title: KO Input

data_processing:
Sequencing reads were trimmed for adaptors before aligned to mouse genome mm10 using bowtie2 (v2.4.2) with default parameters.
Peaks were called using MACS2 (v2.2.7.1) with q less than 0.01.
Peak annotation was performed with Homer (v4.11)
heatmaps and average binding profiles were generated by DeepTools (v3.5.2).
Assembly: mm10
Supplementary files format and content: Bigwig

source_name: Bone Marrow

extract_protocol: For TAF1 ChIP-seq, library was constructed with the ThruPLEX DNA-seq kit. For PoII ChIP-seq, on-bead tagmentation was performed with immunoprecipitated DNA using a Nextera XT kit.

treatment_protocol: Purified Lin- cells were fixed with 1% formaldehyde for 10min at RT and lysed in buffer containing 0.1% SDS, 1% Triton, 1mM EDTA, 16.7 mM Tris and 167mM NaCl. The samples were sonicated with a Bioruptor Pico (Diagenode) for 14 cycles (30s on/off) and debris was removed by centrifugation.

value: Bone Marrow

value: Lineage negative Bone marrow cells

value: Taf1 KO


title: HFSCs/Hg Vehicle-3

status: Public on Jul 07 2025

type: RNA

city: Tokyo

first: Yasuaki

last: Mohri

address: 4-6-1 Shirokanedai, Minato-ku

country: Japan

institute: The Institute of Medical Science, The University of Tokyo

description: Gene expression after 3days in vehicle-treated HFSCs/Hg

hyb_protocol: 1.69 µg of Cy3-labelled cDNAs were hybridized on Agilent SurePrint G3 Mouse GE v2 8x60K Microarray for 17 hours at 65°C . After hybridization, slides were washed with Gene Expression Wash Buffer 1 (Agilent) at room temperature and Gene Expression Wash Buffer 2 (Agilent) at37℃, then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the DNA Microarray Scanner (Agilent) using one color scan setting for 8x60k array slides.

data_processing: The scanned images were analyzed with Feature Extraction Software 10.7.1.1 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities. Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

label: Cyamin-3 (Cy3)

molecule: total RNA

organism: Mus musculus

source_name: epidermis, K15(Hi)/ITGA6(Hi)/ScaI(-), Vehicle, 3days, replicate 3

label_protocol: 0.5 µg cDNA  were labeled with Cyanine-3 (Cy3) using Exo-Klenow fragment enzyme.

extract_protocol: HFSCs/HG were sorted with FACS AriaII directly into Buffer RLT (Qiagen) for RNA extraction. Total mRNAs were purified with an RNeasy Micro Kit (Qiagen) following the standard procedures.

treatment_protocol: After the depilation, the mice were topically applied with Vehicle or DMBA. Single epidermal cell suspensions were obtained and K15-EGFP(Hi)/ITGA6(Hi)/Scal(-) cells were selected as HFSCs/HG with FACS AriaII.

tag: tissue

value: Hair follicle stem cells/Hair germ

tag: Sex

value: male

tag: treatment

value: vehicle


title: Control_Day0_2

type: SRA

city: Miami

first: Stephen

middle: D.

last: Nimer

state: FL

address: 1120 NW 14th Street

department: Sylvester Comprehensive Cancer Center

country: USA

institute: University of Miami

description:
Control_Day0_2
TPM_Macrophage_Differentiation.csv

library_source: transcriptomic

data_processing:
nf-core/rnaseq v 3.6
Sequence reads were processed using the nf-core RNA-seq pipeline with default parameters, for pre-processing, alignment and QC, selecting RSEM as aligner
Reads from RSEM were loaded into DESeq2 v 1.38.3 with tximport v 1.26.1, for time-series analysis
Assembly: mm10
Supplementary files format and content: comma separated (.csv) files include TPM values for each Sample

source_name: Bone marrow

growth_protocol: HSPCs were cultured in 20% Horse Serum (HS, Sigma-Aldrich, H1138) IMDM supplemented with mouse SCF ( PeproTech, 250-03) and IL-3 (PeproTech, 213-13) to expand myeloid cells for 3 days; then half of these cells were cultured in IMDM with mouse cytokines (SCF, IL-3 and G-CSF (PeproTech, 250-05)) for 2 days, and then G-CSF alone for the last 2 days to granulocyte differentiation; and the other half were forced to differentiate toward macrophages in 20% HS IMDM supplemented with mouse GM-CSF (Biolegend, 576302) and M-CSF (PeproTech, 315-02) for 2 days and M-CSF alone for the last 2 days. All cytokines were used at concentration of 50 ng/ml.

extract_protocol:
Total RNA was purified using RNeasy Plus Mini Kit (Qiagen, 74136).
Libraries were generated with KAPA Stranded RNA-Seq Library Preparation Kit

value: Bone marrow

tag: time point

tag: cell type

value: hematopoietic stem progenitor cells

tag: genotype

value: WT

value: In vitro differentiation


title: small EVs_50z_HC

city: Brno

first: Robin

last: Jugas

address: Kamenice 5

country: Czech Republic

institute: CEITEC MU

hyb_protocol: Samples were hybridized using Affymetrix hybridization kit materials • Heat cocktails at 99° for 5 minutes, then at 45°C for 5 minutes • Transfer 200 μl of hyb solution to each array, then tape holes and parafilm. • Hybridize 16 hours at 45° at 60rpm• Fluidics washing is FS450_0001

scan_protocol: Affymetrix Gene ChIP Scanner 3000 7G

data_processing:
Data were processed using R package oligo and custom made probe annotation. Background subtraction, normalization and summarization was done with RMA algorithm.
Clariom_D_Human.r1.pgf
Clariom_D_Human.r1.mps

label: biotin

organism: Homo sapiens

source_name: blood serum small exctracellular vesicles

label_protocol: The fragmented cDNA was labeled by TdT using the proprietary DNA labeling reagent that is covalently linked to biotin according to the manufacturer's recommendations.

growth_protocol: not applicable

extract_protocol: Small EVs were isolated from 150 µl of sera. After the sample passed onto the column, 800 μl of 1X PBS was applied to the column. The fraction containing small EVs was eluted by applying 500 μl of 1X PBS to the column and collected. All samples were treated with proteinase K (20 mg/mL, 10 µl) and RNase Cocktail Enzyme Mix (20 000 U/mL, 5 µl) at 37 °C for 10 min. Finally, SUPERase·In RNase Inhibitor (20 U/μL, 4 µl) was added and mixed well. Total RNA including small RNAs was isolated from small EVs using Monarch® Total RNA Miniprep Kit (New England Biolabs) according to the manufacturer’s recommendations, treated with DNase I, and eluted with 50 μl of DEPC-treated water.

treatment_protocol: All samples were centrifuged at 1500 × g for 10 min at 4 °C and then at 10000 × g for 20 min at 4 °C.

tag: condition

value: HC

tag: gender

value: female

tag: age

tag: diagnosis

value: not applicable

tag: clinical stage

tag: localization


title: HFSCs/Hg DMBA-1

description: Gene expression after 3days in DMBA-treated HFSCs/Hg

source_name: epidermis, K15(Hi)/ITGA6(Hi)/ScaI(-), DMBA, 3days, replicate 1

value: DMBA


title: hiPSC kucg-2 CRIPSRi Ribo-Seq ZNF598 RING disome rep1

city: Martinsried

first: Danny

last: Nedialkova

address: Am Klopferspitz 18

country: Germany

institute: Max Planck Institute of Biochemistry

description: Library name: Sample 15

library_source: other

data_processing:
Sequencing libraries were demultiplexed and adapter-trimmed with Cutadapt v2.5. Trimmed reads longer than 10 nt were aligned to a human ribosomal RNA reference using Bowtie v1.2.2 (Langmead 2009) with the following options: -p 40 -S --best. rRNA-filtered reads were aligned to GRCh38.p13 using STAR v2.6.1c (Dobin 2013) with the following options: --outFilterMultimapNmax 1 --outSAMtype BAM SortedByCoordinate --outFilterMismatchNmax 0 --alignEndsType Local --seedSearchStartLmax 14 --alignIntronMax 10000 --outFilterIntronMotifs RemoveNoncanonicalUnannotated --quantMode TranscriptomeSAM --outSAMattributes NH HI AS nM NM MD.
A custom reference transcriptome annotation was built for the GRCh38.p13 genome based on the Matched Annotation from the NCBI and EMBL-EBI (MANE) and the best scoring transcript annotated in APPRIS (Rodriguez 2013)(https://apprisws.bioinfo.cnio.es/pub/current_release/datafiles/homo_sapiens/GRCh38/appris_data.appris.txt). For all the genes, we extrapolate the MANE-annotated transcript. For genes without a MANE-annotated transcript, the best-scoring transcript in APPRIS was chosen as the principal isoform. For multiple best-scoring transcripts associated with the same gene, the longest isoform was selected. When multiple best-scoring transcripts had the same length, a random one was chosen as the principal isoform. This reference set was further filtered for transcripts with coding regions ending with a UAG/UAA/UGA stop codon, having a three-base periodicity, and not containing unidentified bases in the open reading frame. We retained known transcripts with non-AUG start codons (e.g., EIF4G2) or containing UGA codons re-coded as selenocysteine, and curated the remaining set by manually removing mis-annotations that resulted in multiple transcripts per Ensembl gene ID. and filtering out 18 transcripts associated with pseudoautosomal regions on the Y chromosome (PAR_Y). The resulting reference contained 19,759 protein-coding transcripts and was used for ribosome footprint and matched RNA-seq read alignment.
Assembly: GRCh38
Supplementary files format and content: csv; read counts for protein-coding genes
Library strategy: Ribo-Seq

molecule: other

source_name: cell line

extract_protocol:
Cells were quickly washed with ice cold PBS supplemented with 100 µg/ml cycloheximide (CHX) and snap-frozen in liquid nitrogen. Plates were thawed on ice and cells were scraped off the plate in 400 µl polysome lysis buffer (20 mM Tris pH=7.4, 150 mM NaCl, 5 mM MgCl2, 1% Triton-X100, 1 mM DTT, 100 µg/ml CHX, 25 U/ml Turbo DNase), 0.1% NP-40, 10 µg/ml aprotinin, 20 µM leupeptin, 2.5 µM pepstatin A, 0.5 mM AEBSF and 1x Phosphatase Inhibitor Cocktail. Samples were vortexed vigorously, triturated through a 26G gauge needle, and spun down for 7 minutes at 16,000xg/ 4°C. Supernatant was transferred to a new tube. 20 µg RNA in 200 µl polysome lysis buffer were digested with 50 U RNase I for 45 minutes at 2,000 rpm/22°C.
Ribosome footprint libraries were prepared essentially as described (McGlincy and Ingolia, 2017; Wu 2019) with minor modifications. RNase I digestion was stopped by addition of 100 U Superase In and extracts were loaded on a sucrose cushion. The pellet was dissolved in 400 µl LiDS/LET lysis buffer and RNA was extracted with the acid phenol protocol. Fragments in the range of 19 to 32 nucleotides (monosomes) or 50 to 80 nt (disomes) were isolated by gel size selection, with T4 PNK and ligated to pre-adenylated adapters containing 5 random nucleotides at their 5’ ends (McGlinzy 2017) with T4 RNA Ligase 2 (truncated KQ). Adapter-ligated RNA was subjected to rRNA depletion using the Ribo-Seq riboPOOL h/m/r depletion kit (siTOOLs). The rRNA-depleted footprints were reverse-transcribed with Protoscript II and cDNA was circularized with recombinant TS2126 RNA ligase 1 (commercially available as CircLigase). Libraries were constructed from circularized cDNA with KAPA HiFi DNA Polymerase and single-end sequencing was performed on a NextSeq 550 platform (Illumina).

tag: cell line

value: kucg-2 CRISPRi hiPSC

value: Human induced pluripotent stem cells

value: -DOX


title: small EVs_48z_HC


title: RNA-Seq of Cranberry Hybrids, Cold Treatment: Stevens, 0 minutes, replicate 2

city: Encinitas

first: Audrey

last: Dickinson

state: California

address: 300 Quail Gardens Dr

department: Science and Conservation

institute: San Diego Botanic Garden

description: Library name: Vhyb_ST.C.T0.R2

data_processing:
Sequencing runs were basecalled using the Dorado v5.0.0 super-high accuracy model with a quality threshold of Q9 and a 200 base pair cutoff.
Reads were aligned using minimap2 v2.28-r1209 against Helixer-generated (v0.3.2) coding sequences (CDS) from either V. macrocarpon, V. oxycoccos, or a concatenated hybrid reference, as appropriate. Only primary alignments were retained.
Transcript abundance was quantified using Salmon v1.6.0.
Assembly: V. macrocarpon, V. oxycoccos (Kawash et al., 2022)
Supplementary files format and content: Quantification table output from Salmon. Rows represent genes in each sample. Columns represent length, effective length, TPM, and the number of reads mapping to each transcript.

molecule: polyA RNA

organism: Vaccinium macrocarpon

source_name: Leaf

growth_protocol: All plants were maintained in a greenhouse in Chatsworth, New Jersey, USA, prior to the temperature stress experiments. Each F1 hybrid with the same genotype identifier were clonally propagated from seedling progeny by cuttings. Experimental material consisted of V. macrocarpon, V. oxycoccos, and their F1 hybrids. Experiments were conducted in mid to late September during the growing season, prior to cold acclimation.

extract_protocol:
Approximately 50 mg of leaf tissue was processed per sample. Total nucleic acids were isolated using a CTAB-based method (Daverdin et al., 2017). RNA was precipitated from total nucleic acid using 10M LiCl overnight, pelleted, and resuspended in nuclease-free water. Samples were treated with DNase (Optizyme, Fisherbrand #BP81071), followed by chloroform treatment, sodium acetate precipitation, ethanol washing, and final resuspension in nuclease-free water.
Full-length cDNA was synthesized from 200 ng of total RNA per sample using the Oxford Nanopore cDNA-PCR Sequencing Kit (SQK-PCB111.24). PCR amplification used barcoded primers (16 cycles), and barcoded cDNA from nine samples was pooled per run. ONT Rapid Adapter Kit (EXP-RAA114) was used to prepare libraries for sequencing with R10.4.1 flow cells and V14 chemistry. Sequencing was performed on the PromethION platform for 72 hours.

treatment_protocol: For temperature stress experiments, plants were acclimated for three days at 21 °C under a 12 h day/night cycle. For heat stress, incubators were pre-set to 45 °C and samples were harvested at 0 min (T0), 15 min (T1, 39.7 °C), and 30 min (T2, 47 °C). For cold stress, incubators were set to 2 °C and samples were harvested at T0, 60 min (T1, 10.5 °C), and 95 min (T2, 3 °C). Whole leaves were collected and snap frozen in liquid nitrogen, then stored in RNAlater ICE.

value: Leaf

tag: time

tag: temperature

tag: cultivar

value: Stevens


title: HFSCs/Hg Vehicle-2

source_name: epidermis, K15(Hi)/ITGA6(Hi)/ScaI(-), Vehicle, 3days, replicate 2


title: RNA-Seq of Cranberry Hybrids, Cold Treatment: Stevens, 60 minutes, replicate 1

description: Library name: Vhyb_ST.C.T1.R1


title: KO PoII

library_source: genomic

molecule: genomic DNA

value: Bone Marrow

tag: antibody

value: Lineage negative Bone marrow cells

value: Taf1 KO


title: Control PoII

tag: tissue


title: Control Input


title: HFSCs/Hg Vehicle-1

source_name: epidermis, K15(Hi)/ITGA6(Hi)/ScaI(-), Vehicle, 3days, replicate 1

value: Hair follicle stem cells/Hair germ

tag: Sex

value: male

value: vehicle


title: RNA-Seq of Cranberry Hybrids, Cold Treatment: Stevens, 0 minutes, replicate 3

description: Library name: Vhyb_ST.C.T0.R3

tag: treatment


title: small EVs_41z_HC


title: hiPSC kucg-2 CRIPSRi Ribo-Seq ZNF598 RING disome rep2

description: Library name: Sample 16


title: hiPSC kucg-2 CRIPSRi Ribo-Seq ZNF598 KD disome rep2

description: Library name: Sample 14

value: +DOX


title: KO-2 TAF1


title: Control_Day0_1

description:
Control_Day0_1
TPM_Macrophage_Differentiation.csv

value: Bone marrow

tag: time point

value: hematopoietic stem progenitor cells

value: WT

value: In vitro differentiation


title: RNA-Seq of Cranberry Hybrids, Cold Treatment: Stevens, 0 minutes, replicate 1

description: Library name: Vhyb_ST.C.T0.R1


title: small EVs_34z_HC

value: HC

value: female

value: not applicable


title: small EVs_37z_HC


title: KO-1 TAF1

tag: cell type


title: RNA-Seq of Cranberry Hybrids, Heat Treatment: Stevens, 30 minutes, replicate 3

description: Library name: Vhyb_ST.H.T3.R3


title: hiPSC kucg-2 CRIPSRi Ribo-Seq ZNF598 KD disome rep1

description: Library name: Sample 13

value: kucg-2 CRISPRi hiPSC

value: Human induced pluripotent stem cells


title: RNA-Seq of Cranberry Hybrids, Heat Treatment: Stevens, 30 minutes, replicate 1

description: Library name: Vhyb_ST.H.T2.R1

value: Leaf

value: Stevens


title: hiPSC kucg-2 CRIPSRi Ribo-Seq disome rep2

description: Library name: Sample 12

value: -DOX


title: hiPSC kucg-2 CRIPSRi Ribo-Seq ZNF598 RING 4EGI-1 monosome rep2

description: Library name: Sample 10

value: -DOX, 5µM 4EGI-1


title: RNA-Seq of Cranberry Hybrids, Heat Treatment: Stevens, 30 minutes, replicate 2

description: Library name: Vhyb_ST.H.T2.R2


title: hiPSC kucg-2 CRIPSRi Ribo-Seq disome rep1

description: Library name: Sample 11


title: small EVs_38z_HC


title: small EVs_32z_HC


title: small EVs_2z_HC


title: RNA-Seq of Cranberry Hybrids, Heat Treatment: Stevens, 15 minutes, replicate 3

description: Library name: Vhyb_ST.H.T1.R3


title: Control-2 TAF1

value: Bone Marrow

value: Lineage negative Bone marrow cells

tag: genotype


title: small EVs_39z_HC

tag: condition


title: Control-1 TAF1


title: hiPSC kucg-2 CRIPSRi Ribo-Seq ZNF598 RING 4EGI-1 monosome rep1

description: Library name: Sample 9


title: small EVs_27z_HC

tag: gender

value: male


title: RNA-Seq of Cranberry Hybrids, Heat Treatment: Stevens, 15 minutes, replicate 2

description: Library name: Vhyb_ST.H.T1.R2


title: hiPSC kucg-2 CRIPSRi Ribo-Seq 4EGI-1 monosome rep2

description: Library name: Sample 8


title: RNA-Seq of Cranberry Hybrids, Heat Treatment: Stevens, 15 minutes, replicate 1

description: Library name: Vhyb_ST.H.T1.R1


title: small EVs_29z_HC

tag: age


title: small EVs_275z_HC

tag: diagnosis


title: TAF1_KO_1

data_processing:
nf-core/atacseq v1.2.1
Sequence reads were processed using the nf-core ATAC-seq pipeline with default parameters, for pre-processing, alignment, QC, and generating tracks and peaks call and further processing, selecting the narrowpeak option
The Differentially Accessible regions were generated by the nf-core ATAC-seq pipeline and were merged with the annotations from HOMER for further analysis of the distribution of significant regions
Heatmaps were generated using deeptools v 3.5.1
Coverage curve for nucleosome positions were generated using ATACseqQC v 1.22.0
Assembly: GRCm38
Supplementary files format and content: BigWig

extract_protocol:
The fragmented DNA was purified by DNA Clean and Concentrator-5 Kit (Zymo Research, D4014) according to manufacturer's instruction.
Sequencing library was generated with 5 to 7 cycles of amplification using NEBNext 2x Master Mix (NEB, M0541S) and uniquely indexed i7/i5 primer pairs.

treatment_protocol: Cells were treated with Dnase I for 30 min at 37C to remove the dead cells and DNA debris.

value: Taf1 KO


title: hiPSC kucg-2 CRIPSRi Ribo-Seq 4EGI-1 monosome rep1

description: Library name: Sample 7


title: Control_3

value: Bone marrow


title: RNA-Seq of Cranberry Hybrids, Heat Treatment: Stevens, 0 minutes, replicate 3

description: Library name: Vhyb_ST.H.T0.R3


title: hiPSC kucg-2 CRIPSRi Ribo-Seq monosome rep2

description: Library name: Sample 6


title: RNA-Seq of Cranberry Hybrids, Heat Treatment: Stevens, 0 minutes, replicate 2

description: Library name: Vhyb_ST.H.T0.R2


title: small EVs_206z_HC

tag: clinical stage


title: hiPSC kucg-2 CRIPSRi Ribo-Seq monosome rep1

description: Library name: Sample 5


title: Control_2

value: hematopoietic stem progenitor cells


title: TAF1_KO_2


title: small EVs_204z_HC

tag: localization


title: Control_1

value: WT


title: RNA-Seq of Cranberry Hybrids, Heat Treatment: Stevens, 0 minutes, replicate 1

description: Library name: Vhyb_ST.H.T0.R1


title: hiPSC kucg-2 CRIPSRi Ribo-Seq ZNF598 RING monosome rep2

description: Library name: Sample 4

tag: cell line


title: RNA-Seq of Cranberry Hybrids, Cold Treatment: 7_5, 95 minutes, replicate 3

description: Library name: Vhyb_7_5.C.T2.R3

organism:
Vaccinium macrocarpon
Vaccinium oxycoccos

tag: time

value: Pilgrim x NJ96-82


title: small EVs_203z_HC

value: HC


title: RNA-Seq of Cranberry Hybrids, Cold Treatment: 7_5, 95 minutes, replicate 2

description: Library name: Vhyb_7_5.C.T2.R2

tag: temperature


title: Old_early anagen_rep 3

data_processing:
Bcl2fastq (v2.17.1.14) was used to process the original image data for base calling and preliminary quality analysis.
Low quality reads and contaminations were filtered out prior to data analysis using Cutadapt (version 1.9.1). (1) remove the adapter sequences (2) remove the 5' or 3' end bases containing N’s or with quality values below 20 (3) remove reads that are less than 75 bp in length after trimming
The filtered data were subsequently aligned to the reference genome using Hisat2 (v2.0.1) (Nat Methods. 2015) with default parameters.
Gene expression was calculated as FPKM (fragments per kilobases per million reads) based on read counts from HT-seq (V 0.6.1) (Mortazavi, 2008).
Assembly: Mus_musculus_GRCm39.104_Ensembl
Supplementary files format and content: .xls file include FPKM values

source_name: Old early anagen

extract_protocol:
Total RNA was purified using the RNeasy Micro Kit (Qiagen) according to the manufacturer's protocol.
RNA libraries for RNA-seq were prepared using the SMARTER stranded RNA-Seq Kit.

treatment_protocol: Single cell suspensions were obtained from the skin and then EGFP(Hi)/ITGA6(Hi)/ScaI(-) cells were sorted with FACS AriaII directly into Buffer RLT (Qiagen) for RNA extraction.

value: Skin

value: Hair follicle stem cells/hair germ

value: K15-EGFP Tg/+

value: Hair depilation


title: hiPSC kucg-2 CRIPSRi Ribo-Seq ZNF598 RING monosome rep1

description: Library name: Sample 3

value: kucg-2 CRISPRi hiPSC

value: Human induced pluripotent stem cells


title: Old_early anagen_rep 2


title: hiPSC kucg-2 CRIPSRi Ribo-Seq ZNF598 KD monosome rep2

description: Library name: Sample 2

value: +DOX


title: RNA-Seq of Cranberry Hybrids, Cold Treatment: 7_5, 95 minutes, replicate 1

description: Library name: Vhyb_7_5.C.T2.R1

value: Leaf

tag: cultivar


title: Old_early anagen_rep 1


title: RNA-Seq of Cranberry Hybrids, Cold Treatment: 7_5, 60 minutes, replicate 3

description: Library name: Vhyb_7_5.C.T1.R3


title: small EVs_52z_HC

value: not applicable


title: small EVs_195z_HC


title: small EVs_222z_HC

value: female


title: 260423S,mpt4,batch 15

city: South San Francisco

last: Zhou

address: 170 Harbor Way

institute: Neurona Therapeutics

description:
Library name: pl58mpt4
10x Genomics

library_source: transcriptomic single cell

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregating were made using the Cell Ranger software v7 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Seurat V4 was used for QC, clustering and data visualization
Assembly: GRCh38
Supplementary files format and content: A Seurat project with information of gene counting, cell clustering, PCA and UMAP visualization

source_name: interneurons

extract_protocol:
Total nuclei from dissected mouse cortices were extracted and stained with an antibody against human-specific nuclear antigen to enrich human cells using fluorescence-activated nuclear sorting (FANS). Sorted nuclei were loaded onto 10X Genomics chip G or chip M (HT) for capture and barcoding.
Library construction was performed according to the manufacter’s instructions (single cell 3’v3 protocol, 10x Genomics).

value: interneurons

value: sorted

value: post-transplant


title: small EVs_192z_HC


title: small EVs_189z_HC

value: male


title: small EVs_198z_HC


title: RNA-Seq of Cranberry Hybrids, Cold Treatment: 7_5, 60 minutes, replicate 2

description: Library name: Vhyb_7_5.C.T1.R2


title: hiPSC kucg-2 CRIPSRi Ribo-Seq ZNF598 KD monosome rep1

description: Library name: Sample 1


title: 220720S2,mpt12,batch 12

description:
Library name: pr13mpt12
10x Genomics


title: RNA-Seq of Cranberry Hybrids, Cold Treatment: 7_5, 60 minutes, replicate 1

description: Library name: Vhyb_7_5.C.T1.R1


title: small EVs_177z_HC


title: Old_telogen_rep 3

source_name: Old telogen

value: non treatment


title: Young_early anagen_rep 2

source_name: Young early anagen


title: RNA-Seq of Cranberry Hybrids, Cold Treatment: 7_5, 0 minutes, replicate 3

description: Library name: Vhyb_7_5.C.T0.R3

value: Pilgrim x NJ96-82


title: Young_early anagen_rep 3


title: 220720S2,mpt6,batch 12

description:
Library name: pr13mpt6
10x Genomics


title: RNA-Seq of Cranberry Hybrids, Cold Treatment: 7_5, 0 minutes, replicate 2

description: Library name: Vhyb_7_5.C.T0.R2


title: Old_telogen_rep 2


title: 220720S2,pre,batch 12

description:
Library name: pr13pre
10x Genomics

value: pre-transplant


title: Old_telogen_rep 1

value: Skin


title: small EVs_174z_HC

value: HC


title: small EVs_175z_HC


title: RNA-Seq of Cranberry Hybrids, Cold Treatment: 325_33, 95 minutes, replicate 3

description: Library name: Vhyb_325_33.C.T2.R3

value: NJ96-20 x Stevens


title: small EVs_163z_HC


title: 150120S,mpt18,batch 6

description:
Library name: pr4mpt18
10x Genomics


title: Young_telogen_rep 3

source_name: Young telogen

value: Hair follicle stem cells/hair germ

value: K15-EGFP Tg/+


title: small EVs_172z_HC


title: 220720S2,mpt3,batch 12

description:
Library name: pr13mpt3
10x Genomics


title: small EVs_169z_HC


title: RNA-Seq of Cranberry Hybrids, Cold Treatment: 7_5, 0 minutes, replicate 1

description: Library name: Vhyb_7_5.C.T0.R1


title: Young_early anagen_rep 1

value: Hair depilation


title: 150120S,mpt12,batch 6

description:
Library name: pr4mpt12
10x Genomics


title: Young_telogen_rep 2


title: RNA-Seq of Cranberry Hybrids, Cold Treatment: 325_33, 95 minutes, replicate 1

description: Library name: Vhyb_325_33.C.T2.R1


title: RNA-Seq of Cranberry Hybrids, Cold Treatment: 325_33, 95 minutes, replicate 2

description: Library name: Vhyb_325_33.C.T2.R2


title: Young_telogen_rep 1


title: 150120S,mpt6,batch 6

description:
Library name: pr4mpt6
10x Genomics


title: RNA-Seq of Cranberry Hybrids, Cold Treatment: 325_33, 60 minutes, replicate 3

description: Library name: Vhyb_325_33.C.T1.R3


title: small EVs_157z_HC


title: ESC_Stag3OEStag1Stag2dKO_HiC_2

city: Kyoto

first: Yukihiro

last: Yabuta

state: Kyoto

address: Yoshida-Konoe-cho, Sakyo-ku

department: Anatomy and Cell Biology

institute: Kyoto University, Graduate school of medicine

data_processing:
Sequences were first trimmed using fastp v0.21.0 with default options and the --detect_adapter_for_pe flag.
Trimmed sequences were then processed using HiCUP v0.8.0 with default options and di-tag length range set to 0-800, with bowtie v2.4.2 as the aligner.
hicup2juicer was then used to produce di-tag files subsequently ingested with Juicer tools v1.22.01 for the creation of .hic files.
The same set of di-tag files were also used to create multi-resolution cooler files using cooler v0.8.10 with default options.
Additionally, VEHiCLE commit 7a43401 was used to de-noise 10 kb-resolution contact maps for visualization with published pre-trained models.
Denoised matrices were displayed for individual samples in isolation, whereas differential matrices between two conditions were derived using the original balanced matrices without denoising.
Assembly: mm10
Supplementary files format and content: bw files are bigwig files of  compartment score generated from cooltools call-compartments and oriented using GC content
Supplementary files format and content: mcool files are multi-resolution cooler files containing balance-normalized count matrices

source_name: BDF1-2-1 Blimp1-mVenus reporter; Stella-ECFP reporter (BVSC)

extract_protocol:
in situ Hi-C library preparation was performed as described previously (Nagano et al., 2022). We used the whole harvested cells for mESCs  and FACS-sorted AAG-positive cells for GSCs. 2.5 x 106 cells were used for one replicate. The cells were fixed by 1% formaldehyde (Sigma) /HBSS and lysed in lysis buffer (10 mM Tris-HCl pH8.0, 10 mM NaCl, 0.2% NP-40) for 30 min on ice with frequent inversion. The cells were digested by 500 U of DpnII (NEB) overnight at 37°C. Following biotin filling (Thermo Fisher Scientific, 19524-016; NEB, M0210S), proximity ligation (Thermo Fisher Scientific, 15224090) and reverse crosslinking, DNA was purified by ethanol precipitation and sheared to 200-400bp fragments using Covaris E220 sonicator (Covaris) at 4°C (10% Duty Factor, 200 cycles/burst, 175 W Peak Incident Power, 110 s). Ligation fragments containing biotin were immobilized on MyOne Streptavidin T1 beads (Thermo Fisher Scientific)
Library preparation was performed using NEB library preparation kit (NEB, E7645S; NEB, E7335S) according to manufacturer’s guidance. The libraries were amplified 8 cycles and DNA fragments between 300-800bp were selected using AMPure XP beads (Corning).

value: ESC


title: 150120S,mpt3,batch 6

description:
Library name: pr4mpt3
10x Genomics


title: RNA-Seq of Cranberry Hybrids, Cold Treatment: 325_33, 60 minutes, replicate 2

description: Library name: Vhyb_325_33.C.T1.R2

value: Leaf


title: ESC_Stag3OEStag1Stag2dKO_HiC_1

value: BDF1-2-1 Blimp1-mVenus reporter; Stella-ECFP reporter (BVSC)


title: 010519S1,mpt1,batch 2

description:
Library name: 523mpt1
10x Genomics


title: RNA-Seq of Cranberry Hybrids, Cold Treatment: 325_33, 0 minutes, replicate 3

description: Library name: Vhyb_325_33.C.T0.R3


title: small EVs_159z_HC

value: not applicable


title: small EVs_155z_HC


title: 150120S,pre,batch 6

description:
Library name: pr4prer
10x Genomics

value: interneurons


title: small EVs_154z_HC


title: RNA-Seq of Cranberry Hybrids, Cold Treatment: 325_33, 60 minutes, replicate 1

description: Library name: Vhyb_325_33.C.T1.R1


title: GSC_Stag1Stag3dKO_HiC_2

source_name: Acrosin-EGFP; beta-Actin-EGFP (AAG)

value: Acrosin-EGFP; beta-Actin-EGFP (AAG)

value: GSC


title: small EVs_153z_HC

value: male


title: 010519S1,dpt14,batch 2

description:
Library name: 523dpt14
10x Genomics

value: sorted

value: post-transplant


title: small EVs_145z_HC


title: 010519S1,div30,batch 2

description:
Library name: 523div30
10x Genomics

value: in-vitro,co-culture


title: GSC_Stag1Stag2dKO_HiC_1


title: RNA-Seq of Cranberry Hybrids, Cold Treatment: 309_19, 95 minutes, replicate 3

description: Library name: Vhyb_309_19.C.T2.R3

value: Ben Lear x NJ96-127


title: GSC_Stag1Stag2dKO_HiC_2


title: 010519S1,pre,batch 2

description:
Library name: 523pre
10x Genomics

value: pre-transplant


title: small EVs_136z_HC

value: HC

value: female


title: 010519S1,mpt6,batch 2

description:
Library name: 523mpt6
10x Genomics


title: RNA-Seq of Cranberry Hybrids, Cold Treatment: 325_33, 0 minutes, replicate 2

description: Library name: Vhyb_325_33.C.T0.R2

value: NJ96-20 x Stevens


title: small EVs_130z_HC


title: RNA-Seq of Cranberry Hybrids, Cold Treatment: 325_33, 0 minutes, replicate 1

description: Library name: Vhyb_325_33.C.T0.R1


title: 200319S,mpt18,batch 1

description:
Library name: MB461mpt18
10x Genomics


title: GSC_Stag2Stag3dKO_HiC_1


title: GSC_Stag3KO_HiC_2

value: Stag3 KO


title: RNA-Seq of Cranberry Hybrids, Cold Treatment: 309_19, 95 minutes, replicate 2

description: Library name: Vhyb_309_19.C.T2.R2


title: GSC_Stag1Stag3dKO_HiC_1


title: small EVs_126z_HC


title: GSC_Stag3KO_HiC_1


title: small EVs_135z_HC


title: RNA-Seq of Cranberry Hybrids, Cold Treatment: 309_19, 95 minutes, replicate 1

description: Library name: Vhyb_309_19.C.T2.R1


title: 200319S,mpt6,batch 1

description:
Library name: MB461mpt6
10x Genomics


title: 280120S,EOPs,batch 14

description:
Library name: MS34v3_S
10x Genomics

extract_protocol:
Single cell suspensions from each manufacturing lot were prepared after thawing cryopreserved cells, and loaded onto 10X Genomics standard chip G, according to manufacturer's instructions
Library construction was performed according to the manufacter’s instructions (single cell 3’v3 protocol, 10x Genomics).

value: End of Process


title: CardioGRKO, LV, ZT12, rep5

city: Durham

first: John

last: Cidlowski

state: NC

address: 111 T.W. Alexander Drive

institute: NIEHS

data_processing:
Alignment using STAR (V 2.5.1).
Read count was produced with featureCount (subread, Version 1.5.1)
Statistical analysis done with DEseq2 (v 1.38.3)
DEG was obtained using adjusted pvalue <0.05
Assembly: mm10
Supplementary files format and content: FeatureCount, count level data

source_name: left ventricle free wall

extract_protocol:
Male GRflox and cardioGRKO mice approximately 9-13 weeks of age were sacrificed at ZT0 or ZT12 by cervical dislocation. Hearts were removed and perfused with Tyrode solution.  The left ventricular free wall was dissected from the heart and frozen in liquid nitrogen. Total RNA was isolated from the left ventricular free wall using Qiagen RNeasy mini kit.
LV RNA concentration was determined via Qubit, and RNA integrity was determined via Tapestation.  A TruSeq RNA kit (Illumina, San Diego, CA) was utilized to prepare the poly(A)-enriched RNA-seq libraries that were sequenced on the Illumina NovaSeq 6000 in a 75-base paired-end mode according to the manufacturer’s protocol.

value: left ventricle free wall

tag: strain

value: Male

value: GRfl/fl alphaMHCCre/+ (CardioGRKO)


title: GSC_Stag2Stag3dKO_HiC_2


title: RNA-Seq of Cranberry Hybrids, Cold Treatment: 309_19, 0 minutes, replicate 3

description: Library name: Vhyb_309_19.C.T0.R3

tag: tissue

value: Leaf


title: RNA-Seq of Cranberry Hybrids, Cold Treatment: 309_19, 60 minutes, replicate 3

description: Library name: Vhyb_309_19.C.T1.R3


title: CardioGRKO, LV, ZT12, rep3

tag: Sex


title: 220720S2,EOPs,batch 12

description:
Library name: PR13v3_S
10x Genomics

value: interneurons

tag: treatment


title: small EVs_128z_HC

value: not applicable


title: small EVs_120z_HC

value: male


title: CardioGRKO, LV, ZT12, rep1

tag: time point


title: small EVs_20-76_CRC

value: CRC

value: distal


title: small EVs_20-83_CRC

value: proximal


title: small EVs_101z_HC


title: RNA-Seq of Cranberry Hybrids, Cold Treatment: 309_19, 60 minutes, replicate 2

description: Library name: Vhyb_309_19.C.T1.R2

value: Ben Lear x NJ96-127


title: 200319S,mpt1,batch 1

description:
Library name: MB461mpt1
10x Genomics

tag: cell type

value: sorted

value: post-transplant


title: RNA-Seq of Cranberry Hybrids, Cold Treatment: 309_19, 60 minutes, replicate 1

description: Library name: Vhyb_309_19.C.T1.R1

tag: genotype


title: GRflox, LV, ZT12, rep5

value: GRfl/fl (GRflox)


title: RNA-Seq of Cranberry Hybrids, Cold Treatment: 12_3, 95 minutes, replicate 1

description: Library name: Vhyb_12_3.C.T2.R1

value: Stevens x NJ96-95


title: CardioGRKO, LV, ZT12, rep4


title: 070120S,EOPs,batch 13

description:
Library name: GS34v3_S
10x Genomics


title: small EVs_114z_HC

tag: condition

value: HC


title: RNA-Seq of Cranberry Hybrids, Cold Treatment: 12_3, 60 minutes, replicate 3

description: Library name: Vhyb_12_3.C.T1.R3


title: RNA-Seq of Cranberry Hybrids, Cold Treatment: 309_19, 0 minutes, replicate 2

description: Library name: Vhyb_309_19.C.T0.R2


title: small EVs_20-366_CRC

tag: gender

value: female


title: GRflox, LV, ZT12, rep2

value: left ventricle free wall


title: small EVs_20-371_CRC

tag: age


title: RNA-Seq of Cranberry Hybrids, Cold Treatment: 309_19, 0 minutes, replicate 1

description: Library name: Vhyb_309_19.C.T0.R1


title: 220720S1,EOPs,batch 11

description:
Library name: PR13v2_S
10x Genomics

value: End of Process


title: CardioGRKO, LV, ZT12, rep2

value: Male

value: GRfl/fl alphaMHCCre/+ (CardioGRKO)


title: GRflox, LV, ZT12, rep3


title: 010720S,EOPs,batch 10

description:
Library name: PR12_S
10x Genomics

value: interneurons


title: 251219S,EOPs,batch 5

description:
Library name: PR2_S
10x Genomics


title: GRflox, LV, ZT12, rep1


title: RNA-Seq of Cranberry Hybrids, Cold Treatment: 12_3, 95 minutes, replicate 2

description: Library name: Vhyb_12_3.C.T2.R2

value: Leaf


title: 100620S,EOPs,batch 9

description:
Library name: PR11_S
10x Genomics


title: small EVs_20-52_CRC

value: male

tag: diagnosis


title: GRflox, LV, ZT12, rep4


title: small EVs_20-48_CRC

value: CRC

tag: clinical stage


title: 200520S2,EOPs,batch 8

description:
Library name: PR10r41_S
10x Genomics


title: RNA-Seq of Cranberry Hybrids, Cold Treatment: 12_3, 0 minutes, replicate 3

description: Library name: Vhyb_12_3.C.T0.R3


title: 200520S1,EOPs,batch 7

description:
Library name: PR10_S
10x Genomics


title: 010519S2,EOPs,batch 3

description:
Library name: seqm528
10x Genomics


title: RNA-Seq of Cranberry Hybrids, Cold Treatment: 12_3, 0 minutes, replicate 1

description: Library name: Vhyb_12_3.C.T0.R1


title: CardioGRKO, LV, ZT0, rep4


title: 150120S,EOPs,batch 6

description:
Library name: PR4_S
10x Genomics


title: RNA-Seq of Cranberry Hybrids, Cold Treatment: 12_3, 60 minutes, replicate 2

description: Library name: Vhyb_12_3.C.T1.R2


title: small EVs_20-319_CRC

tag: localization

value: distal


title: RNA-Seq of Cranberry Hybrids, Cold Treatment: 12_3, 60 minutes, replicate 1

description: Library name: Vhyb_12_3.C.T1.R1


title: RNA-Seq of Cranberry Hybrids, Heat Treatment: 12_3, 30 minutes, replicate 2

description: Library name: Vhyb_12_3.H.T2.R2


title: CardioGRKO, LV, ZT0, rep5


title: small EVs_20-283_CRC


title: small EVs_20-311_CRC


title: 111219S,EOPs,batch 4

description:
Library name: PR1_S
10x Genomics


title: small EVs_20-292_CRC


title: GRflox, LV, ZT0, rep5


title: RNA-Seq of Cranberry Hybrids, Cold Treatment: 12_3, 0 minutes, replicate 2

description: Library name: Vhyb_12_3.C.T0.R2


title: CardioGRKO, LV, ZT0, rep3


title: 260423S,mpt1,batch 15

description:
Library name: pl58mpt1
10x Genomics


title: ND561 Recurrent Tumor Model SOX4KO

city: Philadelphia

first: Gregory

last: Donahue

state: PA

address: 3400 Civic Center Blvd, Bldg 421

department: Cell & Developmental Biology

institute: The University of Pennsylvania

description: CAR T cells were manufactured from healthy donor T cells and injected into tumor bearing mice. TILs were extracted from recurrent tumors and T cells were FACS sorted for 10x library prep

data_processing:
Data were aligned to a custom assembly of the GRCh38 genome that contains the mesothelin-directed chimeric antigen receptor sequence (CAR-Ligand) as a separate contig. Aligned tags were filtered for match quality, and then barcodes and unique molecular identifiers were counted using the Cell Ranger v3.1.0 command cellranger count.
Assembly: GRCh38 (hg38) with M5CAR ligand DNA sequence added
Supplementary files format and content: We include expression matrix files with barcodes and features (the output of cellranger count) which can be used to see the expression level of genes in each cell. Additionally, for the patient samples we provide *.cloupe files for visualization in the Loupe browser. Some of the CAE model samples (from donor ND561) were sequenced on two flowcells, and the results of these are included separately (*FC1* and *FC2*) to reproduce the downstream analysis in our study.

source_name: recurrent tumor TILs

growth_protocol: T cells were isolated from patient ascites fluid, recurrent tumors growing in mice, or healthy donor T cells following chronic antigen stimulation in vitro

extract_protocol:
Followed manufacturers protocol (10x single cell RNA-seq v3.1)
scRNA-seq libraries were generated using a Chromium Single-Cell 3’ v3.1 Library and Gel Bead Kit (10x Genomics) following the manufacturer’s protocol. Briefly, for recurrent mouse tumor and chronic antigen stimulation assays, CD8+ T cells were sorted by FACS and washed with ice-cold PBS + 0.04% BSA. After washing, 15,000 cells were loaded onto the chromium controller to generate single-cell gel beads in emulsion. For patient samples, approximately 35,000-100,000 CD3+ T cells were sorted by FACS and cells were washed twice with ice-cold PBS + 0.04% BSA and spun down at 600g for 5 minutes. After washing, cells were resuspended in up to 45 ml of ice-cold PBS + 0.04% BSA. Five microliters of cell suspension were mixed with 5 ml of trypan blue, and cell numbers were counted via hemacytometer under the microscope. Approximately 10,000-16,000 cells were loaded to create the gel bead in emulsion. Following reverse transcription, gel beads in emulsion were disrupted and barcoded complementary DNA was isolated and amplified. After fragmentation, end repair, and poly A tailing, sample indexes were added and amplified following the manufacturer’s protocol. The final libraries were quality control checked and sequenced on an Illumina NextSeq 500.  Patient 04 was sequenced with a 75-cycle kit with parameters Read 1: 28, Read 2: 56, Index 1: 8, Index 2: 0 and patient 05 with a 150-cycle kit with parameters Read 1: 28, Read 2: 91, Index 1: 8, Index 2: 0. After fragmentation, end repair, and poly A tailing, sample indexes were added and amplified following the manufacturer’s protocol. The final libraries were quality control checked and sequenced on an Illumina NextSeq 500.  Patient 04 was sequenced with a 75-cycle kit with parameters Read 1: 28, Read 2: 56, Index 1: 8, Index 2: 0 and patient 05 with a 150-cycle kit with parameters Read 1: 28, Read 2: 91, Index 1: 8, Index 2: 0.

treatment_protocol: T cells were sorted by FACs and single cell RNA-seq libraries were prepared

value: recurrent tumor TILs

tag: t cell_source

tag: genetic background


title: small EVs_20-305_CRC


title: RNA-Seq of Cranberry Hybrids, Heat Treatment: 12_3, 15 minutes, replicate 3

description: Library name: Vhyb_12_3.H.T1.R3

tag: time

tag: temperature


title: 010519S1,EOPs,batch 2

description:
Library name: MB90v2Batch523Eplus
10x Genomics


title: CardioGRKO, LV, ZT0, rep2

tag: strain


title: small EVs_20-280_CRC


title: RNA-Seq of Cranberry Hybrids, Heat Treatment: 12_3, 30 minutes, replicate 3

description: Library name: Vhyb_12_3.H.T3.R3

tag: tissue

tag: cultivar


title: Patient 05 T cells

description: CD3+ T cells were sorted from patient PBMCs and 10x genomics single cell v3.1 RNA-seq libraries were prepared

source_name: patient ascites fluid 26 days post CAR T infusion

value: patient PBMCs


title: 200319S,EOPs,batch 1

description:
Library name: MB461
10x Genomics

tag: treatment

value: sorted


title: CardioGRKO, LV, ZT0, rep1

tag: Sex

tag: time point


title: ND539 Recurrent Tumor Model SOX4KO


title: RNA-Seq of Cranberry Hybrids, Heat Treatment: 12_3, 15 minutes, replicate 1

description: Library name: Vhyb_12_3.H.T1.R1

tag: genotype


title: GRflox, LV, ZT0, rep2


title: Patient 04 T cells

source_name: patient ascites fluid 7 days post CAR T infusion


title: small EVs_20-226_CRC

source_name: blood serum small exctracellular vesicles

tag: condition

value: proximal


title: small EVs_20-267_CRC

tag: gender


title: GRflox, LV, ZT0, rep1

value: GRfl/fl (GRflox)


title: testis_BdE

city: Changchun

first: Tong

last: Chen

state: Jilin

address: No. 5333, Xi'an Road, Lvyuan District

country: China

institute: Jilin University

data_processing:
Cellranger standard processing
**Cell filter** Seurat allows to easily explore QC metrics and filter cells, we can visualize gene and molecule counts, plot their relationship, and exclude cells with a clear outlier number of genes detected as potential multiplets. Followed criteria were used to filter cells: 1.gene counts 500-Inf per cell. 2.UMI counts 3. the percentage of mitochondrial genes < 25% %(customized). 4.DoubletFinder for detecting doublets.
**Cell clustering** Cell clustering contains the following steps: 1)Normalizing the data After removing unwanted cells from the dataset, the next step is to normalize the data. By default, we employ a global-scaling normalization method “LogNormalize” that normalizes the gene expression measurements for each cell by the total expression.
PCA(Principal component analysis): To overcome the extensive technical noise in any single gene for scRNA-seq data, Seurat clusters cells based on their PCA scores, with each PC essentially representing a ‘metagene’ that combines information across a correlated gene set.
t-SNE (t-distributed Stochastic Neighbor Embedding) visualization: Seurat continues to use t-SNE as a powerful tool to visualize and explore these datasets. The tSNE aims to place cells with similar local neighborhoods in high-dimensional space together in low-dimensional space.
Assembly: Mus_musculus.GRCm38.96
Supplementary files format and content: Tap-separated values files and matrix files

source_name: testis

extract_protocol:
The aorta tissue was dissected into five segments and the single cell suspension was obtained by enzymatic digestion. The cell pellet was resuspended in 50 μl of 1× PBS (0.04% BSA). The overall cell viability was confirmed by trypan blue exclusion , which needed to be above 85%, single cell suspensions were counted using a haemocytometer/ Countess II Automated Cell Counter and concentration adjusted to 700-1200 cells/μl.
Single-cell suspensions were loaded to 10x Chromium to capture 5000 single cell according to the manufacturer’s instructions of 10X Genomics Chromium Single-Cell 3’ kit (V3) .The following cDNA amplification and library construction steps were performed according to the standard protocol. Libraries were sequenced on an Illumina NovaSeq 6000 sequencing system (paired-end multiplexing run,150bp)

value: testis

value: dEXO+Busulfan


title: small EVs_20-128_CRC

tag: age


title: small EVs_20-160_CRC

tag: diagnosis


title: small EVs_20-220_CRC

tag: clinical stage


title: GRflox, LV, ZT0, rep4


title: RNA-Seq of Cranberry Hybrids, Heat Treatment: 12_3, 30 minutes, replicate 1

description: Library name: Vhyb_12_3.H.T2.R1

value: Stevens x NJ96-95


title: GRflox, LV, ZT0, rep3

value: left ventricle free wall


title: small EVs_20-113_CRC

tag: localization


title: ND561 Recurrent Tumor Model WT

tag: t cell_source

value: WT


title: testis_BE

value: EXO+Busulfan


title: RNA-Seq of Cranberry Hybrids, Heat Treatment: 12_3, 0 minutes, replicate 3

description: Library name: Vhyb_12_3.H.T0.R3


title: RNA-Seq of Cranberry Hybrids, Heat Treatment: 12_3, 0 minutes, replicate 1

description: Library name: Vhyb_12_3.H.T0.R1


title: HEK293 CRIPSRi RNA-Seq ZNF598 KD + RING rep2

description:
tpm_hek293_znf598_kd_ring_r2
RNA_tpm_all.csv

data_processing:
3’ adapters were trimmed using Trim Galore v0.6.4 with default settings, retaining reads of length ≥20.
Reads were aligned to the GRCh38 human genome using STAR v2.6.1c with the following parameters: --outSAMtype BAM SortedByCoordinate --outFilterMultimapNmax 1 --outFilterMismatchNmax 1 --quantMode TranscriptomeSAM GeneCounts. featureCounts v1.6.2 was used to count reads overlapping a filtered set of protein coding gene annotations from the GENCODE basic gene annotation. Differential gene expression analysis was performed using DESEq2 v1.38.1 with default settings and gene counts from featureCounts.
Assembly: GRCh38
Supplementary files format and content: RNA_tpm_all.csv

source_name: CRISPRi HEK293

extract_protocol:
Cells were lysed in LiDS/LET buffer (5% LiDS in 20 mM Tris, 100 mM LiCl, 2 mM EDTA, 5 mM DTT, pH7.4, 100 μg/ml Proteinase K). Lysates were incubated at 60°C for 10 minutes, pushed 10 times through a 1-ml syringe with a 26G needle, and mixed by vortexing. Two volumes of cold acid phenol (pH 4.3), 1/10 volume 1-Bromo-3-chloropropane and 50 µg glycogen were added. Samples were mixed vigorously by vortexing, followed by centrifuging at 10,000 g, 4°C. The aqueous phase was transferred to a new tube and the phenol/BCP extraction was repeated. RNA was by the addition of 3 volumes of 100% ethanol and incubation at -20°C for 30 min. Pellets were washed with 80% ethanol, air-dried, and resuspended in RNase-free water.
250 ng of total RNA were used for mRNA-Seq library preparation with the Universal Plus RNA-seq with NuQuant kit (Tecan, #0361). Libraries were sequenced on a NextSeq 500 platform.

tag: cell line

value: CRISPRi HEK293

tag: cell type

value: human embryonic kidney cells

value: + DOX

value: ZNF598 KD + ZNF598 RING expression


title: HEK293 CRIPSRi RNA-Seq ZNF598 KD + RING rep1

description:
tpm_hek293_znf598_kd_ring_r1
RNA_tpm_all.csv


title: RNA-Seq of Cranberry Hybrids, Heat Treatment: 12_3, 15 minutes, replicate 2

description: Library name: Vhyb_12_3.H.T1.R2

source_name: Leaf

value: Leaf

tag: time

tag: temperature


title: RNA-Seq of Cranberry Hybrids, Heat Treatment: 12_3, 0 minutes, replicate 2

description: Library name: Vhyb_12_3.H.T0.R2

tag: tissue


title: small EVs_20-151_CRC

value: CRC

value: female

value: distal


title: small EVs_20-109_CRC


title: small EVs_20-114_CRC


title: CM kucg-2 CRIPSRi sgRNA survival screen ctrl rep2

description: custom seq primer 1

data_processing:
sgRNA-seq datasets were processed following the ScreenProcessing pipeline (Horlbeck 2016, https://github.com/mhorlbeck/ScreenProcessing) with minor modifications. Briefly, sequencing reads were aligned and counted against the full sgRNA library sequences using the ScreenProcessing script fastgz_to_counts.py. This was done separately for the two primer sets used for library generation (see methods for Pooled CRISPRi screens) as sequencing datasets from each primer set requires different trimming parameters based on the location and direction of each primer. For primer set 1, the script was run with --trim_start 1 --trim_end 20 to select the first 20 nt, while for primer set 2 --trim_start 20 --trim_end 39 was used to select the last 20 nt. We modified the fastgz_to_counts.py script by adding a parameter --revcomp, which we additionally supplied to the counting for primer set 2 to allow the alignment of the reverse complement of these sequences originating from library construction with a reverse primer.
Following sgRNA counting, process_experiments.py was run for phenotype calculations. As input, the supplied config file was edited to contain the paths to the counts files generated in the first step. sgRNA analysis was conducted for each cell and screen type by comparing matched endpoint samples to their respective T0 samples. Pseudocounts of one were added for zero-count sgRNAs only using pseudocount_behavior = zeros only and pseudocount = 1. sgRNA-level data were collapsed by transcript using collapse_to_transcripts = True. For negative control sets, ten pseudogenes per gene were automatically generated, with a total of 16 000 pseudogenes using generate_pseudogene_dist = auto, pseudogene_size = 10 and num_pseudogenes = 16000. sgRNAs that had less than 50 reads were excluded from the analysis by setting minimum_reads = 50.
Gene-avegared sgRNA log2 fold changes were calculated by normalizing sgRNA log2 enrichment of the average top three sgRNAs using calculate_ave = True and best_n = 3. Mann-Whitney p-values were calculated using the average log2 fold change from all nine sgRNAs per target gene by setting calculate_mw = True.
Assembly: GRCh38
Supplementary files format and content: sgRNA_all_counts.csv

source_name: kucg-2 CRISPRi hiPSC

extract_protocol:
5*106 cells were harvested per screen and gDNA was extracted using the Nucleospin Blood Kit (Macherey&Nagel).
Per screening condition, 20 μg of DNA was amplified using NEBNext Ultra II Q5 Mix with two primer sets flanking the sgRNA sequence
sgRNA-seq with costum sequencing primer

value: kucg-2 CRISPRi hiPSC

value: cardiomyocytes

tag: screen type

value: survival

value: -DOX

value: sgRNA pool


title: small EVs_19-54_CRC

value: proximal


title: small intestinal crypts, Vil-CREPT-WT, 5 dpi

city: Beijing

first: Tingwei

last: Lan

address: Tsinghua University, Haidian District

department: School of Medicine

institute: Tsinghua University

description: GEXSCOPE

data_processing:
Raw reads from scRNA-seq were processed with fastQC and fastp to remove low quality reads, and cutadapt was used to remove poly-A tails and adaptor sequences. Filtered reads were mapped to the reference genome GRCm38 and counted with GRCm38.92 annotation using STAR. Gene counts and UMI counts were acquired by the featureCounts software. Expression matrix files were generated based on gene counts and UMI counts.
Assembly: GRCm38
Supplementary files format and content: expression matrix files

source_name: small intestine

extract_protocol:
The mouse small intestines were harvested and cut longitudinally, then washed with ice-cold PBS with Penicillin (200 U/ml) + Streptomycin (200 μg/ml) for three times to remove intestinal content. The small intestines were then cut into roughly 5-mm-long pieces and incubated in 2 mM EDTA solution prepared with PBS at 4℃ for 30 min. The solution was replaced with fresh ice-cold PBS after the incubation, and the intestinal crypts were isolated by vigorous shaking for 1 min. After the tissue pieces settled by gravity, the supernatant was passed through 70-μm cell strainers. The intestinal crypts were collected by centrifuging the filtered supernatant at 350×g 4℃ for 5 min. The intestinal crypts were suspended in GEXSCOPE Intestine Dissociation Solution (Singleron Biotechnologies) and rotated at 37℃ for 10 min, with mixing every 5 min. The mixture was then filtered with a 40-μm cell strainer and centrifuged at 350×g at 4℃ for 5 min. The cell pellet was resuspended with 1 ml mouse ENR medium and subjected to FACS to sort viable single cells. Propidium iodide (5 μg/ml) was added 5 min before flow cytometry to remove injured cells. The sorted cells were collected by centrifugation at 350×g at 4℃ for 5 min and re-suspended in ice-cold PBS with the concentration of 1×10^5 cells/ml.
The single cell suspension was loaded onto a microfluidic chip (GEXSCOPE Single Cell RNA-seq Kit, Singleron Biotechnologies) and scRNA-seq libraries were generated according to the manufacturer’s instructions.

value: small intestine

value: intestinal crypt cells

value: CREPT f/f

tag: treatment

value: 10 Gy irradiation, 5 dpi


title: CM kucg-2 CRIPSRi sgRNA survival screen rep2

description: custom seq primer 1


title: small intestinal crypts, Vil-CREPT-WT, 3 dpi

description: GEXSCOPE

value: 10 Gy irradiation, 3 dpi


title: CM kucg-2 CRIPSRi sgRNA survival screen rep1

description: custom seq primer 1

value: + DOX


title: testis_BP

value: testis

value: PBS+Busulfan


city: Los Angeles

first: Riki

last: Kawaguchi

state: CA

address: 760 Westwood Plaza, Room 37-420

department: Department of Psychiatry and Neurology Department of Psychiatry

institute: University of California, Los Angeles

description:
Library name: Stroke_P4_26
mouse cerebral white matter microglia  P4 stroke 26

data_processing:
Basecalls/demultiplexing performed using Illumina Bcl2fastq2 v 2.20
Alignment to mouse genome using STAR spliced read aligner
Counting reads using HTSeq with homo sapiens  genome GRCm38 as reference
Normalization using trimmed mean of M values method, and differential expression analysis using Biocoductor packages.
Assembly: GRCm38
Supplementary files format and content: counts

source_name: mouse cerebral white matter

extract_protocol:
NucleoSpin® RNA XS (Macherey-Nagel)
Takara SMART-Seq v4 Ultra low Input RNA kit

value: microglia

value: mouse cerebral white matter

value: stroke


title: CM kucg-2 CRIPSRi sgRNA diff screen ctrl rep2

description: custom seq primer 1

value: kucg-2 CRISPRi hiPSC

value: differentiation + survival


title: RNA-Seq of Cranberry Hybrids, Heat Treatment: 7_5, 15 minutes, replicate 1

description: Library name: Vhyb_7_5.H.T1.R1

value: Leaf

tag: cultivar

value: Pilgrim x NJ96-82


title: RNA-Seq of Cranberry Hybrids, Cold Treatment: 12_3, 95 minutes, replicate 3

description: Library name: Vhyb_12_3.C.T2.R3

value: Stevens x NJ96-95


title: small EVs_19-38_CRC

value: CRC

value: male

value: distal


title: small intestinal crypts, Vil-CREPT-KO, 5 dpi

description: GEXSCOPE

value: small intestine

value: intestinal crypt cells

value: Villin-cre;CREPT f/f


title: small EVs_20-104_CRC


title: RNA-Seq of Cranberry Hybrids, Heat Treatment: 7_5, 30 minutes, replicate 3

description: Library name: Vhyb_7_5.H.T2.R3


title: RNA-Seq of Cranberry Hybrids, Heat Treatment: 7_5, 0 minutes, replicate 3

description: Library name: Vhyb_7_5.H.T0.R3


title: RNA-Seq of Cranberry Hybrids, Heat Treatment: 7_5, 30 minutes, replicate 2

description: Library name: Vhyb_7_5.H.T2.R2


title: CM kucg-2 CRIPSRi sgRNA survival screen ctrl rep1

description: custom seq primer 1

value: cardiomyocytes

value: survival

value: -DOX

value: sgRNA pool


description:
Library name: Stroke_P4_24
mouse cerebral white matter microglia  P4 stroke 24

value: microglia

value: mouse cerebral white matter


title: small intestinal crypts, Vil-CREPT-KO, 3 dpi

description: GEXSCOPE

value: 10 Gy irradiation, 3 dpi


title: RNA-Seq of Cranberry Hybrids, Heat Treatment: 7_5, 30 minutes, replicate 1

description: Library name: Vhyb_7_5.H.T2.R1


description:
Library name: Stroke_P4_23
mouse cerebral white matter microglia  P4 stroke 23

value: stroke


title: RNA-Seq of Cranberry Hybrids, Heat Treatment: 7_5, 15 minutes, replicate 3

description: Library name: Vhyb_7_5.H.T1.R3

value: Leaf


title: CM kucg-2 CRIPSRi sgRNA diff screen rep2

description: custom seq primer 1

value: kucg-2 CRISPRi hiPSC

value: differentiation

value: + DOX


description:
Library name: Stroke_P4_22
mouse cerebral white matter microglia  P4 stroke 22


title: CM kucg-2 CRIPSRi sgRNA diff screen rep1

description: custom seq primer 1


title: RNA-Seq of Cranberry Hybrids, Heat Treatment: 7_5, 15 minutes, replicate 2

description: Library name: Vhyb_7_5.H.T1.R2

value: Pilgrim x NJ96-82


description:
Library name: Stroke_P4_21
mouse cerebral white matter microglia  P4 stroke 21


title: small EVs_19-458_CRC

value: CRC

value: male

value: distal


title: RNA-Seq of Cranberry Hybrids, Heat Treatment: 7_5, 0 minutes, replicate 1

description: Library name: Vhyb_7_5.H.T0.R1


description:
Library name: Stroke_P4_25
mouse cerebral white matter microglia  P4 stroke 25


title: small EVs_19-34_CRC

value: proximal


title: small EVs_19-398_CRC

value: female


title: CM kucg-2 CRIPSRi sgRNA diff screen ctrl rep1

description: custom seq primer 1

value: cardiomyocytes

value: differentiation + survival


title: HEK293 CRIPSRi RNA-Seq HBS1L KD rep2

data_processing:
3’ adapters were trimmed using Trim Galore v0.6.4 with default settings, retaining reads of length ≥20.
Reads were aligned to the GRCh38 human genome using STAR v2.6.1c with the following parameters: --outSAMtype BAM SortedByCoordinate --outFilterMultimapNmax 1 --outFilterMismatchNmax 1 --quantMode TranscriptomeSAM GeneCounts. featureCounts v1.6.2 was used to count reads overlapping a filtered set of protein coding gene annotations from the GENCODE basic gene annotation. Differential gene expression analysis was performed using DESEq2 v1.38.1 with default settings and gene counts from featureCounts.
Assembly: GRCh38
Supplementary files format and content: RNA_tpm_all.csv
Supplementary files format and content: RNA_count_all.csv

value: CRISPRi HEK293

value: HBS1L KD


description:
Library name: Stroke_P4_20
mouse cerebral white matter microglia  P4 stroke 20

value: microglia

value: mouse cerebral white matter


title: RNA-Seq of Cranberry Hybrids, Heat Treatment: 325_33, 30 minutes, replicate 1

description: Library name: Vhyb_325_33.H.T2.R1

value: NJ96-20 x Stevens


title: HEK293 CRIPSRi RNA-Seq NT rep2

value: human embryonic kidney cells

value: scrambled sgRNA control


title: small EVs_19-463_CRC


title: small EVs_19-211_CRC


title: RNA-Seq of Cranberry Hybrids, Heat Treatment: 325_33, 15 minutes, replicate 3

description: Library name: Vhyb_325_33.H.T1.R3

value: Leaf


title: HEK293 CRIPSRi RNA-Seq NT rep1

value: + DOX


title: small EVs_19-352_CRC


title: small EVs_19-310_CRC


title: RNA-Seq of Cranberry Hybrids, Heat Treatment: 7_5, 0 minutes, replicate 2

description: Library name: Vhyb_7_5.H.T0.R2

value: Pilgrim x NJ96-82


title: HEK293 CRIPSRi RNA-Seq ZNF598 KD rep2

value: ZNF598 KD


title: HEK293 CRIPSRi RNA-Seq HBS1L KD rep1


title: HEK293 CRIPSRi RNA-Seq ZNF598 KD rep1


description:
Library name: Stroke_P4_19
mouse cerebral white matter microglia  P4 stroke 19

value: stroke


title: RNA-Seq of Cranberry Hybrids, Heat Treatment: 325_33, 30 minutes, replicate 3

description: Library name: Vhyb_325_33.H.T2.R3


title: small EVs_19-182_CRC

value: CRC

value: distal


description:
Library name: Stroke_P2_17
mouse cerebral white matter microglia  P2 stroke 17


description:
Library name: Stroke_P2_16
mouse cerebral white matter microglia  P2 stroke 16


title: hiPSC kucg-2 CRIPSRi RNA-Seq ZNF598 KD rep2

value: kucg-2 CRISPRi hiPSC

value: Human induced pluripotent stem cell


title: RNA-Seq of Cranberry Hybrids, Heat Treatment: 325_33, 30 minutes, replicate 2

description: Library name: Vhyb_325_33.H.T2.R2


title: RNA-Seq of Cranberry Hybrids, Heat Treatment: 325_33, 0 minutes, replicate 3

description: Library name: Vhyb_325_33.H.T0.R3


title: RNA-Seq of Cranberry Hybrids, Heat Treatment: 325_33, 15 minutes, replicate 2

description: Library name: Vhyb_325_33.H.T1.R2


description:
Library name: Stroke_P2_15
mouse cerebral white matter microglia  P2 stroke 15


description:
Library name: Stroke_P4_18
mouse cerebral white matter microglia  P4 stroke 18


title: small EVs_19-379_CRC

value: female

value: proximal


title: small EVs_19-281_CRC


title: hiPSC kucg-2 CRIPSRi RNA-Seq HBS1L KD rep2

value: HBS1L KD


title: RNA-Seq of Cranberry Hybrids, Heat Treatment: 325_33, 15 minutes, replicate 1

description: Library name: Vhyb_325_33.H.T1.R1


description:
Library name: Stroke_P2_11
mouse cerebral white matter microglia  P2 stroke 11

value: microglia


title: small EVs_19-133_CRC


title: small EVs_19-160_CRC


title: small EVs_19-142_CRC

value: male


title: RNA-Seq of Cranberry Hybrids, Heat Treatment: 325_33, 0 minutes, replicate 1

description: Library name: Vhyb_325_33.H.T0.R1

value: NJ96-20 x Stevens


title: hiPSC kucg-2 CRIPSRi RNA-Seq ZNF598 KD rep1


description:
Library name: Stroke_P2_10
mouse cerebral white matter microglia  P2 stroke 10

value: mouse cerebral white matter


description:
Library name: Stroke_P2_9
mouse cerebral white matter microglia  P2 stroke 9


title: hiPSC kucg-2 CRIPSRi RNA-Seq HBS1L KD rep1


title: hiPSC kucg-2 CRIPSRi RNA-Seq rep1

value: -DOX

value: WT


title: small EVs_18-69_CRC


title: RNA-Seq of Cranberry Hybrids, Heat Treatment: 309_19, 30 minutes, replicate 1

description: Library name: Vhyb_309_19.H.T2.R1

value: Leaf

value: Ben Lear x NJ96-127


description:
Library name: Stroke_P2_6
mouse cerebral white matter microglia  P2 stroke 6


title: RNA-Seq of Cranberry Hybrids, Heat Treatment: 309_19, 30 minutes, replicate 3

description: Library name: Vhyb_309_19.H.T2.R3


title: hiPSC kucg-2 CRIPSRi RNA-Seq ZNF598 RING rep1

value: ZNF598 RING expression


title: RNA-Seq of Cranberry Hybrids, Heat Treatment: 309_19, 30 minutes, replicate 2

description: Library name: Vhyb_309_19.H.T2.R2


title: RNA-Seq of Cranberry Hybrids, Heat Treatment: 325_33, 0 minutes, replicate 2

description: Library name: Vhyb_325_33.H.T0.R2


title: hiPSC kucg-2 CRIPSRi RNA-Seq ZNF598 RING rep2


title: hiPSC kucg-2 CRIPSRi RNA-Seq NT rep2

value: + DOX

value: scrambled sgRNA control


description:
Library name: Stroke_P2_5
mouse cerebral white matter microglia  P2 stroke 5

value: stroke


title: hiPSC kucg-2 CRIPSRi RNA-Seq NT rep1

value: kucg-2 CRISPRi hiPSC


title: small EVs_18-503_CRC

value: CRC

value: distal


description:
Library name: Stroke_P2_2
mouse cerebral white matter microglia  P2 stroke 2


title: hiPSC kucg-2 CRIPSRi RNA-Seq rep2

value: Human induced pluripotent stem cell


title: small EVs_18-477_CRC


title: RNA-Seq of Cranberry Hybrids, Heat Treatment: 309_19, 15 minutes, replicate 3

description: Library name: Vhyb_309_19.H.T1.R3


title: OK6>mCherry-NLS,cac RNAi(attP2) type I MNs, bio rep 4

city: Berkeley

first: Caroline

last: Cypranowska

address: 271 Weill Hall #3200

department: Molecular & Cell Biology

institute: University of California, Berkeley

description:
Library name: OK6-CAC-209
Column name in raw_counts.txt: OK6-CAC-209

data_processing:
Fastq files for each library were analyzed with FastQC (version 0.11.7) to check for quality and trimmed with Trimmomatic (version 0.38) with parameters SLIDINGWINDOW:4:20 MINLEN:20 ILLUMINACLIP:adapter.fa:2:40:15 to remove low quality reads and to remove adapter sequences.
Trimmed reads were aligned to a custom reference genome built from Berkeley Drosophila Genome Project (dm6, release 95), including the pUAST-mCherry-NLS vector sequence for the detection of mCherry mRNA reads. Samples with the dsRNA construct were mapped to the custom genome build described along with the sequence of the specific dsRNA construct. Mapping was performed with HISAT2 (version 2.1.0).  The counts matrix was generated with featureCounts from Subread (v1.6.4). Genes with fewer than 5 read counts across two libraries were considered undetectable and removed from downstream analysis.
Differential expression between knockdown conditions was calculated with DESeq2 (version 1.26.0) using the built-in median of ratios method to normalize the read counts for each gene prior to comparison with wild type controls.
Assembly: dm6
Supplementary files format and content: Tab-delimited output of featureCounts for each Sample

organism: Drosophila melanogaster

source_name: ventral nerve cord

growth_protocol: Drosophila larvae were raised to the 3rd instar stage on cornmeal and molasses media in an incubator at 25°C. Female parents bearing the OK6-Gal4 driver, UAS-mCherry-NLS and UAS-Dcr2 transgenes were crossed with male parents bearing either the attP2 empty vector or RNAi construct to obtain control and knockdown progeny. Larvae were screened for mCherry fluorescence in the ventral nerve cord immediately prior to dissection of ventral nerve cord.

extract_protocol:
Larvae were washed twice with PBS, followed by a wash in 70% ethanol and a final wash in PBS before being placed in a droplet of Schneider's complete media with 10% FBS for ventral nerve cord dissection. Ventral nerve cord tissue was sequentially recovered for each larva dissected in ice cold Schneider's media with 10% FBS, pooled by the appropriate genotype. Dissected tissue was rinsed three times in Schneider's media containing 1.5 mM EDTA and 1.5 mM L-Cysteine. Cells were dissociated in Schneider's media with 1.5 mM EDTA, 1.5 mM L-Cysteine, papain, and 1.25 mg/mL collagenase type-I at 25C on a nutator for 5 minutes and then triturated 30 times with a P200 pipette. The incubation and trituration step was repeated once before the tissue was sheared 7 times with a 27G1/2 needle. The dissociation reaction was quenched with the addition of Schneider's media with 10% FBS. Dissociated cells were passed through a 40 uM cell strainer, spun down at 0.7xg for 7 minutes before being resuspended in 1 mL of Schneider's media with 5% FBS. Cells were stained with 0.3 uM of Sytox Green to assess viability before being sorted on a BD Influx Cell Sorter or BD FACS Aria. Cells were sorted for high mCherry fluorescence and low Sytox Green fluorescence. Sorted cells were recovered in RLT buffer with 3.5 mM BME from the QIAGEN RNEasy Micro kit and processed according to manufacturer's instruction omitting the DNase digestion step.
Libraries were prepared with the Takara SMART-Seq v4 Ultra Low Input RNA kit. cDNA was fragmented with a Covaris S220 Focused-ultrasonicator and libraries were constructed with the KAPA HyperPrep kit. Truncated universal stub adapters were ligated to the fragmented cDNA. PCR amplification with indexed primers was used to complete the adapter sequence and enrich the libraries for adapter-ligated cDNAs. Libraries were sequenced on a NovaSeq X instrument.

value: ventral nerve cord

value: motor neuron

value: cac knockdown


title: small EVs_18-42_CRC

value: male


description:
Library name: Con_P2_14
mouse cerebral white matter microglia  P2 control 14

value: microglia

value: mouse cerebral white matter

value: control


title: Neuron kucg-2 CRIPSRi sgRNA sur screen rep3

extract_protocol:
5*106 cells were harvested per screen and gDNA was extracted using the Nucleospin Blood Kit (Macherey&Nagel).
Per screening condition, 20 μg of DNA was amplified using NEBNext Ultra II Q5 Mix with two primer sets flanking the sgRNA sequence
sgRNA-seq with custom sequencing primer

value: neurons

value: survival

value: sgRNA pool

tag: custom seq primer

value: primer 1


title: small EVs_18-415_CRC

extract_protocol: Small EVs were isolated from 150 µl of sera. After the sample passed onto the column, 800 μl of 1X PBS was applied to the column. The fraction containing small EVs was eluted by applying 500 μl of 1X PBS to the column and collected. All samples were treated with proteinase K (20 mg/mL, 10 µl) and RNase Cocktail Enzyme Mix (20 000 U/mL, 5 µl) at 37 °C for 10 min. Finally, SUPERase·In RNase Inhibitor (20 U/μL, 4 µl) was added and mixed well. Total RNA including small RNAs was isolated from small EVs using Monarch® Total RNA Miniprep Kit (New England Biolabs) according to the manufacturer’s recommendations, treated with DNase I, and eluted with 50 μl of DEPC-treated water.

value: female


title: small EVs_18-383_CRC


description:
Library name: Con_P2_13
mouse cerebral white matter microglia  P2 control 13


title: OK6>mCherry-NLS,cac RNAi(attP2) type I MNs, bio rep 2

description:
Library name: OK6-CAC-207
Column name in raw_counts.txt: OK6-CAC-207

tag: genotype


title: OK6>mCherry-NLS,cac RNAi(attP2) type I MNs, bio rep 3

description:
Library name: OK6-CAC-208
Column name in raw_counts.txt: OK6-CAC-208


description:
Library name: Con_P2_12
mouse cerebral white matter microglia  P2 control 12

tag: condition


title: Neuron kucg-2 CRIPSRi sgRNA sur screen ctrl rep3

value: -DOX


title: Neuron kucg-2 CRIPSRi sgRNA sur screen rep1

value: kucg-2 CRISPRi hiPSC

value: + DOX


description:
Library name: Con_P2_8
mouse cerebral white matter microglia  P2 control 8


title: Neuron kucg-2 CRIPSRi sgRNA sur screen rep2


description:
Library name: Con_P2_7
mouse cerebral white matter microglia  P2 control 7


title: Neuron kucg-2 CRIPSRi sgRNA sur screen ctrl rep2


title: OK6>mCherry-NLS,cac RNAi(attP2) type I MNs, bio rep 1

description:
Library name: OK6-CAC-206
Column name in raw_counts.txt: OK6-CAC-206


title: Neuron kucg-2 CRIPSRi sgRNA sur screen ctrl rep1


title: OK6>mCherry-NLS,empty(attP2) type I MNs, bio rep 4

description:
Library name: OK6-ATTP2-206
Column name in raw_counts.txt: OK6-ATTP2-206

value: WT


title: small EVs_18-424_CRC

value: CRC

tag: gender

value: proximal


title: small EVs_18-356_CRC

tag: age


description:
Library name: Con_P2_4
mouse cerebral white matter microglia  P2 control 4


title: small EVs_18-332_CRC

tag: diagnosis

value: distal


title: OK6>mCherry-NLS,empty(attP2) type I MNs, bio rep 2

description:
Library name: OK6-ATTP2-204
Column name in raw_counts.txt: OK6-ATTP2-204

value: ventral nerve cord

value: motor neuron


title: small EVs_18-368_CRC

value: male

tag: clinical stage


title: small EVs_18-253_CRC

tag: localization


title: small EVs_18-273_CRC


title: small EVs_18-339_CRC


title: Neuron kucg-2 CRIPSRi sgRNA diff screen rep3

value: differentiation

value: primer 2


title: OK6>mCherry-NLS,empty(attP2) type I MNs, bio rep 3

description:
Library name: OK6-ATTP2-205
Column name in raw_counts.txt: OK6-ATTP2-205


description:
Library name: Con_P2_1
mouse cerebral white matter microglia  P2 control 1

value: microglia

value: mouse cerebral white matter

value: control


title: OK6>mCherry-NLS,empty(attP2) type I MNs, bio rep 5

description:
Library name: OK6-ATTP2-208
Column name in raw_counts.txt: OK6-ATTP2-206


title: small EVs_18-239_CRC


title: Neuron kucg-2 CRIPSRi sgRNA diff screen rep2

value: neurons

value: sgRNA pool


title: OK6>mCherry-NLS,empty(attP2) type I MNs, bio rep 1

description:
Library name: OK6-ATTP2-202
Column name in raw_counts.txt: OK6-ATTP2-202


title: Neuron kucg-2 CRIPSRi sgRNA diff screen rep1


description:
Library name: hisat_A12p
mouse cerebral white matter astrocyte stroke  12

value: astrocyte

value: stroke


description:
Library name: hisat_A11p
mouse cerebral white matter astrocyte stroke  11


title: ChIP_anti_SMC_BWX4504_42C_IPTG1h

city: Bloomington

first: Xindan

last: Wang

state: IN

address: 1001 E 3rd St

department: Biology

institute: Indiana University at Bloomington

data_processing:
Reads from each end of a DNA fragment were represented in each of the two FASTQ files generated by Illumina paired-end sequencing.
For Bacillus subtilis Hi-C, we mapped reads in each FASTQ file back to the genome of Bacillus subtilis PY79 (NCBI Reference Sequence: NC_022898.1) independently by Bowtie version 2.1.0 to preserve the order of reads. All the processing steps afterwards were performed using an in-house Perl scripts.  For ChIP-seq and WGS, we mapped reads in each FASTQ file back to the genome of Bacillus subtilis PY79 (NCBI Reference Sequence: NC_022898.1) using CLC genomics workbench 8.0, and exported .csv file.
For Hi-C, the two resulting SAM files were then merged together. Unaligned reads were discarded.
For Hi-C, the Bacillus subtilis (PY79) genome was divided into HindIII restriction fragments. Each aligned read was sorted into its corresponding restriction fragment. We inferred that a DNA fragment resulted from non-ligation or self-ligation if reads from both ends were from the same restriction fragment; these reads were discarded. Only DNA fragments for which the reads came from different restriction fragments were retained and used for construction of a Hi-C contact map.
For Hi-C, the genomes of Bacillus subtilis (PY79) was then divided into bins 10 kb and the remaining reads were allocated to their corresponding bin. We then counted the number of fragments having reads with in different bins. A raw Hi-C contact map is the matrix of read counts in which each entry, mij, indicates the number of fragments with ends mapping to bins i and j. The raw Hi-C contact map/matrix is biased due to the uneven distribution of restriction enzyme sites and, to a lesser extent, differences in GC content and the mappability of individual reads. We normalized raw contact maps using an iterative normalization procedure (Imakaev et al., 2012 PMID: 22941365). Essentially, we converted the number of interactions, or read counts, into Hi-C scores by applying the following equation and iteratively repeating it for the resulting contact map after each cycle:  mij =mij * (total reads) / (total reads in bin i * total reads in bin j). The iterative procedure was repeated until the maximum relative error of the total number of Hi-C scores in a bin was less than 10-5. Resulting matrices were normalized so that Hi-C scores for each row and column sum to 1. Subsequent analysis and visualization was done using R scripts.
Assembly: Bacillus subtilis PY79 (NCBI Reference Sequence: NC_022898.1)
Supplementary files format and content: Files ending with .matrix.txt: tab-delimited text files of the iteratively-corrected Hi-C contact maps/matrices. Files ending with .csv files are comma-separated values files of ChIP-seq/WGS results.

organism: Bacillus subtilis PY79

source_name: Bacillus subtilis PY79

extract_protocol:
Wild type and mutant cells of Bacillus subtilis PY79 growing in CH were crosslinked using 3% formaldehyde and then lysed by treatment of lysosome and 1% SDS as previouly discribed (Wang et al 2015).
Standard library construction protocol was used for Illumina Nextseq500/Nextseq2000 sequencing platforms. Illumina Truseq indexes were used.

value: Bacillus subtilis PY79

value: Bacterial

value: parS at -1degree, yhdG::Phyperspank-opt.rbs-yneE (sirA) (phleo)

value: Cells were grown in CH medium at 30degreeC for 2h, then shifted to 42degreeC and treated with 1mM ITPG for an hour


description:
Library name: hisat_A8p
mouse cerebral white matter astrocyte stroke  8


title: Neuron kucg-2 CRIPSRi sgRNA diff screen ctrl rep3

value: kucg-2 CRISPRi hiPSC

value: -DOX


description:
Library name: hisat_A7p
mouse cerebral white matter astrocyte stroke  7


title: small EVs_18-121_CRC

data_processing:
Data were processed using R package oligo and custom made probe annotation. Background subtraction, normalization and summarization was done with RMA algorithm.
Clariom_D_Human.r1.pgf
Clariom_D_Human.r1.mps

value: CRC

value: female

value: distal


title: WGS_BWX4504_42C_IPTG1h


title: Neuron kucg-2 CRIPSRi sgRNA diff screen ctrl rep1

value: differentiation

value: primer 2


description:
Library name: hisat_A4p
mouse cerebral white matter astrocyte stroke  4

value: mouse cerebral white matter


title: small EVs_17-94_CRC

value: proximal


title: small EVs_17-49_CRC


title: small EVs_18-171_CRC

value: male


description:
Library name: hisat_A3p
mouse cerebral white matter astrocyte stroke  3


title: NPC kucg-2 CRIPSRi sgRNA diff screen rep3

value: neuronal progenitor cells

value: + DOX

value: sgRNA pool


title: WGS_BWX5297_42C_HPUraIPTG20min_T45

value: Bacillus subtilis PY79

value: parSdelta9 no a.b., -59degree parS no a.b, deltaspo0J::spec, yvbJ::Pspank spo0J (deltaparS) (cat), dnaB134 (ts) zhb-83::Tn917 (erm)

value: Cells were grown in CH medium at 30degreeC for 2h, then shifted up to 42degreeC for 45min, then shifted down to 30degreeC for 15min, next shifted up to 42degreeC for 10min. Then 1mM IPTG and 162 µM HPUra were added into the cell culture and the cells were  incubated at 42degreeC for another 20min


title: WGS_BWX5297_42C_HPUraIPTG15min_T40

value: Bacterial

value: Cells were grown in CH medium at 30degreeC for 2h, then shifted up to 42degreeC for 45min, then shifted down to 30degreeC for 15min, next shifted up to 42degreeC for 10min. Then 1mM IPTG and 162 µM HPUra were added into the cell culture and the cells were  incubated at 42degreeC for another 15min


title: NPC kucg-2 CRIPSRi sgRNA diff screen rep2

value: kucg-2 CRISPRi hiPSC


title: NPC kucg-2 CRIPSRi sgRNA diff screen rep1


title: small EVs_17-445_CRC

value: CRC


title: Neuron kucg-2 CRIPSRi sgRNA diff screen ctrl rep2

value: neurons

value: -DOX


description:
Library name: hisat_A9p
mouse cerebral white matter astrocyte control 9

value: astrocyte

value: control


title: B cells, BCR, Spleen 3

city: Zurich

first: Eanna

last: Fennell

address: Winterthurerstrasse 190

department: Institute of Experimental Immunology

country: Switzerland

institute: University of Zurich

description:
Library name: Spleen_3_Plate_3203_3
10x Genomics

data_processing:
Raw reads were processed with Cellranger (version 7.2.0).
Assembly: GRCh38.p13 - Release 42 & EBV genome, strain B95-8
Supplementary files format and content: Tab separate values and matrix files
Library strategy: scBCR-Seq

source_name: Spleen

extract_protocol:
B cells (CD45+CD19+) sorted from the dissociated spleens of EBV infected mice. The quality of the single-cell suspension was evaluated with a hemocytometer under a Leica DM IL LED Fluo microscope, and the quantity was assessed using an automated cell counter (LUNA-FX7, Logos). Approximately 20,000 cells per sample were loaded into the 10X Chromium controller.
Library preparation followed the manufacturer's guidelines specified in the Chromium Next GEM Single Cell 5' Reagent Kits User Guide (v2 Chemistry Dual Index) with BCR sequencing. For sequencing, the resulting libraries were processed on an Illumina NovaSeq X platform with a 150 bp paired-end reads configuration. An average depth of approximately 50,000 reads per cell was achieved during sequencing.

treatment_protocol: EBV infection

value: Spleen

value: B cells

value: EBV-infected


title: B cells, RNA, Spleen 3

description:
Library name: Spleen_3_Plate_3202_3
10x Genomics

data_processing:
Raw reads were processed with Cellranger (version 7.2.0).
Assembly: GRCh38.p13 - Release 42 & EBV genome, strain B95-8
Supplementary files format and content: Tab separate values and matrix files


title: NPC kucg-2 CRIPSRi sgRNA diff screen ctrl rep3

value: neuronal progenitor cells

value: differentiation

value: primer 2


title: small EVs_17-70_CRC

value: male

value: distal


title: NPC kucg-2 CRIPSRi sgRNA diff screen ctrl rep2

value: sgRNA pool


title: B cells, BCR, Spleen 2

description:
Library name: Spleen_2_Plate_3203_2
10x Genomics


description:
Library name: hisat_A5p
mouse cerebral white matter astrocyte control 5

value: mouse cerebral white matter


description:
Library name: hisat_A10p
mouse cerebral white matter astrocyte control 10


title: small EVs_17-369_CRC

value: proximal


title: small EVs_17-370_CRC


title: B cells, RNA, Spleen 2

description:
Library name: Spleen_2_Plate_3202_2
10x Genomics


description:
Library name: hisat_A6p
mouse cerebral white matter astrocyte control 6


title: NPC kucg-2 CRIPSRi sgRNA diff screen ctrl rep1

value: kucg-2 CRISPRi hiPSC


title: small EVs_17-365_CRC

value: CRC

value: female


title: NPC kucg-2 CRIPSRi sgRNA growth screen rep3

value: growth

value: + DOX

value: primer 1


description:
Library name: hisat_A2p
mouse cerebral white matter astrocyte control 2

value: astrocyte

value: control


title: small EVs_17-339_CRC


title: B cells, BCR, Spleen 1

description:
Library name: Spleen_1_Plate_3203_1
10x Genomics

value: Spleen

value: B cells

value: EBV-infected


title: NPC kucg-2 CRIPSRi sgRNA growth screen rep2

value: neuronal progenitor cells


description:
Library name: hisat_A1p
mouse cerebral white matter astrocyte control 1


title: B cells, RNA, Spleen 1

description:
Library name: Spleen_1_Plate_3202_1
10x Genomics


description:
Library name: hisat_N10p
mouse cerebral white matter OPC stroke 10

value: OPC

value: stroke


title: small EVs_17-338_CRC

value: male


title: NPC kucg-2 CRIPSRi sgRNA growth screen rep1

value: sgRNA pool


title: small EVs_17-295_CRC

value: distal


title: induced pluripotent stem cell-derived fibroblasts co-cultured with keratinocytes, replicate 3

city: Berlin

first: January

last: Weiner

address: Charitéplatz 1

department: CUBI

institute: Berlin Institute of Health, Charité Medical University of Berlin

description: Library name: A16

data_processing:
Reads were mapped to human genome using the STAR aligner v. 2.7.3a. Raw counts were derived using the featureCounts program and GENCODE genome annotation v. 25.
Assembly: GRCh38 p7
Supplementary files format and content: TSV file with raw counts data

growth_protocol: Human tissue material and maintenance The human iPSC lines used in this study were BIHi005-A, KCL-004, and KCL-011. The BIHi005-A line was obtained from the iPSC biobank maintained at the Berlin Institute of Health (Berlin, Germany), with detailed information regarding the donor, cell line derivation, ethical approval, and third-party availability accessible at the Human Pluripotent Stem Cell Registry (https://hpscreg.eu/cell-line/BIHi005-A). The derivation and use of KCL-004 and KCL-011 iPSC lines were approved by the UK National Health Service Research Ethics Committee under Reference 11/LO/0295. Informed consent was obtained from all donors, and all experiments adhered to the principles outlined in the WMA Declaration of Helsinki and the NIH Belmont Report. No financial inducements were offered for donation. Jejunal-organoids were obtained from Technische Universität Berlin who generated organoids from patient material with ethical approval from the University of Würzburg's ethics committee (Approval 37/16)29. ASC-jejunal cells were cultured in EIF medium as organoids for expansion and seeded on Matrigel-coated transwells (1:50) for monolayer formation for subsequent terminal differentiation. Normal Primary human keratinocytes and dermal fibroblasts were isolated from juvenile foreskin according to established standard procedures (with written, informed consent and ethical approval from Charité Ethics Board, approval #EA1/081/13). KCs were cultivated in EpiLife supplemented with Human Keratinocyte Growth Supplement (Thermo Scientific). human bronchial epithelial cells (NHBE) and lung fibroblasts were purchased from Epithelix. Normal human bronchial epithelial cells were cultured in PneumaCult Ex Plus (STEMCELL Technologies). Human intestinal fibroblasts were purchased from ScienCell. Cardiac fibroblasts were obtained as a gift from Prof. Sophie van Linthout. Primary fibroblasts were cultured in Fibroblast growth medium (FGM: DMEM (Sigma, D6546) supplemented with 10% FBS, 2mM L-glutamine and 400U/ml Penicillin/Streptomycin). iPSC maintenance and iFB generation The cells were cultured in E8 MDC-HomeBrew medium. Cells were passaged using TrypLE Express and plated in culture medium supplemented with iMatrix-511 (NP892-011, Reprocell) and 10µM Y-27632 (1254, Tocris). Medium was refreshed daily. iPSCs were differentiated into iFBs by adapting a previously published protocol 28 after being seeded at 2x104 cells/cm2 on iMatrix-511 in E8 medium with 10µM Y-27632. The next day, differentiation began in CnT-PR-F +10% FBS +25ng/mL BMP4, transitioning to Fibroblast Growth Medium (FGM) on Day 4. From Days 6–10, 10µM SB-43125 was added to prevent myofibroblast transition. Basic iFB characterisation is found in Fig. S1. Generation of iPSC-CMs At ~90% iPSC confluence, cardiac differentiation was initiated in RPMI + B27 (minus insulin) with CHIR99021 (8µM Day 0; 4µM Day 1), followed by 5µM IWR-1 on Day 3. On Day 7, cells were switched to RPMI + B27 (plus insulin). Spontaneous contractions typically began aroundDays 8–10. All media from Days 0–7 contained 30µM L-ascorbic acid.

extract_protocol:
Total RNA was extracted from iFBs. Briefly, models were lysed in PureLink RNA Mini Kit lysis buffer. RNA was isolated according to the manufacturer’s protocol. Total RNA was quantified, and cDNA was synthesised, using iScriptTM cDNA Synthesis Kit. The subsequent RT-qPCR was performed using SYBR Green I Master Mix (Bio-Rad Laboratories). 18S served as a Housekeeping gene control.
For library preparation, we used the Novogene NGS RNA Library Prep Set (PT042). Polyadenylated mRNA was enriched with oligo(dT)25 beads, randomly fragmented, and reverse-transcribed using random hexamers. The resulting double-stranded cDNA underwent purification, end-repair, A-tailing, and adapter ligation before PCR enrichment with indexed P5 and P7 primers. After quality checks via Qubit 2.0, real-time PCR, and Bioanalyzer 2100, libraries were pooled and sequenced on the Illumina Novaseq X platform (paired-end 150, PE150).

treatment_protocol: Co-culture of iFBs Setup Preparation of iFBs On day 10 post-differentiation initiation, iFBs were passaged using 0.25% trypsin-EDTA for 5minutes at 37°C. Following detachment, cells were collected, counted using a hemocytometer, and resuspended in culture medium. For co-culture experiments, iFBs were seeded at 3x104 cells/cm2 onto the Matrigel-coated basal side of inverted transwell inserts. Cells were allowed to adhere and settle for 45 minutes at 37°C in a humidified incubator with 5% CO₂. The inserts were then placed into standard culture wells containing FGM supplemented with 10 μM Y-27632 for submerged culture. Cells were maintained under these conditions for 24 hours prior to the introduction of organ-specific cell types. Direct Co-Culture Setup The following day, keratinocytes, NHBEs, iPSC-derived cardiomyocytes, or ASC-derived jejunal cells (Fig. S2) were seeded on the apical side of the transwell insert at a cell density of 3x104 cm2. This configuration allowed separation of iFBs and organ-specific cells by only the thin, permeable transwell membrane, thereby constituting a direct co-culture system. Direct co-cultures were maintained for 7 days in respective media (RPMI/B27 for cardiac, EpiLife for dermal, PneumaCult ExPlus for pulmonary, EIF for intestinal). iFBs were then collected for analysis; control iFBs were maintained separately but in the same media for direct comparison. Indirect Co-Culture Setup For indirect co-culture, iFBs were seeded on a Matrigel-coated plate; a transwell with organ-specific cells was placed above. After 7 days, some co-cultures were harvested, while others had the insert removed and were cultured for another 7 days to assess the persistence of co-culture effects.

tag: medium

value: keratinocyte medium

value: co-cultured with keratinocytes

tag: replicate


description:
Library name: hisat_N8p
mouse cerebral white matter OPC stroke 8

tag: cell type

value: mouse cerebral white matter


title: small EVs_17-288_CRC

value: CRC


title: small EVs_17-314_CRC

value: female

value: proximal


title: NPC kucg-2 CRIPSRi sgRNA growth screen ctrl rep1

tag: cell line

value: kucg-2 CRISPRi hiPSC

value: growth

value: -DOX

value: primer 1


title: induced pluripotent stem cell-derived fibroblasts co-cultured with cardiomyocytes, replicate 2

description: Library name: A23

value: cardiomyocyte medium

value: co-cultured with cardiomyocytes


title: induced pluripotent stem cell-derived fibroblasts co-cultured with keratinocytes, replicate 2

description: Library name: A17


title: small EVs_17-268_CRC


title: HEK293 CRIPSRi sgRNA growth screen rep2

value: CRISPRi HEK293

value: human embryonic kidney cells

value: + DOX


description:
Library name: hisat_N5p
mouse cerebral white matter OPC stroke 5

value: OPC

value: stroke


title: NPC kucg-2 CRIPSRi sgRNA growth screen ctrl rep2

value: neuronal progenitor cells

value: sgRNA pool


title: small EVs_17-21_CRC

value: male

value: distal


title: NPC kucg-2 CRIPSRi sgRNA growth screen ctrl rep3


title: HEK293 CRIPSRi sgRNA growth screen ctrl rep3


title: induced pluripotent stem cell-derived fibroblasts co-cultured with intestinal cells, replicate 3

description: Library name: A21

value: intestinal cell medium

value: co-cultured with intestinal cells


title: small EVs_17-138_CRC

value: CRC


description:
Library name: hisat_N3p
mouse cerebral white matter OPC stroke 3

value: mouse cerebral white matter


title: induced pluripotent stem cell-derived fibroblasts co-cultured with intestinal cells, replicate 2

description: Library name: A20


description:
Library name: hisat_N2p
mouse cerebral white matter OPC stroke 2


title: HEK293 CRIPSRi sgRNA growth screen rep3

value: growth


description:
Library name: hisat_N1p
mouse cerebral white matter OPC stroke 1


title: small EVs_17-248_CRC

value: proximal


title: HEK293 CRIPSRi sgRNA growth screen rep1

value: primer 1


title: induced pluripotent stem cell-derived fibroblasts co-cultured with cardiomyocytes, replicate 1

description: Library name: A22

value: cardiomyocyte medium

value: co-cultured with cardiomyocytes


description:
Library name: hisat_N11p
mouse cerebral white matter OPC control 11

value: control


title: small EVs_17-242_CRC

value: female


title: HEK293 CRIPSRi sgRNA growth screen ctrl rep2

value: CRISPRi HEK293

value: human embryonic kidney cells

value: -DOX


title: small EVs_17-149_CRC


description:
Library name: hisat_N7p
mouse cerebral white matter OPC control 7

value: OPC


title: induced pluripotent stem cell-derived fibroblasts co-cultured with intestinal cells, replicate 1

description: Library name: A19


description:
Library name: hisat_N9p
mouse cerebral white matter OPC control 9


title: HEK293 CRIPSRi sgRNA growth screen ctrl rep1

value: sgRNA pool


title: induced pluripotent stem cell-derived fibroblasts co-cultured with bronchial epithelial cells, replicate 2

description: Library name: A25

value: bronchial epithelial cell medium


title: induced pluripotent stem cell-derived fibroblasts co-cultured with bronchial epithelial cells, replicate 3

description: Library name: A26


title: induced pluripotent stem cell-derived fibroblasts co-cultured with bronchial epithelial cells, replicate 1

description: Library name: A27


title: small EVs_16-74_CRC

value: male


title: hiPSC kucg-2 CRIPSRi sgRNA growth screen rep1

value: kucg-2 CRISPRi hiPSC

value: Human induced pluripotent stem cell

value: + DOX


description:
Library name: hisat_N4p
mouse cerebral white matter OPC control 4

value: mouse cerebral white matter


description:
Library name: hisat_N6p
mouse cerebral white matter OPC control 6


title: hiPSC kucg-2 CRIPSRi sgRNA growth screen rep3

value: growth


title: induced pluripotent stem cell-derived fibroblasts grown in keratinocyte medium, replicate 3

description: Library name: A6

value: keratinocyte medium

value: grown in keratinocyte medium


title: hiPSC kucg-2 CRIPSRi sgRNA growth screen rep2

value: primer 1


description:
Library name: hisat_T16p
mouse cerebral white matter pericyte stroke 16

value: pericyte

value: stroke


title: small EVs_16-307_CRC

value: CRC

value: distal


title: small EVs_16-232_CRC


description:
Library name: hisat_T13p
mouse cerebral white matter pericyte stroke 13


title: small EVs_16-22_CRC

value: female


title: hiPSC kucg-2 CRIPSRi sgRNA growth screen ctrl rep3

value: -DOX


title: induced pluripotent stem cell-derived fibroblasts grown in cardiomyocyte medium, replicate 3

description: Library name: A12

value: cardiomyocyte medium

value: grown in cardiomyocyte medium


title: small EVs_16-217_CRC


title: induced pluripotent stem cell-derived fibroblasts grown in keratinocyte medium, replicate 2

description: Library name: A5


title: hiPSC kucg-2 CRIPSRi sgRNA growth screen ctrl rep1

value: sgRNA pool


title: small EVs_16-188_CRC


title: induced pluripotent stem cell-derived fibroblasts grown in cardiomyocyte medium, replicate 2

description: Library name: A11


title: small EVs_16-173_CRC

value: male


title: small EVs_16-72_CRC


description:
Library name: hisat_T12p
mouse cerebral white matter pericyte stroke 12


title: hiPSC kucg-2 CRIPSRi sgRNA growth screen ctrl rep2

value: kucg-2 CRISPRi hiPSC

value: Human induced pluripotent stem cell


title: induced pluripotent stem cell-derived fibroblasts grown in keratinocyte medium, replicate 1

description: Library name: A4


description:
Library name: hisat_T10p
mouse cerebral white matter pericyte stroke 10

value: mouse cerebral white matter


description:
Library name: hisat_T7p
mouse cerebral white matter pericyte stroke 7


title: Subcutaneous fat 3

city: BLACKSBURG

first: Zhendong

last: Tan

state: VA

address: 175 West Campus Drive

institute: Virginia Tech

description:
Library name: sample 8
bSF4

data_processing:
The raw RNA-seq reads were filtered using Trimmomatic v0.39 to remove low-quality reads and reads containing adapters
Clean reads were aligned to the bovine reference genome ARS-UCD 2.0 using STAR v2.7.11a
Gffread v0.12.18 was used to convert the genomic annotation files from gff to gtf format
FeatureCounts (v2.0.2) was used to estimate the read counts
Differential expression analysis was performed using the DESeq2 (v1.42.0) R package
Genes with Benjamini–Hochberg approach adjusted P value < 0.05 and |log2fold change| ≥ 1 were designated as differentially expressed genes (DEGs)
Assembly: ARS-UCD 2.0
Supplementary files format and content: comma separated file contains gene expression profile that includes list of all genes that are differentially expressed

organism: Bos taurus

source_name: Adipose tissue

extract_protocol:
Total RNA was extracted using TRIzol reagent (Zymo Research, Irvine, CA) and the Direct-zol RNA MiniPrep Plus Kit (Zymo Research)
Total RNA was extracted and fragmented, followed by first-strand cDNA synthesis using random hexamer primers. Second-strand cDNA synthesis was performed using a dUTP mix. The resulting double-stranded cDNA was purified using the AMPure XP system. After end repair and adaptor ligation, the adaptor-linked cDNA was again purified with the AMPure XP system and enriched through 10 cycles of PCR. The final cDNA library was purified using the AMPure XP system, pooled, and paired-end sequenced on an Illumina platform.

treatment_protocol: Intramuscular and subcutaneous adipose tissue was collected from five adult Heifers, all of which were angus cross breed.

value: Adipose tissue

tag: tissue type

value: Subcutaneous fat

tag: Sex

value: Female

tag: Stage

value: Adult


title: Subcutaneous fat 5

description:
Library name: sample 10
bSF6

tag: tissue


title: induced pluripotent stem cell-derived fibroblasts grown in intestinal cell medium, replicate 2

description: Library name: A8

value: intestinal cell medium

tag: treatment

value: grown in intestinal cell medium


title: Subcutaneous fat 4

description:
Library name: sample 9
bSF5


description:
Library name: hisat_T4p
mouse cerebral white matter pericyte stroke 4

value: pericyte

value: stroke


description:
Library name: Con_P2_3
mouse cerebral white matter microglia  P2 control 3

value: microglia

value: control


title: small EVs_15-414_CRC

value: CRC

value: female

value: distal


description:
Library name: hisat_T15p
mouse cerebral white matter pericyte control 15


title: small EVs_15-85_CRC


title: small EVs_15-411_CRC

value: male

value: proximal


title: induced pluripotent stem cell-derived fibroblasts grown in cardiomyocyte medium, replicate 1

description: Library name: A10

value: cardiomyocyte medium

value: grown in cardiomyocyte medium


title: induced pluripotent stem cell-derived fibroblasts grown in bronchial epithelial cell medium, replicate 3

description: Library name: A15

value: bronchial epithelial cell medium


title: small EVs_15-42_CRC


description:
Library name: hisat_T11p
mouse cerebral white matter pericyte control 11

value: mouse cerebral white matter


title: small EVs_16-120_CRC


description:
Library name: hisat_T1p
mouse cerebral white matter pericyte stroke 1


title: induced pluripotent stem cell-derived fibroblasts grown in intestinal cell medium, replicate 3

description: Library name: A9


description:
Library name: hisat_T3p
mouse cerebral white matter pericyte stroke 3


title: Intramuscular fat 4

description:
Library name: sample 4
bIF5

value: Adipose tissue

value: Intramuscular fat

value: Female


title: Subcutaneous fat 2

description:
Library name: sample 7
bSF3

value: Subcutaneous fat

value: Adult


title: induced pluripotent stem cell-derived fibroblasts co-cultured with cardiomyocytes, replicate 3

description: Library name: A24

value: co-cultured with cardiomyocytes


title: induced pluripotent stem cell-derived fibroblasts grown in bronchial epithelial cell medium, replicate 1

description: Library name: A13


title: Subcutaneous fat 1

description:
Library name: sample 6
bSF2


title: small EVs_15-303_CRC


description:
Library name: hisat_T6p
mouse cerebral white matter pericyte control 6

value: pericyte


title: Intramuscular fat 5

description:
Library name: sample 5
bIF6


title: induced pluripotent stem cell-derived fibroblasts grown in standard medium, replicate 2

description: Library name: A2

value: standard medium

value: grown in standard medium


description:
Library name: hisat_T14p
mouse cerebral white matter pericyte control 14

value: control