title: CD22.BBζ-CD22.28ζ CAR T cells stimulated with CD22 protein coated beads for 4 hours replicate2

description: Library name: 4hrCD22Bsti109-110_Rep2


title: CD22.BBζ-CD22.28ζ CAR T cells stimulated with CD22 protein coated beads for 4 hours replicate1

status: Public on Aug 13 2025

type: SRA

city: Philadelphia

first: E

middle: JOHN

last: WHERRY

state: PA

address: 421 Curie Blvd,354 BRB II/III

department: Systems Pharmacology       and Translational Therapeutics,Institute for Immunology

country: USA

institute: University of Pennsylvania

description: Library name: 4hrCD22Bsti109-110_Rep1

library_source: transcriptomic

data_processing:
RNA sequencing reads were aligned to hg19 build of human genome using STAR-2.5.2a
The aligned reads were quantified using feature counts function from the Subread package
Merged counts for all the samples are normalized and analyzed using R package DESeq2 for identifying differentially expressed genes between groups of interest
Assembly: hg19
Supplementary files format and content: Merged counts file
Supplementary files format and content: Normalized counts file

molecule: total RNA

organism: Homo sapiens

source_name: Primary Human T cells

growth_protocol: Primary human T cells were activated with anti-CD3/28 coated beads, transduced with either CD19.BBζ, CD19.28ζ, or both vectors, and expanded for 7-9 days to generate CARTs

extract_protocol:
non-transfected (NTF), CD19.BBζ-CD19.28ζ, CD19.BBζ and CD19.28ζ CAR T cells after incubation with CD19 protein coated beads, CD22.BBζ-CD22.28ζ, CD22.BBζ and CD22.28ζ CAR T cells after CD22 protein coated beads , and STD CD19.BBζ-CD19.28ζ, MTDs CD19.28ζ-CD22.BBζ and CD19.BBζ-CD22.28ζ after CD19&CD22 protein coated beads ,All stimulations were for 4 hours
All the replicates for the 4hr stimulated cells were extracted for RNA and libraries were created for transcriptional analysis

treatment_protocol: T cells were electroporated with various CAR RNA and one day later CAR T cells were stimulated with CD19 , CD22 ,or CD19&CD22  protein coated beads

tag: cell line

value: Primary Human T cells


title: CD22.BBζ CAR T cells stimulated with CD22 protein coated beads for 4 hours replicate3

description: Library name: 4hrCD22Bsti109_Rep3


title: CD22.BBζ CAR T cells stimulated with CD22 protein coated beads for 4 hours replicate2

description: Library name: 4hrCD22Bsti109_Rep2


title: Non-transfected T cells stimulated with CD19 protein coated beads for 4 hours replicate2

description: Library name: 4hrCD19BstiNTF_Rep2


title: CD22.BBζ CAR T cells stimulated with CD22 protein coated beads for 4 hours replicate1

description: Library name: 4hrCD22Bsti109_Rep1


title: Non-transfected T cells stimulated with CD19 protein coated beads for 4 hours replicate1

description: Library name: 4hrCD19BstiNTF_Rep1


title: Non-transfected T cells stimulated with CD19 protein coated beads for 4 hours replicate3

description: Library name: 4hrCD19BstiNTF_Rep3


title: Non-transfected T cells stimulated with CD19&CD22 protein coated beads for 4 hours replicate3

description: Library name: 4hrCD1922BstiNTF_Rep3


title: left brain, Day 10, open-field, fish 20E2

city: University Park

first: Jason

last: Keagy

address: 410 Forest Resources Bldg

department: Ecosystem Science and Management

institute: Penn State University

description:
Library name: 1B1_20E2
3'TagSeq

data_processing:
We conducted quality control checks using fastqc (v0.11.8).
Next, reads were aligned to the Gasterosteus aculeatus Ensembl BROAD S1 draft genome (version 92) using STAR (v2.2.3a) with alignment rates of 70.43±1.55%
We used htseq (v0.9.1) to count gene transcripts.
Assembly: Gasterosteus aculeatus Ensembl BROAD S1 draft genome (version 92)
Supplementary files format and content: Tab deliminated text file containing raw read counts with samples in columns and genes in rows. Each sample has six columns corresponding to the six lanes of sequencing.

molecule: polyA RNA

organism: Gasterosteus aculeatus

source_name: left brain

extract_protocol:
Each subject was killed by rapid cervical dissection and the brain was immediately dissected under a microscope in a Sylgaard 184-lined petri-dish. Half of the brain was placed in RNAlater, stored at 4C overnight, and transferred to -20C until RNA extraction. We extracted RNA using Macherey-Nagel NucleoSpin 96 RNA kits with an Eppendorf EpMotion 5075v liquid-handling robot.
242 samples (1.5 μg of RNA in 37.5 μl of RNase-free water) were sent to the Genomic Sequencing and Analysis Facility (GSAF) at the University of Texas at Austin for 3’Tag-seq library preparation and sequencing (6 lanes of Illumina HiSeq 2500, 100 nt reads).

tag: tissue

value: left brain

tag: treatment

value: Day 10

tag: condition

value: open-field

tag: Sex

value: female


title: Non-transfected T cells stimulated with CD19&CD22 protein coated beads for 4 hours replicate2

description: Library name: 4hrCD1922BstiNTF_Rep2


title: Non-transfected T cells stimulated with CD22 protein coated beads for 4 hours replicate1

description: Library name: 4hrCD22BstiNTF_Rep1


title: CD19.28ζ CAR T cells stimulated with CD19 protein coated beads for 4 hours replicate3

description: Library name: 4hrCD19Bsti106_Rep3


title: Non-transfected T cells stimulated with CD19&CD22 protein coated beads for 4 hours replicate1

description: Library name: 4hrCD1922BstiNTF_Rep1


title: Tax-induced productive infection with BLV in YR2 cells

city: Namur

first: Damien

last: Coupeau

address: Rue de Bruxelles, 61

department: Namur Research Institute for Life Sciences

country: Belgium

institute: University of Namur

data_processing:
Viral reads recovery (alignment using BWA mem -a -T15) (BWA v0.7.11)
Adapter trimming (Trimmomatic v0.39. Included the trimming of the adapters, quality trimming (Sliding Window 4:15), and a minimal length filter of 70 nucleotides
PCR duplicates removal (dedupe.sh (BBMap v1.0))
vCircTrappist v1.0 pipeline for circRNA-originating reads identification (including Samtools v1.10 and BWA v0.7.11)
Assembly: KX905135.1 ; KT122858.1 ; AC_000008.1 ; NC_001436.1 ; EF523390.1
Supplementary files format and content: tab-delimited text file including raw circRNA-derived reads count, circularization sites sequences, splicing pattern, strandness of the reads, 5' and 3' positions of the circularization sites, max size of the circRNAs, colocalized genes, common k-mers between circularization sites, viral segment, read identifiers

organism: Ovis aries

extract_protocol:
RNA was extracted using TRI-reagent (Thermofisher) and 4ug were sent to sequencing (Novogene).
1µg of total RNA was sent to Novogene for the library preparation and sequencing. Library preparation include : ribosomal depletion, linear RNA degradation, RNA fragmentation, reverse transcription, second strand synthesis (using dUTPs), end-repair, A-tailing, adapter ligation, enzyme digestion to remove dUTPs-containing second strand cDNAs, size selection, PCR amplification

tag: genotype

value: LTaxSN

value: BLV-infected


title: CD19.28ζ CAR T cells stimulated with CD19 protein coated beads for 4 hours replicate2

description: Library name: 4hrCD19Bsti106_Rep2


title: Tax-induced productive infection with BLV in L267 cells


title: CD19.28ζ CAR T cells stimulated with CD19 protein coated beads for 4 hours replicate1

description: Library name: 4hrCD19Bsti106_Rep1


title: CD19.BBζ-CD19.28ζ CAR T cells stimulated with CD19 protein coated beads for 4 hours replicate2

description: Library name: 4hrCD19Bsti105-106_Rep2


title: astrocyte_P17_ATAC_rep2

city: Daejeon

first: Inkyung

last: Jung

address: KAIST, 291 Daehak-ro, Yuseong-gu

department: Biological Sciences

country: South Korea

institute: KAIST

library_source: genomic

data_processing:
Reads were trimmed for adapters and minimum length of 20 and shorten reads to 75 using cutadapt version 1.18.
RNA-seq reads were aligned to the mm10 using STAR version 2.7.3a. ATAC-seq reads were aligned to the mm10 using bowtie2 version 2.3.4.
For RNA-seq, expected count, TPM, and FPKM were calculated using a RSEM v1.3.1.
For ATAC-seq, reads that have MAPQ smaller than 30, not in proper pairs, or mapping to mitochondrial DNA were discarded. PCR duplicates were removed using Picard's MarkDuplicates (v2.21.3). Then, reads were shifted using alignmentSieve v3.1.3 with the option --ATACshift. Peak calling was performed using macs2 callpeak v2.1.2 with the option: -q 0.01 --nomodel --extsize 200 --shift -100 --keep-dup all.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include gene level expected count, TPM, and FPKM values for each sample derived from RSEM for RNA-seq. narrowPeak for ATAC-seq.

molecule: genomic DNA

organism: Mus musculus

source_name: Astrocyte

extract_protocol:
RNA was extraced for each astrocyte sample using NucleoSpin RNA XS (Macherey-Nagel) for RNA-seq. Nuclei of PBS washed monocytes was isolated using lysis buffer for ATAC-seq.
Amplified cDNA from total RNA was obtained using Ovation RNA-Seq System V2 (NuGEN) and RNA-seq libraries was prepared using TruSeq Stranded mRNA (Illumina). For ATAC-seq, Tagment DNA TDE1 Enzyme and Buffer Kit (Illumina) was used for tagmentation reaction. After cleaning up using MinElute PCR Purification Kit (Qiagen), PCR amplication was done. Finally, size selection was done with AMPure XP (Beckman Coulter).
RNA-seq and ATAC-seq

tag: cell type

value: Astrocyte


title: astrocyte_P30_ATAC_rep1


title: CD19.BBζ-CD19.28ζ CAR T cells stimulated with CD19 protein coated beads for 4 hours replicate3

description: Library name: 4hrCD19Bsti105-106_Rep3


title: astrocyte_P30_ATAC_rep2


title: CD19.BBζ-CD19.28ζ CAR T cells stimulated with CD19 protein coated beads for 4 hours replicate1

description: Library name: 4hrCD19Bsti105-106_Rep1


title: astrocyte_P17_ATAC_rep1


title: CD19.BBζ CAR T cells stimulated with CD19 protein coated beads for 4 hours replicate3

description: Library name: 4hrCD19Bsti105_Rep3


title: astrocyte_P7_ATAC_rep2


title: CD19.BBζ CAR T cells stimulated with CD19 protein coated beads for 4 hours replicate2

description: Library name: 4hrCD19Bsti105_Rep2


title: CD19.BBζ CAR T cells stimulated with CD19 protein coated beads for 4 hours replicate1

description: Library name: 4hrCD19Bsti105_Rep1


title: astrocyte_P3_ATAC_rep2


title: CD22.BBζ-CD22.28ζ CAR T cells stimulated with CD19&CD22 protein coated beads for 4 hours replicate3

description: Library name: 4hrCD1922Bsti109-110_Rep3


title: astrocyte_P1_ATAC_rep2


title: astrocyte_P3_ATAC_rep1


title: CD22.BBζ-CD22.28ζ CAR T cells stimulated with CD19&CD22 protein coated beads for 4 hours replicate2

description: Library name: 4hrCD1922Bsti109-110_Rep2


title: astrocyte_P1_ATAC_rep1


title: astrocyte_E18.5_ATAC_rep2


title: CD22.BBζ-CD22.28ζ CAR T cells stimulated with CD19&CD22 protein coated beads for 4 hours replicate1

description: Library name: 4hrCD1922Bsti109-110_Rep1


title: CD19.28ζ-CD22.BBζ CAR T cells stimulated with CD19&CD22 protein coated beads for 4 hours replicate2

description: Library name: 4hrCD1922Bsti106-109_Rep2


title: astrocyte_P7_ATAC_rep1


title: astrocyte_E18.5_ATAC_rep1


title: CD19.28ζ-CD22.BBζ CAR T cells stimulated with CD19&CD22 protein coated beads for 4 hours replicate1

description: Library name: 4hrCD1922Bsti106-109_Rep1


title: astrocyte_E16.5_ATAC_rep1


title: CD19.BBζ-CD22.28ζ CAR T cells stimulated with CD19&CD22 protein coated beads for 4 hours replicate1

description: Library name: 4hrCD1922Bsti105-110_Rep1


title: CD19.BBζ-CD22.28ζ CAR T cells stimulated with CD19&CD22 protein coated beads for 4 hours replicate2

description: Library name: 4hrCD1922Bsti105-110_Rep2


title: CD19.28ζ-CD22.BBζ CAR T cells stimulated with CD19&CD22 protein coated beads for 4 hours replicate3

description: Library name: 4hrCD1922Bsti106-109_Rep3


title: CD19.BBζ-CD19.28ζ CAR T cells stimulated with CD19&CD22 protein coated beads for 4 hours replicate3

description: Library name: 4hrCD1922Bsti105-106_Rep3


title: astrocyte_P30_RNA_rep1


title: astrocyte_P17_RNA_rep2


title: CD19.BBζ-CD19.28ζ CAR T cells stimulated with CD19&CD22 protein coated beads for 4 hours replicate2

description: Library name: 4hrCD1922Bsti105-106_Rep2


title: astrocyte_E16.5_ATAC_rep2


title: astrocyte_P17_RNA_rep1


title: CD19.BBζ-CD19.28ζ CAR T cells stimulated with CD19&CD22 protein coated beads for 4 hours replicate1

description: Library name: 4hrCD1922Bsti105-106_Rep1


title: CD19.BBζ-CD22.28ζ CAR T cells stimulated with CD19&CD22 protein coated beads for 4 hours replicate3

description: Library name: 4hrCD1922Bsti105-110_Rep3


title: astrocyte_P30_RNA_rep2


title: MKN45_Nutlin-3_24h

city: Chiba

first: Masaki

last: Fukuyo

address: 1-8-1 Inohana, Chuo-ku

department: Department of Molecular Oncology

country: Japan

institute: Chiba University

data_processing:
Illumina Casava1.8.2 software used for basecalling.
Read were aligned with HISAT2.
Fragments per kilobase of exon model per million mapped fragments (FPKM) were calculated using Cufflinks v2.0.2.
Assembly: hg19
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample.

source_name: Human gastric epithelial cancer cell line MKN45

growth_protocol: SNU-719, SNU-1, AGS, MKN45, MKN7, MKN74, TMK1, KATO-III and GES1 were grown in RPMI 1640 with 10% FBS,  penicillin-streptomycin. IM95 was grown in DMEM with 10% FBS,  penicillin-streptomycin and 10 mg/L human recombinant insulin. YCCEL1, WI-38 and IMR-90 were grown in MEM with 10% FBS,  penicillin-streptomycin and Non-Essential Amino Acids .

extract_protocol:
Total RNA was collected using RNeasy (Invitrogen, Carlsbad, CA)
Libraries for RNA-seq were prepared using the TruSeq Stranded mRNA Sample Prep Kit (Illumina).

tag: stimulation

tag: time


title: astrocyte_P7_RNA_rep2


title: GFP+CD25+CD4+ cells from Cre+FLEX4(Tim-3 KO) MC38 tumor Mouse3 exp2

city: Pittsburgh

first: Lawrence

middle: P.

last: Kane

address: 5051 Centre Ave.

department: Immunology

institute: University of Pittsburgh

description: Library name: Tim-3_KO-3_500_cells_C3_S29

data_processing:
FASTq reads were quality checkedand  mapped with GRCm38 ref genome usingCLC genomics workbench V25 default setting
Map reads were quantified  using CLC genomics workbench
Raw count data was downloaded from CLC genomics and uploaded to Partekflow
raw count data was normalized using TMM and differential expression was performed using ANOVA in Partekflow12.4.2
Assembly: GRCm39
Supplementary files format and content: CSV file with raw counts per sample

source_name: MC38 Tumor

extract_protocol:
MC38 tumor ( Day 12) was taken out and enzymetically digested to make single cell suspension, negatively magnetically purified to mostly get untouched CD4 cells, these cells were then sorted based on CD45+CD90.2+CD4+CD25+GFP+ directly into RNA lysis buffer.(Tim-3 stain was included to confirm effective Knockout of Tim-3 in Tim-3 KO(FLEX4) mouse.
SmartSeq cDNA / Nextera XT libraries

treatment_protocol: Mouse prior to Tumor implantation were administered Tamoxifen I.P

value: MC38 Tumor

value: Treg cells

value: Tamoxifen  prior to tumor implantation

value: Day 12 post Tumor implantation


title: MKN45_DMSO_24h

value: DMSO


title: AGS_RG7388_24h

source_name: Human gastric epithelial cancer cell line AGS

value: AGS


title: astrocyte_P7_RNA_rep1


title: MKN45_RG7388_24h


title: GFP+CD25+CD4+ cells from Cre+FLEX4(Tim-3 KO) MC38 tumor Mouse2 exp2

description: Library name: Tim-3_KO-2_500_cells_B3_S28


title: AGS_Nutlin-3_24h


title: AGS_DMSO_24h


title: astrocyte_P3_RNA_rep2


title: IM95_RG7388_24h

source_name: Human gastric epithelial cancer cell line IM95


title: astrocyte_P3_RNA_rep1


title: GFP+CD25+CD4+ cells from Cre control MC38 tumor Mouse3 exp2

description: Library name: WT3_500_cells_G1_S26


title: IM95_Nutlin-3_24h


title: astrocyte_P1_RNA_rep2


title: GFP+CD25+CD4+ cells from Cre+FLEX4(Tim-3 KO) MC38 tumor Mouse1 exp2

description: Library name: Tim-3_KO-1_500_cells_A3_S27


title: IM95_DMSO_24h


title: SNU-1_Nutlin-3_24h

source_name: Human gastric epithelial cancer cell line SNU-1


title: GFP+CD25+CD4+ cells from Cre control MC38 tumor Mouse2 exp2

description: Library name: WT2_500_cells_F1_S25


title: SNU-1_DMSO_24h


title: astrocyte_P1_RNA_rep1


title: YCCEL1_RG7388_24h

source_name: Human gastric epithelial cancer cell line YCCEL


title: astrocyte_E18.5_RNA_rep3


title: SNU-1_RG7388_24h


title: GFP+CD25+CD4+ cells from Cre control MC38 tumor Mouse1 exp2

description: Library name: WT1_500_cells_E1_S24


title: YCCEL1_Nutlin-3_24h


title: astrocyte_E18.5_RNA_rep2


title: YCCEL1_DMSO_24h


title: GFP+CD25+CD4+ cells from Cre+FLEX4(Tim-3 KO) MC38 tumor Mouse2 exp1

description: Library name: E2_Flex4_5_S22


title: astrocyte_E18.5_RNA_rep1


title: SNU-719_RG7388_24h

source_name: Human gastric epithelial cancer cell line SNU-719


title: GFP+CD25+CD4+ cells from Cre+FLEX4(Tim-3 KO) MC38 tumor Mouse3 exp1

description: Library name: F2_Flex4_6_S23


title: SNU-719_DMSO_24h


title: SNU-719_Nutlin-3_24h


title: SNU-1_shMDM2_d3

value: SNU-1 + shMDM2


title: GFP+CD25+CD4+ cells from Cre+FLEX4(Tim-3 KO) MC38 tumor Mouse1 exp1

description: Library name: A2_Flex41_S21


title: SNU-1_shNT_d0

value: SNU-1 + shNT


title: astrocyte_E16.5_RNA_rep1


title: astrocyte_E16.5_RNA_rep2


title: SNU-719_shMDM2_d0

value: SNU-719 + sMDM2


title: SNU-719_shMDM2_d3


title: GFP+CD25+CD4+ cells from Cre control MC38 tumor Mouse1 exp1

description: Library name: A1_WT1_S18


title: SNU-719_shNT_d3

value: SNU-719 + shNT


title: SNU-1_shMDM2_d0


title: GFP+CD25+CD4+ cells from Cre control MC38 tumor Mouse3 exp1

description: Library name: F1_WT6_S20


title: whole blood of subject 240

type: genomic

city: Budapest

first: Ferenc

last: Torma

state: Pest

address: Alkotas st. 42-48

department: Research Institute of Sport Science

country: Hungary

institute: Hungarian University of Sports Science

description: Genomic DNA from whole blood of a healthy subject

hyb_protocol: Bisulphite converted DNA was amplified, fragmented and hybridized to human Infinium MethylationEPIC BeadChip (Illumina) using standard Illumina protocol

scan_protocol: Arrays were imaged using BeadArray Reader (HiScan) and standard recommended Illumina scanner setting

data_processing:
minfi version 1.52.1 and ChAMP version 2.36.0
processed value definition: Beta values (linked as supplementary file on Series record)

label: Cy3 and Cy5

source_name: Whole blood

label_protocol: Standard Illumina Protocol

extract_protocol: Whole blood DNA was extracted using a silica membrane–based protocol.

value: Whole blood

tag: age


title: ATACseq, KmgKD, rep1

city: Stanford

first: Neuza

last: Reis Matias

state: CA

address: 279 Campus Drive

department: Developmental Biology

institute: Stanford University

description:
Library name: ATACseq_KmgKD_rep1
75bp

data_processing:
trim adaptors and low quality bases. trim_galore/0.4.1
map with bwa/0.7.10
create bigwig files with bedtools/2.25.0 and bedGraphToBigWig
Assembly: dm6
Supplementary files format and content: BigWig files normalized by library sizes

organism: Drosophila melanogaster

source_name: Testes

extract_protocol:
For each technical replicate, 10~20 pairs of testes from < 1 day old male flies were dissected in PBS on ice, and immediately digested for 8 minutes at room temperature in 0.5mg/ml of dispase (Worthington LS02109) and 0.5mg/ml of collagenase XI (Sigma C7657) dissolved in PBS with 0.3mM of CaCl2. Testis were washed once in cold PBS and broken open by pipetting 7 ~ 10 times in 50ul of cold PBS. Cells were spun down at 2000rpm for 1min, cold lysis buffer (Buenrostro et al. 2015) added, and the pellet gently resuspended by flicking the tube. After another 2000rpm 2min spin, 20ul of transposase mix from the Nextera Kit (Illumina, cat. no. FC-121-1030) was added and the pellet gently resuspended by flicking the tube. The reaction was incubated at 30oC for 25min with the tube flicked once during incubation.
The DNA was purified using Qiagen MinElute column (Qiagen 28004) and the entire sample used for PCR with NEBNext (NEB M0541S) for a total of 8~9 amplification cycles.

value: Testes

value: bamGAL4/ KmgRNAi

value: Fly crosses were kept for 3 days at 25°C. Adults were then flipped to a new bottle, while the eggs and early larvae were shifted to 29°C. Testes were dissected from 0–2 day old males in 1xPBS.


title: whole blood of subject 237

value: female


title: whole blood of subject 239


title: SNU-1_shNT_d3


title: sgNDUFA5_1_SCM_replicate3

first: Katherine

last: Aird

institute: University of Pittsburgh School of Medicine

description: Library name: K3

data_processing:
Demultiplexed and quality-filtered mRNA-Seq reads were then aligned to human reference genome (GRCh38) using STAR (v.2.6.1)
Differential expression analysis was done using DESeq2 (v2_1.6.3)
Assembly: hg38
Supplementary files format and content: Tab delimited text file includes FPKMs for all samples

growth_protocol: Ovcar8 cells were cultured in RPMI 1640 + 5% FBS

extract_protocol:
RNA was harvested by Trizol followed by a Qiagen clean up column with a DNAse step.
The cDNA libraries were prepared using NEBNext Ultra 2 RNA Library Prep Kit for Illumina (New England Biolabs; Cat.# E7775)

treatment_protocol: Cells were cultured in conditioned media and RPMI 1640 + 5% in a 1:1 ratio

value: High grade serous ovarian cancer

value: NDUFA5 knockout 1

value: Senescent cell conditioned media


title: whole blood of subject 236


title: Myocardial infarction s/p retroviral PHF7 intramyocardial injection  [snATAC-seq]

city: Dallas

first: kenian

last: chen

state: TX

address: 5323 Harry Hines Boulevard

department: Population and Data Science

institute: UTsouthwestern

library_source: genomic single cell

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger Arc software 2.0.0 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: mm10
Supplementary files format and content: filtered .h5 matrix files

source_name: heart

extract_protocol:
Heart nuclei were extracted using a modified version of a previously described protocol in ref (PMID: 34382019). Hearts were dissected, snap-frozen, and stored at -80C. For each conditions n=1-3 hearts were pooled together. Hearts were thawed for 5 min on ice and the minced with scissors in 1 ml cold lysis buffer (10 mM Tris-HCl pH7.4, 10 mM NaCl, 3 mM MgCl2, 0.1% NonidetTM P40, 1 mM DTT, 1 U/μl RNase inhibitor in Nuclease-Free Water). After 2 min, 4 ml of cold lysis buffer was added, and hearts were lysed for 5 min at 4 °C. 10 ml of cold wash buffer (PBS, BSA 2%, and 0.2 U/μl RNase inhibitor from Roche) was added, and the lysate was dounced with 20 strokes of a loose pestle. The homogenate was filtered with 70 μm and 40 μm cell strainers. Nuclei were pelleted by centrifugation for 5 min at 500 × g at 4 °C. Nuclei were resuspended in 0.5 ml of wash buffer. Nuclei were resuspended in 0.5 ml of wash buffer and 2 μl of anti-Nuclear Pore Complex conjugated antibody (Biolegend, 682203) to stain all nuclei. After 15 min, nuclei were pelleted by centrifugation for 5 min at 500 × g at 4 °C. Then the nuclei were resuspended in 300 μl of wash buffer and filtered with 30μm cell strainers. More than 200,000 nuclei were FACS sorted with a BD FACSAria III and the BD FACSDIVA and FlowJo v10.8.1 software. Nuclei were pelleted by centrifugation for 10 min at 500 × g at 4 °C and then resuspended in 200 μl of ATAC lysis buffer (10 mM Tris-HCl pH7.4, 10 mM NaCl, 3 mM MgCl2, 0.01% Tween-20, 0.01% NonidetTM P40, 0.001% Digitonin, 1% BSA, 1 mM DTT, 1U/ul RNase inhibitor in Nuclease-Free Water). After 2 min, 1.3 ml of ATAC wash buffer (10 mM Tris-HCl pH7.4, 10 mM NaCl, 3 mM MgCl2, 0.1% Tween-20, 1 mM DTT, 1% BSA, 1U/μl RNase inhibitor in Nuclease-Free Water) was added. Nuclei were pelleted by centrifugation for 10 min at 500 × g at 4 °C and resuspended in 20 μl of diluted nuclei buffer from 10X genomics.
Library was performed according to the manufacter’s instructions (Next GEM single-cell Multiome ATAC+ Gene expression kit). Briefly, Post GEM-incubation Cleanup using DynaBeads MyOne Silane Beads was followed by Pre-Amplification PCR (72 °C for 5 min, 98 °C for 3 min, cycled 7 × 98 °C for 20 s, 63 °C for 30 s, 72 °C for 1 min). After cleanup with SPRIselect Reagent Kit, ATAC library was generated (98 °C for 45 s, cycled 8 × 98 °C for 20 s, 67 °C for 30 s, 72 °C for 20 s) and purified with SPRIselect Reagent Kit. The fragment size estimation of the resulting ATAC libraries was assessed with Agilent TapeStation D1000 HS (Agilent) and quantified using the QubitTM double stranded DNA (dsDNA) High-Sensitivity HS assay (ThermoFisher Scientific). SnATAC-seq libraries were then sequenced by pair with a HighOutput flowcel using an Illumina Nextseq 500 with the following mode: Read 1N - 63 cycles, i7 index – 8 cycles, i5 index - 24 cycles *(8 dark cycles and 16 cycles on i5), Read 2N - 63 cycles. SnRNA-seq libraries were constructed by performing the following steps: cDNA Amplification, SPRIselect cleanup, Fragmentation, End reair and A tailing, SPRIselect cleanup, and Adaptor ligation, SPRIselect cleanup, Samplex index PCR and SPRIselect cleanup size selection. The fragment size estimation of the resulting libraries was assessed with Agilent TapeStation D1000 (Agilent) and quantified using the QubitTM double stranded DNA (dsDNA) High-Sensitivity HS assay (ThermoFisher Scientific).

treatment_protocol: Following myocardial infarction (MI) with permanent left anterior descending artery ligation, mice received a single intramyocardial injection (28uL) of concentrated retrovirus bearing emtpy control, PHF7, PT or PMT cocktail. Mice were exposed to tamoxifen chow diet continuously until hearts were harvested at four weeks post-MI.

value: heart

value: heart nuclei


title: sgNDUFA5_1_SCM_replicate2

description: Library name: K2


title: whole blood of subject 231


title: sgNDUFA5_1_SCM_replicate1

description: Library name: K1


title: whole blood of subject 230

value: male


title: GFP+CD25+CD4+ cells from Cre control MC38 tumor Mouse2 exp1

description: Library name: C1_WT3_S19

value: MC38 Tumor

value: Treg cells

value: Tamoxifen  prior to tumor implantation

value: Day 12 post Tumor implantation


title: Cachexia - PBMC_EOCX_F

city: Tainan City

first: Po-Hsien

middle: Joseph

last: Huang

address: 1 University Rd.

department: Biochemistry and Molecular Biology

country: Taiwan

institute: National Cheng Kung University

library_source: transcriptomic single cell

data_processing:
10x Genomics Cell Ranger pipeline v6.0.2 (https://support.10xgenomics.com) was used to process the raw Illumina sequencing files to generate fastq files and align the sequencing reads to mouse reference(mm10, GENCODE vM23/Ensembl 98), which passed the pipeline-internal QC,  to generate gene-barcode matrix by default settings.
Assembly: mm10
Supplementary files format and content: UMI reads count were calculated by Cell Ranger v6.0.2

source_name: PBMC

growth_protocol:
The KPC (LSL-KrasG12D;Trp53fl/fl;Pdx1-Cre) mouse model is a frequently-used transgenic animal approach for in vivo understanding of PDAC initiation and progression. The pancreatic tissue specifically expressed the KrasG12D allele and conditionally floxed knockout of Trp53 wild-type alleles by expressing Pdx1 promoter-driven Cre recombinase to generate the spontaneously pancreatic cancer in mice. The body weights of KPC mice were monitored and recorded every two days per week. When the bodyweight reduced up to 15-20 % or until the age of 60 ± 3 days, the mice were sacrificed for pancreatic tumor cryopreservation.
The preserved cryo-pancreatic tumor was weighed between 100-250 mg and washed twice with 1x PBS for transplanting subcutaneously into wild-type C57BL/6 mice of the age of 8 weeks. The mice's body weights were monitored and recorded every two days per week. In addition, the PBMC and allograft of early-onset and late-onset mice were collected simultaneously when the early-onset mice lost their body weight up to 15-20 %.

extract_protocol:
PBMC Isolation: After anesthesia of the mouse, the cardiac puncture blood was collected with a final working conc. of 5 mM EDTA. The Histopaque (density 1.088 mg/mL, Sigma-Aldrich) was used for PMBC isolation with centrifugation of 400 x g for 40 min without brake. The RBC lysis buffer (R7757, Sigma-Aldrich) was used to reduce the RBC in the collected PBMC if needed. After repeated two washes of 1x PBS, the PBMC cells were kept in PBS+0.04% BSA for ~1x106 cells/mL (700~1200 cells/µL) at room temperature and immediately proceeded to the 10x Genomics.
Allograft Pancreatic Tumor Cells Isolation: The dissected allograft tumor was rinsed with 1% penicillin-streptomycin in PBS two times and cut into a size of about 1-3 mm3 with surgical scissors. Replacing the tissue into a digestion buffer including 0.15 mg/mL collagenase IV, 0.15 mg/mL dispase II and 0.1% FBS in DMEM for 37°C incubation for 90 minutes. The digested tissue mixture was filtered with a 70 μm strainer (BIOLOGLX) and neutralized the digested enzyme with the same volume of 10% FBS DMEM. The cells were centrifuged with 450 x g for 5 minutes, re-suspended within DMEM containing 10% FBS for ~1x106 cells/mL (700~1200 cells/µL), and immediately proceeded to the 10x Genomics.
We prepared scRNA-seq libraries on the 10x Genomics Chromium Controller at the National Institute of Cancer Research of National Health Research Institutes following the Chromium Next GEM Single Cell 3’ Reagent Kits v3.1 to the manufacturer’s guidelines (https://support.10xgenomics.com/single-cell-gene-expression/library-prep/doc/user-guide-chromium-single-cell-3-reagent-kits-user-guide-v31-chemistry). At the initial step, each sample of 43.2 μL containing approximately 18,500 cells suspension with more than 90 % cells viability was prepared for GEM generation and barcoding. In addition, each cDNA library was prepared for a target of 10,000 cells.

treatment_protocol: KPC mice fingers or tails were collected around 2-3 weeks after birth. Each collected tissue was digested in a solution containing 50 mM Tris-HCl, 100 mM EDTA, 100 mM NaCl, pH8.0 in 70 μL of NF water added with 10 μL of 1 mg/mL proteinase K. The mixture was incubated at 55°C on the rotated shaker overnight for tissue digestion. According to the manufacturer's manual, the magnetic beads (AMPure XP, Beckman Coulter) purified the mouse genomic DNA. In addition, each genotype of the transgenic mouse was determined by genotyping PCR products electrophoresis via 2% agarose gel.

value: PBMC

tag: cachexia state

value: EOCX

value: Female


title: ATACseq, KmgKD, rep4

description:
Library name: ATACseq_KmgKD_rep4
75bp

value: Testes


title: whole blood of subject 23

value: Whole blood


title: SNU-719_shNT_d0

value: SNU-719 + shNT


title: ATACseq, KmgKD, rep3

description:
Library name: ATACseq_KmgKD_rep3
75bp

value: bamGAL4/ KmgRNAi

value: Fly crosses were kept for 3 days at 25°C. Adults were then flipped to a new bottle, while the eggs and early larvae were shifted to 29°C. Testes were dissected from 0–2 day old males in 1xPBS.


title: whole blood of subject 242


title: Myocardial infarction s/p retroviral PMT intramyocardial injection [snRNA-seq]

description:
PMT
PMT_filtered_feature_bc_matrix.h5

value: pMXs-PHF7, pMXs-Mef2c, pMXs-Tbx5


title: ATACseq, KmgKD, rep2

description:
Library name: ATACseq_KmgKD_rep2
75bp


title: sgControl_SCM_replicate3

description: Library name: J3

value: High grade serous ovarian cancer

value: NDUFA5 wild type

value: Senescent cell conditioned media


title: Myocardial infarction s/p retroviral PT intramyocardial injection [snRNA-seq]

description:
PT
PT_filtered_feature_bc_matrix.h5

value: heart

value: heart nuclei

value: pMXs-PHF7, pMXs-Tbx5


title: whole blood of subject 243

value: female


title: whole blood of subject 241


title: whole blood of subject 23BEA


title: whole blood of subject 238


title: Myocardial infarction s/p retroviral PHF7 intramyocardial injection [snRNA-seq]

description:
PHF7
PHF7_filtered_feature_bc_matrix.h5


title: Myocardial infarction s/p retroviral Empty intramyocardial injection [snRNA-seq]

description:
GFP
GFP_filtered_feature_bc_matrix.h5

value: pMXs-Empty


title: sgControl_SCM_replicate2

description: Library name: J2


title: sgNDUFA5_2_SCM_replicate2

description: Library name: L2

value: NDUFA5 knockout 2


title: whole blood of subject 228


title: Cachexia - PBMC_PreCX_F

value: PBMC

value: PreCX


title: sgControl_SCM_replicate1

description: Library name: J1


title: whole blood of subject 225


title: Myocardial infarction s/p retroviral PMT intramyocardial injection  [snATAC-seq]


title: sgNDUFA5_2_SCM_replicate3

description: Library name: L3


title: whole blood of subject 234


title: sgNDUFA5_2_PCM_replicate3

description: Library name: I3

value: Proliferative conditioned media


title: Cachexia - Allograft_PreCX_F

source_name: Allograft

value: Allograft

value: Female


title: Myocardial infarction s/p retroviral PT intramyocardial injection  [snATAC-seq]


title: Cachexia - PBMC_PreCX_M

value: Male


title: whole blood of subject 235

value: Whole blood


title: whole blood of subject 233

value: male


title: whole blood of subject 232


title: whole blood of subject 231BEA


title: sgNDUFA5_2_SCM_replicate1

description: Library name: L1

value: High grade serous ovarian cancer


title: Myocardial infarction s/p retroviral Empty intramyocardial injection [snATAC-seq]


title: whole blood of subject 22BEA


title: whole blood of subject 229


title: whole blood of subject 220


title: whole blood of subject 221


title: whole blood of subject 227


title: Cachexia - Allograft_EOCX_F

value: EOCX


title: whole blood of subject 224


title: Cachexia - Allograft_PreCX_M


title: whole blood of subject 219


title: whole blood of subject 223


title: whole blood of subject 226


title: sgNDUFA5_2_PCM_replicate2

description: Library name: I2


title: whole blood of subject 222


title: sgNDUFA5_2_PCM_replicate1

description: Library name: I1


title: whole blood of subject 218


title: whole blood of subject 22


title: Cachexia - Allograft_EOCX_M


title: sgNDUFA5_1_PCM_replicate3

description: Library name: H3

value: NDUFA5 knockout 1


title: whole blood of subject 21BEA


title: sgNDUFA5_1_PCM_replicate2

description: Library name: H2


title: sgNDUFA5_1_PCM_replicate1

description: Library name: H1


title: whole blood of subject 217


title: Cachexia - PBMC_EOCX_M


title: whole blood of subject 215


title: whole blood of subject 216


title: Participant60_Month_6_Fast

type: RNA

city: Banjul

first: Ismaila

middle: L.

last: Manneh

address: Atlantic Blvd

department: VIT

country: Gambia

institute: MRCG at LSHTM

description: SAMPLE 296

hyb_protocol: 65°C overnight

scan_protocol: Nanostring reader

data_processing: nSolver and Rosalind

source_name: Blood

growth_protocol: Whole blood preserved in PAXgene tube and stored in -80 until needed

extract_protocol: RNA extraction

treatment_protocol: Left at Room temperature overnight

value: Blood

tag: paticipant

tag: timepoint

tag: response

value: Fast

tag: outcome

value: Cure


title: Participant48_Month_6_Fast

description: SAMPLE 294


title: sgControl_PCM_replicate3

description: Library name: G3

value: NDUFA5 wild type


title: whole blood of subject 214


title: Participant60_Month_4_Fast

description: SAMPLE 295


title: whole blood of subject 213


title: sgControl_PCM_replicate2

description: Library name: G2


title: whole blood of subject 210


title: whole blood of subject 212

value: female


title: Participant48_Month_4_Fast

description: SAMPLE 293


title: sgControl_PCM_replicate1

description: Library name: G1


title: whole blood of subject 208


title: whole blood of subject 20BEA


title: NKYS cells, AZA, rep 2

city: Guangzhou

first: Jianfeng

last: Chen

address: 651East Dongfeng Road

country: China

institute: SYSUCC

description: Library name: NKYS-5aza-rep2

data_processing:
Raw reads were filtered and cleaned by fastp software.
adpators were removed by trim_galore
Aliments were performed followed by STAR instruction
featureCounts were used for counting
Assembly: GRCh38, mm10
Supplementary files format and content: CSV file contain counts for each sample

source_name: NKYS

growth_protocol: EG7-OVA cellls were cultured in RPMI1640 medium supplemented with 10% FBS and 1% P/S. EG7-OVA cellls were cultured in RPMI1640 medium supplemented with 10% FBS, 1% P/S and 100 IU/mL IL-2.

extract_protocol:
total RNA was harvested using Trizol reagent (Invitrogen).
RNA libraries were prepared using standard Illumina protocols.

treatment_protocol: 1.EG7-OVA cells were plated into 6-well plate and treated with DMSO,  azacytidine 1.5μM or decitabine 0.2μM at 0h, 24h, 48h; then harvest cells for RNA extraction at 72h.  2.NKYS cells were plated into 6-well plate and treated with DMSO or  azacytidine 1.0μM at 0h, 24h, 48h; then harvest cells for RNA extraction at 72h.

value: NKYS

value: human NK/T cell lymphoma cells

value: WT

value: azacytidine 1.0μM


title: whole blood of subject 207


title: Participant46_Month_6_Fast

description: SAMPLE 292


title: whole blood of subject 21


title: NKYS cells, DMSO, rep 2

description: Library name: NKYS-CTRL-rep2

value: DMSO


title: whole blood of subject 206


title: Participant45_Month_6_Slow

description: SAMPLE 290

value: Slow


title: whole blood of subject 202


title: NKYS cells, DMSO, rep 1

description: Library name: NKYS-CTRL-rep1


title: whole blood of subject 203


title: whole blood of subject 200


title: whole blood of subject 2


title: whole blood of subject 211


title: Participant45_Month_4_Slow

description: SAMPLE 289


title: whole blood of subject 201


title: Participant26_Month_4_Fast

description: SAMPLE 288


title: Du145, MS023-treated, Replica #2

city: Istanbul

first: Hamzah

last: Syed

address: Rumelifeneri Yolu

department: School of Medicine

country: Turkey

institute: Koç University

data_processing:
STAR was used to align Fastq files to the latest human reference transcriptome
Salmon was used for quantification
Tximport and DEseq2 used for normalisation of counts
Assembly: GRCh38
Supplementary files format and content: XLSX files of all sample counts

growth_protocol: Du145 cancer cells (ATCC no. HTB-81) were cultured in RPMI 1640 medium (Gibco, 11875093) supplemented with 10% FBS (Biowest, S1810), 1% penicillin-streptomycin (Biowest, L0022), and incubated at 37°C, 5% CO2 in a humidified environment.

extract_protocol:
Total RNA was extracted with NucleoSpin™ RNA Plus Isolation Kit (Macherey Nagel, 740984)
BGI undertook this protocol

treatment_protocol: Du145 cells were seeded on 6 well plate at a cell density of 120.000 cell/well. Next day, cells were treated with Type I PRMT inhibitor MS023 at a final concentration of 5 µM for 72 h. After 72 h of treatment, cells were trypsinized and proceeded with RNA isolation step.

value: MS023 treatment (5 µM, 72 h)


title: whole blood of subject 20

value: Whole blood


title: whole blood of subject 209

value: male


title: Participant14_Month_6_Fast

description: SAMPLE 286


title: NKYS cells, AZA, rep 1

description: Library name: NKYS-5aza-rep1


title: whole blood of subject 19BEA


title: Participant24_Month_4_Slow

description: SAMPLE 287


title: whole blood of subject 1BEA


title: whole blood of subject 199


title: Du145, Non-treated, Replica #3


title: Du145, MS023-treated, Replica #1


title: Participant46_Month_4_Fast

description: SAMPLE 291


title: whole blood of subject 197


title: whole blood of subject 198


title: Participant11_Baseline_NA

description: SAMPLE 285

value: Baseline


title: whole blood of subject 196


title: Du145, Non-treated, Replica #2


title: Participant70_Month_6_Slow

description: SAMPLE 284


title: whole blood of subject 195


title: Du145, Non-treated, Replica #1


title: whole blood of subject 194


title: Participant70_Month_4_Slow

description: SAMPLE 283


title: Du145, MS023-treated, Replica #3


title: whole blood of subject 193


title: miRNA hESC, Dicer-null, Rep2

city: New York

first: Seungjae

last: Lee

state: NY

address: 430 East 67th St.

department: Department of Developmental Biology

institute: Sloan-Kettering Institute

data_processing:
After removing adaptor sequences of the small RNA sequencing libraries using Cutadapt, the reads were collapsed subsequently to remove PCR artifacts using fastx_collapser, and 5' and 3' end linker sequences were clipped using fastx_clipper. The remaining small RNA reads were mapped to the hg38 genome assembly, and small RNA counts are normalized by spike-in reads in each library. Differential small RNA expression analysis was performed by Bioconductor R package Limma.
Assembly: hg38
Supplementary files format and content: csv file includes spike-in normalized miRNA counts

source_name: embryo

extract_protocol:
To analyze small RNAs, we isolated biologically independent total RNA samples from hESC cells using Trizol (Invitrogen)
One milligram of total RNA was used to generate small RNA libraries for each sample. After adding 1 μL of QIAseq TM miRNA Library QC Spike-Ins (QIAGEN) to the total RNA, a 3' linker was ligated to it in a reaction containing 100 mM 3' linker, T4 RNA Ligase 2, truncated KQ (NEB), 10% PEG8000, 1x RNA ligation buffer, and 20 U RNase OUT overnight at 17°C. The 48-57 nucleotide sized 3' linker-ligated small RNAs were purified using 12% Urea-PAGE gel with radio-labeled oligonucleotides serving as size-markers. Subsequently, the small RNA-linker hybrid was subjected to a 5’ ligation reaction overnight at 17°C containing 100 mM 5' adaptor, 20% PEG8000, 1x RNA ligase buffer, 1 mM ATP, 20 U RNaseOUT, and 5 U T4 RNA ligase 1. The linker-ligated RNAs were then reverse transcribed, PCR amplified using 12 cycles of PCR with forward and Illumina index reverse primers, and purified by 8% non-denaturing acrylamide gel. Sequencing was performed with HiSeq 4000 in SE50 mode.

value: embryo

value: H1 hESCs

value: Human embryonic stem cells


title: whole blood of subject 191


title: Participant69_Month_6_Fast

description: SAMPLE 282

value: Blood

value: Fast


title: miRNA hESC, Dicer-null, Rep1


title: miRNA hESC, Dicer-S1344L homozygous, Rep2


title: Participant69_Month_4_Fast

description: SAMPLE 281

value: Cure


title: whole blood of subject 189

value: female


title: whole blood of subject 18BEA


title: whole blood of subject 186


title: whole blood of subject 187


title: whole blood of subject 184


title: whole blood of subject 192


title: Participant66_Month_6_Slow

description: SAMPLE 278


title: miRNA hESCs, Dicer-S1344L hemizygous, Rep1


title: Participant67_Month_6_Fast

description: SAMPLE 280


title: whole blood of subject 190


title: whole blood of subject 185


title: whole blood of subject 183


title: miRNA hESCs, Dicer-S1344L hemizygous, Rep2


title: Participant66_Month_4_Slow

description: SAMPLE 277


title: whole blood of subject 181


title: whole blood of subject 18


title: miRNA hESC, Dicer-S1344L homozygous, Rep1


title: Participant64_Month_6_Slow

description: SAMPLE 276


title: miRNA hESC, Wild-type, Rep2


title: whole blood of subject 17BEA


title: miRNA hESC, Wild-type, Rep1


title: whole blood of subject 179


title: Participant64_Month_4_Slow

description: SAMPLE 275


title: iCLIP hESC, Dicer-S1344L homozygous, Rep2

data_processing:
The iCLIP library was processed using the CLIP Tool Kit (CTK) from Chaolin Zhang’s lab (PMID: 27797762).
Assembly: hg38
Supplementary files format and content: csv file includes raw miRNA read counts

extract_protocol:
Dicer1 H1 hESCs of the following genotypes (wildtype, pm/fs, pm/pm) were expanded under dox-depleted conditions for 10 days. Two 15 cm dishes of confluent hESCs were used per sample. The cells were UV irradiated with 150mJ/cm2 UVC (254nM wavelength) two times. The cells were then lysed on ice with iCLIP lysis buffer (50 mM Tris-HCl pH7.4, 100 mM NaCl, 1% NP-40, 0.1% SDS, 0.5% SDC, protease inhibitor cocktail (Roche), and 40 U/ml RNaseOUT (Sigma)) for 20 min on ice. TurboDNase (Invitrogen #AM2238, 10U), RNase I (0.05 U/mL) were added subsequently, and samples were incubated at 37°C for 5 min. Treated lysates were immunoprecipitated with anti-Ago2 antibodies (Abnova) or control IgG (MilliporeSigma) coupled with Dynabeads protein G (Thermo Fisher Scientific) for 2 hrs at 4°C with gentle agitation. The immunoprecipitate was washed sequentially with high-stringency buffer, high-salt buffer (50 mM Tris-HCl pH 7.4, 1 M NaCl, 1 mM EDTA, 1% Nonidet P-40, 0.5% sodium deoxycholate, and 0.1% SDS), and PNK wash buffer (20 mM Tris-HCl pH 7.4, 10 mM MgCl2, and 0.2% Tween-20).
The RNAs in the immunoprecipitate were dephosphorylated on the beads with FastAP Thermosensitive alkaline phosphatase (Thermo Fisher Scientific) and radiolabeled in 300 μl mixture: 60 μl 10X PNK buffer (NEB), 5 μl RNaseOUT, 2.0 μl γ-32P-ATP (15 μCi), 7 μl PNK enzyme (NEB M0201) and 222 μl H2O for 20 min at 37°C. The immunoprecipitated materials were washed with the high-salt buffer, and then 3’ linker ligation was carried out 2 hrs at room temperature in 25 μl of mixture: 9 μl H2O, 9 μl 50% PEG-8000 (NEB #B1004), 3 μl 10x T4 RNA ligation buffer (NEB), 0.4 μl RNaseOUT, 0.3 μl ATP (100mM), 0.8 μl DMSO, 2.5 μl T4 RNA ligase 1 (10U/μl – NEB M0204). Protein–RNA complexes were eluted from the beads, electrophoresed on 4–20% Bis-Tris NuPAGE gels (Thermo Fisher Scientific), transferred to nitrocellulose membranes (Whatman), and visualized by autoradiography. The area of the membrane corresponding with proteins that were ~100 kDa (the MW of Ago2) to ~150 kDa in size was excised from each lane of the blot. Excised lanes were treated with proteinase K (MilliporeSigma) and 7M urea (MilliporeSigma). The RNA-adaptor products were purified by acid phenol:chloroform: isoamyl alcohol extraction and ethanol precipitation. Purified RNAs were then subjected to reverse transcription using Superscript III (Thermo Fisher) with adapter-specific RT primers according to the manufacturer’s instruction. Resulted single-stranded cDNA products were purified using ExoSAP-IT (Thermo Fisher Scientific), and ligated to 5’ linker in 20 μL of mixture: 1.1 μl H2O, 2 μl 10x T4 RNA ligase buffer (NEB), 1 μl of 5'-linker, 9 μl 50% PEG-8000 and 0.5 μl of T4 RNA ligase 1 (10U/μl – NEB M0204) at room temperature overnight. Resulted linker-ligated cDNA products were purified using MyONE Silane beads (Thermo Fisher Scientific), and PCR-amplifed. The resulting libraries were gel-purified and sequenced with the Illumina HiSeq platform.


title: whole blood of subject 178


title: Participant67_Month_4_Fast

description: SAMPLE 279


title: whole blood of subject 188


title: whole blood of subject 175


title: iCLIP hESC, Dicer-S1344L homozygous, Rep1


title: Participant39_Month_6_Slow

description: SAMPLE 274


title: whole blood of subject 176


title: whole blood of subject 174


title: iCLIP hESCs, Dicer-S1344L hemizygous, Rep2


title: whole blood of subject 172


title: whole blood of subject 170


title: NIF2 protein kncokout Plasmodium falciparum 3D7 strain, schizont stage, control 3

city: Shenyang

first: Xiaotong

last: Zhu

state: Liaoning

address: No. 77 Puhe Road Shenyang North NEW AREA

department: Department of Immunology

institute: China Medical University

description: Library name: KO_LS3

data_processing:
Raw sequencing reads underwent quality filtering in fastq format and were subjected to adapter trimming using cutadapt v1.13. High-quality reads were aligned to the Plasmodium falciparum 3D7 reference genome (PlasmoDB-68) employing HISAT2 v2.0.4 [97]. Deduplication of reads was conducted with UMI-tools v1.0.0 [52], and quantification was achieved through HTSeq v0.9.1. Differential expression analysis was carried out using DESeq (v1.18.0), with P-values adjusted for false discovery rate (FDR <0.05) following the Benjamini-Hochberg method.
Assembly: mm10
Supplementary files format and content: tab-delimited text files include readsount values for each Sample

organism: Plasmodium falciparum

source_name: parasite infected red blood cells

growth_protocol: P. falciparum 3D7 blood-stage parasites were cultured in O+ human red blood cells (RBCs) at 37°C in an atmosphere consisting of 3% O₂, 5% CO₂, and 92% N₂, using the complete culturing medium (CM), which containing RPMI 1640 medium (Thermo Fisher) supplemented with 0.5% Albumax I.

extract_protocol:
synchronization of the parasites was achieved by isolating late schizonts via 45%/75% Percoll gradients [91], followed by treatment with 5% sorbitol [92], which facilitated the establishment of tightly synchronized ring-stage cultures over a 3-h window.
mRNA was enriched using poly-T oligo-attached magnetic beads. Reverse transcription was performed with SuperScript II (Invitrogen) using random primers. The reaction was then treated with RNaseH to remove the RNA template and cleaned using DNA Clean and Concentrator Kit (Zymo Research). The clustering of the index-coded samples was performed on a cBot Cluster Generation System using TruSeq PE Cluster Kit v3-cBot-HS (Illumia) according to the manufacturer’s instructions. After cluster generation, the library preparations were sequenced using the Illumina platform.

treatment_protocol: nif2 gene was knockout from the genome using selection of integration strategy.

value: parasite infected red blood cells

value: Plasmodium falciparum 3D7

value: NIF2 gene knockout


title: Participant39_Month_4_Slow

description: SAMPLE 273


title: Participant35_Month_4_NA

description: SAMPLE 271

value: Failure


title: Participant35_Month_6_NA

description: SAMPLE 272


title: whole blood of subject 16BEA


title: whole blood of subject 167


title: whole blood of subject 168


title: NIF2 protein kncokout Plasmodium falciparum 3D7 strain, schizont stage, control 1

description: Library name: KO_LS1


title: whole blood of subject 165


title: whole blood of subject 169


title: Participant35_Baseline_NA

description: SAMPLE 269


title: whole blood of subject 166


title: NIF2 protein kncokout Plasmodium falciparum 3D7 strain, trophozoite stage, control 3

description: Library name: KO_T3


title: Participant25_Month_6_NA

description: SAMPLE 268


title: Participant35_Month_2_NA

description: SAMPLE 270


title: whole blood of subject 164


title: whole blood of subject 177


title: whole blood of subject 163


title: whole blood of subject 162


title: whole blood of subject 161


title: NIF2 protein kncokout Plasmodium falciparum 3D7 strain, trophozoite stage, control 2

description: Library name: KO_T2


title: NIF2 protein kncokout Plasmodium falciparum 3D7 strain, trophozoite stage, control 1

description: Library name: KO_T1


title: Participant25_Month_4_NA

description: SAMPLE 267


title: whole blood of subject 160


title: Participant25_Month_2_NA

description: SAMPLE 266


title: NIF2 protein kncokout Plasmodium falciparum 3D7 strain, schizont stage, control 2

description: Library name: KO_LS2


title: whole blood of subject 15BEA


title: whole blood of subject 16


title: NIF2 protein kncokout Plasmodium falciparum 3D7 strain, ring stage, control 3

description: Library name: KO_R3


title: whole blood of subject 159


title: whole blood of subject 158


title: Participant25_Baseline_NA

description: SAMPLE 265


title: whole blood of subject 157


title: NIF2 protein kncokout Plasmodium falciparum 3D7 strain, ring stage, control 2

description: Library name: KO_R2


title: whole blood of subject 156


title: Participant22_Month_4_NA

description: SAMPLE 263


title: whole blood of subject 154


title: whole blood of subject 155


title: whole blood of subject 153


title: Participant22_Month_2_NA

description: SAMPLE 262


title: whole blood of subject 151


title: wild type Plasmodium falciparum 3D7 strain, schizont stage, control 2

description: Library name: WT_LS2

value: WT

value: wild type strain without any additional treatment


title: wild type Plasmodium falciparum 3D7 strain, schizont stage, control 3

description: Library name: WT_LS3


title: wild type Plasmodium falciparum 3D7 strain, schizont stage, control 1

description: Library name: WT_LS1


title: whole blood of subject 15


title: Participant68_Month_6_Fast

description: SAMPLE 260


title: wild type Plasmodium falciparum 3D7 strain, trophozoite stage, control 3

description: Library name: WT_T3


title: whole blood of subject 149


title: Participant68_Month_4_Fast

description: SAMPLE 259


title: whole blood of subject 14BEA


title: whole blood of subject 148


title: whole blood of subject 147


title: wild type Plasmodium falciparum 3D7 strain, trophozoite stage, control 2

description: Library name: WT_T2


title: Participant68_Month_2_Fast

description: SAMPLE 258


title: wild type Plasmodium falciparum 3D7 strain, trophozoite stage, control 1

description: Library name: WT_T1


title: whole blood of subject 146


title: whole blood of subject 145


title: Participant22_Month_6_NA

description: SAMPLE 264


title: NIF2 protein kncokout Plasmodium falciparum 3D7 strain, ring stage, control 1

description: Library name: KO_R1


title: whole blood of subject 144


title: Participant68_Baseline_Fast

description: SAMPLE 257


title: whole blood of subject 143


title: whole blood of subject 142


title: whole blood of subject 150


title: wild type Plasmodium falciparum 3D7 strain, ring stage, control 2

description: Library name: WT_R2


title: whole blood of subject 141


title: Participant22_Baseline_NA

description: SAMPLE 261


title: Participant63_Month_4_NA

description: SAMPLE 255


title: whole blood of subject 140


title: wild type Plasmodium falciparum 3D7 strain, ring stage, control 1

description: Library name: WT_R1


title: Participant63_Month_2_NA

description: SAMPLE 254


title: whole blood of subject 13BEA


title: whole blood of subject 14


title: whole blood of subject 139


title: Sciatic nerve,control for 7 days,rep3

city: Shanghai

first: Jian

last: Zhou

address: No. 600, Yi Shan Road, Shanghai

institute: Shanghai Sixth People's Hospital

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 ploy-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 using Hisat2 v2.0.5 and paired-end clean reads were aligned to the reference genome using Hisat2 v2.0.5.
The mapped reads of each sample were assembled by StringTie in a reference-based approach. StringTie uses a novel network flow algorithm as well as an optional de novo assembly step to assemble and quantitate fulllength transcripts. FeatureCounts v1.6.0 was used to count the reads numbers mapped to each gene.
Genes differential expression analysis was performed by DESeq2 software between two different groups (and by edgeR between two samples). The genes with the parameter of false discovery rate (FDR) below 0.05 and absolute fold change ≥ 1 were considered differentially expressed genes. Differentially expressed genes were then subjected to enrichment analysis of GO functions and KEGG pathways.

organism: Rattus norvegicus

source_name: nerve

extract_protocol:
Total RNA was extracted usingTrizol reagent following the manufacturer's procedure. The total RNA quantity and purity were analysis of Bioanalyzer 2100 and  NanoPhotometer® spectrophotometer, high-quality RNA samples with RIN number > 6.8 were used to construct sequencing library.
After total RNA was extracted, mRNA was purified from total RNA using poly-Toligo-attached magnetic beads. Fragmentation was carried out using divalent cations under elevated temperature in NEBNext First Strand Synthesis Reaction Buffer(5X). First strandcDNA was synthesized using random hexamer primer and M-MuLV Reverse Transcriptase(RNase H-). Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and RNase H. Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. After adenylation of 3’ ends of DNA fragments, NEBNext Adaptor with hairpin loop structure were ligated to prepare for hybridization. In order to select cDNA fragments of preferentially 250~300bp in length, the library fragments were purified with AMPure XP system (Beckman Coulter, Beverly, USA). Then 3 µl USER Enzyme (NEB, USA) was used with size-selected, adaptor-ligated cDNA at 37°C for 15 min followed by 5 min at 95 °C before PCR. Then PCR was performed with Phusion High-Fidelity DNA polymerase, Universal PCR primers and Index (X) Primer. At last, PCR products were purified (AMPure XP system) and library quality was assessed on the Agilent Bioanalyzer 2100 system. The clustering of the index-coded samples was performed on a cBot Cluster Generation System using TruSeq PE Cluster Kit v3-cBot-HS (Illumia) according to the manufacturer instructions. After cluster generation, the library preparations were sequenced on an Illumina Novaseq platform and 150 bp paired-end reads were generated.

value: nerve

tag: strain

value: Sprague-Dawley

value: Sham operation for 7 days


title: Participant63_Baseline_NA

description: SAMPLE 253

value: Baseline


title: whole blood of subject 138

value: Whole blood


title: Sciatic nerve,control for 7 days,rep2


title: whole blood of subject 136

value: male


title: whole blood of subject 137


title: Participant53_Month_4_NA

description: SAMPLE 251

value: Relapse


title: whole blood of subject 134


title: Participant53_Month_6_NA

description: SAMPLE 252

value: Blood


title: L6 DRGs,control for 7 days,rep3

source_name: DRG

value: DRG


title: whole blood of subject 133


title: Participant63_Month_6_NA

description: SAMPLE 256


title: wild type Plasmodium falciparum 3D7 strain, ring stage, control 3

description: Library name: WT_R3


title: whole blood of subject 132


title: Participant53_Month_2_NA

description: SAMPLE 250


title: L6 DRGs,control for 7 days,rep2


title: Participant53_Baseline_NA

description: SAMPLE 249


title: whole blood of subject 130


title: whole blood of subject 13


title: L6 DRGs,control for 7 days,rep1


title: whole blood of subject 131


title: Participant43_Month_6_NA

description: SAMPLE 248


title: Participant43_Month_4_NA

description: SAMPLE 247


title: whole blood of subject 126


title: whole blood of subject 127


title: whole blood of subject 125


title: Participant43_Month_2_NA

description: SAMPLE 246


title: whole blood of subject 135


title: Sciatic nerve,control for 7 days,rep1


title: Participant43_Baseline_NA

description: SAMPLE 245


title: whole blood of subject 123


title: whole blood of subject 124


title: whole blood of subject 122


title: whole blood of subject 121


title: whole blood of subject 120


title: L4 DRGs,control for 7 days,rep3


title: whole blood of subject 12


title: L4 DRGs,control for 7 days,rep2


title: Participant36_Month_4_NA

description: SAMPLE 243


title: Participant36_Month_6_NA

description: SAMPLE 244


title: whole blood of subject 11BEA


title: whole blood of subject 129


title: L4 DRGs,control for 7 days,rep1


title: whole blood of subject 118


title: Participant36_Month_2_NA

description: SAMPLE 242


title: L5 DRGs,control for 7 days,rep3


title: Sciatic nerve,control for 3 days,rep3

value: Sham operation for 3 days


title: whole blood of subject 117


title: Participant36_Baseline_NA

description: SAMPLE 241


title: L5 DRGs,control for 7 days,rep2


title: whole blood of subject 116


title: Sciatic nerve,control for 3 days,rep2


title: whole blood of subject 115

value: female


title: whole blood of subject 114


title: L5 DRGs,control for 7 days,rep1


title: whole blood of subject 112


title: Participant34_Month_4_Slow

description: SAMPLE 239

value: Slow

value: Cure


title: whole blood of subject 110


title: L6 DRGs,control for 3 days,rep3


title: whole blood of subject 111


title: Participant34_Month_2_Slow

description: SAMPLE 238


title: whole blood of subject 119


title: Participant34_Baseline_Slow

description: SAMPLE 237


title: whole blood of subject 11


title: whole blood of subject 109


title: Participant34_Month_6_Slow

description: SAMPLE 240


title: L6 DRGs,control for 3 days,rep1


title: whole blood of subject 108


title: whole blood of subject 106


title: Sciatic nerve,control for 3 days,rep1


title: whole blood of subject 105


title: whole blood of subject 104


title: whole blood of subject 103


title: L5 DRGs,control for 3 days,rep2


title: Participant19_Month_2_NA

description: SAMPLE 234


title: whole blood of subject 102


title: L5 DRGs,control for 3 days,rep1


title: whole blood of subject 113


title: Participant19_Baseline_NA

description: SAMPLE 233


title: whole blood of subject 101


title: whole blood of subject 100


title: Participant5_Month_6_NA

description: SAMPLE 232


title: whole blood of subject 10


title: L4 DRGs,control for 3 days,rep3


title: L6 DRGs,control for 3 days,rep2


title: whole blood of subject 1


title: L4 DRGs,control for 3 days,rep2


title: Participant19_Month_6_NA

description: SAMPLE 236


title: Participant5_Month_4_NA

description: SAMPLE 231


title: L5 DRGs,control for 3 days,rep3


title: whole blood of subject 9BEA


title: whole blood of subject 99


title: whole blood of subject 98


title: L4 DRGs,control for 3 days,rep1


title: Participant5_Baseline_NA

description: SAMPLE 229


title: whole blood of subject 97


title: Participant19_Month_4_NA

description: SAMPLE 235


title: Sciatic nerve,L5 Nerve entrapment for 7 days,rep3

value: rats L5 nerves were compressed for 7days


title: whole blood of subject 95


title: Participant5_Month_2_NA

description: SAMPLE 230

value: Failure


title: whole blood of subject 96


title: whole blood of subject 94


title: Sciatic nerve,L5 Nerve entrapment for 7 days,rep2


title: whole blood of subject 93


title: Participant1_Month_6_NA

description: SAMPLE 228


title: whole blood of subject 92


title: whole blood of subject 91


title: Sciatic nerve,L5 Nerve entrapment for 7 days,rep1


title: Participant1_Month_4_NA

description: SAMPLE 227


title: whole blood of subject 90


title: L6 DRGs,L5 Nerve entrapment for 7 days,rep3


title: Participant1_Month_2_NA

description: SAMPLE 226


title: whole blood of subject 9


title: whole blood of subject 8BEA


title: Participant1_Baseline_NA

description: SAMPLE 225


title: L6 DRGs,L5 Nerve entrapment for 7 days,rep2


title: whole blood of subject 89


title: L6 DRGs,L5 Nerve entrapment for 7 days,rep1


title: whole blood of subject 88


title: whole blood of subject 87


title: Participant62_Month_6_Fast

description: SAMPLE 224

value: Fast


title: whole blood of subject 84


title: L5 DRGs,L5 Nerve entrapment for 7 days,rep2


title: whole blood of subject 85


title: whole blood of subject 83


title: Participant62_Month_4_Fast

description: SAMPLE 223


title: whole blood of subject 81


title: Participant61_Month_6_Slow

description: SAMPLE 222


title: L5 DRGs,L5 Nerve entrapment for 7 days,rep1


title: whole blood of subject 80BEA


title: Participant61_Month_4_Slow

description: SAMPLE 221


title: L4 DRGs,L5 Nerve entrapment for 7 days,rep3


title: L4 DRGs,L5 Nerve entrapment for 7 days,rep2


title: Participant59_Month_6_Fast

description: SAMPLE 220


title: Participant59_Month_4_Fast

description: SAMPLE 219


title: whole blood of subject 8


title: whole blood of subject 80


title: whole blood of subject 7BEA


title: L4 DRGs,L5 Nerve entrapment for 7 days,rep1


title: Participant58_Month_6_Slow

description: SAMPLE 218


title: whole blood of subject 79BEA


title: whole blood of subject 79


title: Sciatic nerve,L5 Nerve entrapment for 3 days,rep3

value: rats L5 nerves were compressed for 3days


title: whole blood of subject 86


title: whole blood of subject 82


title: L5 DRGs,L5 Nerve entrapment for 7 days,rep3


title: whole blood of subject 78BEA


title: whole blood of subject 77BEA


title: Sciatic nerve,L5 Nerve entrapment for 3 days,rep2

value: nerve


title: Participant58_Month_4_Slow

description: SAMPLE 217


title: whole blood of subject 78


title: whole blood of subject 77


title: whole blood of subject 76BEA


title: Participant57_Month_4_Fast

description: SAMPLE 215


title: Participant57_Month_6_Fast

description: SAMPLE 216


title: Sciatic nerve,L5 Nerve entrapment for 3 days,rep1

value: Sprague-Dawley


title: whole blood of subject 76


title: L6 DRGs,L5 Nerve entrapment for 3 days,rep2


title: Participant56_Month_4_Slow

description: SAMPLE 213


title: whole blood of subject 74BEA


title: L6 DRGs,L5 Nerve entrapment for 3 days,rep3


title: Participant56_Month_6_Slow

description: SAMPLE 214


title: whole blood of subject 75BEA


title: whole blood of subject 74


title: whole blood of subject 75


title: whole blood of subject 72BEA


title: L5 DRGs,L5 Nerve entrapment for 3 days,rep3


title: whole blood of subject 73


title: whole blood of subject 72


title: Participant55_Month_6_Slow

description: SAMPLE 212


title: L5 DRGs,L5 Nerve entrapment for 3 days,rep2


title: whole blood of subject 71BEA


title: whole blood of subject 7


title: whole blood of subject 71


title: Participant54_Month_6_Slow

description: SAMPLE 210


title: L4 DRGs,L5 Nerve entrapment for 3 days,rep3


title: whole blood of subject 70BEA


title: Participant55_Month_4_Slow

description: SAMPLE 211


title: Participant54_Month_4_Slow

description: SAMPLE 209


title: whole blood of subject 68BEA


title: whole blood of subject 68


title: whole blood of subject 69


title: L6 DRGs,L5 Nerve entrapment for 3 days,rep1


title: whole blood of subject 69BEA


title: Participant52_Month_6_Fast

description: SAMPLE 208


title: whole blood of subject 67


title: iCLIP hESCs, Dicer-S1344L hemizygous, Rep1

value: embryo

value: H1 hESCs

value: Human embryonic stem cells


title: Participant51_Month_4_Fast

description: SAMPLE 205


title: Participant52_Month_4_Fast

description: SAMPLE 207


title: whole blood of subject 67BEA

value: Whole blood


title: whole blood of subject 73BEA

value: male


title: L4 DRGs,L5 Nerve entrapment for 3 days,rep1


title: L5 DRGs,L5 Nerve entrapment for 3 days,rep1


title: whole blood of subject 66BEA


title: iCLIP hESC, Wild-type, Rep2


title: whole blood of subject 66


title: Participant50_Month_6_Fast

description: SAMPLE 204

value: Blood


title: iCLIP hESC, Wild-type, Rep1


title: whole blood of subject 65


title: Participant50_Month_4_Fast

description: SAMPLE 203


title: whole blood of subject 64


title: whole blood of subject 64BEA


title: whole blood of subject 62BEA


title: L4 DRGs,L5 Nerve entrapment for 3 days,rep2

value: DRG


title: whole blood of subject 63


title: whole blood of subject 61


title: whole blood of subject 63BEA


title: Participant49_Month_4_Slow

description: SAMPLE 201


title: hESC, Dicer-S1344L homozygous, Rep2

data_processing:
After removing 5’ and 3’end Illumina TruSeq adaptor sequences using Cutadapt, the reads were mapped to the hg38 genome assembly using HISAT2
Assembly: hg38
Supplementary files format and content: csv file includes raw counts for each sample

extract_protocol:
RNA was harvested using Trizol (Invitrogen). 1ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using TruSeq RNA Library Prep Kit v2 (Illumina)


title: whole blood of subject 61BEA


title: hESCs, Dicer-S1344L hemizygous, Rep2


title: Participant49_Month_6_Slow

description: SAMPLE 202


title: hESC, Dicer-S1344L homozygous, Rep1


title: Participant44_Month_6_Fast

description: SAMPLE 200


title: whole blood of subject 60


title: Participant51_Month_6_Fast

description: SAMPLE 206


title: whole blood of subject 6


title: Participant44_Month_4_Fast

description: SAMPLE 199


title: hESCs, Dicer-S1344L hemizygous, Rep1


title: Participant42_Month_6_Slow

description: SAMPLE 198


title: hESC, Wild-type, Rep2


title: whole blood of subject 59BEA


title: whole blood of subject 59


title: whole blood of subject 58BEA


title: hESC, Wild-type, Rep1


title: Participant42_Month_4_Slow

description: SAMPLE 197


title: whole blood of subject 57BEA


title: whole blood of subject 58


title: whole blood of subject 57


title: whole blood of subject 56


title: shNdufa5_2_SCM_replicate3

description: Library name: F3

data_processing:
Demultiplexed and quality-filtered mRNA-Seq reads were then aligned to human reference genome (GRCm38) using STAR (v.2.6.1)
Differential expression analysis was done using DESeq2 (v2_1.6.3)
Assembly: mm10
Supplementary files format and content: Tab delimited text file includes FPKMs for all samples

growth_protocol: KPCA.B cells were cultured in DMEM, high glucose + 4% heat inactivated FBS + 2ng/mL EGF + 1X ITS-G

treatment_protocol: Cells were cultured in conditioned media and DMEM, high glucose + 4% heat inactivated FBS + 2ng/mL EGF + 1X ITS-G in a 1:1 ratio

value: High grade serous ovarian cancer

value: Ndufa5 knockdown 2

value: Senescent cell conditioned media


title: whole blood of subject 55BEA

value: female


title: Participant41_Month_6_Fast

description: SAMPLE 196

value: Cure


title: Participant41_Month_4_Fast

description: SAMPLE 195


title: whole blood of subject 55


title: whole blood of subject 54BEA


title: whole blood of subject 53BEA


title: Participant40_Month_6_Slow

description: SAMPLE 194

value: Slow


title: whole blood of subject 54


title: shNdufa5_1_SCM_replicate3

description: Library name: E3

value: Ndufa5 knockdown 1


title: Participant40_Month_4_Slow

description: SAMPLE 193


title: shNdufa5_1_SCM_replicate2

description: Library name: E2


title: Participant38_Month_6_Slow

description: SAMPLE 192


title: whole blood of subject 53


title: whole blood of subject 51BEA


title: whole blood of subject 51


title: shNdufa5_1_SCM_replicate1

description: Library name: E1


title: whole blood of subject 52BEA


title: Participant37_Month_6_Fast

description: SAMPLE 190

value: Fast


title: Participant38_Month_4_Slow

description: SAMPLE 191


title: shControl_SCM_replicate3

description: Library name: D3

value: Ndufa5 wild type


title: whole blood of subject 50


title: whole blood of subject 49BEA


title: whole blood of subject 49


title: whole blood of subject 4BEA


title: shControl_SCM_replicate1

description: Library name: D1


title: shNdufa5_2_SCM_replicate1

description: Library name: F1


title: shNdufa5_2_SCM_replicate2

description: Library name: F2


title: whole blood of subject 48BEA


title: Participant37_Month_4_Fast

description: SAMPLE 189


title: whole blood of subject 48


title: whole blood of subject 5BEA


title: shControl_SCM_replicate2

description: Library name: D2


title: whole blood of subject 47BEA


title: shNdufa5_2_PCM_replicate3

description: Library name: C3

value: Proliferative conditioned media


title: whole blood of subject 47


title: Participant23_Month_4_Slow

description: SAMPLE 187


title: whole blood of subject 46BEA


title: Participant23_Month_2_Slow

description: SAMPLE 186


title: whole blood of subject 46


title: shNdufa5_2_PCM_replicate2

description: Library name: C2


title: whole blood of subject 50BEA


title: shNdufa5_2_PCM_replicate1

description: Library name: C1


title: whole blood of subject 45BEA


title: Participant23_Baseline_Slow

description: SAMPLE 185

value: Baseline


title: Participant23_Month_6_Slow

description: SAMPLE 188


title: whole blood of subject 45


title: Participant21_Month_6_Slow

description: SAMPLE 184


title: whole blood of subject 44


title: whole blood of subject 44BEA


title: shNdufa5_1_PCM_replicate3

description: Library name: B3


title: shNdufa5_1_PCM_replicate2

description: Library name: B2


title: whole blood of subject 42BEA


title: whole blood of subject 43


title: shNdufa5_1_PCM_replicate1

description: Library name: B1


title: whole blood of subject 43BEA


title: Participant21_Month_2_Slow

description: SAMPLE 182


title: whole blood of subject 40BEA


title: Participant20_Month_6_Slow

description: SAMPLE 180


title: shControl_PCM_replicate3

description: Library name: A3


title: shControl_PCM_replicate2

description: Library name: A2


title: whole blood of subject 4


title: whole blood of subject 39BEA


title: whole blood of subject 41


title: EG7-OVA cells, DAC, rep 2

description: Library name: EG7-DAC-rep2

value: mouse T cell lymphoma cells

value: WT

value: decitabine 0.2μM


title: whole blood of subject 3BEA

value: Whole blood

value: male


title: shControl_PCM_replicate1

description: Library name: A1


title: EG7-OVA cells, DAC, rep 1

description: Library name: EG7-DAC-rep1


title: whole blood of subject 40


title: whole blood of subject 42


title: Participant20_Baseline_Slow

description: SAMPLE 177

value: Blood


title: whole blood of subject 38BEA


title: Participant21_Month_4_Slow

description: SAMPLE 183


title: whole blood of subject 37BEA


title: Participant20_Month_2_Slow

description: SAMPLE 178


title: whole blood of subject 41BEA


title: EG7-OVA cells, AZA, rep 2

description: Library name: EG7-AZA-rep2

value: azacytidine 1.5μM


title: whole blood of subject 37


title: whole blood of subject 38


title: Participant21_Baseline_Slow

description: SAMPLE 181


title: whole blood of subject 36BEA


title: EG7-OVA cells, AZA, rep 1

description: Library name: EG7-AZA-rep1


title: Participant18_Month_6_Slow

description: SAMPLE 176


title: whole blood of subject 36


title: EG7-OVA cells, DMSO, rep 3

description: Library name: EG7-CT-rep2

value: DMSO


title: Participant18_Month_2_Slow

description: SAMPLE 174


title: Participant20_Month_4_Slow

description: SAMPLE 179


title: whole blood of subject 39


title: whole blood of subject 34


title: Participant18_Baseline_Slow

description: SAMPLE 173


title: whole blood of subject 33BEA


title: EG7-OVA cells, DMSO, rep 2

description: Library name: EG7-CT-rep1


title: Participant18_Month_4_Slow

description: SAMPLE 175


title: whole blood of subject 33


title: EL4 P3 tumor rep 2

description: Library name: P3_rep2

source_name: tumor

value: tumor


title: whole blood of subject 32


title: EL4 P3 tumor rep 1

description: Library name: P3_rep1


title: whole blood of subject 32BEA

value: female


title: Participant17_Month_6_Fast

description: SAMPLE 172

value: Cure


title: Participant17_Month_4_Fast

description: SAMPLE 171


title: whole blood of subject 31BEA


title: whole blood of subject 317


title: whole blood of subject 316


title: EL4 P0 tumor rep 1

description: Library name: P0_rep1


title: Participant17_Month_2_Fast

description: SAMPLE 170


title: whole blood of subject 314


title: whole blood of subject 313


title: whole blood of subject 35BEA


title: Participant6_Month_6_Fast

description: SAMPLE 168


title: SC4

first: Jia

last: Liu

address: 85 Saint Nicholas Ter

department: Neuroscience

institute: CUNY Advanced Science Research Center

description: Library name: INS6

data_processing:
Sequence reads were trimmed for adaptors using trimmomatic and filtered out low quality reads
Trimmed sequences were mapped to Mm10 using subread-buildindex
Assembly: Mm10
Supplementary files format and content: differential expression analyzed by DEseq2 in csv format

source_name: medial prefrontal cortex

extract_protocol:
RNA was extracted using Rneasy Micro kit. 100ng was used to contruct the library
Library was constructed using KAPA mRNA Hyperprep kit

value: medial prefrontal cortex

value: Male

value: SC


title: Participant17_Baseline_Fast

description: SAMPLE 169

value: Fast


title: whole blood of subject 310


title: SC3

description: Library name: INS5


title: Participant6_Month_4_Fast

description: SAMPLE 167


title: whole blood of subject 31


title: SC2

description: Library name: INS4


title: Participant6_Month_2_Fast

description: SAMPLE 166


title: CFC3

description: Library name: INF12

value: CFC


title: whole blood of subject 306


title: CFC2

description: Library name: INF11


title: whole blood of subject 304


title: whole blood of subject 309


title: SC1

description: Library name: INS1


title: whole blood of subject 308


title: whole blood of subject 312


title: whole blood of subject 302


title: CFC1

description: Library name: INF10


title: whole blood of subject 311


title: Participant6_Baseline_Fast

description: SAMPLE 165

value: Baseline


title: EL4 P0 tumor rep 2

description: Library name: P0_rep2


title: whole blood of subject 315


title: whole blood of subject 30BEA


title: whole blood of subject 300


title: whole blood of subject 30


title: whole blood of subject 305


title: Participant4_Month_4_Slow

description: SAMPLE 163

value: Slow


title: whole blood of subject 303


title: Participant4_Baseline_Slow

description: SAMPLE 161


title: whole blood of subject 29BEA


title: Participant4_Month_2_Slow

description: SAMPLE 162


title: Participant4_Month_6_Slow

description: SAMPLE 164


title: whole blood of subject 301


title: whole blood of subject 298


title: Intermittent Fasting, rep3

city: London

first: Jessica

middle: Sarah

last: Chadwick

address: Du Cane Road

department: Brain Sciences

country: United Kingdom

institute: Imperial College London

data_processing:
Sequence reads and trimmed reads quality control was carried out using FastQC-v0.11.9
Sequence reads were trimmed for adaptor sequence/low-quality sequence using TrimGalore!-v0.6.6 (parameter - Phred33 quality limit: 20)
Trimmed sequence reads were mapped to M25 Gencode reference genome (GrCM38/mm10) and read counts per transcript obtained using Salmon-v1.6.0 in mapping-based mode (parameters- gcBias, seqBias)
Salmon output files were imported and converted for DESeq2 using Tximeta-v1.12.4
Differential gene expression analysis was carried out using DESeq2-v1.34.0 in R-v4.1.2
Normalised counts were generated using the median of ratios method in DESeq2.
Assembly: M25
Supplementary files format and content: tab-delimited txt file represents the raw expression data as TPM, produced by Salmon

source_name: L4-6 DRG

extract_protocol:
RNA was harvested using Rneasy mini kit (Qiagen). Total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using TruSeq Stranded mRNA Library Prep Kit following manufacturer's protocols.

treatment_protocol:
AL or 10d Intermittent Fasting mice were sacrificed after 24 hours.
DRGs were dissociated using 1 mg/ml Dispase II, 2.5 mg/ml Collagenase Type II, and Papain. Released cells were placed into 15% BSA in DMEM gradient to obtain a neuronal enriched cell population

value: L4-6 DRG

value: 8-10 weeks

value: Intermittent Fasting


title: AL Control, rep3

value: ad libitum


title: whole blood of subject 299

value: Whole blood


title: Participant3_Month_6_Slow

description: SAMPLE 160

value: Blood


title: AL Control, rep2


title: whole blood of subject 294


title: whole blood of subject 293


title: Participant3_Baseline_Slow

description: SAMPLE 157


title: AL Control, rep1


title: whole blood of subject 307


title: Intermittent Fasting, rep2


title: whole blood of subject 291

value: male


title: whole blood of subject 2BEA


title: whole blood of subject 297


title: Participant3_Month_4_Slow

description: SAMPLE 159


title: whole blood of subject 296


title: Participant3_Month_2_Slow

description: SAMPLE 158


title: whole blood of subject 295


title: whole blood of subject 28BEA


title: whole blood of subject 289


title: Participant2_Month_6_Fast

description: SAMPLE 156


title: whole blood of subject 292


title: Leptin overexpression, rep3

data_processing:
Sequence reads and trimmed reads quality control was carried out using FastQC-v0.11.9
Sequence reads were trimmed for adaptor sequence/low-quality sequence using TrimGalore!-v0.6.6 (parameter - Phred33 quality limit: 20)
Trimmed sequence reads were mapped to M27 Gencode reference genome (GrCM38/mm10) and read counts per transcript obtained using Salmon-v1.6.0 in mapping-based mode (parameters- gcBias, seqBias)
Salmon output files were imported and converted for DESeq2 using Tximeta-v1.12.4
Differential gene expression analysis was carried out using DESeq2-v1.34.0 in R-v4.1.2
Normalised counts were generated using the median of ratios method in DESeq2.
Assembly: M27 Gencode reference genome (GrCM38/mm10)
Supplementary files format and content: normalised counts generated using the median of ratios method in DESeq2

treatment_protocol:
AAV-GFP or AAV-Leptin-GFP overexpressed mice underwent DCA injury and sacrificed after 24 hours.
DRGs were dissociated using 1 mg/ml Dispase II, 2.5 mg/ml Collagenase Type II, and Papain. Released cells were placed into 15% BSA in DMEM gradient to obtain a neuronal enriched cell population

value: AAV-Leptin-GFP


title: Participant2_Month_4_Fast

description: SAMPLE 155


title: GFP Control, rep3

value: AAV-GFP


title: whole blood of subject 285

data_processing:
minfi version 1.52.1 and ChAMP version 2.36.0
processed value definition: Beta values (linked as supplementary file on Series record)

value: female


title: Intermittent Fasting, rep1


title: Participant16_Month_4_Slow

description: SAMPLE 151

value: Cure


title: Participant2_Month_2_Fast

description: SAMPLE 154


title: whole blood of subject 282


title: Leptin overexpression, rep2

value: Male


title: Leptin overexpression, rep1


title: whole blood of subject 29


title: whole blood of subject 287


title: Participant2_Baseline_Fast

description: SAMPLE 153


title: whole blood of subject 286


title: whole blood of subject 281


title: GFP Control, rep2


title: whole blood of subject 284


title: whole blood of subject 288


title: Participant16_Month_2_Slow

description: SAMPLE 150


title: whole blood of subject 279


title: whole blood of subject 283


title: GFP Control, rep1


title: Participant16_Month_6_Slow

description: SAMPLE 152


title: whole blood of subject 28


title: whole blood of subject 275


title: Participant15_Month_2_Fast

description: SAMPLE 146


title: whole blood of subject 273


title: whole blood of subject 280


title: whole blood of subject 27BEA


title: Participant16_Baseline_Slow

description: SAMPLE 149


title: whole blood of subject 276


title: Participant13_Month_6_Fast

description: SAMPLE 144


title: Participant15_Month_4_Fast

description: SAMPLE 147


title: Participant15_Month_6_Fast

description: SAMPLE 148


title: Participant15_Baseline_Fast

description: SAMPLE 145


title: L4 C. elegans, K21 Treatment, rep5

city: Piscataway

first: Christopher

last: Rongo

state: NJ

address: 190 Frelinghuysen Rd

department: Genetics

institute: Waksman Institute / Rutgers University

description:
Library name: K5
Processed data files contain raw counts

data_processing:
Reads were mapped to the C. elegans genome (WS245) and gene counts generated with STAR 2.5.1a. Normalization and statistical analysis on gene counts were performed with EdgeR using generalized linear model functionality and tagwise dispersion estimates.
Assembly: WS245
Supplementary files format and content: tab delimited file contains raw counts for each sample

organism: Caenorhabditis elegans

source_name: Whole Animal

growth_protocol: Nematodes were cultured on OP50 E. coli seeded on NGM plates

extract_protocol:
Total RNA was isolated from animals using Trizol (Invitrogen) combined with Bead Beater lysis in five biological replicates for each genotype.
An mRNA library (paired-end, 150-bp reads) was prepared for each sample/replicate using Illumina Truseq with PolyA selection (Azenta/GeneWiz).  Libraries were sequenced across two lanes on an Illumina HiSeq2500 (Azenta/GeneWiz), resulting in a range of 27-37M reads per sample, with peak mean phred scores of 38.76.

treatment_protocol: A 50% stock solution of K21 QASD in ethanol was used to create a working stock colloidal suspension of 0.2% K21 in 0.8% ethanol. A 0.8% ethanol solution without K21 used as a vehicle-only control. For treatment, agar plates seeded with OP50 were dosed with 150 L of either K21 or vehicle, and the plate was rotated to ensure the entire surface that contained OP50 was covered in either substance. Plates were then allowed to dry for approximately 20 minutes, allowing the liquid to be absorbed into the surface of the agar. Embryos harvested following bleach isolation were then deposited on the plates and allowed to hatch. Hatched animals were typically assessed once they reached the L4 stage unless otherwise noted.

value: Whole Animal

tag: developmental stage

value: L4 Stage


title: whole blood of subject 27


title: whole blood of subject 277


title: whole blood of subject 274


title: whole blood of subject 26BEA


title: whole blood of subject 272


title: whole blood of subject 271


title: whole blood of subject 270


title: whole blood of subject 267


title: L4 C. elegans, K21 Treatment, rep3

description:
Library name: K3
Processed data files contain raw counts


title: Participant13_Month_4_Fast

description: SAMPLE 143

value: Fast


title: whole blood of subject 266


title: whole blood of subject 264


title: L4 C. elegans, K21 Treatment, rep2

description:
Library name: K2
Processed data files contain raw counts


title: L4 C. elegans, K21 Treatment, rep4

description:
Library name: K4
Processed data files contain raw counts


title: CREB_WT2

city: Aachen

first: Lin

last: Gan

address: Pauwelsstr. 30

department: IZKF

country: Germany

institute: University Hospital Aachen

hyb_protocol: Overnight hybridization of end-labelled cDNA was applied on the MTA 1.0 ST Mouse (Affymetrix) arrays for 18 hours, at 60 rpm, at 45ºC in a Hybridization Oven 645 (Affymetrix). Washing and staining of the arrays were done on an Affymetrix 450 Fluidics Station using the protocol FS450_0001.

scan_protocol: Arrays were scanned on an Affymetrix 3000 7G scanner, as described in the manufacture manual

data_processing: Expression estimates were calculated applying the sst-RMA algorithm in theTranscriptome Analysis Console (TAC)

label: biotin

label_protocol: Total RNA (7.92ng per sample) was processed with the Ovation Pico WTA system V2 Kit (Nugen).

growth_protocol: Experiments were performed with sex- and age-matched 10-12 week-old  Foxp3creCREBfl/fl  and respective WT mice;  Foxp3creCREBfl/fl mice were generated by crossing CREB-flox mice  with C57BL/6 Foxp3-IRES Cre mice.

extract_protocol: Total RNA from isolated CD4+CD25+Nrp1+ (isolated by FACS) was isolated using RNeasy Micro Kit

treatment_protocol: CD4+CD25+  cells were isolated by MACS-separation from spleens, mice were untreated

value: spleen

value: Treg cells

tag: individual

value: CREB-WT


title: Participant13_Month_2_Fast

description: SAMPLE 142

tag: tissue


title: CREB_WT3


title: CREB_KO3

value: CREB-KO


title: whole blood of subject 269

extract_protocol: Whole blood DNA was extracted using a silica membrane–based protocol.


title: CREB_KO2


title: CREB_WT1


title: whole blood of subject 260


title: whole blood of subject 263


title: whole blood of subject 258


title: L4 C. elegans, K21 Treatment, rep1

description:
Library name: K1
Processed data files contain raw counts

tag: treatment


title: whole blood of subject 261


title: L4 C. elegans, vehicle control, rep3

description:
Library name: Ctrl3
Processed data files contain raw counts

value: Vehicle Only


title: Participant13_Baseline_Fast

description: SAMPLE 141

value: Baseline


title: whole blood of subject 26

value: Whole blood


title: L4 C. elegans, vehicle control, rep4

description:
Library name: Ctrl4
Processed data files contain raw counts


title: Participant12_Month_6_Fast

description: SAMPLE 140

value: Blood


title: Participant12_Month_2_Fast

description: SAMPLE 138


title: Participant12_Baseline_Fast

description: SAMPLE 137


title: whole blood of subject 256


title: Participant12_Month_4_Fast

description: SAMPLE 139


title: whole blood of subject 257


title: Participant11_Month_6_Slow

description: SAMPLE 136

value: Slow


title: L4 C. elegans, vehicle control, rep5

description:
Library name: Ctrl5
Processed data files contain raw counts


title: CREB_KO1

value: male


title: whole blood of subject 259


title: L4 C. elegans, vehicle control, rep1

description:
Library name: Ctrl1
Processed data files contain raw counts


title: Participant11_Month_4_Slow

description: SAMPLE 135


title: whole blood of subject 252


title: Participant11_Month_2_Slow

description: SAMPLE 134


title: L4 C. elegans, vehicle control, rep2

description:
Library name: Ctrl2
Processed data files contain raw counts


title: whole blood of subject 262


title: whole blood of subject 251


title: whole blood of subject 25


title: ISG15KO 3 IFN

first: Dusan

last: Bogunovic

address: 650 W 168th Street

department: Pediatrics

institute: Columbia University

description: Library name: Sample_12_ISG15_P3_IFN

data_processing:
FASTQ files were uploaded to BaseSpace (Illumina) and sequence reads were trimmed for adaptor sequence and low-quality reads (<q15) using fastp.
Trimmed sequence reads were uploaded to BaseSpace (Illumina) and mapped to the human genome (hg19)with  the RNA-Seq Alignment (STAR) module
Assembly: hg19
Supplementary files format and content: csv file includes filtered, unnormalized gene-level count matrix for each sample

source_name: hTERT-immortalized fibroblast cell line (patient 3)

growth_protocol: hTERT-immortalized fibroblasts were cultured in DMEM supplemented with 10% fetal bovine serum and antibiotics in humidifed atmosphere with 5% CO2 at 37˚C.

extract_protocol:
Total RNA was extracted using RNeasy spin columns (QIAGEN 74104) following manufacturer’s instructions.
RNA sequencing libraries were prepared and sequenced by Azenta Life Sciences.

treatment_protocol: Cells were left unstimulated or treated with 1000 IU/mL IFN-α2b for 12 hours followed by a 24-hour rest

tag: cell line

value: fibroblast

value: ISG15 knock out

value: 12 hour IFN-a2b stimulation + 24 hour rest


title: whole blood of subject 24BEA

tag: Sex

value: female


title: Participant11_Baseline_Slow

description: SAMPLE 133

value: Cure


title: whole blood of subject 249


title: ISG15KO 3 unstimulated

description: Library name: Sample_11_ISG15_P3

value: hTERT-immortalized fibroblast cell line (patient 3)

tag: genotype

value: unstimulated


title: whole blood of subject 248


title: Participant10_Month_4_Fast

description: SAMPLE 131

value: Fast


title: whole blood of subject 253


title: ISG15KO 2 IFN

description: Library name: Sample_10_ISG15_P2_IFN

source_name: hTERT-immortalized fibroblast cell line (patient 2)

tag: cell type


title: whole blood of subject 255

source_name: Whole blood


title: Participant10_Month_6_Fast

description: SAMPLE 132


title: whole blood of subject 244


title: ISG15KO 2 unstimulated

description: Library name: Sample_9_ISG15_P2

value: hTERT-immortalized fibroblast cell line (patient 2)


title: Participant10_Month_2_Fast

description: SAMPLE 130


title: whole blood of subject 246


title: Participant10_Baseline_Fast

description: SAMPLE 129


title: ISG15KO 1 unstimulated

description: Library name: Sample_7_ISG15_P1

source_name: hTERT-immortalized fibroblast cell line (patient 1)


title: Participant9_Month_6_Slow

description: SAMPLE 128


title: IFNa03

city: Brussels

first: Xiaoyan

last: Yi

state: Brussels

address: Route de Lennik 808

department: Medical Faculty

institute: Université libre de Bruxelles

description:
Library name: Sample 6
hESC-derived NKX2-3GFP+ thyroid follicular cells treated with IFN-a

data_processing:
Raw FASTQ reads were pseudoaligned to the human transcriptome using Salmon (v1.4.0) with default parameters. Transcript-level abundance estimates were summarized to gene-level counts using tximport in R.
Differential gene expression analysis was performed using DESeq2 (v1.38.3) with shrinkage estimation and Benjamini-Hochberg adjusted p-values.
Assembly: GENCODE V36 (GRCh38.p13)
Supplementary files format and content: Gene-level expression matrices in TPM and raw counts were provided.

source_name: Thyroid

growth_protocol: The hESC line HES3 (NKX2-1wt/GFP) was used. These cells were cultured on Matrigel-coated 6-well plates in StemFlex medium (Thermo Scientific) supplemented with 100 U/ml penicillin-streptomycin (Gibco). Differentiation into thyroid follicular cells followed a previously established stepwise protocol. Briefly, cells were treated with 50 ng/ml Activin A for 3 days to induce foregut endoderm, followed by 1 μg/ml doxycycline for 4 days to induce NKX2-1 and PAX8 expression. Progenitors were expanded for 1 week and matured using 300 μM 8-Br-cAMP, 1 mU/ml recombinant human TSH, 50 nM dexamethasone, and 10 μM SB431542. Medium was refreshed every 48 hours. At day 58, cells were harvested for treatment and FACS sorting.

extract_protocol:
NKX2-1GFP+ cells were sorted by FACS (FACS Aria; BD Biosciences) and lysed directly into 700 µl of Qiazol lysis reagent (Qiagen). Total RNA was extracted using the miRNeasy Micro Kit (Qiagen) following the manufacturer’s instructions. RNA quality was verified using the Bioanalyzer 2100 (Agilent) and the RNA 6000 Nano Kit.
RNA libraries were constructed using the Ovation Solo RNA-seq System (NuGEN) according to the manufacturer’s instructions. cDNA libraries were indexed, quantified using the Quant-iT PicoGreen Kit (Life Technologies), and fragment size was verified using the Bioanalyzer 2100 (Agilent) with the DNA 1000 Kit. Libraries were multiplexed and sequenced on the Illumina HiSeq 1500 system (high-output mode, 2 × 100 bp).

treatment_protocol: At day 58 of differentiation, hESC-derived thyroid follicular cells were treated with either 2000 U/ml IFNa or 1000 U/ml IFNg (both from PeproTech) for 24 hours. Control cells received no treatment. Cells were collected after treatment for FACS sorting and RNA extraction.

value: Thyroid

value: Thyroid follicular cell

value: WT

value: IFN-α

tag: batch


title: IFNg03

description:
Library name: Sample 9
hESC-derived NKX2-1GFP+ thyroid follicular cells treated with IFN-g

value: IFN-γ


title: IFNg01

description:
Library name: Sample 7
hESC-derived NKX2-1GFP+ thyroid follicular cells treated with IFN-g


title: IFNa01

description:
Library name: Sample 4
hESC-derived NKX2-1GFP+ thyroid follicular cells treated with IFN-a


title: IFNg02

description:
Library name: Sample 8
hESC-derived NKX2-1GFP+ thyroid follicular cells treated with IFN-g


title: ISG15KO 1 IFN

description: Library name: Sample_8_ISG15_P1_IFN

value: hTERT-immortalized fibroblast cell line (patient 1)


title: Participant9_Month_2_Slow

description: SAMPLE 126

data_processing: nSolver and Rosalind

value: Blood

value: Slow


title: CTRL03

description:
Library name: Sample 3
Control

value: Control


title: Control 3 unstimulated

description: Library name: Sample_5_C21

source_name: hTERT-immortalized fibroblast cell line (C21)

value: fibroblast


title: CTRL02

description:
Library name: Sample 2
Control


title: CTRL01

description:
Library name: Sample 1
Control


title: whole blood of subject 247

first: Ferenc

last: Torma

institute: Hungarian University of Sports Science

value: Whole blood


title: Control 2 IFN

description: Library name: Sample_4_C18_IFN

source_name: hTERT-immortalized fibroblast cell line (C18)

value: 12 hour IFN-a2b stimulation + 24 hour rest


title: whole blood of subject 245

value: female


title: Control 3 IFN

description: Library name: Sample_6_C21_IFN

value: hTERT-immortalized fibroblast cell line (C21)


title: Participant9_Baseline_Slow

description: SAMPLE 125

source_name: Blood

value: Baseline

value: Cure


title: Control 2 unstimulated

description: Library name: Sample_3_C18

value: hTERT-immortalized fibroblast cell line (C18)

value: unstimulated


title: Participant8_Month_6_Fast

description: SAMPLE 124

value: Fast


title: Participant8_Month_4_Fast

description: SAMPLE 123


title: Control 1 unstimulated

description: Library name: Sample_1_C1

source_name: hTERT-immortalized fibroblast cell line (C1)

value: WT


title: IFNa02

description:
Library name: Sample 5
hESC-derived NKX2-2GFP+ thyroid follicular cells treated with IFN-a

value: Thyroid

value: Thyroid follicular cell

value: IFN-α


title: Participant9_Month_4_Slow

description: SAMPLE 127

value: Blood


title: Participant8_Month_2_Fast

description: SAMPLE 122


title: PacBio_KmgKD_rep2

first: Neuza

last: Reis Matias

institute: Stanford University

description:
Library name: PacBio_KmgKD_rep2
(24hr run time) at the Chan Zuckerberg Biohub SF Genomics Platform

data_processing:
Circular consensus sequencing (CCS) and Iso-Seq analysis were performed in SMRT Link v11.0
Data was mapped to Drosophila genome assembly: BDGP6.32 (GCA_000001215.4) using pbmm2 (1.12.0)
Tama (b0.0.0) collapse was used to collapse redundant transcript models (Kuo et al. 2020); -x capped (although our libraries are not 5' capped, this avoids over collapsing), -a 78 (78bp interquantile width that includes 90% of CAGE clusters, from parallel analysis), -z 80 (80bp interquantile width that includes 90% of 3?end clusters, from parallel analysis)
Transcriptome models from each PacBio library were merged into one single transcriptome with Tama (b0.0.0) merge (Kuo et al. 2020); -a 78 (78bp interquantile width that includes 90% of CAGE clusters, from parallel analysis), -z 80 (80bp interquantile width that includes 90% of 3?end clusters, from parallel analysis)
Analysis scripts are available at https://github.com/NeuzaRM/Kmg_FullerPaper2025
Assembly: dm6
Supplementary files format and content: gtf file of the merged transcriptome (control + KmgKD), after quality control and filters. Please see publication for details.

source_name: Testes

extract_protocol:
RNA was extracted from 150 pairs of testes using the RNeasy Plus Mini Kit from QIAGEN (74104)
Iso-Seq SMRTbell® libraries were made following the “Procedure & Checklist – Iso-Seq™ Express Template Preparation for Sequel® and Sequel II Systems”, protocol from PacBio.

value: Testes

value: bamGAL4/ KmgRNAi

value: Fly crosses were kept for 3 days at 25°C. Adults were then flipped to a new bottle, while the eggs and early larvae were shifted to 29°C. Testes were dissected from 0–2 day old males in 1xPBS.


title: Control 1 IFN

description: Library name: Sample_2_C1_IFN

value: hTERT-immortalized fibroblast cell line (C1)

value: fibroblast


title: Participant8_Baseline_Fast

description: SAMPLE 121