title: 36

description: Library name: Patient36


title: ivf200_4cell_control_15

status: Public on Apr 13 2026

type: SRA

city: Philadelphia

first: Colin

last: Conine

state: Pennsylvania

address: 421 Curie Blvd BRB 1213

department: Genetics and Neonatology

country: USA

institute: UPenn Perelman SOM and CHOP

description: Library name: ivf200_4cell_control_15

library_source: transcriptomic

data_processing:
RNA-sequencing Analysis. To exclude low-complexity libraries, single embryos were required to exhibit detectable expression in a minimum number of genes. Thresholds were selected separately for each developmental stage and dataset based on inspection of the distribution of detected genes per sample, using the inflection point preceding the major drop-off in library complexity. Stage-specific cutoffs ranged from 6000-8000 detected genes. Samples failing these criteria were excluded from downstream analyses. Raw gene-level counts were analyzed in R (v4.5.1) using DESeq2 (v1.48.2). Genes were retained if they achieved at least 2.5 counts per million (CPM) in at least 80% of samples within at least one treatment group. Genes failing these criteria were removed from downstream analysis. Differential expression was modeled using a negative binomial generalized linear model with batch (embryo collection date) as a variable and Wald tests were performed to assess differential expression between each treatment level and designated control group. Normalized counts and full differential expression statistics were exported for downstream analysis. Given the limited statistical power of single-embryo sequencing due to the nature of the experimental design, nominal p-values were used for candidate identification, while enrichment and pathway-level analyses incorporated multiple-testing correction.  Computational Analysis for REMORA-AGO. Raw FASTQ files were processed using an adaptation of the MARINE pipeline developed by the Yeo Lab. Adapter trimming and low-quality base removal were performed using Cutadapt, followed by per-sample quality assessment with FastQC. Trimmed reads were aligned to the Mus musculus reference genome (mm10) using STAR, retaining uniquely mapped reads for downstream analysis. Gene-level read quantification was performed using featureCounts. To detect RNA editing events, MARINE applied its internal A-to-I (A→G) editing identification module downstream of STAR alignment and filtered using the dbSNP database mm10 to remove any SNPs.  RNA editing quantification and normalization. Editing counts were aggregated by summing site-levels counts within each gene and genomic region (CDS, 3’UTR, or intron) for each sample. Region definitions and gene/region lengths were derived from the GENCODE mouse GTF (gencode.vM10). Transcript-level intervals were collapsed to gene-level unions by gene symbol. Intronic intervals were defined per gene as the gene body minus the union of annotated exons. For each sample, the number of RNA-seq alignments overlapping CDS, inferred 3’UTRs, or introns were quantified from genome-aligned BAM files using featureCounts in SAF mode, producing region-specific mapped-read denominators. Editing activity was normalized to region length and region-specific library depth by computing editing events per kilobase per million mapped reads (EPKM); EPKM=edit_counts×10^9/(〖mapped_reads〗_region×region_bp). The resulting gene-by-sample EPKM matrices for CDS, 3’UTR, and introns were used for downstream comparisons across experimental conditions.  Statistical identification of miRNA-directed RNA editing targets. To account for small differences in global editing activity across conditions given the nature of embryo microinjections, EPKM values were further normalized within each replicate by scaling to a total of one million, generating edits per million (EPM) values that represent the fraction of total editing attributable to each transcript. Per-gene RNA editing levels were quantified for each single embryo as editing events per million mapped reads (EPM). To stabilize variance and accommodate zero-inflated distributions, EPM values were transformed at the embryo level as log₂(EPM + 1). For each gene, the mean log₂(EPM + 1) was calculated separately across rABE_Ago embryos and rABE_Ago + miR-200c-3p embryos. The change in editing was defined as the difference in these means. Editing abundance was defined as the average of the two group means. These values were visualized in an MA-style plot to separate editing abundance from miR-200c-3p–induced editing shifts. Statistical significance was assessed per gene using an unpaired one-sided Wilcoxon rank-sum test comparing log₂(EPM+1) values between conditions. Genes were required to have data from at least three embryos per group to be tested. Given the limited power and inherent variability of single-embryo RNA-sequencing, nominal p-values were interpreted alongside effect size and reproducibility across embryos.
Assembly: MM10
Supplementary files format and content: xlsx spreadsheet with one tab per /comparison

molecule: polyA RNA

organism: Mus musculus

source_name: 4-cell embryo

growth_protocol: Male (8-12 weeks old) and female (5-7 weeks old) FVB/NJ mice were derived from breeders obtained from Jackson Laboratory (Strain #001800) and maintained in-house.  Mouse parthenogenesis and embryogenesis were performed as previously described9. Briefly, oocytes were isolated from superovulated females and activated to generate parthenotes using KSOM with 10 mM SrCl2, 4 mM EGTA, and 0.05 μg/mL cytochalasin B for 1 hour. In Vitro Fertilization was performed in HTF with 1 mM glutathione with capacitated sperm for 3 hours. Embryos were cultured in KSOM under standard conditions 37°C, 5% CO2, and 5% O2 until microinjection and to the indicated developmental stages. Detailed step-by-step procedures are available in Lee et al., STAR Protocols

extract_protocol:
For sperm RNA and embryo isolations for single embryo RNA-seq see Trigg and Conine et al. 2024
Small RNA sequencing from sperm was performed largely as previously described10. Briefly, total sperm RNA was isolated and size-selected for small RNAs. In contrast to the original protocol (18-40 nucleotides), libraries in this study were size-selected for 18-24 nucleotide fragments to enrich specifically for mature miRNAs. Libraries were prepared using a modified Illumina Tru-Seq small RNA library prep protocol and sequenced on an Illumina NextSeq 1000/2000 platform. Libraries were mapped and normalized to reads per million as described previously (Trigg and Conine 2024).  Single-embryo RNA-sequencing. Following microinjection, individual embryos were collected 28 hours (late 2-cell), 46 hours (4-cell), or 70 hours (compacted morula) post activation or fertilization in 5 μL of TCL buffer (Qiagen, Cat. No. 1070498) with 1% 2-mercaptoethanol. Samples were immediately placed in -80°C until all replicates were collected. Libraries were generated using the SMART-Seq protocol11. Briefly, lysed embryos were isolated using RNAClean-XP beads and polyadenylated RNA was reverse transcribed using Superscript II. cDNA was amplified and indexed using the Nextera XT kit and sequenced on an Illumina NextSeq 1000/2000 platform (paired-end 50 bp, ~5 million reads per sample). Reads were mapped against the Mus musculus (mm10) genome using RSEM.

treatment_protocol: Embryo Microinjection. Cytoplasmic microinjections were performed on parthenotes or embryos as described previously9, delivering ~53 fL of injection solution per embryo. For each experimental replicate, embryos were collected from ~5 females derived from one or two litters, pooled, and randomly assigned to all injection conditions to minimize litter-specific effects. Within each experimental day, all treatments groups were represented in parallel. Embryos were distributed to ensure approximately matched numbers per condition (typically ~8 embryos per group and embryonic stage per replicate), preventing confounding by collection date or maternal origin. At least 24 embryos per condition were collected across three independent biological replicates. In one experiment with high embryo yield and injection efficiency, sufficient embryos were obtained across two replicates to meet this threshold.

tag: tissue

value: 4-cell embryo


title: ivf200_4cell_control_17

description: Library name: ivf200_4cell_control_17


title: 38

city: Kobe

first: Yusei

last: Hosokawa

state: Hyogo

address: 7-5-1 Kusunoki-cho, Chuo-ku

department: 1Division of Diabetes and Endocrinology, Department of Internal Medicine

country: Japan

institute: Kobe University graduate school of medicine

description: Library name: Patient38

data_processing:
Illumina bcl2fastq2-v2.20.0 software used for basecalling.
Trimmomatic program is used to remove adapter sequences and bases with base quality lower than three from the ends. Also using sliding window method, bases of reads that does not qualify for window size 4, and mean quality 15 are trimmed. Afterwards, reads with length shorter than 36bp are dropped to produce trimmed data.
Sequenced reads were mapped to GRCh38 whole genome by using HISAT2 version 2.1.0 with parameter -dta --rna-strandness RF --novel-splicesite-outfile -x -1 -2
FPKM were calculated by using StringTie version 2.1.3b, with parameter --rf -l -o -G -A -e
Assembly: GRCh38
Supplementary files format and content: tab-delimited text files include Read Count, FPKM, TPM values for each Sample

molecule: total RNA

organism: Homo sapiens

source_name: visceral white adipose tissue

extract_protocol:
Total RNA was extracted from tissues with RNeasy minikit (QIAGEN).
RNA libraries for RNA-Seq were Prepared using TruSeq stranded mRNA Library Prep. Kit Following manufacturers Protocols

value: visceral white adipose tissue


title: ivf200_4cell_control_14

description: Library name: ivf200_4cell_control_14


title: ivf200_4cell_control_13

description: Library name: ivf200_4cell_control_13


title: 32

description: Library name: Patient32


title: 30

description: Library name: Patient30


title: 31

description: Library name: Patient31


title: 29

description: Library name: Patient29


title: 27

description: Library name: Patient27


title: parth200_morula_mid_miR200_22

description: Library name: parth200_morula_mid_miR200_22

source_name: Morula parthenote

value: Morula parthenote


title: parth200_morula_mid_miR200_20

description: Library name: parth200_morula_mid_miR200_20


title: 25

description: Library name: Patient25


title: 26

description: Library name: Patient26


title: 33

description: Library name: Patient33


title: 21

description: Library name: Patient21


title: 24

description: Library name: Patient24


title: parth200_morula_mid_miR200_23

description: Library name: parth200_morula_mid_miR200_23


title: parth200_morula_mid_miR200_13

description: Library name: parth200_morula_mid_miR200_13


title: ivf200_4cell_control_10

description: Library name: ivf200_4cell_control_10


title: 23

description: Library name: Patient23


title: parth200_morula_mid_miR200_21

description: Library name: parth200_morula_mid_miR200_21


title: parth200_morula_mid_miR200_9

description: Library name: parth200_morula_mid_miR200_9


title: 19

description: Library name: Patient19


title: parth200_morula_mid_miR200_8

description: Library name: parth200_morula_mid_miR200_8


title: ivf200_4cell_control_12

description: Library name: ivf200_4cell_control_12


title: 18

description: Library name: Patient18


title: 17

description: Library name: Patient17


title: 16

description: Library name: Patient16


title: parth200_morula_mid_miR200_5

description: Library name: parth200_morula_mid_miR200_5


title: parth200_morula_mid_miR200_7

description: Library name: parth200_morula_mid_miR200_7


title: 14

description: Library name: Patient14


title: parth200_morula_mid_miR200_2

description: Library name: parth200_morula_mid_miR200_2


title: 13

description: Library name: Patient13


title: parth200_morula_mid_miR200_12

description: Library name: parth200_morula_mid_miR200_12


title: 34

description: Library name: Patient34


title: 12

description: Library name: Patient12


title: parth200_morula_mid_miR200_1

description: Library name: parth200_morula_mid_miR200_1


title: 9

description: Library name: Patient9


title: parth200_morula_mid_miR200_6

description: Library name: parth200_morula_mid_miR200_6


title: parth200_morula_low_miR200_9

description: Library name: parth200_morula_low_miR200_9


title: parth200_morula_mid_miR200_3

description: Library name: parth200_morula_mid_miR200_3


title: 10

description: Library name: Patient10


title: 15

description: Library name: Patient15


title: parth200_morula_mid_miR200_16

description: Library name: parth200_morula_mid_miR200_16


title: parth200_morula_low_miR200_6

description: Library name: parth200_morula_low_miR200_6


title: 28

description: Library name: Patient28


title: 6

description: Library name: Patient6


title: parth200_morula_low_miR200_26

description: Library name: parth200_morula_low_miR200_26


title: parth200_morula_mid_miR200_18

description: Library name: parth200_morula_mid_miR200_18


title: 22

description: Library name: Patient22


title: 5

description: Library name: Patient5


title: 1

description: Library name: Patient1


title: parth200_morula_mid_miR200_15

description: Library name: parth200_morula_mid_miR200_15


title: parth200_morula_low_miR200_4

description: Library name: parth200_morula_low_miR200_4


title: ivf200_4cell_control_11

description: Library name: ivf200_4cell_control_11


title: parth200_morula_low_miR200_7

description: Library name: parth200_morula_low_miR200_7


title: parth200_morula_low_miR200_24

description: Library name: parth200_morula_low_miR200_24


title: hESC Differentiation Screen

city: Cambridge

first: Nicholas

middle: T

last: Hutchins

state: MA

address: 455 Main St.

institute: Massachusetts Institute of Technology

description: Library name: Sample 2

library_source: transcriptomic single cell

data_processing:
The data was processed using CellRanger (7.1.0) for demultiplexing, barcoding, and aggregation (https://www.10xgenomics.com/support/software/cell-ranger/latest).
Assembly: GRCh38
Supplementary files format and content: Tab separated values and matrix files

source_name: hESC Derived

extract_protocol:
Cells were incubated with dissociated with accutase at 37 C for 30 minutes. They were resuspended inice-cold PBS. Multiseq conjugated oligos were combined according to manufacturer's protocols which briefly included adding the anchor oligo on ice,  followed by the co-anchor, then the barcode. Cells were pelleted, resuspended in PBS + 1% BSA. Cells were sorted using live-dead DAPI staining with FACS. Cells were pooled and prepared for future processing.
Libraries were constructed following the manufacturer's protocol

value: hESC Derived

tag: cell line


title: parth200_morula_low_miR200_3

description: Library name: parth200_morula_low_miR200_3


title: 20

description: Library name: Patient20


title: TransgelinKDCM3

city: Kashiwa-shi

first: Okamoto

last: Ryuji

address: 6-5-1 Kashiwanoha

institute: National cancer center east

data_processing:
HISAT2
Assembly: hg38
Supplementary files format and content: tab-delimited text file includs TPM values for each Samples

source_name: colon cancer

growth_protocol: Primary cultures of harvested fibroblasts were cultured in MF-medium (Toyobo) at 37°C and 5% CO2.

extract_protocol:
Libraries were prepared using the NEBNext poly(A) mRNA magnetic isolation apparatus (New England Biolabs [NEB], Hitchin, UK) and the NEBNext Ultra RNA LibraryPrep Kit for Illumina (NEB).
Gene expression analysis of SPF was performed by RNA sequence. Three SPFs, each established from separate cancer tissue samples, were transfected with sh luc or sh Transgelin#1. After introduction of the sh vector, RNA derived from stimulated and unstimulated cells was extracted by addition of cancer cell culture supernatant. The final analysis was performed using 3 (SPF type) × 2 (2 vectors) × 2 (with or without cancer cell culture supernatant added) for a total of 12 Samples. For Bioanalyzer (Agilent) quality control and next-generation sequencing analysis, total RNA samples were sent to Rhelixa Corporation.

value: colon cancer

tag: cell type

value: Subperitoneal Fibroblast

tag: genotype

value: Transgelin knockdown

tag: treatment

value: Cancer-cell-conditioned medium


title: 4

description: Library name: Patient4


title: Multiseq Barcode Library

description: Library name: Sample 1


title: parth200_morula_low_miR200_23

description: Library name: parth200_morula_low_miR200_23


title: 8

description: Library name: Patient8


title: parth200_morula_low_miR200_21

description: Library name: parth200_morula_low_miR200_21


title: parth200_morula_low_miR200_19

description: Library name: parth200_morula_low_miR200_19


title: TransgelinKDCM1


title: parth200_morula_low_miR200_2

description: Library name: parth200_morula_low_miR200_2


title: parth200_morula_low_miR200_22

description: Library name: parth200_morula_low_miR200_22


title: TransgelinKDCM2


title: parth200_morula_low_miR200_20

description: Library name: parth200_morula_low_miR200_20


title: parth200_morula_low_miR200_18

description: Library name: parth200_morula_low_miR200_18


title: TransgelinKD3

value: non


title: 3

description: Library name: Patient3


title: parth200_morula_low_miR200_16

description: Library name: parth200_morula_low_miR200_16


title: controlCM3

value: luciferase


title: TransgelinKD2


title: controlCM2


title: parth200_morula_low_miR200_17

description: Library name: parth200_morula_low_miR200_17


title: TransgelinKD1


title: controlCM1


title: parth200_morula_low_miR200_13

description: Library name: parth200_morula_low_miR200_13


title: parth200_morula_low_miR200_14

description: Library name: parth200_morula_low_miR200_14


title: control3


title: parth200_morula_low_miR200_12

description: Library name: parth200_morula_low_miR200_12


title: control2


title: parth200_morula_low_miR200_11

description: Library name: parth200_morula_low_miR200_11


title: 2

description: Library name: Patient2


title: parth200_morula_mid_miR200_4

description: Library name: parth200_morula_mid_miR200_4


title: parth200_morula_mid_miR200_11

description: Library name: parth200_morula_mid_miR200_11


title: control1


title: parth200_morula_low_miR200_1

description: Library name: parth200_morula_low_miR200_1


title: human skm post exercise participant 12 (miRNA-seq)

city: Burwood

first: Danielle

last: Hiam

state: Vic

address: 221 Burwood Hwy

department: IPAN

country: Australia

institute: Deakin University

data_processing:
Human skeletal muscle mitochondria and human whole skeletal muscle tissue pools were subsequently loaded on separate lanes on a SP flow cell on the NovaSeq 6000 XP (v1.5) platform. A 2nM loading pool was prepared for each of the whole tissue and isolated mitochondria samples, respectively. Each pool contained 50% gel-excised miRNA region, 25% gel-excised 190 bp region and 25% Phi-X spike-in and was sequenced on a 2x51bp run. Following sequencing, quality control and data pre-processing were performed for read1 only as described for pre-sequencing above. quality control and pre-processing of fastq files (read1 only) were performed using fastp (fastp v0.20.0) (34) to remove the read1 adapter sequence (AGATCGGAAGAGCACACGTCTGAACTCCAGTCA) and filter poor quality reads. Next, reads were mapped using blast (v2.9.0+) with switch -task blastn and word length set to 19 nt to miRbase human mature miRNAs (mature.fa; accessible from miRbase (v22.1) (2); downloaded March 12, 2018). Raw read counts for each mature miRNA were counted using a short perl script.
Assembly: miRbase v22.1
Supplementary files format and content: .csv file includes raw read counts for each miRNA for each sample
Supplementary files format and content: .csv file includes normalised read counts (DEseq2) for each miRNA for each sample

source_name: skeletal muscle (vastus lateralis)

extract_protocol:
For RNA extraction from skeletal muscle tissue, 10-15 mg frozen human skeletal muscle tissue was submerged in 400 μL ice-cold 1x DNA/RNA protection reagent (T2010, New England Biolabs, MA, USA) containing 700-800 mg 1.0mm zirconia/silica beads (11079110z, BioSpec Products, St. Helena, Australia). The tissue was homogenised with mechanical disruption at 6,500rpm for 30 s (MagnaLyser, Roche Diagnostics, NSW, Australia). Next, 30 μL Prot K Reaction Buffer (T2010, New England Biolabs, MA, USA) plus 15 μL Prot K (T2010, New England Biolabs, MA, USA) was added to the tissue homogenate and incubated at 55°C for 5 min. Following incubation, the lysate was briefly vortexed and then centrifuged at 16,000xg for 2 min. The supernatant was transferred to a new tube. RNA extraction was then performed using the Monarch Total RNA Mini Prep Kit (T2010, New England Biolabs, MA, USA) with on-column DNase-I digest as per the manufacturer’s instructions. RNA was eluted from the column in 30 μL nuclease-free water. The eluted RNA was tested for purity and concentration on a Nanodrop One (Thermo Fisher Scientific, MA, USA). If required, RNA was diluted below 25 ng/μL and then the RNA integrity number (RIN) was determined using the HS RNA screentape and reagents (5067-5579 and 5067-5580, Agilent Technologies, CA, USA) on the Agilent 4200 TapeStation.
Small RNA libraries were also prepared from 299 ± 167 ng (n=35) total RNA extracted from whole skeletal muscle tissue using the NEBNext Multiplex Small RNA Library Prep Set (cat# #E7560S, New England Biolabs.) with 3’ and 5’ adapters and reverse transcription primer diluted 0.5x, and 15 PCR cycles to amplify the adapter-ligated library. The cDNA was cleaned, quantified and assessed as described above for mitochondrial small RNA libraries.

tag: Sex

value: male

value: skeletal muscle (vastus lateralis)

value: acute endurance exercise

tag: time


title: parth200_morula_high_miR200_9

description: Library name: parth200_morula_high_miR200_9


title: human skm pre exercise participant 12 (miRNA-seq)

value: pre


title: human skm post exercise participant 11 (miRNA-seq)


title: parth200_morula_high_miR200_7

description: Library name: parth200_morula_high_miR200_7


title: parth200_morula_high_miR200_5

description: Library name: parth200_morula_high_miR200_5


title: parth200_morula_high_miR200_6

description: Library name: parth200_morula_high_miR200_6


title: parth200_morula_high_miR200_4

description: Library name: parth200_morula_high_miR200_4


title: human skm 3hpost exercise participant 10 (miRNA-seq)


title: human skm pre exercise participant 11 (miRNA-seq)


title: parth200_morula_low_miR200_10

description: Library name: parth200_morula_low_miR200_10


title: human skm post exercise participant 10 (miRNA-seq)


title: parth200_morula_high_miR200_3

description: Library name: parth200_morula_high_miR200_3


title: parth200_morula_high_miR200_8

description: Library name: parth200_morula_high_miR200_8


title: human skm 3hpost exercise participant 12 (miRNA-seq)


title: human skm pre exercise participant 8 (miRNA-seq)


title: human skm 3hpost exercise participant 7 (miRNA-seq)


title: parth200_morula_high_miR200_18

description: Library name: parth200_morula_high_miR200_18


title: human skm post exercise participant 7 (miRNA-seq)


title: human skm 3hpost exercise participant 11 (miRNA-seq)


title: parth200_morula_high_miR200_16

description: Library name: parth200_morula_high_miR200_16


title: parth200_morula_high_miR200_14

description: Library name: parth200_morula_high_miR200_14


title: human skm 3hpost exercise participant 6 (miRNA-seq)


title: human skm post exercise participant 6 (miRNA-seq)


title: parth200_morula_high_miR200_11

description: Library name: parth200_morula_high_miR200_11


title: human skm pre exercise participant 7 (miRNA-seq)


title: parth200_morula_high_miR200_22

description: Library name: parth200_morula_high_miR200_22


title: parth200_morula_high_miR200_1

description: Library name: parth200_morula_high_miR200_1


title: parth200_morula_high_miR200_24

description: Library name: parth200_morula_high_miR200_24


title: human skm post exercise participant 9 (miRNA-seq)


title: human skm pre exercise participant 10 (miRNA-seq)


title: parth200_morula_high_miR200_23

description: Library name: parth200_morula_high_miR200_23


title: human skm pre exercise participant 5 (miRNA-seq)


title: human skm 3hpost exercise participant 9 (miRNA-seq)


title: parth200_morula_control_8

description: Library name: parth200_morula_control_8


title: human skm 3hpost exercise participant 4 (miRNA-seq)


title: parth200_morula_control_7

description: Library name: parth200_morula_control_7


title: parth200_morula_high_miR200_2

description: Library name: parth200_morula_high_miR200_2


title: 7

description: Library name: Patient7


title: human skm post exercise participant 4 (miRNA-seq)


title: human skm pre exercise participant 4 (miRNA-seq)


title: parth200_morula_control_6

description: Library name: parth200_morula_control_6


title: parth200_morula_control_5

description: Library name: parth200_morula_control_5


title: parth200_morula_control_4

description: Library name: parth200_morula_control_4


title: human skm 3hpost exercise participant 3 (miRNA-seq)


title: parth200_morula_control_3

description: Library name: parth200_morula_control_3


title: parth200_morula_low_miR200_5

description: Library name: parth200_morula_low_miR200_5


title: parth200_morula_low_miR200_25

description: Library name: parth200_morula_low_miR200_25


title: parth200_morula_control_22

description: Library name: parth200_morula_control_22


title: human skm pre exercise participant 3 (miRNA-seq)


title: parth200_morula_control_9

description: Library name: parth200_morula_control_9


title: human skm pre exercise participant 6 (miRNA-seq)


title: human skm 3hpost exercise participant 5 (miRNA-seq)


title: parth200_morula_high_miR200_21

description: Library name: parth200_morula_high_miR200_21


title: human skm 3hpost exercise participant 8 (miRNA-seq)


title: parth200_morula_high_miR200_20

description: Library name: parth200_morula_high_miR200_20


title: human skm post exercise participant 8 (miRNA-seq)


title: parth200_morula_high_miR200_12

description: Library name: parth200_morula_high_miR200_12


title: human skm post exercise participant 12

description: GENERATE FASTQ

data_processing:
Total RNA libraries were placed in an equimolar pool and sequenced on the NovaSeq 6000 (v1.5) platform on a 150 bp paired-end run. Following sequencing, sequence quality was inspected using fastqc (v0.11.9, Babraham Bioinformatics, UK) and then tabulated using multiqc (v1.13, (35)). RNA-seq reads were mapped to the human transcriptome (GRCh38.p13, downloaded from ENSEMBL v38) using kallisto v0.46.1. Data were then read into RStudio (v4.2.1). Duplicate lane data were aggregated, and transcript level counts were aggregated to gene level counts based on ENSEMBL ID. Genes with an average of less than 10 reads across samples were excluded from downstream analysis.
Assembly: miRbase v22.1
Supplementary files format and content: .csv file includes raw read counts for each miRNA for each sample
Supplementary files format and content: .csv file includes normalised read counts (DEseq2) for each miRNA for each sample

extract_protocol:
For RNA extraction from skeletal muscle tissue, 10-15 mg frozen human skeletal muscle tissue was submerged in 400 μL ice-cold 1x DNA/RNA protection reagent (T2010, New England Biolabs, MA, USA) containing 700-800 mg 1.0mm zirconia/silica beads (11079110z, BioSpec Products, St. Helena, Australia). The tissue was homogenised with mechanical disruption at 6,500rpm for 30 s (MagnaLyser, Roche Diagnostics, NSW, Australia). Next, 30 μL Prot K Reaction Buffer (T2010, New England Biolabs, MA, USA) plus 15 μL Prot K (T2010, New England Biolabs, MA, USA) was added to the tissue homogenate and incubated at 55°C for 5 min. Following incubation, the lysate was briefly vortexed and then centrifuged at 16,000xg for 2 min. The supernatant was transferred to a new tube. RNA extraction was then performed using the Monarch Total RNA Mini Prep Kit (T2010, New England Biolabs, MA, USA) with on-column DNase-I digest as per the manufacturer’s instructions. RNA was eluted from the column in 30 μL nuclease-free water. The eluted RNA was tested for purity and concentration on a Nanodrop One (Thermo Fisher Scientific, MA, USA). If required, RNA was diluted below 25 ng/μL and then the RNA integrity number (RIN) was determined using the HS RNA screentape and reagents (5067-5579 and 5067-5580, Agilent Technologies, CA, USA) on the Agilent 4200 TapeStation.
Total RNA extracted from whole skeletal muscle tissue was prepared for total RNA sequencing externally (Macrogen, South Korea). Total RNA libraries depleted of ribosomal RNA were prepared using the TruSeq stranded Total RNA Library Preparation with RiboZero (human/mouse/rat).


title: parth200_morula_control_11

description: Library name: parth200_morula_control_11


title: human skm post exercise participant 3 (miRNA-seq)


title: human skm 3hpost exercise participant 1 (miRNA-seq)


title: human skm pre exercise participant 11

description: GENERATE FASTQ


title: human skm post exercise participant 2 (miRNA-seq)


title: human skm pre exercise participant 2 (miRNA-seq)


title: parth200_morula_control_18

description: Library name: parth200_morula_control_18


title: parth200_morula_control_19

description: Library name: parth200_morula_control_19


title: parth200_morula_control_16

description: Library name: parth200_morula_control_16


title: parth200_morula_control_13

description: Library name: parth200_morula_control_13


title: parth200_morula_control_14

description: Library name: parth200_morula_control_14


title: parth200_morula_control_2

description: Library name: parth200_morula_control_2


title: human skm 3hpost exercise participant 11

description: GENERATE FASTQ


title: parth200_morula_control_21

description: Library name: parth200_morula_control_21


title: parth200_4cell_mid_miR200_5

description: Library name: parth200_4cell_mid_miR200_5

source_name: 4-cell parthenote

value: 4-cell parthenote


title: human skm 3hpost exercise participant 2 (miRNA-seq)


title: human skm post exercise participant 11

description: GENERATE FASTQ


title: human skm pre exercise participant 10

description: GENERATE FASTQ


title: parth200_morula_control_10

description: Library name: parth200_morula_control_10


title: parth200_morula_control_20

description: Library name: parth200_morula_control_20


title: human skm post exercise participant 1 (miRNA-seq)


title: parth200_morula_control_1

description: Library name: parth200_morula_control_1


title: parth200_4cell_mid_miR200_6

description: Library name: parth200_4cell_mid_miR200_6


title: human skm pre exercise participant 1 (miRNA-seq)


title: human skm post exercise participant 10

description: GENERATE FASTQ


title: human skm pre exercise participant 12

description: GENERATE FASTQ


title: parth200_4cell_mid_miR200_3

description: Library name: parth200_4cell_mid_miR200_3


title: human skm 3hpost exercise participant 12

description: GENERATE FASTQ


title: parth200_4cell_mid_miR200_2

description: Library name: parth200_4cell_mid_miR200_2


title: human skm 3hpost exercise participant 7

description: GENERATE FASTQ


title: parth200_4cell_mid_miR200_24

description: Library name: parth200_4cell_mid_miR200_24


title: human skm post exercise participant 9

description: GENERATE FASTQ


title: parth200_4cell_mid_miR200_4

description: Library name: parth200_4cell_mid_miR200_4


title: parth200_4cell_mid_miR200_8

description: Library name: parth200_4cell_mid_miR200_8


title: parth200_4cell_mid_miR200_7

description: Library name: parth200_4cell_mid_miR200_7


title: human skm post exercise participant 7

description: GENERATE FASTQ


title: human skm post exercise participant 5 (miRNA-seq)


title: parth200_4cell_mid_miR200_9

description: Library name: parth200_4cell_mid_miR200_9


title: parth200_4cell_mid_miR200_22

description: Library name: parth200_4cell_mid_miR200_22


title: human skm 3hpost exercise participant 6

description: GENERATE FASTQ


title: parth200_4cell_mid_miR200_21

description: Library name: parth200_4cell_mid_miR200_21


title: human skm post exercise participant 6

description: GENERATE FASTQ


title: parth200_4cell_mid_miR200_20

description: Library name: parth200_4cell_mid_miR200_20


title: human skm 3hpost exercise participant 8

description: GENERATE FASTQ


title: human skm pre exercise participant 6

description: GENERATE FASTQ


title: human skm post exercise participant 8

description: GENERATE FASTQ


title: human skm 3hpost exercise participant 5

description: GENERATE FASTQ


title: human skm 3hpost exercise participant 9

description: GENERATE FASTQ


title: parth200_morula_control_12

description: Library name: parth200_morula_control_12


title: parth200_4cell_mid_miR200_17

description: Library name: parth200_4cell_mid_miR200_17


title: parth200_4cell_mid_miR200_14

description: Library name: parth200_4cell_mid_miR200_14


title: human skm pre exercise participant 7

description: GENERATE FASTQ


title: parth200_4cell_mid_miR200_12

description: Library name: parth200_4cell_mid_miR200_12


title: human skm pre exercise participant 3

description: GENERATE FASTQ


title: parth200_4cell_mid_miR200_10

description: Library name: parth200_4cell_mid_miR200_10


title: human skm 3hpost exercise participant 2

description: GENERATE FASTQ


title: parth200_4cell_mid_miR200_11

description: Library name: parth200_4cell_mid_miR200_11


title: human skm pre exercise participant 8

description: GENERATE FASTQ


title: human skm 3hpost exercise participant 1

description: GENERATE FASTQ


title: human skm pre exercise participant 2

description: GENERATE FASTQ


title: human skm pre exercise participant 5

description: GENERATE FASTQ


title: human skm post exercise participant 1

description: GENERATE FASTQ


title: parth200_4cell_low_miR200_6

description: Library name: parth200_4cell_low_miR200_6


title: parth200_4cell_low_miR200_7

description: Library name: parth200_4cell_low_miR200_7


title: parth200_4cell_low_miR200_4

description: Library name: parth200_4cell_low_miR200_4


title: Z781

city: Chongqing

first: Xinyu

last: Zhou

address: 1 Youyi Road, Yuzhong District

department: Department of Psychiatry

country: China

institute: The First Affiliated Hospital of Chongqing Medical University

data_processing:
Raw reads were first cleaned by removing reads containing the adapter by using Trimmomatic. FastQC (version0.10.1) was used to assess the quality of raw reads. Clean reads were then aligned to the human reference genome GRCh38 using HISAT2. FeatureCounts was used to count reads mapped to individual genes.
Assembly: GRCh38
Supplementary files format and content: tab-delimited text files include rlogTransformed values for each Sample.

source_name: peripheral blood

extract_protocol:
For each enrolled participant, 2mL fasting venous blood samples were collected in PAXgene Blood RNA Tubes. Total RNA was extracted using the PAXgene Blood RNA Kit (QIAGEN) and isolated from peripheral blood using TRIzol® Reagent according to the manufacturer's protocol.
RNA purification, reverse transcription, library construction, and sequencing were done at Shanghai Majorbio Bio-pharm Biotechnology Co., Ltd. (Shanghai, China) (Illumina, San Diego, CA). A library of RNA-seq transcripts was made with 1μg of total RNA and the Illumina® Stranded mRNA Prep, Ligation from Illumina (San Diego, CA). Messenger RNA was isolated using the polyA selection method with oligo (dT) beads and subsequently fragmented using a fragmentation buffer. The resulting double-stranded cDNA was synthesized using the SuperScript double-stranded cDNA synthesis kit (Invitrogen, CA) with random hexamer primers (Illumina). The synthesized cDNA was then subjected to end-repair, phosphorylation, and 'A' base addition as per Illumina's library construction protocol. The libraries were size selected for cDNA target fragments of 300 bp on 2% Low Range Ultra Agarose, and then PCR amplified using Phusion DNA polymerase (NEB) for 15 PCR cycles. After measuring with Qubit 4.0, the Nova Seq 6000 sequencer was used to read the paired-end RNA-seq library (2 × 150bp read length).

value: peripheral blood

tag: disease state

value: Healthy control (HC)

value: Without Drug therapy


title: parth200_4cell_mid_miR200_1

description: Library name: parth200_4cell_mid_miR200_1


title: human skm post exercise participant 2

description: GENERATE FASTQ


title: human skm post exercise participant 5

description: GENERATE FASTQ


title: parth200_4cell_mid_miR200_18

description: Library name: parth200_4cell_mid_miR200_18


title: Z779


title: parth200_4cell_low_miR200_24

description: Library name: parth200_4cell_low_miR200_24


title: parth200_4cell_mid_miR200_19

description: Library name: parth200_4cell_mid_miR200_19


title: human skm 3hpost exercise participant 4

description: GENERATE FASTQ


title: Z774


title: parth200_4cell_low_miR200_23

description: Library name: parth200_4cell_low_miR200_23


title: human skm 3hpost exercise participant 3

description: GENERATE FASTQ


title: Z761


title: parth200_4cell_low_miR200_22

description: Library name: parth200_4cell_low_miR200_22


title: human skm post exercise participant 3

description: GENERATE FASTQ


title: Z756


title: parth200_4cell_low_miR200_9

description: Library name: parth200_4cell_low_miR200_9


title: parth200_4cell_low_miR200_8

description: Library name: parth200_4cell_low_miR200_8


title: parth200_4cell_low_miR200_21

description: Library name: parth200_4cell_low_miR200_21


title: Z755


title: parth200_4cell_low_miR200_20

description: Library name: parth200_4cell_low_miR200_20


title: Z758


title: parth200_4cell_mid_miR200_13

description: Library name: parth200_4cell_mid_miR200_13


title: parth200_4cell_low_miR200_16

description: Library name: parth200_4cell_low_miR200_16


title: human skm post exercise participant 4

description: GENERATE FASTQ


title: human skm pre exercise participant 1

description: GENERATE FASTQ


title: parth200_4cell_low_miR200_18

description: Library name: parth200_4cell_low_miR200_18


title: Z748


title: parth200_4cell_low_miR200_12

description: Library name: parth200_4cell_low_miR200_12


title: Z712


title: parth200_4cell_mid_miR200_23

description: Library name: parth200_4cell_mid_miR200_23


title: parth200_4cell_low_miR200_13

description: Library name: parth200_4cell_low_miR200_13


title: Z753


title: Z713


title: Z709


title: parth200_4cell_low_miR200_11

description: Library name: parth200_4cell_low_miR200_11


title: parth200_4cell_low_miR200_10

description: Library name: parth200_4cell_low_miR200_10


title: Z723


title: Z707


title: parth200_4cell_low_miR200_5

description: Library name: parth200_4cell_low_miR200_5


title: parth200_4cell_low_miR200_2

description: Library name: parth200_4cell_low_miR200_2


title: Z705


title: Z725


title: parth200_4cell_low_miR200_3

description: Library name: parth200_4cell_low_miR200_3


title: Z703


title: parth200_4cell_high_miR200_6

description: Library name: parth200_4cell_high_miR200_6


title: parth200_4cell_high_miR200_9

description: Library name: parth200_4cell_high_miR200_9


title: Z685


title: parth200_4cell_high_miR200_5

description: Library name: parth200_4cell_high_miR200_5


title: Z683


title: Z682


title: parth200_4cell_low_miR200_1

description: Library name: parth200_4cell_low_miR200_1


title: parth200_4cell_low_miR200_19

description: Library name: parth200_4cell_low_miR200_19


title: parth200_4cell_high_miR200_3

description: Library name: parth200_4cell_high_miR200_3


title: Z681


title: Z737


title: parth200_4cell_high_miR200_2

description: Library name: parth200_4cell_high_miR200_2


title: Z741


title: parth200_4cell_high_miR200_24

description: Library name: parth200_4cell_high_miR200_24


title: Z677


title: parth200_4cell_high_miR200_23

description: Library name: parth200_4cell_high_miR200_23


title: Z673


title: parth200_4cell_high_miR200_21

description: Library name: parth200_4cell_high_miR200_21


title: parth200_4cell_high_miR200_8

description: Library name: parth200_4cell_high_miR200_8


title: Z688


title: parth200_4cell_high_miR200_7

description: Library name: parth200_4cell_high_miR200_7


title: parth200_4cell_high_miR200_4

description: Library name: parth200_4cell_high_miR200_4


title: Z778


title: Z678


title: Z676


title: parth200_4cell_high_miR200_13

description: Library name: parth200_4cell_high_miR200_13


title: Z661


title: Z668


title: parth200_4cell_high_miR200_12

description: Library name: parth200_4cell_high_miR200_12


title: Z646


title: Z655


title: parth200_4cell_high_miR200_16

description: Library name: parth200_4cell_high_miR200_16


title: Z644


title: parth200_4cell_low_miR200_15

description: Library name: parth200_4cell_low_miR200_15


title: parth200_4cell_high_miR200_22

description: Library name: parth200_4cell_high_miR200_22


title: parth200_4cell_low_miR200_14

description: Library name: parth200_4cell_low_miR200_14


title: parth200_4cell_high_miR200_20

description: Library name: parth200_4cell_high_miR200_20


title: Z665


title: Z656


title: parth200_4cell_control_8

description: Library name: parth200_4cell_control_8


title: parth200_4cell_control_9

description: Library name: parth200_4cell_control_9


title: Z635


title: parth200_4cell_control_7

description: Library name: parth200_4cell_control_7


title: parth200_4cell_control_5

description: Library name: parth200_4cell_control_5


title: parth200_4cell_high_miR200_1

description: Library name: parth200_4cell_high_miR200_1


title: parth200_4cell_control_3

description: Library name: parth200_4cell_control_3


title: Z651


title: parth200_4cell_high_miR200_10

description: Library name: parth200_4cell_high_miR200_10


title: parth200_4cell_high_miR200_19

description: Library name: parth200_4cell_high_miR200_19


title: Z632


title: Z633


title: parth200_4cell_high_miR200_15

description: Library name: parth200_4cell_high_miR200_15


title: parth200_4cell_high_miR200_11

description: Library name: parth200_4cell_high_miR200_11


title: Z642


title: parth200_4cell_high_miR200_18

description: Library name: parth200_4cell_high_miR200_18


title: Z664


title: Z631


title: Z638


title: Z636


title: Z630


title: Z652


title: Z621


title: parth200_4cell_control_23

description: Library name: parth200_4cell_control_23


title: parth200_4cell_control_21

description: Library name: parth200_4cell_control_21


title: Z629


title: parth200_4cell_high_miR200_14

description: Library name: parth200_4cell_high_miR200_14


title: Z650


title: parth200_4cell_high_miR200_17

description: Library name: parth200_4cell_high_miR200_17


title: Z617


title: parth200_4cell_control_19

description: Library name: parth200_4cell_control_19


title: Z610


title: Z608


title: parth200_4cell_control_18

description: Library name: parth200_4cell_control_18


title: Z612


title: parth200_4cell_control_4

description: Library name: parth200_4cell_control_4


title: Z625


title: parth200_4cell_control_6

description: Library name: parth200_4cell_control_6


title: parth200_4cell_control_1

description: Library name: parth200_4cell_control_1


title: parth200_4cell_control_20

description: Library name: parth200_4cell_control_20


title: parth200_4cell_control_24

description: Library name: parth200_4cell_control_24


title: parth200_4cell_control_22

description: Library name: parth200_4cell_control_22


title: Z599


title: parth200_4cell_control_16

description: Library name: parth200_4cell_control_16


title: parth200_4cell_control_17

description: Library name: parth200_4cell_control_17


title: Z592


title: Z597


title: parth200_4cell_control_12

description: Library name: parth200_4cell_control_12


title: Z598


title: parth200_4cell_control_10

description: Library name: parth200_4cell_control_10


title: Z627


title: parth200_4cell_control_11

description: Library name: parth200_4cell_control_11


title: Z588


title: parth200_4cell_control_15

description: Library name: parth200_4cell_control_15


title: Z595


title: parth200_2cell_mid_miR200_6

description: Library name: parth200_2cell_mid_miR200_6

source_name: 2-cell parthenote

value: 2-cell parthenote


title: parth200_2cell_mid_miR200_8

description: Library name: parth200_2cell_mid_miR200_8


title: Z583


title: Z590


title: parth200_4cell_control_14

description: Library name: parth200_4cell_control_14


title: parth200_2cell_mid_miR200_26

description: Library name: parth200_2cell_mid_miR200_26


title: Z580


title: parth200_4cell_control_2

description: Library name: parth200_4cell_control_2


title: Z589


title: Z576


title: parth200_2cell_mid_miR200_21

description: Library name: parth200_2cell_mid_miR200_21


title: Z584


title: Z565


title: Z561


title: Z609


title: parth200_2cell_mid_miR200_24

description: Library name: parth200_2cell_mid_miR200_24


title: parth200_2cell_mid_miR200_5

description: Library name: parth200_2cell_mid_miR200_5


title: parth200_2cell_mid_miR200_17

description: Library name: parth200_2cell_mid_miR200_17


title: Z585


title: parth200_2cell_mid_miR200_23

description: Library name: parth200_2cell_mid_miR200_23


title: Z575


title: Z572


title: parth200_2cell_mid_miR200_7

description: Library name: parth200_2cell_mid_miR200_7


title: Z582


title: Z577


title: parth200_4cell_control_13

description: Library name: parth200_4cell_control_13


title: Z570


title: Z559


title: parth200_2cell_mid_miR200_2

description: Library name: parth200_2cell_mid_miR200_2


title: parth200_2cell_mid_miR200_22

description: Library name: parth200_2cell_mid_miR200_22


title: Z569


title: parth200_2cell_mid_miR200_9

description: Library name: parth200_2cell_mid_miR200_9


title: parth200_2cell_mid_miR200_14

description: Library name: parth200_2cell_mid_miR200_14


title: Z528


title: parth200_2cell_mid_miR200_16

description: Library name: parth200_2cell_mid_miR200_16


title: parth200_2cell_mid_miR200_13

description: Library name: parth200_2cell_mid_miR200_13


title: Z560


title: parth200_2cell_mid_miR200_19

description: Library name: parth200_2cell_mid_miR200_19


title: Z571


title: Z581


title: parth200_2cell_mid_miR200_4

description: Library name: parth200_2cell_mid_miR200_4


title: parth200_2cell_mid_miR200_11

description: Library name: parth200_2cell_mid_miR200_11


title: Z615


title: parth200_2cell_mid_miR200_18

description: Library name: parth200_2cell_mid_miR200_18


title: Z518


title: parth200_2cell_mid_miR200_10

description: Library name: parth200_2cell_mid_miR200_10


title: Z521


title: Z516


title: Z507


title: parth200_2cell_low_miR200_8

description: Library name: parth200_2cell_low_miR200_8


title: Z514


title: parth200_2cell_low_miR200_9

description: Library name: parth200_2cell_low_miR200_9


title: parth200_2cell_low_miR200_26

description: Library name: parth200_2cell_low_miR200_26


title: parth200_2cell_low_miR200_3

description: Library name: parth200_2cell_low_miR200_3


title: parth200_2cell_low_miR200_25

description: Library name: parth200_2cell_low_miR200_25


title: parth200_2cell_mid_miR200_1

description: Library name: parth200_2cell_mid_miR200_1


title: parth200_2cell_low_miR200_7

description: Library name: parth200_2cell_low_miR200_7


title: parth200_2cell_low_miR200_24

description: Library name: parth200_2cell_low_miR200_24


title: Z294


title: parth200_2cell_mid_miR200_15

description: Library name: parth200_2cell_mid_miR200_15


title: Z531


title: Z520


title: parth200_2cell_mid_miR200_20

description: Library name: parth200_2cell_mid_miR200_20


title: Z523


title: parth200_2cell_low_miR200_21

description: Library name: parth200_2cell_low_miR200_21


title: parth200_2cell_low_miR200_2

description: Library name: parth200_2cell_low_miR200_2


title: minus_4B_a

city: Bethesda

first: Jon

middle: R.

last: Lorsch

state: MD

address: 49 Convent Dr Building 49 RM 2C08

department: NICHD

institute: NIH

description:
Library name: minus_4B_a
48S Preinitiaiton complex protected mRNA fragments

data_processing:
Remove sequencing adaptors sequence (AGATCGGAAGAGCAC) in the fastq files using cutadapt/4.4, Demultiplex fastq sequences using Linux "grep" function to subset reads containing sample specific barcode at the 3' ends.
Remove non-coding RNA reads using STAR/2.7.10b
Map non-coding RNA removed reads to yeast genome, and Spike-in mRNAs using STAR/2.7.10b, and count 25-34 nt reads mapped to each transcript using "fp-count" function in RiboSeq (https://github.com/ingolia-lab/RiboSeq)
Wiggle files were produced from the alignment files using "wiggle-track" function in RiboSeq (https://github.com/ingolia-lab/RiboSeq), generating two wiggle files, each for genes on the Watson or Crick strand. Wiggle files were normalized by multiplying the size factor "q" (calculate using spike-in RPFs) in the wiggle-track function (-q).
Differential expression analysis of changes in RPF, recruitment efficiency (RE), or relative ribosome occupancy (RRO) values was performed using DESeq2 (Love et al., 2014) using custermerized Size-factors calculated from spike-in RPFs.
Assembly: R64-1-1 S288C Sac cer3 Genome Assembly
Supplementary files format and content: Wiggle files

organism: Saccharomyces cerevisiae BY4741

source_name: Yeast strain

growth_protocol: WT yeast strain was cultured in Yeast Extract–Peptone–Dextrose (YPD) medium to OD600 of ~1. Harvested cells were washed with cold water and stored in -80°C before use.

extract_protocol:
The frozen cell pellet from a 500 ml culture was thawed on ice and mechanically disrupted by vortexing with glass beads three times for 2 min each at maximum speed in a cold room (4°C) in 2 ml of buffer RL (provided in the kit), 3 ml phenol:chloroform:isoamyl alcohol 25:24:1 (pH 5.2) and 3 ml ice cold glass beads. Following 5 min centrifugation at 14000 rpm in a Sorvall LYNX 6000 Superspeed centrifuge using a Fiberlite F14-14 x 50cy rotor, the supernatant was transferred to a fresh tube and total RNA was prepared using a GenElute total RNA purification Maxi kit (Sigma-Aldrich; RNB200) following the manufacturer’s protocol. 400 μg total RNA in 250 μl water was applied to a GeneElute mRNA miniprep kit (Sigma-Aldrich; MRN70-1KT), following the manufacturer’s protocol. The purified total mRNA was treated by 5’-Phosphate-Dependent Exonuclease (Lucigen, TER51020) to degrade RNAs with 5’ monophosphates, such as 18S and 25S ribosomal RNAs, at 0.3 μg/µl mRNA in 1X buffer A (provided in the kit), 1U/µl RiboGuard RNase Inhibitor (Lucigen; RG90925), 0.1 U/µl 5’-Phosphate-Dependent Exonuclease. Following a 1 h incubation at 30°C, the total mRNA was extracted using phenol:chloroform:isoamyl alcohol 25:24:1 (pH 5.2), ethanol precipitated, resuspended in 10 mM Tris (pH 8.0) and stored in -80 °C.
RecSeq sequencing library construction was conducted according to a previously described protocol (McGlincy and Ingolia 2017), with modifications, using identical barcoded linkers (NI-810 to NI-815), RT primer (NI-802) and PCR primers (NI-798, NI-799, NI-822 to NI-824). The RNA fragments purified from 48S PIC RPFs were dephosphorylated using T4 Polynucleotide Kinase (PNK) (NEB; M0201L) and ligated to pre-adenylated linkers (NI-810 to NI-815) containing 5 nt sample barcodes unique for each sample using truncated T4 RNA ligase 2 (K227Q) (NEB; M0351L). Ligated fragments were separated from free linkers on a 15% polyacrylamide TBE-Urea gel and then pooled and purified for reverse transcription using RT primer NI-802 and ProtoScript II Reverse Transcriptase (NEB; M0368S). The ~105 nt cDNAs were separated from free RT primers on a 15% TBE-Urea gel and circularized using CircLigaseII ssDNA Ligase (Biosearch Technologies; CL9021K). PCR was carried out using forward primer NI-798, and reverse primers (NI-799, NI-822 to 824) as already described (McGlincy and Ingolia 2017) .

treatment_protocol: No additional treatment for the cell.

tag: strain

value: Yeast strain

value: MATa his3-del-1 leu2-del-0 met15-del-0 ura3-del-0


title: Z291


title: Z502


title: parth200_2cell_low_miR200_5

description: Library name: parth200_2cell_low_miR200_5


title: parth200_2cell_low_miR200_6

description: Library name: parth200_2cell_low_miR200_6


title: parth200_2cell_low_miR200_19

description: Library name: parth200_2cell_low_miR200_19


title: YZ999

value: Major depressive disorder (MDD)

value: Drug therapy


title: 4E-4G_mrna

description:
Library name: 4E-4G_mrna
RNA-Seq


title: Z501


title: parth200_2cell_low_miR200_4

description: Library name: parth200_2cell_low_miR200_4


title: parth200_2cell_low_miR200_27

description: Library name: parth200_2cell_low_miR200_27


title: Z299


title: Z293


title: minus_4B_b

description:
Library name: minus_4B_b
48S Preinitiaiton complex protected mRNA fragments


title: YZ983


title: parth200_2cell_low_miR200_17

description: Library name: parth200_2cell_low_miR200_17


title: parth200_2cell_low_miR200_16

description: Library name: parth200_2cell_low_miR200_16


title: parth200_2cell_low_miR200_15

description: Library name: parth200_2cell_low_miR200_15


title: plus_4B_b

description:
Library name: plus_4B_b
48S Preinitiaiton complex protected mRNA fragments


title: YZ980


title: parth200_2cell_low_miR200_14

description: Library name: parth200_2cell_low_miR200_14


title: parth200_2cell_low_miR200_22

description: Library name: parth200_2cell_low_miR200_22


title: parth200_2cell_low_miR200_12

description: Library name: parth200_2cell_low_miR200_12


title: plus_4B_a

description:
Library name: plus_4B_a
48S Preinitiaiton complex protected mRNA fragments


title: 4E-4G_240nM_a

description:
Library name: 4E-4G_240nM_a
48S Preinitiaiton complex protected mRNA fragments


title: parth200_2cell_low_miR200_11

description: Library name: parth200_2cell_low_miR200_11


title: 4E-4G_120nM_c

description:
Library name: 4E-4G_120nM_c
48S Preinitiaiton complex protected mRNA fragments


title: YZ964


title: parth200_2cell_low_miR200_10

description: Library name: parth200_2cell_low_miR200_10


title: Z292


title: parth200_2cell_low_miR200_1

description: Library name: parth200_2cell_low_miR200_1


title: YZ962


title: 4E-4G_120nM_b

description:
Library name: 4E-4G_120nM_b
48S Preinitiaiton complex protected mRNA fragments


title: YZ957


title: 40S_mrna

description:
Library name: 40S_mrna.fastq.gz
RNA-Seq


title: parth200_2cell_low_miR200_23

description: Library name: parth200_2cell_low_miR200_23


title: YZ948


title: parth200_2cell_control_4

description: Library name: parth200_2cell_control_4


title: parth200_2cell_low_miR200_20

description: Library name: parth200_2cell_low_miR200_20


title: 4E-4G_240nM_b

description:
Library name: 4E-4G_240nM_b
48S Preinitiaiton complex protected mRNA fragments


title: parth200_2cell_control_8

description: Library name: parth200_2cell_control_8


title: YZ949


title: parth200_2cell_control_6

description: Library name: parth200_2cell_control_6


title: parth200_2cell_control_7

description: Library name: parth200_2cell_control_7


title: 4E-4G_240nM_c

description:
Library name: 4E-4G_240nM_c
48S Preinitiaiton complex protected mRNA fragments


title: parth200_2cell_control_5

description: Library name: parth200_2cell_control_5


title: parth200_2cell_control_27

description: Library name: parth200_2cell_control_27


title: 4E-4G_15nM_b

description:
Library name: 4E-4G_15nM_b
48S Preinitiaiton complex protected mRNA fragments


title: parth200_2cell_control_29

description: Library name: parth200_2cell_control_29


title: 4E-4G_60nM_b

description:
Library name: 4E-4G_60nM_b
48S Preinitiaiton complex protected mRNA fragments


title: YZ936


title: parth200_2cell_control_26

description: Library name: parth200_2cell_control_26


title: YZ942


title: parth200_2cell_control_30

description: Library name: parth200_2cell_control_30


title: parth200_2cell_control_9

description: Library name: parth200_2cell_control_9


title: 4E-4G_120nM_a

description:
Library name: 4E-4G_120nM_a
48S Preinitiaiton complex protected mRNA fragments


title: 4E-4G_15nM_c

description:
Library name: 4E-4G_15nM_c
48S Preinitiaiton complex protected mRNA fragments


title: parth200_2cell_low_miR200_18

description: Library name: parth200_2cell_low_miR200_18


title: parth200_2cell_control_31

description: Library name: parth200_2cell_control_31


title: YZ946


title: YZ940


title: 4E-4G_60nM_a

description:
Library name: 4E-4G_60nM_a
48S Preinitiaiton complex protected mRNA fragments


title: YZ900


title: 4E-4G_60nM_c

description:
Library name: 4E-4G_60nM_c
48S Preinitiaiton complex protected mRNA fragments


title: parth200_2cell_control_18

description: Library name: parth200_2cell_control_18


title: parth200_2cell_control_20

description: Library name: parth200_2cell_control_20


title: 4E-4G_5nM_b

description:
Library name: 4E-4G_5nM_b
48S Preinitiaiton complex protected mRNA fragments


title: YZ903


title: parth200_2cell_control_28

description: Library name: parth200_2cell_control_28


title: parth200_2cell_control_32

description: Library name: parth200_2cell_control_32


title: parth200_2cell_control_3

description: Library name: parth200_2cell_control_3


title: parth200_2cell_control_22

description: Library name: parth200_2cell_control_22


title: parth200_2cell_control_23

description: Library name: parth200_2cell_control_23


title: parth200_2cell_control_11

description: Library name: parth200_2cell_control_11


title: parth200_2cell_control_15

description: Library name: parth200_2cell_control_15


title: 4E-4G_0nM_a

description:
Library name: 4E-4G_0nM_a
48S Preinitiaiton complex protected mRNA fragments


title: 4E-4G_5nM_c

description:
Library name: 4E-4G_5nM_c
48S Preinitiaiton complex protected mRNA fragments


title: parth200_2cell_control_10

description: Library name: parth200_2cell_control_10


title: 40S_60nM_c

description:
Library name: 40S_60nM_c
48S Preinitiaiton complex protected mRNA fragments


title: parth200_2cell_control_17

description: Library name: parth200_2cell_control_17


title: 40S_60nM_b

description:
Library name: 40S_60nM_b
48S Preinitiaiton complex protected mRNA fragments


title: Drug-seq library of CRISPR edited PBMC-derived induced microglia-like cells

city: Boston

first: Liam

last: McCrea

address: 185 Cambridge Street

department: Center for Genomic Medicine

institute: Massachusetts General Hospital

description: Library name: Sample 1

data_processing:
Raw paired-end FASTQ files were trimmed with Trim Galore v0.6.10
Trimmed reads aligned to hg38 using STAR v2.7.11b using "solo" mode and unique molecular identifier count matrices were generated in this step by supplying the list of sequencing barcodes to option –soloCBwhitelist with UMI deduplication as described in the MERCURIUS DRUG-Seq kit documentation (Alithea Genomics, 10841).
Differential expression (DE) was performed with DESeq2.(9) Samples from each knockout (KO) gene well were contrasted to negative control (NTCs) wells.
Assembly: hg38
Supplementary files format and content: demultiplexed sample count matrix

growth_protocol: Peripheral blood mononuclear cells (PBMCs) were isolated from a half leukapheresis pack (Leukopak, HemaCare/Charles River). Leukopak contents were diluted 1:2 with HBSS (Thermo Fisher #14175095). 15ml of Lymphoprep Density Gradient Medium (Stemcell Technologies #07851) was added to 50ml conical tubes, and the diluted leukopak was layered on top. Tubes were centrifuged at 400g for 30 min (brake off). PBMC layers were collected, diluted to 45 ml with HBSS, and washed twice by centrifugation at 300g for 10 min (brake off), resuspending pellets in HBSS between washes. Cells were pooled, counted (Countess II, Thermo Fisher), and after a final spin (300g, 10 min), pellets were resuspended in Cryostor CS10 (Sigma-Aldrich #C2874) , aliquoted, and frozen in a Mr. Frosty container (Thermo Fisher #5100-0001) at -80°C before transfer to liquid nitrogen. Cells remained in Cryostor at room temperature for no more than 10 min prior to freezing; if longer processing was needed, suspensions were split and processed in batches. Frozen PBMCs were thawed at 37°C and transferred into RPMI-1640 (Sigma, #R8758) supplemented with 10% heat-inactivated FBS (Sigma, #12306C) and 1% Penicillin/Streptomycin (Life Technologies, #15140-122). After centrifugation at 300 g for 5 min (brake off), cells were resuspended, counted, and plated at ~500,000 cells/cm² in 6-well tissue culture plates (Corning, #353046) pre-coated with Geltrex (Gibco, #A1413202) for 1 hour. After 24 hours, media was replaced with RPMI-1640 containing 1% Penicillin/Streptomycin, 1% Glutamax (Life Technologies, #35050-061), 100 ng/ml IL-34 (Biolegend, #577904), and 10ng/ml GM-CSF (PeproTech, #300-03). Cells were incubated for 8 days to induce transdifferentiation

extract_protocol:
96-well multiplexed libraries (DRUG-seq) were prepared using the MERCURIUS™ DRUGseq kit (Alithea Genomics, 10841) as per manufacturer instructions. Briefly, cells were washed with 100 µL Dulbecco’s PBS (Gibco, 14190-144) per well, lysed at 4°C with 20 µL/well 1x Cell Lysis Buffer, and clarified by centrifugation (300 × g, 5 min, 4°C). Up to 20 µL supernatant was transferred to a new 96-well PCR plate and stored at -80°C.
For reverse transcription, lysates were thawed and 10 µL was added to wells containing dry barcoded oligo-dT primers (Alithea Genomics, 10513). After resuspension, 10 µL RT Master Mix was added and reverse transcription performed (30 min 50°C, 10 min 85°C, hold at 4°C). Firststrand cDNA was pooled, mixed with 7x DNA binding buffer (Zymo, D4003-1-L), and purified via Zymo-Spin IC column (C1004-50), eluting in 20 µL nuclease-free water. Excess oligo-dT was digested from 17 µL eluate using Exonuclease I, incubating 30 min at 37°C, 20 min at 80°C, and cooling to 4°C. Second-strand synthesis was performed immediately after (addition of 7 µL Second Strand Synthesis reaction mix, 20 min at 37°C, 30 min at 65°C, hold at 4°C). Second-strand cDNA was purified with CleanNGS beads (Bulldog Bio, CNGS005; 0.6x ratio) using a PCR Strip Magnetic Separator (Permagen, MSR812). cDNA concentration was measured using Qubit 1X dsDNA HS Assay Kit (Invitrogen, Q33231); 50–60 ng cDNA was tagmented in a 20 µL reaction (with 4µL of provided Tagmentation Enzyme Buffer) for 7 min at 55°C, then purified with 0.6x CleanNGS beads. The resulting library was pre-amplified with provided kit UDI adapters (10 cycles: 98°C 10 s, 63°C 30 s, 72°C 1 min), then purified twice with 0.7x CleanNGS beads and eluted in 20 µL. Final library quality and concentration were measured on an Agilent 5300 Fragment Analyzer with the HS NGS Fragment Kit (DNF-474-0500). Libraries were sequenced on a NovaSeq X Plus 1.5B flow cell (Read 1: 28 cycles, i7/i5: 8 cycles each, Read 2: 90 cycles).

treatment_protocol: Guide RNAs (Synthego) were resuspended to 25μM. SpCas9 protein (IDT, #1081059) was diluted to 31μM in Duplex buffer (IDT, #11-01-03-01) and combined with gRNAs at a 1:1.5 molar ratio (SpCas9:gRNA) to form ribonucleoprotein (RNP) complexes (~10.8μM final concentration). Complexes were gently mixed by pipetting, incubated for 10min at room temperature, diluted to 7.2µM, and kept on ice until use as 5μl aliquots in 8-strip PCR tubes per 25,000 cells (per reaction). piMGLC culture supernatant was collected, filtered through a 0.22µm Steriflip-GP unit (EMD Millipore, #SCGP00525), and retained as Conditioned Medium for post-nucleofection culture. piMGLCs were washed with DPBS and detached using Accutase (Sigma, #A6964) for 5min at 37°C, centrifuged (300g, 5min), and resuspended in fresh medium. For nucleofection, 25,000cells (for assays) or 75,000 cells for Drug-seq were resuspended in 20µl P3 buffer (Lonza P3 Nucleofection Kit, #V4SP-3096) and mixed with prepared RNPs. Cell-RNP suspensions were transferred into nucleofection cuvettes and nucleofected (Lonza 4-D nucleofector) using program EA-100. After a 10min recovery at room temperature, cells were seeded into Geltrex-coated 96-well plates (Corning, #3904) with 180µl Conditioned Medium (total 200µlperwell) and cultured for 6days.

value: CRISPR knockout


title: parth200_2cell_control_16

description: Library name: parth200_2cell_control_16


title: parth200_2cell_control_24

description: Library name: parth200_2cell_control_24


title: YZ857


title: parth200_2cell_control_19

description: Library name: parth200_2cell_control_19


title: 4E-4G_0nM_b

description:
Library name: 4E-4G_0nM_b
48S Preinitiaiton complex protected mRNA fragments


title: 4E-4G_5nM_a

description:
Library name: 4E-4G_5nM_a
48S Preinitiaiton complex protected mRNA fragments


title: parth200_2cell_control_25

description: Library name: parth200_2cell_control_25


title: 4E-4G_15nM_a

description:
Library name: 4E-4G_15nM_a
48S Preinitiaiton complex protected mRNA fragments


title: YZ897


title: YZ927


title: YZ894


title: 4E-4G_0nM_c

description:
Library name: 4E-4G_0nM_c
48S Preinitiaiton complex protected mRNA fragments


title: parth200_2cell_control_2

description: Library name: parth200_2cell_control_2


title: BR16_ctc_cluster

city: Basel

first: Yongzhan

last: Zhang

address: Otto-Stern-Weg 7 HPL H17.2

country: Switzerland

institute: ETH Zurich

description:
Library name: Sample 20
10X Genomics

data_processing:
Sequencing reads were trimmed from the 3’ end until the final base had a quality score >30, utilizing Trimmomatic (v0.33). Quality assessment of RNA-seq data was performed using FastQC (v0.11.4). Trimmed reads were aligned to the appropriate reference genomes using STAR (v2.7.3a): the human genome (GRCh38) for LM2 samples and the mouse genome (GRCm39) for MVT1 samples. Gene-level expression counts were quantified with HTSeq (v2.0.5), using GENCODE gene annotations (release 44 for human, release M33 for mouse).
FASTQ files were demultiplexed and aligned using Cell Ranger (v6.0.0, 10x Genomics) with default parameters. Reads were aligned to species-specific reference genomes provided by 10x Genomics: refdata-gex-GRCh38-2020-A for human (LM2-NSG, BR16-NSG) samples and refdata-gex-mm10-2020-A for mouse (MVT1-FVB) samples. Doublet removal was performed using DoubletFinder (V2.0), following standard guidelines.
Assembly: GRCh38, mm10
Supplementary files format and content: Tab-seperated values files and matrix files

extract_protocol:
For all cell types, viability assessment and fluorescence-based sorting were performed using a BD FACSAria Fusion cell sorter. Dead cells were excluded using SYTOX blue dead cell stain. Cancer cells were identified and sorted based on fluorescent markers: GFP for LM2 cells, RFP for BR16 cells, and CD90.2 for MVT1 cells, with the latter stained using Alexa Fluor 488 anti-mouse CD90.2 antibody.
Single-cell RNA sequencing libraries were generated using the 10x Genomics Chromium Single Cell 3′ Gene Expression Kit v3. Briefly, viable single-cell suspensions were loaded onto Chromium Single Cell Chips, and libraries were constructed following the manufacturer’s protocol.


title: 40S_30nM_c

description:
Library name: 40S_30nM_c
48S Preinitiaiton complex protected mRNA fragments


title: LM2_ctc_single_m2

description:
Library name: Sample 7
10X Genomics


title: LM2_lung_metastasis_m2

description:
Library name: Sample 6
10X Genomics


title: YZ893


title: YZ888


title: parth200_2cell_control_1

description: Library name: parth200_2cell_control_1


title: BR16_primary_tumor

description:
Library name: Sample 17
10X Genomics


title: LM2_ctc_single_m1

description:
Library name: Sample 3
10X Genomics


title: LM2_lung_metastasis_m1

description:
Library name: Sample 2
10X Genomics


title: YZ844


title: 40S_15nM_b

description:
Library name: 40S_15nM_b
48S Preinitiaiton complex protected mRNA fragments


title: 40S_15nM_c

description:
Library name: 40S_15nM_c
48S Preinitiaiton complex protected mRNA fragments


title: BR16_ctc_single

description:
Library name: Sample 19
10X Genomics


title: 40S_30nM_b

description:
Library name: 40S_30nM_b
48S Preinitiaiton complex protected mRNA fragments


title: LM2_primary_tumor_m1

description:
Library name: Sample 1
10X Genomics


title: LM2_primary_tumor_m2

description:
Library name: Sample 5
10X Genomics


title: YZ856


title: YZ843


title: PBMC TCR, BCG, TBT04301058 D7; TBT04301062 D14; TBT04301097 D0

city: Oxford

first: Shuailin

last: Li

address: Old Road Campus Research Building

country: United Kingdom

institute: University of Oxford

description: Library name: TCR3-b2-PBMC

data_processing:
scRNA-seq Barcode assignment, Unique Molecular Identifier (UMI) tagging, and sequence alignment for the BAL samples were conducted using the Cell Ranger count pipeline (v6.0.1), employing the human reference genome GRCh38 (GENCODE version 32/Ensembl 98) provided by 10x Genomics 48. TCR clonotypes in the BAL samples were determined using the Cell Ranger V(D)J pipeline (v6.0.1), with the GRCh38 Human V(D)J Reference (v7.1.0) from 10x Genomics. For PBMC samples, the Cell Ranger multi pipeline (v6.0.1) was utilized, processing data from the 5’ gene expression, V(D)J, and cell surface protein libraries, using the same human reference genome and V(D)J reference as for the BAL samples. Bulk TCR-seq Alignment of FASTQ files from the bulk TCR-seq data and assembly of TCR sequences were performed using the Cogent NGS Immune Profiler (v1.6, Takara Bio) with the default settings.
Assembly: Human reference genome GRCh38 (GENCODE version 32/Ensembl 98) provided by 10x Genomics, and the  GRCh38 Human V(D)J Reference (v7.1.0) from 10x Genomics.
Supplementary files format and content: scRNA-seq h5 file: gene expression matrix csv file: TCR clone information for each cell Bulk TCR-seq csv file: TCR clone information

source_name: Blood

extract_protocol:
scRNA-seq of BAL samples BAL cells from all three saline controls and three selected volunteers receiving BCG from each group were processed for scRNA-seq. The three volunteers receiving BCG were selected to allow for batched processing with saline controls where possible, followed by consideration of cell availability for single-cell processing. BAL volume was recorded, and tubes from the same volunteer were pooled before being centrifuged (400×g, 10min, maximum brake) to separate the BAL cells from the supernatant BAL fluid (BALF). BAL cells were incubated in 5 ml of red blood cell (RBC) lysis solution (Qiagen #158103) for 5 minutes, followed by washing and resuspension for counting using a Countess II FL (Thermo Fisher #AMQAX1000). Cells were spun at 300×g for 10 minutes at 4°C and resuspended in the R10 medium (no streptomycin), aiming to recover 5000 cells per well. Resuspended cells were transferred on ice to the Oxford Genomics Centre (OGC) for further processing. Group 1 samples initially underwent attempts at Magnetic Cell Separation (MACSTM) bead (Miltenyi Biotec #130-097-043) sorting as part of the original plan to enrich the T cell population, particularly for TCR sequencing. MACSTM CD3 MicroBeads and Magnetic Separation (MS) column (Miltenyi Biotec #130-042-201) were used to positively select CD3+ cells as per the manufacturer’s instructions. Due to technical issues with cell counting equipment at the time, all cells were recombined and sent for sequencing in their original proportions after these attempts at separation, allowing for comparisons across different groups. The BAL samples collected from volunteers in the groups 2 and onwards did not undergo any cell sorting attempts. scRNA-seq of PBMC samples Frozen PBMCs (1 ml) were thawed at 37 °C and gradually diluted into 9 ml of warm R10 medium, followed by centrifugation at 400×g for 7 minutes at room temperature. The pellet was resuspended in 2 ml R10, and cell count and viability were assessed using (Solution 13 Chemometec #910-3013) on the NC-slide A8TM (Chemometec #942-0003). Cells were then spun at 300×g for 5 minutes, resuspended in cell staining buffer at 1×107 cells/ml, and blocked with Human TruStain FcXTM (BioLegend #422301) for 10 minutes at 4 °C. TotalSeq-C cell hashing antibody (2 μl, BioLegend #394661, #394663, #394665) was added and incubated for 30 minutes at 4 °C. Cells were washed three times with staining buffer and resuspended in 100 μl of 0.04% PBS (Sigma #D8537)/BSA (bovine serum albumin, Miltenyi Biotec #130-091-376). Count and viability were reassessed before pooling. Bulk TCR-seq of PBMC samples Frozen PBMC samples were thawed, and around 2 million cells were disrupted in 350 μl of the RLT Plus buffer (Qiagen #1053393) with β-mercaptoethanol (BME, Sigma #M3148) (10 μl/ml). RNA was extracted using the AllPrep DNA/RNA/miRNA Universal Kit (Qiagen #80224) following the manufacturer’s instructions. RNA was eluted into 35 μl of RNase-free water (Thermo Fisher #AM9937) with the concentration quantified by the Nanodrop. RNA was then concentrated using the RNeasy MinElute Cleanup Kit (Qiagen #74204) following the manufacturer’s instructions and eluted into 20 μl of RNase-free water. RNA concentration was quantified using the Nanodrop, and RNA integrity was assessed using the Agilent 4150 TapeStation System. Bulk TCR-seq of AIM+ cells Cells were thawed as they were in the processing of scRNA-seq, except that the cells were resuspended in 2 ml of the R10 medium with 2×benzonase (4 μl/ml, Sigma #E1014). Cells were incubated in 5% CO2 at 37°C for 10 minutes and then counted using Countess II FL. Cells were washed, resuspended, and seeded at a density of 1×106 cells per 100 μl per well in a 96-well U-bottom plate. Cells were incubated with a purified anti-CD40 monoclonal antibody (100 μg/ml; 5 μl per million cells, Miltenyi Biotec #130-094-133) for 15 minutes at room temperature to block CD40-mediated signalling pathways. No washing step was performed between the blocking and stimulation stages. Cells were stimulated with PPD (20 μg/ml), BCG (2×105 CFU/ml, AJ Vaccines) or M.bovis lysate (10 μg/ml, BEI Resources) in a total volume of 200 μl for 24 hours at 37 °C with 5% CO2. Post-incubation, cells were centrifuged at 440×g for 5 minutes. The cell pellet was washed with cold PBS, transferred to a V-bottom plate, and centrifuged again under the same conditions. After discarding the supernatant, cells were stained with a Live/Dead Aqua stain (diluted 1:100 in PBS, Thermo Fisher #L34957) in a total volume of 5 μl for 10 minutes at 4°C. This was followed by staining with a cell surface antibody cocktail for 30 minutes at 4°C. Cells were then washed with 2% BSA/PBS, resuspended in 100 μl of 2% BSA/PBS. AIM+ CD4⁺ or CD8⁺ T cells, identified by co-expression of CD134 and CD137, CD154 and CD134, CD154 and CD137, CD69 and CD134, CD69 and CD137, or CD69 and CD154 , were then sorted using the FACSAria Fusion flow cytometer (BD Biosciences) to 350 μl RLT buffer. RNA was extracted using the Qiagen RNeasy Micro kit (Qiagen #74004) following the manufacturer’s instructions.
scRNA-seq of BAL samples Samples from each volunteer were separated into two Gel beads-in-emulsion (GEM) wells, aiming for 5000 cells per well. 5’ gene expression libraries and V(D)J libraries were generated as per the manufacturer’s instructions. Samples from the Groups 1 and 2 (Batch 1) were processed using the Chromium Next GEM Single Cell V(D)J Reagent kits v1.1 (10x Genomics) and sequenced using a single index configuration. Due to changes in reagents availability, the Chromium Next GEM Single Cell 5’ Reagent Kits v2 (10x Genomics) were used for library construction for Groups 3-5 (Batch 2) samples. Libraries were sequenced using the Illumina NovaSeq 6000 platform to achieve a minimum sequencing depth of 30,000 mean reads per cell with 50% sequencing saturation. scRNA-seq of PBMC samples PBMCs from three donors (1.4×104 cells each) were pooled and processed using the Chromium Next GEM Single Cell 5’ HT Reagent Kit (v2) to generate gene expression, surface protein, and V(D)J libraries, following the manufacturer’s protocols. Libraries were sequenced on the Illumina NovaSeq-X platform (paired-end 150 bp), targeting ≥45,000 reads/cell for gene expression and ≥7,500 reads/cell for V(D)J and surface protein libraries. Bulk TCR-seq of PBMC samples 500-1,000 ng RNA was used as input for TCR library construction using the SMART-Seq Human TCR (with UMIs) kit (Takara Bio #634779). TCR libraries were quantified using the Qubit (Thermo Fisher #Q32851) and TapeStation and sequenced on the Illumina NovaSeq 6000 SP flow cell to achieve a target sequencing depth of 1.5×107 reads per PBMC sample. Bulk TCR-seq of AIM+ cells RNA was then processed and sequenced as mentioned in the Bulk TCR sequencing part, except the target sequencing depth was 1×105 reads per 1,000 sorted cells.

value: Blood


title: PBMC HTO, BCG, TBT04301058 D14; TBT04301062 D0; TBT04301097 D2

description:
Library name: HTO4-GEX-b2-PBMC
S4-b2_filtered_feature_bc_matrix.h5

library_source: other

molecule: protein


title: YZ840


title: LM2_ctc_cluster_m1

description:
Library name: Sample 4
10X Genomics


title: PBMC TCR, BCG, TBT04301058 D2; TBT04301062 D7; TBT04301097 D14

description: Library name: TCR2-b2-PBMC


title: 40S_5nM_c

description:
Library name: 40S_5nM_c
48S Preinitiaiton complex protected mRNA fragments


title: PBMC TCR, BCG, TBT04301058 D0; TBT04301062 D2; TBT04301097 D7

description: Library name: TCR1-b2-PBMC


title: 40S_60nM_a

description:
Library name: 40S_60nM_a
48S Preinitiaiton complex protected mRNA fragments


title: YZ846


title: PBMC HTO, BCG, TBT04301058 D7; TBT04301062 D14; TBT04301097 D0

description:
Library name: HTO3-GEX-b2-PBMC
S3-b2_filtered_feature_bc_matrix.h5


title: 40S_5nM_b

description:
Library name: 40S_5nM_b
48S Preinitiaiton complex protected mRNA fragments


title: LM2_ctc_cluster_m2

description:
Library name: Sample 8
10X Genomics


title: PBMC HTO, BCG, TBT04301058 D2; TBT04301062 D7; TBT04301097 D14

description:
Library name: HTO2-GEX-b2-PBMC
S2-b2_filtered_feature_bc_matrix.h5


title: PBMC GEX, BCG, TBT04301058 D14; TBT04301062 D0; TBT04301097 D2

description:
Library name: GEX4-b2-PBMC
S4-b2_filtered_feature_bc_matrix.h5


title: 40S_15nM_a

description:
Library name: 40S_15nM_a
48S Preinitiaiton complex protected mRNA fragments


title: 40S_30nM_a

description:
Library name: 40S_30nM_a
48S Preinitiaiton complex protected mRNA fragments


title: 40S_5nM_a

description:
Library name: 40S_5nM_a
48S Preinitiaiton complex protected mRNA fragments


title: BR16_lung_metastasis

description:
Library name: Sample 18
10X Genomics


title: YZ855


title: PBMC TCR, BCG, TBT04301058 D14; TBT04301062 D0; TBT04301097 D2

description: Library name: TCR4-b2-PBMC


title: CosMx SMI whole-brain spatial transcriptomics, slide 118Band1182L [118B (Control); 1182L (Control)]

type: RNA

city: Columbia

first: Ai-Ling

last: Lin

state: MO

address: 1101 Hospital Drive

department: Radiology

institute: University of Missouri

description: Sagittal brain section; samples 118B (Control); 1182L (Control); CosMx single-cell spatial transcriptomics; cell segmentation and typing via AtoMx with InSituType

data_processing:
Expression matrices, per-cell metadata, cell boundary polygons, and FOV position files were exported from AtoMx Spatial Informatics Platform. AnnData objects were constructed and negative control probes excluded alongside cells with >10% negative probe counts. Additional filtering excluded cells with fewer than 100 total transcripts or fewer than 20 detected genes, and genes expressed in fewer than 100 cells.  Data were normalized to 1000 counts per cell and log1p-transformed using Scanpy (Python 3.10). Olfactory regions were masked and labeled for exclusion from downstream analysis.
Processed data file - H5AD file (AnnData format): filtered and normalized single-cell expression matrix with cell-level metadata including cell types, sample identity, and QC metrics

label: fluorescent RNA probes

source_name: Sagittal brain sections

label_protocol: fluorescent RNA probes

growth_protocol: 3xTg-AD transgenic mice (B6;129-Tg(APPSwe,tauP301L)1Lfa Psen1tm1Mpm/Mmjax) were obtained from MMRRC at The Jackson Laboratory. Mice were housed on a 12:12 light/dark cycle with ad libitum access to food and water.

extract_protocol: Single-cell spatial transcriptomic profiling was performed on formalin-fixed, paraffin-embedded (FFPE) sagittal brain sections using the NanoString CosMx Spatial Molecular Imager with a high-plex RNA in situ hybridization panel.

treatment_protocol: Mice received a 7-day course of oral antibiotics followed by a 3-day fecal microbiota transplantation (FMT) using donor material from either healthy human donors (Healthy-FMT) or stroke patient donors (Stroke-FMT). Naive control mice received no antibiotic or FMT treatment. At 6.5 months of age, mice were euthanized and brain tissue was collected.

value: brain


title: YZ850


title: YZ829


title: PBMC HTO, BCG D2, TBT04301051 D2; TBT04301059 D2; TBT04301072 D2

description:
Library name: HTO2-GEX-b1-D2-PBMC
S2-b1_filtered_feature_bc_matrix.h5


title: PBMC TCR, BCG D14, TBT04301051 D14; TBT04301059 D14; TBT04301072 D14

description: Library name: TCR4-b1-D14-PBMC


title: PBMC HTO, BCG D7, TBT04301051 D7; TBT04301059 D7; TBT04301072 D7

description:
Library name: HTO3-GEX-b1-D7-PBMC
S3-b1_filtered_feature_bc_matrix.h5


title: CosMx SMI whole-brain spatial transcriptomics, slide 120Land323DY [120L (Stroke_FMT); 323DY (Healthy_FMT)]

description: Sagittal brain section; samples 120L (Stroke_FMT); 323DY (Healthy_FMT); CosMx single-cell spatial transcriptomics; cell segmentation and typing via AtoMx with InSituType


title: CosMx SMI whole-brain spatial transcriptomics, slide 367Rand215L [367R (Healthy_FMT); 215L (Stroke_FMT)]

description: Sagittal brain section; samples 367R (Healthy_FMT); 215L (Stroke_FMT); CosMx single-cell spatial transcriptomics; cell segmentation and typing via AtoMx with InSituType


title: PBMC GEX, BCG D14, TBT04301051 D14; TBT04301059 D14; TBT04301072 D14

description:
Library name: GEX4-b1-D14-PBMC
S4-b1_filtered_feature_bc_matrix.h5


title: YZ831


title: PBMC TCR, BCG D2, TBT04301051 D2; TBT04301059 D2; TBT04301072 D2

description: Library name: TCR2-b1-D2-PBMC


title: CosMx SMI whole-brain spatial transcriptomics, slide 368R [368R (Stroke_FMT)]

description: Sagittal brain section; samples 368R (Stroke_FMT); CosMx single-cell spatial transcriptomics; cell segmentation and typing via AtoMx with InSituType


title: YZ825


title: YZ836


title: PBMC TCR, BCG D7, TBT04301051 D7; TBT04301059 D7; TBT04301072 D7

description: Library name: TCR3-b1-D7-PBMC


title: PBMC HTO, BCG D0, TBT04301051 D0; TBT04301059 D0; TBT04301072 D0

description:
Library name: HTO1-GEX-b1-D0-PBMC
S1-b1_filtered_feature_bc_matrix.h5


title: YZ851


title: YZ835


title: PBMC GEX, BCG, TBT04301058 D0; TBT04301062 D2; TBT04301097 D7

description:
Library name: GEX1-b2-PBMC
S1-b2_filtered_feature_bc_matrix.h5


title: YZ832


title: PBMC GEX, BCG, TBT04301058 D2; TBT04301062 D7; TBT04301097 D14

description:
Library name: GEX2-b2-PBMC
S2-b2_filtered_feature_bc_matrix.h5


title: PBMC HTO, BCG, TBT04301058 D0; TBT04301062 D2; TBT04301097 D7

description:
Library name: HTO1-GEX-b2-PBMC
S1-b2_filtered_feature_bc_matrix.h5


title: PBMC GEX, BCG, TBT04301058 D7; TBT04301062 D14; TBT04301097 D0

description:
Library name: GEX3-b2-PBMC
S3-b2_filtered_feature_bc_matrix.h5


title: YZ834


title: YZ823


title: CosMx SMI whole-brain spatial transcriptomics, slide 217Rand144_2L [217R (Healthy_FMT); 144_2L (Control)]

description: Sagittal brain section; samples 217R (Healthy_FMT); 144_2L (Control); CosMx single-cell spatial transcriptomics; cell segmentation and typing via AtoMx with InSituType


title: PBMC TCR, BCG D0, TBT04301051 D0; TBT04301059 D0; TBT04301072 D0

description: Library name: TCR1-b1-D0-PBMC


title: PBMC GEX, BCG D2, TBT04301051 D2; TBT04301059 D2; TBT04301072 D2

description:
Library name: GEX2-b1-D2-PBMC
S2-b1_filtered_feature_bc_matrix.h5


title: PBMC GEX, BCG D0,  TBT04301051 D0; TBT04301059 D0; TBT04301072 D0

description:
Library name: GEX1-b1-D0-PBMC
S1-b1_filtered_feature_bc_matrix.h5


title: RPF7_T4_sgROSA

city: New York

first: Chritine

last: Chio

state: NY

department: ICG

institute: Columbia Unievristy

description: Library name: RPF7

data_processing:
After sequencing, samples were processed with Eclipsebio's proprietary analysis pipeline (v1). Unique molecular identifiers (UMIs) were pruned from read sequences using UMI-tools (v1.1.1). Next 3' adapters were trimmed from reads using Cutadapt (v3.2). Reads were then mapped to a custom, curated database of repetitive elements and rRNA sequences. All non-repeat mapped reads were mapped to the genome hg38 using STAR (v2.7.7a), during the alignment multimapping reads were not retained. The exclusion of multimapping reads reduces false positive differential and pausing calls. The removal of multimapping reads may lead to underestimates of counts for genes with high rates of pseudogenization or duplication events. PCR duplicates were removed using UMI-tools (v1.1.1). Gene coverage was calculated using Eclipsebio's proprietary feature counting algorithm and ribosome occupancy was calculated by dividing coverage in the ribosome protected footprint (RPF) library by the RNA-Seq library. Differentially expressed and occupied genes were identified using DESeq2. For transcriptome analyses, genomic aligned reads were aligned to the transcriptome with mudskipper (v0.1.0). Transcriptome aligned reads were processed with riboWaltz and custom analysis programs developed by Eclipsebio to determine codon usage, stall sites, 5' UTR loading, and 3' read through. ORF detection was performed on genome alignments using ribotricer (v1.3.3).
Assembly: hg38
Supplementary files format and content: tsv , Files conatin Ribosome occupancy (RO), Ribosome footprints(RPF) and RNA seq differentially expressed genes
Library strategy: Ribo-Seq

source_name: Cell Line

growth_protocol: Monolayer KPC primary pancreatic cancer cells were generated from tumors derived from Trp53+/LSL-R172H, Kras+/LSL-G12D, Pdx1-Cre (KPC) mice (44). HEK293T cell line was from ATCC (Cat# CRL-3216, RRID:CVCL_0063). All cells were cultured in DMEM (Gibco Cat#11995073) supplemented with 10% fetal bovine serum (FBS) (Corning Cat# 35-010-cv) and 1% PS unless stated otherwise.  All cells were cultured at 37 °C with 5% CO2.

extract_protocol:
For each starting sample, cells were lysed and 1 µg of total RNA was isolated for RNA-Seq while 9 µg of total RNA was digested with RNase I to isolate ribosome protected RNA footprints (RPFs). Both sample types were taken through rRNA depletion and RNA-seq samples were heat fragmented. Both sample types then underwent adapter ligation.
Ligated RNA was reverse transcribed, libraries were generated via PCR, and then sequenced on a NextSeq 2000.

value: Cell Line

value: PDA


title: DHCA2

city: Fuzhou

first: xiaochai

last: lv

address: Xin-quan Road

institute: Fujian Medical University Union Hospital

description: Library name: Sample 6

data_processing:
Q30 was used to perform quality control. The adaptor sequences were trimmed and the adaptor-trimmed-reads (>= 15nt) were left by cutadapt software (v1.9.3).
The trimmed reads were aligned to the merged pre-miRNA databases (known pre-miRNA from miRBase plus the newly predicted pre-miRNAs) using Novoalign software (v3.02.12) with at most one mismatch.
The numbers of mature miRNA mapped tags were defined as the raw expression levels of that miRNA. The read counts were normalized by TPM (tag counts per million aligned miRNAs) approach.
Trimmed reads from all samples were pooled, and miRDeep2 software (v2.0.0.5) was used to predict novel miRNAs. Differentially expressed miRNA between two groups were filtered by Fold Change and P-value.
miRNA targets were performed by popular miRNA target prediction softwares, miRNA-targets networks were plotted by cytoscape software (v2.8.0), and the GO and KEGG pathway analysis were performed based on the top 10 differentially expressed miRNA target genes.
Assembly: rn6
Supplementary files format and content: miRNA_Expression.xlsx The table contains the number of miRNA raw counts identified and normalized counts.

organism: Rattus

source_name: Hippocampus

extract_protocol:
Total RNA was extracted using Trizol reagent
The small RNA libraries were constructed with GenSeq® Small RNA Library Prep Kit (GenSeq, Inc.) by following the manufacturer’s instructions. Briefly, 3’ and 5’ adaptors were successively ligated to RNA samples. Then, the adaptor-ligated RNA was reversely transcribed into cDNA, followed by PCR amplification. After amplification, the cDNA libraries were size-selected for miRNA fractions before sequencing and then sequenced in platform.

value: Hippocampus

value: Sprague-Dawley

tag: batch


title: RPF9_T4_sgEIF4G2

description: Library name: RPF9


title: YZ817


title: RPF4_T2_sgROSA

description: Library name: RPF4


title: YZ815


title: YZ818


title: NC4

description: Library name: Sample 4


title: RPF3_T1_sgEIF4G2

description: Library name: RPF3


title: DHCA1

description: Library name: Sample 5


title: YZ814


title: RPF1_T1_sgROSA

description: Library name: RPF1


title: RNASeq8_T4_sgEIF4G2

description: Library name: RNASeq8

data_processing:
After sequencing, samples were processed with Eclipsebio's proprietary analysis pipeline (v1). Unique molecular identifiers (UMIs) were pruned from read sequences using UMI-tools (v1.1.1). Next 3' adapters were trimmed from reads using Cutadapt (v3.2). Reads were then mapped to a custom, curated database of repetitive elements and rRNA sequences. All non-repeat mapped reads were mapped to the genome hg38 using STAR (v2.7.7a), during the alignment multimapping reads were not retained. The exclusion of multimapping reads reduces false positive differential and pausing calls. The removal of multimapping reads may lead to underestimates of counts for genes with high rates of pseudogenization or duplication events. PCR duplicates were removed using UMI-tools (v1.1.1). Gene coverage was calculated using Eclipsebio's proprietary feature counting algorithm and ribosome occupancy was calculated by dividing coverage in the ribosome protected footprint (RPF) library by the RNA-Seq library. Differentially expressed and occupied genes were identified using DESeq2. For transcriptome analyses, genomic aligned reads were aligned to the transcriptome with mudskipper (v0.1.0). Transcriptome aligned reads were processed with riboWaltz and custom analysis programs developed by Eclipsebio to determine codon usage, stall sites, 5' UTR loading, and 3' read through. ORF detection was performed on genome alignments using ribotricer (v1.3.3).
Assembly: hg38
Supplementary files format and content: tsv , Files conatin Ribosome occupancy (RO), Ribosome footprints(RPF) and RNA seq differentially expressed genes


title: DHCA4

description: Library name: Sample 8


title: NC3

description: Library name: Sample 3


title: PBMC HTO, BCG D14, TBT04301051 D14; TBT04301059 D14; TBT04301072 D14

description:
Library name: HTO4-GEX-b1-D14-PBMC
S4-b1_filtered_feature_bc_matrix.h5


title: YZ811


title: YZ830


title: macrophages from the peritoneal cavity, d12 after m204 MTO injection, rep 4

city: Cantoblanco

first: Juan

middle: Carlos

last: Oliveros

state: Madrid

address: Darwin 3

country: Spain

institute: CNB, CSIC

description: Library name: d12_R4

data_processing:
FastQ files were preprocessed first by inspecting raw short-reads for quality with FastQC (Babraham Bioinformatics) and then were quality-filtered and adapter-trimmed with Fastp version 0.23.2 (Chen et al., 2018) (--length_required 50).
Filtered reads were subsequently aligned against mouse genome (Mus_musculus.GRCm39, primary assembly) with RNA-STAR version 2.7.11a (Dobin et al., 2013) (--alignIntronMin 20 --alignIntronMax 100000). Alignment files were first indexed with Samtools version 1.10 (Li et al., 2009).
Aligned reads were then assigned to genes, using the annotation file Mus_musculus.GRCm39.109.gtf, with the function featureCounts of Subread version 2.0.6 (Liao et al., 2013) (-t exon -g gene_id -M --primary -s 2).
Differentially expressed genes (DEGs) were determined with DESEq2 version 1.40.2 (Love et al., 2014) using default parameters.
Assembly: GRCm39
Supplementary files format and content: Tab-delimited text file containing raw counts for each sample

source_name: peritoneal fluid

growth_protocol: Tim4+ resMØs were isolated by FACS from peritoneal cell suspensions from control mice, and from mice at day 12 after MTO injection, after immunofluorescent staining with PECy7-conjugated anti-CD11b (eBioscience), APC-conjugated anti-MHCII (eBioscience) and Brilliant Violet 421-conjugated 14 anti-Tim4 (BD Biosciences); propidium iodide (Sigma) was added for viability staining before sorting. Cells were sorted using a BD FACSAria™ II sorter (BD Biosciences) with a 85 μm nozzle, at the Flow Cytometry Facility of the Centro de Biología Molecular Severo Ochoa (CBMSO, Madrid). FACS-sorted resMØ preparations had a purity > 97%. Sorted cells were subsequently spun at 400g, resuspended in 100 μl of Lysis solution (Invitrogen) and stored at -80ºC until RNA extraction.

extract_protocol:
Total RNA was extracted, from 3 biological replicates per condition, using the RNAqueous-Micro Kit (Invitrogen), according to the manufacturer’s instructions. RNA samples were quantified and checked for integrity using an Agilent 2100 Bioanalyzer (Agilent Technologies).
30 ng of total RNA was used to generate barcoded RNA-seq libraries using the NEBNext Ultra II Directional RNA Library preparation kit (New England Biolabs) according to manufacturer’s instructions. First, poly A+ RNA was purified using poly-T oligo- attached magnetic beads followed by fragmentation and first and second cDNA strand synthesis. Next, cDNA ends were repaired and adenylated. The NEBNext adaptor was then ligated followed by second strand removal, uracile excision from the adaptor and PCR amplification. The size of the libraries was checked using the Agilent 2100 Bioanalyzer and the concentration was determined using the Qubit® fluorometer (ThermoFisher). Libraries were sequenced at a final concentration of 650 pM using a P2 flow cell in a NextSeq 2000 sequencer (Illumina) to generate 100pb single reads.

value: peritoneal fluid

value: macrophage


title: RNASeq4_T2_sgROSA

description: Library name: RNASeq4


title: RNASeq3_T1_sgEIF4G2

description: Library name: RNASeq3


title: KO2_Colon tissue

city: Shanghai

first: Ming

last: Feng

address: 280 S. Chongqing Road

department: Department of Biochemistry and Molecular Cell Biology

institute: Shanghai Jiao Tong University School of Medicine

description:
Library name: KO2_lib
KO2_FPKM

data_processing:
Sequence reads were trimmed for adaptor sequence/low-quality sequence using SOAPnuke.
Trimmed seaence reads were mapped to mm39 using Hisat2.
Read count extraction and normalization were performed using RSEM.
Assembly: mm39
Supplementary files format and content: tab-delimited text file includes FPKM values for each Samples

source_name: Colon

extract_protocol:
Total RNA was isolated using Trizol reagent.
The first step in the workflow involves purifying the poly-A containing mRNA molecules using poly-T oligo-attached magnetic beads; following purification, the mRNA is fragmented into small pieces using divalent cations under elevated temperature, after which the cleaved RNA fragments are copied into first strand cDNA using reverse transcriptase and random primers, followed by second strand cDNA synthesis using DNA Polymerase I and RNase H. These cDNA fragments then have the addition of a single 'A' base and subsequent ligation of the adapter, and the products are then purified and enriched with PCR amplification. We then quantified the PCR yield by Qubit and pooled samples together to make a single strand DNA circle (ssDNA circle), which gave the final library.

value: Colon

value: female

value: ChREBP knockout

value: AOM/DSS


title: macrophages from the peritoneal cavity, d12 after m204 MTO injection, rep 3

description: Library name: d12_R3


title: YZ800

value: peripheral blood

value: Without Drug therapy


title: RNASeq1_T1_sgROSA

description: Library name: RNASeq1


title: macrophages from the peritoneal cavity, d12 after m204 MTO injection, rep 1

description: Library name: d12_R1


title: KO3_Colon tissue

description:
Library name: KO3_lib
KO3_FPKM


title: NC2

description: Library name: Sample 2


title: macrophages from the peritoneal cavity, d12 after m204 MTO injection, rep 2

description: Library name: d12_R2


title: macrophages present in the steady state, rep 3

description: Library name: Ctrl_R3


title: RNASeq7_T4_sgROSA

description: Library name: RNASeq7


title: YZ801

value: Major depressive disorder (MDD)


title: YZ798


title: RPF6_T2_sgEIF4G2

description: Library name: RPF6


title: Infected mice lung, 15 days, bio rep5

city: Shenzhen

first: feng

last: chun

institute: SUSTech

description: Library name: Treatment 5

data_processing:
Quality control of the sequencing data was performed using FastQC, followed by adapter trimming and removal of low-quality reads with Trim Galore. Paired-end alignment was conducted using STAR v2.7.11b, and output files were converted with SAMtools. Read counting was performed using featureCounts, focusing on reads mapped to exonic regions and excluding multi-mapped reads.
Assembly: GCF_000149245.1
Supplementary files format and content: A comma-separated values file containing raw counts, with genes in rows and samples in columns.

source_name: Lung

extract_protocol:
RNA was harvested using GoldHi Plasmid Mini Kit.
RNA libraries for RNA-seq were prepared using standard Illumina protocols.

value: Lung

value: Infected


title: Infected mice lung, 15 days, bio rep4

description: Library name: Treatment 4


title: YZ80

value: Drug therapy


title: DHCA3

description: Library name: Sample 7


title: macrophages present in the steady state, rep 1

description: Library name: Ctrl_R1


title: Infected mice lung, 15 days, bio rep3

description: Library name: Treatment 3


title: YZ795


title: PBMC GEX, BCG D7, TBT04301051 D7; TBT04301059 D7; TBT04301072 D7

description:
Library name: GEX3-b1-D7-PBMC
S3-b1_filtered_feature_bc_matrix.h5

value: Blood


title: YZ794