChIP DNA was then purified using spin columns.
ChIP-Seq library preparation and sequencing reactions were conducted by GENEWIZ, Inc/Azenta US, Inc. (South Plainfield, NJ, USA). ChIP DNA samples were quantified using a Qubit 2.0 Fluorometer (Life Technologies, Carlsbad, CA, USA) and the DNA integrity was checked with a 4200 TapeStation (Agilent Technologies, Palo Alto, CA, USA). An NEBNext Ultra DNA Library Preparation Kit was used, following the manufacturer’s recommendations (Illumina, San Diego, CA, USA). Briefly, the ChIP DNA was end repaired and adapters were ligated after adenylation of the 3’ ends. Adapter-ligated DNA was size selected, followed by clean up and limited cycle PCR enrichment. The ChIP library was validated using a TapeStation and quantified using a Qubit 2.0 Fluorometer, as well as real time PCR (Applied Biosystems, Carlsbad, CA, USA). The sequencing libraries were multiplexed and clustered on one lane of a flowcell. After clustering, the flowcell was loaded on an Illumina Novaseq instrument according to the manufacturer’s instructions (Illumina, San Diego, CA, USA). Sequencing was performed using a 2x150 Paired End (PE) configuration. Image analysis and base calling were conducted by the Novaseq Control Software (NCS). Raw sequence data (.bcl files) generated from the Illumina instrument were converted into fastq files and de-multiplexed using Illumina's bcl2fastq 2.17 software. One mis-match was allowed for index sequence identification.

tag: strain

value: Spinal cord

tag: antibody


title: Mouse_heart_TAC_Sham_8W_Chip1

description:
Library name: p1095_8W_1
SMARTseq2

value: 8 weeks post-surgery


title: Macrophage_LPS_4

description:
Library name: Sample23
Column names in counts_invitro_all_samples.txt: LPS_16_1 and LPS_16_2


title: PAD247

description: Library name: PAD247

value: Control


title: Tonsil_RT, No7


title: Mouse_heart_TAC_Sham_16W_CM_NCM

description:
Library name: p1162_16W
SMARTseq2

value: 16 weeks post-surgery


title: Mouse_heart_TAC_Sham_5D_Chip3

description:
Library name: p1053_5D_2
SMARTseq2


title: unt_3

description:
Library name: unt_3
unt_3

value: bone marrow

value: bone marrow-derived macrophages


title: PAD239

description: Library name: PAD239

value: PAD+CKD


title: Patient HNC0002, PDX sample, Biological Replicate A

description: Library name: HNC0002PRX0A

value: Head and Neck Squamous Cell Carcinoma


title: Macrophage_LPS_CGRP_2

description:
Library name: Sample27
Column names in counts_invitro_all_samples.txt:CGRP_20_1 and CGRP_20_2

value: macrophage


title: Mouse_heart_TAC_Sham_5D_Chip1

description:
Library name: p1053_5D_1
SMARTseq2


title: Tonsil_PPP, No3

value: Tonsil


title: PAD238

description: Library name: PAD238

value: PAD


title: Mouse_heart_TAC_Sham_8W_Chip2

description:
Library name: p1095_8W_2
SMARTseq2


title: Tonsil_PPP/PAO, No1


title: RNA-seq of cardiac cells from Myh6-dCas9VPR/Klf15 KO mice 6

description: Single cell RNA sequencing performed on cardiac cells isolated using a modified Langendorff Perfusion protocol. Libraries were prepared using ICELL8 system and sequenced on a HiSeq4000 platform. Sequences were processed using Cogent NGS analysis pipeline.

data_processing:
Sequences were aligned to the reference genome Mus musculus (mm9 version 102) using STAR aligner v. 2.5.2a, allowing for 2 mismatches within 50 bases. Read counting was performed using featureCounts v. 1.5.0-p1. Normalization and differential expression analysis were conducted using Seurat.
Assembly: mm9 version 102
Supplementary files format and content: The processed data files are in .rda format containing raw counts, normalized read counts and differential expression analysis results.

extract_protocol:
Cardiac cells were isolated from whole hearts using a modified Langendorff Perfusion protocol. Hearts were perfused with a buffer containing NaCl, HEPES, KCl, glucose, Na-pyruvate, MgCl2, taurine, and 2,3-butadione monoxime, followed by a buffer supplemented with CaCl2 and Liberase DH. Reactions were stopped with a buffer containing bovine serum albumin and CaCl2. Hearts were minced and homogenized into a single cell suspension. Cells were distributed on Matrigel-coated coverslips for live cell imaging using an Axio Imager M2 with ZEN software. RNA was extracted from isolated cardiac cells using standard protocols. RNA quality was assessed by measuring the RNA integrity number (RIN) using a Fragment Analyzer HS Total RNA Kit (Advanced Analytical Technologies, Inc.).
Library preparation for RNA-Seq was performed at the Next Generation Sequencing Facility, Institute of Human Genetics, University Medical Center Göttingen. Cells were distributed on ICELL8 250v Chips. Single alive cells were identified using Hoechst 33342 and propidium iodide staining. Complementary DNA synthesis was performed by oligo-dT priming in a one-step RT-PCR reaction. P5 and P7 indexing primers, Terra Polymerase, and Reaction Buffer were used for library preparation. Transposase enzyme and reaction buffer (Tn5 mixture) were added to each well. Final libraries were amplified, pooled, purified, and size-selected with Agencourt AMPureXP magnetic beads to obtain an average library size of 500 bp. Libraries were sequenced on a HiSeq4000 (Illumina) to obtain ~3·10^5 reads per cell (single-end, 50 bp).

treatment_protocol: Four to six-month-old mice were injected with 1x10^12 vg/g rAAV2/9-TRISPR-Klf15 or rAAV2/9-TRISPR-NT, respectively diluted in 0.9% NaCl, via the tail vein. Injected adult mice underwent transverse aortic constriction surgery (TAC) using a 26G blunt cannula or sham surgery (control). Pressure overload by aortic ligation was determined by measuring the ratio between blood flow velocities in right and left carotid arteries. TAC mice with a blood flow gradient <60% were excluded. Echocardiography was performed four and eight weeks post-surgery, and hearts were harvested 12-16 weeks post-surgery.

value: Cardiac cells

value: Myh6-dCas9VPR/Klf15 KO

value: rAAV2/9-TRISPR-Klf15 injection


title: PAD243

description: Library name: PAD243


title: NN4_D14

description:
Library name: Sample19
read_count_NN4_D14

data_processing:
SOAPnuke
The raw data contains reads of low quality, reads with adaptor sequences and reads with high levels of N base. Those reads need to be filtered before the data analysis for reliability analysis results.
HISAT was used to align the clean reads to the reference genome
Bowtie2 was used to align the clean reads to the reference genes
Assembly: GCF_015227675.2_mRatBN7.2
Supplementary files format and content: csv files include count values for each sample

organism: Rattus norvegicus

source_name: periodontal healing tissue

growth_protocol: Samples were collected from experimental animals at different time points.

extract_protocol:
RNA was harvest with PureLink RNA extraction kit (Thermofisher). A total of 55μl at concentration above 10ng/μl RNA for each sample was used for the construction of sequencing libraries.
Library construction was performed by BGI using the DNBSEQ platform. Sequencing libraries were generated using the BGI mRNA-seq Library Prep Kit following the manufacturer’s protocol.

value: periodontal healing tissue

value: Mixed cells

value: WT

value: periodontal bone defect and sensory denervation

tag: time

value: Day 14


title: RNA-seq of cardiac cells from Myh6-dCas9VPR/Klf15 KO mice 5

value: heart


title: NN4_D7

description:
Library name: Sample 34
read_count_NN4_D7


title: Has2 Overexpression, Replicate 4

city: Louisville

first: Richa

last: Singhal

state: KY

address: 580 S Preston Street, Baxter II Building, Office 321B

department: Medicine

institute: University of Louisville

description:
Library name: R77 _Has2
STC304_18_S18

data_processing:
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 (mm39) using Star version 2.6.
Read counts for gene regions were obtained with HTSeq v.0.10.0 using Ensembl annotations (GRCm39).
Assembly: mm39/GRCm39
Supplementary files format and content: tab-delimited file includes raw counts for each sample

source_name: Heart

growth_protocol: Fibroblasts were grown in DMEM/F-12 with GlutaMAX. Fetal Bovin Serum, Insulin-Transferrin-Selenium, Penicillin-Streptomycin, and basic fibroblast growth factor was added to the base media. Fibroblasts were plated at a ratio of 1 heart per 75 cm2 (10 mL/flask) and allowed to sediment for 2 h. Cardiac fibroblast media was changed following 2 h, 24 h, and subsequently every 2 d until reaching 70–80% confluency.

extract_protocol:
Tissue was disrupted and total RNA isolated using Trizol extraction followed by DNAse treatment
TruSeq Stranded mRNA Library Prep Kit for Illumina was used for library prep

treatment_protocol: Cardiac fibroblasts from Has2fl/fl mice were treated at P2. Cells (7 x 105) were plated in 60 mm dishes and allowed to adhere to the bottom of the dish overnight. Cells were then serum starved for 24 h. To treat, fibroblasts were given Cre adenovirus (Vector Biolabs 1045N), a Has2 overexpression adenovirus (Vector Biolabs), or GFP adenovirus as the control. After 5 hours, cells were given fresh media with 20 ng/mL of bFGF and TGFb, respectively. After 48 hours of stimulation, the cells were collected and total RNA was isolated from it.

value: Heart

value: Male

value: Fibroblast

value: Wild Type

value: Has2 Overexpression

tag: group


title: PAD236

description: Library name: PAD236

value: gastrocnemius muscle

value: CKD


title: NN3_D7

description:
Library name: Sample 33
read_count_NN3_D7


title: NN2_D7

description:
Library name: Sample 32
read_count_NN2_D7


title: Spinal cord Runx1 ChIP Replicate 2

value: Spinal cord

value: Runx1 (rabbit polyclonal, ab23980, lot# 1017033-4, Abcam)


title: RNA-seq of cardiac cells from Myh6-dCas9VPR/Klf15 KO mice 4

value: Cardiac cells

value: Myh6-dCas9VPR/Klf15 KO


title: NN1_D7

description:
Library name: Sample 31
read_count_NN1_D7

value: periodontal healing tissue


title: Spinal cord Runx1 ChIP Replicate 3

source_name: Runx1 (rabbit polyclonal, ab23980, lot# 1017033-4, Abcam)


title: Macrophage_LPS_3

description:
Library name: Sample22
Column names in counts_invitro_all_samples.txt: LPS_15_1 and LPS_15_2

value: macrophage

value: LPS stimulation


title: PAD234

description: Library name: PAD234


title: PAD241

description: Library name: PAD241

value: Control


title: Has2 Overexpression, Replicate 3

description:
Library name: R76 _Has2
STC304_13_S13


title: Macrophage_LPS_5

description:
Library name: Sample24
Column names in counts_invitro_all_samples.txt:  LPS_17_1 and LPS_17_2

value: WT


title: NN3_D3

description:
Library name: Sample16
read_count_NN3_D3

value: Mixed cells

value: periodontal bone defect and sensory denervation

value: Day 3


title: PAD227

description: Library name: PAD227


title: Has2 Overexpression, Replicate 2

description:
Library name: S648 _Has2
STC304_8_S8

value: Heart

value: Female

value: Fibroblast


title: RNA-seq of cardiac cells from Myh6-dCas9VPR/Klf15 KO mice 2

value: heart

value: rAAV2/9-TRISPR-Klf15 injection


title: NN2_D14

description:
Library name: Sample15
read_count_NN2_D14

value: Day 14


title: Macrophage_LPS_CGRP_1

description:
Library name: Sample26
Column names in counts_invitro_all_samples.txt: CGRP_19_1 and CGRP_19_2

value: LPS and CGRP stimulation


title: NN3_D14

description:
Library name: Sample17
read_count_NN3_D14


title: RNA-seq of cardiac cells from Myh6-dCas9VPR/Klf15 KO mice 1

value: Cardiac cells


title: PAD233

description: Library name: PAD233

value: gastrocnemius muscle

value: CKD


title: PAD237

description: Library name: PAD237


title: NN1_D14

description:
Library name: Sample13
read_count_NN1_D14

value: periodontal healing tissue


title: Control, Replicate 3

description:
Library name: R76_GFP
STC304_11_S11

value: Male

value: Wild Type

value: GFP


title: Control, Replicate 2

description:
Library name: S648_GFP
STC304_6_S6

value: Control


title: PAD226

description: Library name: PAD226

value: PAD


title: NN1_D3

description:
Library name: Sample12
read_count_NN1_D3

value: Mixed cells

value: WT

value: periodontal bone defect and sensory denervation

value: Day 3


title: PAD224

description: Library name: PAD224


title: PAD223

description: Library name: PAD223


title: Mut aIL2 Th2 3

city: Bethesda

first: Tom

last: Hill

state: Maryland

address: NIHBC 10 - CLINICAL CENTER BG RM 11N244A, 10 CENTER DR

institute: NIAID

data_processing:
Reads trimmed with trimGalore
Reads mapped with STAR aligned
expression quantified with RSEM
Assembly: mm10
Supplementary files format and content: expression txt file

source_name: Lung

extract_protocol:
polyA mRNA isolation
NEB Next library protocol

value: Lung

tag: genotype/treatment

value: Mut aIL2 Th2


title: NN4_D3

description:
Library name: Sample18
read_count_NN4_D3


title: Macrophage_LPS_2

description:
Library name: Sample21
Column names in counts_invitro_all_samples.txt: LPS_14_1 and LPS_14_2

value: macrophage

value: LPS stimulation


title: spinal microglia_Runx1 Knock-out, tamoxifen treated

description: FACS sorted cells: 22,800 cells; Recovered: 2,600 cells

data_processing:
All raw FASTQs reads were aligned to the mouse GRCm38.p5 (primary assembly) reference genome using the STAR algorithm and quantified through the 10X Genomics Cellranger v2.0.1 single cell pipeline, with default and recommended parameter. Only mapped reads were used for normalization before aggregating cells. The resulting gene-barcode matrix was imported into Seurat (v2.1.0 ) R toolkit for quality control and all downstream analysis. All functions were run with default or recommended parameters, unless specified otherwise. Low-quality cells were excluded from the overall experiment. Gene expression was log normalized to a scale factor of 10,000. To begin unsupervised clustering of cells, a selection of highly variable genes was obtained and used to calculate up to 75 principal components. The significance of principal components was determined using JackStraw analysis and by creating a PCElbowPlot. Expression of selected marker genes across cell clusters identified by graph-based clustering was used to select particular cell types for all subsequent analysis. Differential and marker gene analysis of cells defined by FACS sorting sample or graph-clustering was also run in Seurat using the negative binomial test for genes expressed by at least 25% of cells in the defined cell group being compared.
Genome_build: mm10 (GRCm38.p5)
Supplementary_files_format_and_content: Filtered gene - barcode matrix output from CellRanger

source_name: Knock-out

extract_protocol:
4 weeks following first tamoxifen, mice were perfused, spinal cords were extruded and enzymatically dissociated with 2mg/ml collagenase-4 for 30 min at 37 oC. Cell suspensions were subsequenty strained and centrifuged before removing debris using a Percoll gradient. Liberated single cells were re-suspended in 1% bovine serum album in HBSS for FACS purification. For FACS purification, forward and side scatter gates were used to exclude debris, and cell doublets, then cx3cr1-YFP cells were identified and collected.
Libraries were prepared according to 10X Genomics ChromiumTM Single Cell 3’ Reagent Guidelines v2 Chemistry as per the manufacturer’s protocol. In brief, single cells were sorted into 1% BSA–PBS and partitioned into Gel Bead-In-EMulsions (GEMs) using 10xTM GemCodeTM Technology. This process lysed cells and enabled barcoded reverse transcription of RNA, generating full-length cDNA from poly-adenylated mRNA. DynaBeads® MyOneTM Silane magnetic beads were used to remove leftover biochemical reagents, then cDNA was amplified by PCR over 10 cycles. Quality control size gating was used to select cDNA amplicon size prior to library construction. Read 1 primer sequences were added to cDNA during GEM incubation. P5 primers, P7 primers, i7 sample index, and Read 2 primer sequences were added during library construction. Quality control and cDNA quantification was performed using Agilent D1000 ScreenTape System. Next Generation Sequencing was done using Illumina HiSeq 4000 PE (75 bp paired-end reads) with a targeted sequencing depth of ~75,000-100,000 reads/cell.

treatment_protocol: Cre-recombination was induced with five once daily intraperitoneal injections of tamoxifen (1mg/day, Sigma-Aldrich), vehicle injections were used as a control in wild-type mice.

tag: background strain

tag: transgenic strain

value: tamoxifen

value: Runx1 Knock-out

tag: facs strategy

value: YFP+positive

tag: library preparation

value: 10X Genomics Single Cell RNAseq v2


title: PAD222

description: Library name: PAD222

tag: tissue

value: gastrocnemius muscle

tag: disease state


title: Control, Replicate 4

description:
Library name: R77_GFP
STC304_16_S16

value: Heart

value: Male

tag: cell type

value: Fibroblast

tag: genotype

value: Wild Type


title: NN2_D3

description:
Library name: Sample14
read_count_NN2_D3

value: periodontal healing tissue

value: Mixed cells

tag: treatment


title: Control, Replicate 1

description:
Library name: S643_GFP
STC304_1_S1

tag: Sex

value: Female

value: Control

value: GFP


title: RNA-seq of cardiac cells from Myh6-dCas9VPR/Klf15 KO mice 3

description: Single cell RNA sequencing performed on cardiac cells isolated using a modified Langendorff Perfusion protocol. Libraries were prepared using ICELL8 system and sequenced on a HiSeq4000 platform. Sequences were processed using Cogent NGS analysis pipeline.

value: heart

tag: cell line

value: Cardiac cells

value: Myh6-dCas9VPR/Klf15 KO

value: rAAV2/9-TRISPR-Klf15 injection


title: WT aIL2 Th2 3

value: Lung

value: WT aIL2 Th2


title: Has2 Overexpression, Replicate 1

description:
Library name: S643 _Has2
STC304_3_S3

value: Has2 Overexpression


title: Mut Control Th2 3

value: Mut Control Th2


title: spinal microglia_wild type, Vehicle treated

description: FACS sorted cells: 23,500 cells; Recovered: 4,500 cells

source_name: Wild type

value: vehicle

value: Wild type

value: YFP+positive

value: 10X Genomics Single Cell RNAseq v2


title: Macrophage_LPS_1

description:
Library name: Sample20
Column names in counts_invitro_all_samples.txt: LPS_13_1 and LPS_13_2

value: macrophage

value: WT

value: LPS stimulation


title: PAD221

description: Library name: PAD221

source_name: gastrocnemius muscle

value: gastrocnemius muscle

value: Control


title: Hyal2 Overexpression Replicate_4

description:
Library name: S418_Hyal2
IL0054_18_38_S18

extract_protocol:
Tissue was disrupted and total RNA isolated using Trizol extraction followed by DNAse treatment
NEBNext Ultra II RNA Library Prep Kit for Illumina was used for library prep

treatment_protocol: Cardiac fibroblasts from Hyal2fl/fl mice were treated at P2. Cells (7 x 105) were plated in 60 mm dishes and allowed to adhere to the bottom of the dish overnight. Cells were then serum starved for 24 h. To treat, fibroblasts were given Cre adenovirus (Vector Biolabs 1045N), a Hyal2 overexpression adenovirus (Vector Biolabs), or GFP adenovirus as the control. After 5 hours, cells were given fresh media with 20 ng/mL of bFGF and TGFb, respectively. After 48 hours of stimulation, the cells were collected and total RNA was isolated from it.

value: Heart

value: Male

value: Fibroblast

value: Wild Type C57BL/6J

value: Hyal2 Overexpression


title: Con4_D7

description:
Library name: Sample10
read_count_Con4_D7

value: periodontal healing tissue

value: Mixed cells

value: peridontal bone defect

value: Day 7


title: Hyal2 Exon 2 knock out Replicate_4

description:
Library name: S418_Cre
IL0054_17_37_S17

value: Hyal2 Exon 2 knock out

value: Cre


title: Con4_D14

description:
Library name: Sample11
read_count_Con4_D14

value: Day 14


title: PAD219

description: Library name: PAD219


title: Control + TGFB Replicate_4

description:
Library name: S418_Gfp_Tgfb
IL0054_19_39_S19

value: Control + TGFB


title: Con3_D7

description:
Library name: Sample8
read_count_Con3_D7

value: WT


title: Con3_D3

description:
Library name: Sample7
read_count_Con3_D3

value: Day 3


title: PAD225

description: Library name: PAD225

value: gastrocnemius muscle

value: PAD+CKD


title: Mut aIL2 Th2 2

value: Lung

value: Mut aIL2 Th2


title: PAD218

description: Library name: PAD218

value: Control


title: Con3_D14

description:
Library name: Sample9
read_count_Con3_D14


title: Mut Control Th2 2

value: Mut Control Th2


title: WT aIL2 Th2 2

value: WT aIL2 Th2


title: Con2_D14

description:
Library name: Sample6
read_count_Con2_D14

value: periodontal healing tissue


title: Control Replicate_4

description:
Library name: S418_Gfp
IL0054_16_36_S16

value: Heart

value: Male

value: Fibroblast

value: Wild Type C57BL/6J

value: GFP


title: Hyal2 Exon 2 knock out + TGFB Replicate_4

description:
Library name: S418_Cre_Tgfb
IL0054_20_40_S20

value: Hyal2 Exon 2 knock out + TGFB


title: PAD217

description: Library name: PAD217


title: WT Control Th2 3

value: WT Control Th2


title: Con2_D3

description:
Library name: Sample4
read_count_Con2_D3

value: Mixed cells

value: WT

value: peridontal bone defect


title: PAD220

description: Library name: PAD220

value: gastrocnemius muscle

value: PAD


title: PAD216

description: Library name: PAD216

value: PAD+CKD


title: Con2_D7

description:
Library name: Sample5
read_count_Con2_D7

value: Day 7


title: Mut Control Th2 1

value: Lung

value: Mut Control Th2


title: PAD209

description: Library name: PAD209


title: WT Control Th2 2


title: Con1_D7

description:
Library name: Sample2
read_count_Con1_D7

value: periodontal healing tissue


title: Hyal2 Exon 2 knock out + TGFB Replicate_3

description:
Library name: S417_Cre_Tgfb
IL0054_15_35_S15

value: Heart


title: PAD207

description: Library name: PAD207

value: Control


title: Mut aIL2 Th2 1

value: Mut aIL2 Th2


title: Con1_D14

description:
Library name: Sample3
read_count_Con1_D14

value: Day 14


title: PAD205

description: Library name: PAD205


title: PAD206

description: Library name: PAD206


title: Control + TGFB Replicate_2

description:
Library name: S496_Gfp_Tgfb
IL0054_09_29_S9

value: Female

value: Fibroblast

value: Wild Type C57BL/6J

value: Control + TGFB


title: Hyal2 Overexpression Replicate_3

description:
Library name: S417_Hyal2
IL0054_13_33_S13

value: Male

value: Hyal2 Overexpression


title: WT aIL2 Th2 1

value: WT aIL2 Th2


title: PAD210

description: Library name: PAD210

value: gastrocnemius muscle

value: PAD


title: WT Control Th2 1

value: WT Control Th2


title: MH7A_Control_3

city: Guangzhou

first: Yisi

last: Cai

address: No. 1023 South Shatai Road, Baiyun District

department: School of Traditional Chinese Medicine

institute: Southern Medical university

hyb_protocol: Each slide was hybridized with 1.65μg Cy3-labeled cRNA using Gene Expression Hybridization Kit (Cat.# 5188-5242, Agilent technologies, Santa Clara, CA, US) in Hybridization Oven (Cat.# G2545A, Agilent technologies, Santa Clara, CA, US), according to the manufacturer’s instructions. After 17 hours hybridization, slides were washed in staining dishes (Cat.# 121, Thermo Shandon, Waltham, MA, US) with Gene Expression Wash Buffer Kit(Cat.# 5188-5327, Agilent technologies, Santa Clara, CA, US), followed the manufacturer’s instructions.

scan_protocol: Slides were scanned by Agilent Microarray Scanner (Cat#G2565CA, Agilent technologies, Santa Clara, CA, US) with default settings, Dye channel: Green, Scan resolution=3μm, PMT 100%, 20bit. Data were extracted with Feature Extraction software 10.7 (Agilent technologies, Santa Clara, CA, US).

data_processing: Raw data were normalized by Quantile algorithm, limma packages in R.

source_name: MH7A cells without treatment

label_protocol: Total RNA was amplified and labeled by Low Input Quick Amp Labeling Kit, One-Color (Cat.# 5190-2305, Agilent technologies, Santa Clara, CA, US), following the manufacturer’s instructions. Labeled cRNA were purified by RNeasy mini kit (Cat.# 74106, QIAGEN, GmBH, Germany).

extract_protocol: Total RNA was extracted using TRIZOL Reagent (Cat#15596-018, Life technologies, Carlsbad, CA,US) following the manufacturer’s instructions and checked for a RIN number to inspect RNA integrity by an Agilent Bioanalyzer 2100 (Agilent technologies, Santa Clara, CA, US). Qualified total RNA was further purified by RNeasy mini kit (Cat#74106, QIAGEN, GmBH, Germany) and RNase-Free DNase Set (Cat#79254, QIAGEN, GmBH, Germany).

value: MH7A cells


title: Control Replicate_3

description:
Library name: S417_Gfp
IL0054_11_31_S11

value: GFP


title: Control + TGFB Replicate_3

description:
Library name: S417_Gfp_Tgfb
IL0054_14_34_S14


title: Mut Control Th1 3

value: Lung

value: Mut Control Th1


title: PAD204

description: Library name: PAD204

value: Control


title: Control Replicate_2

description:
Library name: S496_Gfp
IL0054_06_26_S6

value: Heart


title: Hyal2 Exon 2 knock out Replicate_3

description:
Library name: S417_Cre
IL0054_12_32_S12

value: Hyal2 Exon 2 knock out

value: Cre


title: Hyal2 Overexpression Replicate_2

description:
Library name: S496_Hyal2
IL0054_08_28_S8

value: Female

value: Fibroblast


title: WT aIL2 Th1 3

value: WT aIL2 Th1


title: Hyal2 Exon 2 knock out + TGFB Replicate_1

description:
Library name: S421_Cre_Tgfb
IL0054_05_25_S5

value: Wild Type C57BL/6J

value: Hyal2 Exon 2 knock out + TGFB


title: Mut aIL2 Th1 2

value: Mut aIL2 Th1


title: PAD201

description: Library name: PAD201

value: gastrocnemius muscle


title: LNCaPE-shPDGFC3

city: chongqing

first: bingqian

last: deng

address: Gaotanyan street 30

institute: Army Medical University

description:
Library name: Sample6
Column name in raw_counts_All_Samples.txt:shPDGFC3

data_processing:
CLC Genomics  Workbench v11.1.0
Sequence reads were trimmed for adaptor sequence/low-quality sequence using CLC genomic benchwork (parameter- Quality limit:0.05)
Trimmed sequence reads were mapped to GrCM38/mm10 using CLC genomic benchwork (parameters- mismath cost: 2 insertion cost: 3 deletion cost: 3 length fraction: 0.8 similarity fraction: 0.8)
Read count extraction and normalization were performed using CLC genomic benchwork
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample
Supplementary files format and content: csv files include FPKM values for each Sample

source_name: LNCaP

growth_protocol: Cell lines were cultured and maintained in DMEM  supplemented with 10% fetal bovine serum, and the culture environment was set at 37 °C and 5% CO₂.

extract_protocol:
Total RNA was extracted from cell  by Trizol reagent. 1μg of  total RNA was used for the construction secquencing libraries.
The cDNA libraries of each pooled RNA sample for single-end sequencing were prepared using Ion Total RNA-Seq Kit v2.0 (Life Technologies) according to the manufacturer’s instructions.

value: LNCaP

value: tumor cell

value: shPDGFC


title: WT Control Th1 3

value: WT Control Th1


title: MH7A_Control_1

value: MH7A cells


title: PAD255

description: Library name: PAD255

extract_protocol:
total RNA isolated using Zymo Direct-Zol RNA isolation kit
Illumina library preparation performed by Azenta Life Sciences

value: PAD+CKD


title: Mut aIL2 Th1 3

value: Lung


title: Patient HNC0008, PDX sample, Biological Replicate A

description: Library name: HNC0008PRX0A

extract_protocol:
total RNA was extracted using the miRNeasy Mini Kit (Qiagen) according to the manufacturer’s protocol. RNA quantity and integrity were assessed using an Agilent 2100 Bioanalyzer with the RNA 6000 Nano Kit (Agilent).
total RNA was processed using the Kapa Hyper Plus with ribo-erase RNA Library Prep Kit (Roche) by the Health and Life Sciences Genomics Core Technology Unit at Queen’s University Belfast and sequenced on a HiSeq-X instrument (Illumina) by BGI Genomics using 150-bp paired-end reads, aiming for 30M+ reads per sample.

value: Hypopharynx

value: Head and Neck Squamous Cell Carcinoma


title: Con1_D3

description:
Library name: Sample1
read_count_Con1_D3

value: periodontal healing tissue

value: Mixed cells

value: WT

value: peridontal bone defect

value: Day 3


title: MH7A_Control_2


title: Hyal2 Exon 2 knock out Replicate_2

description:
Library name: S496_Cre
IL0054_07_27_S7

value: Heart

value: Female

value: Fibroblast

value: Wild Type C57BL/6J

value: Hyal2 Exon 2 knock out

value: Cre


title: MH7A_DGNTG treated_2

source_name: MH7A cells with 4mg/mL DGNTG treatment


title: PAD203

description: Library name: PAD203

value: gastrocnemius muscle

value: Control


title: Mut Control Th1 2

value: Mut Control Th1


title: MH7A_DGNTG treated_3

value: MH7A cells


title: Hyal2 Overexpression Replicate_1

description:
Library name: S421_Hyal2
IL0054_03_23_S3

value: Hyal2 Overexpression


title: LNCaPE-shPDGFC2

description:
Library name: Sample5
Column name in raw_counts_All_Samples.txt:shPDGFC2

value: LNCaP

value: tumor cell

value: shPDGFC


title: Hyal2 Exon 2 knock out + TGFB Replicate_2

description:
Library name: S496_Cre_Tgfb
IL0054_10_30_S10

value: Hyal2 Exon 2 knock out + TGFB


title: WT Control Th1 2

value: Lung

value: WT Control Th1


title: Control + TGFB Replicate_1

description:
Library name: S421_Gfp_Tgfb
IL0054_04_24_S4

value: Heart

value: Control + TGFB


title: Mut aIL2 Th1 1

value: Mut aIL2 Th1


title: LNCaPE-shNC1

description:
Library name: Sample1
Column name in raw_counts_All_Samples.txt:shNC1

value: shNC


title: LNCaPE-shNC2

description:
Library name: Sample2
Column name in raw_counts_All_Samples.txt:shNC2


title: Ctrl hippocampal microglia p3w replication2

city: Shanghai

first: Zhu

last: wei

address: siping road 1239

institute: tongji university

description: Library name: Ctrl_rna_2

data_processing:
Adapter trimming was done using Trim Galore (v0.6.5), and reads were aligned to the mouse genome (mm10) using Bowtie2 (v2.4.5). Duplicates were marked with SAMtools (v1.3.1), and gene counts and TPMs were calculated using HTSeq (v2.0.3). Genes with total counts <10 were excluded. Differential expression analysis was performed using DESeq2 (v1.32.0), with Benjamini–Hochberg correction.
Assembly: mm10
Supplementary files format and content: tab-delimited text file including raw counts for each sample

source_name: hippocampus microglia

extract_protocol:
total RNA were extract by RNAisoPlus(TAKARA, 9109). RNA from 3000 microglia were used for the construction of sequencing library
library constraction was performed with the protocol of SMARTer Stranded Total RNA-Seq Kit v2(Takara, 634411)

value: hippocampus microglia

tag: age

value: postpartum 3 weeks


title: WT aIL2 Th1 2

value: WT aIL2 Th1


title: FGR hippocampal microglia p3w replication3

description: Library name: FGR_rna_3


title: LNCaPE-shPDGFC1

description:
Library name: Sample4
Column name in raw_counts_All_Samples.txt:shPDGFC1


title: Mut Control Th1 1


title: Hyal2 Exon 2 knock out Replicate_1

description:
Library name: S421_Cre
IL0054_02_22_S2

value: Female

value: Fibroblast

value: Wild Type C57BL/6J

value: Hyal2 Exon 2 knock out

value: Cre


title: MH7A_DGNTG treated_1

value: MH7A cells


title: FGR hippocampal microglia p3w replication1

description: Library name: FGR_rna_1


title: Ctrl hippocampal microglia p3w replication3

description: Library name: Ctrl_rna_3


title: WT aIL2 Th1 1


title: Porcine embryo, IVF-derived, hatched blastocyst stage, rep2

city: Cheongju

first: Cheng-Lin

last: Zhan

address: Chungdae-ro 1, Seowon-Gu

country: South Korea

institute: Chungbuk National University

description:
Library name: EmbryoRNAseq_IVF_HatchedBlastocyst_rep2
IVF_HBL-2

data_processing:
To get high-quality clean reads, reads were filtered by fastp (version 0.18.0) to remove reads that contain adapters, more than 10% of unknown nucleotides(N), and more than 50% of low-quality (Q-value≤20) bases.
Short reads were aligned to the rRNA database using Bowtie2 [2] (v2.2.8). The resulting rRNA-mapped reads were removed, and the remaining clean reads were used for gene assembly and abundance calculation.
An index of the reference genome was built, and paired-end clean reads were mapped to the reference genome using HISAT2.4 and other parameters set as a default. The reference genome used in this study is ncbi_GCF_000003025.6.
Use the StringTie (v 1.3.1) to assemble the mapped reads of every sample in a reference-based approach. For each transcript, the expression abundance and variations were quantified by calculating a fragment per kilobase of transcript per million mapped reads (FPKM) value using RSEM software.
Assembly: Sscrofa11.1
Supplementary files format and content: tab-delimited text file includes raw counts, FPKM, TPM for each Sample

organism: Sus scrofa

source_name: porcine preimplantation embryo

extract_protocol:
Total RNA was extracted using a TRIzol reagent kit (Invitrogen, Carlsbad, CA, USA) according to the manufacturer’s protocol. RNA quality was assessed using an Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA, USA) and verified by RNase-free agarose gel electrophoresis.
After total RNA extraction, the eukaryotic mRNA was enriched with Oligo(dT) beads. The enriched mRNA was fragmented into short fragments using a fragmentation buffer and reverse transcribed into cDNA using the NEBNext Ultra RNA Library Prep Kit for Illumina (NEB #7530; New England Biolabs, Ipswich, MA, USA). The purified double-stranded cDNA fragments were end-repaired, a base was added and ligated to Illumina sequencing adapters. The ligation reaction was purified using AMPure XP Beads (1.0X) and PCR was performed to amplify the ligation products.The resulting cDNA library sequencing was performed on the Illumina HiseqTM 2500/4000 by Gene Denovo Biotechnology Co., Ltd (Guangzhou, China) with a sequenc-ing strategy of Paired-end 150 bp (PE150).

value: porcine preimplantation embryo

value: preimplantation embryonic cells


title: Ctrl hippocampal microglia p3w replication1

description: Library name: Ctrl_rna_1


title: FGR hippocampal microglia p3w replication2

description: Library name: FGR_rna_2


title: shS_Sample 3

city: Beijing

first: Xiao-Hui

last: Tan

address: 8, Xishiku Street, Xicheng District

institute: Peking University First Hospital

description: Library name: Sample 6

data_processing:
Illumina Casava1.7 software
Sequence reads were trimmed for adaptor sequence/low-quality sequence using Cutadapt (version 2.7)
Trimmed sequence reads were mapped to GRCh38.111 (human) using Hisat2 (version 2.0.5).
The output SAM (sequencing alignment/map) files were converted to BAM (binary alignment/map) files and sorted using SAM tools (version 1.3.1).
Gene abundance was expressed as fragments per kilobase of exon per million reads mapped (FPKM). Stringtie software was used to count the fragment within each gene, and the TMM algorithm was used for normalization.
Assembly: hg38
Supplementary files format and content: Matrix table with FPKM values and counts for each sample

growth_protocol: HEK293T was maintained in DMEM cell culture medium supplemented with 10% fetal bovine serum (FBS) and antibiotics in a humidified atmosphere with 5% CO2 at 37℃.

extract_protocol:
The total RNA was extracted using Trizol (Invitrogen) following the manufacturer's procedure. The quality and integrity of each sample were checked using the Agilent BioAnalyzer 2100 (Agilent RNA 6000 nano kit) and a NanoDrop ND-1000 spectrophotometer (NanoDrop Technology, Rockland, DE). 50 μg of RNA was used as input material for the RNA sample preparations.
Paired-end libraries were synthesized by using the mRNA-seq Lib Prep Kit for Illumina (ABclonal, Wuhan, Hubei, China).

treatment_protocol: Following 24h growth, HEK293T was transfected with the corresponding lentivirus vector and selected using puromycin.

value: Human embryonic kidney epithelial-like cell

value: transfected with shSRPK1 lentivirus vector


title: Control Replicate_1

description:
Library name: S421_Gfp
IL0054_01_21_S1

value: Heart

value: Control

value: GFP


title: Porcine embryo, IVF-derived, hatched blastocyst stage, rep1

description:
Library name: EmbryoRNAseq_IVF_HatchedBlastocyst_rep1
IVF_HBL-1


title: shS_Sample 2

description: Library name: Sample 5


title: LNCaPE-shNC3

description:
Library name: Sample3
Column name in raw_counts_All_Samples.txt:shNC3

value: LNCaP

value: tumor cell

value: shNC


title: Mut aIL2 Th0 3

value: Lung

value: Mut aIL2 Th0


title: FGR_microglia_H3K9me3_replication_3

description: Library name: FGR_H3K9me3_3

data_processing:
Adapter trimming was done using Trim Galore (v0.6.5)
reads were aligned to the mouse genome (mm10) using Bowtie2 (v2.4.5).
Duplicates were marked with SAMtools (v1.3.1)
callpeak were execute by MACS2 (v2.2.7.1)
Differentially enriched regions analysis was performed using Diffbind (v3.12.0). Annotation of peaks was performed by ChIPpeakAnno(v3.36.1)
Assembly: mm10
Supplementary files format and content: narrowpeaks, bigwig

extract_protocol:
DNA obtained by isopropanol precipitation method
library constructed fellow a protocol of KAPA HyperPrep Kits(Roche, KR0961)

value: hippocampus microglia

value: postpartum 3 week


title: WT Control Th1 1

value: WT Control Th1


title: Mut Control Th0 3

value: Mut Control Th0


title: shCtrl_Sample 3

description: Library name: Sample 3

value: transfected with shCtrl lentivirus vector


title: FGR_microglia_H3K9me3_replication_2

description: Library name: FGR_H3K9me3_2


title: shS_Sample 1

description: Library name: Sample 4


title: Porcine embryo, IVF-derived, 4-cell stage, rep2

description:
Library name: EmbryoRNAseq_IVF_4Cell_rep2
IVF_4C-2

value: porcine preimplantation embryo


title: WT aIL2 Th0 3

value: WT aIL2 Th0


title: FGR_microglia_H3K9me3_replication_1

description: Library name: FGR_H3K9me3_1


title: FGR_microglia_H3K27ac_replication_3

description: Library name: FGR_H3K27ac_3


title: RNA-seq of EHM sample 19

data_processing:
Sequences were aligned to the reference genome Homo sapiens (hg38 version 96) using STAR aligner v. 2.5.2a, allowing for 2 mismatches within 50 bases. Read counting was performed using featureCounts v. 1.5.0-p1. Normalization and differential expression analysis were conducted using DESeq2.
Assembly: Homo sapiens (hg38)
Supplementary files format and content: The processed data files are in tab-delimited text format containing normalized read counts and differential expression analysis results.

growth_protocol: Engineered heart muscle (EHM) were generated by combining lentivirally transduced (NT gRNAs or KLF15 gRNAs expression vector, 5 days pre-casting) CRISPRa (Schoger et al. Stem Cell Res. 2020) hiPSC-cardiomyocytes with human foreskin fibroblasts in a bovine collagen matrix as described before (Tiburcy et al. STAR Protoc. 2020). EHM were cultured in IMDM supplemented with 4% B27 minus insulin, 100 ng/mL IGF-1, 5 ng/mL VEGF165, 10 ng/mL FGF-2, 100 U/mL penicillin, 100 µg/mL streptomycin, and 5 ng/mL TGF-β1 for 3 days, then without TGF-β1 from day 4 onwards. From day 14 until the end of the experiment, EHM were cultured in alpha-MEM supplemented with 4% B27 minus insulin, 1% MEM non-essential amino acids, 100 ng/mL IGF-1, 5 ng/mL VEGF165, 10 ng/mL FGF-2, 100 U/mL penicillin, and 100 µg/mL streptomycin.

extract_protocol:
RNA was extracted using Trizol/Chloroform followed by isopropanol precipitation. RNA quality was assessed by measuring the RNA integrity number (RIN) using a Fragment Analyzer HS Total RNA Kit (Advanced Analytical Technologies, Inc.).
RNA quality was assessed using a Fragment Analyzer HS Total RNA Kit. Libraries were prepared using Illumina Stranded Total RNA Prep with Ribo-Zero Plus. The size range of cDNA libraries was determined with the SS NGS Fragment Kit. Accurate quantification was performed using the DeNovix DS-Series System. Sequencing was done on a NovaSeq 6000, 100 cycles, with 25 Mio reads/sample.

treatment_protocol: CRISPR hiPSC-cardiomyocytes were lentivirally transduced with either non-targeted control (NT) gRNAs or KLF15 gRNAs targeted to the human KLF15 5' upstream transcriptional start site region before casting EHM. On day 28, EHM groups were subdivided into two groups: the flexible silcone pole culture group (Flex, control) or the fixed metal pole holders group (Fix, stress) to induce mechanical stress. Both groups were cultured under the otherwise same conditions for an additional 7 days.

value: EHM (hiPSC derived Cardiomyocytes + human foreskin fibroblasts

value: CRISPRa + KLF15 gRNA

value: Stressed (Fix)


title: Porcine embryo, IVF-derived, 4-cell stage, rep3

description:
Library name: EmbryoRNAseq_IVF_4Cell_rep3
IVF_4C-3

value: preimplantation embryonic cells


title: FGR_microglia_H3K9ac_replication_3

description: Library name: FGR_H3K9ac_3


title: WT Control Th0 3

value: WT Control Th0


title: shCtrl_Sample 2

description: Library name: Sample 2

value: Human embryonic kidney epithelial-like cell


title: WT aIL2 Th0 2


title: Porcine embryo, IVF-derived, hatched blastocyst stage, rep3

description:
Library name: EmbryoRNAseq_IVF_HatchedBlastocyst_rep3
IVF_HBL-3


title: RNA-seq of EHM sample 18

source_name: CRISPRa (Schoger et al. Stem Cell Res. 2020)


title: Porcine embryo, IVF-derived, blastocyst stage, rep3

description:
Library name: EmbryoRNAseq_IVF_Blastocyst_rep3
IVF_BL-3


title: Porcine embryo, IVF-derived, blastocyst stage, rep2

description:
Library name: EmbryoRNAseq_IVF_Blastocyst_rep2
IVF_BL-2


title: Mut aIL2 Th0 2


title: FGR_microglia_H3K27ac_replication_1

description: Library name: FGR_H3K27ac_1


title: Mut Control Th0 2


title: Porcine embryo, IVF-derived, 4-cell stage, rep1

description:
Library name: EmbryoRNAseq_IVF_4Cell_rep1
IVF_4C-1


title: FGR_microglia_H3K27ac_replication_2

description: Library name: FGR_H3K27ac_2


title: Porcine embryo, IVF-derived, blastocyst stage, rep1

description:
Library name: EmbryoRNAseq_IVF_Blastocyst_rep1
IVF_BL-1


title: Porcine embryo, in vivo–derived, hatched blastocyst stage, rep2

description:
Library name: EmbryoRNAseq_InVivo_HatchedBlastocyst_rep2
invivo_HBL-2


title: FGR_microglia_H3K9ac_replication_2

description: Library name: FGR_H3K9ac_2


title: RNA-seq of EHM sample 16

value: CRISPRa (Schoger et al. Stem Cell Res. 2020)


title: Porcine embryo, in vivo–derived, hatched blastocyst stage, rep1

description:
Library name: EmbryoRNAseq_InVivo_HatchedBlastocyst_rep1
invivo_HBL-1


title: WT Control Th0 2


title: Porcine embryo, in vivo–derived, blastocyst stage, rep2

description:
Library name: EmbryoRNAseq_InVivo_Blastocyst_rep2
invivo_BL-2


title: RNA-seq of EHM sample 9

value: CRISPRa + NT gRNA


title: RNA-seq of EHM sample 17


title: Mut Control Th0 1

value: Lung


title: RNA-seq of EHM sample 15


title: Porcine embryo, in vivo–derived, blastocyst stage, rep1

description:
Library name: EmbryoRNAseq_InVivo_Blastocyst_rep1
invivo_BL-1


title: WT aIL2 Th0 1


title: shCtrl_Sample 1

description: Library name: Sample 1


title: Mut aIL2 Th0 1

value: Mut aIL2 Th0


title: WT Control Th0 1


title: Luc

city: 杭州

first: wei

last: zhang

state: 浙江省

address: 浙江省杭州市钱塘区下沙街道东方街150中国科学院杭州医学研究所

institute: 浙江工业大学

description:
Library name: Sample 1
10×Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v2.1.1(https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: Mouse mm10
Supplementary files format and content: Tab-separated values (TSV) files for gene expression matrices; matrix files containing unique molecular identifier (UMI) counts per gene per cell

source_name: Tumor tissue

extract_protocol:
Fresh mouse tumor tissues were harvested and immediately placed in ice-cold HBSS supplemented with Mg²⁺ and 0.04% (w/v) BSA. Under sterile conditions, the tissues were minced into 1–2 mm³ pieces, then resuspended in digestion buffer (HBSS with Mg²⁺, containing 2 mg/ml collagenase IV, 0.2 mg/ml hyaluronidase, and 40 U/ml DNase I) and incubated at 37°C for 45–60 minutes with gentle shaking. Digestion was terminated by adding an equal volume of FACS buffer (HBSS + 2% FBS + 5 mM EDTA), and the resulting suspension was filtered through a 70 μm cell strainer to remove undigested tissue debris, followed by centrifugation at 300×g for 5 minutes at 4°C. The collected cell pellet was washed twice with FACS buffer, and cell viability and concentration were assessed via Trypan Blue staining to ensure a viability rate of >80% and a final cell concentration of 700–1,200 cells/μl in HBSS containing 0.04% BSA.
The prepared cell suspension, reaction mixture (Master Mix + Sample), 10X Barcode Gel Beads (VDJ 5’ Gel Beads v1.1), and Partitioning Oil were loaded into separate wells of a Chromium Next GEM Chip G. Through the microfluidic “single cross” system, Gel Beads-in-Emulsions (GEMs) were formed. To achieve single-cell resolution, cells were subjected to limited dilution during GEM generation, resulting in 90–99% of GEMs being cell-free and the remaining GEMs typically containing a single cell. All generated GEMs were pooled together, followed by Gel Bead dissolution and cell lysis within each GEM. The Gel Beads consist of a gel matrix and oligonucleotides conjugated to magnetic beads. Upon dissolution, the Gel Beads release a large quantity of primer sequences, which are composed of: (i) Illumina TruSeq Read 1 sequencing primer, (ii) a 16-nt 10X Barcode (unique to each Gel Bead), (iii) a 10-nt unique molecular identifier (UMI), and (iv) a 13-nt Template Switch Oligo (TSO). The released oligonucleotides were mixed with the lysed cells and Master Mix (containing RT reagents and RT primers) to perform reverse transcription, yielding full-length cDNA sequences tagged with the 10X Barcode. After reverse transcription, the oil-in-water emulsion was disrupted using a Recovery Agent. The cDNA was then recovered, purified, and amplified with DNA polymerase. Following cDNA amplification, an aliquot of the cDNA from a single sample was split into 2–3 portions, which were separately used for TCR/BCR enrichment and library construction, as well as 5’ transcriptome library construction, according to the experimental design. V(D)J Enrichment and Library Construction: The constant (C) regions of TCR and BCR genes are highly conserved. Nested PCR was performed using outer and inner primers designed against these C regions to specifically enrich cDNA fragments containing the V(D)J regions. The enriched cDNA was fragmented by enzymatic digestion, and fragments of appropriate size were selected. After end repair, A-tailing, and ligation of Read 2 sequencing primers, the cDNA library containing P5 and P7 adapters was constructed via PCR.

treatment_protocol: PDE6G-expressing tumor models (experimental group) were immunized with PDE6G mRNA-LNP vaccine

value: Tumor tissue

value: Tumor cells


title: FGR_microglia_H3K9ac_replication_1

description: Library name: FGR_H3K9ac_1

value: hippocampus microglia

value: postpartum 3 week


title: FGR_microglia_H3K4me3_replication_1

description: Library name: FGR_H3K4me3_1


title: Mut_Control_Naive 3


title: FGR_microglia_H3K4me3_replication_2

description: Library name: FGR_H3K4me3_2


title: RNA-seq of EHM sample 8


title: FGR_microglia_H3K4me3_replication_3

description: Library name: FGR_H3K4me3_3


title: Mouse, Lung,  Saline_1

city: Chengdu

first: Bisen

last: Ding

address: Renmin South Road

institute: State Key Laboratory of Biotherapy

description: Library name: Saline_1

data_processing:
The cellranger pipeline (version 3.1.0, 10X Genomics) was used to process raw sequencing output.
Assembly: mm10
Supplementary files format and content: Cell Ranger software output files (barcodes.tsv, features.tsv, matrix.mtx, or filtered_feature_bc_matrix.h5)

source_name: lung

extract_protocol:
The homogenized lung tissues were suspended in DMEM medium (C11995500BT, GIBCO) containing 1 mg/mL type I collagenase (C8140，Solarbio), 1 mg/mL type IV collagenase (C8160，Solarbio), 1 mg/mL Dispase II (D6430，Solarbio), and 0.2 mg/mL DNAase (D8071, Solarbio) at 37°C for 30 min. The digested lung tissues were filtered through a 70 μm filter membrane (BS-70-XBS, biosharp), and the filtrate was centrifuged and treated with red blood cell lysis buffer (R1010, Solarbio) for 10 min, centrifuged again under the same conditions, the pellet was washed once with sterile PBS (C10010500BT, GIBCO), and centrifuged again under the same conditions. Cell pellet was resuspended again with MACS mixture (2 mM EDTA, 0.1% BSA, 1% penicillin/streptomycin/antimitotic in DPBS) to obtain lung single cell suspension.
Single-cell ATAC sequencing (scATAC-seq) and single-cell RNA sequencing (scRNA-seq) were performed using the 10X Chromium 3′ v3 kit (10X Genomics, Pleasanton, CA) according to the manufacturer's instructions.

value: lung

value: saline


title: RNA-seq of EHM sample 6


title: FGR_microglia_Input

description: Library name: FGR_Input


title: Ctrl_microglia_H3K9me3_replication_2

description: Library name: Ctrl_H3K9me3_2


title: RNA-seq of EHM sample 2

value: Control = CT (healthy, flex)


title: Ctrl_microglia_H3K9me3_replication_1

description: Library name: Ctrl_H3K9me3_1


title: Ctrl_microglia_H3K9me3_replication_3

description: Library name: Ctrl_H3K9me3_3


title: D2 5-5 mouse embryonic stem cells, H3K27ac (ChIP), biological replicate2

city: Bar Harbor

first: Christopher

middle: Lee

last: Baker

state: ME

address: 600 Main Street

department: Research

institute: The Jackson Laboratory

description: Library name: chip70

data_processing:
Adaptors were trimmed from reads using trimmomatic (version 0.39). Samples were mapped using hisat2 (version 2.2.1). Duplicate reads were removed using PicardTools (version 2.0.1).  Peaks were called using MACS (version 1.4.2). A comprehensive set of open chromatin locations (i.e., peakome) was generated by combining all peaks identified across a strain and  and peaks overlapping by 1 bp merged using bedtools (version 2.9.2). For H3K9me3 ChIP, peak counts were gathered against previously identified chromatin accessibility peaks (Byers, et. al., EMBO Journal, 2021.). Read matrices were TMM-normalized and log2-transformed downstream differential analysis of histone modification using edgeR.
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes raw counts for each sample
Supplementary files format and content: bigwig files for each sample

growth_protocol: Cells were grown in DMEM high glucose base medium supplemented with 15% fetal bovine serum, 1X Pen/Strep, 2 mM GlutaMAX, 1 mM sodium pyruvate, 0.1 mM MEM NEAA, 0.1 mM 2-Mercaptoethanol, 103 IU LIF, 1 μM PD0325901, and 3 μM CHIR99021

extract_protocol:
Cells were fixed with 1% formaldehyde for 10 minutes. 3 million cells were lysed, fragmented using Mnase, and immunoprecipitated.
Libraries were constructed using the KAPA HyperPrep Kit. Libaries were sequenced to a depth of ~ 40 million reads with 75 bp on an Illumina NextSeq.

tag: strain

value: mouse embryonic stem cells

tag: chip antibody

value: H3K27ac (abcam, #ab4729)


title: Ctrl_microglia_H3K27ac_replication_2

description: Library name: Ctrl_H3K27ac_2


title: D2 203 mouse embryonic stem cells, H3K27ac (ChIP), biological replicate3

description: Library name: chip69


title: B6 4-4 mouse embryonic stem cells, H3K27ac (ChIP), biological replicate2

description: Library name: chip72


title: Samples_I_K_barcode

city: Pittsburgh

first: Curtis

last: McCloskey

state: PA

address: 5051 Centre Avenue office 2043

institute: University of Pittsburgh

description:
10x Genomics
RUN6_Barcode

data_processing:
Raw sequencing reads were aligned using CellRanger 3.1.0
MULTI-seq sample barcode libraries were trimmed to 28bp using Trimmomatic v0.36 prior to demultiplexing.
MULTIseq sample barcode alignment and classification were performed using the deMULTIplex R package (https://github.com/chris-mcginnis-ucsf/MULTI-seq) with barcodes in the MULTI_batch_barcodes.csv
Further doublet removal and QC was performed as described in the paper, RAW and normalized count matrix files are supplied here that are post-doublet removal and QC
Assembly: GRCh38-3.0.0 Human genome
Supplementary files format and content: Expression libraries: gene-cell matrix provided as raw and normalized UMI counts post-demultiplexing, doublet removal and QC as described in the paper, along with metadata for each cell. Raw fastq files for barcode libraries and transcriptome libraries are supplied.

source_name: primary human breast

extract_protocol:
Cells were lysed in droplets in the 10x Chromium system
10x Genomics Single Cell 3' Reagent Kit (v3 Chemistry)

value: primary human breast

value: Non-carrier (mutneg)


title: Mut_Control_Naive 2


title: D2 2-9 mouse embryonic stem cells, H3K27ac (ChIP), biological replicate1

description: Library name: chip68


title: WT_Control_Naive 2


title: 0009533_Br1412-teen

city: BALTIMORE

first: Xin Zhi

last: Fang

state: MD

address: 615 N Wolfe St

department: Biostatistics

institute: Johns Hopkins University

hyb_protocol: Probe hybridization, ligation, and amplification were performed by 10x Genomics.

scan_protocol: The Xenium instrument was used for automated imaging and onboard processing of the data.

source_name: dentate gyrus (DG)

growth_protocol: Human dentate gyrus (DG) was dissected from frozen (-80℃), unfixed postmortem human tissue. 10-micron coronal sections were obtained by cryosectioning. RNAscope smFISH was performed on tissue sections to confirm the inclusion of full laminar organization spanning layer 1 though white matter. Tissue blocks containing these full laminar organization were then cryosectioned to collect 10-micron coronal sections onto microscopy slides for Xenium.

extract_protocol: Xenium slides were fixed and permeabilized according to 10X Genomics’ Xenium In Situ for Fresh Frozen Tissues – Fixation & Permeabilization Protocol (CG000581, Rev C).

value: dentate gyrus (DG)


title: Samples_E_F_barcode

description:
10x Genomics
RUN4_Barcode

value: BRCA2 mutation


title: B6 5-1 mouse embryonic stem cells, H3K27ac (ChIP), biological replicate3

description: Library name: chip73


title: WT_Control_Naive 3

extract_protocol:
polyA mRNA isolation
NEB Next library protocol


title: Ctrl_microglia_H3K27ac_replication_1

description: Library name: Ctrl_H3K27ac_1


title: Ctrl_microglia_H3K9ac_replication_3

description: Library name: Ctrl_H3K9ac_3


title: D2 203 mouse embryonic stem cells, H3K9me3 (ChIP), biological replicate3

description: Library name: D2-203

value: H3K9me3 (Active Motif, #39161)


title: 0009533_Br6023-elderly

data_processing: The Xenium instrument was used for automated imaging and onboard processing of the data.

label_protocol: Probe hybridization, ligation, and amplification were performed by 10x Genomics.


title: Samples_E_F

description:
10x Genomics
MULTI_UMI_count_matrix_RAW.csv
MULTI_UMI_count_matrix.csv
RUN4_3pr_v3


title: 0009524_Br8533-infant


title: RNA-seq of EHM sample 4

value: CRISPRa (Schoger et al. Stem Cell Res. 2020)

value: EHM (hiPSC derived Cardiomyocytes + human foreskin fibroblasts

value: CRISPRa + NT gRNA


title: RNA-seq of EHM sample 5


title: RNA-seq of EHM sample 1


title: Ctrl_microglia_H3K27ac_replication_3

description: Library name: Ctrl_H3K27ac_3


title: Ctrl_microglia_H3K9ac_replication_1

description: Library name: Ctrl_H3K9ac_1


title: 0009524_Br2720-adult


title: Sample_D_barcode

description:
10x Genomics
RUN5_Barcode

value: BRCA1 mutation


title: WT_Control_Naive 1

value: Lung


title: Sample_D

description:
10x Genomics
MULTI_UMI_count_matrix_RAW.csv
MULTI_UMI_count_matrix.csv
RUN5_3pr_v3


title: B6 5-1 mouse embryonic stem cells, H3K9me3 (ChIP), biological replicate3

description: Library name: B6-51


title: Ctrl_microglia_H3K4me3_replication_3

description: Library name: Ctrl_H3K4me3_3

value: hippocampus microglia


title: RNA-seq of EHM sample 3


title: Ctrl_microglia_H3K4me3_replication_2

description: Library name: Ctrl_H3K4me3_2

value: postpartum 3 week


title: B6 4-4 mouse embryonic stem cells, H3K9me3 (ChIP), biological replicate2

description: Library name: B6-44


title: PDE6G

address: 浙江省杭州市钱塘区下沙街道东方街150中国科学院杭州医学研究所

description:
Library name: Sample 2
10×Genomics

value: Tumor tissue

value: Tumor cells


title: hypoxia, gcn2, rep3

city: Qingdao

first: Chengdong

state: Shandong

address: 5 Yushan Rd

institute: Ocean University of China

description:
Library name: Sample 12
hyp_gcn2_3

data_processing:
Raw sequencing data (FASTQ format) were processed using fastp to remove low-quality reads and obtain clean reads.
HISAT2 (v2.2.1) was used to build an index of the reference genome, and paired-end clean reads were aligned to the reference genome using HISAT2.
featureCounts (v2.0.6) was employed to quantify the number of reads mapped to each gene. Gene expression levels were subsequently calculated as fragments per kilobase of transcript per million mapped reads (FPKM) based on gene length and mapped read counts.
Assembly: GRCz11
Supplementary files format and content: tab-delimited text file includes FPKM for each Sample

organism: Danio rerio

source_name: whole larvae

growth_protocol: Zebrafish embryos and larvae were raised at 28.5 °C in embryo rearing solution.

extract_protocol:
Total RNA was extracted using TRIzol reagent, and mRNA was purified from total RNA using poly(T) oligo–attached magnetic beads.
Sequencing libraries were generated using NEBNext Ultra RNA Library Prep Kit for Illumina (NEB, USA, Catalog #: E7530L) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample.

value: whole larvae

value: gcn2 knockout

value: hypoxia


title: Samples_I_K

description:
10x Genomics
MULTI_UMI_count_matrix_RAW.csv
MULTI_UMI_count_matrix.csv
RUN6_3pr_v3

value: primary human breast


title: Mut_Control_Naive 1


title: D2 5-5 mouse embryonic stem cells, H3K9me3 (ChIP), biological replicate2

description: Library name: D2-55

value: mouse embryonic stem cells


title: Ctrl_microglia_Input

description: Library name: Ctrl_Input


title: hypoxia, gcn2, rep2

description:
Library name: Sample 11
hyp_gcn2_2


title: FGR_scRNA_hippocampus_microglia

description: Library name: FGR_scRNA

data_processing:
The raw data were processed using Cell Ranger (v3.0)
clustering and visualization were performed using the Seurat (v5.0)
pseudotime analysis was performed using monocle (v2.30.1)
Functional clustering analysis were done via DAVID
Assembly: mm10
Supplementary files format and content: cellranger output files

extract_protocol:
Tem119 positive cells were sorted by FACS and washed once with PBS.
library was performed according to the manufacter's instructions (single cell 3` v2 protocol 10x Genomics) by BGI Genomics Co., Ltd

value: postpartum 3 weeks


title: Samples_C_J_barcode

description:
10x Genomics
RUN3_Barcode

value: mixed sample (BRCA1 mutation, Non-carrier (mutneg))


title: slide-5548

source_name: dlPFC

label_protocol: Probe hybridization, ligation, amplification, autofluorescence quenching,  and nuclei staining was performed as specified in CG000581 (Rev C, 10x Genomics) using the 266 gene human  brain panel (Xenium Human Brain Gene Expression Panel, Part No.1000599)be hybridization, ligation, and amplification were performed by 10x Genomics.

growth_protocol: Human dorsolateral prefrontal cortex (dlPFC) was dissected from frozen (-80℃), unfixed postmortem human tissue. 10-micron coronal sections were obtained by cryosectioning. RNAscope smFISH was performed on tissue sections to confirm the inclusion of full laminar organization spanning layer 1 though white matter. Tissue blocks containing these full laminar organization were then cryosectioned to collect 10-micron coronal sections onto microscopy slides for Xenium.

value: dlPFC


title: slide-5434

hyb_protocol: Probe hybridization, ligation, amplification, autofluorescence quenching,  and nuclei staining was performed as specified in CG000581 (Rev C, 10x Genomics) using the 266 gene human  brain panel (Xenium Human Brain Gene Expression Panel, Part No.1000599)


title: B6 4-1mouse embryonic stem cells, H3K9me3 (ChIP), biological replicate1

description: Library name: B6-41

value: H3K9me3 (Active Motif, #39161)


title: Ctrl_microglia_H3K9ac_replication_2

description: Library name: Ctrl_H3K9ac_2


title: B6 4-1 mouse embryonic stem cells, H3K27ac (ChIP), biological replicate1

description: Library name: chip71

value: H3K27ac (abcam, #ab4729)


title: Samples_C_J

description:
10x Genomics
MULTI_UMI_count_matrix_RAW.csv
MULTI_UMI_count_matrix.csv
RUN3_Multiseq_3pr_v3


title: Samples_B_G_barcode

description:
10x Genomics
RUN1_Barcode

value: mixed sample (BRCA1 mutation, BRCA2 mutation)


title: Samples_A_H_barcode

description:
10x Genomics
RUN2_Barcode


title: Ctrl_scRNA_hippocampus_microglia

description: Library name: Ctrl_scRNA


title: D2 2-9 mouse embryonic stem cells, H3K27ac (HiChIP), biological replicate1

description: Library name: D2-29-k27-10cyc

data_processing:
HiChIP reads were processed using HiC-Pro (v2.11.4) with the following parameters: N_CPU = 4, SORT_RAM = 768M REFERENCE_GENOME = mm10 LIGATION_SITE = GATCGATC MIN_FRAG_SIZE = 30 MAX_FRAG_SIZE =100000 MIN_INSERT_SIZE = 30 MAX_INSERT_SIZE = 600. Long-range interactions were called with hichipper (v.0.7.8b0) using H3K27ac ChIP-seq peaks generated in this paper. PET counts were imported into RStudio (version 4.1) using diffloop (v1.22.0). Before filtering data, read matrices were TMM-normalized. Anchors of interactions were not merged and interactions less than 5,000 bp were filtered out. P-values were adjusted using an FDR cutoff of 0.01. Interactions were filtered for at least four read counts in at least two samples before identifying differential interactions using DESeq2 within the diffloop package. Significant differential interactions were cutoff at FDR < 0.2.
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes raw counts for each sample
Library strategy: HiChIP

extract_protocol:
Cells were fixed with 1% formaldehyde for 10 minutes.
Samples were processed as described in Mumbach, et al., 2016, using DpnII (NEB, R05443) with the following modifications. 1) biotin incorporation was performed at 23°C for 4 hours with interval shaking (10 sec at 900 rpm, 5 min off). 2) Ligation was performed at 16°C for 4 hours with interval shaking (1 min at 500 rpm, 4 min off). 3) Samples were sheared using a Diagenode Biorupter with the following parameters: tube size = 1.5 mL, time on = 30 sec, time off = 30 sec, cycle # = 8. 4) A total of 3 µL of H3K27ac antibody (Abcam #ab4729) was added to the sample and incubated at 4°C overnight with rotation. 5) After ChIP washes, samples were resuspended in 20 µL removal of biotin-dATP master mix: 5 µL 10X NEB Buffer 2.1, 0.125 µL of dATP and dGTP at 10 mM each, 5 µL T4 DNA polymerase (NEB, M0203), and 39.8 µL distilled water. Samples were incubated at 20°C for 4 hours with interval shaking (1 min at 400 rpm, 4 min off). Lastly, size selection of libraries was performed using a two-sided selection with AMPureXP beads. Briefly, 22.5 µL of beads were added to the sample to capture fragments less than 700 bp. Supernatant was transferred to a new tube and 13.5 µL of beads were added to the supernatant sample to capture fragments greater than 300 bp. Libraries were eluted in 50 µL 10 mM Tris pH 8.0. Libraries were quantified using qPCR against Illumina primers and then paired end sequenced with read length of 75 bp to a sequencing depth of 200 million reads per sample over two Illumina NextSeq runs.


title: Ctrl_microglia_H3K4me3_replication_1

description: Library name: Ctrl_H3K4me3_1


title: WGBS FGR hippocampal microglia p3w replication2

description: Library name: FGR_WGBS_2

data_processing:
Adapter trimming was done using Trim Galore (v0.6.5)
clean data were mapped to the genome of the mouse genome (mm10) using Bismark, mapping rate and bisulfite conversion rate of each sample were then calculated.
Differentially Methylated Site (DMS) and Differentially Methylated Regions (DMR) analysis were performed by methylKit (v1.28.0).
Assembly: mm10
Supplementary files format and content: txt file including the numbers of T and C and the methylation ratio in methylation site, BigWig

extract_protocol:
Then genomic DNA was extract by Wizard Genomic DNA purification Kit(Promega, A1120). And DNA fragmented by sonication to a mean size of approximately 250bp (Covaris, M220)
the ligated DNA was bisulfite-converted using the MethylCode™ Bisulfite Conversion Kit (Invitrogen, MECOV50), and the construction of library follow the protocol of  EpiArt® DNA Methylation Library Kit for Illumina V3 (Vazyme, NE103)


title: D2 2-9 mouse embryonic stem cells, H3K9me3 (ChIP), biological replicate1

description: Library name: D2-29


title: hypoxia, wt, rep2

description:
Library name: Sample 8
hyp_wt_2

value: WT


title: D2 5-5 mouse embryonic stem cells, H3K27ac (HiChIP), biological replicate2

description: Library name: D2-55-k27-8cyc


title: WGBS FGR hippocampal microglia p3w replication1

description: Library name: FGR_WGBS_1


title: Samples_B_G

description:
10x Genomics
MULTI_UMI_count_matrix_RAW.csv
MULTI_UMI_count_matrix.csv
RUN1_Multiseq_3pr_v3


title: VECs, siPALMD, rep3

city: BEIJING

first: YINGCHUN

last: HAN

address: No.2, Anzhen Road, Chaoyang District

institute: ANZHEN HOSPITAL

data_processing:
Perl script was used to filter the original data (Raw Data). The steps are: 1) Trim Smart-seq2 public primer sequence from the Reads (If the length of trimmed Reads is lower than 30bp, reads should be discarded. If it is PE sequence, both of the reads must be removed ); 2) Remove the contaminated reads for adapters (The contaminated reads for adapters was defined that the Read Bases contained more than 5bp of adapter sequences. If either one of the PE Reads was polluted, we will remove both ends of the reads); 3) Remove the low quality reads (The low quality reads was defined that the number of Reads Bases whose phred Quality value was less than or equal to 19 accounted for more than 15% . If either one of the PE Reads defined as low quality, we will remove both ends of the reads); 4) Remove the reads whose N base more than 5% for total bases (If either one of the PE Reads had high Ns bases, we will remove both ends of the reads).
The reference genomes and the annotation file were downloaded from ENSEMBL database (http://www.ensembl.org/index.html). Bowtie2 v2.2.3 was used for building the genome index, and Clean Data was then aligned to the reference genome using HISAT2 v2.1.0. HISAT2 is the successor to TopHat2 , which uses a modified BWT algorithm to convert reference genomes to index for faster speed and fewer resources
FPKM (Fragments Per Kilobase Millon Mapped Reads) was then calculated to estimate the expression level of genes
Assembly: Homo_sapiens.GRCh38.84
Supplementary files format and content: FPKM (Fragments Per Kilobase Millon Mapped Reads) was then calculated to estimate the expression level of genes

source_name: primary cells

extract_protocol:
Total RNA was extracted from the tissues using Trizol (Invitrogen, Carlsbad, CA, USA) according to the manual instructions. 1 ug of total RNA was used for the construction of sequencing libraries.
A total amount of 1 μg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext® Ultra™ RNA Library Prep Kit for Illumina® (#E7530L, NEB, USA) following the manufacturer’s recommendations and index codes were added to attribute sequences to each sample. Briefly, mRNA was purified from total RNA using poly-T oligo-attached magnetic beads. Fragmentation was carried out using divalent cations under elevated temperature in NEBNext First Strand Synthesis Reaction Buffer (5X). First strand cDNA was synthesized using random hexamer primer and RNase H. Second strand cDNA synthesis was subsequently performed using buffer, dNTPs, DNA polymerase I and RNase H. The library fragments were purified with QiaQuick PCR kits and elution with EB buffer, then terminal repair,A-tailing and adapter added were implemented. The aimed products were retrieved and PCR was performed, then the library was completed

value: primary cells

value: valvular endothelial cells

value: siPALMD


title: normoxia, gcn2, rep3

description:
Library name: Sample 6
nor_gcn2_3

value: normoxia


title: VECs, siPALMD, rep2


title: Samples_A_H

description:
10x Genomics
MULTI_UMI_count_matrix_RAW.csv
MULTI_UMI_count_matrix.csv
RUN2_Multiseq_3pr_v3