title: E1_N_SR_L05

description: Library name: Sample 44


title: 142_SMARTER_M_67

status: Public on Sep 30 2025

type: SRA

city: Ulm

first: Emil

last: Chteinberg

address: Albert-Einstein-Allee 11

country: Germany

institute: Ulm University Medical Center

description:
HTG EdgeSeq Pan B-Cell Lymphoma Panel
RNA (amplified oligo nucleotide probes)

library_source: transcriptomic

data_processing:
FASTQ Files using Illumina BaseSpace BCL to FASTQ software version 2.2.0 and Illumina Local Run Manager Software version 2.0.0.
FASTQ Files were analyzed with HTG EdgeSeq Parser software version 5.5 to generate raw counts for a total of 298 genes.
Assembly: Assembly: GRCh38.p13
Supplementary files format and content: raw counts
Supplementary files format and content: log2(Count per million+1)

molecule: total RNA

organism: Homo sapiens

source_name: Diffuse large B-ell lymphoma

extract_protocol:
Three hundred sixty DLBCLs tissues were processed. Using 5 ¬µm unstained FFPE sections. The optimal amounts of tissue for each HTG EdgeSeq panB Lymphoma assay. The sample preparation as performed according to the manufacturer’s instructions.
Probe_captured FFPE samples for EdgeSeq panB Lymphoma assay were amplified¨ and indexed via polymerase chain reaction (PCR) using the master mix (OneTaq HotStart 2X MasterMix in GC Buffer (New England Biolabs Inc., Ipswich, MA, USA), and indexing primers according to manufacturer’s instructions. The following library cleanup was performed using AMPure XP beads according to manufacturer’s instructions
Targeted mRNA Sequencing using HTG EdgeSeq Pan B_Cell Lymphoma Panel assay

tag: cell type

value: Diffuse large B-ell lymphoma

tag: tissue-fixation

value: FFPE

tag: Sex

value: M

tag: age


title: E1_N_SR_L02

city: Baltimore

first: Atul

last: Daiwile

state: MD

address: 251 Bayview Blvd,

department: MNRB

country: USA

institute: NIDA

description: Library name: Sample 43

data_processing:
Image analysis and base calling were conducted by the HiSeq Control Software (HCS). Raw sequence data (.bcl files) generated from Illumina HiSeq was converted into fastq files and de-multiplexed using Illumina's bcl2fastq 2.17 software. One mismatch was allowed for index sequence identification.
After investigating the quality of the raw data, sequence reads were trimmed to remove possible adapter sequences and nucleotides with poor quality using Trimmomatic v.0.36. The trimmed reads were mapped to the Rattus norvegicus reference genome available on ENSEMBL using the STAR aligner v.2.5.2b. The STAR aligner is a splice aligner that detects splice junctions and incorporates them to help align the entire read sequences. BAM files were generated as a result of this step. Unique gene hit counts were calculated by using feature Counts from the Subread package v.1.5.2. Only unique reads that fell within exon regions were counted.
After extraction of gene hit counts, the gene hit counts were added to the table
Assembly: Rattus norvegicus Rnor6.0
Supplementary files format and content: tab-delimited text file includes raw counts fro each sample

molecule: polyA RNA

organism: Rattus norvegicus

source_name: Nuclues Accumbens

extract_protocol:
RNA was extracted using the protocol from RNeasy Mini Handbook (Qiagen)
RNA samples were quantified using Qubit 2.0 Fluorometer (Life Technologies, Carlsbad, CA, USA) and RNA integrity was checked using Agilent TapeStation 4200 (Agilent Technologies, Palo Alto, CA, USA). RNA sequencing libraries were prepared using the NEBNext Ultra II RNA Library Prep Kit for Illumina following manufacturer’s instructions (NEB, Ipswich, MA, USA). Briefly, mRNAs were first enriched with Oligo(dT) beads. Enriched mRNAs were fragmented for 15 minutes at 94 °C. First strand and second strand cDNAs were subsequently synthesized. cDNA fragments were end repaired and adenylated at 3’ends, and universal adapters were ligated to cDNA fragments, followed by index addition and library enrichment by limited-cycle PCR. The sequencing libraries were validated on the Agilent TapeStation (Agilent Technologies, Palo Alto, CA, USA), and quantified by using Qubit 2.0 Fluorometer (Invitrogen, Carlsbad, CA) as well as by quantitative PCR (KAPA Biosystems, Wilmington, MA, USA). The sequencing libraries were clustered on two flowcell lanes. After clustering, the flowcells were loaded on the Illumina HiSeq instrument (4000 or equivalent) according to manufacturer’s instructions. The samples were sequenced using a 2x150bp Paired End (PE) configuration.

treatment_protocol:
Rats were randomly segregated into two groups of saline (n = 6) or METH (0.1 mg/kg /infusion) (n = 18). On each training day, rats were trained to lever press on a fixed-ratio-1 (FR1) schedule for three 3-h daily sessions (total 9 h/d) with 30 min off intervals in between each session to intravenously self-administer (SA) METH for 20 days.
Subsequently, all METH SA rats were given the opportunity to earn METH accompanied by a concurrent delivery of a 0.5-s foot-shock through the grid floor at 50% of the reinforced lever-presses. We set the initial footshock at 0.18 mA and increased the foot-shock intensity by 0.06 mA up to a final current of 0.36 mA (with a total of 9 punishment days). After 9 days of foot-shock we identified two phenotypes. Some rats continued to take METH in presence of aversive stimuli (foot-shock 0.18 to 0.36mA) we termed those rats shock-resistant (SR), whereas some rats decrease their reinforced lever responding and we called them shock-sensitive (SS)

tag: tissue

value: Nuclues Accumbens

value: Neural tissue

tag: genotype

value: WT

tag: treatment

value: METH Shock Resistant


title: Wild_type_control_GMCSF_replicate_03

city: New Haven

first: Andrés

last: Hidalgo

address: 10 Amistad Street

institute: Yale University

description:
Library name: WT_C_GM_03
S6_WT_C_GM_03

data_processing:
FastQ files for each sample were obtained using CASAVA v1.8 software (Illumina). Reads were further processed with RTA v1.18.66.3. FastQ files for each sample were obtained using bcl2fastq v2.20.0.422 software (Illumina). Sequencing reads were further processed as follows: Illumina adapters were trimmed and low-quality reads removed with Cutadapt v4.9 (10.14806/ej.17.1.200) (overlap = 7bp, minimum read length = 30bp). Quality control of the processed reads was done with fastQC. RSEM v1.3.1 was used to quantify expression levels against the mouse genome reference GRCm38  (default options). The count data were processed and normalized using limma v3.46 and edgeR v3.32.1, which were also used to perform pairwise differential expression analyses. To identify genes whose expression significantly varies across conditions, we applied a Likelihood Ratio Test (LRT) using DESeq2 v1.30.1, allowing the detection of global effects of a factor without the need to specify individual contrasts. The resulting significant genes were then clustered using the k-means algorithm from the stats package v4.0.3.
Sequenced reads were trimmed using cutadapt
Reads were quantified using RSEM
Assembly: GRCm38.84
Supplementary files format and content: raw counts matrix
Supplementary files format and content: tab delimited text file includes raw counts for each sample

organism: Mus musculus

source_name: HoxB8-Derived Neutrophils

extract_protocol:
RNA from HoxB8-derived neutrophils was extracted using RNAeasy micro kit (Quiagen ®). RNA quality was checked using capillary electrophoresis (Agilent). Samples were submitted for whole RNA next generation sequencing in the Genomics Unit of CNIC. 200 ng of total RNA was used to generate barcoded RNA sequencing libraries using the NEBNext Ultra RNA Library preparation kit (New England Biolabs). Libraries were sequenced with HiSeq2500 (Illumina) to generate 50-nucleotide single reads, with a minimum of eight million reads per sample.
RNA integrity was assessed using Agilent Bioanalyzer 2100, with RNA integrity numbers (RIN) between 9.8 and 10.0. RNA samples were processed by Novogene (Munich, Germany) for library preparation and sequencing, and all samples passed the quality control criteria. Strand-specific libraries were generated based on Novogene´s standard protocol. Samples were sequenced on an Illumina platform to produce 150 bp pairwise reads (PE150) per sample.

treatment_protocol: Culture of HoxB8 cells. For the flow cytometry and bulk RNA sequencing experiments, HoxB8 progenitors at day 3.5 of differentiation were seeded in 96-well plates at a density of 50,000 cells per well. Cells were cultured in complete DMEM medium (vehicle) or treated with GM-CSF (10ng/ml) for 48h, following the same conditions described for primary bone marrow neutrophil cultures. Vehicle or GM-CSF treated cells were collected at 48h after treatment for the analysis.

value: HoxB8-Derived Neutrophils

value: GM-CSF


title: Wild_type_control_GMCSF_replicate_02

description:
Library name: WT_C_GM_02
S5_WT_C_GM_02


title: 1419_RICOVER_noRTh_M_71


title: Wild_type_control_vehicle_replicate_03

description:
Library name: WT_C_VEH_03
S3_WT_C_VEH_03

value: Vehicle


title: Wild_type_control_GMCSF_replicate_01

description:
Library name: WT_C_GM_01
S4_WT_C_GM_01


title: E1_N_CT_R12

description: Library name: Sample 42

value: Control


title: E1_N_CT_R11

description: Library name: Sample 41


title: E1_N_CT_R06

description: Library name: Sample 40


title: E1_N_SR_R07

description: Library name: Sample 47


title: Wild_type_control_vehicle_replicate_02

description:
Library name: WT_C_VEH_02
S2_WT_C_VEH_02


title: 1416_RICOVER_noRTh_F_64

value: F


title: 141_SMARTER_F_68


title: 1414_RICOVER_noRTh_F_67


title: BMSCs, α-Asaronel, replicate5

city: Guangzhou

first: Li

last: Tong

address: Jingxi

country: China

institute: Nanfang Hospital

data_processing:
CLC Genomics Workbench v11.0.1
Sequence reads were trimmed for adaptor sequence/low-quality sequence using CLC genomic benchwork (parameter-quality limit:0.05)
Trimmed sequence reads were mapped to grcm38/mm10 using CLC genomic benchwork (parameters-mismath cost: 2 inserion cost: 3 deleion cost: 3 lenoth fraction. 0.8  simarly fraction:0.8)
Read count extraction and normalization were performed using CLC genomic benchwork
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample
Supplementary files format and content: tab-delimited text files include TPM values for each Sample

source_name: Bone marrow mesenchymal stem cells

growth_protocol: The sedimented bone marrow was then resuspended in DMEMsupplemented with 15% fetal bovine serum  and 1% penicillin-streptomycin

extract_protocol:
Total RNA was extracted using Trizol (Invitrogen) and assessed for quantity and purity with a Bioanalyzer 2100 and RNA 6000 Nano LabChip kit (Agilent),  with all samples having RNA integrity numbers (RIN) above 7.0. Approximately 10 μg of RNA was purified by isolating poly (A) mRNA with poly-T magnetic beads (Invitrogen) and fragmented using divalent cations at elevated temperatures.
Fragmented RNA was reverse transcribed into cDNA with the mRNA-Seq Sample Preparation Kit (Illumina),  generating libraries with an average insert size of 300 bp (±50 bp).

treatment_protocol: Osteogenic differentiation was induced in osteogenic induction medium,  which was described as consisting of basal growth medium supplemented with 100 nM dexamethasone (Sigma-Aldrich,  USA),  10 mM sodium β-glycerophosphate (Sigma-Aldrich,  USA) and 50 μM ascorbic acid (Sigma-Aldrich,  USA).

value: Bone marrow mesenchymal stem cells

value: BMSCs

value: osteogenic differentiation

tag: agent

value: α-Asaronel


title: E1_N_CT_R05

description: Library name: Sample 39


title: Wild_type_control_vehicle_replicate_01

description:
Library name: WT_C_VEH_01
S1_WT_C_VEH_01


title: BMSCs, α-Asaronel, replicate3


title: Wild_type_JunB_OVEREXPRESSED_vehicle_replicate_03

description:
Library name: WT_JB_VEH_03
S9_WT_JB_VEH_03


title: BMSCs, α-Asaronel, replicate4


title: 1406_RICOVER_noRTh_M_75


title: BMSCs, α-Asaronel, replicate2


title: BMSCs, α-Asaronel, replicate1


title: 1403_RICOVER_noRTh_F_77


title: E1_N_CT_L11

description: Library name: Sample 37


title: BMSCs, control, replicate6

value: control


title: BMSCs, control, replicate5


title: E1_N_CT_L12

description: Library name: Sample 38


title: BMSCs, control, replicate4


title: 1400_RICOVER_noRTh_M_69

value: Diffuse large B-ell lymphoma


title: E1_M_SS_R10

description: Library name: Sample 36

source_name: Midbrain

value: Midbrain

value: METH Shock Sensitive


title: BMSCs, control, replicate3


title: 140_SMARTER_F_68

value: FFPE


title: BMSCs, control, replicate2


title: E1_M_SS_R08

description: Library name: Sample 35

value: Neural tissue


title: BMSCs, α-Asaronel, replicate6

value: WT


title: BMSCs, control, replicate1


title: JB3, lung neutrophils, Mrp8 CRE JunB f/f

data_processing:
Sequenced reads were trimmed using cutadapt
Reads were quantified using RSEM
Assembly: GRCm38.84
Supplementary files format and content: raw counts matrix
Supplementary files format and content: tab delimited text file includes raw counts for each sample

source_name: lung neutrophils sorted from Mrp8 CRE JunB f/f mice

extract_protocol:
Blood and tissue neutrophils from 10-12 week-old male mice  were FACS sorted using CD45, CD11b, Ly6G and DAPI labeling, with typical purities > 95%. Total RNA was prepared with the RNA Extraction RNeasy Plus Mini-kit (QIAGEN)
cDNA amplification from neutrophil RNA and generation of index-tagged sequencing libraries were carried out using the Ovation Single Cell RNA-Seq System (NuGEN Technologies, San Carlos CA). Libraries were quantified using the dsDNA HS assay with the Qubit fluorometer (Life Technologies, Carlsbad, California). Average library size and size distribution were determined using a High Sensitivity DNA assay in an Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara CA). Libraries were normalized to 10nM using Tris-Cl 10mM, pH8.5 with 0.1% Tween 20.

value: lung

value: Neutrophils

value: Mrp8 CRE JunB f/f


title: 14_DENSER_F_79


title: E1_M_SS_R03

description: Library name: Sample 34


title: BM3, Bone Marrow neutrophils, Mrp8 WT JunB f/f

source_name: Bone Marrow neutrophils sorted from Mrp8 WT JunB f/f mice

value: Bone Marrow

value: Mrp8 WT JunB f/f


title: DNX1895, Blood neutrophils, Mrp8 WT JunB f/f

source_name: Blood neutrophils sorted from Mrp8 WT JunB f/f mice

value: Blood


title: 1399_4_RICOVER_noRTh_M_61

value: M


title: E1_M_SS_R02

description: Library name: Sample 33


title: DNX2085, Blood neutrophils, Mrp8 WT JunB f/f


title: DNX2076, Blood neutrophils, Mrp8 WT JunB f/f


title: 1399_3_RICOVER_noRTh_M_61


title: E1_M_SS_L03

description: Library name: Sample 31


title: BM1, Bone Marrow neutrophils, Mrp8 WT JunB f/f


title: 1394_RICOVER_noRTh_M_73


title: DNX1893, Blood neutrophils, Mrp8 WT JunB f/f


title: WT5, lung neutrophils, Mrp8 WT JunB f/f

source_name: lung neutrophils sorted from Mrp8 WT JunB f/f mice


title: WT7, lung neutrophils, Mrp8 WT JunB f/f


title: E1_M_SR_R09

description: Library name: Sample 30

value: METH Shock Resistant


title: 1392_RICOVER_noRTh_M_77


title: E1_M_SR_R07

description: Library name: Sample 29


title: JB4, lung neutrophils, Mrp8 CRE JunB f/f


title: JB5, lung neutrophils, Mrp8 CRE JunB f/f


title: 1391_RICOVER_noRTh_M_77


title: 1390_RICOVER_noRTh_M_66


title: BM2, Bone Marrow neutrophils, Mrp8 WT JunB f/f


title: PBMC, GCSF+ISO, replicate 5

city: Tucson

first: Richard

last: Simpson

state: AZ

address: 1501 N Campbell Avenue, CRC building Rm 5340

department: School of Nutritional Sciences & Wellness

institute: University Of Arizona

description:
Library name: ISO.010 Post
10x Genomics

library_source: transcriptomic single cell

data_processing:
FastQ files were converted into expression matrices using the “cellranger count” function provided by Cell Ranger 6.0.1
Assembly: GRCh38
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Blood

extract_protocol:
Peripheral blood mononuclear cells (PBMCs) were isolated from 6mL of ACD whole blood, collected at baseline and after a 20-min ISO infusion, by density gradient centrifugation (Cytiva Ficoll-PaqueTM, Fisher Scientific, Hampton, NH) and cryopreserved for later analysis. Isolated PBMCs were then resuspended in a PBS/RNAlater solution and delivered to the University of Arizona Genetics Core for single cell RNA sequencing (scRNAseq) analysis using the 10x Genomics platform.
Targeted Gene Expression libraries generated from Chromium Single Cell 5’ Gene Expression and Chromium Single Cell V(D)J libraries comprised standard Illumina paired-end constructs which begin with P5 and end with P7. The gene expression libraries were quantified, normalized, pooled, and sequenced on an Illumina NextSeq500 sequencer.

value: PBMCs

value: GCSF+ISO


title: E1_M_SR_L10

description: Library name: Sample 28


title: PBMC, GCSF+ISO, replicate 3

description:
Library name: ISO.006 Post
10x Genomics


title: PBMC, GCSF+ISO, replicate 2

description:
Library name: ISO.004 Post
10x Genomics


title: E1_M_SR_L08

description: Library name: Sample 27


title: 1388_RICOVER_noRTh_M_71


title: 1398_RICOVER_noRTh_M_63


title: PBMC, GCSF+ISO, replicate 4

description:
Library name: ISO.007 Post
10x Genomics


title: E1_M_SS_L04

description: Library name: Sample 32


title: PBMC, GCSF+ISO, replicate 1

description:
Library name: ISO.001 Post
10x Genomics


title: E1_M_SR_L05

description: Library name: Sample 26


title: 1387_RICOVER_noRTh_M_64


title: PBMC, GCSF, replicate 5

description:
Library name: ISO.010 Pre
10x Genomics

value: GCSF


title: E1_M_SR_L02

description: Library name: Sample 25


title: 1384_RICOVER_noRTh_M_68

value: Diffuse large B-ell lymphoma


title: PBMC, GCSF, replicate 3

description:
Library name: ISO.006 Pre
10x Genomics


title: WT4, lung neutrophils, Mrp8 WT JunB f/f


title: E1_M_CT_R12

description: Library name: Sample 24

value: Midbrain

value: Control


title: PBMC, GCSF, replicate 2

description:
Library name: ISO.004 Pre
10x Genomics


title: U937 cells, TNRC18 KO, H3K27ac, 16 hr  rep1

city: North Chicago

first: Fedik

last: Rahimov

state: IL

address: 1 N. Waukegan Road

department: Genomics Research Center

institute: AbbVie

description: Library name: TNRC18KO16R1-K27

library_source: genomic

data_processing:
Sequencing data were demultiplexed and reads with sgRNA sequences were quantified using custom Perl scripts. Given that the position of the sgRNA could vary per read, the primer sequences flanking the sgRNA were considered. Sequences in between the flanking primers were extracted and then compared to sequences in the sgRNA library. Only sequences with no mismatches were used in the calculation of guide-level read counts. Samples with a minimum of 80% reads mapping to a sgRNAs were considered for further analysis. Through the edgeR Bioconductor package,  reads were normalized between samples using the trimmed mean of M values (TMM) method. Differential analysis of guide level counts was performed using the limma R Bioconductor package. Gene level effects were considered as the median log fold change of the four guides associated with each gene. Statistically significant genes were identified by aggregating differential sgRNAs ranked consistently higher at gene level using the robust rank aggregation (RRA) method.
Assembly: GRCh38
Supplementary files format and content: Processed data listed in column processed data file are bedgraph files.
Library strategy: CUT&Tag

molecule: genomic DNA

growth_protocol: U937 cells were maintained in RPMI 1640 (Gibco) supplemented with 10% heat inactivated fetal bovine serum (FBS, Gibco) and 1% Pen/Strep (Gibco).

extract_protocol:
Genomic DNA was extracted using Quick-DNA FFPE Kit (Zymo Research).
Active Motif's protocol for Cut&Tag was followed. Briefly, Tagmented DNA was PCR amplified with i5 and i7 primers. Paired end sequencing 70 cycles.

treatment_protocol: U937 cells were maintained in RPMI 1640 media (Gibco) supplemented with 10% heat inactivated fetal bovine serum (FBS, Gibco) and 1% Pen/Strep (Gibco). Cells were differentiated by addition of 10 ng/ml phorbol 12-myristate 13-acetate (PMA, Sigma, P1585) for 24 hours and treated with 100 mg/ml lipopolysaccharide (LPS) (Sigma, L26375MG) for 0 or 16 hours.

tag: cell line

value: pro-monocytic cell

value: 16 hr LPS

tag: chip antibody

value: anti-H3K27Ac (Active Motif, 91193)


title: 1380_RICOVER_noRTh_F_71

value: FFPE

value: F


title: 1382_RICOVER_noRTh_F_62


title: PBMC, GCSF, replicate 1

description:
Library name: ISO.001 Pre
10x Genomics


title: 1376_RICOVER_noRTh_F_75


title: E1_M_CT_R11

description: Library name: Sample 23

value: Neural tissue

value: WT


title: E1_M_CT_R06

description: Library name: Sample 22


title: U937 cells, TNRC18 KO, H3K27ac, 16 hr  rep2

description: Library name: TNRC18KO16R2-K27


title: U937 cells, TNRC18 KO, H3K27ac, 0 hr rep2

description: Library name: TNRC18KO0R2-K27

value: 0 hr


title: U937 cells, WT, H3K27ac, 16 hr rep1

description: Library name: WT16R1-K27


title: E1_M_CT_L12

description: Library name: Sample 20


title: 1378_RICOVER_noRTh_F_71


title: U937 cells, TNRC18 KO, H3K27ac, 0 hr rep1

description: Library name: TNRC18KO0R1-K27


title: U937 cells, WT, H3K27ac, 16 hr rep2

description: Library name: WT16R2-K27


title: U937 cells, WT, H3K27ac, 0 hr rep1

description: Library name: WT0R1-K27


title: U937 cells, WT, H3K27ac, 0 hr rep2

description: Library name: WT0R2-K27


title: E1_M_CT_L11

description: Library name: Sample 19


title: 1374_RICOVER_noRTh_M_70


title: PBMC, GCSF, replicate 4

description:
Library name: ISO.007 Pre
10x Genomics

value: Blood


title: Presort3

description:
Library name: Presort3
Presort 3

data_processing:
Sequencing data were demultiplexed and reads with sgRNA sequences were quantified using custom Perl scripts. Given that the position of the sgRNA could vary per read, the primer sequences flanking the sgRNA were considered. Sequences in between the flanking primers were extracted and then compared to sequences in the sgRNA library. Only sequences with no mismatches were used in the calculation of guide-level read counts. Samples with a minimum of 80% reads mapping to a sgRNAs were considered for further analysis. Through the edgeR Bioconductor package,  reads were normalized between samples using the trimmed mean of M values (TMM) method. Differential analysis of guide level counts was performed using the limma R Bioconductor package. Gene level effects were considered as the median log fold change of the four guides associated with each gene. Statistically significant genes were identified by aggregating differential sgRNAs ranked consistently higher at gene level using the robust rank aggregation (RRA) method.
Assembly: GRCh38
Supplementary files format and content: Count matrix showing guide counts for all samples in a tab-delimited text file
Library strategy: CRISPR Screen

extract_protocol:
Genomic DNA was extracted using Quick-DNA FFPE Kit (Zymo Research).
PCR reactions containing up to 10 μg genomic DNA in each reaction were performed using ExTaq DNA Polymerase with primers to amplify the sgRNAs. Samples were then purified with SPRIselect beads, mixed and sequenced on a NextSeq 500 by 75-bp single-end sequencing.

treatment_protocol: 120 million U937 cells that stably express Cas9 and an LC3 autophagy reporter, were infected with the Brunello sgRNA library (76,441 sgRNAs targeting 19,114 genes) at multiplicity of infection (MOI) = 0.3 in three biological replicates. Following puromycin selection, cells were differentiated with phorbol-12-myristate-13-acetate (PMA) and treated with lipopolysaccharide (LPS) for 24 hours. 40 million cells were collected as presort for genomic DNA extraction for each replicate. Greater than 120 million cells per replicate were then processed and stained for intracellular IL-1β at 10 million cells/ml. Cell populations expressing the top and bottom 10% IL-1β levels were enriched using a FACSAria Fusion cell sorter (BD Biosciences). At least four million IL-1βlow and IL-1βhigh cells were collected for genomic DNA extraction. PCR reactions containing up to 10 μg genomic DNA in each reaction were performed using ExTaq DNA Polymerase with primers to amplify the sgRNAs. Samples were then purified with SPRIselect beads, mixed and sequenced on a NextSeq 500.

value: CRISPR-Cas9 knockout


title: Presort2

description:
Library name: Presort2
Presort 2


title: E1_D_SS_R10

description: Library name: Sample 18

source_name: Dorsal striatum

value: Dorsal striatum

value: METH Shock Sensitive


title: Presort1

description:
Library name: Presort1
Presort 1


title: IL1b, High, Rep3

description:
Library name: IL1b-High-Rep3
High 3


title: 1372_RICOVER_noRTh_F_63


title: 1368_RICOVER_noRTh_M_64

value: M


title: E1_D_SS_R03

description: Library name: Sample 16


title: U937 cells, rs748670681-TT rep 6, 24hr LPS treatment rep 2

description: Library name: U937TNRC18Risk624hrLPS2

data_processing:
FastQ files were aligned to human genome reference using STAR (v2.7.10b) with GRCh38 primary assembly (v2.7.4a) gene annotations. Gene expression levels were counted using featureCounts (v2.4.3). Differential expression was compared using the test in limma R package (v3.54.2).
UMI-labeled reads were deduplicated using UMI-tools.
Assembly: GRCh38
Supplementary files format and content: Count matrix showing CPM values in a tab-delimited text file

growth_protocol: Cells were maintained in RPMI 1640 (Gibco) supplemented with 10% heat inactivated fetal bovine serum (FBS, Gibco) and 1% Pen/Strep (Gibco).

extract_protocol:
Total RNA was isolated using the Direct-zol RNA Miniprep Plus kit (R2072, Zymo Research)
500 nanograms of total RNA were used for NEBNext Ultra II Directional RNA Library Prep Kit (NEB # E7760L). Poly-A selection (NEBNext Poly (A) Magnetic Isolation Module; NEB # E7490) and cDNA synthesis were performed according to NEB protocol. The NEBNext UMI RNA Adaptors were diluted 50-fold in ice-cold UMI Adaptor dilution buffer. Ligation reaction was purified using Ampure XP beads. (Beckman Coulter, # A63881) and the adaptor ligated cDNA was amplified with 12 cycles of PCR with NEBNext Primer Mix (96 Unique Dual Index UMI Adaptors RNA set1, (NEB #E7416). Equimolar amounts of the samples were then pooled and sequenced using NextSeq 500/550 70 base read lengths in paired-end mode.

treatment_protocol: Cells were differentiated by addition of 10 ng/ml phorbol 12-myristate 13-acetate (Sigma, P1585) for 24 hours and treated with 100 mg/ml lipopolysaccharide (LPS) (Sigma, L26375MG)for designated times.

value: LPS


title: E1_D_SS_L03

description: Library name: Sample 13


title: E1_D_SS_R08

description: Library name: Sample 17


title: E1_M_CT_R05

description: Library name: Sample 21


title: IL1b, High, Rep2

description:
Library name: IL1b-High-Rep2
High 2


title: 1365_RICOVER_noRTh_F_68

value: Diffuse large B-ell lymphoma


title: IL1b, Low, Rep2

description:
Library name: IL1b-Low-Rep2
Low 2


title: IL1b, High, Rep1

description:
Library name: IL1b-High-Rep1
High 1


title: IL1b, Low, Rep1

description:
Library name: IL1b-Low-Rep1
Low 1


title: E1_D_SS_R02

description: Library name: Sample 15


title: 1363_RICOVER_noRTh_F_67


title: E1_D_SS_L04

description: Library name: Sample 14


title: U937 cells, rs748670681-TT rep 6, vehicle treatment rep 1

description: Library name: U937TNRC18Risk6Veh1

value: Vehicle


title: 1358_RICOVER_noRTh_M_67


title: E1_D_SR_R09

description: Library name: Sample 12

value: METH Shock Resistant


title: U937 cells, rs748670681-TT rep 3, 24hr LPS treatment rep 2

description: Library name: U937TNRC18Risk324hrLPS2

value: pro-monocytic cell


title: 1364_RICOVER_noRTh_M_76


title: U937 cells, rs748670681-TT rep 6, 24hr LPS treatment rep 1

description: Library name: U937TNRC18Risk624hrLPS1


title: IL1b, Low, Rep3

description:
Library name: IL1b-Low-Rep3
Low 3


title: 1354_RICOVER_noRTh_M_67


title: U937 cells, rs748670681-TT rep 6, vehicle treatment rep 3

description: Library name: U937TNRC18Risk6Veh3


title: 1361_RICOVER_noRTh_F_65


title: 1360_RICOVER_noRTh_M_70


title: U937 cells, rs748670681-TT rep 3, 24hr LPS treatment rep 3

description: Library name: U937TNRC18Risk324hrLPS3


title: U937 cells, rs748670681-TT rep 6, vehicle treatment rep 2

description: Library name: U937TNRC18Risk6Veh2


title: E1_D_SR_R07

description: Library name: Sample 11


title: U937 cells, rs748670681-TT rep 3, 24hr LPS treatment rep 1

description: Library name: U937TNRC18Risk324hrLPS1


title: U937 cells, rs748670681-TT rep 6, 24hr LPS treatment rep 3

description: Library name: U937TNRC18Risk624hrLPS3


title: E1_D_SR_L10

description: Library name: Sample 10


title: U937 cells, rs748670681-TT rep 3, vehicle treatment rep 3

description: Library name: U937TNRC18Risk3Veh3


title: U937 cells, rs748670681-TT rep 3, vehicle treatment rep 1

description: Library name: U937TNRC18Risk3Veh1


title: E1_D_SR_L08

description: Library name: Sample 9


title: U937 cells, rs748670681-TT rep 1, 24hr LPS treatment rep 3

description: Library name: U937TNRC18Risk124hrLPS3


title: 135_SMARTER_F_76


title: U937 cells, rs748670681-TT rep 3, vehicle treatment rep 2

description: Library name: U937TNRC18Risk3Veh2


title: E1_D_SR_L05

description: Library name: Sample 8


title: 135_RICOVER_60_F_79


title: E1_D_SR_L02

description: Library name: Sample 7


title: 1349_RICOVER_noRTh_F_70


title: 1348_RICOVER_noRTh_M_69


title: U937 cells, rs748670681-TT rep 1, 24hr LPS treatment rep 1

description: Library name: U937TNRC18Risk124hrLPS1


title: U937 cells, rs748670681-TT rep 1, 24hr LPS treatment rep 2

description: Library name: U937TNRC18Risk124hrLPS2


title: E1_D_CT_R12

description: Library name: Sample 6

value: Control


title: E1_D_CT_R11

description: Library name: Sample 5


title: U937 cells, rs748670681-TT rep 1, vehicle treatment rep 2

description: Library name: U937TNRC18Risk1Veh2


title: 1344_RICOVER_noRTh_F_75


title: 1342_RICOVER_noRTh_F_61


title: E1_D_CT_R05

description: Library name: Sample 3


title: 133_SMARTER_F_68


title: U937 cells, rs748670681-TT rep 1, vehicle treatment rep 3

description: Library name: U937TNRC18Risk1Veh3


title: U937 cells, WT rep 3, 24hr LPS treatment rep 1

description: Library name: U937WT324hrLPS1


title: E1_D_CT_L12

description: Library name: Sample 2


title: U937 cells, WT rep 3, vehicle treatment rep 3

description: Library name: U937WT3Veh3


title: E1_D_CT_R06

description: Library name: Sample 4


title: 1343_RICOVER_noRTh_F_73


title: 132_MegaCHOEP_III_M_23


title: U937 cells, WT rep 2, 24hr LPS treatment rep 2

description: Library name: U937WT224hrLPS2


title: U937 cells, WT rep 2, 24hr LPS treatment rep 3

description: Library name: U937WT224hrLPS3


title: U937 cells, rs748670681-TT rep 1, vehicle treatment rep 1

description: Library name: U937TNRC18Risk1Veh1


title: 131_SMARTER_M_61


title: U937 cells, WT rep 3, vehicle treatment rep 1

description: Library name: U937WT3Veh1


title: U937 cells, WT rep 3, 24hr LPS treatment rep 2

description: Library name: U937WT324hrLPS2


title: U937 cells, WT rep 2, vehicle treatment rep 3

description: Library name: U937WT2Veh3


title: U937 cells, WT rep 3, 24hr LPS treatment rep 3

description: Library name: U937WT324hrLPS3


title: 12

city: Krakow

first: Tomasz

last: Szmatoła

state: Małopolskie

address: Mickiewicza 21

department: OMEI

country: Poland

institute: University of Agriculture in Krakow

description: Library name: Sample 12

data_processing:
Quality control, FastQC, v0.11.9
Filtering, Flexbar, 3.5.0
Alignment, STAR, 2.7.5c
Reads counting, Htseq-count, 1.99.2
Reads normalization, DESeq2 3.16
Assembly: EquCab3
Supplementary files format and content: Processed data files include raw read counts for all samples in tabular format, text files (.txt)

organism: Equus caballus

source_name: chorionic girdle

extract_protocol:
Standard procedure of  PureLink™ RNA Mini Kit (Ambion) with DNAse treatment
Standard protocol of VAHTS Universal V8 RNA-seq Library Prep Kit for Illumina

value: chorionic girdle


title: U937 cells, WT rep 2, vehicle treatment rep 2

description: Library name: U937WT2Veh2


title: U937 cells, WT rep 1, 24hr LPS treatment rep 3

description: Library name: U937WT124hrLPS3


title: 11

description: Library name: Sample 11


title: U937 cells, WT rep 2, vehicle treatment rep 1

description: Library name: U937WT2Veh1


title: U937 cells, WT rep 3, vehicle treatment rep 2

description: Library name: U937WT3Veh2


title: U937 cells, WT rep 1, 24hr LPS treatment rep 2

description: Library name: U937WT124hrLPS2


title: 13_DENSER_F_79

value: FFPE


title: 10

description: Library name: Sample 10


title: U937 cells, WT rep 1, 24hr LPS treatment rep 1

description: Library name: U937WT124hrLPS1


title: 1289_RICOVER_60_M_72


title: U937 cells, WT rep 1, vehicle treatment rep 3

description: Library name: U937WT1Veh3


title: U937 cells, WT rep 2, 24hr LPS treatment rep 1

description: Library name: U937WT224hrLPS1


title: U937 cells, WT rep 1, vehicle treatment rep 1

description: Library name: U937WT1Veh1


title: 1283_RICOVER_60_F_61

value: F


title: U937 cells, WT rep 1, vehicle treatment rep 2

description: Library name: U937WT1Veh2


title: 9

description: Library name: Sample 9


title: U937 cells, TNRC18 knockout, 24hr LPS treatment rep 2

description: Library name: U937TNRC18KOA01A0224hrLPS2

value: TNRC18 knockout


title: 1287_RICOVER_60_M_75


title: 8

description: Library name: Sample 8

source_name: allantochorion

value: allantochorion


title: 1304_RICOVER_60_F_61


title: U937 cells, TNRC18 knockout, 24hr LPS treatment rep 3

description: Library name: U937TNRC18KOA01A0224hrLPS3


title: 1269_RICOVER_60_M_74


title: E1_D_CT_L11

description: Library name: Sample 1

value: Neural tissue

value: WT


title: U937 cells, non-template control, 24hr LPS treatment rep 2

description: Library name: U937NTC124hrLPS2


title: U937 cells, non-template control, 24hr LPS treatment rep 1

description: Library name: U937NTC124hrLPS1


title: 4

description: Library name: Sample 4


title: 7

description: Library name: Sample 7


title: U937 cells, TNRC18 knockout, vehicle treatment rep 3

description: Library name: U937TNRC18KOA01A02Veh3


title: U937 cells, TNRC18 knockout, vehicle treatment rep 2

description: Library name: U937TNRC18KOA01A02Veh2


title: 6

description: Library name: Sample 6


title: 128_SMARTER_M_74


title: U937 cells, TNRC18 knockout, vehicle treatment rep 1

description: Library name: U937TNRC18KOA01A02Veh1


title: 126_SMARTER_F_76


title: U937 cells, non-template control, 24hr LPS treatment rep 3

description: Library name: U937NTC124hrLPS3


title: U937 cells, non-template control, vehicle treatment rep 1

description: Library name: U937NTC1Veh1


title: NT gRNA Veh  [CUT&RUN]

city: Research Triangle Park

first: Francesco

middle: John

last: DeMayo

state: North Carolina

address: 111 T W Alexander Dr

department: DIR

institute: NIEHS

description: Library name: Sample9

data_processing:
Reads from CUT&RUN were trimmed of adapter sequences using Trim Galore! (https://www.bioinformatics.babraham.ac.uk/projects/trim_galore/; Version 0.6.10) with default settings except for specifying paired-end validation.
Trimmed sequences were aligned to hg38 and E. coli K-12 MG1655 genomes using bowtie2 (Version 2.5.2) with maximum fragment length 2,000, forward-reverse mate orientation, local read alignment, and no mixed or discordant read alignments.
Alignment files were deduplicated using Picard (http://broadinstitute.github.io/picard; Version 3.2.0) and filtered for reads with MAPQ 5 using samtools (Version 1.18).
Processed reads from replicate samples were concatenated and converted from paired-end format to fragment representation in BED format, then peak calls were performed via MACS2 (Version 2.2.9.1) with the callpeaks function and parameters “-f BED -g hs -q 0.001 --keep-dup all --nomodel --extsize 100”, using IgG samples as background control. Prior to downstream analysis, peaks overlapping blacklist regions were discarded.
Assembly: hg38 genome (GCF_000001405.40)
Supplementary files format and content: consensus.bed files contain consensus peaks in bed format for each condition.
Supplementary files format and content: bigwig files contain Ecoli spike-in normalized bed files for each sample.
Library strategy: CUT&Run

source_name: THESC

growth_protocol: CRISPR engineered cells were maintained in DMEM/F-12 supplemented with 10% Fetal Bovine Serum and 4ug/mL Blasticidin. Cells were cultured and grown in a 5% CO2 and 37°C incubator. Cell media was changed every three days and cells were passaged before reaching 90% confluency.

extract_protocol:
Targeted DNA amplicons were isolated using the Epicypher CUTANA Cut&Run Kit Version 3 with antibodies targeting PGR and control antibody IgG.
PGR Cut&Run was conducted using a 1:25 dilution of the PGR antibody (Santa Cruz; Cat. No. sc-7208) incubated in antibody incubation buffer overnight at 4C. Targeted DNA amplicons were purified using the Qiagen QIAquick PCR Purification Kit (Qiagen, Hilden, Germany). Sequencing libraries were prepared using the NEBNext Ultra II DNA library preparation kit for Illumina (New England Biolabs, Ipswich, MA, USA), with 13 cycles of PCR amplification. The libraries were sequenced by the NIEHS sequencing core.

treatment_protocol: Cell culture media was changed to low serum media containing DMEM/F12 supplemented with 2% Fetal Bovine Serum (FBS) and 1% penicillin-streptomycin. 24 hours later, cells were treated with 1uM Medroxyprogesterone Acetate (MPA) or 0.01% EtOH (vehicle) in OptiMEM with 2% Charcoal Stripped Serumand 1% Penicillin-Streptomycin for 3 hours.

value: THESC

value: Endometrial Stromal Cells

value: Vehicle (0.01% ethanol)

tag: batch


title: U937 cells, TNRC18 knockout, 24hr LPS treatment rep 1

description: Library name: U937TNRC18KOA01A0224hrLPS1


title: 1248_RICOVER_60_F_78


title: 1247_RICOVER_60_F_77


title: Promoter gRNA Veh R2 [CUT&RUN]

description: Library name: Sample6

value: PGRB-dominant


title: 5

description: Library name: Sample 5


title: U937 cells, non-template control, vehicle treatment rep 2

description: Library name: U937NTC1Veh2


title: 3

description: Library name: Sample 3


title: 126_RICOVER_60_F_72


title: 1235_RICOVER_60_F_66


title: IgG-Ab NT gRNA Veh

description: Library name: Sample1

data_processing:
Reads from CUT&RUN were trimmed of adapter sequences using Trim Galore!  Version 0.6.10 with default settings except for specifying Illumina adapter sequences and paired-end validation.
Trimmed sequences were aligned to hg38 genome using bowtie2 (Version 2.5.2).
Alignment files were processed using Picard (http://broadinstitute.github.io/picard; Version 3.2.0) for duplicate removal and samtools (Version 1.18) to filter for reads with MAPQ  5
Assembly: hg38 genome (GCF_000001405.40)
Supplementary files format and content: bigwig files
Library strategy: CUT&Run

extract_protocol:
Targeted DNA amplicons were isolated using the Epicypher CUTANA Cut&Run Kit Version 3 with antibodies targeting PGR and control antibody IgG.
A total of 550,000 cells per sample were collected in DNA LoBind 1.5mL tubes containing wash buffer. Cells were captured with BioMag Plus Concavalin A beads and incubated with FOXO1 antibody (Cell Signaling Technologies, Cat. No. 2880, clone C29H4; 1:50) or IgG antibody (1:100) supplied by the CUTANA kit overnight at 4°C in antibody incubation buffer. After washing away antibodies, pAG-MNase generated by the NIEHS proteomics core was added and incubated for 30 minutes at room temperature. After washing, CaCl2 was added and incubated for 30 minutes in an aluminum cold block placed in ice. The protein-DNA complexes were released by incubating at 37°C for 10 minutes. DNA was purified using the Qiagen MiniElute PCR Purification Kit. Sequencing libraries were prepared using the NEBNext Ultra II DNA library preparation kit for Illumina  according to the manufacturer’s instructions, with 14 cycles of PCR amplification. The PCR products were quantified using the Qubit dsDNA HS Assay Kit and quality control was performed with Bioanalyzer DNA Analysis. The libraries were sequenced by the NIEHS sequencing core.

treatment_protocol: Cells were treated with 10nM E2 or 0.01% EtOH (vehicle) in OptiMEM with 2% Charcoal Stripped Serumand 1% Penicillin-Streptomycin for 24 hours.


title: 122_DENSER_F_67


title: S22-063-170

city: Praha 6

first: Karel

last: Muller

address: Rozvojová 263

department: Lab. of hormonal regulations in plants

country: Czech Republic

institute: Institute of Experimenal Botany of the Czech Academy of Sciences

data_processing:
reads were quality filterred by rcorrector and Trimmomatic
transcript quantification and normalization done by Salmon v1.3.0 with parameters--seqBias, --gcBias, --PosBias, --numBootstraps 30
Assembly: Chara braunii assembly Cbr_1.0
Supplementary files format and content: sf files generated by Salmon software, include TPM values

organism: Chara braunii

source_name: whole thalli with rhizoids

growth_protocol: Chara braunii was maintained on soil-agar medium in cultivation chamber at 22°C with a 14/10 light-day cycle and light intensity of 15 µE m-2 s-1.

extract_protocol:
FavorPrep Plant Total RNA Mini kit (Favorgen Biotech Corp)
NEBNext Ultra II Directional RNA Library prep kit

value: whole thalli with rhizoids

tag: strain


title: U1U2 gRNAs Veh R1 [CUT&RUN]

description: Library name: Sample1

value: PGRA/B-equivalent


title: S22-063-169

source_name: whole thalli without rhizoids

value: whole thalli without rhizoids


title: Promoter gRNA MPA R3

description: Library name: Sample18

data_processing:
Adapter trimming, optical deduplication, and PCR deduplication were performed using BBMap v39.01
Reads were mapped to the hg38 genome (GCF_000001405.40) using STAR v2.6.0c
Differential expression analysis was performed using edgeR v4.2.2 in R v4.4.1
Assembly: hg38 genome (GCF_000001405.40)
Supplementary files format and content: raw_counts.csv contains the raw counts data for each sample, with genes at row titles and samples as column titles.
Supplementary files format and content: normalized_counts_log2cpm.csv contains normalized counts using the log2 of counts per million method.

extract_protocol:
The total RNA of the cells was isolated using Qiagen RNeasy RNA mini prep kit with Qiagen on-column DNase digestion following the manufacturer’s instructions.
Illumina Tru-seq Stranded mRNA library kit with IDT for Illumina TruSeq RNA UD-96 barcodes

treatment_protocol: Cell culture media was changed to low serum media containing DMEM/F12 supplemented with 2% Fetal Bovine Serum (FBS) and 1% penicillin-streptomycin. 24 hours later, cells were treated with 1uM Medroxyprogesterone Acetate (MPA) or 0.01% EtOH (vehicle) in OptiMEM with 2% Charcoal Stripped Serumand 1% Penicillin-Streptomycin for 72 hours.

value: 1uM Medroxyprogesterone Acetate (MPA)


title: 1

description: Library name: Sample 1


title: Promoter gRNA MPA R1

description: Library name: Sample16


title: Promoter gRNA Veh R2

description: Library name: Sample14


title: S22-063-168

value: NIES


title: S22-063-167


title: 123_RICOVER_60_M_71

value: Diffuse large B-ell lymphoma

value: M


title: U1U2 gRNAs MPA R3

description: Library name: Sample12


title: U1U2 gRNAs MPA R2

description: Library name: Sample11


title: U1U2 gRNAs MPA R1

description: Library name: Sample10


title: 2

description: Library name: Sample 2


title: 12_DENSER_M_70

value: FFPE


title: U1U2 gRNAs Veh R3

description: Library name: Sample9


title: Promoter gRNA Veh R1

description: Library name: Sample13


title: U1U2 gRNAs Veh R1

description: Library name: Sample7


title: S22-063-164


title: Promoter gRNA MPA R2 [CUT&RUN]

description: Library name: Sample8


title: 1175_RICOVER_60_M_73


title: S22-063-163

source_name: whole thalli

value: whole thalli


title: 1164_RICOVER_60_M_75

source_name: Diffuse large B-ell lymphoma


title: Promoter gRNA Veh R1 [CUT&RUN]

description: Library name: Sample5


title: Promoter gRNA MPA R1 [CUT&RUN]

description: Library name: Sample7


title: 124_RICOVER_60_F_70

value: F


title: S22-063-162


title: NT gRNA MPA R1

description: Library name: Sample4


title: S22-063-172


title: U937 cells, non-template control, vehicle treatment rep 3

description: Library name: U937NTC1Veh3

value: pro-monocytic cell

value: Vehicle


title: NT gRNA Veh R2

description: Library name: Sample2

value: WT


title: U1U2 gRNAs MPA R2 [CUT&RUN]

description: Library name: Sample4

value: THESC


title: 1148_RICOVER_60_M_65


title: U1U2 gRNAs MPA R1 [CUT&RUN]

description: Library name: Sample3

value: Endometrial Stromal Cells


title: S22-063-171


title: U1U2 gRNAs Veh R2 [CUT&RUN]

description: Library name: Sample2

value: Vehicle (0.01% ethanol)


title: Hfq_R3

city: Würzburg

first: Manuel

last: Velasco Gomariz

address: Josef-Schneider-Straße 2/D15

institute: Helmholtz Institute for RNA-based Infection Research (HIRI)

description: Library name: CC_Hfq_R3_RILseq

data_processing:
Pipeline for Chimeric fragment (https://github.com/maltesie/ChimericFragments) from Siemers M et al 2024 (doi: 10.1093/nargab/lqae035)
Assembly: NCBI Reference Sequence: NC_011916.1
Supplementary files format and content: xlsx file including single and chimeric fragments
Library strategy: RIL-seq

organism: Caulobacter vibrioides

growth_protocol: Growth in PYE-Medium, 200 rpm shaking, 30 °C until OD 1

extract_protocol:
Melamed S. et al 2018 (DOI: 10.1038/nprot.2017.115)
Melamed S. et al 2018 (DOI: 10.1038/nprot.2017.115)/RNAtag-seq protocol from Shishkin AA et al 2015 (DOI: 10.1038/nmeth.3313)

treatment_protocol: 80,000 μJ/cm2 of 254-nm UV irradiation

value: Wt


title: experiment_H001AS8_P23_sci-iPS-2sec dataset on hPSC derived Cardiomyocytes DD23

city: Torino

first: Elisa

last: Balmas

address: via Nizza 52

department: Department of molecular biotechnology and life sciences

country: Italy

institute: University of Torino

description:
differentiation DD23
RT_primers_conditions.txt
sci_RNA_cds_monocle_cell_info.txt
sci_RNA_cds_monocle_counts_norm.txt
sci_RNA_cds_monocle_ceount_prenorm.txt
sci_RNA_cds_monocle_processed.txt

data_processing:
Illumina base calls for iPS2-sci-seq were converted to fastq and demultiplexed with bcl2fastq v2.20.0.422, using i7 and i5 PCR indexes.
count data were obtained from fastq files with the catcheR_scicount function  implemented in our catcheR package https://github.com/alessandro-bertero/catcheR
Reads 1 and 2 were concatenated, adaptor trimmed with TrimGalore 0.6.10, aligned with STAR 2.5.1b to human GRCh38 (GENECODE v21/Ensembl77) gene annotation, and filtered to have a MAPQ score equal of higher than 30 with samtools 1.7. Uniquely mapping reads were extracted, and reads with identical UMI, RT index, and tagmentation site were collapsed as PCR duplicates. RT_primers_conditions.txt file was used to demultiplex the first level of indexing.  Samtools and bedtools 2.27.1 were used to calculate the percentage of ribosomal RNA and to assign reads to genes. Reads were finally assigned to nuclei by further demultiplexing with the RT indexes. Cells with less than 500 UMI were filtered out as noise/low quality. The remaining sparse count matrix was converted to a complete count matrix with the sparsetodense function of Monocle 2.22.
shRNA and cell barcodes have been identified with catcheR_scicatch function implemented in our catcheR package https://github.com/alessandro-bertero/catcheR (this allow to link the cell ID to a cell perturbation)
Assembly: custom reference combining human reference genome (hg19), mouse reference genome (mm10), built by UW genome research (Seattle,WA) and used for Cao J et al. 2017 PMID: 28818938
Supplementary files format and content: sci_RNA_cds_monocle_cell_info.txt is the annotation file post QC and processing
Supplementary files format and content: sci_RNA_cds_monocle_counts_norm.txt normalized read count post QC and processing
Supplementary files format and content: sci_RNA_cds_monocle_counts_prenorm.txt unnormalized read count post QC and processing
Supplementary files format and content: sci_RNA_cds_monocle_processed.rds full post QC and processing single cell dataset file

source_name: hPSC derived cardiomyocytes

growth_protocol: hPSC were differentiated into cardiomyocites with RBA media.

extract_protocol:
Nuclear extraction by IGEPAL 0.3% ipotonic buffer. PFA fixation. RNAse inhibitors have been used during all steps to avoid RNA degradation.
2-level indexing sci-RNAseq protocol for the gene expression library and the barcode library. shRNA barcodes have been enriched during RT and PCR indexing by a nested PCR binding the TET repressor.
sci-RNASeq 2 levels of combinatorial indexing

treatment_protocol: hPSC tranfected in pool with iPS-2seq plasmids in AAVS1 locus (multiple perturbations in pool). shRNA expression has been induced throughout differentiation with Tetracycline. hPSC derived cardiomyocytes were cultured for 23 days with tetracycline. Then Harvested at single cell suspension and processed for nuclear extraction.

value: hPSC derived cardiomyocytes

value: hPSC derived cardiomyocytes DD23

value: Tetracycline


title: experiment_H001AS8_P21_sci-iPS-2sec dataset on hPSC derived Cardiomyocytes DD23


title: Hfq_R2

description: Library name: CC_Hfq_R2_RILseq


title: 120_RICOVER_60_M_74


title: Promoter gRNA Veh R3

description: Library name: Sample15

value: PGRB-dominant


title: experiment_H001AS8_P19_sci-iPS-2sec dataset on hPSC derived Cardiomyocytes DD23


title: experiment_H001AS8_P17_sci-iPS-2sec dataset on hPSC derived Cardiomyocytes DD23


title: 1190_RICOVER_60_M_75


title: 1128_RICOVER_60_F_79


title: S22-063-166

value: whole thalli without rhizoids

value: NIES


title: 1081_RICOVER_60_M_67

value: Diffuse large B-ell lymphoma

value: M


title: Wt_R4

description: Library name: CC_Wt_R4_RILseq

source_name: Wt


title: experiment_H001AS8_P15_sci-iPS-2sec dataset on hPSC derived Cardiomyocytes DD23


title: 119_DENSER_M_65

value: FFPE


title: Promoter gRNA MPA R2

description: Library name: Sample17

value: 1uM Medroxyprogesterone Acetate (MPA)


title: 1060_RICOVER_60_F_71

value: F


title: 118_DENSER_F_69


title: U1U2 gRNAs Veh R2

description: Library name: Sample8

value: PGRA/B-equivalent


title: experiment_H001AS8_P13_sci-iPS-2sec dataset on hPSC derived Cardiomyocytes DD23


title: 106_DENSER_F_61


title: NT gRNA MPA R3

description: Library name: Sample6

value: WT


title: Wt_R2

description: Library name: CC_Wt_R2_RILseq


title: Zygote_sRNA_Rep2

city: Kolkata

first: ZHUMUR

last: GHOSH

address: EN 80, Sector V, Bidhan Nagar

country: India

institute: Bose Institute

data_processing:
Linux and R
Read quality was assessed for each samples (both long and small RNAseq data) using FastQC and low-quality reads (quality <32) were removed using Cutadapt3.4.
The trimmed long RNA reads were mapped to the Mouse mm10 reference genome retrieved from Ensembl using spliced aligner tool Hisat2 2.1.0. SAMtools 0.1.19 was used to sort and index the BAM files. Transcript counts were generated using FeatureCounts, followed by batch correction with ComBat-seq and Diffrential analysis with DESeq2.
For miRNA detection, for both online and in-house datasets, the trimmed small RNA reads were aligned with mature mouse miRNA sequences retrieved from miRBase Release 22 using Megablast. In-house custom scripts have been used to detect the general profile for each group followed by differential analysis using DESeq2.
Assembly: mm10
Supplementary files format and content: tab delimited text files include transcript counts for each sample

source_name: Zygote (1 cell stage)

extract_protocol:
Total RNA was isolated Qiagen using miRNeasy Mini Kit according to manufacturer's protocol.
RNA sequencing libraries were prepared with Illumina-compatible NEBNext® UltraTM II Directional RNA Library Prep Kit (New England BioLabs, MA, USA), according to manufacturer’s instructions, at Genotypic Technology Pvt. Ltd., Bangalore, India.
Small RNA sequencing (SmRNA) library for oocyte and sperm was prepared using the NEXTflexTM Small RNA-Seq Kit v3 (Bioo Scientfic Corporation, Austin, Texas, U.S.A.), at Genotypic Technology Pvt. Ltd., Bangalore, India, following manufacturer’s instructions.
Small RNA sequencing (smRNA) libraries for zygote was prepared with QIAseq® miRNA Library Kit (Cat: 331502) protocol (Qiagen, Maryland, U.S.A.) at Genotypic Technology Pvt. Ltd., Bangalore, India.

value: Zygote (1 cell stage)

value: Balb/c


title: experiment_H001AS8_P10_sci-iPS-2sec dataset on hPSC derived Cardiomyocytes DD23


title: 104_DENSER_F_63

data_processing:
FASTQ Files using Illumina BaseSpace BCL to FASTQ software version 2.2.0 and Illumina Local Run Manager Software version 2.0.0.
FASTQ Files were analyzed with HTG EdgeSeq Parser software version 5.5 to generate raw counts for a total of 298 genes.
Assembly: Assembly: GRCh38.p13
Supplementary files format and content: raw counts
Supplementary files format and content: log2(Count per million+1)

extract_protocol:
Three hundred sixty DLBCLs tissues were processed. Using 5 ¬µm unstained FFPE sections. The optimal amounts of tissue for each HTG EdgeSeq panB Lymphoma assay. The sample preparation as performed according to the manufacturer’s instructions.
Probe_captured FFPE samples for EdgeSeq panB Lymphoma assay were amplified¨ and indexed via polymerase chain reaction (PCR) using the master mix (OneTaq HotStart 2X MasterMix in GC Buffer (New England Biolabs Inc., Ipswich, MA, USA), and indexing primers according to manufacturer’s instructions. The following library cleanup was performed using AMPure XP beads according to manufacturer’s instructions
Targeted mRNA Sequencing using HTG EdgeSeq Pan B_Cell Lymphoma Panel assay


title: NT gRNA MPA R2

description: Library name: Sample5

value: THESC

value: Endometrial Stromal Cells


title: Arabidopsis thaliana, odr1-2, seeds imbibed in 300mM mannitol for 12 h, rep3

city: Shenzhen

first: Ling

last: Ding

address: No 7,Pengfei Road,Dapeng District

institute: Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences

description:
Library name: m49-M_3
Column name in allSample.count.xlsx and allSample.TPM.xlsx: m49-M_3

data_processing:
Quality control and filtering of raw sequencing data were performed using fastp (version 0.23.1)
Filtered reads were aligned to the reference genome using hisat2 (2.2.1)
Gene expression levels were quantified using htseq (version 2.0.5)
Assembly: Arabidopsis Information Resource 10 genome (TAIR10)
Supplementary files format and content: The TPM expression matrix file includes gene IDs and corresponding expression values for each sample.
Supplementary files format and content: The Gene Count Matrix file comprises gene IDs and the raw counts of reads that mapped to each gene in every sample.

organism: Arabidopsis thaliana

source_name: seeds

growth_protocol: Arabidopsis thaliana were grown in a controlled environment at 22°C with a 16-hour light and 8-hour dark cycle.

extract_protocol:
The extraction of RNA was carried out with the FastPure Plant Total RNA Isolation Kit (Vazyme, RC401), strictly following the protocol provided by the manufacturer.
Messenger RNA was purified from total RNA using poly-T oligo-attached magnetic beads. After fragmentation, the first strand cDNA was synthesized using random hexamer primers followed by the second strand cDNA synthesis. The library was ready after end repair, A-tailing, adapter ligation, size selection, amplification, and purification.

treatment_protocol:
After-ripened seeds stratified at 4°C for 2 days and then imbibed in 300mM mannitol for 12 hours
RNA extraction was performed after a 12-hour soaking period in either distilled water or mannitol solution (300mM). The mannitol treatment was used to simulate osmotic stress, while distilled water served as the control.

value: seeds

tag: Stage

value: After-ripened seeds

value: mannitol


title: S22-063-165

value: whole thalli with rhizoids


title: 102_RICOVER_60_F_76


title: NT gRNA Veh R3

description: Library name: Sample3

value: Vehicle (0.01% ethanol)


title: Wt_R1

description: Library name: CC_Wt_R1_RILseq

value: Wt


title: 116_DENSER_M_67

value: Diffuse large B-ell lymphoma


title: S22-063-161

value: whole thalli


title: NT gRNA Veh R1

description: Library name: Sample1


title: experiment_H001AS8_P08_sci-iPS-2sec dataset on hPSC derived Cardiomyocytes DD23

value: hPSC derived cardiomyocytes

value: hPSC derived cardiomyocytes DD23

value: Tetracycline


title: Arabidopsis thaliana, odr1-2, seeds imbibed in 300mM mannitol for 12 h, rep1

description:
Library name: m49-M_1
Column name in allSample.count.xlsx and allSample.TPM.xlsx: m49-M_1


title: experiment_H001AS8_P24_sci-iPS-2sec dataset on hPSC derived Cardiomyocytes DD23


title: Hfq_R4

description: Library name: CC_Hfq_R4_RILseq


title: experiment_H001AS8_P07_sci-iPS-2sec dataset on hPSC derived Cardiomyocytes DD23


title: 114_DENSER_M_65

value: FFPE

value: M


title: experiment_H001AS8_P22_sci-iPS-2sec dataset on hPSC derived Cardiomyocytes DD23


title: experiment_H001AS8_P20_sci-iPS-2sec dataset on hPSC derived Cardiomyocytes DD23


title: 111_RICOVER_60_M_68


title: Arabidopsis thaliana, odr1-2, seeds imbibed in water for 12 h, rep3

description:
Library name: m49-ck_3
Column name in allSample.count.xlsx and allSample.TPM.xlsx: m49-ck_3

treatment_protocol:
After-ripened seeds stratified at 4°C for 2 days and then imbibed in water for 12 hours
RNA extraction was performed after a 12-hour soaking period in either distilled water or mannitol solution (300mM). The mannitol treatment was used to simulate osmotic stress, while distilled water served as the control.

value: water


title: Sperm_sRNA_Rep1

source_name: Sperm

value: Sperm

value: Balb/c


title: 101_RICOVER_60_F_67

value: F


title: experiment_H001AS8_P18_sci-iPS-2sec dataset on hPSC derived Cardiomyocytes DD23


title: Hfq_R1

description: Library name: CC_Hfq_R1_RILseq


title: experiment_H001AS8_P16_sci-iPS-2sec dataset on hPSC derived Cardiomyocytes DD23


title: experiment_H001AS8_P04_sci-iPS-2sec dataset on hPSC derived Cardiomyocytes DD23


title: Arabidopsis thaliana, odr1-2, seeds imbibed in water for 12 h, rep1

description:
Library name: m49-ck_1
Column name in allSample.count.xlsx and allSample.TPM.xlsx: m49-ck_1

value: seeds


title: CC_CL-4

city: Pirassununga

first: Flavio

middle: Vieira

last: Meirelles

state: Sao Paulo

address: Duque de caxias

department: Veterinary Medicine

country: Brazil

institute: University of Sao Paulo

description:
cumulus cells transcriptome
cumulus_count_table.txt
cumulus_count_table.txt

data_processing:
Trimgalore / cutadapt
STAR/Bismark
featurecounts
DEESEQ2/methylKit
PCIT / CETF
Assembly: ARS-UCD 1.2
Supplementary files format and content: Raw counts for each sample in .txt file
Supplementary files format and content: NDA

organism: Bos taurus

source_name: Cumulus cell

extract_protocol:
The SMART-Seq®HT kit (Takara Bio, USA) / EpiTect Fast Bisulfite
NextEra XT Stranded mRNA Sample Prep kit following manufacturer instructions/NEBNext Ultra II DNA library

value: Cumulus cell

value: Diploid

value: Cumulus cell_Diploid


title: 100_DENSER_F_64


title: experiment_H001AS8_P14_sci-iPS-2sec dataset on hPSC derived Cardiomyocytes DD23


title: Arabidopsis thaliana, Col-0, seeds imbibed in 300mM mannitol for 12 h, rep3

description:
Library name: col-M_3
Column name in allSample.count.xlsx and allSample.TPM.xlsx: col-M_3

value: After-ripened seeds

value: mannitol


title: experiment_H001AS8_P03_sci-iPS-2sec dataset on hPSC derived Cardiomyocytes DD23


title: Wt_R3

description: Library name: CC_Wt_R3_RILseq

value: Wt


title: Arabidopsis thaliana, Col-0, seeds imbibed in 300mM mannitol for 12 h, rep2

description:
Library name: col-M_2
Column name in allSample.count.xlsx and allSample.TPM.xlsx: col-M_2


title: experiment_H001AS8_P06_sci-iPS-2sec dataset on hPSC derived Cardiomyocytes DD23


title: experiment_H001AS8_P02_sci-iPS-2sec dataset on hPSC derived Cardiomyocytes DD23


title: experiment_H001AS8_P12_sci-iPS-2sec dataset on hPSC derived Cardiomyocytes DD23


title: RA-FLSs cells, SH_SNORD3_3

city: Hong Kong

first: chunhao

last: cao

address: Hong Kong

department: School of Chinese Medicine

country: Hong Kong

institute: Hong Kong Baptist University

description: Library name: Sample11

data_processing:
1. **Quality Control**: Raw sequencing reads were assessed using FastQC to check the quality of the data.
2. **Trimming**: Adapters and low-quality bases were removed using Trimmomatic.
3. **Alignment**: Cleaned reads were aligned to the reference genome (Homo sapiens GRCh38) using HISAT2.
4. **Conversion**: SAM files generated by HISAT2 were converted to BAM files using SAMtools.
5. **Feature Counting**: Gene-level quantification was performed using featureCounts.
Assembly: hg38
Supplementary files format and content: CSV
Supplementary files format and content: Text files generated by featureCounts containing the read counts per gene for each sample.

source_name: synovial tissue

growth_protocol: RA-FLSs were maintained in DEME supplemented with 20%  fetal bovine serum (FBS) and  1% penicillin-streptomycin. And  cells were maintained at 37°C humid atmosphere with 5% CO2.

extract_protocol:
RNA was harvested using TransZol UP Plus RNA Kit.
RNA quality was assessed using the Agilent 2100 Bioanalyzer. High-quality RNA samples with RIN (RNA Integrity Number) > 7.0 were used for library construction. Libraries were prepared using the NEBNext Ultra RNA Library Prep Kit for Illumina, following the manufacturer's instructions. Indexed libraries were then sequenced on an Illumina HiSeq 4000 platform to generate 150 bp paired-end reads.

treatment_protocol: Stable SNORD3 knockdown and expression  RA-FLSs were generated using lentiviruses expressing human SNORD3 shRNA  targeting the SNORD3 cloned in pLKO.1 vector, and lentiviruses expressing human  SNORD3 cloned in pCDH vector. Transduced cells were selected with puromycin.

value: synovial tissue

value: RA-FLSs

value: fibroblast-like synoviocytes cells

value: SNORD3 knockdown


title: experiment_H001AS8_P11_sci-iPS-2sec dataset on hPSC derived Cardiomyocytes DD23

value: hPSC derived cardiomyocytes

value: hPSC derived cardiomyocytes DD23

value: Tetracycline


title: 1058_RICOVER_60_F_64

value: Diffuse large B-ell lymphoma

value: FFPE


title: experiment_H001AS8_P01_sci-iPS-2sec dataset on hPSC derived Cardiomyocytes DD23


title: Arabidopsis thaliana, Col-0, seeds imbibed in 300mM mannitol for 12 h, rep1

description:
Library name: col-M_1
Column name in allSample.count.xlsx and allSample.TPM.xlsx: col-M_1


title: Zygote_sRNA_Rep1

value: Zygote (1 cell stage)

value: Balb/c


title: RA-FLSs cells, SH_SNORD3_1

description: Library name: Sample9


title: experiment_H001AS8_O23_sci-iPS-2sec dataset on hPSC derived Cardiomyocytes DD23


title: RA-FLSs cells, SH-Vector_3

description: Library name: Sample8

value: WT


title: experiment_H001AS8_O22_sci-iPS-2sec dataset on hPSC derived Cardiomyocytes DD23


title: experiment_H001AS8_P09_sci-iPS-2sec dataset on hPSC derived Cardiomyocytes DD23


title: Oocyte_sRNA_Rep2

source_name: Oocyte

value: Oocyte


title: CC_BL-1

value: Cumulus cell

value: Diploid

value: Cumulus cell_Diploid


title: Arabidopsis thaliana, odr1-2, seeds imbibed in 300mM mannitol for 12 h, rep2

description:
Library name: m49-M_2
Column name in allSample.count.xlsx and allSample.TPM.xlsx: m49-M_2

value: seeds

value: After-ripened seeds

value: mannitol


title: 1018_RICOVER_60_F_67

description:
HTG EdgeSeq Pan B-Cell Lymphoma Panel
RNA (amplified oligo nucleotide probes)

value: F


title: Oocyte_sRNA_Rep1


title: Liver, WT, TNF, rep4

city: Gent

first: Steven

last: Timmermans

address: Technologiepark 71

country: Belgium

institute: VIB-UGent

description:
Library name: sample15
WT_TNF-4

data_processing:
Reads were quality checked with fastQC and preprocessed (adapter removal) with TRIMMOMATIC v0.34 (ILLUMINACLIP & MINLEN filters)
Reads were mapped to the mm39 reference genome with STAR (2.7.10b) and the gencode M30 and read counts were directly obtained using the "--quantMode GeneCounts" parameter for STAR
Differential expression analysis was done using the DESeq2 package, with the FDR set at 5%
Assembly: mm39
Supplementary files format and content: tab delimited count matrix with the raw counts per sample

source_name: Liver

growth_protocol: All mice were housed in individually ventilated cages at conventional housing conditions (22°C, 14/10h light/dark cycle, dark phase starting at 9 p.m.) in a specific pathogen-free facility. Food (chow diet consisting of 18% proteins, 4.5% fibers, 4.5% fat and 6.3% ashes, Provimi Kliba SA) and water were given at libitum

extract_protocol:
Total RNA was isolated with Aurum Total RNA mini Kit (Bio-Rad) following the manufacturer’s instructions
Library preparation was done using the illumina truseq stranded library kit for sequencing with a Cloudbreak sequencing kit on the element AVITI according the the manufacturer's instructions

treatment_protocol: Mice were injected with PBS (control) or TNF (35 µg) in a volume of 200µl per 20g bodyweight. 8 hours after injection livers were isolated and prepared for RNA-seq

value: Liver

value: TNF

tag: time after_injection

tag: volume injected

tag: tnf dose


title: RA-FLSs cells, OE_SNORD3_3

description: Library name: Sample6

value: synovial tissue

value: RA-FLSs

value: fibroblast-like synoviocytes cells

value: SNORD3 overexpression


title: Liver, WT, TNF, rep3

description:
Library name: sample14
WT_TNF-3


title: 1013_RICOVER_60_F_65

value: Diffuse large B-ell lymphoma

value: FFPE


title: Sperm_sRNA_Rep2

value: Sperm

value: Balb/c


title: RA-FLSs cells, OE_SNORD3_2

description: Library name: Sample5


title: Arabidopsis thaliana, odr1-2, seeds imbibed in water for 12 h, rep2

description:
Library name: m49-ck_2
Column name in allSample.count.xlsx and allSample.TPM.xlsx: m49-ck_2

value: water


title: experiment_H001AS8_P05_sci-iPS-2sec dataset on hPSC derived Cardiomyocytes DD23

value: hPSC derived cardiomyocytes

value: hPSC derived cardiomyocytes DD23

value: Tetracycline


title: SH-SY5Y cells, siPCBP2-2

city: Chongqing

first: Lu

last: Wang

address: 1 Youyi Road, Yuzhong District

institute: the First Affiliated Hospital of Chongqing Medical University

description: Library name: si_ActD0h_2

data_processing:
Raw read quality was assessed using FastQC (v0.10.1). Adapter trimming and removal of low_x001E_quality bases were performed with Cutadapt, producing clean reads. Clean reads were aligned to the Homo sapiens reference genome GRCh38 using HISAT2 (v2.2.1) with default parameters unless stated; strandedness was set according to the dUTP protocol.
Alignment metrics and mapping rates were summarized with samtools. Transcript assembly and quantification were performed with StringTie (v2.1.6) against the Ensembl gene annotation, generating per_x001E_gene and per_x001E_transcript FPKM/TPM and count tables. Gene_x001E_level raw counts were extracted from StringTie output using prepDE.py (bundled with StringTie) to create a genes × samples count matrix.
Differential expression analysis was conducted in R (v3.6) using DESeq2 (v1.22.2) and edgeR (v3.22.5); lowly expressed genes were filtered, size_x001E_factor normalization was applied, and results were corrected for multiple testing using Benjamini–Hochberg FDR.
Alternative splicing events were detected using rMATS (v4.1.1) with default settings, reporting SE/RI/A5SS/A3SS/MXE events and FDR_x001E_adjusted P values.Normalized expression values and the sample metadata were exported for downstream analyses and are provided as processed files.
Assembly: Human, Homo sapiens; reference genome assembly: GRCh38. Gene annotation from Ensembl release 110; gene biotypes defined according to Ensembl (https://asia.ensembl.org/info/genome/genebuild/biotypes.html). Alignments were performed with HISAT2 v2.2.1; libraries are strand-specific (dUTP protocol; strandedness: RF).
Supplementary files format and content: gene_counts.tsv: gene-by-sample raw count matrix (rows = Ensembl gene IDs from Ensembl release 110; columns = samples). gene_tpm.tsv: per-gene normalized expression values (TPM) computed with StringTie v2.1.6. transcript_tpm.tsv (optional): transcript-level TPM from StringTie v2.1.6. DEG_results_DESeq2.tsv: differential expression results generated in R v3.6 using DESeq2 v1.22.2 (and/or edgeR v3.22.5), including log2 fold change, P value, and FDR (Benjamini–Hochberg). rMATS_events_SE/RI/A5SS/A3SS/MXE.txt: alternative splicing events from rMATS v4.1.1 with PSI, ΔPSI, P value, and FDR. sample_metadata.tsv: sample annotations (condition, replicate, library type, strandedness = RF, read length, platform). QC_reports: FastQC v0.10.1 HTML/TXT for raw/clean reads. Optional: bigWig coverage tracks (RPM-normalized) per sample for genome browser visualization.

extract_protocol:
Total RNA was isolated from [tissue/cell type] using TRIzol reagent (Thermo Fisher, cat. 15596018) following the manufacturer’s instructions. RNA quantity and purity were assessed with a NanoDrop ND‑1000 (NanoDrop, Wilmington, DE, USA), and RNA integrity was evaluated on an Agilent 2100 Bioanalyzer (Agilent, CA, USA). Samples with concentration > 50 ng/μL, RIN > 7.0, and total RNA amount > 1 μg were carried forward for library preparation.
Poly(A)+ mRNA was captured from total RNA using oligo(dT) magnetic beads (Dynabeads Oligo(dT), Thermo Fisher, cat. 25‑61005) with two rounds of selection. Purified mRNA was fragmented at 94°C for 5–7 min using the NEBNext Magnesium RNA Fragmentation Module (NEB, cat. E6150S). First‑strand cDNA was synthesized with SuperScript II Reverse Transcriptase (Invitrogen, cat. 1896649). Second‑strand cDNA was generated using E. coli DNA Polymerase I (NEB, cat. M0209) and RNase H (NEB, cat. M0297), incorporating dUTP (Thermo Fisher, cat. R0133) for strand specificity. End repair was performed to generate blunt ends, an A base was added to each 3′ end, and sequencing adapters with 3′‑T overhangs were ligated. Size selection and purification were carried out with magnetic beads. Uracil‑DNA glycosylase (UDG; NEB, cat. M0280) digestion was used to enforce strand specificity, followed by PCR amplification (95°C 3 min; 8 cycles of 98°C 15 s, 60°C 15 s, 72°C 30 s; final extension 72°C 5 min) to generate libraries with an average insert size of ~300 bp ± 50 bp.


title: Liver, WT, TNF, rep2

description:
Library name: sample13
WT_TNF-2

value: WT


title: RA-FLSs cells, OE_SNORD3_1

description: Library name: Sample4


title: 101_DENSER_F_67

city: Ulm

first: Emil

last: Chteinberg

address: Albert-Einstein-Allee 11

institute: Ulm University Medical Center


title: CC_CL-3

value: Cumulus cell

value: Diploid

value: Cumulus cell_Diploid


title: RA-FLSs cells, OE_Vector_3

description: Library name: Sample3


title: 1_DENSER_M_69

value: M


title: CC_CL-2


title: CC_CL-1


title: CC_BL-4


title: RA-FLSs cells, OE_Vector_2

description: Library name: Sample2

value: synovial tissue


title: experiment_H001AS8_O24_sci-iPS-2sec dataset on hPSC derived Cardiomyocytes DD23


title: Arabidopsis thaliana, Col-0, seeds imbibed in water for 12 h, rep3

description:
Library name: col-ck_3
Column name in allSample.count.xlsx and allSample.TPM.xlsx: col-ck_3

value: seeds

value: After-ripened seeds


title: CC_BL-3


title: Arabidopsis thaliana, Col-0, seeds imbibed in water for 12 h, rep2

description:
Library name: col-ck_2
Column name in allSample.count.xlsx and allSample.TPM.xlsx: col-ck_2


title: experiment_H001AS8_O16_sci-iPS-2sec dataset on hPSC derived Cardiomyocytes DD23


title: RA-FLSs cells, OE_Vector_1

description: Library name: Sample1

value: RA-FLSs

value: fibroblast-like synoviocytes cells


title: CC_BL-2


title: Arabidopsis thaliana, Col-0, seeds imbibed in water for 12 h, rep1

description:
Library name: col-ck_1
Column name in allSample.count.xlsx and allSample.TPM.xlsx: col-ck_1


title: RA-FLSs cells, SH-Vector_1

description: Library name: Sample7


title: 643_GES11_10273_hippocampus_CAST_EiJ_female

city: Bar Harbor

first: Gary

last: Churchill

state: Maine

address: 600 Main St

institute: The Jackson Laboratory

data_processing:
raw counts quantified by EMASE
Assembly: GRCm39
Supplementary files format and content: hippocampus_ensembl_v105_gene_counts.txt

source_name: hippocampus

extract_protocol:
Total hippocampal RNA was isolated using the Life Technologies TRIzol Plus RNA purification kit with on-column DNase-digestion step.
RNA-Seq libraries were prepared using the TruSeq kit (Illumina Inc., San Diego, CA) according to the manufacturer’s protocols.

value: female

value: hippocampus


title: RA-FLSs cells, SH_SNORD3_2

description: Library name: Sample10

value: SNORD3 knockdown


title: 642_GES11_10262_hippocampus_CAST_EiJ_female


title: experiment_H001AS8_O21_sci-iPS-2sec dataset on hPSC derived Cardiomyocytes DD23


title: Liver, Slc25a13 KO, TNF, rep3

description:
Library name: sample7
KO_TNF-3

value: Liver

value: Slc25a13 KO

value: TNF


title: S24

city: New Haven

first: Andrés

last: Hidalgo

address: 10 Amistad Street

institute: Yale University

description: Library name: S24

data_processing:
Sequenced reads were trimmed using cutadapt
Reads were quantified using RSEM
Assembly: GRCh38_113
Supplementary files format and content: raw counts matrix
Supplementary files format and content: tab delimited text file includes raw counts for each sample

source_name: cell culture of human derived BM neutrophils

extract_protocol:
We used the NucleoSpin RNA Mini Kit (Macherey-Nagel, cat. no. 740955.50), following the manufacturer's instructions. RNA concentration was assessed with Qubit 2.0 (Thermo Fisher), a total amount of 400 ng RNA were sequenced.
RNA integrity was assessed using Agilent Bioanalyzer 2100, with RNA integrity numbers (RIN) between 9.8 and 10.0. RNA samples were processed by Novogene (Munich, Germany) for library preparation and sequencing, and all samples passed the quality control criteria. Strand-specific libraries were generated based on Novogene´s standard protocol. Samples were sequenced on an Illumina platform to produce 150 bp pairwise reads (PE150) per sample.

value: GCSF 1n/ul + IFNb 10 ng/ul

tag: time


title: SH-SY5Y cells, siPCBP2-3

description: Library name: si_ActD0h_3


title: experiment_H001AS8_O20_sci-iPS-2sec dataset on hPSC derived Cardiomyocytes DD23

value: hPSC derived cardiomyocytes

tag: cell type

value: hPSC derived cardiomyocytes DD23

value: Tetracycline


title: experiment_H001AS8_O13_sci-iPS-2sec dataset on hPSC derived Cardiomyocytes DD23


title: Liver, Slc25a13 KO, TNF, rep2

description:
Library name: sample6
KO_TNF-2


title: experiment_H001AS8_O19_sci-iPS-2sec dataset on hPSC derived Cardiomyocytes DD23


title: Liver, WT, TNF, rep1

description:
Library name: sample12
WT_TNF-1

value: WT


title: 639_GES11_10239_hippocampus_CAST_EiJ_female


title: SH-SY5Y cells, siPCBP2-1

description: Library name: si_ActD0h_1


title: Liver, Slc25a13 KO, TNF, rep4

description:
Library name: sample8
KO_TNF-4


title: experiment_H001AS8_O14_sci-iPS-2sec dataset on hPSC derived Cardiomyocytes DD23


title: SH-SY5Y cells, NC-3

description: Library name: NC_ActD0h_3


title: Liver, WT, PBS, rep3

description:
Library name: sample11
WT_PBS-3

value: PBS


title: 462_GES11_10182_hippocampus_WSB_EiJ_male

value: male


title: P21

description: Library name: P21

value: cell culture of human derived BM neutrophils

value: GCSF 1n/ul  RNA direct


title: experiment_H001AS8_O17_sci-iPS-2sec dataset on hPSC derived Cardiomyocytes DD23


title: O20

description: Library name: O20

value: GCSF 1n/ul + GM-CSF 10 ng/ul


title: SH-SY5Y cells, NC-2

description: Library name: NC_ActD0h_2


title: experiment_H001AS8_O09_sci-iPS-2sec dataset on hPSC derived Cardiomyocytes DD23


title: Liver, WT, PBS, rep2

description:
Library name: sample10
WT_PBS-2


title: 458_GES11_10148_hippocampus_WSB_EiJ_male


title: Liver, Slc25a13 KO, TNF, rep1

description:
Library name: sample5
KO_TNF-1


title: SH-SY5Y cells, NC-1

description: Library name: NC_ActD0h_1


title: Liver, WT, PBS, rep1

description:
Library name: sample9
WT_PBS-1


title: experiment_H001AS8_O18_sci-iPS-2sec dataset on hPSC derived Cardiomyocytes DD23


title: M18

description: Library name: M18

value: GCSF 1n/ul + TGFb 10ng/ul


title: T25

description: Library name: T25


title: 641_GES11_10251_hippocampus_CAST_EiJ_female

value: female


title: L17

description: Library name: L17

value: GCSF 1n/ul Unstimulated


title: K16

description: Library name: K16


title: experiment_H001AS8_O12_sci-iPS-2sec dataset on hPSC derived Cardiomyocytes DD23


title: AdipoqF2KO mice sample 3

city: Chicago

first: Chioma

last: Nnyamah

state: Illinois

address: 840 South Wood Street, Suite 1020N, MC 787

institute: University of Illinois at Chicago

description:
Library name: Sample 7
feature counts document named: Knockout5_S15.txt

data_processing:
Raw sequencing reads were first trimmed to remove residual adapter sequences and low-quality bases. Adapter trimming was performed using Trimmomatic with the Illumina TruSeq adapter sequence CTGTCTCTTATACACATCT provided in Illumina Adapter Sequences v14 (Document #1000000002694).
Trimmed reads were then aligned to the mouse reference genome using the STAR aligner. Gene-level read quantification was performed using featureCounts, and differential expression analysis and normalization were conducted using DESeq2.
Assembly: Mouse genome GRCm38 (mm10), Ensembl annotation release [e.g., v98]
Supplementary files format and content: tab delimited text files contain feature counts for samples with matched names e.g. file named Control1_S9.txt contains feature count data for raw file named Control1_S1_R1_001.fastq

source_name: Jejunum Mucosa

growth_protocol: Male Adipoq-F2-KO mice were generated by crossing FFA2 floxed mice (FFA2^fl/fl) with Adiponectin-Cre transgenic mice (RRID: IMSR_JAX:028020). Littermate Adipoq-F2-KO and FFA2^fl/fl control mice were co-housed from birth under a 12-hour light/dark cycle at ambient temperature and given ad libitum access to Teklad LM-485 normal chow and water. Mice were aged to 12 weeks before initiation of treatment protocol.

extract_protocol:
Jejunal mucosal scrapings were collected immediately following euthanasia by scraping the luminal surface of opened jejunum segments on ice. Tissue samples were flash-frozen in liquid nitrogen and stored at −80 °C until RNA extraction. Total RNA was extracted using TRIzol Reagent (Life Technologies) following the manufacturer's protocol. Phase separation was performed using chloroform, and the aqueous RNA phase was recovered and purified using the RNeasy Mini Kit (Qiagen). RNA integrity was confirmed by bioanalyzer before sequencing.
RNA libraries were constructed using the Illumina TruSeq Stranded mRNA Library Prep Kit, which includes poly-A selection to enrich for mRNA. Libraries were sequenced on an Illumina NovaSeq X Plus system using single-end 75bp reads according to manufacturer protocols.

treatment_protocol: At 12 weeks of age, mice were transitioned from normal chow to either a custom-modified Western diet supplemented with 10% fructooligosaccharides (FOS; D20021208, Research Diets, Inc.) for a total of 2 weeks until a difference in weight became evident between genotypes. Mice were immediately euthanized for tissue collection. No antibiotics or other pharmacological agents were administered.

value: Jejunum Mucosa

value: Mixed cell type (jejunum mucosa)

value: Western Diet + 10% Fructooligosaccharides/2 weeks/ thermoneutral housing


title: experiment_H001AS8_O15_sci-iPS-2sec dataset on hPSC derived Cardiomyocytes DD23


title: experiment_H001AS8_O11_sci-iPS-2sec dataset on hPSC derived Cardiomyocytes DD23


title: R23

description: Library name: R23


title: 452_GES11_10092_hippocampus_WSB_EiJ_female

value: hippocampus


title: experiment_H001AS8_O10_sci-iPS-2sec dataset on hPSC derived Cardiomyocytes DD23


title: 459_GES11_10159_hippocampus_WSB_EiJ_male


title: J10

description: Library name: J10


title: Liver, Slc25a13 KO, PBS, rep3

description:
Library name: sample3
KO_PBS-3

value: Liver

value: Slc25a13 KO


title: N19

description: Library name: N19

value: GCSF 1n/ul + IFNb 10 ng/ul


title: Liver, Slc25a13 KO, PBS, rep2

description:
Library name: sample2
KO_PBS-2


title: I9

description: Library name: I9


title: experiment_H001AS8_O07_sci-iPS-2sec dataset on hPSC derived Cardiomyocytes DD23

value: hPSC derived cardiomyocytes

value: hPSC derived cardiomyocytes DD23

value: Tetracycline


title: experiment_H001AS8_O08_sci-iPS-2sec dataset on hPSC derived Cardiomyocytes DD23


title: 457_GES11_10137_hippocampus_WSB_EiJ_male

value: male


title: Q22

description: Library name: Q22

value: cell culture of human derived BM neutrophils


title: Liver, Slc25a13 KO, PBS, rep1

description:
Library name: sample1
KO_PBS-1

value: PBS


title: Liver, Slc25a13 KO, PBS, rep4

description:
Library name: sample4
KO_PBS-4


title: 454_GES11_10114_hippocampus_WSB_EiJ_female


title: FFA2 fl/fl control mice sample 4

description:
Library name: Sample 4
feature counts document named: Control5_S12.txt

value: FFA2 fl/fl


title: FFA2 fl/fl control mice sample 3

description:
Library name: Sample 3
feature counts document named: Control4_S11.txt


title: 442_GES11_10022_hippocampus_NZO_HlLtJ_male


title: experiment_H001AS8_O03_sci-iPS-2sec dataset on hPSC derived Cardiomyocytes DD23

description:
differentiation DD23
RT_primers_conditions.txt
sci_RNA_cds_monocle_cell_info.txt
sci_RNA_cds_monocle_counts_norm.txt
sci_RNA_cds_monocle_ceount_prenorm.txt
sci_RNA_cds_monocle_processed.txt


title: 437_GES11_997_hippocampus_NZO_HlLtJ_male


title: AdipoqF2KO mice sample 4

description:
Library name: Sample 8
feature counts document named: Knockout6_S16.txt


title: H8

description: Library name: H8

value: GCSF 1n/ul + TGFb 10ng/ul


title: experiment_H001AS8_O02_sci-iPS-2sec dataset on hPSC derived Cardiomyocytes DD23


title: experiment_H001AS8_O06_sci-iPS-2sec dataset on hPSC derived Cardiomyocytes DD23


title: AdipoqF2KO mice sample 2

description:
Library name: Sample 6
feature counts document named: Knockout4_S14.txt


title: experiment_H001AS8_O05_sci-iPS-2sec dataset on hPSC derived Cardiomyocytes DD23


title: 436_GES11_996_hippocampus_NZO_HlLtJ_male


title: E5

description: Library name: E5

value: GCSF 1n/ul + GM-CSF 10 ng/ul


title: experiment_H001AS8_O04_sci-iPS-2sec dataset on hPSC derived Cardiomyocytes DD23


title: D4

description: Library name: D4


title: 451_GES11_10081_hippocampus_WSB_EiJ_female

value: female


title: C57BL/6J mice injected with LPS and anti IL10R antibody 72hr_3

city: Irvine

first: William Lucas

middle: Paredes

last: Wadley

email: wwadley@uci.edu, Lucas.wadley@gmail.com

state: CA

address: 845 Health Sciences Road

department: Biological Chemistry

institute: University of California Irvine

description: Library name: [D33_LPS_aIL10R]

data_processing:
Fastq data files were converted to BAM files using HISAT2 v2.2.0 and aligned against GRCm38 genome using default settings. Raw counts were extracted from BAM files using Subread function featureCounts v2.1.1 under default settings, probe counts were saved onto a csv file. An associated meta data csv file was created for differential analysis. Differentially expressed genes (DEGs) were elucidated in R v4.3.2 using DESeq2. Gene ontology analysis was additionally done in R. Plots were generated in RStudio. Gene set enrichment analysis (GSEA) was performed the GSEA v4.3.3 software.
Assembly: Fastq data files were converted to BAM files using HISAT2 v2.2.0 and aligned against GRCm38 genome using default settings.
Supplementary files format and content: Raw counts RNA seq data

source_name: Hematopoietic stem and progenitor cells

extract_protocol:
Wild-type C57BL/6J mice were intraperitoneally injected with 5mg LPS (L2880; Sigma-Aldrich) with or without 100mg IL-10R blocking antibody (112702; BioLegend), or phosphate buffered saline (DPBS; 14200075; ThermoFisher Scientific) for 72 or 24 hours prior to BM harvest for cell sorting using BD FACSAria Fusion sorter at the UCI Institute of Immunology Flow Cytometry Facility. Cells were sorted, using the HSPC staining protocol aforementioned, into RNA lysis buffer (R1060; Zymo-Research) and immediately processed using Zymo-Research Quick-RNA MiniPrep kit for RNA isolation as per manufacture’s protocol (R1058; Zymo-Research).
Samples were stored at -20°C until sequencing at the UCI Genomics Research and Technology HUB.

value: Hematopoietic stem and progenitor cells


title: 453_GES11_10103_hippocampus_WSB_EiJ_female


title: AdipoqF2KO mice sample 1

description:
Library name: Sample 5
feature counts document named: Knockout2_S13.txt

value: Jejunum Mucosa

value: Mixed cell type (jejunum mucosa)


title: 441_GES11_10011_hippocampus_NZO_HlLtJ_male

value: hippocampus


title: experiment_H001AS8_O01_sci-iPS-2sec dataset on hPSC derived Cardiomyocytes DD23


title: G7

description: Library name: G7

value: GCSF 1n/ul Unstimulated


title: experiment_H001AS8_N21_sci-iPS-2sec dataset on hPSC derived Cardiomyocytes DD23


title: C57BL/6J mice injected with LPS and anti IL10R antibody 72hr_2

description: Library name: [D32_LPS_aIL10R]


title: 429_GES11_991_hippocampus_NZO_HlLtJ_female


title: F6

description: Library name: F6

value: GCSF 1n/ul  RNA direct


title: experiment_H001AS8_N19_sci-iPS-2sec dataset on hPSC derived Cardiomyocytes DD23


title: 426_GES11_988_hippocampus_NZO_HlLtJ_female


title: A1

description: Library name: A1

value: GCSF 1n/ul RNA direct


title: S17_D30_IFN_03

description: Library name: S17_D30_IFN

data_processing:
Sequenced reads were trimmed using cutadapt
Reads were quantified using RSEM
Assembly: GRCh38.113
Supplementary files format and content: raw counts matrix
Supplementary files format and content: tab delimited text file includes raw counts for each sample

source_name: Human iPS cells (SCTi003-A

extract_protocol:
Total RNA was extracted from cell cultures using the RNA Extraction RNeasy Plus Mini-kit (QIAGEN)
200 ng of total RNA was used to generate barcoded RNA sequencing libraries using the NEBNext Ultra RNA Library preparation kit (New England Biolabs). Libraries were sequenced with HiSeq2500 (Illumina) to generate 50-nucleotide single reads, with a minimum of eight million reads per sample. FastQ files for each sample were obtained using CASAVA v1.8 software (Illumina). Reads were further processed with RTA v1.18.66.3. FastQ files for each sample were obtained using bcl2fastq v2.20.0.422 software (Illumina).

value: Human iPS cells (SCTi003-A

value: IFNB


title: C57BL/6J mice injected with LPS and anti IL10R antibody 72hr_1

description: Library name: [D31_LPS_aIL10R]


title: experiment_H001AS8_N18_sci-iPS-2sec dataset on hPSC derived Cardiomyocytes DD23

value: hPSC derived cardiomyocytes

value: hPSC derived cardiomyocytes DD23

value: Tetracycline


title: S12_D30_TGFB_01

description: Library name: S12_D30_TGFB

value: TGFB


title: 419_GES11_983_hippocampus_PWK_PhJ_male

value: male


title: C57BL/6J mice injected with LPS 72hr_1

description: Library name: [D31_LPS]


title: FFA2 fl/fl control mice sample 2

description:
Library name: Sample 2
feature counts document named: Control2_S10.txt

value: FFA2 fl/fl

value: Western Diet + 10% Fructooligosaccharides/2 weeks/ thermoneutral housing


title: 417_GES11_981_hippocampus_PWK_PhJ_male


title: experiment_H001AS8_N24_sci-iPS-2sec dataset on hPSC derived Cardiomyocytes DD23


title: 416_GES11_980_hippocampus_PWK_PhJ_male


title: 422_GES11_985_hippocampus_PWK_PhJ_male


title: S2_D11_02

description: Library name: S2_D11


title: C57BL/6J mice injected with LPS and anti IL10R antibody 24hr_2

description: Library name: [D12_LPS_aIL10R]


title: experiment_H001AS8_N14_sci-iPS-2sec dataset on hPSC derived Cardiomyocytes DD23


title: 412_GES11_978_hippocampus_PWK_PhJ_female

value: female


title: FFA2 fl/fl control mice sample 1

description:
Library name: Sample 1
feature counts document named: Control1_S9.txt


title: 435_GES11_995_hippocampus_NZO_HlLtJ_female


title: C57BL/6J mice injected with LPS 24hr_2

description: Library name: [D12_LPS]

value: Hematopoietic stem and progenitor cells


title: 413_GES11_979_hippocampus_PWK_PhJ_female


title: experiment_H001AS8_N15_sci-iPS-2sec dataset on hPSC derived Cardiomyocytes DD23


title: experiment_H001AS8_N22_sci-iPS-2sec dataset on hPSC derived Cardiomyocytes DD23


title: 430_GES11_992_hippocampus_NZO_HlLtJ_female


title: S15_D30_IFN_01

description: Library name: S15_D30_IFN


title: C3

description: Library name: C3

value: cell culture of human derived BM neutrophils

value: GCSF 1n/ul + TGFb 10ng/ul


title: C57BL/6J mice injected with LPS 72hr_3

description: Library name: [D33_LPS]


title: 398_GES11_971_hippocampus_CAST_EiJ_male

value: hippocampus


title: experiment_H001AS8_N20_sci-iPS-2sec dataset on hPSC derived Cardiomyocytes DD23


title: B2

description: Library name: B2

value: GCSF 1n/ul Unstimulated


title: experiment_H001AS8_N12_sci-iPS-2sec dataset on hPSC derived Cardiomyocytes DD23


title: S14_D30_TGFB_03

description: Library name: S14_D30_TGFB


title: C57BL/6J mice injected with LPS 72hr_2

description: Library name: [D32_LPS]


title: experiment_H001AS8_N23_sci-iPS-2sec dataset on hPSC derived Cardiomyocytes DD23


title: experiment_H001AS8_N09_sci-iPS-2sec dataset on hPSC derived Cardiomyocytes DD23


title: 395_GES11_968_hippocampus_CAST_EiJ_male


title: S3_D16_01

description: Library name: S3_D16


title: S20_D30_GMCSG_03

description: Library name: S20_D30_GMCSG

value: GM+CSF


title: S22_Blood_N_2

description: Library name: S22_Blood_N

source_name: Neutrophils from human blood

value: Neutrophils from human blood


title: experiment_H001AS8_N17_sci-iPS-2sec dataset on hPSC derived Cardiomyocytes DD23


title: C57BL/6J mice PBS control Day 0_2

description: Library name: Control 2


title: experiment_H001AS8_N16_sci-iPS-2sec dataset on hPSC derived Cardiomyocytes DD23


title: S9_D30_VEH_01

description: Library name: S9_D30_VEH

value: Human iPS cells (SCTi003-A

value: PBS


title: C57BL/6J mice injected with LPS and anti IL10R antibody 24hr_3

description: Library name: [D13_LPS_aIL10R]


title: C57BL/6J mice injected with LPS 24hr_3

description: Library name: [D13_LPS]


title: experiment_H001AS8_N07_sci-iPS-2sec dataset on hPSC derived Cardiomyocytes DD23

value: hPSC derived cardiomyocytes


title: S1_D11_01

description: Library name: S1_D11


title: 385_GES11_960_hippocampus_A/J_male

value: A/J


title: experiment_H001AS8_N13_sci-iPS-2sec dataset on hPSC derived Cardiomyocytes DD23

value: hPSC derived cardiomyocytes DD23

value: Tetracycline


title: 408_GES11_974_hippocampus_PWK_PhJ_female


title: 406_GES11_972_hippocampus_PWK_PhJ_female


title: S5_D20_01

description: Library name: S5_D20


title: experiment_H001AS8_N06_sci-iPS-2sec dataset on hPSC derived Cardiomyocytes DD23


title: 382_GES11_957_hippocampus_A/J_male

value: male


title: WT_2

city: Hangzhou

first: Boya

last: Zhang

state: Zhejiang

address: Qingchun East Road

institute: Department of dermatology,Sir Run Run Shaw Hospital, Zhejiang University, School of Medicine

description: Library name: Sample5

data_processing:
The raw paired end reads were trimmed and quality controlled by fastp with default parameters
Then clean reads were separately aligned to reference genome with orientation mode using HISAT2 software
The mapped reads of each sample were assembled by StringTie in a reference-based approach.
To identify DEGs ( differential expression genes) between two different samples, the expression level of each transcript was calculated according to the transcripts per million reads (TPM) method
Supplementary files format and content: tab-delimited text files include TPM values for each Sample

source_name: skin

extract_protocol:
Total RNA from each sample was extracted using TRIzol® Reagent according to the manufacturer’s instructions (Invitrogen, Carlsbard, CA, USA) and genomic DNA was removed using DNase I (TaKara, Shiga, Japan)
The RNA-seq transcriptome librariy was prepared following Illumina® Stranded mRNA Prep Ligation from Illumina (San Diego, CA) using 1μg of total RNA.

value: skin


title: S16_D30_IFN_02

description: Library name: S16_D30_IFN

value: IFNB


title: experiment_H001AS8_N11_sci-iPS-2sec dataset on hPSC derived Cardiomyocytes DD23


title: experiment_H001AS8_N03_sci-iPS-2sec dataset on hPSC derived Cardiomyocytes DD23


title: C57BL/6J mice PBS control Day 0_5

description: Library name: Control 5


title: experiment_H001AS8_N10_sci-iPS-2sec dataset on hPSC derived Cardiomyocytes DD23


title: S23_iPSCs_01

description: Library name: S23_iPSCs


title: HTRA1_3

description: Library name: Sample3


title: C57BL/6J mice injected with LPS and anti IL10R antibody 24hr_1

description: Library name: D11_LPSaIL10R


title: S13_D30_TGFB_02

description: Library name: S13_D30_TGFB

value: TGFB


title: 396_GES11_969_hippocampus_CAST_EiJ_male


title: S8_D25_02

description: Library name: S8_D25


title: C57BL/6J mice injected with LPS 24hr_1

description: Library name: D11_LPS

value: Hematopoietic stem and progenitor cells


title: experiment_H001AS8_N08_sci-iPS-2sec dataset on hPSC derived Cardiomyocytes DD23


title: S10_D30_VEH_02

description: Library name: S10_D30_VEH


title: 393_GES11_966_hippocampus_CAST_EiJ_male


title: C57BL/6J mice PBS control Day 0_4

description: Library name: Control 4


title: 372_GES11_949_hippocampus_A/J_female

value: female


title: S18_D30_GMCSG_01

description: Library name: S18_D30_GMCSG


title: C57BL/6J mice PBS control Day 0_3

description: Library name: Control 3


title: HTRA1_1

description: Library name: Sample1


title: S21_Blood_N_1

description: Library name: S21_Blood_N


title: 367_GES11_946_hippocampus_NOD_ShiLtJ_male


title: 384_GES11_959_hippocampus_A/J_male


title: S7_D25_01

description: Library name: S7_D25


title: WT_3

description: Library name: Sample6


title: S24_iPSCs_02

description: Library name: S24_iPSCs


title: experiment_H001AS8_N05_sci-iPS-2sec dataset on hPSC derived Cardiomyocytes DD23


title: Hs578T, LY3, 0.1, R3

city: Leiden

first: Bob

last: van de Water

state: Leiden

address: Einsteinweg 55

country: Netherlands

institute: Leiden University

description: Library name: I17-1234-G06-A6

data_processing:
Alignment was performed using the STAR aligner (version 2.4.2a) against the human GRCh38 reference genome.
Marking duplicates, sorting and indexing were performed using Sambamba (version 0.6.6).
Counts per gene were quantified using HTseq based on the ENSEMBL gene annotation for GRCH38 (release 84).
Data was normalized and differential gene expression was determined using DESeq2.
Assembly: GRCh38 (release 84)
Supplementary files format and content: .txt format containing raw counts

growth_protocol: Hs578T cells were maintained in RPMI-1640 medium with L-glutamine and 25 mM HEPES, supplemented with 10% FBS and penicillin/streptomycin

extract_protocol:
RNA was isolated with the RNeasy Plus Mini Kit (Qiagen) following manufacturer's instructions.
DNA libraries were prepared from the samples with the TruSeq Stranded mRNA Library Prep Kit.

treatment_protocol: Hs578T cells were treated with the negative solvent control DMSO (0.1%) or the inhibitors I-73 (0.1 and 0.316 μM), D10-81 (0.1 μM), Y3-21 (0.1 μM) for 6 hours prior to collection of RNA.  For combination treatments, cells were treated with I-73 (0.1 μM), lapatinib (3.16 μM) and a combination thereof for 6 hours prior to collection of RNA.

value: Breast cancer cell line


title: 362_GES11_941_hippocampus_NOD_ShiLtJ_male

value: hippocampus


title: BMDM IFNy 5

city: Schlieren

first: Florence

last: Vallelian

address: Wagistrasse 12

department: Department of Internal Medicine

country: Switzerland

institute: University Hospital and University of Zurich

description: Library name: M5_BMDM_IFNy

data_processing:
Read alignment using STAR (version 2.7.11b)
Read summarization using featureCounts (Rsubread version 2.22.1)
Assembly: Mus_musculus/GENCODE/GRCm39/Annotation/Release_M37-2025-07-03
Supplementary files format and content: .txt: Contains feature (gene) counts

source_name: BMDM

growth_protocol: BM cells were isolated by flushing the femurs and tibias of 7- to 12-week-old C57BL/6J mice and then passed through a 70-μm filter. The BM cells were plated at a density of 3 x 105 cells/ml on tissue culture-treated 60 mm UpCell dishes (Nunc™ UpCell™, ThermoFisher) in complete RPMI-1640 medium (10% fetal calf serum (FCS), 1% L-glutamine and 1% P/S) supplemented with 100 ng/ml recombinant mouse M-CSF (PeproTech). On day 3, half of the medium was replaced. Cultures were treated on day 3 or 4  with IL-4 (20 ng/ml, PeproTech), IL-10 (100 ng/ml), TGF-β (100 ng/ml), or IFNγ (20 ng/ml, PeproTech). The BM cells were harvested for analysis on day 7 from the temperature-responsive cell culture plates after cooling to room temperature. Cells were washed twice in PBS and centrifuged (300g, 10 min) before processing.

extract_protocol:
RNA was extracted from macrophages using the RNeasy Mini kit (Qiagen) according to the manufacturer's protocol, including on-column DNase I treatment.
RNA quality was validated on an Agilent Technologies 4150 Tapestation using  RNA Screentapes, and only samples with an RNA integrity number (RIN) of > 9 were used for sequencing. cDNA libraries were generated at the Functional Genomics Center Zurich (FGCZ) from RNA samples using the Illumina Stranded mRNA Prep ligation kit following the manufacturer’s instructions. The quality and concentration of the libraries were determined using an Agilent Technologies 4200 Tapestation with DNA Screentapes. The libraries were pooled in equimolar amounts and sequenced on an Illumina NovaSeq X Plus sequencer (paired-end 150 bp) with a depth of at least 20 million reads per sample.

value: BMDM

value: IFNy


title: Hs578T, LY3, 0.1, R2

description: Library name: I17-1234-D05-A6


title: experiment_H001AS8_N04_sci-iPS-2sec dataset on hPSC derived Cardiomyocytes DD23

source_name: hPSC derived cardiomyocytes


title: experiment_H001AS8_M19_sci-iPS-2sec dataset on hPSC derived Cardiomyocytes DD23


title: 356_GES11_936_hippocampus_NOD_ShiLtJ_female


title: WT_1

description: Library name: Sample4


title: BMDM TGFb 4

description: Library name: M4_BMDM_TGFb

value: TGFb


title: experiment_H001AS8_M18_sci-iPS-2sec dataset on hPSC derived Cardiomyocytes DD23


title: 377_GES11_954_hippocampus_A/J_female


title: 354_GES11_934_hippocampus_NOD_ShiLtJ_female


title: C57BL/6J mice PBS control Day 0_1

description: Library name: Control 1


title: experiment_H001AS8_N02_sci-iPS-2sec dataset on hPSC derived Cardiomyocytes DD23