title: LM_KSFM_1_Diff6_d29_06052022_B_A03_S14_R2

city: Nijmegen

first: Jo Huiqing

last: Zhou

address: Geert Grooteplein 26/28

country: Netherlands

institute: Radboud University

description: Library name: LM_KSFM_1_Diff6_d29_06052022_B_A03_S14_R1

data_processing:
Preprocessing was performed using the seq2science rna-seq workflow (v0.9.5)
Assembly: GRCh38.p13
Supplementary files format and content: tab-delimited text files include counts for each iKC sample

source_name: Skin

growth_protocol: iPSC1 from Soares et al., 2019 (doi: 10.1073/pnas.1908180116) were cultured on VTN XF-coated plates in E8F medium at 37C + 5% CO2. For differentiation into keratinocytes, single iPSC were obtained with accutase and seeded at 1000/cm2 density on geltrex (for KSFM condition) or geltrex-collagen I (for CnT-30 condition) coated plates in E8F medium with revitacell. After two days, medium was changed to KSFM or CnT-30 with 1um RA and 10ng/ml BMP4 and refreshed every other day. Cells in KSFM were split at day 7 with accutase, and cells in CnT-30 not but both were stimulated with ROCK inhibitor Y-27632 from this day onwards. RA and BMP4 were removed from day 15 onwards and cells were collected at day 30 for RNA sequencing.

extract_protocol:
Total RNA was isolated using the E.Z.N.A. Total RNA Kit I (Omega Bio-Tek)
400ng of RNA per sample and the KAPA RNA HyperPrep kit with RiboErase (human/mouse/rat [HMR]) (Kapa Biosystems) were used. Fragmentation and priming was executed at 94°C for 6 min. A 1.5-μM stock (NEXTflex DNA barcodes; Bioo Scientific) was used for adapter ligation. Eight cycles of library amplification and a 0.8× bead-based cleanup. High-sensitivity DNA bioanalyzer (Agilent Technologies) was used to determine the library size, and to measure the library concentration the DeNovix double-stranded DNA (dsDNA) high-sensitivity assay was performed. Sequencing was done with the Illumina NextSeq 500 instrument and 42bp-paired end reads were generated.

treatment_protocol: See growth protocol, but summarized two weeks of RA/BMP4 of which the second also with ROCKi, and the remaining two weeks without RA/BMP4 and still with ROCKi.

value: Skin

value: iPSC-derived

value: keratinocytes

value: KSFM


title: TAF8 ChIP-nexus Control rep3

status: Public on Dec 19 2025

type: SRA

city: Kansas City

first: Melanie

last: Weilert

state: MO

country: USA

institute: Stowers Institute for Medical Research

description: Library name: kc167_dmso_taf8_nexus_3

library_source: genomic

data_processing:
ChIP-nexus data were first preprocessed by trimming and reassigning fixed and random barcode sequence information, stored as read names for use in downstream processing.
Reads were next trimmed to remove adapter sequences using Cutadapt (v.4.2) and aligned to the dm6 genome assembly using bowtie2 (v.2.3.5.1)
Using aligned coordinates alongside the stored fixed and random barcode sequence information, reads were deduplicated. Coverage was generated by collecting only the first “stop” base of each aligned read.
Across each relevant condition and TF, ChIP-nexus reads were pooled across replicates to generate the final high-coverage samples. Normalized reads-per-million (RPM) coverage was generated by scaling all base-resolution ChIP-nexus coverage relative to the total aligned reads, described previously.
Assembly: Drosophila melanogaster UCSC dm6
Supplementary files format and content: Bigwig files of positive and negative strands for each replicate and single base-pair resolution.

molecule: genomic DNA

organism: Drosophila melanogaster

source_name: Kc167 cells

growth_protocol: Drosophila melanogaster Kc167 cells were grown at 25 °C in HyClone SFX-Insect Cell Culture Media.

extract_protocol:
10e7 Kc167 cells were fixed with 1% formaldehyde in culture media at room temperature for 10 min with rotation. Fixed cells were washed with cold PBS, incubated with Orlando and Paro’s Buffer (0.25% Triton X-100, 10 mM EDTA, 0.5 mM EGTA, 10 mM Tris-HCl pH 8.0, with freshly added Protease Inhibitor) for 10 min at room temperature with rotation, and then centrifuged and re-suspended in ChIP Buffer (10 mM Tris-HCl, pH 8.0; 140 mM NaCl; 0.1% SDS; 0.1% sodium deoxycholate; 0.5% sarkosyl; 1% Triton X-100, with freshly added Protease Inhibitor). Sonication was performed with a Bioruptor Pico for five rounds of 30 s on and 30 s off. Chromatin extracts were then centrifuged at 16,000 g for 5 min at 4° C. Supernatants were used for ChIP.
NOTE: This sample was prepared following a previous version of the ChIP-nexus protocol. Chromatin extracts were added to the antibody-bound beads (10 ug antibody per 50 ul Dynabeads Protein A + 50 ul Dynabeads Protein G) and incubated at 4°C overnight with rotation and then washed with Nexus washing buffer A to D (wash buffer A: 10 mM Tris-EDTA, 0.1% Triton X-100, wash buffer B: 150 mM NaCl, 20 mM Tris-HCl, pH 8.0, 5 mM EDTA, 5.2% sucrose, 1.0% Triton X-100, 0.2% SDS, wash buffer C: 250 mM NaCl, 5 mM Tris-HCl, pH 8.0, 25 mM HEPES, 0.5% Triton X-100, 0.05% sodium deoxycholate, 0.5 mM EDTA, wash buffer D: 250 mM LiCl, 0.5% IGEPAL CA-630, 10 mM Tris-HCl, pH 8.0, 0.5% sodium deoxycholate, 10 mM EDTA). End repair and dA-tailing were performed using the NEBNext End Repair Module and the NEBNext dA-Tailing Module. ChIP-nexus adaptors with mixed fixed barcodes (CTGA, TGAC, GACT, ACTG) were ligated with Quick T4 DNA ligase and converted to blunt ends with Klenow fragment and T4 DNA polymerase. The samples were treated with lambda exonuclease and RecJf exonuclease. After each enzymatic reaction, the chromatin was washed with the Nexus washing buffers A to D and Tris buffer (10 mM Tris, pH 7.5, 8.0, or 9.5, depending on the next enzymatic step). The chromatin was then eluted and subjected to reverse crosslinking and ethanol precipitation. Purified single-stranded DNA was then circularized with CircLigase, annealed with oligonucleotides complementary to the BamHI restriction site and linearized by BamHI digestion. The linearized single-stranded DNA was purified by ethanol precipitation and subjected to PCR amplification with NEBNext High-Fidelity 2X PCR Master Mix and ChIP-nexus primers.

treatment_protocol: Transcription inhibitors were added directly into SFX media. Cells were treated with 10 μM triptolide (TOCRIS Bioscience, 3253; dissolved in DMSO) at room temperature for 1h. Equivalent amounts of DMSO treatment (2%) were used as the control.

tag: cell line

value: Kc167 cells

tag: chip antibody

value: custom anti-TAF8 rabbit polyclonal, Zeitlinger Lab, TAF8 - U7893CL140-7

tag: treatment

value: DMSO


title: LM_KSFM_1_Diff6_d29_06052022_A_A02_S10_R2

description: Library name: LM_KSFM_1_Diff6_d29_06052022_A_A02_S10_R1

library_source: transcriptomic

molecule: total RNA

organism: Homo sapiens

tag: tissue

tag: cell type


title: total RNAs from GFP tagged CG31510 fly ovary with polyA selection replicate3

city: Vienna

first: Julius

middle: Fabian

last: Brennecke

address: Dr. Bohr Gasse 3

country: Austria

institute: IMBA-Institute for Molecular Biotechnology

description: Library name: GFP_CG31510_rep3

data_processing:
reads were trimmed by removal of the adaptor sequences and to a length of 18-200 bases
reads mapping to the Drosophila melanogaster rRNA precursor and the mitochondrial genome using Bowtie (release 1.2.2) with 0 mismatches were excluded
reads were mapped to the Drosophila melanogaster genome using STAR (v.2.5.2b)
reads mapping to rRNA, tRNA, mitoRNA were excluded
Assembly: dm6
Supplementary files format and content: all mapping and unique mapping bigwig files for sense and antisense

molecule: polyA RNA

source_name: fly ovaries

growth_protocol: flies were maintained at 25 °C under a 12-hour light/dark cycle. For ovary sample collections, flies were aged for 2-3 days and placed on apple juice agar supplemented with fresh yeast paste for 2 days.

extract_protocol:
RNA was extracted using NucleoSpin® RNA Kit from Macherey-Nagel
Libraries were prepared using a NEBNext Ultra Directional RNA Library Prep Kit for Illumina (NEB)

value: fly ovaries


title: TAF9 ChIP-nexus Control rep3

description: Library name: kc167_dmso_taf9_nexus_3

value: custom anti-TAF9 rabbit polyclonal, Zeitlinger Lab, TAF9 - 529220-34


title: TAF8 ChIP-nexus Control rep2

description: Library name: kc167_dmso_taf8_nexus_2


title: Osteoblast day3

type: RNA

city: Obu

first: Kiyoaki

last: Ishii

state: Aichi

address: Morioka-cho 7-430

country: Japan

institute: Natuional center for geriatrics and gerontology

description: Gene expression in mouse MSCs cultured for 3 day

hyb_protocol: 600 ng of Cy3-labeled cRNA was hybridized to the Agilent SurePrint G3 Mouse Gene Expression v2 microarray for 17 h at 65°C using the Gene Expression Hybridization Kit.

scan_protocol: Microarrays were scanned using an Agilent DNA Microarray Scanner (Model G2565CA).

data_processing: Raw data were extracted using Feature Extraction Software (v12.0) and normalized using the 75th percentile shift method in GeneSpring GX (Agilent).

organism: Mus musculus

source_name: osteogenic-induced MSCs (3 days)

label_protocol: cRNA was synthesized and labeled with Cy3 using the Low Input Quick Amp Labeling Kit, One-Color (Agilent Technologies).

growth_protocol: Mouse primary MSCs were isolated from bone marrow and cultured in αMEM supplemented with 10% FBS, 100 U/mL penicillin, and 100 μg/mL streptomycin. Osteogenic differentiation was induced by addition of 50 μg/mL ascorbic acid and 10 mM β-glycerophosphate for 3 or 21 days.

extract_protocol: Total RNA was extracted using ISOSPIN Cell and Tissue RNA (NIPPON GENE) according to the manufacturer’s instructions. RNA quality was verified using an Agilent 2100 Bioanalyzer.

treatment_protocol: Cells were maintained in a humidified incubator at 37°C with 5% CO2. Medium was changed every 2–3 days.

tag: Sex

value: male

tag: age

value: 8 weeks


title: small RNA-seq analyis of small RNA expression changes in CG31510 and CG7065 KD OSCs

data_processing:
reads were trimmed by removal of the adaptor sequences and to a length of 18-200 bases
reads mapping to the Drosophila melanogaster rRNA precursor and the mitochondrial genome using Bowtie (release 1.2.2) with 0 mismatches were excluded
reads were mapped to the Drosophila melanogaster TE consensus using Bowtie (release 1.2.2) with 0 mismatches for genome wide analysis
Assembly: dm6
Supplementary files format and content: all mapping and unique mapping bigwig files for sense and antisense

source_name: OSCs

growth_protocol: OSCs were grown in M3 medium supplemented with 10% fetal bovine serum, insulin, glutathion and fly extract in hunidified incubator with 2.5% CO2 at 27º C

extract_protocol:
small RNAs were purified though TrapR column, followed by pheno Chloroform extraction
Small RNA-seq was performed according to the TraPR method, Grentzinger et al. (2020)

value: OSCs


title: MSC day0

description: Gene expression in mouse MSCs cultured for 0 day

source_name: primary mouse mesenchymal stem cells


title: TAF7 ChIP-nexus 1 h Triptolide treatment rep3

description: Library name: kc167_triptolide_taf7_nexus_3

value: custom anti-TAF7 rabbit polyclonal, Zeitlinger Lab, TAF7 - U1266BL120-6

value: 10 uM Triptolide


title: LM_KSFM_1_Diff52_d29_25032022_A01_S20_R2

description: Library name: LM_KSFM_1_Diff52_d29_25032022_A01_S20_R1


title: Siberian Hamster, POA, 4wk, Rep 4

city: Glasgow

first: Calum

last: Stewart

address: Jarrett Building, University of Glasgow

country: United Kingdom

institute: University of Glasgow

description: Library name: POA_352

data_processing:
Raw reads were demultiplexed and basealled using guppy basecaller
Porechop was used to trim adapters
Filtlong used to select long reads (>25 reads)
Minimap2 used to align reads to Mus musculus genome (GCRm39)
Transcript expression levels generated  using Salmon
Assembly: GRCm39
Supplementary files format and content: Expression matrix (CPM)

organism: Phodopus sungorus

source_name: POA

extract_protocol:
RNA was extracted using the Qiagen RNEasy plus mini-kit
RNA Libraries were constructed using the PCR_cDNA sequencing barcoding kit (SQK-PCB109, Oxford Nanopore) as per manufacturers instructions

value: POA

value: 4wk SD


title: Osteoblast day21

description: Gene expression in mouse MSCs cultured for 21 day

source_name: osteogenic-induced MSCs (21 days)


title: total RNAs from GFP tagged CG31510 fly ovary with polyA selection replicate1

description: Library name: GFP_CG31510_rep1


title: Siberian Hamster, POA, 4wk, Rep 3

description: Library name: POA_351


title: TAF7 ChIP-nexus 1 h Triptolide treatment rep1

description: Library name: kc167_triptolide_taf7_nexus_1


title: total RNAs from CG31510 frameshift fly ovary with polyA selection replicate2

description: Library name: CG31510_null_rep2


title: LM_CnT30_1_difff6_d29_06052022_B_A08_S19_R2

description: Library name: LM_CnT30_1_difff6_d29_06052022_B_A08_S19_R1


title: LM_CnT30_1_Diff52_d32_28032022_A04_S12_R2

description: Library name: LM_CnT30_1_Diff52_d32_28032022_A04_S12_R1


title: total RNAs from CG31510 frameshift fly ovary with polyA selection replicate3

description: Library name: CG31510_null_rep3


title: Siberian Hamster, POA, 4wk, Rep 2

description: Library name: POA_332


title: Siberian Hamster, POA, 4wk, Rep 1

description: Library name: POA_333


title: LM_CnT30_1_difff6_d29_06052022_A_A05_S17_R2

description: Library name: LM_CnT30_1_difff6_d29_06052022_A_A05_S17_R1


title: Siberian Hamster, POA, LD, Rep 6

description: Library name: POA_417

value: LD


title: total RNAs from CG31510 frameshift fly ovary with polyA selection replicate1

description: Library name: CG31510_null_rep1


title: TAF7 ChIP-nexus Control rep2

description: Library name: kc167_dmso_taf7_nexus_2


title: Siberian Hamster, POA, 4wk, Rep 5

description: Library name: POA_314


title: Siberian Hamster, POA, LD, Rep 5

description: Library name: POA_141


title: Blood, PD362, Healthy control

city: Busan

first: Jungho

last: Kim

address: 57, Oryundae-ro, Geumjeong-gu, Busan, Republic of Korea

department: Department of Clinical Laboratory Science, College of Health Sciences

country: South Korea

institute: Catholic University of Pusan

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence (using fastx_trimmer), then mapped to hg19 (UCSC) whole genome using Bowtie2
Read count extraction using bedtools.
Assembly: hsa
Supplementary files format and content: tab-delimited text files include read count values for each Sample

source_name: Blood

extract_protocol:
RNA was harvested using PAXgene Blood miRNA kit (QIAGEN). 500 ng of total RNA was used for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using EBNext Multiplex Small RNA Library Prep kit standard protocols.

value: Blood

value: Blood cell

tag: subject status

value: Healthy control


title: Siberian Hamster, POA, LD, Rep 4

description: Library name: POA_238


title: Blood, PD371, Healthy control


title: Blood, PD348, Healthy control


title: TAF6 ChIP-nexus Control rep2

description: Library name: kc167_dmso_taf6_nexus_2

value: custom anti-TAF6 rabbit polyclonal, Zeitlinger Lab, TAF6 - U1266BL120-3


title: total RNAs from CG31510 and CG7065 germline KD in fly ovary with polyA selection replicate3

description: Library name: MTD_shCCG31510_CG7065_rep3


title: Siberian Hamster, POA, LD, Rep 3

description: Library name: POA_247


title: TAF6 ChIP-nexus 1 h Triptolide treatment rep1

description: Library name: kc167_triptolide_taf6_nexus_1

value: Kc167 cells


title: total RNAs from w1118 fly ovary with polyA selection replicate3

description: Library name: w1118_rep3


title: TAF6 ChIP-nexus 1 h Triptolide treatment rep3

description: Library name: kc167_triptolide_taf6_nexus_3


title: TAF7 ChIP-nexus Control rep3

description: Library name: kc167_dmso_taf7_nexus_3


title: Siberian Hamster, POA, LD, Rep 2

description: Library name: POA_248


title: total RNAs from w1118 fly ovary with polyA selection replicate1

description: Library name: w1118_rep1


title: total RNAs from w1118 fly ovary with polyA selection replicate2

description: Library name: w1118_rep2


title: Blood, PD350, Healthy control


title: TAF6 ChIP-nexus Control rep1

description: Library name: kc167_dmso_taf6_nexus_1


title: Siberian Hamster, POA, LD, Rep 1

description: Library name: POA_205


title: Blood, PD344, Healthy control


title: Siberian Hamster, AVPV, 32wk, Rep 6

description: Library name: AVPV_161

source_name: AVPV

value: AVPV

value: 32wk SD


title: total RNAs from CG31510 and CG7065 germline KD in fly ovary with polyA selection replicate2

description: Library name: MTD_shCCG31510_CG7065_rep2

value: fly ovaries


title: TAF5 ChIP-nexus 1 h Triptolide treatment rep2

description: Library name: kc167_triptolide_taf5_ap_nexus_2

value: custom anti-TAF5 rabbit polyclonal, Zeitlinger Lab, TAF5 (AP) - U7893CL140-5AP


title: total RNAs from CG31510 and CG7065 germline KD in fly ovary with polyA selection replicate1

description: Library name: MTD_shCCG31510_CG7065_rep1


title: Blood, PD339, Healthy control


title: TAF5 ChIP-nexus 1 h Triptolide treatment rep3

description: Library name: kc167_triptolide_taf5_ap_nexus_3


title: Siberian Hamster, AVPV, 32wk, Rep 5

description: Library name: AVPV_113


title: total RNAs from CG7065 germline KD in fly ovary with polyA selection replicate3

description: Library name: MTD_shCG7065_rep3


title: Blood, PD337, Healthy control


title: total RNAs from GFP tagged CG31510 fly ovary with polyA selection replicate2

description: Library name: GFP_CG31510_rep2


title: Siberian Hamster, AVPV, 32wk, Rep 4

description: Library name: AVPV_152


title: TAF5 ChIP-nexus Control rep3

description: Library name: kc167_dmso_taf5_ap_nexus_3

value: DMSO


title: total RNAs from CG7065 germline KD in fly ovary with polyA selection replicate2

description: Library name: MTD_shCG7065_rep2


title: TAF5 ChIP-nexus Control rep1

description: Library name: kc167_dmso_taf5_ap_nexus_1


title: Blood, PD331, Healthy control


title: Siberian Hamster, AVPV, 32wk, Rep 3

description: Library name: AVPV_153


title: TAF4 ChIP-nexus 1 h Triptolide treatment rep3

description: Library name: kc167_triptolide_taf4_nexus_3

value: custom anti-TAF4 rabbit polyclonal, Zeitlinger Lab, TAF4 - U7893CL140-3


title: total RNAs from CG7065 germline KD in fly ovary with polyA selection replicate1

description: Library name: MTD_shCG7065_rep1


title: Blood, PD311, Healthy control


title: total RNAs from CG31510 germline KD in fly ovary with polyA selection replicate3

description: Library name: MTD_shCG31510_rep3


title: Blood, PD284, latent tuberculosis infection

value: subjects with latent tuberculosis infection


title: TAF4 ChIP-nexus 1 h Triptolide treatment rep1

description: Library name: kc167_triptolide_taf4_nexus_1


title: Siberian Hamster, AVPV, 32wk, Rep 1

description: Library name: AVPV_149


title: TAF4 ChIP-nexus Control rep3

description: Library name: kc167_dmso_taf4_nexus_3


title: Blood, PD282, latent tuberculosis infection


title: total RNAs from CG31510 germline KD in fly ovary with polyA selection replicate1

description: Library name: MTD_shCG31510_rep1


title: TAF3 ChIP-nexus 1 h Triptolide treatment rep3

description: Library name: kc167_triptolide_taf3_nexus_3

value: custom anti-TAF3 rabbit polyclonal, Zeitlinger Lab, TAF3 - U7724CL140-9


title: Blood, PD281, latent tuberculosis infection


title: Siberian Hamster, AVPV, 28wk, Rep 5

description: Library name: AVPV_172

value: 28wk SD


title: total RNAs from Piwi germline KD in fly ovary with polyA selection replicate3

description: Library name: MTD_shPiwi_rep3


title: Blood, PD279, latent tuberculosis infection


title: TAF4 ChIP-nexus Control rep1

description: Library name: kc167_dmso_taf4_nexus_1


title: Blood, PD332, Healthy control


title: TAF3 ChIP-nexus 1 h Triptolide treatment rep2

description: Library name: kc167_triptolide_taf3_nexus_2

value: 10 uM Triptolide


title: Blood, PD277, latent tuberculosis infection


title: Siberian Hamster, AVPV, 28wk, Rep 4

description: Library name: AVPV_163


title: total RNAs from Piwi germline KD in fly ovary with polyA selection replicate2

description: Library name: MTD_shPiwi_rep2


title: Siberian Hamster, AVPV, 32wk, Rep 2

description: Library name: AVPV_160


title: Siberian Hamster, AVPV, 28wk, Rep 3

description: Library name: AVPV_165


title: total RNAs from Piwi germline KD in fly ovary with polyA selection replicate1

description: Library name: MTD_shPiwi_rep1


title: TAF3 ChIP-nexus Control rep3

description: Library name: kc167_dmso_taf3_nexus_3


title: Blood, PD276, latent tuberculosis infection


title: total RNAs from control germline KD in fly ovary with polyA selection replicate3

description: Library name: MTD_shwhite_rep3


title: Blood, PD275, latent tuberculosis infection


title: Siberian Hamster, AVPV, 28wk, Rep 2

description: Library name: AVPV_162


title: TAF3 ChIP-nexus Control rep2

description: Library name: kc167_dmso_taf3_nexus_2


title: total RNAs from control germline KD in fly ovary with polyA selection replicate2

description: Library name: MTD_shwhite_rep2


title: total RNAs from CG31510 germline KD in fly ovary with polyA selection replicate2

description: Library name: MTD_shCG31510_rep2


title: Blood, PD274, latent tuberculosis infection


title: TAF2 ChIP-nexus 1 h Triptolide treatment rep3

description: Library name: kc167_triptolide_taf2_nexus_3

value: custom anti-TAF2 rabbit polyclonal, Zeitlinger Lab, TAF2 - U4123BK150-9


title: Siberian Hamster, AVPV, 28wk, Rep 1

description: Library name: AVPV_174


title: Siberian Hamster, AVPV, 28wk, Rep 6

description: Library name: AVPV_175


title: total RNAs from control germline KD in fly ovary with polyA selection replicate1

description: Library name: MTD_shwhite_rep1


title: Siberian Hamster, AVPV, 24wk, Rep 6

description: Library name: AVPV_178

value: 24wk SD


title: Siberian Hamster, AVPV, 24wk, Rep 5

description: Library name: AVPV_188


title: TAF2 ChIP-nexus 1 h Triptolide treatment rep1

description: Library name: kc167_triptolide_taf2_nexus_1


title: gys2 knockout, liver, biol rep 7

city: Minami-ku, Sagamihara

first: Fumiya

last: Furukawa

state: Kanagawa

address: 1-15-1, Kitazato

department: Marine Biosciences

institute: Kitasato University

description: Library name: 189

data_processing:
Read 1 reads were used for quantification using fastp (version 0.23.4) (Chen et al., 2018), bwa mem (0.7.17-r1188) (Li, 2013), and salmon (v1.10.2) (Patro et al., 2017) on zebrafish GRCz11 transcriptome reference ver 111.
Assembly: Danio_rerio.GRCz11.cdna.all.fa
Supplementary files format and content: csv-delimited text file includes rawcnt values for each Sample

organism: Danio rerio

source_name: liver

growth_protocol: The zebrafish (Danio rerio) strains AB was maintained under a 14-h light/10-h dark cycle. The water temperature was kept at 28.5°C.

extract_protocol:
Each tissue was separated and the total RNA was extracted by direct-TRI method (Ujibe et al., 2021, Bio Protoc 11: e4136).
3’ mRNA-Seq were conducted according to the Lasy-Seq ver. 1.1 protocol (https://sites.google.com/view/lasy-seq/) (Kamitani et al. 2019; Kashima et al. 2021). Briefly, total RNA was reverse transcribed using an RT primer with index and SuperScript IV reverse transcriptase (Thermo Fisher Scientific, Waltham, MA, USA). Then, all RT mixtures of the samples were pooled and purified using an equal volume of AMpure XP beads (Beckman Coulter, Brea, CA, USA) according to the manufacturer’s instructions. Second strand synthesis was conducted on the pooled samples using RnaseH (5 U/μL, Enzymatics, Beverly, MA, USA), and DNA polymerase I (10 U/μL, Enzymatics, Beverly, MA, USA). To avoid the carryover of large amounts of rRNAs, the mixture was subjected to Rnase treatment using Rnase T1 (Thermo Fisher Scientific, Waltham, MA, USA). Then, purification was conducted with a 0.8× volume of Ampure XP beads. Fragmentation, end-repair, and A-tailing were conducted using 5× WGS Fragmentation Mix (Enzymatics, Beverly, MA, USA). The Adapter for Lasy-Seq was ligated using 5× Ligation Mix (Enzymatics, Beverly, MA, USA), and the adapter-ligated DNA was purified twice with a 0.8× volume of Ampure XP beads. After optimisation of PCR cycles for library amplification by qPCR using Evagreen, 20× in water (Biotium, Fremont, CA, USA) and the QuantStudio5 Real-Time PCR System (Applied Biosystems, Waltham, MA, USA), the library was amplified using KAPA HiFi HotStart ReadyMix (KAPA BIOSYSTEMS, Wilmington, MA, USA) on the ProFlex PCR System (Applied Biosystems, Waltham, MA, USA). The amplified library was purified with an equal volume of Ampure XP beads. One microliter of the library was then used for electrophoresis using a Bioanalyzer 2100 with the Agilent High Sensitivity DNA kit (Agilent Technologies, Santa Clara, CA, USA) to check for quality. Then, sequencing of 150-bp paired-end reads was performed using HiSeq X Ten (Illumina, San Diego, CA, USA) by Macrogen, Inc. (Seoul, Korea).

value: liver

tag: strain

value: AB

tag: developmental stage

value: adult

tag: genotype

value: gys2 knockout


title: gys2 knockout, liver, biol rep 8

description: Library name: 190


title: Blood, PD270, latent tuberculosis infection

value: Blood

value: Blood cell


title: Siberian Hamster, AVPV, 24wk, Rep 4

description: Library name: AVPV_180

value: AVPV


title: Siberian Hamster, AVPV, 24wk, Rep 3

description: Library name: AVPV_196


title: TAF2 ChIP-nexus Control rep3

description: Library name: kc167_dmso_taf2_nexus_3

value: Kc167 cells


title: Blood, PD246, latent tuberculosis infection


title: TAF2 ChIP-nexus Control rep1

description: Library name: kc167_dmso_taf2_nexus_1


title: gys2 knockout, liver, biol rep 6

description: Library name: 188


title: TAF1 ChIP-nexus 1 h Triptolide treatment rep2

description: Library name: kc167_triptolide_taf1_p1_nexus_2

value: custom anti-TAF1 rabbit polyclonal, Zeitlinger Lab, TAF1 (P1) - U7893CL140-11


title: Blood, PD244, latent tuberculosis infection


title: gys2 knockout, liver, biol rep 5

description: Library name: 187


title: TAF1 ChIP-nexus 1 h Triptolide treatment rep1

description: Library name: kc167_triptolide_taf1_p1_nexus_1


title: gys2 knockout, liver, biol rep 4

description: Library name: 186


title: Siberian Hamster, AVPV, 24wk, Rep 1

description: Library name: AVPV_181


title: Siberian Hamster, AVPV, 24wk, Rep 2

description: Library name: AVPV_187


title: Blood, PD237, latent tuberculosis infection


title: TAF1 ChIP-nexus Control rep3

description: Library name: kc167_dmso_taf1_p1_nexus_3

value: DMSO


title: Blood, PD271, latent tuberculosis infection


title: gys2 knockout, liver, biol rep 3

description: Library name: 185


title: TBP ChIP-nexus non treated rep3

description: Library name: kc167_nt_tbp_nexus_2

value: custom anti-TBP rabbit polyclonal, Zeitlinger Lab, TBP - U4123BK150-6 (1738)

value: Non treated


title: Siberian Hamster, AVPV, 20wk, Rep 3

description: Library name: AVPV_231

value: 20wk SD


title: wild type, liver, biol rep 8

description: Library name: 182

value: wild type


title: Blood, PD137, patient at diagnossis

value: patient


title: Siberian Hamster, AVPV, 20wk, Rep 6

description: Library name: AVPV_213


title: Blood, PD236, latent tuberculosis infection

value: subjects with latent tuberculosis infection


title: TAF1 ChIP-nexus Control rep2

description: Library name: kc167_dmso_taf1_p1_nexus_2


title: Blood, PD231, latent tuberculosis infection


title: Siberian Hamster, AVPV, 20wk, Rep 2

description: Library name: AVPV_226


title: gys2 knockout, liver, biol rep 2

description: Library name: 184


title: Blood, PD137, patient after completion of treatment

value: anti-tuberculosis treamtent


title: gys2 knockout, liver, biol rep 1

description: Library name: 183

value: liver


title: Siberian Hamster, AVPV, 20wk, Rep 5

description: Library name: AVPV_217


title: Blood, PD129, patient during treatment


title: Siberian Hamster, AVPV, 20wk, Rep 4

description: Library name: AVPV_216


title: TBP ChIP-nexus non treated rep1

description: Library name: kc167_nt_tbp_nexus_1


title: Blood, PD137, patient during treatment


title: Blood, PD129, patient after completion of treatment


title: wild type, liver, biol rep 7

description: Library name: 181

value: AB


title: wild type, liver, biol rep 5

description: Library name: 179

value: adult


title: TBP ChIP-nexus 1 h Triptolide treatment rep1

description: Library name: kc167_triptolide_tbp_k_nexus_1

value: custom anti-TBP rabbit polyclonal, Kadonaga Lab, TBP - Kadonaga lab 517

value: 10 uM Triptolide


title: TBP ChIP-nexus 1 h Triptolide treatment rep3

description: Library name: kc167_triptolide_tbp_k_nexus_3


title: wild type, liver, biol rep 6

description: Library name: 180


title: TBP ChIP-nexus Control rep1

description: Library name: kc167_dmso_tbp_k_nexus_1


title: Siberian Hamster, AVPV, 20wk, Rep 1

description: Library name: AVPV_214


title: Siberian Hamster, AVPV, 16wk, Rep 6

description: Library name: AVPV_244

value: 16wk SD


title: Blood, PD129, patient at diagnossis

value: Blood

value: Blood cell


title: Siberian Hamster, AVPV, 16wk, Rep 5

description: Library name: AVPV_265

value: AVPV


title: wild type, liver, biol rep 4

description: Library name: 178


title: wild type, liver, biol rep 3

description: Library name: 177


title: Blood, PD127, patient during treatment


title: c.elegans, Day 3, Refed, rep 3

city: Dallas

first: Peter

middle: M

last: Douglas

state: Texas

address: 6000 Harry Hines Blvd

department: Department of Molecular Biology

institute: University of Texas Southwestern Medical Center at Dallas

description: Library name: EC3_1

data_processing:
raw reads were trimmed and mapped using CLC genomics workbench (v23) default settings. CLC was also used for statistical analysis to idenify DEGs and generate expression browsers.
Assembly: WBcel235
Supplementary files format and content: tab delimeted text files include raw total counts for each sample

organism: Caenorhabditis elegans

source_name: whole-body

growth_protocol: 20°C on HT115 bacteria and NGM plates supplemented with IPTG and Carbenicillin

extract_protocol:
Whole worm RNA was extracted using Trizol with freeze/thawing and vortexing.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Collection of worms at Day 1 whom have been fed their whole life, Day 2 whom have been fasted for 24 hours (complete removal of food), and Day 3 whom have been refed on food for 24 hours.

value: whole-body

tag: day

tag: RNAi

value: EV RNAi

value: wildtype

value: Refed

tag: biological repeat

value: biological repeat 3


title: Siberian Hamster, AVPV, 16wk, Rep 4

description: Library name: AVPV_283


title: Blood, PD127, patient after completion of treatment

value: patient


title: c.elegans, Day 3, Refed, rep 4

description: Library name: EC4_1

value: biological repeat 4


title: c.elegans, Day 3, Refed, rep 2

description: Library name: EC2_1

value: biological repeat 2


title: TBP ChIP-nexus Control rep2

description: Library name: kc167_dmso_tbp_k_nexus_2

value: Kc167 cells

value: DMSO


title: Siberian Hamster, AVPV, 16wk, Rep 3

description: Library name: AVPV_255


title: Blood, PD127, patient at diagnossis


title: Blood, PD120, patient after completion of treatment

value: anti-tuberculosis treamtent


title: gys2 knockout, muscle, biol rep 8

description: Library name: 174

source_name: muscle

value: muscle

value: AB

value: adult

value: gys2 knockout


title: Siberian Hamster, AVPV, 16wk, Rep 2

description: Library name: AVPV_251

value: 16wk SD


title: Blood, PD120, patient during treatment

value: Blood

value: Blood cell


title: c.elegans, Day 2, Fasted, rep 3

description: Library name: CB3_1

value: whole-body

value: EV RNAi

value: Fasted


title: gys2 knockout, muscle, biol rep 7

description: Library name: 173


title: wild type, liver, biol rep 2

description: Library name: 176

value: liver

value: wild type


title: Siberian Hamster, AVPV, 12wk, Rep 5

description: Library name: AVPV_280

value: AVPV

value: 12wk SD


title: Blood, PD120, patient at diagnossis

value: patient


title: Siberian Hamster, AVPV, 12wk, Rep 6

description: Library name: AVPV_277


title: gys2 knockout, muscle, biol rep 6

description: Library name: 172


title: c.elegans, Day 2, Fasted, rep 4

description: Library name: CB4_1

value: wildtype

value: biological repeat 4


title: Blood, PD118, patient after completion of treatment

value: anti-tuberculosis treamtent


title: Siberian Hamster, AVPV, 16wk, Rep 1

description: Library name: AVPV_252


title: wild type, liver, biol rep 1

description: Library name: 175

value: AB


title: gys2 knockout, muscle, biol rep 5

description: Library name: 171

value: muscle

value: adult


title: c.elegans, Day 3, Refed, rep 1

description: Library name: EC1_1

value: Refed

value: biological repeat 1


title: Siberian Hamster, AVPV, 12wk, Rep 4

description: Library name: AVPV_278


title: c.elegans, Day 2, Fasted, rep 1

description: Library name: CB1_1


title: Blood, PD118, patient during treatment

value: Blood

value: Blood cell


title: gys2 knockout, muscle, biol rep 4

description: Library name: 170

value: gys2 knockout


title: c.elegans, Day 1, Fed, rep 4

description: Library name: AA4_1

value: whole-body

value: EV RNAi

value: Fed


title: gys2 knockout, muscle, biol rep 3

description: Library name: 169


title: Siberian Hamster, AVPV, 12wk, Rep 2

description: Library name: AVPV_276

value: AVPV


title: Siberian Hamster, AVPV, 12wk, Rep 3

description: Library name: AVPV_289

value: 12wk SD


title: Blood, PD118, patient at diagnossis

value: patient


title: c.elegans, Day 1, Fed, rep 3

description: Library name: AA3_1

value: wildtype

value: biological repeat 3


title: c.elegans, Day 2, Fasted, rep 2

description: Library name: CB2_1

value: Fasted

value: biological repeat 2


title: Blood, PD117, patient after completion of treatment

value: anti-tuberculosis treamtent


title: c.elegans, Day 1, Fed, rep 2

description: Library name: AA2_1


title: gys2 knockout, muscle, biol rep 2

description: Library name: 168

value: muscle

value: AB

value: adult


title: Siberian Hamster, AVPV, 8wk, Rep 6

description: Library name: AVPV_305

value: 8wk SD


title: wild type, muscle, biol rep 8

description: Library name: 166

value: wild type


title: Blood, PD117, patient at diagnossis

value: Blood

value: Blood cell


title: Siberian Hamster, AVPV, 8wk, Rep 5

description: Library name: AVPV_397


title: c.elegans, Day 1, kin-19, rep 4

description: Library name: K4_1

data_processing:
raw reads were trimmed and mapped using CLC genomics workbench (v23) default settings. CLC was also used for statistical analysis to idenify DEGs and generate expression browsers.
Assembly: WBcel235
Supplementary files format and content: tab delimeted text file includes raw total counts for each sample

extract_protocol:
Whole worm RNA was extracted using Trizol with freeze/thawing and vortexing.
RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: Collection of worms at Day 1 whom have been fed their whole life on either empty vector control RNAi or kin-19 RNAi.

value: whole-body

value: kin-19 RNAi

value: knockdown

value: Biol rep 4


title: Blood, PD116, patient after completion of treatment

value: patient


title: c.elegans, Day 1, kin-19, rep 3

description: Library name: K3_1

value: wildtype

value: Biol rep 3


title: Blood, PD116, patient during treatment


title: Siberian Hamster, AVPV, 8wk, Rep 3

description: Library name: AVPV_398

value: AVPV


title: c.elegans, Day 1, kin-19, rep 2

description: Library name: K2_1

value: Biol rep 2


title: Blood, PD116, patient at diagnossis


title: c.elegans, Day 1, kin-19, rep 1

description: Library name: K1_1

value: Biol rep 1


title: wild type, muscle, biol rep 4

description: Library name: 162

value: muscle


title: Siberian Hamster, AVPV, 8wk, Rep 1

description: Library name: AVPV_310


title: Siberian Hamster, AVPV, 12wk, Rep 1

description: Library name: AVPV_292

value: 12wk SD


title: Siberian Hamster, AVPV, 8wk, Rep 2

description: Library name: AVPV_399


title: Blood, PD112, patient after completion of treatment

value: anti-tuberculosis treamtent


title: Blood, PD112, patient during treatment


title: Blood, PD117, patient during treatment


title: wild type, muscle, biol rep 3

description: Library name: 161

value: AB

value: adult


title: c.elegans, Day 1, Fed, rep 1

description: Library name: AA1_1

value: EV RNAi

value: Fed

value: biological repeat 1


title: gys2 knockout, muscle, biol rep 1

description: Library name: 167

value: gys2 knockout


title: Blood, PD112, patient at diagnossis

value: Blood

value: Blood cell


title: Siberian Hamster, AVPV, 4wk, Rep 5

description: Library name: AVPV_314

value: 4wk SD


title: Siberian Hamster, AVPV, 4wk, Rep 6

description: Library name: AVPV_356


title: Siberian Hamster, AVPV, 8wk, Rep 4

description: Library name: AVPV_306

value: 8wk SD


title: wild type, muscle, biol rep 2

description: Library name: 160

value: wild type


title: Siberian Hamster, AVPV, 4wk, Rep 4

description: Library name: AVPV_352

value: AVPV


title: wild type, muscle, biol rep 6

description: Library name: 164


title: c.elegans, Day 1, EV, rep 2

description: Library name: EV2_1

value: whole-body

value: wildtype

value: control

value: Biol rep 2


title: wild type, muscle, biol rep 1

description: Library name: 159

value: muscle


title: wild type, muscle, biol rep 7

description: Library name: 165

value: AB


title: c.elegans, Day 1, EV, rep 1

description: Library name: EV1_1

value: Biol rep 1


title: wild type, muscle, biol rep 5

description: Library name: 163

value: adult


title: Blood, PD111, patient during treatment

value: patient

value: anti-tuberculosis treamtent


title: 40482_LAT_CTRL

city: Sacramento

first: Bradley

last: Ander

state: CA

address: 2805 50th Street - Room 2434

department: Neurology

institute: University of California, Davis

description: Library name: 40482lat

library_source: transcriptomic single cell

data_processing:
Raw FASTQ reads were demultiplexed using the SpliT-Pipe protocol from the manufacturer and aligned to the RheMac10 genome. Gene annotations for the rhesus macaque were augmented by use of the Comparative Annotation Toolkit (CAT) which takes into consideration genes with homology across species.
Assembly: RheMac10
Supplementary files format and content: Tab-separated values files and matrix files

organism: Macaca mulatta

source_name: brain

extract_protocol:
Single nucleus suspensions were made following minor modifications to a validated 10x Genomics demonstrated protocol (Nuclei Isolation from Cell Suspensions and Tissue for Single Cell RNA Sequencing (CG000124 revE). Briefly, samples were mechanically homogenized in lysis buffer before undergoing cycles of washing and centrifugation. The pellet was resuspended and passed through a 40μm cell strainer. Single nucleus suspensions were fixed according to specifications of the Nuclei Fixation Kit (Parse Biosciences, Seattle, WA (formerly known as SplitBio), SB1003). Aliquots of each fixed sample were counted in duplicate. Fixed suspensions were stored at -80oC until all samples were ready for library preparation.
Libraries were prepared by the UC Davis Genomics Core using the Whole Transcriptome Kit (Parse Biosciences; EC-W01030) according to manufacturer protocol and sequenced on Illumina NovaSeq 6000 S4 (PE150) which targeted a total of 4167 nuclei/region/case and resulted in a total of 56k reads/nucleus.

value: brain

value: male

tag: tissue region

value: amygdala

tag: tissue subregion

value: lateral nucleus

tag: experimental group

value: CTRL


title: c.elegans, Day 1, EV, rep 4

description: Library name: EV4_1

value: EV RNAi

value: Biol rep 4


title: Siberian Hamster, AVPV, 4wk, Rep 3

description: Library name: AVPV_351

value: AVPV

value: 4wk SD


title: Siberian Hamster, AVPV, 4wk, Rep 2

description: Library name: AVPV_332


title: 40360_LAT_MIA

description: Library name: 40360lat

value: MIA


title: c.elegans, Day 1, EV, rep 3

description: Library name: EV3_1

value: whole-body

value: wildtype

value: control

value: Biol rep 3


title: SVA RNA, cultured in human lung carcinoma (LC) cell line, sample 2

city: Blacksburg

first: Chang

last: Lu

state: VA

address: 235 Goodwin Hall, 635 Prices Fork Road, Virginia Tech

department: Chemical Engineering

institute: Virginia Tech

description: Library name: SVA-Viral-Extract-2

data_processing:
1000 read fastq files are generated by ONT MinKNOW software in real time using Guppy basecaller (ONT, v5.0.16) with Qscore cutoff of 8
Real-time monitoring performed using ONT Epi2me custom genome alignment workfow
Alignment performed using minimap2 (v2.28)
Bigwig files generated using deepTools bamCoverage (v3.5.6)
Alignments visualized using Integrative genomics viewer (IGV) (v2.15.4)
Assembly: NC_011349.1
Supplementary files format and content: fastq, bigwig

organism: Sus scrofa domesticus

source_name: Human Lung Carcinoma (LC)

extract_protocol:
SVA positive vesicular fluid samples were taken from SVA positive pigs (as confirmed by RT-PCR). Collected fluid was immersed in oral fluid from the test subject. Oral fluid was collected from healthy pigs as controls. These samples were stored at -80°C until processing. RNA from VFE samples underwent the same Trizol extraction procedure with libraries generated the same day to minimize RNA degradation.
Nanopore sequencing libraries were generated in a microfluidic device, which also previously performs RT-LAMP and bead purification. A brief description is as follows: 1) 1µl of sample was added to a premade mixture of 12.5µl LAMP mastermix (M1700S, New England Bio), 9µl H2O, and 2.5µl LAMP primer mix, then loaded into the microfluidic device; 2) The device is placed on a hotplate to perform isothermal amplification at 65°C for 60 min; 3) The device is then removed from the hotplate, allowed to briefly cool, then loaded with SPRI paramagnetic beads for DNA isolation (SPRIselect, Beckman Coulter) ; 4) a magnet is applied underneath the device to immobilize the beads; 5) 75% ethanol solution is loaded to wash the beads; 6) a mixture of ONT fragmentation solution is loaded into the device and DNA is eluted into the solution from the bead surface (Oxford Nanopore RBK004); 7) The device is incubated for 5 min for fragmentation and barcoding of DNA; 8) A fresh tubing is plugged into the microfluidic outlet and then the library is flushed out, ready for pooling. 4-8 samples are pooled per sequencing run, with 1ul sequencing adaptor  (Oxford Nanopore RBK004)solution added to the pooled libraries.

tag: cell line

value: Human Lung Carcinoma (LC)


title: 40482_CE_CTRL

description: Library name: 40482ce

value: central nucleus


title: Siberian Hamster, AVPV, 4wk, Rep 1

description: Library name: AVPV_333


title: Blood, PD108, patient after completion of treatment

value: Blood

value: Blood cell

value: patient

value: anti-tuberculosis treamtent


title: SVA RNA, cultured in human lung carcinoma (LC) cell line, sample 3

description: Library name: SVA-Viral-Extract-3


title: SVA RNA, cultured in human lung carcinoma (LC) cell line, sample 1

description: Library name: SVA-Viral-Extract-1


title: SVA RNA, cultured in human lung carcinoma (LC) cell line, tube based library prep

description: Library name: SVA-Viral-Extract-Tube


title: Blood, PD108, patient during treatment


title: Blood, PD111, patient after completion of treatment


title: Siberian Hamster, AVPV, LD, Rep 6

description: Library name: AVPV_417

value: LD


title: Blood, PD108, patient at diagnossis


title: Siberian Hamster, AVPV, LD, Rep 5

description: Library name: AVPV_141


title: Healthy control, oral fluid, subject 16

description: Library name: HC-S3

source_name: Saliva

value: Saliva


title: Blood, PD107, patient after completion of treatment


title: 988_LAT_MIA

description: Library name: 988lat

value: brain

value: male

value: amygdala

value: lateral nucleus


title: Healthy control, oral fluid, subject 15

description: Library name: HC-S2


title: Siberian Hamster, AVPV, LD, Rep 4

description: Library name: AVPV_238

value: AVPV


title: 988_CE_MIA

description: Library name: 988ce

value: MIA


title: Blood, PD107, patient during treatment


title: Siberian Hamster, AVPV, LD, Rep 3

description: Library name: AVPV_247


title: Blood, PD111, patient at diagnossis


title: 827_LAT_MIA

description: Library name: 827lat


title: 827_CE_MIA

description: Library name: 827ce


title: Siberian Hamster, AVPV, LD, Rep 2

description: Library name: AVPV_248


title: SVA-positive vesicular fluid sample, subject 7, tube based library prep

description: Library name: SVA-VFE-S7-Tube

source_name: Vesicular lession

value: Vesicular lession


title: Blood, PD107, patient at diagnossis


title: SVA-positive vesicular fluid sample, subject 7

description: Library name: SVA-VFE-S7


title: Siberian Hamster, AVPV, LD, Rep 1

description: Library name: AVPV_205


title: Blood, PD101, patient after completion of treatment


title: 478_LAT_CTRL

description: Library name: 478lat

value: CTRL


title: SVA-positive vesicular fluid sample, subject 6

description: Library name: SVA-VFE-S6


title: GAS d-perR-infected HMEC-1 cells, bio rep 4, dual RNA-seq

city: Taipei City

first: Shu-Wei

middle: Marcia

last: Su

address: No. 155, Sec. 2, Linong St, Beitou District

country: Taiwan

institute: National Yang Ming Chiao Tung University

description: Total RNA treated with DNase I and ribosomal RNA depletion

data_processing:
Raw sequencing data quality was analyzed using Fastp (version 0.23.2), and the sequencing adapters and low-quality reads were trimmed and removed using STAR (version 2.7.9a). The reads were aligned to the GAS NZ131 reference genome (NCBI accession number, NC_011375.1) and human reference genome (hg38) using the featureCounts (version 2.0.4). The differential gene expression analysis was performed separately for HMEC-1 cells and GAS and normalized using DESeq2. The genes with a Padj < 0.05 and a log2 fold change ≥ 1 or ≤ −1 were considered to be differentially expressed genes (DEGs). Gene ontology (GO) term enrichment analysis of the DEGs was performed using the Blast2GO tool.
Assembly: GAS NZ131 reference genome (NCBI accession number, NC_011375.1) and human reference genome (hg38)
Supplementary files format and content: Tab-delimited text files including raw counts for each sample

organism:
Streptococcus pyogenes
Homo sapiens

growth_protocol: HMEC-1 cells were cultured in endothelial cell growth medium M200 (Thermo Fisher Scientific) with addition of low serum growth supplement (Thermo Fisher Scientific) and 10% fetal bovine serum and incubated at 37°C in 5% CO2. For GAS infection model, HMEC-1 cells were seeded in 6-well (3 × 105 cells per well) culture plates for overnight. Next day, the refreshed GAS (OD600=0.5; mid-log phase) grown in tryptic soy broth containing 0.5% yeast extract (TSBY) were collected, washed, and resuspended in M200 medium.

extract_protocol:
To extract total RNAs of HMEC-1 cells and intracellular GAS, we resuspended the cell pellets in the lysozyme buffer (Geneaid) containing acid-treated silica beads (0.1 mm) (Sigma). The cells were mechanically broken by vortexing, followed by the RNA isolation procedure of GENEzol TriRNA Bacterial Kit (Geneaid), according to the manufacturer’s recommendation. The total RNAs for dual RNA-seq analysis were further evaluated using the Eukaryote Total RNA Nano Kit for 2100 Bioanalyzer system (Agilent). The RNAs that obtained the RNA integrity number greater than 9 were used for subsequent library preparation of dual RNA-seq analysis.
The high quality total RNAs (HMEC-1 cells and GAS) were treated with DNase I and ribosomal RNA depletion (Ribo-Zero rRNA Removal Kits; Illumina), prior to library preparation (Stranded Total RNA Prep kit; Illumina) and NextSeq2000 sequencing (2x100 bp paired-end sequencing) (Illumina).

treatment_protocol: To infect HMEC-1 cells, we then added the freshly prepared GAS in the seeded cell wells at a multiplicity of infection (MOI) of 50 for infection. After 30 min of infection, the extracellular GAS in the medium was removed, and the cells were washed twice with PBS buffer. Subsequently, the cells were inoculated for another half of hour (in total 1 h post-infection point) with M200 containing antibiotic gentamicin (125 µg/mL). For dual RNA-seq analyses, HMEC-1 cells containing intracellular GAS were collected from 6-well plates at 1 h post-infection, followed by trypsin-EDTA detachment and washed in M200 medium. The cell pellets were then preserved in the RNAlater stabilization solution (Thermo Fisher Scientific) at -80ºC until use.

value: Human microvascular endothelial cell line-1

value: d-perR mutant strain

value: 1 h infection


title: 478_CE_CTRL

description: Library name: 478ce

value: central nucleus


title: Blood, PD101, patient at diagnossis

value: Blood

value: Blood cell


title: Blood, PD101, patient during treatment

value: patient

value: anti-tuberculosis treamtent


title: SVA-positive vesicular fluid sample, subject 5, tube based library prep

description: Library name: SVA-VFE-S5-Tube


title: GAS WT-infected HMEC-1 cells, bio rep 4, dual RNA-seq

value: Wild-type strain


title: 335_LAT_CTRL

description: Library name: 335lat

value: brain


title: GAS d-perR-infected HMEC-1 cells, bio rep 3, dual RNA-seq


title: N3

city: Guangzhou

first: Yanteng

last: Xu

state: Guangdong

address: 600# Tianhe Road

department: Centre for Nanomedicine

country: China

institute: The Third Affiliated Hospital of Sun Yat-sen University

description: Library name: NNNVs3

data_processing:
Subsequently, unique sequences with length in 18~25 nucleotide were mapped to specific species precursors in miRBase 22.1 by BLAST search to identify known miRNAs and novel 3p- and 5p- derived miRNAs. Length variation at both 3' and 5' ends and one mismatch inside of the sequence were allowed in the alignment. The unique sequences mapping to specific species mature miRNAs in hairpin arms were identified as known miRNAs. The unique sequences mapping to the other arm of known specific species precursor hairpin opposite to the annotated mature miRNA-containing arm were considered to be novel 5p- or 3p-derived miRNA candidates. The remaining sequences were mapped to other selected species precursors (with the exclusion of specific species) in miRBase 22.1 by BLAST search, and the mapped pre-miRNAs were further BLASTed against the specific species genomes to determine their genomic locations.  The above two we defined as known miRNAs. The unmapped sequences were BLASTed against the genomes, and the hairpin RNA structures containing sequences were predicated from the flank 120 nt sequences using RNAfold software (http://rna.tbi.univie.ac. at/cgi-bin/RNAfold.cgi). The criteria for secondary structure prediction were: (1) number of nucleotides in one bulge in stem (≤12) (2) number of base pairs in the stem region of the predicted hairpin (≥16) (3) cutoff of free energy (kCal/mol ≤-15) (4) length of hairpin (up and down stems + terminal loop ≥50) (5) length of hairpin loop (≤200). (6) number of nucleotides in one bulge in mature region (≤4) (7) number of biased errors in one bulge in mature region (≤2) (8) number of biased bulges in mature region (≤2) (9) number of errors in mature region (≤4) (10) number of base pairs in the mature region of the predicted hairpin (≥12) (11) percent of mature in stem (≥80).
Assembly: miRBase 22.1
Supplementary files format and content: tab-delimited text files include raw and normalized count values for each sample

extract_protocol:
Total RNA was extracted using Trizol reagent (Invitrogen, CA, USA) following the manufacturer's procedure
Approximately 5 µg of total RNA were used to prepare nine small RNA librariesaccording to the protocol of TruSeq Small RNA Sample Prep Kits (Illumina, San Diego, CA, USA). And then the libraries were sequenced by Illumina Hiseq 2500 at the LC-BIO following the vendor’s recommended protocol. Raw reads were subjected to an in-house program, ACGT101-miR (LC Sciences, Houston, Texas, USA) to remove adapter dimers, junk, low complexity, common RNA families (rRNA, tRNA, snRNA, snoRNA) and repeats.

value: murine neural stem cell


title: SVA-positive vesicular fluid sample, subject 5

description: Library name: SVA-VFE-S5


title: 40360_CE_MIA

description: Library name: 40360ce

value: male

value: amygdala


title: 335_CE_CTRL

description: Library name: 335ce


title: N2

description: Library name: NNNVs2


title: Healthy control, oral fluid, subject 14

description: Library name: HC-S1

value: Saliva


title: SVA-positive vesicular fluid sample, subject 4

description: Library name: SVA-VFE-S4


title: GAS WT-infected HMEC-1 cells, bio rep 3, dual RNA-seq


title: N1

description: Library name: NNNVs1


title: SVA-positive vesicular fluid sample, subject 3

description: Library name: SVA-VFE-S3


title: GAS d-perR-infected HMEC-1 cells, bio rep 2, dual RNA-seq


title: 318_CE_MIA

description: Library name: 318ce

value: MIA


title: MnI2

description: Library name: MnINNVs2


title: MnI3

description: Library name: MnINNVs3


title: GAS WT-infected HMEC-1 cells, bio rep 2, dual RNA-seq


title: SVA-positive vesicular fluid sample, subject 2

description: Library name: SVA-VFE-S2

value: Vesicular lession


title: GAS d-perR-infected HMEC-1 cells, bio rep 1, dual RNA-seq


title: 295_LAT_CTRL

description: Library name: 295lat

value: lateral nucleus

value: CTRL


title: MnI1

description: Library name: MnINNVs1


title: 295_CE_CTRL

description: Library name: 295ce


title: GAS WT-infected HMEC-1 cells, bio rep 1, dual RNA-seq

value: Human microvascular endothelial cell line-1


title: SVA-positive vesicular fluid sample, subject 1

description: Library name: SVA-VFE-S1


title: Short read scRNA-seq mouse hippocampus sequencing with RPS2-STAMP rep 1

status: Public on Dec 18 2025

city: La Jolla

first: Brian

last: Yee

address: 9500 Gilman Dr

department: Health

institute: UCSD

description:
Library name: biol rep 1
Single-cell sequencing of Ribo-STAMP-expressing mouse hippocampus

data_processing:
Aligned with cellranger-3.0.0 to mm10 + tdTomato reference
Doublet removal with Scrublet
QC filtering: removed low-quality cells and genes, mitochondrial filtering, replicate-specific Gm42418 filtering
CPM and log normalization. Raw edits were normalized by Stamp expression via regression. EPR = normed edits / raw reads
BBKNN batch correction, cell type assignment with marker genes using Scanpy
Assembly: mm10
Supplementary files format and content: Barcodes: cell barcodes (barcodes.tsv.gz)
Supplementary files format and content: Features: gene IDs and names (features.tsv.gz). Matrix: gene expression counts in Matrix Market format (matrix.mtx.gz)
Supplementary files format and content: Adatas (.h5ad files): filtered and normalized counts (shortread_normed_counts_adata_*), filtered and Stamp normalized edits (shortread_normed_edits_adata_*), filtered EPR adata (shortread_epr_adata_*)
Supplementary files format and content: MARINE output of raw edits: raw_edits_per_cell_per_gene_*.tsv

source_name: Hippocampus

growth_protocol: P22 C57BL/6J mice stereotactically injected with EF1a-Ribo-STAMP virus in dorsal hippocampus. Processed 72h post-injection at P25.

extract_protocol:
Hippocampi dissected from perfused brains, enzymatically dissociated with Papain/DNaseI, filtered, and resuspended at 1200 cells/µl.
10x Genomics Chromium Next GEM Single Cell 3' v3.4. Target: 10,000 cells/replicate, 100,000 reads/cell on Illumina NextSeq 200.

value: Hippocampus

value: Mixed

value: Injection in dHC with 800 nL EF1a-Ribo STAMP virus

tag: batch


title: Short read scRNA-seq mouse hippocampus sequencing with RPS2-STAMP rep 2

description:
Library name: biol rep 2
Single-cell sequencing of Ribo-STAMP-expressing mouse hippocampus

tag: treatment


title: WT_treatment2_R2

city: IRAPUATO

first: ALFREDO

last: HERRERA ESTRELLA

state: GUANAJUATO

address: Libramiento Norte León Km 9.6

department: UGA-LANGEBIO

country: Mexico

institute: CINVESTAV

description:
Library name: Sample 8
Column name in raw_counts.txt: 05mMPhi_R2

data_processing:
RNA-Seq data quality was assessed using FastQC v0.11.8 and SOAPnuke with default parameters to remove adapters and low-quality reads. High-quality reads were aligned to the T. atroviride reference genome (https://mycocosm.jgi.doe.gov/Triat2/Triat2.home.html) using HISAT2. Reads were quantified using the “featureCounts” function of the Rsubread package of R.
Assembly: Trichoderma atroviride v2.0 (https://mycocosm.jgi.doe.gov/Triat2/Triat2.home.html)
Supplementary files format and content: raw_counts.txt

organism: Trichoderma atroviride

source_name: Mycelium

extract_protocol:
RNA was extracted using the TRIzol method and its quality was assessed using the 2100 Bioanalyzer (Agilent)
RNA libraries for sequencing were prepared according to the MGIEasy RNA library prep method (2 x 150) for RNA-Seq libraries

tag: tissue

value: Mycelium

value: WT

value: 1 mM Pi + 0.5 mM Phi

tag: time

value: day 3


title: WT_treatment1_R2

description:
Library name: Sample 5
Column name in raw_counts.txt: 01mMPhi_R2

value: 1 mM Pi + 0.1 mM Phi


title: WT_treatment2_R3

description:
Library name: Sample 9
Column name in raw_counts.txt: 05mMPhi_R3


title: Short read scRNA-seq mouse hippocampus sequencing with RPS2-STAMP rep 3

description:
Library name: biol rep 3
Single-cell sequencing of Ribo-STAMP-expressing mouse hippocampus

tag: cell type


title: 318_LAT_MIA

description: Library name: 318lat

value: brain

tag: Sex


title: WT_treatment1_R1

description:
Library name: Sample 4
Column name in raw_counts.txt: 01mMPhi_R1


title: WT_control_1mMPi_R2

description:
Library name: Sample 2
Column name in raw_counts.txt: control_R2

value: 1 mM Pi control


title: WT_control_1mMPi_R1

description:
Library name: Sample 1
Column name in raw_counts.txt: control_R1


title: WT_control_1mMPi_R3

description:
Library name: Sample 3
Column name in raw_counts.txt: control_R3


title: TAM_cGAMPnp2

city: Hsinchu

first: Hsin mei

last: Lee

address: Guangfu Rd.

institute: National Tsing Hua University

description:
Library name: TAM_cGAMPnp2
10X Genomics

data_processing:
The Cell Ranger  (v9.0.1) was used for read trimming, genome alignment, sample demultiplexing, barcode processing and UMI counting. Sequence data were mapped onto the mouse reference genome (mm10) by using “cellranger multi”. The Unique molecular identifier (UMI) count matrix would be generated and then imported into R (4.1.0), analyzed with Seurat (4.1.1)
Assembly: Mouse mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Tumor

growth_protocol: Murine PDAC Ak4.4 cells were orthotopically implanted in the pancrea of 6-8-week-old female FVB mice. 10^5 Ak4.4 cells were injected in the pancrea through a 28-gauge needle.

extract_protocol:
Tumour tissues were cut into small pieces and digested at 37°C for 30 min by incubation with collagenase type 1A (1.5 mg/mL) and hyaluronidase (1.5 mg/mL) in DMEM. The cells were then filtered with 40 um cell strainers followed by a centrifugation at 3000 rpm for 10 min. Following washes with 1% BSA in PBS, red blood cells were removed using 1× ACK lysis buffer. Dead cells were subsequently deleted using a dead cell removal kit and MS columns, and the resulting viable single-cell suspensions were used for downstream single-cell RNA sequencing.
Single cells were processed through the GemCode Single Cell Platform using the Chromium Fixed RNA Kit, Mouse Transcriptome (10X Genomics, Pleasanton) according to  the manufacturer’s protocol. In brief, Cell suspensions were fixed with paraformaldehyde. After probe hybridization, Cells were pooled and loaded onto a Chromium Single-Cell Chip Q along with the reverse transcription (RT) master mix and single cell TL gel beads, aiming for 40000 cells per channel. Following generation of single-cell gel bead-in-emulsions (GEMs), reverse transcription was performed using a Applied Biosystems™ Veriti™ 96-Well Thermal Cycler (Thermo Fisher Scientific, USA). Amplified cDNA was purified using SPRIselect beads and converted to the sequencing library according to the manufacturer’s protocol. Library was sequenced on an Illumina NovaSeq X platform following read length: 150 bp Read 1 (16bp single cell barcode, 10x barcode; 12bp Unique molecular identifier, UMI), 150 bp Read 2 (transcript insert), 10 bp i7 Index (sample index), 10 bp i5 Index (sample index)

treatment_protocol: The experimental design involved orthotopically implanted murine PDAC (Ak4.4) cells in FVB mice, followed by IV administration of TAM-cGAMPnp on day 9, 11, 13, and 15 post-inoculation. Subsequent transcriptome analysis of the tumors was performed on day 16.

value: Tumor

value: PDAC

value: TAM-cGAMPnp


title: Control1

description:
Library name: Control1
10X Genomics

value: control


title: SVA-positive vesicular fluid sample, subject 2, tube based library prep

description: Library name: SVA-VFE-S2-Tube

value: Vesicular lession


title: 3 dpa-rep1-IgG

city: New York

first: Jingli

last: Cao

state: NY

department: Cell & Developmental Biology

institute: Weill Cornell Medical College

description: Library name: 3 dpa-rep1-IgG

data_processing:
CUT&TAG data were processed and analyzed following a step-by-step pipeline (dx.doi.org/10.17504/protocols.io.bjk2kkye). Reads were trimmed for adaptors using Trimmomatic (v0.39) before aligning to the DanRer10 genome using Bowtie2 (v2.5.3) with parameters for 10-700 bp length. Peaks were called using SEACR (v1.3) with p-value < 0.01.
Assembly: DanRer10
Supplementary files format and content: bigWig, called peaks
Library strategy: CUT&Tag

source_name: heart

growth_protocol: in vivo

extract_protocol:
Hearts were isolated at 3 dpa together with the uninjured control (2 biological replicates each) on ice and washed several times to remove blood cells.  Ventricles were digested in an Eppendorf tube with 0.5 ml HBSS plus 0.13 U/ml Liberase DH (Roche) at 37°C, while stirring gently with a Spinbar® magnetic stirring bar (Bel-Art Products).  Supernatants were collected every 5 min and neutralized with sheep serum.  Dissociated cells were spun down and re-suspended in DMEM plus 10% fetal bovine serum (FBS) medium and sorted using a Sony MA900 sorter for EGFP+ cells (uninjured) and EGFP+mScarlet+ (3 dpa).
Nuclei preparation and CUT&TAG library preparation using rabbit anti-H3K4me1 antibody (Abcam, ab8895) were performed using the EpiCypher CUTANA™ CUT&Tag Kit following the manual. Two replicates with 5,000-12,000 nuclei for each sample were used.

treatment_protocol: standard heart amputation injury

value: heart

value: primary epicardial cells

value: epicardial cell

value: wild-type

value: heart injury


title: 3 dpa-rep2-IgG

description: Library name: 3 dpa-rep2-IgG


title: 3 dpa-rep2-H3K4me1

description: Library name: 3 dpa-rep2-H3K4me1


title: 3 dpa-rep1-H3K4me1

description: Library name: 3 dpa-rep1-H3K4me1


title: WT_treatment1_R3

description:
Library name: Sample 6
Column name in raw_counts.txt: 01mMPhi_R3

value: Mycelium


title: WT_treatment2_R1

description:
Library name: Sample 7
Column name in raw_counts.txt: 05mMPhi_R1

value: WT


title: control-rep1-IgG

description: Library name: control-rep1-IgG


title: control-rep1-H3K4me1

description: Library name: control-rep1-H3K4me1


title: control-rep2-H3K4me1

description: Library name: control-rep2-H3K4me1


title: Adar KO (sgRNA #1) ER-Hoxb8 macrophages grown for 7div with 10um baricitinib, Replicate 3

city: Philadelphia

first: Frederick

middle: Chris

last: Bennett

state: PA

address: 3501 Civic Center Blvd

institute: University of Pennsylvania

description: Library name: A11

data_processing:
All pre-processing steps were run using Terminal. FastQ files were downloaded from BaseSpace (Illumina) and concatenated across lanes using the “cat” function. All files were processed using FastP (Chen et al., 2018; Chen, 2023) to filter reads and trim Illumina adaptors, as well as FastQC (Andrews, 2014) to assess quality. All files were determined to be of sufficient quality for subsequent downstream processing. Reads were pseudoaligned to the mouse GRCm39 cDNA transcriptome (Ensembl release 99; Schneider et al., 2017; Zerbino et al., 2018) using Kallisto (version 0.46.0; Bray et al., 2016) and run through MultiQC (Ewels et al., 2016) for a final quality check after mapping.
All post-processing steps were run using RStudio (R Core Team, 2022). Transcripts were summarized to the gene level through tximport (version 1.14.2; Soneson et al., 2015) with abundance counts calculated via TPM and then normalized using TMM via edgeR (Robinson et al., 2010; McCarthy et al., 2012; Chen et al., 2016). Hierarchical cluster dendrograms were created using the “dist” function (method = euclidean) and “hclust” function (method = complete) and were visualized with the plot function. PCA plots were created using the “prcomp” function. Differential gene expression analysis was performed using linear modeling via limma (Ritchie et al., 2015), and differentially expressed genes (DEGs) were decided by applying an FDR cutoff of 0.05, a counts per million (CPM) cutoff of +1, and a Log2(FC) cutoff of +/- 2. Linear models and R2 values were created using the “lm” function. All output plots were visualized with ggplot2 (Wickham, 2016).
Assembly: mouse GRCm39 cDNA transcriptome
Supplementary files format and content: normalized_counts.tsv file contains transcript abundance counts calculated as described above for all samples

growth_protocol: Hoxb8s grown in RPMI media (Invitrogen, 7240047) supplemented with 1 mM Na-Pyruvate (Invitrogen, 11360070), 0.0005 mM beta-estradiol (Sigma Aldrich, E2758), and 10 ng/mL GM-CSF (Peprotech, 315-03). All cells were differentiated in DMEM media (ThermoFisher, 10569010), 10% FBS (VWR, 89510-186), 1% Penn/Strep (Invitrogen, 15140122), supplemented with 30 ng/mL murine M-CSF (Peprotech, 315-02) for 7 days unless noted otherwise. All cells kept at 5% C02 at 37C with media changes every 2-3 days.

extract_protocol:
For in vitro populations, RNA was extracted using the Qiagen RNeasy Mini Kit (74104) according to manufacturer’s instructions. For in vivo populations, cells were isolated and FACS sorted into TRIZol LS reagent.  Cells were briefly vortexed and 0.2 volumes of chloroform (Sigma, C2432-500ML) were added. Cells were again vortexed, incubated for 3 m at RT, and then centrifuged at 12,000xg for 15 m at 4c. The upper aqueous phase was then collected and 1 volume of fresh 70% EtOH was added. Cells were again vortexed and then run through the Qiagen RNeasy Micro Kit (74004) according to manufacturer’s instructions. Isolated RNA was stored at -80.
Sequencing libraries were prepared in-house using either 40 ng or 8ul RNA per sample, depending on if RIN scores and concentrations were able to be calculated, using the NEBNext Single Cell/Low Input RNA Library Prep Kit for Illumina (NEB, E6420) according to manufacturer’s instructions.

treatment_protocol: Cells were treated with 0uM, 0.00064uM, 0.16uM, 0.4uM, or 10uM Baricitinib (Selleck Chemicals, S2851) with each media change.

value: Cas9 het; Adar KO

value: 10um baricitinib


title: Adar KO (sgRNA #1) ER-Hoxb8 macrophages grown for 7div with 0.4um baricitinib, Replicate 1

description: Library name: A7

value: 0.4um baricitinib


title: Adar KO (sgRNA #1) ER-Hoxb8 macrophages grown for 7div with 10um baricitinib, Replicate 4

description: Library name: A16


title: Adar KO (sgRNA #1) ER-Hoxb8 macrophages grown for 7div with 10um baricitinib, Replicate 2

description: Library name: A6


title: Adar KO (sgRNA #1) ER-Hoxb8 macrophages grown for 7div with 0.4um baricitinib, Replicate 3

description: Library name: A17


title: Adar KO (sgRNA #1) ER-Hoxb8 macrophages grown for 7div with 0.016um baricitinib, Replicate 3

description: Library name: A18

value: 0.016um baricitinib


title: Adar KO (sgRNA #1) ER-Hoxb8 macrophages grown for 7div with 0.016um baricitinib, Replicate 2

description: Library name: A13


title: Adar KO (sgRNA #1) ER-Hoxb8 macrophages grown for 7div with 10um baricitinib, Replicate 1

description: Library name: A1


title: Adar KO (sgRNA #1) ER-Hoxb8 macrophages grown for 7div with 0.016um baricitinib, Replicate 1

description: Library name: A8


title: Adar KO (sgRNA #1) ER-Hoxb8 macrophages grown for 7div with 0.4um baricitinib, Replicate 2

description: Library name: A12


title: Adar KO (sgRNA #1) ER-Hoxb8 macrophages grown for 7div with 0.0006um baricitinib, Replicate 2

description: Library name: A9

value: 0.0006um baricitinib


title: Adar KO (sgRNA #1) ER-Hoxb8 macrophages grown for 7div with 0.0006um baricitinib, Replicate 3

description: Library name: A19


title: Adar KO (sgRNA #1) ER-Hoxb8 macrophages grown for 7div with 0um baricitinib, Replicate 2

description: Library name: A10

value: 0um baricitinib


title: control-rep2-IgG

description: Library name: control-rep2-IgG


title: Adar KO (sgRNA #1) ER-Hoxb8 macrophages grown for 7div with 0um baricitinib, Replicate 1

description: Library name: A5


title: NTC ER-Hoxb8 macrophages grown for 7div with 10um baricitinib, Replicate 3

description: Library name: N16

value: Cas9 het; NTC


title: Adar KO (sgRNA #1) ER-Hoxb8 macrophages grown for 7div with 0um baricitinib, Replicate 3

description: Library name: A15


title: Microplastics (repl. 1)  vs. Control (repl. 1)

city: Bayreuth

first: Alfons

middle: R

last: Weig

address: Universitaetsstrasse 30

department: Genomics and Bioinformatics

country: Germany

institute: University of Bayreuth

description: Biological replicate PVC 1, Biological replicate control 1;  microplastic animals, exposed to PVC with or without DINP;  harvested when carrying the 7th brood

hyb_protocol: Hybridization and washing if the Microarrays was perfomed as described in the Low Input Quick Amp Labeling Kit (Agilent Technologies)

scan_protocol: Microarrays were scanned using a high-resolution scanner G2505C (Agilent Technologies) and Agilent's Feature Extraction software (v. 11.5.1.1) was used to quantify hybridization signals;

data_processing: Data were processed using LIMMA: background correction (normexp), normalized within arrays (loess), normalized between arrays (Aquantile);

organism: Daphnia magna

source_name: animal, microplastics, replicate 1

label_protocol: RNA was labelled using the Low Input Quick Amp Labeling Kit (Agilent Technologies, Santa Clara, CA, USA);

growth_protocol: Age synchronized, juvenile D. magna (less than 24h old) were placed into 50 ml of semiatrifical medium, fed with S. oliquus equalling a carbon conentration of 1.5 mg per Liter (after 6 days a reduction to 1 mg per Liter occured), a full medium change occured after 14 days

extract_protocol: Total RNA was extracted using the RNeasy Microarray Tissue Kit (Qiagen GmbH, Hilden, Germany);

treatment_protocol: Daphnai were fed with a 1:10 ratio of PVC or PVC+DINP to algae cells (Scenedesmus obliquus)

value: Belgian clone BL2.2

value: whole organism

source_name: animal, control treatment, replicate 1


title: Microplastics/Plasticizers (repl. 2)  vs. Control (repl. 2), dye-swap

description: Biological replicate control 2, Biological replicate PVC+DINP 2; Control animals, untreated; microplastic animals, exposed to PVC with or without DINP;  harvested when carrying the 7th brood

source_name: animal, microplastics and plasticizers, replicate 2

source_name: animal, control treatment, replicate 2


title: Adar KO (sgRNA #1) ER-Hoxb8 macrophages grown for 7div with 0.0006um baricitinib, Replicate 1

description: Library name: A4


title: Control (repl. 1)  vs. Microplastics/Plasticizers (repl. 1)

description: Biological replicate control 1, Biological replicate PVC+DINP 1; Control animals, untreated; microplastic animals, exposed to PVC with or without DINP;  harvested when carrying the 7th brood

source_name: animal, microplastics and plasticizers, replicate 1


title: Control (repl. 2)  vs. Microplastics/Plasticizers (repl. 2)


title: NTC ER-Hoxb8 macrophages grown for 7div with 10um baricitinib, Replicate 2

description: Library name: N11


title: Microplastics (repl. 1)  vs. Microplastics/Plasticizers (repl. 1)

description: Biological replicate PVC 1, Biological replicate PVC+DINP 1; microplastic animals, exposed to PVC with or without DINP;  harvested when carrying the 7th brood


title: NTC ER-Hoxb8 macrophages grown for 7div with 0.4um baricitinib, Replicate 3

description: Library name: N12


title: Microplastics/Plasticizers (repl. 1)  vs. Control (repl. 1), dye-swap


title: NTC ER-Hoxb8 macrophages grown for 7div with 0.016um baricitinib, Replicate 3

description: Library name: N13


title: NTC ER-Hoxb8 macrophages grown for 7div with 0.016um baricitinib, Replicate 1

description: Library name: N3


title: Control (repl. 2)  vs. Microplastics (repl. 2), dye-swap

description: Biological replicate control 2, Biological replicate PVC 2; Control animals, untreated; microplastic animals, exposed to PVC with or without DINP;  harvested when carrying the 7th brood

source_name: animal, microplastics, replicate 2


title: NTC ER-Hoxb8 macrophages grown for 7div with 0.4um baricitinib, Replicate 4

description: Library name: N17


title: NTC ER-Hoxb8 macrophages grown for 7div with 0.016um baricitinib, Replicate 4

description: Library name: N18


title: NTC ER-Hoxb8 macrophages grown for 7div with 0.4um baricitinib, Replicate 2

description: Library name: N7


title: NTC ER-Hoxb8 macrophages grown for 7div with 0um baricitinib, Replicate 3

description: Library name: N20


title: NTC ER-Hoxb8 macrophages grown for 7div with 0.016um baricitinib, Replicate 2

description: Library name: N8


title: NTC ER-Hoxb8 macrophages grown for 7div with 0.0006um baricitinib, Replicate 1

description: Library name: N4


title: NTC ER-Hoxb8 macrophages grown for 7div with 0.0006um baricitinib, Replicate 3

description: Library name: N14


title: NTC ER-Hoxb8 macrophages grown for 7div with 0.0006um baricitinib, Replicate 2

description: Library name: N9


title: NTC ER-Hoxb8 macrophages grown for 7div with 0um baricitinib, Replicate 2

description: Library name: N10


title: Microplastics/Plasticizers (repl. 2)  vs. Microplastics (repl. 2), dye-swap

description: Biological replicatePVC 2, Biological replicate PVC+DINP 2; Control animals, untreated; microplastic animals, exposed to PVC with or without DINP;  harvested when carrying the 7th brood


title: Adar KO (sgRNA #2) macrophages after 7div, Replicate 5

description: Library name: A2-Mac-5


title: Adar KO (sgRNA #2) macrophages after 7div, Replicate 4

description: Library name: A2-Mac-4


title: Adar KO (sgRNA #2) macrophages after 7div, Replicate 2

description: Library name: A2-Mac-2


title: NTC ER-Hoxb8 macrophages grown for 7div with 0.4um baricitinib, Replicate 1

description: Library name: N2


title: Adar KO (sgRNA #2) macrophages after 7div, Replicate 3

description: Library name: A2-Mac-3


title: NTC macrophages after 7div, Replicate 3

description: Library name: NTC-3


title: Adar KO (sgRNA #2) macrophages after 7div, Replicate 1

description: Library name: A2-Mac-1


title: NTC macrophages after 7div, Replicate 1

description: Library name: NTC-1


title: Adar KO (sgRNA #2) progenitors made from transducing Cas9 het ER-Hoxb8s, Replicate 2

description: Library name: A2-Prog-2


title: Adar KO (sgRNA #2) progenitors made from transducing Cas9 het ER-Hoxb8s, Replicate 3

description: Library name: A2-Prog-3


title: Adar KO (sgRNA #2) progenitors made from transducing Cas9 het ER-Hoxb8s, Replicate 1

description: Library name: A2-Prog-1


title: Adar KO (sgRNA #1) macrophages after 7div, Replicate 3

description: Library name: Adar1-3


title: NTC ER-Hoxb8 macrophages grown for 7div with 10um baricitinib, Replicate 1

description: Library name: N1


title: NTC macrophages after 7div, Replicate 2

description: Library name: NTC2-2-Redo


title: Adar KO (sgRNA #1) progenitors made from transducing Cas9 het ER-Hoxb8s, Replicate 3

description: Library name: AdarProg3


title: Adar KO (sgRNA #1) macrophages after 7div, Replicate 2

description: Library name: Adar1-2


title: NTC progenitors made from transducing Cas9 het ER-Hoxb8s, Replicate 3

description: Library name: NTC2Prog3


title: Unmanipulated microglia isolated from FVB WT mouse; no injection, Replicate 9

description: Library name: YSWT2

source_name: Mg

value: brain

value: Mg


title: Adar KO (sgRNA #1) progenitors made from transducing Cas9 het ER-Hoxb8s, Replicate 2

description: Library name: AdarProg2


title: Unmanipulated microglia isolated from FVB WT mouse; no injection, Replicate 5

description: Library name: WT5


title: NTC ER-Hoxb8 macrophages grown for 7div with 0um baricitinib, Replicate 1

description: Library name: N5


title: NTC progenitors made from transducing Cas9 het ER-Hoxb8s, Replicate 2

description: Library name: NTC2Prog2


title: Unmanipulated microglia isolated from FVB WT mouse; no injection, Replicate 2

description: Library name: WT2


title: NTC progenitors made from transducing Cas9 het ER-Hoxb8s, Replicate 1

description: Library name: NTC2Prog1


title: Adar KO (sgRNA #1) progenitors made from transducing Cas9 het ER-Hoxb8s, Replicate 1

description: Library name: AdarProg1


title: Unmanipulated microglia isolated from FVB WT mouse; no injection, Replicate 7

description: Library name: WT7


title: Unmanipulated microglia isolated from FVB WT mouse; no injection, Replicate 8

description: Library name: YSWT1


title: ER-Hoxb8 ICT inj. into CSF1R KO brain; re-isolated back out, Replicate 6

description: Library name: WTHox4Lo


title: Unmanipulated microglia isolated from FVB WT mouse; no injection, Replicate 4

description: Library name: WT4


title: Unmanipulated microglia isolated from FVB WT mouse; no injection, Replicate 3

description: Library name: WT3


title: Adar KO (sgRNA #1) macrophages after 7div, Replicate 1

description: Library name: Adar1-1


title: Unmanipulated microglia isolated from FVB WT mouse; no injection, Replicate 1

description: Library name: WT1


title: ER-Hoxb8 ICT inj. into CSF1R KO brain; re-isolated back out, Replicate 2

description: Library name: GFPHox2


title: ER-Hoxb8 ICT inj. into CSF1R KO brain; re-isolated back out, Replicate 5

description: Library name: WTHox2Lo


title: BM ICT inj. into CSF1R KO brain; re-isolated back out, Replicate 6

description: Library name: BM7

source_name: BM

value: BM


title: ER-Hoxb8 ICT inj. into CSF1R KO brain; re-isolated back out, Replicate 1

description: Library name: GFPHox1


title: ER-Hoxb8 ICT inj. into CSF1R KO brain; re-isolated back out, Replicate 4

description: Library name: WTHox1Lo


title: Unmanipulated microglia isolated from FVB WT mouse; no injection, Replicate 6

description: Library name: WT6


title: BM ICT inj. into CSF1R KO brain; re-isolated back out, Replicate 3

description: Library name: BM3


title: BM ICT inj. into CSF1R KO brain; re-isolated back out, Replicate 1

description: Library name: BM1


title: ER-Hoxb8 macrophages grown for 7div from FVB Cas9 Mouse, Replicate 2

description: Library name: d7Hox2

value: Cas9 het


title: ER-Hoxb8 macrophages grown for 7div from FVB Cas9 Mouse, Replicate 1

description: Library name: d7Hox1


title: ER-Hoxb8 cells grown for 4div from FVB Cas9 Mouse, Replicate 2

description: Library name: d4Hox2


title: BM ICT inj. into CSF1R KO brain; re-isolated back out, Replicate 5

description: Library name: BM6


title: BM ICT inj. into CSF1R KO brain; re-isolated back out, Replicate 4

description: Library name: BM5


title: ER-Hoxb8 cells grown for 4div from FVB Cas9 Mouse, Replicate 1

description: Library name: d4Hox1


title: Macrophages grown for 7div from FVB WT BM, Replicate 3

description: Library name: wBM_1


title: ER-Hoxb8 Progenitors from FVB Cas9 Mouse, Replicate 2

description: Library name: d0Hox2


title: Monocytes isolated from FVB WT BM, Replicate 3

description: Library name: Mono3


title: Macrophages grown for 7div from FVB WT BM, Replicate 1

description: Library name: Mac1


title: Monocytes isolated from FVB WT BM, Replicate 1

description: Library name: Mono1


title: Progenitors isolated from FVB WT BM, Replicate 3

description: Library name: Prog3


title: ER-Hoxb8 cells grown for 4div from FVB Cas9 Mouse, Replicate 3

description: Library name: d4Hox3


title: BM ICT inj. into CSF1R KO brain; re-isolated back out, Replicate 2

description: Library name: BM2


title: ER-Hoxb8 Progenitors from FVB Cas9 Mouse, Replicate 3

description: Library name: d0Hox3


title: Macrophages grown for 7div from FVB WT BM, Replicate 2

description: Library name: Mac3


title: ER-Hoxb8 ICT inj. into CSF1R KO brain; re-isolated back out, Replicate 3

description: Library name: GFPHox4


title: Monocytes isolated from FVB WT BM, Replicate 2

description: Library name: Mono2


title: Progenitors isolated from FVB WT BM, Replicate 1

description: Library name: Prog1


title: Progenitors isolated from FVB WT BM, Replicate 2

description: Library name: Prog2


title: ER-Hoxb8 macrophages grown for 7div from FVB Cas9 Mouse, Replicate 3

description: Library name: d7Hox3


title: ER-Hoxb8 Progenitors from FVB Cas9 Mouse, Replicate 1

description: Library name: d0Hox1


title: Sst_Gaba.male.9mo

first: Joseph

last: Ecker

address: 10010 North Torrey Pines Road

department: Genomic Analysis Laboratory

institute: HHMI-Salk-Institute

description:
Library name: sample 104
read length: 151

data_processing:
Reads trimed with Cutadapt for adapters and low quality bases (Phred score >= 20)
The resulting files are mapped to in-silico bisulfite converted reference genome using Hisat3n.
The raw BAM file will be filtered using samtools to filter reads by MAPQ > 10 and use Picard to remove PCR duplicates
Tab-delimited files (ALLC files) describing the quantity of unmethylated and methylated cytosine base calls will be generated with in-house developing package using the filtered BAM files
Assembly: mm10
Supplementary files format and content: tab-delimited files (ALLC files) describing the quantity of unmethylated and methylated cytosine base calls. Columns are: 1. Chromosome, 2. Position, 3. Strand, 4. Cytosin Context, 5. methylated base call, 6. total mapped base call, 7. not used, place holder column
Library strategy: snmC-seq3

extract_protocol:
Mouse brains were dissected.
Library prepared following protocol discribed in Luo, Chongyuan, Angeline Rivkin, Jingtian Zhou, Justin P. Sandoval, Laurie Kurihara, Jacinta Lucero, Rosa Castanon, et al. 2018. “Robust Single-Cell DNA Methylome Profiling with snmC-seq2.” Nature Communications 9 (1): 3824.

treatment_protocol: The nuclei were isolated and sorted into 384-well plates using previous methods21. Briefly, single-nuclei were stained with AlexaFluor488-conjugated anti-NeuN antibody (MAB377X, Millipore) and Hoechst 33342 (62249, ThermoFisher) followed by FANS using a BD Influx sorter with single-cell (1 drop single) mode.

value: male


title: Vip_Gaba.male.9mo

description:
Library name: sample 107
read length: 151


title: Sst_Gaba.male.8wk

description:
Library name: sample 103
read length: 151


title: Sst_Gaba.male.18mo

description:
Library name: sample 102
read length: 151


title: STR_D2_Gaba.male.8wk

description:
Library name: sample 94
read length: 151


title: STR_Gaba.male.9mo

description:
Library name: sample 98
read length: 151


title: SUB-ProS_Glut.male.8wk

description:
Library name: sample 100
read length: 151


title: STR_Gaba.male.8wk

description:
Library name: sample 97
read length: 151


title: Vip_Gaba.male.8wk

description:
Library name: sample 106
read length: 151


title: STR_Gaba.male.18mo

description:
Library name: sample 96
read length: 151


title: Vip_Gaba.male.18mo

description:
Library name: sample 105
read length: 151


title: STR_D1_Sema5a_Gaba.male.18mo

description:
Library name: sample 90
read length: 151


title: STR_D1_Gaba.male.8wk

description:
Library name: sample 88
read length: 151


title: STR_D1_Sema5a_Gaba.male.9mo

description:
Library name: sample 92
read length: 151


title: STR_D1_Gaba.male.18mo

description:
Library name: sample 87
read length: 151


title: STR_D1_Gaba.male.9mo

description:
Library name: sample 89
read length: 151


title: STR_D1_Sema5a_Gaba.male.8wk

description:
Library name: sample 91
read length: 151


title: STR-PAL_Chst9_Gaba.male.9mo

description:
Library name: sample 86
read length: 151


title: SUB-ProS_Glut.male.9mo

description:
Library name: sample 101
read length: 151


title: STR-PAL_Chst9_Gaba.male.8wk

description:
Library name: sample 85
read length: 151


title: STR_D2_Gaba.male.18mo

description:
Library name: sample 93
read length: 151


title: STR-PAL_Chst9_Gaba.male.18mo

description:
Library name: sample 84
read length: 151


title: SUB-ProS_Glut.male.18mo

description:
Library name: sample 99
read length: 151


title: Pvalb_Gaba.male.9mo

description:
Library name: sample 83
read length: 151


title: Pvalb_Gaba.male.8wk

description:
Library name: sample 82
read length: 151


title: Pvalb_Gaba.male.18mo

description:
Library name: sample 81
read length: 151


title: STR_D2_Gaba.male.9mo

description:
Library name: sample 95
read length: 151


title: PB_Evx2_Glut.male.9mo

description:
Library name: sample 80
read length: 151


title: PB_Evx2_Glut.male.8wk

description:
Library name: sample 79
read length: 151


title: PB_Evx2_Glut.male.18mo

description:
Library name: sample 78
read length: 151


title: PAG_Glut.male.9mo

description:
Library name: sample 77
read length: 151


title: PAG_Glut.male.8wk

description:
Library name: sample 76
read length: 151


title: PAG_Glut.male.18mo

description:
Library name: sample 75
read length: 151


title: PAG-PPN_Pax5_Sox21_Gaba.male.18mo

description:
Library name: sample 72
read length: 151


title: PAG-PPN_Pax5_Sox21_Gaba.male.9mo

description:
Library name: sample 74
read length: 151


title: Oligo_NN.male.18mo

description:
Library name: sample 69
read length: 151


title: Oligo_NN.male.8wk

description:
Library name: sample 70
read length: 151


title: OPC_NN.male.8wk

description:
Library name: sample 67
read length: 151


title: OPC_NN.male.9mo

description:
Library name: sample 68
read length: 151


title: PAG-PPN_Pax5_Sox21_Gaba.male.8wk

description:
Library name: sample 73
read length: 151


title: OPC_NN.male.18mo

description:
Library name: sample 66
read length: 151


title: Microglia_NN.male.9mo

description:
Library name: sample 65
read length: 151


title: Oligo_NN.male.9mo

description:
Library name: sample 71
read length: 151


title: Microglia_NN.male.8wk

description:
Library name: sample 64
read length: 151


title: Microglia_NN.male.18mo

description:
Library name: sample 63
read length: 151


title: MEA-COA_Glut.male.8wk

description:
Library name: sample 61
read length: 151


title: MEA-COA_Glut.male.9mo

description:
Library name: sample 62
read length: 151


title: MEA-COA_Glut.male.18mo

description:
Library name: sample 60
read length: 151


title: MEA-BST_Gaba.male.9mo

description:
Library name: sample 59
read length: 151


title: MEA-BST_Gaba.male.18mo

description:
Library name: sample 57
read length: 151


title: MEA-BST_Gaba.male.8wk

description:
Library name: sample 58
read length: 151


title: Lamp5_Gaba.male.9mo

description:
Library name: sample 56
read length: 151


title: Lamp5_Gaba.male.18mo

description:
Library name: sample 54
read length: 151


title: Lamp5_Gaba.male.8wk

description:
Library name: sample 55
read length: 151


title: LDT-PCG-CS_Gata3_Lhx1_Gaba.male.9mo

description:
Library name: sample 53
read length: 151


title: LDT-PCG-CS_Gata3_Lhx1_Gaba.male.8wk

description:
Library name: sample 52
read length: 151


title: LDT-PCG-CS_Gata3_Lhx1_Gaba.male.18mo

description:
Library name: sample 51
read length: 151


title: LA-BLA-BMA-PA_Glut.male.9mo

description:
Library name: sample 50
read length: 151


title: LA-BLA-BMA-PA_Glut.male.18mo

description:
Library name: sample 48
read length: 151


title: L6bCT_ENT_Glut.male.9mo

description:
Library name: sample 47
read length: 151


title: L6bCT_ENT_Glut.male.8wk

description:
Library name: sample 46
read length: 151


title: L6_IT_CTX_Glut.male.9mo

description:
Library name: sample 44
read length: 151


title: L6_CT_CTX_Glut.male.9mo

description:
Library name: sample 41
read length: 151


title: L6_IT_CTX_Glut.male.18mo

description:
Library name: sample 42
read length: 151


title: L5_NP_CTX_Glut.male.9mo

description:
Library name: sample 38
read length: 151


title: L6_IT_CTX_Glut.male.8wk

description:
Library name: sample 43
read length: 151


title: L6_CT_CTX_Glut.male.18mo

description:
Library name: sample 39
read length: 151


title: L5_NP_CTX_Glut.male.18mo

description:
Library name: sample 36
read length: 151


title: L6_CT_CTX_Glut.male.8wk

description:
Library name: sample 40
read length: 151


title: L5_IT_CTX_Glut.male.9mo

description:
Library name: sample 35
read length: 151


title: L6bCT_ENT_Glut.male.18mo

description:
Library name: sample 45
read length: 151


title: L5_IT_CTX_Glut.male.8wk

description:
Library name: sample 34
read length: 151


title: L5_NP_CTX_Glut.male.8wk

description:
Library name: sample 37
read length: 151


title: L5_IT_CTX_Glut.male.18mo

description:
Library name: sample 33
read length: 151


title: L5_ET_CTX_Glut.male.9mo

description:
Library name: sample 32
read length: 151


title: L45_IT_CTX_Glut.male.8wk

description:
Library name: sample 28
read length: 151


title: L45_IT_CTX_Glut.male.9mo

description:
Library name: sample 29
read length: 151


title: L5_ET_CTX_Glut.male.8wk

description:
Library name: sample 31
read length: 151


title: L5_ET_CTX_Glut.male.18mo

description:
Library name: sample 30
read length: 151


title: L23_IT_PPP_Glut.male.9mo

description:
Library name: sample 26
read length: 151


title: L45_IT_CTX_Glut.male.18mo

description:
Library name: sample 27
read length: 151


title: L23_IT_PPP_Glut.male.8wk

description:
Library name: sample 25
read length: 151


title: L23_IT_ENT_Glut.male.9mo

description:
Library name: sample 23
read length: 151


title: L23_IT_ENT_Glut.male.8wk

description:
Library name: sample 22
read length: 151


title: L23_IT_PPP_Glut.male.18mo

description:
Library name: sample 24
read length: 151


title: LA-BLA-BMA-PA_Glut.male.8wk

description:
Library name: sample 49
read length: 151


title: L23_IT_ENT_Glut.male.18mo

description:
Library name: sample 21
read length: 151


title: L23_IT_CTX_Glut.male.9mo

description:
Library name: sample 20
read length: 151


title: L23_IT_CTX_Glut.male.8wk

description:
Library name: sample 19
read length: 151


title: L23_IT_CTX_Glut.male.18mo

description:
Library name: sample 18
read length: 151


title: DG_Glut.male.8wk

description:
Library name: sample 16
read length: 151


title: CEA-BST_Gaba.male.9mo

description:
Library name: sample 14
read length: 151


title: CEA-BST_Gaba.male.18mo

description:
Library name: sample 12
read length: 151


title: CA3_Glut.male.8wk

description:
Library name: sample 10
read length: 151


title: CA3_Glut.male.18mo

description:
Library name: sample 9
read length: 151


title: CA3_Glut.male.9mo

description:
Library name: sample 11
read length: 151


title: CA1-ProS_Glut.male.9mo

description:
Library name: sample 8
read length: 151


title: CA1-ProS_Glut.male.18mo

description:
Library name: sample 6
read length: 151


title: Astro-TE_NN.male.8wk

description:
Library name: sample 4
read length: 151


title: Astro-TE_NN.male.18mo

description:
Library name: sample 3
read length: 151


title: Astro-NT_NN.male.9mo

description:
Library name: sample 2
read length: 151


title: Astro-NT_NN.male.8wk

description:
Library name: sample 1
read length: 151


title: Astro-NT_NN.male.18mo

description:
Library name: sample 0
read length: 151


title: AB378_3

city: nanjing

first: Jiaquan

last: Lin

address: Hankou road

institute: nanjing university

description:
Library name: AB378_3
FPKM.AB378_3

data_processing:
Reads obtained from the sequencing machines includes raw reads containing adapters or low quality bases which will affect the following assembly and analysis. Thus, to get high quality clean reads, reads were further filtered by Cutadapt (https://cutadapt.readthedocs.io/en/stable/,version:cutadapt-1.9). We aligned reads of all samples to the research species reference genome using HISAT2 (https://daehwankimlab.github.io/hisat2/,version:hisat2-2.2.1) package, which initially remove a portion of the reads based on quality information accompanying each read and then maps the reads to the reference genome.
The mapped reads of each sample were assembled using StringTie (http://ccb.jhu.edu/software/stringtie/,version:stringtie-2.1.6) with default parameters. Then, all transcriptomes from all samples were merged to reconstruct a comprehensive transcriptome using gffcompare software(http://ccb.jhu.edu/software/stringtie/gffcompare.shtml,version:gffcompare-0.9.8). After the final transcriptome was generated, StringTie and ballgown (http://www.bioconductor.org/packages/release/bioc/html/ballgown.html) were used to estimate the expression levels of all transcripts and perform expression abundance for mRNAs by calculating FPKM (fragment per kilobase of transcript per million mapped reads) value.
Genes differential expression analysis was performed by DESeq2 software between two different groups (and by edgeR between two samples). The genes with the parameter of false discovery rate (FDR) below 0.05 and absolute fold change ≥ 2 were considered differentially expressed genes. Differentially expressed genes were then subjected to enrichment analysis of GO functions and KEGG pathways.
Assembly: GRCm39
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

source_name: primary microglia

extract_protocol:
Total RNA was extracted using Trizol reagent (thermofisher, 15596018) following the manufacturer's procedure. The total RNA quantity and purity were analysis of Bioanalyzer 2100 and RNA 6000 Nano LabChip Kit (Agilent, CA, USA, 5067-1511) , high-quality RNA samples with RIN number > 7.0 were used to construct sequencing library.
mRNA was purified from total RNA (5ug) using Dynabeads Oligo (dT) (Thermo Fisher, CA, USA) with two rounds of purification. Following purification, the mRNA was fragmented into short fragments using divalent cations under elevated temperature (Magnesium RNA Fragmentation Module (NEB, cat.e6150, USA) under 94℃ 5-7min). Then the cleaved RNA fragments were reverse-transcribed to create the cDNA by SuperScript™ II Reverse Transcriptase (Invitrogen, cat. 1896649, USA), which were 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 then added to the blunt ends of each strand, preparing them for ligation to the indexed adapters. Each adapter contained a T-base overhang for ligating the adapter to the A-tailed fragmented DNA. 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. The average insert size for the final cDNA librarys were 300±50 bp. At last, we performed the 2×150bp paired-end sequencing (PE150) on an Illumina NovaseqTM 6000 following the vendor's recommended protocol.

value: primary microglia

value: Microglia

value: A β oligomers+miR-378a-3p mimics


title: AB378_2

description:
Library name: AB378_2
FPKM.AB378_2

value: WT


title: AB5

description:
Library name: AB5
FPKM.AB5

value: A β oligomers+negative control mimics


title: AB378_1

description:
Library name: AB378_1
FPKM.AB378_1


title: AB4

description:
Library name: AB4
FPKM.AB4


title: AB378_5

description:
Library name: AB378_5
FPKM.AB378_5


title: AB1

description:
Library name: AB1
FPKM.AB1


title: AB3

description:
Library name: AB3
FPKM.AB3


title: AB2

description:
Library name: AB2
FPKM.AB2


title: DG_Glut.male.18mo

description:
Library name: sample 15
read length: 151

source_name: brain


title: CEA-BST_Gaba.male.8wk

description:
Library name: sample 13
read length: 151


title: CA1-ProS_Glut.male.8wk

description:
Library name: sample 7
read length: 151


title: DG_Glut.male.9mo

description:
Library name: sample 17
read length: 151


title: TM+ Rep4, INPUT

city: Austin

first: Muyoung

state: TX

address: 2506 Speedway

department: Molecular Biosciences

institute: University of Texas at Austin

description: Library name: TM+ Rep4, INPUT

data_processing:
ChIP-seq samples were adapter-trimmed by TrimGalore v0.6.10 (https://github.com/FelixKrueger/TrimGalore), aligned by Bowtie v2.5.1 (Langmead & Salzberg, 2012), then processed with Samtools v1.20 (Danecek et al, 2021) and Picard MarkDuplicates v3.0.0 (http://broadinstitute.github.io/picard).
Peak calling was performed using Macs3 v3.0.1 (Zhang et al, 2008), and the heatmap was generated using DeepTools v3.5.5 (Ramírez et al, 2016).
Assembly: mm10
Supplementary files format and content: bigWig (except for input samples)

source_name: embryonic stem cells

extract_protocol:
Cells were cross-linked with 1% formaldehyde (Fisher Bioreagents, BP531-500) for 7 minutes at room temperature, and the reaction was quenched by adding glycine (Fisher Scientific, BP381-1) to a final concentration of 0.125 M. The bioChIP protocol was conducted as previously described (Kim et al, 2009). Genomic DNA was sheared to an average fragment size of ~200 bp using a Bioruptor sonicator (Diagenode). Cross-linked chromatin was pre-cleared with Protein A agarose beads (Thermofisher, 10008D) and subsequently subjected to immunoprecipitation using Dynabeads MyOne Streptavidin T1 (Invitrogen, 65602).
Library preparation was performed using the NEBNext® Ultra™ DNA Library Prep Kit (NEB, 7103L)

treatment_protocol: bioChIP-seq was performed on PREB- and PREBΔTM-OE ES cells treated with 0.5 µg/mL doxycycline for 24 hours.

value: embryonic stem cells