title: AIM_exp2_G3_S2_GEX

description:
Library name: AIM_exp2_G3_S2_GEX
totalSeqC_feature_ref_AIM_exp2.csv


title: S56_J121_T1 [S56-2_S60_L001]

status: Public on Nov 07 2025

type: SRA

city: Canyon

first: Matthew

middle: Adam

last: Scott

state: TX

address: 3201 Russell Long Blvd

department: Large Animal Clinical Sciences

country: USA

institute: Texas A&M University

library_source: transcriptomic

data_processing:
Illumina RTA v3 software was used for basecalling.
Read quality was assessed in FastQC v0.11.9
Read trimming was performed with Trimmomatic v0.39 with parameters for a 4-base pair sliding window and removing read segments below a minimum base quality score of 20, read length of less than 28 bases, leading and trailing basepairs below a quality score of 3, and removal of all Illumina Universal adaptors.
Read mapping and indexing was performed with HISAT2 v2.1.1, using the bovine whole genome assembly ARS-UCD1.3; parameters -p 14 --dta -x GCF_002263795.2_ARS-UCD1.3
Read assembly and quantification was performed with StringTie v2.2.0 with parameters -p 14 -G GCF_002263795.2_ARS-UCD1.3_genomic.gff, followed by stringtie --merge -p 14 -G GCF_002263795.2_ARS-UCD1.3_genomic.gff -o mergefile.gtf, and stringtie -e -p 14 -G mergefile.gtf -o. A read count matrix was generated with prepDE3.py with parameters python prepDE3.py  -l 150 -i mergelist.txt. ComBat-Seq within sva was used to account for lane bias. Differential expression analysis was performed with edgeR v3.36.0 and glmmSeq v0.2.0.
Assembly: GCF_002263795.2
Supplementary files format and content: Comma-delimited text file of raw gene counts for each sample

molecule: total RNA

organism: Bos taurus

source_name: Whole blood

extract_protocol:
Total RNA was isolated via Tempus Spin RNA Isolation Kits (Applied Biosystems), per product instruction.
RNA libraries were prepared for sequencing using Illumina Stranded mRNA library preparation kits, using standard Illumina protocols.

treatment_protocol: All samples were collected into Tempus RNA Blood tubes (Applied Biosystems) and stored per product recommendation the same day of collection.

tag: tissue

value: Whole blood

tag: ID

tag: timepoint

tag: vaccinated

value: no

tag: marketing

value: direct

tag: treated for_brd

value: yes

tag: sequencing lane


title: S58_J123_T1 [S58_S61_L001]

value: auction


title: Ctr Brain 2BAct Diet P14 03

city: Chicago

first: Brian

last: Popko

state: IL

address: 7601 Morton Medical Research Building, 320 East Superior Street

department: Neurology

institute: Northwestern Feinberg School of Medicine

data_processing:
Adapters were trimmed from reads using cutadapt version 1.13
Trimmed reads were aligned using STAR version 020201
Gene counting was performed using htseq-count version 0.6.1p1
Differential expression was performed using DESeq2 version 1.14.1
Assembly: mm10
Supplementary files format and content: tab-delimited text file with raw counts for each sample

organism: Mus musculus

source_name: Brain

extract_protocol:
The Aurum™ Total RNA Fatty and Fibrous Tissue Module kit (from Bio Rad #7326870) was used for RNA extractions.
Directional mRNA libraries were prepared using Illumina UDI Kits per the manufacturer’s instructions

value: Brain

tag: genotype

value: WT

tag: treatment

value: P14, 2BAct Diet


title: MDMs, HIV+Moderate, IL1B_2

city: La Jolla

first: Jerel

last: Fields

state: CA

address: 5320 La Jolla Hermosa Ave

department: Psychiatry

institute: University of California, San Diego

description:
Library name: HIV+Moderate (IL1B)2
D10-I2_643027385

data_processing:
Using the Illumina NovaSeq 6000 platform, libraries were sequenced on a NovaSeq S4 flow cell, with initial quality control checks, including per-base sequence quality, GC content, and sequence duplication levels conducted using FastQC (v0.11.9).
Clean reads were aligned to the hg38 human reference genome using STAR aligner (v2.7.9a) with default parameters on the Illumina BaseSpace Sequence Hub platform.
Differential expression analysis was conducted using DESeq2 (v1.30.0) in R (v4.0.5), with genes displaying a false discovery rate (FDR) < 0.05 considered significantly differentially expressed.
Assembly: Human (hg38)
Supplementary files format and content: Comma Separated Spreadsheet (.csv) files include raw gene transcript counts

organism: Homo sapiens

source_name: monocyte-derived macrophages

growth_protocol: Isolated monocytes were cultured in IMDM supplemented with 10% human serum plus 1% penicillin/streptomycin and maintained in a humidified incubator at 5% CO2 and 37°C. Media was renewed every 48-72 hours over the 7-day differentiation period.

extract_protocol:
RNA collection was performed using RNeasy Plus Mini Kits from Qiagen. Following NanoDrop quantification, a total of 80 ng of mRNA per sample was used for library construction.
Illumina Stranded mRNA Prep, according to manufacturer's instructions.

treatment_protocol: MDMs were treated with media containing IL1B (I; 20 ng/mL), CBD (C; 30 μM), or both C+I for 6 hours.

tag: disease state

value: HIV Positive

tag: condition

value: Moderate

tag: cell type

value: monocyte-derived macrophages

tag: donor

value: Donor 10 (D10)


title: AIM_exp2_G3_S1_GEX

first: Ester

last: Marina-Zarate

state: California

address: 9420 Athena Cir

institute: La Jolla Institute for Immunology

description:
Library name: AIM_exp2_G3_S1_GEX
totalSeqC_feature_ref_AIM_exp2.csv

library_source: transcriptomic single cell

data_processing:
The demultiplexing, barcoded processing, and gene counting were made using the Cell Ranger software v7.1.0
Assembly: Mmul10
Supplementary files format and content: Tab-separated values files and matrix files

organism: Macaca mulatta

source_name: Blood

extract_protocol:
Frozen PBMC and LN FNA samples were thawed in R10 media (RPMI + 10% FBS, 1x penicillin/streptomycin, 1x GlutaMAX), and counted. Cells were washed with FACS buffer (2% FBS in PBS) and stained first with fluorescent antigen probes. MD39 (MD39 WT) and MD39 epitope knock-out (MD39 KO) probes were prepared by mixing fluorophore-conjugated streptavidin (SA) with biotinylated antigen probes added in small increments every 15 minutes for a total of 1 hour in PBS at room temperature. MD39 KO probe was added for 15 min at 4 °C and then incubated with MD39 WT probes for an additional 15 min. Without washing, cells were stained with surface antibodies for an additional 30 min at 4 °C. For sorting, anti-human Total-Seq-C hashtag antibodies (Biolegend) were individually added to each sample at a concentration of 1 µg/5 million cells at the time of addition of the master mix. Cells were washed twice with FACS buffer. Cells were sorted on a FACSymphony S6 (BD Biosciences) or a FACSAria II (BD Biosciences).
Sorted AIM+ CD4 T cells from PBMCs and sorted LN FNA CD4 T cell populations were loaded onto a Chromium Next GEM Single Cell 5' v2 chip and processed using the Chromium Controller, following the manufacturer's protocol (10X Genomics).Indexed V(D)J, Feature Barcode, and Gene Expression (GEX) libraries were prepared using the Feature Barcoding Kit (10X Genomics) and sequenced on a NovaSeq 6000 (Illumina). Custom rhesus macaque primers for TCRβ and TCRα constant regions were used. Forward and reverse primers were used at a final concentration of 1 µM.

treatment_protocol: HIV Env trimer MD39 with adjuvant SMNP immunizations

value: Blood


title: MDMs, HIV+Moderate, IL1B_1

description:
Library name: HIV+Moderate (IL1B)1
D10-I1_643019398


title: Jimpy Brain 2BAct Diet P14 01

value: Jimpy


title: S55_J117_T1 [S55-2_S58_L001]


title: S54_J115_T1 [S54_S56_L001]


title: MDMs, HIV+Moderate, Vehicle_2

description:
Library name: HIV+Moderate (Control)2
D10-V2_643019408

value: Vehicle


title: MDMs, HIV+Moderate, Vehicle_1

description:
Library name: HIV+Moderate (Control)1
D10-V1_643031390


title: AIM_exp2_G2_S1_GEX

description:
Library name: AIM_exp2_G2_S1_GEX
totalSeqC_feature_ref_AIM_exp2.csv


title: AIM_exp2_G1_S2_GEX

description:
Library name: AIM_exp2_G1_S2_GEX
totalSeqC_feature_ref_AIM_exp2.csv


title: S52_J111_T1 [S52_S54_L001]


title: Ctr Brain Ctr Diet P14 01

value: P14, Control Diet


title: AIM_exp1_G4_GEX

description:
Library name: AIM_exp1_G4_GEX
totalSeqC_feature_ref_AIM_exp1.csv


title: MDMs, HIV+Naïve, CBD_3

description:
Library name: HIV+Naïve (CBD)3
D18-C3_643033393

value: Naïve

value: CBD

value: Donor 18 (D18)


title: S51_J110_T1 [S51_S53_L001]

value: Whole blood

value: no


title: S63_J014_T2 [S63_S66_L001]

value: yes

value: direct


title: AIM_exp1_G2_GEX

description:
Library name: AIM_exp1_G2_GEX
totalSeqC_feature_ref_AIM_exp1.csv


title: Ctr Brain 2BAct Diet P14 02

value: Brain

value: WT


title: AIM_exp2_G2_S2_GEX

description:
Library name: AIM_exp2_G2_S2_GEX
totalSeqC_feature_ref_AIM_exp2.csv


title: S53_J112_T1 [S53_S55_L001]


title: Wk59_TFH_S6_GEX

description:
Library name: Wk59_TFH_S6_GEX
totalSeqC_feature_ref_wk59.csv

source_name: Lymph node

value: Lymph node


title: MDMs, HIV+Moderate, Vehicle_3

description:
Library name: HIV+Moderate (Control)3
D10-V3_643027391

value: HIV Positive

value: Moderate


title: Ctr Brain Ctr Diet P14 03


title: Wk59_TFH_Fusion_GEX

description:
Library name: Wk59_TFH_Fusion_GEX
totalSeqC_feature_ref_wk59.csv


title: MDMs, HIV+Naïve, CBD_2

description:
Library name: HIV+Naïve (CBD)2
D18-C2_643029390

value: monocyte-derived macrophages


title: Ctr Brain Ctr Diet P14 02


title: AIM_exp2_G1_S1_GEX

description:
Library name: AIM_exp2_G1_S1_GEX
totalSeqC_feature_ref_AIM_exp2.csv

value: Blood


title: MDMs, HIV+Naïve, CBD+IL1B_3

description:
Library name: HIV+Naïve (C+I)3
D18-CPLUSI3_643029403


title: S50_J108_T1 [S50_S52_L001]


title: Jimpy Brain 2BAct Diet P7 04

value: Jimpy

value: P7, 2BAct Diet


title: MDMs, HIV+Naïve, CBD+IL1B_2

description:
Library name: HIV+Naïve (C+I)2
D18-CPLUSI2_643019416


title: MDMs, HIV+Naïve, CBD+IL1B_1

description:
Library name: HIV+Naïve (C+I)1
D18-CPLUSI1_643033396


title: Jimpy Brain Ctr Diet P7 03

value: P7, Control Diet


title: Wk55_TFH_S6_GEX

description:
Library name: Wk55_TFH_S6_GEX
totalSeqC_feature_ref_wk55.csv


title: Jimpy Brain 2BAct Diet P7 03


title: AIM_exp1_G1G3_GEX

description:
Library name: AIM_exp1_G1G3_GEX
totalSeqC_feature_ref_AIM_exp1.csv


title: S49_J107_T1 [S49_S51_L001]

value: auction


title: Jimpy Brain Ctr Diet P7 02


title: MDMs, HIV+Naïve, IL1B_2

description:
Library name: HIV+Naïve (IL1B)2
D18-I2_643019423

value: Naïve


title: S44_J091_T1 [S44_S46_L001]


title: Wk55_TFH_Fusion_GEX

description:
Library name: Wk55_TFH_Fusion_GEX
totalSeqC_feature_ref_wk55.csv


title: Ctr Brain 2BAct Diet P14 01

value: P14, 2BAct Diet


title: Jimpy Brain 2BAct Diet P7 02


title: MDMs, HIV+Naïve, IL1B_1

description:
Library name: HIV+Naïve (IL1B)1
D18-I1_643030403

value: Donor 18 (D18)


title: Jimpy Brain Ctr Diet P7 01


title: S43_J089_T1 [S43_S45_L001]

value: Whole blood

value: no


title: Ctr Brain 2BAct Diet P7 03


title: Wk55_NonTFH_S6_GEX

description:
Library name: Wk55_NonTFH_S6_GEX
totalSeqC_feature_ref_wk55.csv


title: S48_J104_T1 [S48_S50_L001]

value: yes

value: direct


title: S47_J103_T1 [S47_S49_L001]


title: Jimpy Brain 2BAct Diet P7 01

value: Brain


title: MDMs, HIV+Naïve, CBD_1

description:
Library name: HIV+Naïve (CBD)1
D18-C1_643019411

value: CBD


title: Jimpy Brain Ctr Diet P7 04


title: S42_J088_T1 [S42_S44_L001]


title: S46_J097_T1 [S46_S48_L001]


title: MDMs, HIV+Naïve, IL1B_3

description:
Library name: HIV+Naïve (IL1B)3
D18-I3_643029409

value: HIV Positive


title: MDMs, HIV+Naïve, Vehicle_1

description:
Library name: HIV+Naïve (Control)1
D18-V1_643029412

value: Vehicle


title: Ctr Brain 2BAct Diet P7 01

value: WT


title: Wk48_TFH_Fusion_GEX

description:
Library name: Wk48_TFH_Fusion_GEX
totalSeqC_feature_ref_wk48.csv

value: Lymph node


title: Ctr Brain Ctr Diet P7 04


title: S45_J092_T1 [S45_S47_L001]


title: S39_J085_T1 [S39_S41_L001]


title: MDMs, HIV+Naïve, Vehicle_3

description:
Library name: HIV+Naïve (Control)3
D18-V3_643035395

value: monocyte-derived macrophages


title: Wk48_NonTFH_S6_GEX

description:
Library name: Wk48_NonTFH_S6_GEX
totalSeqC_feature_ref_wk48.csv


title: Wk59_NonTFH_Fusion_GEX

description:
Library name: Wk59_NonTFH_Fusion_GEX
totalSeqC_feature_ref_wk59.csv


title: Wk48_NonTFH_Fusion_GEX

description:
Library name: Wk48_NonTFH_Fusion_GEX
totalSeqC_feature_ref_wk48.csv


title: Ctr Brain 2BAct Diet P7 02

value: P7, 2BAct Diet


title: MDMs, HIV+Naïve, Vehicle_2

description:
Library name: HIV+Naïve (Control)2
D18-V2_643019425


title: Wk30_TFH_Fusion_GEX

description:
Library name: Wk30_TFH_Fusion_GEX
totalSeqC_feature_ref_wk30.csv


title: S37_J082_T1 [S37_S39_L001]


title: Ctr Brain Ctr Diet P7 01

value: P7, Control Diet


title: Wk55_NonTFH_Fusion_GEX

description:
Library name: Wk55_NonTFH_Fusion_GEX
totalSeqC_feature_ref_wk55.csv


title: MDMs, HIV-Naïve, CBD_2

description:
Library name: HIV-Naïve (CBD)2
D8-C2_643003363

value: HIV Negative

value: Donor 8 (D8)


title: Wk48_TFH_S6_GEX

description:
Library name: Wk48_TFH_S6_GEX
totalSeqC_feature_ref_wk48.csv


title: er mutant, CLE41 overexpressor, rep4

city: Durham

first: Wenbin

last: Wei

address: Stockton Road

department: Biosciences

country: United Kingdom

institute: Durham University

data_processing:
RNA-seq data were aligned to the TAIR10 (EnsemblePlants, release 58) genome sequence with corresponding gtf file using STAR (v 2.7.11a) to obtain read count per gene.
Assembly: TAIR10
Supplementary files format and content: tab-delimited text files include raw count per gene, one file per sample

organism: Arabidopsis thaliana

source_name: 5-week-old hypocotyls

growth_protocol: Arabidopsis thaliana (Columbia ecotype) plants were grown at 22 °C on a 16 h/8 h light/dark cycle. Seeds were surface-sterilized with absolute ethyl alcohol for 5 min and 75% ethanol for 15 min, then washed three-four times with sterilized distilled water under aseptic conditions. Surface-sterilized seeds were germinated on half-strength Murashige and Skoog (MS) medium in an incubator. After seven days, the seedlings were transferred into soil.

extract_protocol:
RNA was extracted from 5-week-old Arabidopsis hypocotyls using ReliaPrep™ RNA Miniprep
Libraries were prepared by Novogene. Messenger RNA was purified from total RNA using poly-T oligo-attached magnetic beads. After fragmentation, the first strand cDNA was synthesized using random hexamer primers followed by the second strand cDNA synthesis. The library was ready after end repair, A-tailing, adapter ligation, size selection, amplification, and purification.

value: 5-week-old hypocotyls

value: er mutant, CLE41 overexpressor


title: S41_J087_T1 [S41_S43_L001]

value: Whole blood

value: auction


title: S40_J086_T1 [S40_S42_L001]

value: no

value: yes


title: MDMs, HIV-Naïve, CBD+IL1B_2

description:
Library name: HIV-Naïve (C+I)2
D8-CPLUSI2_643010368

value: Naïve


title: er mutant, CLE41 overexpressor, rep3


title: Wk30_NonTFH_S6_GEX

description:
Library name: Wk30_NonTFH_S6_GEX
totalSeqC_feature_ref_wk30.csv


title: S34_J076_T1 [S34_S36_L001]

value: direct


title: S38_J084_T1 [S38_S40_L001]


title: MDMs, HIV-Naïve, IL1B_3

description:
Library name: HIV-Naïve (IL1B)3
D8-I3_643001369


title: er mutant, CLE41 overexpressor, rep2


title: S33_J075_T1 [S33_S35_L001]


title: Wk30_NonTFH_Fusion_GEX

description:
Library name: Wk30_NonTFH_Fusion_GEX
totalSeqC_feature_ref_wk30.csv


title: Ctr Brain Ctr Diet P7 03

value: Brain


title: MDMs, HIV-Naïve, CBD+IL1B_1

description:
Library name: HIV-Naïve (C+I)1
D8-CPLUSI1_642993358


title: MDMs, HIV-Naïve, IL1B_2

description:
Library name: HIV-Naïve (IL1B)2
D8-I2_643001368


title: Ctr Brain Ctr Diet P7 02


title: Wk27_TFH_S6_GEX

description:
Library name: Wk27_TFH_S6_GEX
totalSeqC_feature_ref_wk27.csv


title: MDMs, HIV-Naïve, IL1B_1

description:
Library name: HIV-Naïve (IL1B)1
D8-I1_642995357


title: MDMs, HIV-Naïve, CBD_3

description:
Library name: HIV-Naïve (CBD)3
D8-C3_642997359

value: CBD


title: S36_J081_T1 [S36_S38_L001]


title: Wk30_TFH_2_S6_GEX

description:
Library name: Wk30_TFH_2_S6_GEX
totalSeqC_feature_ref_wk30.csv


title: MDMs, HIV-Naïve, Vehicle_3

description:
Library name: HIV-Naïve (Control)3
D8-V3_643036397

value: Vehicle


title: Wk30_TFH_1_S6_GEX

description:
Library name: Wk30_TFH_1_S6_GEX
totalSeqC_feature_ref_wk30.csv

value: Lymph node


title: MDMs, HIV-Naïve, CBD+IL1B_3

description:
Library name: HIV-Naïve (C+I)3
D8-CPLUSI3_643001367

value: monocyte-derived macrophages


title: MDMs, HIV-Naïve, Vehicle_2

description:
Library name: HIV-Naïve (Control)2
D8-V2_643036396


title: S35_J078_T1 [S35_S37_L001]


title: MDMs, HIV-Naïve, CBD_1

description:
Library name: HIV-Naïve (CBD)1
D8-C1_642993355


title: Wk27_NonTFH_S6_GEX

description:
Library name: Wk27_NonTFH_S6_GEX
totalSeqC_feature_ref_wk27.csv


title: er mutant, rep4

value: er mutant


title: Wk27_NonTFH_Fusion_GEX

description:
Library name: Wk27_NonTFH_Fusion_GEX
totalSeqC_feature_ref_wk27.csv


title: S30_J062_T1 [S30_S32_L001]


title: S32_J071_T1 [S32_S34_L001]


title: S28_J059_T1 [S28_S30_L001]


title: Wk27_TFH_Fusion_GEX

description:
Library name: Wk27_TFH_Fusion_GEX
totalSeqC_feature_ref_wk27.csv


title: CLE41 overexpressor, rep3

value: CLE41 overexressor


title: CLE41 overexpressor, rep2


title: Wk24_TFH_Fusion_GEX

description:
Library name: Wk24_TFH_Fusion_GEX
totalSeqC_feature_ref_wk24.csv


title: er mutant, rep3


title: S31_J068_T1 [S31_S33_L001]


title: MCF7, LHPP KO, biol rep 3

first: Jeffrey

last: Reina

address: 10010 N Torrey Pines Rd

institute: Salk Institute for Biological Studies

data_processing:
Performed by Novogen Co. (Sacramento, CA, USA)
Remove reads with adapter contamination. Remove reads when uncertain nucleotides constitute more than 10 percent of either read (N > 10%). Remove reads when low quality nucleotides (Base Quality less than 5) constitute more than 50 percent of the read (Yan et al, 2011).
Perform alignments with HISAT2 to the reference (Mortazavi et al., 2008).
Assembly: hg38
Supplementary files format and content: Microsoft Excel file includes FPKM values for each sample, one file for MDA-MB-231 cells and one for MCF7 cells

growth_protocol: Cells were cultured in DMEM supplemented with 10% fetal bovine serum and 1% penicillin/streptomycin at 37°C with 5% CO2.

extract_protocol:
Cells grown to 70-90% confluence in 10 cm plates were washed twice with cold PBS, then collected using 600 μL of TRIzol reagent (Invitrogen, 15596018). Total RNA was extracted using the Direct-zol RNA miniprep kit (Zymo Research, R2050).
Messenger RNA was purified from total RNA using poly-T oligo-attached magnetic beads. After fragmentation, the first strand cDNA was synthesized using random hexamer primers, followed by the second strand cDNA synthesis using either dUTP for directional library or dTTP for non-directional library. Performed by Novogene Co. (Sacramento, CA, USA)

tag: cell line

value: breast cancer cells

value: LHPP KO


title: S27_J055_T1 [S27_S29_L001]


title: CLE41 overexpressor, rep1

value: 5-week-old hypocotyls


title: MCF7, LHPP KO, biol rep 2


title: MCF7, LHPP KO, biol rep 1


title: Wk24_TFH_1_S6_GEX

description:
Library name: Wk24_TFH_1_S6_GEX
totalSeqC_feature_ref_wk24.csv


title: MDMs, HIV-Naïve, Vehicle_1

description:
Library name: HIV-Naïve (Control)1
D8-V1_643036395

value: HIV Negative

value: Donor 8 (D8)


title: S29_J061_T1 [S29_S31_L001]

value: Whole blood

value: auction


title: er mutant, rep2


title: Wk24_TFH_2_Fusion_GEX

description:
Library name: Wk24_TFH_2_Fusion_GEX
totalSeqC_feature_ref_wk24.csv


title: Wild type, rep2

value: Wild type


title: Wk24_NonTFH_S6_GEX

description:
Library name: Wk24_NonTFH_S6_GEX
totalSeqC_feature_ref_wk24.csv


title: S25_J051_T1 [S25_S27_L001]

value: no


title: Wild type, rep1


title: MCF7, WT, biol rep 3

value: WT


title: Zebrafish head, wounded, scRNA

city: Melbourne

first: Michelle

last: Meier

address: 305 Grattan Street

country: Australia

institute: Peter MacCallum Cancer Centre

description:
10X Chromium (Single cell 3' V3)
D10026_Level_01_SeuratObject.RDS.gz

data_processing:
Sequencing quality was assessed using FastQC v0.11.6 and MultiQC v1.7 viewer for aggregated reports. Cell Ranger count (and aggr where appropriate) was used to generate count files. Doublets were identified from the filtered aggregated count files using Scrublet  in Python version 3.6. Sequence reads corresponding to ribosomal and global genes were removed, cells filtered according to library size and mitochondrial content, normalised, followed by UMAP dimension reduction, clustering (louvain) and cell-cycle analysis using Seurat for R statistical software. The quality of the dataset was evaluated before and after normalisation using both custom plots and built-in functions in Seurat and scater.  Cluster solutions were evaluated, and most appropriate resolution selected using ClusTree, and cluster identity was defined using key markers of phenotype
Assembly: Zebrafish: GRCz11 (Ensembl 102), Mouse: mm10-3.0.0
Supplementary files format and content: cellranger output filtered_feature_bc_matrix: barcode, feature and count matrices
Supplementary files format and content: Seurat object of all cells after quality control filtering in RDS format

organism: Danio rerio

source_name: Head

extract_protocol:
Library preparation and sequencing was performed at the Molecular Genomics Core Facility (Peter MacCallum Cancer Centre).  Single cell suspensions from FACS were spun down and a cell count was performed to determine post-sort viability and cell concentration. Single cell suspension was partitioned and barcoded using the 10X Genomics Chromium iX Controller (10X Genomics) and the Single Cell 3' Library and Gel Bead Kit (Zebrafish dataset: V3.1; 10X Genomics;  PN-1000121, Mouse dataset V2).  The cells were loaded onto the Chromium Single Cell Chip G (10X Genomics; PN-1000120) to target 10,000 cells
Gel bead in Emulsion (GEM) generation and barcoding, cDNA amplification, and library construction was performed according to the 10X Genomics Chromium User Guide. The resulting single cell transcriptome libraries contained unique sample indices for each sample. The libraries were quantified on the Agilent TapeStation 4200 using High Sensitivity D1000 ScreenTape and reagents (Agilent, 5067-5585, 5067-5584). Single cell transcriptome libraries were pooled in equimolar ratios before being sequenced (Zebrafish dataset: Illumina NovaSeq 6000, Mouse dataset: Illumina NextSeq 500) using S4 300-cycle chemistry. Read1 supplies the cell barcode and UMI, i7 and i5 the sample indexes, and Read2 the 3’ sequence of the transcript. Sequencing read lengths were trimmed to 28bp (Read1), 10bp (i7 index), 10bp (i5 index), 91bp (Read2), ensuring compatibility with the 10X Genomics analysis software, Cell Ranger. After sequencing, fastq files were generated using bcl2fastq2 (v.2.20.0.422)

value: Head

tag: age

tag: transgenic

tag: facs

value: kdrl (mCherry) positive and pdgfrb (GFP) negative

tag: internal id

tag: cellranger


title: S24_J050_T1 [S24_S26_L001]

tag: tissue

tag: ID

tag: timepoint

value: direct

value: yes


title: MCF7, WT, biol rep 2


title: Wk24_NonTFH_Fusion_GEX

description:
Library name: Wk24_NonTFH_Fusion_GEX
totalSeqC_feature_ref_wk24.csv

value: Lymph node


title: S23_J047_T1 [S23_S25_L001]

tag: vaccinated

tag: marketing

tag: treated for_brd


title: MDA-MB-231, LHPP KO, biol rep 3

tag: genotype


title: S22_J045_T1 [S22_S24_L001]

tag: sequencing lane


title: Wk24_leftLN_TFH_S6_GEX

description:
Library name: Wk24_leftLN_TFH_S6_GEX
totalSeqC_feature_ref_wk24leftLN.csv


title: MCF7, WT, biol rep 1


title: Wild type, rep3


title: Wk24_leftLN_NonTFH_S6_GEX

description:
Library name: Wk24_leftLN_NonTFH_S6_GEX
totalSeqC_feature_ref_wk24leftLN.csv


title: LP46, CD4+CCR5+

city: Covington

first: Joseph

last: Mudd

state: LA

address: 18703 Three Rivers Road

department: Division of Immunology

institute: TNPRC

description: Library name: LP46-CCR5

data_processing:
TCR sequencing data were processed using Cogent NGS Immune Profiler Software (version 2.0) with standard parameters and the human genome as the alignment reference, in accordance with the TCRv2 protocol.
Assembly: hg38
Supplementary files format and content: Tab-Separated Values (.tsv) TRUST4 files
Library strategy: TCR-Seq

source_name: Blood, PBMC

extract_protocol:
Collected samples were homogenized with a 20-gauge needle and syringe. RNA isolation on homogenized samples was performed using the RNeasy micro kit (Qiagen; catalog 74004), with the addition of 350 µl RLT and 10% 2-mercaptoethanol (Millipore Sigma; catalog M6250), following manufacturer’s instructions.
TCR library generation was performed using SMARTer Human TCR a/b profiling kit v2 (TCRv2; TakaraBio; catalog 634478).

value: Blood, PBMC

value: Primary T cells


title: Wk24_leftLN_TFH_Fusion_GEX

description:
Library name: Wk24_leftLN_TFH_Fusion_GEX
totalSeqC_feature_ref_wk24leftLN.csv


title: Wk24_leftLN_NonTFH_Fusion_GEX

description:
Library name: Wk24_leftLN_NonTFH_Fusion_GEX
totalSeqC_feature_ref_wk24leftLN.csv


title: MDA-MB-231, LHPP KO, biol rep 2

value: breast cancer cells


title: S21_J043_T1 [S21_S23_L001]


title: Zebrafish head, unwounded, scRNA


title: S20_J041_T1 [S20_S22_L001]


title: KC43, CD4+CCR5+

description: Library name: KC43-CCR5


title: S19_J037_T1 [S19_S21_L001]


title: Wk16_TFH_S6_GEX

description:
Library name: Wk16_TFH_S6_GEX
totalSeqC_feature_ref_wk16.csv


title: MDA-MB-231, WT, biol rep 3


title: Wk16_TFH_Fusion_GEX

description:
Library name: Wk16_TFH_Fusion_GEX
totalSeqC_feature_ref_wk16.csv


title: MDA-MB-231, LHPP KO, biol rep 1

value: LHPP KO


title: S18_J036_T1 [S18_S20_L001]


title: S17_J034_T1 [S17_S19_L001]


title: MDA-MB-231, WT, biol rep 2


title: MDA-MB-231, WT, biol rep 1


title: EM83, CD4+CCR5+

description: Library name: EM83-CCR5


title: Wk16_NonTFH_S6_GEX

description:
Library name: Wk16_NonTFH_S6_GEX
totalSeqC_feature_ref_wk16.csv


title: LP46, CD4+CMV-specific

description: Library name: LP46-AIM-CMV


title: LP17, CD4+CCR5+

description: Library name: LP17-CCR5


title: Wk16_NonTFH_Fusion_GEX

description:
Library name: Wk16_NonTFH_Fusion_GEX
totalSeqC_feature_ref_wk16.csv


title: LP17, CD4+CMV-specific

description: Library name: LP17-AIM-CMV


title: KC43, CD4+CMV-specific

description: Library name: KC43-AIM-CMV


title: Wk16_Intermediate_S6_GEX

description:
Library name: Wk16_Intermediate_S6_GEX
totalSeqC_feature_ref_wk16.csv


title: R255X-MUT_hCO_bulk RNA-seq_3

first: Alysson

middle: R.

last: Muotri

address: 2880 Torrey Pines Scenic Drive - Room 3005

institute: UCSD

description:
Library name: Sample 6
Column name in bulk_RNA-seq Featurecounts.xlsx: R255X-MUT_hCO_3

data_processing:
Raw sequencing reads were subjected to quality control and preprocessing using standard pipelines. Initial quality assessment of the raw FASTQ files was performed using FastQC v0.11.9 to evaluate read quality scores, sequence length distribution, and the presence of adapter sequences. Adaptor trimming was carried out using Cutadapt v3.4, specifically targeting Nextera transposase adapter sequences as recommended by Illumina. Post-trimming quality checks were repeated with FastQC to ensure adapter removal and assess read length distribution after trimming. Trimmed reads were aligned to the human reference genome GRCh38.p14 using Bowtie2 v2.5.1. SAM files generated during alignment were converted to BAM format using SAMtools v1.17. Quantification of gene-level expression was performed using “featureCounts” from the Subread package v2.1.0. to assign reads to genomic features based on the GRCh38.p14 GTF annotation file. rRNA genes were excluded, and low-expressed genes (fewer than 10 counts in over 50% of samples) were filtered out. The final count matrix was used for downstream analyses in R v4.4.2.
Assembly: GRCh38
Supplementary files format and content: bulk_RNA-seq Featurecounts.xlsx includes raw counts for each sample
Supplementary files format and content: bulk_RNA-seq_metadata.xlsx includes metadata information for each sample

source_name: brain organoid

growth_protocol: Human cerebral organoids

extract_protocol:
Total RNA was extracted from pooled organoids using TRIzol Reagent (Invitrogen, 15596026-100ML), and up to 5 µg of RNA was subsequently treated with DNaseI (Roche, 04716728001), according to the manufacturer’s instructions. RNA was stored at - 80 ºC until further use.
Bulk RNA-seq libraries were prepared using the Illumina Stranded Total RNA kit and pair-end sequenced on a single lane of a NovaSeq X Plus (Illumina) flow cell with a 10% PhiX target.

value: brain organoid

value: Neural progenitors and neurons

value: Patient 2042

value: week 6 of differentiation


title: S26_J052_T1 [S26_S28_L001]

value: Whole blood

value: auction


title: R255X-MUT_hCO_bulk RNA-seq_4

description:
Library name: Sample 7
Column name in bulk_RNA-seq Featurecounts.xlsx: R255X-MUT_hCO_4


title: S15_J031_T1 [S15-2_S16_L001]

value: no


title: R255X-MUT_hCO_bulk RNA-seq_2

description:
Library name: Sample 5
Column name in bulk_RNA-seq Featurecounts.xlsx: R255X-MUT_hCO_2


title: JJ72, CD4+CMV-specific

description: Library name: JJ72-AIM-CMV


title: JJ72, CD4+CCR5+

description: Library name: JJ72-CCR5


title: Wk10_TFH_S6_GEX

description:
Library name: Wk10_TFH_S6_GEX
totalSeqC_feature_ref_wk10.csv


title: R255X-MUT_hCO_bulk RNA-seq_1

description:
Library name: Sample 4
Column name in bulk_RNA-seq Featurecounts.xlsx: R255X-MUT_hCO_1


title: S13_J029_T1 [S13_S13_L001]


title: EM83, CD4+CMV-specific

description: Library name: EM83-AIM-CMV


title: S12_J028_T1 [S12_S12_L001]


title: Wk10_TFH_Fusion_GEX

description:
Library name: Wk10_TFH_Fusion_GEX
totalSeqC_feature_ref_wk10.csv


title: R255X-WT_hCO_bulk RNA-seq_3

description:
Library name: Sample 3
Column name in bulk_RNA-seq Featurecounts.xlsx: R255X-WT_hCO_3


title: S11_J026_T1 [S11_S11_L001]


title: Wk10_NonTFH_S6_GEX

description:
Library name: Wk10_NonTFH_S6_GEX
totalSeqC_feature_ref_wk10.csv


title: Wk10_NonTFH_Fusion_GEX

description:
Library name: Wk10_NonTFH_Fusion_GEX
totalSeqC_feature_ref_wk10.csv


title: R255X-WT_hCO_bulk RNA-seq_2

description:
Library name: Sample 2
Column name in bulk_RNA-seq Featurecounts.xlsx: R255X-WT_hCO_2


title: S16_J033_T1 [S16-2_S18_L001]


title: S10_J025_T1 [S10_S10_L001]


title: S9_J024_T1 [S9_S9_L001]


title: 55 days of embryonic period_1

city: Hohhot

first: Hai

last: erhan

state: Inner Mongolia

address: Inner Mongolia Key Laboratory of Sheep & Goat Genetics Breeding and Reproduction

country: China

institute: Inner Mongolia Agricultural University

data_processing:
Subsequently, unique sequences with length in 18~25 nucleotide were mapped to specific species precursors in miRBase 22.0 by BLAST search to identify known miRNAs and novel 3p- and 5p- derived miRNAs.
Assembly: CVASU_BBG_1.0
Supplementary files format and content: excel,expression profiles
Supplementary files format and content: excel,expression profiles

organism: Capra hircus

source_name: lateral skin tissue

extract_protocol:
Total RNA was extracted using Trizol reagent (Invitrogen, CA, USA) following the manufacturer's procedure
small RNA sequencing of cashmere goat skin epithelial cells

value: lateral skin tissue

value: epithelial cells

value: somatic cells


title: S14_J030_T1 [S14_S14_L001]

value: direct


title: Wk16_Intermediate_Fusion_GEX

description:
Library name: Wk16_Intermediate_Fusion_GEX
totalSeqC_feature_ref_wk16.csv


title: R255X-WT_CO3, R255X-MUT_CO3, R255X-WT_TA3, R255X-MUT_TA3

description:
Library name: Pool 4
10x Genomics

data_processing:
ScRNA-seq reads were processed with Cell Ranger multi v8.0.1 using the prebuilt 10X GRCh38 reference refdata-gex-GRCh38-2024-A and including introns. Further processing, such as demultiplexing, dimensionality reduction, clustering, and visualization, was performed in R v4.4.2 with Seurat v5.0.0. Demultiplexed datasets were filtered to retain high-quality cells. Only cells containing between 800 and 10,000 sequenced genes, a UMI count below 40,000, and a proportion of mitochondrial and ribosomal genes less than 15% and 30%, respectively, were retained. The Gruffi algorithm (v.1.5.6) (Vértesy et al., 2022) was used to identify and remove cells with a transcriptional signature of cellular stress (thresholds: GO:0006096, 1.124; GO:0034976, 0.464; GO:0042063, 0.948). Expression matrices were log-normalized and scaled, and dimensionality reduction was performed using principal component analysis (PCA) on the top 2,000 genes with the highest standardized variance (vst selection method). The top 40 principal components were used to batch correct libraries using Harmony v1.2.3, and the top 25 Harmony embeddings were used for UMAP visualization (for hTAs, the top 18 Harmony embeddings were used).
The first 12 harmony embeddings were used to identify telencephalic clusters, with clustering at resolution 0.7 and 1 yielding the most reliable cell type identification. hCO clusters were annotated using known marker genes expressed on the developing human neocortex 57: aRG (clusters 11 and 12 at resolution 0.7, and cluster 14 at resolution 1), oRG (cluster 10 at resolution 0.7), cycling NPCs (cluster 15 at resolution 0.7, and cluster 17 at resolution 1), IPs (cluster 4 at resolution 0.7, and cluster 2 at resolution 1), excitatory immature neurons (clusters 1, 13, and 14 at resolution 0.7, and clusters 0, 10, and 16 at resolution 1), excitatory infragranular neurons (cluster 3, 6, 8, 9, and 11 at resolution 1), excitatory supragranular neurons (clusters 1, 4, 5, 7, and 15 at resolution 1), and CGE interneurons (cluster 16 at resolution 0.7, and cluster 18 at resolution 1). hTA clusters were annotated similarly, but clustering was only performed at resolution 0.7: RG (cluster 9), cycling NPCs (clusters 10, 15, and 16), IPs (cluster 2), excitatory immature neurons (clusters 0, 1, and 14), excitatory infragranular neurons (cluster 5 and 11), excitatory supragranular neurons (clusters 3, 4, 6, 7, and 8), MGE interneurons (cluster 13), and OPCs (cluster 12).
Assembly: GRCh38
Supplementary files format and content: barcodes.tsv.gz, features.tsv.gz, matrix.mtx.gz are provided for each multiplexed pool

growth_protocol: Human cerebral organoids and telencephalic assembloids.

extract_protocol:
Multiplexing was performed with antibody-based cell hashing. Library preparation was performed according to the manufacter’s instructions (GEM-X Single Cell 3’ Kit v.4 protocol, 10x Genomics).
Antibody-based cell hashing was performed using 0.5 µg of TotalSeqTM-B anti-human antibodies against β2-microglobulin and CD298 (BioLegend: 394631, 394633, 394635, and 394637), according to the manufacturer’s instructions. To generate single-cell GEMs (Gel Beads in Emulsion), 40,000 live cells of the multiplexed pool were loaded per channel (to give an estimated recovery of 10,000 cells per channel) onto a Chromium GEM-X Single Cell Chip (10X Genomics, PN-1000690). The gene expression library was prepared with the GEM-X Single Cell 3' Kit v.4 (10X Genomics, PN-1000691), and the hashtag-oligo library was prepared with the GEM-X Single Cell 3' Feature Barcode Kit (10X Genomics, PN-1000702). ScRNA-seq libraries were then pooled and pair-end sequenced in a NovaSeq X flowcell (Illumina) with a targeted sequencing depth per cell of 50,000 gene expression reads and 5,000 surface barcode reads.

value: week 17 of differentiation


title: S8_J020_T1 [S8_S8_L001]

value: yes


title: AGS_H3K27ac_BAY_plus_Uridine, ChIP

city: Guangzhou

first: Guodi

last: Cai

state: Guangdong Province

address: 132, Waihuandonglu, Daxue Cheng

department: School Of Pharmaceutical Sciences

institute: Sun Yat-Sen university

library_source: genomic

data_processing:
Sequencing tags were mapped against the Homo sapiens (Human) reference genome (hg19) using Bowtie 2.
Uniquely mapped tags were used for peak calling by MACS(2.1.0) to identify regions of ChIP-Seq enrichment over background.
A q value threshold of enrichment of 5 x 10^-2 was used for all data sets. by using ngs.plot (https://github.com/shenlab-sinai/ngsplot)
Normalized genome-wide signal coverage tracks from raw read alignment files were built by MACS2, fold-enrichment normalized wiggle files were generated by MACS by comparing ChIP treatment against input control, UCSC tools (http://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/bedGraphToBigWig/bedClip) and bedTools (http://code.google.com/p/bedtools/).
Visualization of ChIP-seq singnal at enriched genomic regions(avgprof and heatmap) was achieved
Assembly: hg19
Supplementary files format and content: bigwig files were generated using MACS2 and UCSC tools

molecule: genomic DNA

source_name: AGS

growth_protocol: AGS cells were cultured in RPMI1640 supplemented with 10% FBS. Cells were grown at 37 °C in 5% CO2 incubators.

extract_protocol:
Cell preparation, crosslinking, nuclei preparation and chromatin shearing was following truChIP® Chromatin Shearing Kit (Covaris), according to the manufacturer’s instruction. Chromatin fragments were precipitated by using H3K27ac (Abcam; ab4729) antibodies and Protein G beads, washed, and treated with Proteinase K and RNAse A. Purified ChIP DNA was then used for library generation.
Libraries were quantified with the Bioanalyzer 2100 (Agilent) and sequenced in single-end 50-bp mode on the Illumina HiSeq 2000 Sequencer (BGI, Wuhan, China).

treatment_protocol: AGS cells were treated with vehicle, BAY (5 nM) or BAY (5 nM) plus Uridine (100 μM) for 24 h before harvested.

value: AGS

value: gastric adenocarcinoma cells

value: WT

tag: treatment

value: BAY plus Uridine


title: AGS_H3K27ac_BAY, ChIP

tag: cell type

value: BAY


title: Wk08_TFH_Fusion_GEX

description:
Library name: Wk08_TFH_Fusion_GEX
totalSeqC_feature_ref_wk8.csv

value: Lymph node


title: Wk08_NonTFH_S6_GEX

description:
Library name: Wk08_NonTFH_S6_GEX
totalSeqC_feature_ref_wk8.csv


title: R255X-WT_CO1, R255X-MUT_CO1, R255X-WT_TA1, R255X-MUT_TA1

description:
Library name: Pool 2
10x Genomics

value: brain organoid

value: Neural progenitors and neurons

value: Patient 2042


title: AGS_H3K27ac_Vehicle, ChIP

value: Vehicle


title: Wk08_NonTFH_Fusion_GEX

description:
Library name: Wk08_NonTFH_Fusion_GEX
totalSeqC_feature_ref_wk8.csv


title: R133C-WT_CO1, R133C-WT_CO2, R133C-MUT_CO1

description:
Library name: Pool 1
10x Genomics

value: Patient 2036


title: Wk04_TFH_S6_GEX

description:
Library name: Wk04_TFH_S6_GEX
totalSeqC_feature_ref_wk4.csv


title: S6_J018_T1 [S6_S6_L001]

value: Whole blood

value: no


title: 55 days of embryonic period_3

value: lateral skin tissue

value: epithelial cells

value: somatic cells


title: 55 days of embryonic period_2


title: AGS_Input_BAY


title: Wk08_TFH_S6_GEX

description:
Library name: Wk08_TFH_S6_GEX
totalSeqC_feature_ref_wk8.csv


title: S4_J016_T1 [S4_S4_L001]

value: direct


title: AGS_Input_Vehicle

value: AGS


title: Run8: 5x post-COV, 6x Control

city: Rostock

first: Brigitte

last: Müller-Hilke

address: Schillingallee 70

department: Core Facility for Cell Sorting and Cell Analysis

country: Germany

institute: Rostock University Medical Center

description:
Library name: WTA8
Run 7 and 8 had to be analyzed together

data_processing:
BD Rhapsody™ Sequence Analysis Pipeline 2.2.1
Velocyto to create loom-file
Assembly: GRCh38
Supplementary files format and content: Counts per Cell in h5mu- and MatrixMarket formats.
Supplementary files format and content: Spliced/Unspliced counts in loom-format

source_name: PBMC

extract_protocol:
RNA was harvested using the single-cell capture and cDNA synthesis protocol on the BD Rhapsody Single-Cell Analysis System according to the manufacturer's protocol.
RNA libraries for scRNA-seq were prepared using the Library Preparation Protocol for mRNA Whole Transcriptome Analysis and Sample Tag using the BD Rhapsody System according to the manufacturer's instructions.

treatment_protocol: Cryopreserved cells were thawed using the 10X Genomics Cryopreservation Protocol for Fresh Frozen Human Peripheral Blood.

value: PBMC


title: Wk04_TFH_Fusion_GEX

description:
Library name: Wk04_TFH_Fusion_GEX
totalSeqC_feature_ref_wk4.csv


title: Run7: 6x post-COV, 5x Control

description:
Library name: WTA7
Run 7 and 8 had to be analyzed together


title: R255X-WT_hCO_bulk RNA-seq_1

description:
Library name: Sample 1
Column name in bulk_RNA-seq Featurecounts.xlsx: R255X-WT_hCO_1

value: week 6 of differentiation


title: Wk04_NonTFH_S6_GEX

description:
Library name: Wk04_NonTFH_S6_GEX
totalSeqC_feature_ref_wk4.csv


title: S7_J019_T1 [S7_S7_L001]

value: yes


title: S3_J014_T1 [S3_S3_L001]


title: AR-6

city: Beijing

first: Feng

last: Xiaoxuan

address: No. 35 Qinghua East Road, Haidian District

institute: Beijing Forestry University

data_processing:
Raw data (raw reads) of fastq format were firstly processed using Trimmomatic
The reads containing ploy-N and the low quality reads were removed to obtain the clean reads
The clean reads were assembled into expressed sequence tag clusters (contigs) and de novo assembled into transcripts by Trinity (vesion: 2.4) with paired-end method.
Assembly: No genome build/assembly
Supplementary files format and content: Use the eXpress software to calculate the expression level of Unigene (FPKM)

organism: Prunus incisa

source_name: Prunus subgenus Cerasus × Incisa 'Gotenba zakura'

extract_protocol:
Total RNA was extracted using TRIzol reagent according to the manufacturer’s protocol.
Libraries were constructed using VAHTS Universal V6 RNA-seq Library Prep Kit for Illumina according to the manufacturer’s instructions.

value: aerial roots

tag: growth


title: Run5: 6x post-COV, 5x Control

description: Library name: WTA5


title: R255X-WT_CO2, R255X-MUT_CO2, R255X-WT_TA2, R255X-MUT_TA2

description:
Library name: Pool 3
10x Genomics

tag: cell line

value: week 17 of differentiation


title: Run6: 5x post-COV, 6x Control

description: Library name: WTA6


title: S2_J013_T1 [S2_S2_L001]


title: AR-5


title: Wk04_leftLN_TFH_S6_GEX

description:
Library name: Wk04_leftLN_TFH_S6_GEX
totalSeqC_feature_ref_wk4leftLN.csv

value: Lymph node


title: S5_J017_T1 [S5_S5_L001]


title: Mouse meninges, LDL uptake enriched, rep2, scRNA

description:
10X Chromium (Single cell 3' V2)
D10009_Level_01_SeuratObject.RDS.gz

source_name: Meninges

value: Meninges

tag: age

value: 3 months

value: GFP positive

value: WT


title: Run3: 6x post-COV, 5x Control

description: Library name: WTA3


title: Run2: 5x post-COV, 6x Control

description: Library name: WTA2


title: S1_J011_T1 [S1_S1_L001]

value: Whole blood


title: AGS_Input_BAY_plus_Uridine

value: gastric adenocarcinoma cells

value: BAY plus Uridine


title: Wk04_leftLN_NonTFH_Fusion_GEX

description:
Library name: Wk04_leftLN_NonTFH_Fusion_GEX
totalSeqC_feature_ref_wk4leftLN.csv


title: AR-2


title: Run4: 5x post-COV, 6x Control

description: Library name: WTA4


title: Wk04_leftLN_TFH_Fusion_GEX

description:
Library name: Wk04_leftLN_TFH_Fusion_GEX
totalSeqC_feature_ref_wk4leftLN.csv


title: Wk04_leftLN_NonTFH_S6_GEX

description:
Library name: Wk04_leftLN_NonTFH_S6_GEX
totalSeqC_feature_ref_wk4leftLN.csv


title: AR-1

value: bark


title: Run1: 6x post-COV, 5x Control

description: Library name: WTA1


title: Mouse meninges, LDL uptake enriched, rep1, scRNA


title: HeLa_TurboID-H1.2_rep1  PLAMseq

city: Sevilla

first: Román

last: González-Prieto

address: Americo Vespucio 24

country: Spain

institute: CABIMER

description:
Library name: HeLa_TurboID-H1.2_rep1
Cell lines expressing TurboID-H1.2 construction

data_processing:
Raw sequencing reads were aligned to the telomere-to-telomere (T2T-CHM13v2.0) reference genome with Rsubread, allowing multimapping but retaining only the best-mapped location for each read. Duplicate reads from BAM files were removed with samtools markdup, thus only properly paired and non-duplicated reads were retained for downstream analysis. Bigwig files were build with bamCoverage function from Deeptools2, using a bin size of 1 and CPM normalization.
Assembly: T2T-CHM13v2.0
Supplementary files format and content: Bigwig files

source_name: HeLa

growth_protocol: DMEM (4,5g/L glucose, L-glutamine and sodium pyruvate), 10% Fetal Bovine Serum, 1x Penicillin/Streptomycin. Cells were culture at 37ºC at 5% CO2.

extract_protocol:
Cells were fixed with 1% formaldehyde for 20 minutes. After quenching and cell lysis, chromatin was sonicated using a E220 focused-ultrasonicator (Covaris).
PLAMseq libraries of H1.4 and H1.0 samples were prepared using Tn5 transposase (tagmentation) 5 minutes 37ºC. Then, NEBNext® High-Fidelity 2X PCR Master Mix was used for PCR amplification and library indexing (Nextera DNA Indexes i5 and i7) according to the following program: 72°C for 5 minutes; 98°C for 30 seconds, 9-10 cycles of 98°C for 10 seconds, 63°C for 30 seconds, and 72°C for 30 seconds, final holding stage 72ºC 5 minutes. PCR product was double purified using 0.7 and 0.15 volumnes of Seramag Beads (Cytiva). PLAMseq libraries of CTCF, POL2RI and H1.2 samples were prepared using the ThruPLEX DNA-Seq kit of Takara (cat. N. R400675).

treatment_protocol: Biotin 50μM 10 minutes 37ºC

value: HeLa

value: Human cervical cancer

value: 1x Biotin 10min


title: Wk04_NonTFH_Fusion_GEX

description:
Library name: Wk04_NonTFH_Fusion_GEX
totalSeqC_feature_ref_wk4.csv


title: Clp_Saline_Rep11

status: Public on Nov 06 2025

city: Albany

first: Ramon

last: Bossardi Ramos

state: Ny

address: 43 New Scotland Avenue

department: Department of Molecular and Cellular Physiology

institute: Albany Medical College

description: Library name: ATAC_Sample_11

data_processing:
Adapters and low-quality sequences were removed using Trim Galore (v0.6.10). Reads were aligned to the human genome (hg38) using Bowtie2 (v2.4.4) with parameters optimized for ATAC-seq. PCR duplicates, mitochondrial reads, and reads mapping to ENCODE blacklist regions were removed. Peaks were called using MACS3 (v3.0.0a7) with the --nomodel --shift -100 --extsize 200 options. BigWig files for visualization were generated using deepTools (v3.5.1).
Assembly: mm10
Supplementary files format and content: BigWig File

source_name: Kidney

growth_protocol: Male C57BL/6 mice (8–12 weeks old) were housed under specific pathogen-free conditions with ad libitum access to food and water. All procedures were approved by the Institutional Animal Care and Use Committee. Mice were randomly assigned to experimental groups.

extract_protocol:
Kidney tissues were enzymatically digested into single-cell suspensions, and endothelial cells were enriched using anti-CD31 magnetic-microbeads according to the manufacturer’s protocol. CD31⁺ cells were lysed in Trizol reagent (Thermo Fisher Scientific), and total RNA was purified using RNeasy Micro columns (Qiagen) with on-column DNase digestion to eliminate genomic DNA contamination.
ATAC-seq libraries were prepared using the Nextera DNA Library Preparation Kit (Illumina) according to the Omni-ATAC protocol. Libraries were PCR-amplified, purified with AMPure XP beads (Beckman Coulter), quantified by Qubit and qPCR, and sequenced on an Illumina NovaSeq 6000 platform using 150 bp paired-end reads.

treatment_protocol: To model post-sepsis inflammatory memory, mice underwent cecal ligation and puncture (CLP) or sham surgery (first hit). After a recovery period, mice were challenged intranasally with either Streptococcus pneumoniae (1×10⁶ CFU) or PBS (second hit). Endothelial cells were isolated from lung and kidney tissues at defined timepoints corresponding to acute and memory phases of the response.

value: Kidney

value: endothelial cells


title: Sham_Saline_Rep12

description: Library name: ATAC_Sample_12


title: Sham_Saline_Rep8

description: Library name: ATAC_Sample_8


title: Clp_Sp_Rep9

description: Library name: ATAC_Sample_9


title: AR-4


title: Sham_Sp_Rep7

description: Library name: ATAC_Sample_7


title: Clp_Saline_Rep2

description: Library name: ATAC_Sample_2


title: Sham_Saline_Rep3

description: Library name: ATAC_Sample_3


title: Clp_Saline_Rep5

description: Library name: ATAC_Sample_5


title: Clp_Sp_Rep6

description: Library name: ATAC_Sample_6


title: Faa1 knockout, rep5 [20191030_Jose_10]

city: Gent

first: Inge

middle: N. A.

last: Van Bogaert

address: Coupure Links, 653

department: Department of Biotechnology

country: Belgium

institute: Ghent University

data_processing:
Adapter and quality trimming of raw sequencing reads was done with cutadapt (v1.18)
Trimmed reads were mapped against the Yarrowia lipolytica (GCA_000002525.1) reference genome with STAR (v2.6.0c)
Feature counting was done with rsem_calculate_expression (RSEM v1.3.1) with the --strand-specific option
Feature counts were normalized in R (v3.6.0) using the edgeR (v3.26.8) package
Assembly: GCA_000002525.1
Supplementary files format and content: CountTable.csv: comma-delimited text file (csv) includes raw feature count values for each sample
Supplementary files format and content: normCounts.csv: comma-delimited text file (csv) includes normalized feature counts as CPM values for each sample

organism: Yarrowia lipolytica

source_name: Liquid culture

growth_protocol: 3C medium was used (10% glucose monohydrate, 1% yeast extract, 0.1% urea). This medium contains a higher concentration of glucose than usual to achieve a high C/N ratio, which stimulates lipid production. Y. lipolytica strains were incubated at 28°C and on a rotatory shaker at 200 rpm for liquid media for 4 days.

extract_protocol:
The WT and Δfaa1 Y. lipolytica strains were inoculated overnight in 5 ml of 3C media. The grown cultures were reinoculated in 5 ml of 3C in quintuplicates with a starting OD600 of 0.1. After 48 hours, when fatty acids are already present in the extracellular medium, cells were harvested by centrifugation and lysed using liquid nitrogen. Then, RNA was extracted using the RNeasy Midi kit (Qiagen) following the recommended protocol.
Sequencing libraries were constructed with the Quantseq 3’ mRNA library FWD kit  (Lexogen) according the manufacturer's protocols.

value: Liquid culture

value: Yeast

value: xpr2 and faa1 deletion


title: Faa1 knockout, rep3 [20191030_Jose_8]


title: Sham_Sp_Rep10

description: Library name: ATAC_Sample_10


title: Clp_Sp_Rep1

description: Library name: ATAC_Sample_1


title: AR-3

value: aerial roots


title: Faa1 knockout, rep2 [20191030_Jose_7]


title: Wildtype-like, rep4 [20191030_Jose_4]

value: xpr2 deletion


title: Wildtype-like, rep5 [20191030_Jose_5]


title: Wildtype-like, rep2 [20191030_Jose_2]


title: Wildtype-like, rep3 [20191030_Jose_3]


title: Bulk brain R2

city: Stanford

first: Ian

last: Guldner

address: 290 Jane Stanford Way

department: Neuro

institute: Stanford University

description:
Library name: WB2
Col name: WB2

data_processing:
Novogene performed data processing steps, providing a count table. The following is provided by Novogene in relation to data processing steps: Original image data file from high-throughput sequencing platforms (like Illumina) is transformed to sequenced reads (called Raw Data or Raw Reads) by CASAVA base recognition (Base Calling). Raw data are stored in FASTQ(fq) format files. The error rate for each base can be transformed by the Phred score as in equation 1. "e" represents sequencing error rate, "Qphred" represents base quality values of Illumina platforms (equation 1: Qphred = -10log10(e)). Raw reads were filtered as follows:Remove reads with adapter contamination; Remove reads when uncertain nucleotides constitute more than 10 percent of either read (N > 10%).; Remove reads when low quality nucleotides (Base Quality less than 5) constitute more than 50 percent of the read. Performed alignments with HISAT2 to the reference.
Mapping: hisat2 2.2.1; Default parameters
Quantification: featureCounts 2.0.; Default parameters
Assembly: Mus Musculus(GRCm39/mm39)
Supplementary files format and content: txt file, samples as column names, genes as row names, raw counts provided

growth_protocol: Standard mouse husbandry conditons

extract_protocol:
Qiazol lysis followed by Qiagen miRNAeasy protocol.
Novogene contructed the library. The following is provided by Novogene in relation to library constructoin: Messenger RNA was purified from total RNA using poly-T oligo-attached magnetic beads. After fragmentation, the first strand cDNA was synthesized using random hexamer primers, followed by the second strand cDNA synthesis using  dTTP.  After end repair, A-tailing, adapter ligation, size selection, amplification, and purification, the library was ready for sequencing.

value: Brain

value: All brain cells

tag: batch


title: Bulk brain R5

description:
Library name: WB5
Col name: WB5


title: Bulk brain R1

description:
Library name: WB1
Col name: WB1


title: Bulk brain R3

description:
Library name: WB3
Col name: WB3


title: Microglia R5

description:
Library name: MG5
Col name: MG5

value: microglia


title: Microglia R4

description:
Library name: MG4
Col name: MG4


title: Microglia R2

description:
Library name: MG2
Col name: MG2


title: Microglia R1

description:
Library name: MG1
Col name: MG1


title: Faa1 knockout, rep4 [20191030_Jose_9]


title: Meninges infected 4

city: Manchester

first: Matthew

middle: Christopher

last: Sinton

state: Greater Manchester

address: Core Technology Facility

department: Division of Immunology, Immunity to Infection and Respiratory Medicine

institute: University of Manchester

description: Library name: Men_I4

data_processing:
Raw data (raw reads) of fastq format were firstly processed through in-house Perl scripts. In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing poly-N and low quality reads from raw data. At the same time, Q20, Q30 and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality
Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built 3 using Hisat2 v2.0.5 and paired-end clean 1 reads were aligned to the reference genome using Hisat2 v2.0.5. We selected Hisat2 as the mapping tool for that Hisat2 can generate a database of splice junctions based on the gene model annotation file and thus a better mapping result than other non-splice mapping tools.
featureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene. FPKM, expected number of Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced, considers the effect of sequencing depth and gene length for the reads count at the same time, and is currently the most commonly used method for estimating gene expression levels.
Assembly: GRCm39
Supplementary files format and content: Tab-delimited file contains raw counts for all samples
Supplementary files format and content: Tab-delimited file contains raw counts for all samples

molecule: polyA RNA

growth_protocol: Mice were group housed at room temperatire under 12h light 12h dark conditions

extract_protocol:
Qiagen Rneasy Kit
Library construction was performed by Novogene. Messenger RNA was purified from total RNA using poly-T oligo-attachedmagnetic beads. After fragmentation, the first strand cDNA was synthesized using random hexamer primers followed by the secondstrand cDNA synthesis. The library was ready after end repair, A-tailing, adapter ligation, size selection, amplification, and purification. After library quality control, different libraries were pooled based on the effective concentration and targeted data amount, then subjected to Illumina sequencing. The basic principle of sequencing is "Sequencing by Synthesis", where fluorescently labelled dNTPs, DNA polymerase, and adapter primers are added to the sequencing flow cell for amplification. As each sequencing cluster extends its complementary strand, the addition of each fluorescently labelled dNTP releases a corresponding fluorescence signal. The sequencer captures these fluorescence signals and converts them into sequencing peaks through computer software, thereby obtaining the sequence information of the target fragment.

treatment_protocol: Mice were infected with ~2,000 T. brucei parasites via intraperitoneal injection on day 0, and monitored until day 25, alongside naïve control mice

value: Meninges

tag: strain

tag: Sex

value: Female

value: Infected


title: Meninges infected 1

description: Library name: Men_I1


title: Meninges naïve 3

description: Library name: Men_N3

value: Naïve


title: Meninges naïve 4

description: Library name: Men_N4


title: Meninges infected 2

description: Library name: Men_I2


title: Meninges infected 3

description: Library name: Men_I3


title: Meninges naïve 2

description: Library name: Men_N2


title: Sham_Sp_Rep4

description: Library name: ATAC_Sample_4

value: WT


title: Meninges naïve 1

description: Library name: Men_N1


title: Faa1 knockout, rep1 [20191030_Jose_6]


title: Microglia R3

description:
Library name: MG3
Col name: MG3


title: Spleen infected 1

description: Library name: Sp_I1

source_name: Spleen

value: Spleen


title: Spleen infected 3

description: Library name: Sp_I3


title: Spleen infected 4

description: Library name: Sp_I4


title: Bulk brain R4

description:
Library name: WB4
Col name: WB4

source_name: Brain


title: Spleen naïve 2

description: Library name: Sp_N2


title: Wildtype-like, rep1 [20191030_Jose_1]


title: Spleen infected 2

description: Library name: Sp_I2


title: Spleen naïve 3

description: Library name: Sp_N3


title: Skull bone marrow infected 2

description: Library name: skBM_I2

source_name: Skull bone marrow

value: Skull bone marrow


title: Skull bone marrow infected 1

description: Library name: skBM_I1


title: Spleen naïve 1

description: Library name: Sp_N1


title: Skull bone marrow naïve 4

description: Library name: skBM_N4


title: Skull bone marrow infected 3

description: Library name: skBM_I3


title: Skull bone marrow infected 4

description: Library name: skBM_I4


title: Skull bone marrow naïve 3

description: Library name: skBM_N3


title: Skull bone marrow naïve 1

description: Library name: skBM_N1


title: Femur bone marrow infected 4

description: Library name: fBM_I4

source_name: Femur bone marrow

value: Femur bone marrow


title: Femur bone marrow infected 3

description: Library name: fBM_I3


title: Femur bone marrow naïve 3

description: Library name: fBM_N3


title: Femur bone marrow infected 1

description: Library name: fBM_I1


title: Femur bone marrow naïve 2

description: Library name: fBM_N2


title: Femur bone marrow infected 2

description: Library name: fBM_I2


title: bloodstream ZC3H41-depleted replicate C

city: Armilla

first: Antonio

middle: M

last: Estevez

state: Granada

address: Avda. del Conocimiento 17

department: Lopez-Neyra

institute: CSIC

data_processing:
TruSeq RNA Single Indexes (set A&B)
The resulting 75-nt paired end sequences were checked for quality using FastQC, and
mapped to the T. brucei genome using the ‘align’ program of the Subread package with options nTrim5=4, nTrim3=1, unique=TRUE
Reads assignment to mRNAs/lncRNAs and counting were carried out using the ‘featureCounts’ program of the Subread package (options -p -B -C -O -Q 20)
Replicates were compared to control trypanosomes (S16 or 449 parental cell lines) using the edgeR program
Assembly: TREU927, version 5.1
Supplementary files format and content: featureCounts output, tab-delimited text file

organism: Trypanosoma brucei brucei

source_name: bloodstream S16

growth_protocol: Grown in HMI-9 medium at 37ºC (bloodstream) or SDM-79 medium at 28ºC (procyclic)

extract_protocol:
Cells were centrifuged and RNA was extracted using the RNeasy Mini Kit (Qiagen)
TruSeq Stranded mRNA® Illumina

treatment_protocol: ± 1 µg/ml tetracycline for RNAi induction

value: bloodstream S16


title: Spleen naïve 4

description: Library name: Sp_N4


title: Femur bone marrow naïve 1

description: Library name: fBM_N1


title: Femur bone marrow naïve 4

description: Library name: fBM_N4


title: bloodstream ZC3H41-depleted replicate B


title: procyclic control replicate C

source_name: procyclic 449

value: procyclic 449


title: procyclic DRBD3-depleted replicate C


title: procyclic DRBD3-depleted replicate B


title: procyclic control replicate B


title: procyclic control replicate A


title: bloodstream DRBD3-depleted replicate C


title: procyclic DRBD3-depleted replicate A


title: bloodstream ZC3H41-depleted replicate A


title: bloodstream DRBD3-depleted replicate A


title: Skull bone marrow naïve 2

description: Library name: skBM_N2


title: bloodstream control replicate B


title: bloodstream DRBD3-depleted replicate B


title: bloodstream control replicate A


title: deltaRG_dBET_5hG1_r1

city: Worcester

first: Allana

last: Schooley

state: MA

address: 368 Plantation St

department: Systems Biology

institute: UMass Medical School

description: Library name: deltaRG_dBET_5hG1_r1

data_processing:
Hi-C libraries were processed using the distiller-nf pipeline (Goloborodko et al. 2022), version 0.3.4
paired-end reads were mapped to hg38 human reference genome using bwa mem (Li 2013) in a single-sided fashion (-SP); read alignments were parsed and classified into pairwise interactions, or pairs, by parse from the pairtools package (Open2C et al. 2024b), version 1.0.2, additional `--walk-policy all` option was used in order to rescue multi-way interactions (walks); after the removal of duplicates, uniquely mapped and rescued pairs were further filtered according to their alignment quality (MAPQ > 30), and subsequently aggregated into binned contact matrices in the cooler format (Abdennur and Mirny 2020) at 1, 2, 5, 10, 25, 50, 100, 250, 500 and 1000 kb resolutions;  contact matrices were normalized using the iterative correction normalization (Imakaev et al. 2012) with the default parameters
Assembly: hg38
Supplementary files format and content: mcool (cooler) files for each replicate library and a pooled replicate mcool for each treatment/timepoint

source_name: cell line

growth_protocol: Cells were synchronized and arrested in prometaphase and either RanGAP1-AID or Nup93-AID was degraded 2 hours prior to release from nocodazole block. Cells were sorted in prometaphase, telophase, cytokinesis, and G1 of the cell cycle (5h). A G1 depletion was also performed 3.5h after mitotic release and cells were allowed to progress in G1 for a total of 10h.

extract_protocol:
Cells were fixed with FA/DSG and digested with DdeI/DpnII according to Hi-C 3.0 (Lafontaine et al 2021)
Libraries were constructed using either Illumina TruSeq DNA LT Kit indexed adapters or NEBNext Multiplex Oligos

treatment_protocol: control Nup93-AID (ctrlN93) or IAA-treated Nup93-AID (deltaN93) or control RanGAP1-AID (ctrlRG) or IAA-treated RanGAP1-AID (deltaRG) DLD-1 cells

value: cell line

value: control 5h G1, dBET6, replicate 1


title: deltaRG_JQ1_5hG1_r2

description: Library name: deltaRG_JQ1_5hG1_r2

value: control 5h G1, JQ1, replicate 2


title: deltaRG_JQ1_5hG1_r1

description: Library name: deltaRG_JQ1_5hG1_r1

value: control 5h G1, JQ1, replicate 1


title: Splenic CD8+ T cells, But, rep2

first: Lachlan

last: Dryburgh

state: Victoria

address: 792 Elizabeth Street

department: The Department of Microbiology and Immunology,  The University of Melbourne

institute: The Peter Doherty Institute for Infection and Immunity

description: Library name: mouse3_butyrate

data_processing:
cellranger v4 pipeline.
Counts loaded into Seurat v4.3 object.
Filtered for cell quality and doublet/empty cells.
Normalization,scaled and dimensional reduction with PCA.
Nearest neighbour clustering and UMAP generated from PCA.
Assembly: refdata-gex-mm10-2020-A
Supplementary files format and content: filtered_gex.rds.gz filtered Seurat object.
Supplementary files format and content: features.tsv.gz, barcodes.tsv.gz matrix.mtx.gz raw counts output from cellranger.

growth_protocol: Spleens from gBT-I.CD45.1 mice were harvested and meshed through a 70 µM sieve with PBS and single cell suspensions exposed to gB498-505-pulsed B6 splenocytes in the presence of 6 µg LPS. Cells were incubated at 37°C at 6.5% CO2 and split 1:2 in RP-10 with 12.5 U/ml recombinant human IL-2  daily from day 2 as described previously.

extract_protocol:
Viable CD8+Vα2+ single cells from control and butyrate treated gBT-I cells in vitro cultures were purified by flow cytometry using a BD Influx (> 98% purity), resuspended in 0.04% BSA and filtered through a 70 µm sieve before being captured in droplets for library preparation.
Library preparation was done using the 10X Genomics Chromium Single Cell 3' V3.1 chemistry.

treatment_protocol: Activated gBT-I cells were treated with 0.5 mM sodium butyrate (But) or PBS (Ctrl)  in vitro starting on day 3 following activation as published previously (Bachem et al. Immunity 2019).

value: CD8+ T cells

value: gBT-I.CD45.1 tg

value: Butyrate


title: Splenic CD8+ T cells, Ctrl, rep2

description: Library name: mouse3_nobutyrate

value: PBS


title: Splenic CD8+ T cells, But, rep1

description: Library name: mouse2_butyrate


title: ctrlRG_dBET_5hG1_r2

description: Library name: ctrlRG_dBET_5hG1_r2

value: control 5h G1, dBET6, replicate 2


title: ctrlRG_dBET_5hG1_r1

description: Library name: ctrlRG_dBET_5hG1_r1


title: ctrlRG_JQ1_5hG1_r2

description: Library name: ctrlRG_JQ1_5hG1_r2


title: Splenic CD8+ T cells, Ctrl, rep1

description: Library name: mouse2_nobutyrate


title: ctrlRG_JQ1_5hG1_r1

description: Library name: ctrlRG_JQ1_5hG1_r1


title: ctrlRG_3p5hG1_delta_10h_r2

description: Library name: ctrlRG_3p5hG1_delta_10h_r2

value: control, 0-3.5h, auxin 3.5-10h, G1, replicate 2


title: deltaRG_dBET_5hG1_r2

description: Library name: deltaRG_dBET_5hG1_r2


title: bloodstream control replicate C


title: Muscle, baseline, SIE group, Participant #2

first: Javier

last: Botella

address: Ballarat road

institute: Victoria University

description: Library name: 02SIEPRE

data_processing:
Quality check: FASTQC
Alignment: STAR
quantification: RSEM
differential expression: limma/edgeR
Assembly: Reference genome: UCSC hg38
Supplementary files format and content: Genes by samples as total counts or counts per million

source_name: Skeletal muscle - Vastus lateralis

extract_protocol:
RNA was extracted from whole muscle samples using the Rneasy Kit from Qiagen and following the manufacturer's protocol.
Following BGI's recommended protocol

value: Skeletal muscle - Vastus lateralis

tag: time

value: baseline

tag: group

value: SIE group

tag: participant

value: Participant #2


title: Muscle, +24h, SIE group, Participant #2

description: Library name: 02SIE24H

tag: tissue


title: Muscle, +2.5h, SIE group, Participant #3

description: Library name: 03SIE03H

value: Participant #3


title: Muscle, +2.5h, SIE group, Participant #2

description: Library name: 02SIE03H


title: deltaRG_3p5hG1_delta_10h_r1

description: Library name: deltaRG_3p5hG1_delta_10h_r1

value: auxin-treated, 0-10h G1, replicate 1


title: Muscle, baseline, SIE group, Participant #3

description: Library name: 03SIEPRE


title: deltaRG_3p5hG1_r2

description: Library name: deltaRG_3p5hG1_r2

value: auxin-treated 3.5h G1, replicate 2


title: ctrlRG_3p5hG1_ctrl_10h_r1

description: Library name: ctrlRG_3p5hG1_ctrl_10h_r1

value: cell line

value: control, 0-10h G1, replicate 1


title: deltaRG_3p5hG1_r1

description: Library name: deltaRG_3p5hG1_r1

value: auxin-treated, 3.5h G1, replicate 1


title: Muscle, +2.5h, MICE group, Participant #3

description: Library name: 03MIE03H

value: MICE group


title: Muscle, baseline, SIE group, Participant #1

description: Library name: 01SIEPRE

value: Participant #1


title: deltaRG_3p5hG1_delta_10h_r2

description: Library name: deltaRG_3p5hG1_delta_10h_r2

value: auxin-treated 0-10h G1, replicate 2


title: Muscle, +24h, MICE group, Participant #3

description: Library name: 03MIE24H


title: ctrlRG_3p5hG1_r2

description: Library name: ctrlRG_3p5hG1_r2

value: control, 3.5h G1, replicate 2


title: ctrlRG_3p5hG1_r1

description: Library name: ctrlRG_3p5hG1_r1

value: control, 3.5h G1, replicate 1


title: deltaRG_cyto_r2

description: Library name: deltaRG_cyto_r2

value: auxin-treated, cytokinesis, replicate 2


title: Muscle, +24h, MICE group, Participant #2

description: Library name: 02MIE24H


title: Muscle, +2.5h, MICE group, Participant #2

description: Library name: 02MIE03H


title: Muscle, baseline, MICE group, Participant #2

description: Library name: 02MIEPRE


title: ctrlRG_3p5hG1_delta_10h_r1

description: Library name: ctrlRG_3p5hG1_delta_10h_r1

value: control, 0-3.5h, auxin 3.5-10h, G1, replicate 1


title: Muscle, +24h, MICE group, Participant #1

description: Library name: 01MIE24H

value: Skeletal muscle - Vastus lateralis


title: ctrlRG_cyto_r2

description: Library name: ctrlRG_cyto_r2

value: control, cytokinesis, replicate 2


title: ctrlRG_telo_r2

description: Library name: ctrlRG_telo_r2

value: control, telophase, replicate 2


title: ctrlRG_3p5hG1_ctrl_10h_r2

description: Library name: ctrlRG_3p5hG1_ctrl_10h_r2

value: control, 0-10h G1, replicate 2


title: rna_si3e_normoxia_a

city: Aurora

first: Neelanjan

last: Mukherjee

state: Colorado

address: Research Complex 1 South, 12801 E 17th Ave

department: Biochemistry and Molecular Genetics

institute: University of Colorado School of Medicine

description: Library name: NM2023_0106

data_processing:
Adapters were trimmed with Cutadapt (Martin et al, 2011). UMIs were trimmed and collapsed using UMI-tools (Smith et al, 2017). Salmon (Patro et al, 2017) was used for quantifying transcript levels from RNA-seq and Ribo-seq libraries using GENCODEv26 transcriptome assembly. Briefly, Salmon data were imported using the tximport (Soneson et al, 2015).  Transcript expression was quantified using Salmon v1.6 (12). Quality of ribosome sequencing data, including ribosome footprint length, p-site positioning, and three-nucleotide periodicity, was assessed using Ribowaltz (Lauria et al, 2018).
Assembly: GRCh38
Supplementary files format and content: tabular file containing salmon quantification (raw reads and TPMs) for all samples

growth_protocol: Cells were cultured in incubators at 37 ℃ with 5% CO2 and ~21% O2 (atmospheric). MCF7SIX1 cells (Clone A13) (derived from human female breast cancer cells) were generated as previously described (Ford et al, 1998). The MCF7SIX1 cells were cultured Dulbecco’s High Glucose Modified Eagle Medium (DMEM, Hyclone SH30022.01), with which 10% fetal bovine serum (FBS, Corning 35-010-CV), and 2 mM L-glutamine (L-glut, Hyclone SH30034.02) were supplemented. The MDA-MB-231 cells were cultured with Dulbecco’s High Glucose Modified Eagle Medium (DMEM, Hyclone SH30022.01), with which 5% fetal bovine serum (FBS, Corning 35-010-CV), 2 mM L-glutamine (L-glut, Hyclone SH30034.02), were supplemented.

extract_protocol:
Ribosome profiling was performed as described previously with a few modifications (Calviello et al, 2016). The lysis buffer contained 100 ug/mL cycloheximide. Following lysis and clarification by centrifugation, total RNA was quantified using the Qubit RNA BR assay kit. A portion of the lysate was reserved as input sample for RNASeq preparation. Total RNA was extracted using the DirectZol RNA Microprep kit (ZYMO Research) following the manufacturer’s instructions with on-column DNase I treatment.  Ribosomal RNA was depleted from total RNA using our previously described RNaseH-based method (Baldwin et al, 2021), then input into the KAPA RNA Hyper prep RNAseq library prep kit (Roche) according to manufacturer’s instructions with dual-index adapters, followed by quality check of the final libraries by Qubit dsDNA HS assay and Tapestation High Sensitivity D1000 screentape. Libraries were pooled and submitted for paired-end 150 bp sequencing on the Illumina NovaSeq6000 platform to a depth of 40 million paired end reads per library.
The remaining lysate was used as input into the ribosome footprinting reaction with 750 U RNase I (Invitrogen Ambion). The digestion was stopped with SUPERaseIN followed by recovery of monosomes with equilibrated Microspin S-400 HR (GE) columns. Trizol LS was added to the monosome-containing elution and RNA isolated with the ZYMO Directzol microprep kit with on-column DNase I treatment. The isolated RNA was depleted of rRNA using the siTOOLs riboPOOLs kit for ribosome profiling. The samples were resolved on a 15% TBE-Urea PAGE gel and ribosome protected fragments (RPFs) 28-29 nt in size were extracted and recovered. RPFs were treated with T4-PNK then used as input into the Qiagen QIAseq miRNA library prep kit with provided single index adapters. Libraries were pooled and submitted for paired-end 150 bp sequencing on the Illumina NovaSeq 6000 S4 platform to a depth of 50 million paired end reads per library (Novogene Corporation Inc.).

treatment_protocol: To provide a hypoxic environment, cells were placed in either a modular hypoxic chamber and filled with a premixed gas comprised of 1% O2, or the cells were placed in a BioSpherix hypoxic chamber flushed with N2 and CO2 gas. The O2 and CO2 concentrations in the BioSpherix chamber were maintained at 1% and 5%, respectively, using a carbon dioxide & oxygen controller (BioSpherix). These conditions were maintained constant throughout the course of the experiments. After hypoxic incubation was completed, quick lysis (<3 min) of the cells was necessary to prevent reoxygenation from affecting our results. ON-TARGETplus siRNA SMARTPools were ordered specifically for eIF3e (cat #: L-010518-00-0010) and eIF3d (cat #: L-017556-00-0010) from Horizon Discovery. ON-TARGETplus non-targeting pool (cat # D-001810-10) was always used as a control. siRNA transfections occurred in 25% OPTIMEM Reduced serum media and 75% full growth media (cat # 31985062). siRNAs were added to the media mixture at a concentration of 7.5 nM for 5 minutes prior to the addition of 1.875 mL Lipofectamine RNAI MAX transfection reagent (cat # 13778150) per 1 mL of media. siRNA:lipofectamine mixtures were incubated for 20 minutes before adding it directly onto the cell culture overnight. siRNA knockdowns were assessed 48-72 hours after the addition of the siRNAs.  8430 and 209 were resuspended in DMSO to a working solution concentration of 20 mM. All experiments with 8430 and 209 were used at 20 mM (1:1000 dilution) with DMSO as a vehicle control.

value: breast cancer

value: SIX1 OE

value: eIF3e siRNA


title: Muscle, +24h, SIE group, Participant #1

description: Library name: 01SIE24H

value: SIE group


title: Muscle, +2.5h, MICE group, Participant #1

description: Library name: 01MIE03H


title: Muscle, baseline, MICE group, Participant #1

description: Library name: 01MIEPRE

value: baseline


title: Muscle, +24h, MICE group, Participant #12

description: Library name: 12MIE24H

value: Participant #12


title: rna_si3d_normoxia_a

description: Library name: NM2023_0105

value: eIF3d siRNA


title: Muscle, +2.5h, SIE group, Participant #1

description: Library name: 01SIE03H

value: Participant #1


title: Muscle, baseline, MICE group, Participant #12

description: Library name: 12MIEPRE

value: MICE group


title: rna_si3d_hypoxia_a

description: Library name: NM2023_0102

value: eIF3d siRNA and hypoxia


title: rna_si3e_hypoxia_a

description: Library name: NM2023_0103

value: eIF3e siRNA and hypoxia


title: Muscle, +24h, MICE group, Participant #11

description: Library name: 11MIE24H

value: Participant #11


title: Muscle, baseline, MICE group, Participant #3

description: Library name: 03MIEPRE

value: Participant #3


title: Muscle, +2.5h, MICE group, Participant #12

description: Library name: 12MIE03H

value: Skeletal muscle - Vastus lateralis


title: rna_sictrl_normoxia_a

description: Library name: NM2023_0104

value: scramble siRNA


title: Muscle, +2.5h, MICE group, Participant #11

description: Library name: 11MIE03H


title: ribo_si3d_normoxia_a

description: Library name: NM2023_0045

data_processing:
Adapters were trimmed with Cutadapt (Martin et al, 2011). UMIs were trimmed and collapsed using UMI-tools (Smith et al, 2017). Salmon (Patro et al, 2017) was used for quantifying transcript levels from RNA-seq and Ribo-seq libraries using GENCODEv26 transcriptome assembly. Briefly, Salmon data were imported using the tximport (Soneson et al, 2015).  Transcript expression was quantified using Salmon v1.6 (12). Quality of ribosome sequencing data, including ribosome footprint length, p-site positioning, and three-nucleotide periodicity, was assessed using Ribowaltz (Lauria et al, 2018).
Assembly: GRCh38
Supplementary files format and content: tabular file containing salmon quantification (raw reads and TPMs) for all samples
Library strategy: Ribo-Seq


title: Muscle, baseline, MICE group, Participant #11

description: Library name: 11MIEPRE


title: ribo_si3e_normoxia_a

description: Library name: NM2023_0046


title: Muscle, +24h, MICE group, Participant #10

description: Library name: 10MIE24H

value: Participant #10


title: rna_sictrl_hypoxia_a

description: Library name: NM2023_0101

value: scramble siRNA and hypoxia


title: deltaRG_telo_r2

description: Library name: deltaRG_telo_r2

value: cell line

value: auxin-treated, telophase, replicate 2


title: Muscle, baseline, MICE group, Participant #10

description: Library name: 10MIEPRE


title: Muscle, +2.5h, SIE group, Participant #12

description: Library name: 12SIE03H


title: ribo_sictrl_normoxia_a

description: Library name: NM2023_0044

value: breast cancer

value: SIX1 OE


title: Muscle, +2.5h, MICE group, Participant #10

description: Library name: 10MIE03H


title: ribo_si3d_hypoxia_a

description: Library name: NM2023_0042


title: ribo_si3e_hypoxia_a

description: Library name: NM2023_0043


title: Muscle, +24h, SIE group, Participant #12

description: Library name: 12SIE24H

value: SIE group


title: ribo_sictrl_hypoxia_a

description: Library name: NM2023_0041


title: Muscle, +24h, SIE group, Participant #11

description: Library name: 11SIE24H


title: Muscle, +2.5h, SIE group, Participant #11

description: Library name: 11SIE03H


title: Muscle, +24h, SIE group, Participant #10

description: Library name: 10SIE24H


title: Muscle, +2.5h, SIE group, Participant #10

description: Library name: 10SIE03H


title: Roots, Yunquera, Spring, Ind2

city: Malaga

first: Vanessa

middle: Viviana

last: Castro Rodriguez

state: Malaga

address: Universidad de Malaga

institute: Universidad de Malaga

description: Library name: PAPBL4R

data_processing:
Original image data file from high-throughput sequencing platforms (like Illumina) is transformed to sequenced reads (called Raw Data or Raw Reads) by CASAVA base recognition (Base Calling). Raw data are stored in FASTQ(fq) format files.
The raw reads were cleaned of adapter contamination. Reads were removed if uncertain nucleotides constituted more than 10% of either read (N > 10%) or if low-quality nucleotides (base quality < 5) made up more than 50% of the read.
Alignments were performed with HISAT2 (Mortazavi et al., 2008) to the reference.
Transcript expression was obtained using featureCounts (Liao et al., 2013)
Assembly: The same assembled reference transcriptome used in the GSE189122 (GEO accession) experiment
Supplementary files format and content: raw_counts.txt. Tab-delimited text files include raw counts for each sample.The column gene_id is the sequence identifier.

organism: Abies pinsapo

source_name: Roots

growth_protocol: Abies Pinsapo needles and roots from 30-50 yr-old trees were sampled at Sierra de Las Nieves (Málaga, Spain) at two different locations: Puerto Saucillo-Yunquera (lower ecotone, 1100-1200 m asl) and Cañada del Cuerno-Ronda (upper ecotone, 1700-1800 m asl). The harvesting was carried out in September (2022) and May (2023), in six independent trees.

extract_protocol:
RNA total extraction was carried out following the method described by Canales et al. (2012). For RNA extractions from roots, the NucleoSpin RNA Plant kit (Cat. No. 740120.50, Macherey-Nagel, Düren, Germany) was used according to the manufacturer’s instructions. Initial RNA quantification of the samples was performed using NanoPhotometer N60 spectrophotometer (Implen) (Fisher Scientific, Leicestershire, UK), and sample purity was evaluated based on 260/280 and 260/230 ratios. RNA integrity was verified through agarose gel electrophoresis and further assessed using a Fragment Analyzer System with the Agilent DNF-472 HS RNA Kit (Agilent, CA, USA). Only samples with a RIN greater than 7 were included in subsequent analyses.
Two types of libraries were prepared for the study: non-directional and directional. The non-directional library involved messenger RNA purification, RNA fragmentation, and first-strand cDNA synthesis using random hexamer primers, followed by second-strand cDNA synthesis with dUTP. For the directional library, dTTP was used for second-strand cDNA synthesis.

value: Roots

tag: month

value: May

tag: year

value: 30-50 years old

tag: biological replicate


title: Needles, Ronda, Spring, Ind3

description: Library name: PAPBT8NT

source_name: Needles

value: Needles


title: Muscle, baseline, SIE group, Participant #11

description: Library name: 11SIEPRE

value: baseline


title: Roots, Ronda, Spring, Ind1

description: Library name: PAPBT6R


title: Roots, Ronda, Spring, Ind3

description: Library name: PAPBT8R


title: Muscle, +24h, MICE group, Participant #9

description: Library name: 09MIE24H

value: MICE group

value: Participant #9


title: Needles, Ronda, Spring, Ind2

description: Library name: PAPBT7NT


title: Roots, Ronda, Spring, Ind2

description: Library name: PAPBT7R


title: Roots, Yunquera, Spring, Ind1

description: Library name: PAPBL3R


title: Needles, Ronda, Spring, Ind1

description: Library name: PAPBT6NT


title: Muscle, baseline, SIE group, Participant #10

description: Library name: 10SIEPRE


title: Muscle, +2.5h, MICE group, Participant #9

description: Library name: 09MIE03H


title: Muscle, baseline, MICE group, Participant #9

description: Library name: 09MIEPRE


title: Needles, Yunquera, Spring, Ind2

description: Library name: PAPBL4NT


title: Muscle, +24h, MICE group, Participant #8

description: Library name: 08MIE24H

value: Participant #8


title: Needles, Yunquera, Spring, Ind1

description: Library name: PAPBL3NT


title: Muscle, baseline, SIE group, Participant #12

description: Library name: 12SIEPRE

value: Skeletal muscle - Vastus lateralis

value: Participant #12


title: Roots, Ronda, Autumn, Ind3

description: Library name: APBT8R

value: September


title: Muscle, +2.5h, MICE group, Participant #8

description: Library name: 08MIE03H


title: Roots, Ronda, Autumn, Ind2

description: Library name: APBT7R


title: Muscle, baseline, MICE group, Participant #8

description: Library name: 08MIEPRE


title: Muscle, +24h, SIE group, Participant #9

description: Library name: 09SIE24H


title: Roots, Yunquera, Spring, Ind3

description: Library name: PAPBL5R


title: Muscle, +2.5h, SIE group, Participant #9

description: Library name: 09SIE03H


title: Roots, Ronda, Autumn, Ind1

description: Library name: APBT6R


title: Roots, Yunquera, Autumn, Ind3

description: Library name: APBL5R


title: Roots, Yunquera, Autumn, Ind2

description: Library name: APBL4R


title: Roots, Yunquera, Autumn, Ind1

description: Library name: APBL3R


title: Needles, Ronda, Autumn, Ind3

description: Library name: APBT8NT


title: Needles, Ronda, Autumn, Ind2

description: Library name: APBT7NT


title: Muscle, baseline, SIE group, Participant #9

description: Library name: 09SIEPRE


title: Muscle, +2.5h, MICE group, Participant #7

description: Library name: 07MIE03H

value: Participant #7


title: Muscle, +24h, MICE group, Participant #7

description: Library name: 07MIE24H


title: Needles, Yunquera, Autumn Ind3

description: Library name: APBL5NT


title: Muscle, baseline, MICE group, Participant #7

description: Library name: 07MIEPRE


title: Muscle, +24h, SIE group, Participant #8

description: Library name: 08SIE24H


title: Muscle, +24h, SIE group, Participant #7

description: Library name: 07SIE24H


title: Needles, Yunquera, Spring, Ind3

description: Library name: PAPBL5NT


title: Needles, Yunquera, Autumn, Ind1

description: Library name: APBL3NT


title: Needles, Ronda, Autumn, Ind1

description: Library name: APBT6NT


title: Needles, Yunquera, Autumn, Ind2

description: Library name: APBL4NT


title: Muscle, baseline, SIE group, Participant #8

description: Library name: 08SIEPRE


title: Muscle, +2.5h, SIE group, Participant #8

description: Library name: 08SIE03H


title: DLD-1 cells, replicate 3, RanGAP1 control, hour 5, no 4sU labeling

description:
Library name: rep3_0m5
SLAM-seq, 5 hours post-arrest release

data_processing:
*library strategy: SLAM-seq
Adapter trimming was performed using trimmomatic ILLUMINACLIP with TruSeq3 adapter sequences. Replicate 1 fastq files were subsampled to median read depth of replicate 2 and replicate 3 samples using seqtk. Replicate 2 and 3 reads (2x150 PE reads) were trimmed to 100nt reads for concordance with replicate 1 (2x100 PE reads). fastq.gz files here are raw reads wtihout trimming or subsampling.
Adapter trimmed, subsampled/length trimmed reads were aligned to Ensembl GRCh38v95 with Hisat-3n v2.2.1-3n-0.0.3, specifying T>C conversions (--base-change T,C)
TPMs were calculated using Kallisto quant v0.48.0. TPM files here are computed from adapter-trimmed and subsampled (rep1) / length trimmed (rep2 and rep3) fastq files.
Assembly: Ensembl GRCh38v95
Supplementary files format and content: Tab-delimited text files include transcript lengths, effective lengths, estimated counts, and computed TPMs for total RNA.

extract_protocol:
Total RNA harvested in TRIzol reagent in DNA LoBind tubes. 10% 4sU-labeled and unlabeled ERCC spike-ins added proportional to harvested cell number. RNA extracted with Zymo RNA Clean & Concentrate columns.
3ug total RNA was taken into ribosomal RNA depletion (Z. Zhang et al., 2012). rRNA-depleted RNA was treated with 10mM iodoacetamide to alkylate 4sU bases (Herzog et al., 2017). 100ng rRNA-depleted, IAA-treated RNA per sample was used as input to NEBNext Ultra II directional RNA library prep kit and libraries were prepared according to manufacturer's recommendations. Library quality was assessed on Agilent TAPE station.

treatment_protocol: 1 hour of 1mM 4sU labeling where noted

value: colorectal adenocarcinoma

tag: genotype

value: WT

value: pro-metaphase cell cycle arrest

value: hour 5


title: Muscle, +2.5h, SIE group, Participant #7

description: Library name: 07SIE03H

value: SIE group


title: Muscle, baseline, SIE group, Participant #7

description: Library name: 07SIEPRE


title: DLD-1 cells, replicate 3, RanGAP1 KD, hour 5, 1 hour 4sU labeling

description:
Library name: rep3_p5
SLAM-seq, 5 hours post-arrest release

value: RanGAP1 knockdown (AID)


title: Muscle, +2.5h, MICE group, Participant #6

description: Library name: 06MIE03H

value: Participant #6


title: DLD-1 cells, replicate 3, RanGAP1 KD, hour 4, 1 hour 4sU labeling

description:
Library name: rep3_p4
SLAM-seq, 4 hours post-arrest release

value: hour 4


title: DLD-1 cells, replicate 3, RanGAP1 control, hour 0, no 4sU labeling

description:
Library name: rep3_0m0
SLAM-seq, cell cycle arrested (pro-metaphase)

value: hour 0


title: Muscle, baseline, MICE group, Participant #6

description: Library name: 06MIEPRE

value: baseline


title: DLD-1 cells, replicate 3, RanGAP1 KD, hour 3, 1 hour 4sU labeling

description:
Library name: rep3_p3
SLAM-seq, 3 hours post-arrest release

value: hour 3


title: Muscle, +24h, SIE group, Participant #6

description: Library name: 06SIE24H


title: DLD-1 cells, replicate 3, RanGAP1 KD, hour 2, 1 hour 4sU labeling

description:
Library name: rep3_p2
SLAM-seq, 2 hours post-arrest release

value: hour 2


title: Muscle, +2.5h, SIE group, Participant #6

description: Library name: 06SIE03H


title: Muscle, baseline, SIE group, Participant #6

description: Library name: 06SIEPRE


title: DLD-1 cells, replicate 3, RanGAP1 KD, hour 1, 1 hour 4sU labeling

description:
Library name: rep3_p1
SLAM-seq, 1 hour post-arrest release

value: hour 1


title: Muscle, +2.5h, SIE group, Participant #5

description: Library name: 05SIE03H

value: Skeletal muscle - Vastus lateralis

value: Participant #5


title: DLD-1 cells, replicate 3, RanGAP1 control, hour 5, 1 hour 4sU labeling

description:
Library name: rep3_m5
SLAM-seq, 5 hours post-arrest release


title: DLD-1 cells, replicate 3, RanGAP1 control, hour 4, 1 hour 4sU labeling

description:
Library name: rep3_m4
SLAM-seq, 4 hours post-arrest release


title: Muscle, +24h, MICE group, Participant #5

description: Library name: 05MIE24H

value: MICE group


title: Muscle, baseline, SIE group, Participant #5

description: Library name: 05SIEPRE


title: Muscle, +24h, SIE group, Participant #5

description: Library name: 05SIE24H


title: Muscle, baseline, MICE group, Participant #5

description: Library name: 05MIEPRE


title: Muscle, +24h, MICE group, Participant #4

description: Library name: 04MIE24H

value: Participant #4


title: DLD-1 cells, replicate 3, RanGAP1 control, hour 3, 1 hour 4sU labeling

description:
Library name: rep3_m3
SLAM-seq, 3 hours post-arrest release

value: colorectal adenocarcinoma


title: DLD-1 cells, replicate 3, RanGAP1 control, hour 0, 1 hour 4sU labeling

description:
Library name: rep3_m0
SLAM-seq, cell cycle arrested (pro-metaphase)

value: WT


title: Muscle, +2.5h, MICE group, Participant #4

description: Library name: 04MIE03H


title: Muscle, +2.5h, MICE group, Participant #5

description: Library name: 05MIE03H


title: DLD-1 cells, replicate 3, RanGAP1 KD, hour 0, 1 hour 4sU labeling

description:
Library name: rep3_p0
SLAM-seq, cell cycle arrested (pro-metaphase)

value: pro-metaphase cell cycle arrest


title: DLD-1 cells, replicate 2, RanGAP1 control, hour 5, no 4sU labeling

description:
Library name: rep2_0m5
SLAM-seq, 5 hours post-arrest release

value: hour 5


title: DLD-1 cells, replicate 2, RanGAP1 control, hour 0, no 4sU labeling

description:
Library name: rep2_0m0
SLAM-seq, cell cycle arrested (pro-metaphase)


title: DLD-1 cells, replicate 3, RanGAP1 control, hour 1, 1 hour 4sU labeling

description:
Library name: rep3_m1
SLAM-seq, 1 hour post-arrest release


title: DLD-1 cells, replicate 3, RanGAP1 control, hour 2, 1 hour 4sU labeling

description:
Library name: rep3_m2
SLAM-seq, 2 hours post-arrest release


title: Muscle, +24h, MICE group, Participant #6

description: Library name: 06MIE24H


title: DLD-1 cells, replicate 2, RanGAP1 KD, hour 5, 1 hour 4sU labeling

description:
Library name: rep2_p5
SLAM-seq, 5 hours post-arrest release


title: DLD-1 cells, replicate 2, RanGAP1 KD, hour 4, 1 hour 4sU labeling

description:
Library name: rep2_p4
SLAM-seq, 4 hours post-arrest release


title: DLD-1 cells, replicate 2, RanGAP1 KD, hour 3, 1 hour 4sU labeling

description:
Library name: rep2_p3
SLAM-seq, 3 hours post-arrest release


title: Muscle, +2.5h, SIE group, Participant #4

description: Library name: 04SIE03H

value: SIE group


title: Muscle, +24h, SIE group, Participant #4

description: Library name: 04SIE24H


title: Muscle, baseline, SIE group, Participant #4

description: Library name: 04SIEPRE


title: DLD-1 cells, replicate 2, RanGAP1 KD, hour 2, 1 hour 4sU labeling

description:
Library name: rep2_p2
SLAM-seq, 2 hours post-arrest release

value: RanGAP1 knockdown (AID)


title: DLD-1 cells, replicate 2, RanGAP1 KD, hour 0, 1 hour 4sU labeling

description:
Library name: rep2_p0
SLAM-seq, cell cycle arrested (pro-metaphase)


title: Muscle, +24h, SIE group, Participant #3

description: Library name: 03SIE24H

value: Participant #3


title: NAc, L33, Female, Naïve, IP

city: Portland

first: Marina

last: Guizzetti

state: OR

address: 3710 SW US Veterans Hospital Rd

department: Behavioral Neuroscience

institute: Oregon Health & Science University; Portland VA Research Service

description: Library name: L33FNNIP

data_processing:
Raw sequencing reads were quality assessed with FastQC v0.11.9
Sequencing reads were trimmed with Trimmomatic v0.39
Trimmed reads were aligned to the mouse reference genome from Ensembl (GRCm38) with the STAR aligner v2.7.10b
The Ensembl annotation gtf file GRCm38.99 was used during alignment to define gene regions and to obtain gene counts from the ReadsPerGene output files from STAR.
Assembly: GRCm38
Supplementary files format and content: comma separated file, read-counts per gene

source_name: Nucleus accumbens

extract_protocol:
Translating Ribosome Affinity Purification (TRAP) was carried out on nucleus accumbens brain punches to isolate astrocyte translating RNA. An aliquot was saved prior to the TRAP procedure to serve as input samples which represents the bulk-tissue RNA.
RNA libraries were generated with Takara’s SMART-Seq PLUS kit according to manufacturers protocol.

treatment_protocol: Animals underwent the CIE-2BC protocol for 5 rounds of CIE for dependent animals.

value: Nucleus accumbens

value: Female

tag: fraction

value: IP

value: Naïve

value: L


title: DLD-1 cells, replicate 2, RanGAP1 control, hour 5, 1 hour 4sU labeling

description:
Library name: rep2_m5
SLAM-seq, 5 hours post-arrest release

tag: treatment


title: DLD-1 cells, replicate 2, RanGAP1 KD, hour 1, 1 hour 4sU labeling

description:
Library name: rep2_p1
SLAM-seq, 1 hour post-arrest release

tag: cell type

value: hour 1


title: DLD-1 cells, replicate 2, RanGAP1 control, hour 4, 1 hour 4sU labeling

description:
Library name: rep2_m4
SLAM-seq, 4 hours post-arrest release

value: hour 4


title: NAc, L30, Female, Naïve, Input

description: Library name: L30FNNin

value: Input


title: NAc, L33, Female, Naïve, Input

description: Library name: L33FNNin


title: NAc, L32, Male, Naïve, Input

description: Library name: L32MNNin

value: Male


title: NAc, L31, Male, Naïve, IP

description: Library name: L31MNNIP


title: NAc, L32, Male, Naïve, IP

description: Library name: L32MNNIP


title: DLD-1 cells, replicate 2, RanGAP1 control, hour 3, 1 hour 4sU labeling

description:
Library name: rep2_m3
SLAM-seq, 3 hours post-arrest release

value: hour 3


title: DLD-1 cells, replicate 2, RanGAP1 control, hour 2, 1 hour 4sU labeling

description:
Library name: rep2_m2
SLAM-seq, 2 hours post-arrest release

value: colorectal adenocarcinoma

value: hour 2


title: DLD-1 cells, replicate 2, RanGAP1 control, hour 0, 1 hour 4sU labeling

description:
Library name: rep2_m0
SLAM-seq, cell cycle arrested (pro-metaphase)

value: WT

value: pro-metaphase cell cycle arrest

value: hour 0


title: NAc, L31, Male, Naïve, Input

description: Library name: L31MNNin


title: Muscle, baseline, MICE group, Participant #4

description: Library name: 04MIEPRE

value: Skeletal muscle - Vastus lateralis

value: baseline

value: MICE group

value: Participant #4


title: DLD-1 cells, replicate 1, RanGAP1 control, hour 0, no 4sU labeling

description:
Library name: rep1_0m0
SLAM-seq, cell cycle arrested (pro-metaphase)


title: NAc, L30, Female, Naïve, IP

description: Library name: L30FNNIP

value: Nucleus accumbens

value: Female

value: IP


title: DLD-1 cells, replicate 1, RanGAP1 control, hour 5, no 4sU labeling

description:
Library name: rep1_0m5
SLAM-seq, 5 hours post-arrest release

value: hour 5


title: NAc, L29, Female, Dependent, IP

description: Library name: L29FVNIP

value: Dependent

value: L


title: NAc, L29, Female, Dependent, Input

description: Library name: L29FVNin

value: Input


title: DLD-1 cells, replicate 1, RanGAP1 KD, hour 4, 1 hour 4sU labeling

description:
Library name: rep1_p4
SLAM-seq, 4 hours post-arrest release

value: RanGAP1 knockdown (AID)

value: hour 4


title: DLD-1 cells, replicate 1, RanGAP1 KD, hour 5, 1 hour 4sU labeling

description:
Library name: rep1_p5
SLAM-seq, 5 hours post-arrest release

value: colorectal adenocarcinoma


title: NAc, L28, Male, Naïve, Input

description: Library name: L28MNNin

value: Male

value: Naïve


title: NAc, L27, Female, Naïve, IP

description: Library name: L27FNNIP


title: DLD-1 cells, replicate 1, RanGAP1 KD, hour 3, 1 hour 4sU labeling

description:
Library name: rep1_p3
SLAM-seq, 3 hours post-arrest release

value: pro-metaphase cell cycle arrest

value: hour 3


title: NAc, L28, Male, Naïve, IP

description: Library name: L28MNNIP


title: DLD-1 cells, replicate 1, RanGAP1 KD, hour 2, 1 hour 4sU labeling

description:
Library name: rep1_p2
SLAM-seq, 2 hours post-arrest release

value: hour 2


title: DLD-1 cells, replicate 1, RanGAP1 KD, hour 1, 1 hour 4sU labeling

description:
Library name: rep1_p1
SLAM-seq, 1 hour post-arrest release

value: hour 1


title: NAc, L26, Male, Dependent, IP

description: Library name: L26MVNIP


title: DLD-1 cells, replicate 2, RanGAP1 control, hour 1, 1 hour 4sU labeling

description:
Library name: rep2_m1
SLAM-seq, 1 hour post-arrest release

value: WT


title: DLD-1 cells, replicate 1, RanGAP1 control, hour 5, 1 hour 4sU labeling

description:
Library name: rep1_m5
SLAM-seq, 5 hours post-arrest release


title: NAc, L26, Male, Dependent, Input

description: Library name: L26MVNin

value: Nucleus accumbens


title: NAc, L25, Female, Dependent, IP

description: Library name: L25FVNIP

value: Female


title: DLD-1 cells, replicate 1, RanGAP1 control, hour 4, 1 hour 4sU labeling

description:
Library name: rep1_m4
SLAM-seq, 4 hours post-arrest release


title: NAc, L25, Female, Dependent, Input

description: Library name: L25FVNin


title: NAc, L24, Female, Naïve, Input

description: Library name: L24FNNin


title: NAc, L23, Male, Naïve, Input

description: Library name: L23MNNin


title: DLD-1 cells, replicate 1, RanGAP1 control, hour 3, 1 hour 4sU labeling

description:
Library name: rep1_m3
SLAM-seq, 3 hours post-arrest release


title: NAc, K21, Male, Dependent, IP

description: Library name: K21MVNIP

value: IP

value: K


title: DLD-1 cells, replicate 1, RanGAP1 control, hour 0, 1 hour 4sU labeling

description:
Library name: rep1_m0
SLAM-seq, cell cycle arrested (pro-metaphase)

value: hour 0


title: NAc, L27, Female, Naïve, Input

description: Library name: L27FNNin

value: L


title: NAc, K21, Male, Dependent, Input

description: Library name: K21MVNin

value: Input

value: Dependent


title: NAc, K20, Female, Naïve, IP

description: Library name: K20FNNIP