title: CD8_NA_0h_rep2

data_processing:
We sequenced the same libraries twice due to sharrower reads from the first sequencing. First sequencing generated files were named "first_batch_*" and second sequencing generated files were named "second_batch_*". Each run is represented by a separate SRR ID. We first trimmed adapter sequences before aligning reads to the GRCh38 human genome assembly with Bowtie 2.  We used FastQC (http://www.bioinformatics.babraham.ac.uk/ projects/fastqc/) to obtain sequence quality control metrics both before and after read trimming. We obtained alignment summary metrics with Picard tools (http://broadinstitute.github.io/ picard). We retained reads that mapped uniquely to the primary assembly with MAPQ >= 30 and re- moved optical duplicates. We shifted cut sites by +4bp and −5bp on positive and negative strands, respectively.
We used MACS2 to call ATAC-seq peaks within individual samples using a q < 0.2 threshold. For each library, we use ataqv to calculate TSS enrichment and the fraction of reads in peaks (FRiP). We excluded peaks within ENCODE blacklist regions.
We used Markov clustering to identify a preliminary set of consensus features across libraries. Edges were weighted by the proportion of overlapping bases between each pair of peaks. Peaks that did not overlap with at least one peak from another library were excluded from further analysis. After clustering, we deﬁned preliminary clusters to be the maximal (union) coordinates of all constituent peaks.
We used a two-state Hidden Markov Model to identify the central, maximally replicated portion of each preliminary feature. Consensus features were deﬁned as the maximal extent of all “open” segments within each cluster.
We used featureCounts to quantitate the number of reads within each peak for each library. Outliers were identiﬁed through principal component analysis.
Genome_build: hg38
Supplementary_files_format_and_content: count matrix

extract_protocol: Human naïve CD4+/CD8+ T cells were stimulated with anti-CD3/CD28 w/wo IFN-b (500U/ml). ATAC-seq samples were collected from 2h, 8h, 72h timepoints.


title: CD8_NA_0h_rep1

status: Public on Jan 31 2022

type: SRA

city: New Haven

first: Tomokazu

middle: S

last: Sumida

state: CT

address: 300 George St,, 3rd floor room349

department: Neurology

country: USA

institute: Neurology, Yale School of Medicine

library_source: genomic

molecule: genomic DNA

organism: Homo sapiens

source_name: primary T cells

tag: cell type

tag: treatment

tag: time points


title: heart: 751

city: Los Angeles

first: Calvin

last: Pan

address: 675 Charles Young Dr South

institute: UCLA

library_source: transcriptomic

data_processing:
Reads were quantified against mouse transcriptome reference from GRCm38.p6 (Ensembl release 97) using kallisto v0.46
Gene counts and TPM values were tabulated with tximport.
Genome_build: GRCm38.p6
Supplementary_files_format_and_content: *.txt files are tab-delimited text containing either gene counts or gene TPMs

molecule: total RNA

organism: Mus musculus

extract_protocol:
Total RNA from mouse heart samples (one mouse per strain) was purified using the Qiagen miRNeasy kit (Qiagen cat#217004) per the manufacturer’s instructions.
Libraries were prepared using the Nugen Universal Plus mRNA kit (Tecan Genomics Inc, Redwood City, CA)

treatment_protocol: Mice were fed a chow diet for 8 weeks, followed by a high-fat/high-sucrose diet for 8 weeks.  Tissues were collected at 16 weeks of age.

tag: tissue

value: heart

tag: strain

tag: Sex

value: M


title: genomic DNA from LDRC_567_1S

type: genomic

city: Houston

first: Oxana

middle: Yu.

last: Naumova

state: TX

address: 4849 Calhoun Rd, TIMES, Rm 373

department: Psychology

institute: University of Houston

description: normal development

hyb_protocol: Bisulphite converted DNA was amplified, fragmented and hybridised to the Illumina Infinium MethylationEPIC Beadchip using standard Illumina protocol

scan_protocol: Arrays were imaged using iScan in accodance to the standard recommended Illumina scanner setting

data_processing: Illumina GenomeStudio Methylation Module v1.8

label: Cy5 and Cy3

source_name: saliva LDRC_567_1S

label_protocol: Standard Illumina Protocol

extract_protocol: T-cells from blood samples were isolated using monoclonal anti-biotin antibody coupled to MicroBeads according to standard instructions. Genomic DNA was extracted (1) from T-cells using the Qiagen DNeasy Kit, (2) from blood samples using the Qiagen  FlexiGene kit, and (3) from the Oragene (OGR-50) saliva samples using the DNA Genotek prepIT.L2P reagents. All the procedures have been performed according to the manufacturer's protocol

tag: gender

value: Male

value: saliva

tag: disease state

value: normal


title: CD4_con_96h_1

data_processing:
After sequencing, adapter sequences and poor-quality bases (quality score < 3) were trimmed with Trimmomatic. Remaining bases were trimmed if their average quality score in a 4 bp sliding window fell below 5. FastQC was used to obtain quality control metrics before and after trimming. Remaining reads were aligned to the GRCh38 human genome with STAR 2.5.244. We used Picard to remove optical duplicates and to compile alignment summary statistics and RNA-seq summary statistics. After alignment, reads were quantitated to gene level with RSEM45 using the Ensembl annotation. Normalized Fragments Per Kilobase Million (FPKM) expression values
Genome_build: hg38
Supplementary_files_format_and_content: count matrix

molecule: polyA RNA

growth_protocol: Naïve CD4+ T cells (CD4+/CD25neg/CD127+/CD45ROneg/CD45RA+) and naïve CD8+ T cells (CD8++/CD25neg/CD127+/CD45ROneg/CD45RA+) were sorted on a FACSAria (BD Biosciences). Sorted cells were plated in 96-well round-bottom plates (Corning) and cultured in RPMI 1640 medium supplemented with 5 % Human serum, 2 nM L-glutamine, 5 mM HEPES, and 100 U/ml penicillin, 100 g/ml streptomycin, 0.5 mM sodium pyruvate, 0.05 mM nonessential amino acids, and 5% human AB serum (Gemini Bio-Products).

extract_protocol:
Total RNA was extracted using RNeasy Micro Kit (QIAGEN), or ZR-96 Quick-RNA kit (Zymo Research), according to the manufacturer’s instructions.
cDNAs were generated from isolated RNAs using SMART-Seq v4 Ultra Low Input RNA Kit for sequencing (Takara/Clontech). Barcoded libraries were generated by the Nextera XT DNA Library Preparation kit (Illumina) and sequenced with a 2x100 bp paired-end protocol on the HiSeq 4000 Sequencing System (Illumina).

treatment_protocol: Cells were seeded (30,000-50,000/wells) into wells pre-coated with anti-human CD3 (2 ug/ml, clone UCHT1, BD Biosciences) along with soluble anti-human CD28 (1ug/ml, clone 28.2, BD Biosciences) in the presence or absence of human IFN beta (500 U/ml: Pestka Biomedical Laboratories) without adding IL-2.

value: con


title: CD8_IFNb_8h_rep3

value: IFNb


title: CD8_IFNb_72h_1


title: genomic DNA from LDRC_481_1T

description: normal development

source_name: T cells LDRC_481_1T

value: T cells


title: CD8_NA_0h_rep3


title: heart: 747

value: F


title: CD8_IFNb_8h_rep2


title: CD8_IFNb_72h_rep3


title: CD8_IFNb_8h_rep1


title: heart: 742


title: heart: 734


title: CD4_IFNb_72h_1


title: CD8_con_72h_1


title: CD4_con_72h_1


title: CD8_IFNb_48h_1


title: CD8_IFNb_72h_rep2


title: heart: 722


title: heart: 732


title: CD8_IFNb_72h_rep1


title: heart: 716


title: heart: 698


title: heart: 714


title: CD8_IFNb_2h_rep1


title: CD4_con_48h_1


title: CD8_IFNb_2h_rep2


title: CD4_IFNb_48h_1


title: CD8_con_48h_1


title: heart: 695


title: CD8_Control_8h_rep2

value: Control


title: heart: 692


title: CD8_con_96h_1


title: CD4_IFNb_16h_1


title: CD4_con_16h_1


title: heart: 686

value: CBA/J


title: CD8_Control_8h_rep1


title: CD8_IFNb_8h_1


title: CD8_Control_72h_rep2


title: CD8_con_8h_1


title: heart: 679


title: CD8_Control_72h_rep1


title: heart: 676


title: CD4_con_8h_1


title: CD8_Control_2h_rep1


title: heart: 673


title: CD8_con_4h_1


title: CD8_Control_2h_rep2


title: CD8_IFNb_16h_1


title: heart: 671


title: CD8_IFNb_2h_rep3


title: CD4_NA_0h_rep3


title: heart: 645


title: CD8_Control_8h_rep3


title: CD4_IFNb_4h_1


title: heart: 654


title: CD8_IFNb_4h_1


title: heart: 690


title: CD8_con_16h_1


title: CD4_con_4h_1


title: CD4_NA_0h_rep1


title: heart: 682

value: BUB/BnJ


title: CD8_Control_72h_rep3


title: CD8_Control_2h_rep3


title: CD4_NA_0h_rep2


title: CD8_IFNb_2h_1


title: CD4_IFNb_8h_rep3


title: heart: 627


title: CD8_con_2h_1


title: heart: 616

value: RIIIS/J


title: CD4_IFNb_8h_1


title: CD4_IFNb_8h_rep2


title: heart: 614


title: heart: 585

value: PL/J


title: CD4_IFNb_72h_rep3


title: CD4_con_2h_1


title: CD4_IFNb_2h_1


title: CD8_IFNb_1h_1


title: heart: 583


title: heart: 581


title: CD4_IFNb_72h_rep2


title: CD8_con_1h_1


title: CD4_IFNb_8h_rep1


title: CD4_IFNb_72h_rep1


title: heart: 643


title: CD4_IFNb_2h_rep1


title: heart: 575


title: CD8_naïve_0h_1


title: CD4_IFNb_2h_rep3


title: heart: 571


title: CD4_naive_0h_1


title: CD4_con_1h_1


title: CD4_IFNb_2h_rep2


title: heart: 567


title: heart: 561


title: CD4_Control_8h_rep3


title: heart: 556


title: CD4_Control_8h_rep2


title: Subject 2 CD11c+ ATMs

city: Ann Arbor

first: Lindsey

middle: A

last: Muir

state: MI

address: 1600 Huron Parkway B520

institute: University of Michigan

data_processing:
Checked quality of the raw reads data for each sample using FastQC (version v0.11.3)
aligned reads using TopHat (version 2.0.13) and Bowtie2 (version 2.2.1.) using default parameter settings plus “--b2-very-sensitive”
Ran FastQC for a second round of quality control (post-alignment)
Genome_build: hg19
Supplementary_files_format_and_content: tab delimited text files containing raw counts, regularized log transformation of raw counts, and depth normalized counts (FPKM) generated using DESeq2 (version 1.14.1)
Supplementary_files_format_and_content: raw counts
Supplementary_files_format_and_content: depth normalized counts (FPKM)
Supplementary_files_format_and_content: rlog normalized counts

source_name: Omental adipose tissue

extract_protocol:
Samples were thawed at 37°C , run through QIAshredder columns for sample homogenization, and purified using an RNeasy Mini Kit (Qiagen).
The University of Michigan Sequencing Core confirmed RNA integrity on an Agilent 2100 Bioanalyzer (RIN 7.9-10 after one freeze/thaw of purified RNA), and samples were then processed with the Pico Input Mammalian SMARTer® Stranded Total RNA-Seq Kit (Clontech).

treatment_protocol: Human adipose tissue macrophages (ATMs) were isolated from samples of human omental adipose tissue collected from three subjects with obesity during bariatric surgery. Single cell suspensions of stromal vascular cells were obtained from adipose tissue after fine mincing by hand using surgical scissors (DR Instruments, 4SB) and digestion in 3 mg/ml collagenase II (Life Technologies, 17101015) in a 50 mL conical tube with approximately 2 grams tissue in 10 mL enzyme solution. Digests were agitated on a rocker at 37°C for 30 minutes, shaking tubes by hand at 5-minute intervals, followed by filtration through a 100 μm cell strainer and NH4Cl red blood cell lysis. Digest and wash buffer was Hank’s balanced salt solution with calcium/magnesium (Gibco) and 0.5% bovine serum albumin (Sigma-Aldrich). Single cell suspensions were stained for sorting using CD45 PerCP-Cy5.5 (Thermo Fisher Scientific 45-0459-41, RRID:AB_10718244, clone Hl30), CD64 PE (BioLegend 305008, RRID:AB_314492, clone 10.1), CD11c PE-Cy7 (BioLegend 301608, RRID:AB_389351, clone 3.9), CD206 APC-Cy7 (BioLegend 321119, RRID:AB_2144932, clone 15-2).  A Beckman Coulter MoFlo Astrios was used for cell sorting (University of Michigan Flow Cytometry Core), with gating to identify live, non-aggregated, CD45+CD64+ ATMs, followed by gating for ATM subtypes using CD11c and CD206. Cells were sorted into into 50% fetal bovine serum in phosphate buffered saline. Sorted cells were centrifuged at 400 x g for 10 minutes at 4°C and supernatant removed. Up to 250,000 cells were lysed by vortexing pellets in 1 ml 1% beta-mercaptoethanol/RLT buffer (Qiagen), and lysate was stored at -80°C.

value: CD64+CD206-CD11c+ ATMs


title: CD4_Control_8h_rep1


title: heart: 552


title: Subject 1 CD11c+ ATMs


title: CD4_Control_72h_rep2


title: CD4_IFNb_1h_1


title: Subject 3 DP ATMs

value: CD64+CD206+CD11c+ ATMs


title: Subject 2 DP ATMs


title: heart: 550


title: CD4_Control_72h_rep1


title: heart: 543

value: AKR/J


title: Subject 1 DP ATMs


title: heart: 547

value: heart


title: Subject 2 CD206+ ATMs

value: CD64+CD206+CD11c- ATMs


title: CD4_Control_2h_rep1


title: Subject 3 CD11c+ ATMs


title: Subject 3 CD206+ ATMs


title: heart: 536

value: M


title: heart: 540


title: CD4_Control_2h_rep2


title: Subject 1 CD206+ ATMs


title: CD4_Control_2h_rep3


title: heart: 563


title: heart: 521


title: heart: 524


title: heart: 529

value: SEA/GnJ


title: heart: 393


title: CR Pool 5 GL2 - Rep 4 gfp +

city: Columbus

first: Jeffrey

last: Parvin

state: Ohio

address: 250 Lincoln Tower, 1800 Cannon Drive

department: Biomedical Informatics

institute: Ohio State University

description:
Sample 66
pool5cis.h5

data_processing:
FASTQ files containing either barcodes for each sample and the barcode-map for each library were used as input for the software package Enrich2.
Enrich2 was used to count the barcodes, associate each barcode with a nucleotide variant, and then translate and count both the unique-nucleotide and unique-amino acid variants.
Barcodes assigned to variants containing insertions or deletions were removed from analysis.
The counts for each protein variant were converted to frequencies by dividing by the total number of variant counts for each sample by Enrich2.
The ratio of the frequency of each variant in the GFP positive population over its frequency in the GFP negative population was calculated by Enrich2.
That ratio for each variant was then normalized to the GFP+/GFP- ratio for the wild-type sequence at ln(GFP+/GFP-) = 0 by Enrich2. That is the score.
Genome_build: genome_build.txt
Supplementary_files_format_and_content: hdf5 files with counts and scores. Columns names are descriptive, _- denotes noGFP, _+ denotes GFP samples.

source_name: HeLa

growth_protocol: Ten 10 cm tissue-culture plates of HeLaDR-FRT cells at 90% confluency were each transfected with 10 μg of the pcDNA5/FRT BRCA1 variant library and 20 μg of pOG44 to express the flippase enzyme (Starita et al., 2018). Transfections were done with 30 μl Lipofectamine (Thermo Fisher) and 1 ml of Opti-MEM per plate according to manufacturer’s instructions.  Transfected cells were kept in DMEM media containing 1% GlutaMAX, 1% Sodium Pyruvate and 10% Fetal Bovine Serum. Cells were incubated at 37˚C for 24 hr to facilitate transfection, moved to 30˚C for 24 hr for optimal flippase activity, and then back to 37˚C for hygromycin resistance expression. 72 hr after the transfection, cells were transferred to twenty 15 cm plates containing selection media (fresh DMEM supplemented with 50% filter-sterilized conditioned media, 10% fetal bovine serum, 1% GlutaMax, 1% Sodium Pyruvate and 550 μg/mL Hygromycin-B). After 24 hrs, the hygromycin-resistant cells were washed with sterile phosphate-buffered saline (PBS), and selection media was replaced. After approximately 1 week, cell colonies were counted. Pool 4 had 102,000 colonies, pool 5 had 108,000 colonies, and pool 6 had 113,000 colonies. After another week, cells were resuspended in 20 mL of culture media and mixed thoroughly. 15 mL of resuspended cells were frozen into 1 mL aliquots. The remaining cells were plated on 15 cm plates and passaged for another week to ensure loss of unintegrated BRCA1 expression plasmid before performing multiplexed HDR reporter experiments.

extract_protocol:
DNeasy Blood & Tissue Kit, eluted in 200 ul H2O. To amplify the barcode from gDNA from the GFP-positive and negative populations were spread over 8-16 reactions containing 250 ug of gDNA each (220K‚Äì440K genome equivalents by weight given HeLa triploid genome ~9 pg). Reactions also contained Kapa2G Robust Polymerase (Kapa Biosystems), a primer that annealed to the SV40 promoter 5‚Äô of the integrated plasmid and a primer adjacent to the barcode (SV40_F and newpc5bc_nexteraR). PCR was performed using the following conditions [95C, 5 min; {95C, 40s, 65C, 30s, 72C, 3 min} x ~28 cycles; 72C, 10 min]. The reactions produce a ~3,700 base amplicon specifically from integrated plasmids. The reactions for each sample were combined and the amplicons were purified by 0.5X Ampure and eluted with 10 mM Tris at 10% of the original reaction volume. 10% of the eluted PCR volume was re-amplified with primers containing sample indexes and Illumina cluster generating sequences (pc5bc_p5_F, nextIndex). Reactions also contained Kapa2G Robust Polymerase and 0.5X SYBR green II (ThermoFisher). PCR reactions are monitored on a Mini-opticon qPCR machine (Bio-Rad) and removed during exponential amplification using the following conditions [95C, 3 min; {95C, 20s, 65C, 30s, 72C, 20s} x 5-10 cycles]. The PCR reaction produced a 350-base amplicon that was purified using a double-Ampure protocol. First the large DNA fragments were removed by precipitation by addition of 0.6X volume Ampure beads to the reactions. Then the 350-base amplicons were purified from the supernatant using 0.9X volume Ampure beads. The samples were multiplexed and the barcodes and sample indexes were sequenced (single read, pcDNA5_barcodeSeq_F) on a Nextseq 500 High Output 75 base kit.
pcDNA5-FRT/TO-HA-BRCA1 was digested with NheI-HF and SbfI-HF (New England Biosciences), and the 1700 bp fragment containing amino acids 1294-1863 was cloned into the pUC19 plasmid. For experiments mutagenizing amino acids 1557-1768, the pcDNA5-FRT/TO-HA-BRCA1 plasmid was modified to include regions of homology for Illumina sequencing (pcDNA5-FRT/TO-HA-BRCA1-Blue). Three site-saturation mutagenesis libraries – pool 4 (amino acids 1769-1863), pool 5 (amino acids 1673-1768) and pool 6 (amino acids 1577-1672) – were constructed using inverse PCR mutagenesis (Jain and Varadarajan, 2014) with KaPa HiFi HotStart ReadyMix. 30 base mutagenic primers were designed for each codon, with hand mixed NNN (pools 5 and 6) and NNK (pool 4) (N = ACTG, K = GT) bases at the 5′ end of the sense oligonucleotide. Ligations were pooled together, phosphorylated and self-ligated as previously described (Jain and Varadarajan, 2014). Cells were transformed into MAX Efficiency DH5α competent cells (Thermo Fisher), and 10 μl was plated on an agar plate with ampicillin (0.1 mg/mL) while the remaining 990 μl were added to 250 ml LB media with ampicillin (0.1 mg/mL). Plates were counted after 24 hr incubation and libraries with at least 10,000 colonies (approximately five-fold library coverage) were purified using the Qiagen Maxiprep kit. Pool 4 had approximately 86,000 colonies, pool 5 had 85,000 colonies, and pool 6 had 104,200 colonies. PCR (7-10 cycles) was used to isolate the mutagenized BRCA1 fragment and add a 16-base degenerate barcode to variants (primers NheI-Fwd-Long and BRCA1-AscI-Barcode-XhoI-Gib-Rev for pool 4, BRCA1-NheI-Fwd-Long and BRCA1-SbfI-Barcode-Rev for pools 5 and 6). The BRCA1 fragment was ligated back into pcDNA5-FRT/TO-HA-BRCA1 using Gibson assembly (Smith et al., 2009) and transformed into MAX Efficiency DH5α competent cells. Pool 4 had 46,300 independent plasmid variants, pool 5 had 10,400 plasmids, and pool 6 had 11,900 plasmids. Barcodes were amplified from gDNA over 18  reactions, each containing 250 ng of gDNA. PCR reactions were done using Kapa2G Robust  Polymerase for 22-23 cycles. For pool 4, the primers Pool4-Nest1-Fwd and FRT-LacZ-Rev were  used and for pools 5 and 6 the primers CTerm56-Nest1-Fwd and FRT-LacZ-Rev were used.  The resultant ~750 bp fragment was purified with 0.6X AmpurePB beads and eluted in 40 μl 10  mM Tris (pH 8). 125 ng of PCR product was re-amplified with primers containing sample  indexes and Illumina cluster-generating sequences using Kapa2G Robust Polymerase. The  resultant 150 bp (pool 4) or 170 bp (pools 5 and 6) amplicon was purified using double Ampure  purification (0.6X and 0.8X). The samples were combined, and barcodes and sample indexes  (Seq-i70x and Seq-i50x primers) were sequenced on the HiSeq 4000 at the Nationwide  Children’s Hospital Genomic Services Laboratory.

treatment_protocol:
(Samples 1- 48 ) HDR assays for each pool were performed in quadruplicate, two replicates at a time. For two replicates, integrated variant libraries were seeded at 70% confluency in 48 wells across two 24-well plates. The next day, each well was transfected with 30 pmol of siRNA, 1.5 μl of Oligofectamine (Thermo Fisher), and 31 μl of Opti-MEM per manufacturer’s recommendations. For each experiment, two wells were treated with siRNA targeting the BRCA1 coding region, 16 wells were treated with control siRNA, and 30 wells were treated with siRNA targeting the BRCA1 3′UTR, to which integrated BRCA1 variants were resistant. Cells were transferred to four 6-well tissue culture plates 24 hr after transfection. 48 hr after the Oligofectamine transfection, wells were transfected with 5 pmol siRNA, 3 μl of Lipofectamine 2000 (Thermo Fisher), 250 μl Opti-MEM and 3 μg of expression plasmid containing the restriction endonuclease I-SceI (pCBASceI) to induce a double-strand break. If HDR is functional, the break is repaired by gene conversion with the second GFP allele, and cells become GFP+ (Pierce et al., 2001; Ransburgh et al., 2010). After 48 hr, two wells for each siRNA condition were analyzed for GFP expression by observing 10,000 cells using the FACSCalibur machine at the OSUCCC Analytical Cytometry Shared Resource. Experiments proceeded if cells treated with control siRNA and BRCA1 3′UTR siRNA were between 7-9% and 4-7% GFP respectively, and if cells treated with BRCA1 coding sequence siRNA were between 1-2% GFP. 72 hr after Lipofectamine transfection, cells were pooled according to treatment and sorted by FACS using the Aria III in the OSUCCC Analytical Cytometry Shared Resource. Cells were resuspended and pooled in filter-sterilized sorting buffer containing 1X PBS (Ca2+- and Mg2+-free), 5 mM EDTA, 25 mM HEPES (pH 7.0), and 1% heat-inactivated fetal bovine serum dialyzed against Ca2+ and Mg2+ PBS. 10% of pooled cells for each sample were saved as input. A minimum of 264,000 GFP+ cells and a maximum of two million GFP- cells were collected per pool. Genomic DNA (gDNA) was extracted from GFP+, GFP- and input cells with a DNeasy Blood & Tissue Kit (QIAGEN) according to manufacturer’s instructions. DNA was eluted into 200 μl of Buffer EB (Qiagen).
(Sample 49-66) HeLaDR-FRT cells integrated with BRCA1 mutagenic pools were seeded at 40-50% confluency in 6-well dishes. Transfections were carried out using siRNA to BRCA1 3¢UTR, BRCA1 coding sequence or control siRNA (5 pmol) using Opti-MEM and Oligofectamine per manufacturer instructions. For each replicate, two wells were transfected each with control or BRCA1 3¢UTR siRNA, and one well was transfected with BRCA1 coding sequence siRNA. 24 hrs later, cells were split 1:3. Transfections were repeated on cells 48 hours after the first transfection. 48 hours after the second transfection, three 15 cm plates were seeded with 250,000 cells each for cells treated with siRNA to BRCA1 3¢UTR, and six 15 cm plates were seeded with 250,000 cells each for cells treated with control siRNA. Remaining cells were split between RNA extraction and protein isolation. Endogenous BRCA1 depletion was confirmed using qRT-PCR and total BRCA1 depletion was confirmed using immunoblotting. Following confirmation of endogenous BRCA1 depletion, the three 15 cm plates for each transfection condition (control and BRCA1 3¢UTR) were treated with 7.5 μM cisplatin (Selleckchem). After two hours of treatment, cells were washed with PBS and culture media was replaced. Five days after cisplatin treatment, cells were collected and gDNA was isolated using the DNeasy Blood & Tissue Kit as detailed for multiplex HDR reporter assays.

tag: cell line

value: HeLa

tag: functional assay

value: cisplatin-resistance

tag: population

value: gfp +


title: CR Pool 5 GL2 - Rep 2 gfp +

description:
Sample 64
pool5cis.h5


title: CR Pool 5 GL2 - Rep 3 gfp +

description:
Sample 65
pool5cis.h5


title: CR Pool 5 GL2 - Rep 1 gfp +

description:
Sample 63
pool5cis.h5


title: CD4_Control_72h_rep3


title: heart: 377


title: CR Pool 5 BRCA1 - Rep 4 gfp +

description:
Sample 61
pool5cis.h5


title: CR Pool 5 BRCA1 - Rep 3 gfp +

description:
Sample 60
pool5cis.h5


title: CR Pool 5 BRCA1 - Input

description:
Sample 62
pool5cis.h5

value: Input


title: heart: 320


title: heart: 318

value: LG/J


title: heart: 368


title: CR Pool 5 BRCA1 - Rep 2 gfp +

description:
Sample 59
pool5cis.h5


title: heart: 307


title: heart: 315


title: CR Pool 5 BRCA1 - Rep 1 gfp +

description:
Sample 58
pool5cis.h5


title: heart: 302

value: F


title: heart: 255

value: MA/MyJ


title: heart: 298


title: heart: 254


title: heart: 273


title: CR Pool 4 GL2 - Rep 4 gfp +

description:
Sample 57
pool4cis.h5


title: CR Pool 4 GL2 - Rep 3 gfp +

description:
Sample 56
pool4cis.h5


title: CR Pool 4 GL2 - Rep 2 gfp +

description:
Sample 55
pool4cis.h5


title: heart: 220


title: heart: 224


title: CR Pool 4 BRCA1 - Input

description:
Sample 53
pool4cis.h5


title: CR Pool 4 BRCA1 - Rep 3 gfp +

description:
Sample 51
pool4cis.h5


title: CR Pool 4 BRCA1 - Rep 4 gfp +

description:
Sample 52
pool4cis.h5


title: CR Pool 4 BRCA1 - Rep 2 gfp +

description:
Sample 50
pool4cis.h5


title: CR Pool 4 BRCA1 - Rep 1 gfp +

description:
Sample 49
pool4cis.h5


title: heart: 200


title: heart: 194


title: heart: 188


title: heart: 196


title: HDR Pool 6 GL2 - Rep 2 gfp -

description:
Sample 46
pool6hdr.h5

value: homology-directed repair

value: gfp -


title: HDR Pool 6 GL2 - Rep 3 gfp -

description:
Sample 47
pool6hdr.h5


title: heart: 183


title: HDR Pool 6 GL2 - Rep 1 gfp -

description:
Sample 45
pool6hdr.h5


title: HDR Pool 6 GL2 - Rep 4 gfp -

description:
Sample 48
pool6hdr.h5


title: heart: 180


title: HDR Pool 6 GL2 - Rep 4 gfp +

description:
Sample 44
pool6hdr.h5


title: HDR Pool 6 GL2 - Rep 2 gfp +

description:
Sample 42
pool6hdr.h5


title: heart: 211


title: heart: 179


title: MCD2_026

city: Changsha

first: Lin

last: Ye

address: 139 Renmin Middle Road, Furong district, Changsha

country: China

institute: Central South University

data_processing:
The raw reads (raw sequencing FASTQ files) are selected for a DSP pipeline run
The raw reads are processed for high quality(if more than 50% base's Phred Q <=19), the adapters(for SE,if the adapter contamination length is greater than 5bp; for PE, if one read has adapter contamination, then both reads are removed) are removed, and the paired-end reads are merged
The reads are aligned to the DSP readout tag sequence identifier barcodes, then PCR duplicates are removed by matching on the Unique Molecular Index (UMI)
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every Regions of Interest (ROIs)

source_name: Kidney

extract_protocol:
Formalin-fixed paraffin-embedded renal tissues were used.
After the GeoMx DSP system has completed collection, each GeoMx DSP aspirate in the collection plate contains photocleaved DNA oligos comprised of an RNA analyte identifier, a unique molecular identifier (UMI) barcode, and primer binding sites. When PCR is performed on the aspirates, Illumina adapter sequences and unique dual sample indices are added. Following a pooling purification and quality control process, the final library is ready for sequencing on an Illumina NGS platform using a dualindex workflow.

value: Kidney

tag: disease

value: MCD


title: MCD2_027


title: HDR Pool 6 GL2 - Rep 1 gfp +

description:
Sample 41
pool6hdr.h5


title: HDR Pool 6 GL2 - Rep 3 gfp +

description:
Sample 43
pool6hdr.h5


title: heart: 218


title: MCD2_025


title: heart: 161

value: BALB/cJ


title: HDR Pool 6 BRCA1 - Rep 4 gfp -

description:
Sample 40
pool6hdr.h5


title: MCD2_023


title: heart: 144


title: HDR Pool 6 BRCA1- Rep 3 gfp -

description:
Sample 39
pool6hdr.h5


title: HDR Pool 6 BRCA1 - Rep 2 gfp -

description:
Sample 38
pool6hdr.h5


title: HDR Pool 6 BRCA1 - Rep 1 gfp -

description:
Sample 37
pool6hdr.h5


title: MCD1_012


title: heart: 137


title: MCD1_011


title: HDR Pool 6 BRCA1 - Rep 4 gfp +

description:
Sample 36
pool6hdr.h5


title: heart: 133


title: HDR Pool 6 BRCA1- Rep 3 gfp +

description:
Sample 35
pool6hdr.h5


title: HDR Pool 6 BRCA1 - Rep 2 gfp +

description:
Sample 34
pool6hdr.h5


title: MCD1_010


title: heart: 122


title: MCD1_007


title: heart: 174


title: MCD1_006


title: HDR Pool 5 GL2 - Rep 4 gfp -

description:
Sample 32
Pool5_barcodes_exp.h5


title: heart: 119


title: heart: 166

value: SWR/J


title: heart: 125

value: heart


title: HDR Pool 5 GL2 - Rep 3 gfp -

description:
Sample 31
Pool5_barcodes_exp.h5


title: heart: 115

value: FVB/NJ


title: MCD1_004

value: ANCA


title: MCD2_024


title: heart: 110

value: KK/HlJ

value: M


title: ANCA1_024


title: HDR Pool 5 GL2- Rep 2 gfp -

description:
Sample 30
Pool5_barcodes_exp.h5

value: HeLa


title: heart: 107


title: CR Pool 4 GL2 - Rep 1 gfp +

description:
Sample 54
pool4cis.h5

value: cisplatin-resistance

value: gfp +


title: ANCA1_022


title: HDR Pool 5 GL2 - Rep 1 gfp -

description:
Sample 29
Pool5_barcodes_exp.h5


title: heart: 103

source_name: BTBR T<+> tf/J_F

value: BTBR T<+> tf/J


title: HDR Pool 5 GL2 - Rep 4 gfp +

description:
Sample 28
Pool5_barcodes_exp.h5


title: ANCA3_020


title: heart: 100

source_name: BTBR T<+> tf/J_M


title: ANCA1_021


title: ANCA3_019


title: heart: 131


title: HDR Pool 6 BRCA1 - Rep 1 gfp +

description:
Sample 33
pool6hdr.h5


title: heart: 95


title: heart: 89

value: F


title: heart: 83


title: ANCA3_017


title: MCD1_005


title: ANCA1_018


title: heart: 75

value: NON/ShiLtJ


title: HDR Pool 5 GL2 - Rep 1 gfp +

description:
Sample 25
Pool5_barcodes_exp.h5

value: homology-directed repair


title: HDR Pool 5 BRCA1 - Rep 4 gfp -

description:
Sample 24
Pool5_barcodes_exp.h5

value: gfp -


title: HDR Pool 5 GL2 - Rep 3 gfp +

description:
Sample 27
Pool5_barcodes_exp.h5


title: HDR Pool 5 GL2- Rep 2 gfp +

description:
Sample 26
Pool5_barcodes_exp.h5


title: ANCA2_015

value: Kidney


title: ANCA3_016


title: HDR Pool 5 BRCA1 - Rep 3 gfp -

description:
Sample 23
Pool5_barcodes_exp.h5


title: HDR Pool 5 BRCA1 - Rep 2 gfp -

description:
Sample 22
Pool5_barcodes_exp.h5


title: heart: 72


title: heart: 63


title: HDR Pool 5 BRCA1 - Rep 1 gfp -

description:
Sample 21
Pool5_barcodes_exp.h5


title: ANCA2_014


title: HDR Pool 5 BRCA1 - Rep 4 gfp +

description:
Sample 20
Pool5_barcodes_exp.h5


title: ANCA2_013


title: heart: 62


title: heart: 56


title: ANCA2_012


title: HDR Pool 5 BRCA1 - Rep 2 gfp +

description:
Sample 18
Pool5_barcodes_exp.h5


title: heart: 48


title: ANCA2_011


title: ANCA1_006


title: ANCA2_009


title: HDR Pool 5 BRCA1 - Rep 1 gfp +

description:
Sample 17
Pool5_barcodes_exp.h5


title: heart: 4


title: HDR Pool 4 GL2 - Rep 4 gfp +

description:
Sample 12
pool4hdr.h5


title: HDR Pool 4 GL2 - Rep 2 gfp -

description:
Sample 14
pool4hdr.h5


title: ANCA1_008


title: heart: 42

value: SJL/J


title: HDR Pool 4 GL2 - Rep 1 gfp -

description:
Sample 13
pool4hdr.h5


title: PAH7: gDNA from circulating CD04+ T cells from PAH7

city: Naples

first: Claudio

last: Napoli

state: Italy

address: P.za Miraglia, 2

country: Italy

institute: University of Campania "L. Vanvitelli"

description: SSc

data_processing:
Raw reads were assessed for quality with FastQC v011.8 and trimmed with TrimGalore v0.6.3 with the default settings
Trimmed reads were then mapped to the in silico bisulfite converted human reference genome (GRCh38) by using Bismark v.0.22.1 with and non directional parameter applied
Only the uniquely mapped reads were used to make cytosine methylation calls by using bismark methylation extractor
Differentially methylated CpGs (dmCpGs) were identified by using the R package methylKit (v1.10.0)
Genome_build: GRCh38
Supplementary_files_format_and_content: For each sample, the bismark methylation extractor output is reported and contains the genome-wide cytosine methylation report  The genome-wide cytosine methylation output file is tab-delimited in the following format:  <chromosome>  <position>  <strand>  <count methylated>  <count non-methylated>  <C-context>  <trinucleotide context>

source_name: PAH CD04+ T cells

extract_protocol:
gDNA samples from CD04+ cells were immediately extracted by using DNeasy Blood & Tissue Kit (Qiagen), according to manufacturer’s indications
All libraries were prepared by TruSeq Library Prep Kit (Illumina) and bisulfite conversion was obtained by using the EZ DNA Methylation-Gold Kit (Zymo Research).

value: PAH

value: CD04+ T cells


title: heart: 38

value: heart

value: BALB/cJ


title: HDR Pool 4 GL2 - Rep 3 gfp -

description:
Sample 15
pool4hdr.h5


title: heart: 17


title: ANCA1_007

value: ANCA


title: PAH5: gDNA from circulating CD04+ T cells from PAH5

description: portopulmonary


title: C57BL/6J_Y47

data_processing:
Reads were quantified against mouse transcriptome reference from GRCm38.p6 (Ensembl release 97) using kallisto v0.46
Genome_build: mm10
Supplementary_files_format_and_content: *.txt files are tab-delimited text containing gene counts

source_name: heart

extract_protocol:
Total RNA from mouse heart samples was purified using the Qiagen miRNeasy kit (Qiagen cat#217004) per the manufacturer’s instructions.
Libraries were prepared using the Nugen Universal Plus mRNA kit (Tecan Genomics Inc, Redwood City, CA)

tag: diet

value: High-fat diet + L-NAME


title: C57BL/6J_Y49

value: M


title: HDR Pool 4 GL2 - Rep 4 gfp -

description:
Sample 16
pool4hdr.h5

value: HeLa


title: ANCA2_010


title: C57BL/6J_Y16


title: HDR Pool 5 BRCA1 - Rep 3 gfp +

description:
Sample 19
Pool5_barcodes_exp.h5


title: HDR Pool 4 GL2 - Rep 2 gfp +

description:
Sample 10
pool4hdr.h5


title: C57BL/6J_Y14


title: HDR Pool 4 GL2 - Rep 3 gfp +

description:
Sample 11
pool4hdr.h5


title: ANCA1_005


title: PAH3: gDNA from circulating CD04+ T cells from PAH3

description: idiopathic


title: ANCA1_004


title: PAH2: gDNA from circulating CD04+ T cells from PAH2

description: idiopathic


title: ANCA1_003


title: C57BL/6J_Y13


title: PAH6: gDNA from circulating CD04+ T cells from PAH6

description: SSc


title: HDR Pool 4 GL2 - Rep 1 gfp +

description:
Sample 9
pool4hdr.h5


title: ANCA1_002


title: ANCA1_001


title: C57BL/6J_Y12


title: PAH4: gDNA from circulating CD04+ T cells from PAH4

description: idiopathic


title: CTRL6: gDNA from circulating CD04+ T cells from CTRL6

description: normal

source_name: normal CD04+ T cells

value: CTRL


title: C57BL/6J_Y11


title: C57BL/6J_Y10


title: HDR Pool 4 BRCA1 - Rep 4 gfp -

description:
Sample 8
pool4hdr.h5


title: ANCA4_021


title: CTRL7: gDNA from circulating CD04+ T cells from CTRL7

description: normal


title: ANCA4_018


title: C57BL/6J_YF9


title: CTRL4: gDNA from circulating CD04+ T cells from CTRL4

description: normal


title: HDR Pool 4 BRCA1 - Rep 3 gfp -

description:
Sample 7
pool4hdr.h5


title: HDR Pool 4 BRCA1 - Rep 1 gfp -

description:
Sample 5
pool4hdr.h5


title: C57BL/6J_YF20


title: PAH1: gDNA from circulating CD04+ T cells from PAH1

description: idiopathic


title: CTRL2: gDNA from circulating CD04+ T cells from CTRL2

description: normal


title: CTRL5: gDNA from circulating CD04+ T cells from CTRL5

description: normal


title: HDR Pool 4 BRCA1 - Rep 3 gfp +

description:
Sample 3
pool4hdr.h5

value: gfp +


title: ANCA4_017


title: ANCA4_019


title: HDR Pool 4 BRCA1 - Rep 2 gfp +

description:
Sample 2
pool4hdr.h5


title: C57BL/6J_YF15


title: CTRL1: gDNA from circulating CD04+ T cells from CTRL1

description: normal


title: ANCA4_016


title: HDR Pool 4 BRCA1 - Rep 2 gfp -

description:
Sample 6
pool4hdr.h5


title: ANCA4_022


title: HDR Pool 4 BRCA1 - Rep 4 gfp +

description:
Sample 4
pool4hdr.h5


title: HDR Pool 4 BRCA1 - Rep 1 gfp +

description:
Sample 1
pool4hdr.h5


title: C57BL/6J_YF11


title: CTRL3: gDNA from circulating CD04+ T cells from CTRL3

description: normal


title: A549_input

city: Frederick

first: Yinling

last: Hu

state: MARYLAND

address: NCI/CIP, Building 567, 1050 Boyles  St.

department: NCI

institute: NIH

data_processing:
Basecalls performed using RTA 2.4.6.
Samples were trimmed for adapters using trimmomatic software Trimmomatic 0.36 before the alignment.
ChIP-seq reads were aligned to the hg38 genome assembly using Bowtie2 2.2.6.
Library complexity is measured by uniquely aligned reads using picard’s (Picard 2.4.1) markduplicate utility.
wig files were generated using deeptools;Scores represent RPKM
Genome_build: hg38
Supplementary_files_format_and_content: bigwig

source_name: A549 cells

growth_protocol: A549 cells were cultured in DMEM medium supplemented with with 10% FBS. Cells were routinely generated by re-plating d 3 cultures(typically 1 × 10e6 cells into a 10cm dish).

extract_protocol:
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with IKKα antibody.
ChIP-seq samples were pooled and sequenced on NextSeq using TruSeq ChIP Library Prep Kit (IP-202- 1012).

value: epithelial

tag: chip antibody


title: C57BL/6J_YF13

value: F


title: C57BL/6J_YF12


title: ANCA4_015


title: FeSO4 Treg cells rep2

city: Xihu District, Hangzhou

first: Xing

last: Chang

state: Zhejiang

address: No.18 Shilongshan Road Cloud Town

department: School of Life Sciences

institute: Westlake University

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence by using Trim Galore v0.6.7, and masked for low-complexity or low-quality sequence, then mapped to mm10 whole genome using STAR v2.7.9a.
Sequence reads count is calculated using featureCounts
Genome_build: mm10
Supplementary_files_format_and_content: Raw_gene_counts_matrix.txt

source_name: Tregs differentiation in vitro

growth_protocol: iTreg differentiation condition medium :anti-IL4 (5 ug/mL), anti-IFNγ (5 ug/mL; R46A2), rhIL2 (100 U/mL, Peprotech) and 5 ng/mL rhTGF-β(RD systems).

extract_protocol:
Total RNA was isolated with RNeasy plus kit (Qiagen, CA)
RNA libraries were prepared for sequencing using standard Illumina protocols

value: spleen

value: FeSO4 (50 μM)  for 4 days


title: ANCA4_013


title: A549_IKKα

value: IKKα (14A231, Novus)


title: C57BL/6J_Y8

value: Control diet


title: FeSO4 Treg cells rep1


title: ANCA4_003

value: Kidney


title: C57BL/6J_YF18


title: volunteer 31

type: RNA

city: Granada

first: Julio

middle: Ramon

last: Plaza Diaz

state: Granada

address: Avda. del Conocimiento s/n

department: Biochemistry and Molecular Biology II

country: Spain

institute: University of Granada

hyb_protocol: Following fragmentation, 5,5 µg of cDNA were hybridized using the GeneChip Hybridization, Wash and Stain kit from Affymetrix

scan_protocol: GeneChips were scanned using the GeneTitan™ from Affymetrix

data_processing: The data were analyzed with the Command Console (AGCC 3.1, Affymetrix®) and the Expression Console (EE 1.1, Affymetrix®)

label: biotin

source_name: Muscle biopsies

label_protocol: The label process was performed using he WT Terminal Labeling kit de Affymetrix with deoxynucleotidyl transferase linked to biotin

extract_protocol:
RNA extraction was performed using the RNeasy Mini kit and Qiacube system according to the manufacturer's instructions.
1.3 µg of total RNA was utilized in the cDNA synthesis with theOne Cycle cDNA Synthesis kit de Affymetrix according to the manufacturer's instructions.
The resulting cDNA was fragmented using Uracil DNA Glycosylase) and APE1 (Apurinic/apyrimidinic endonuclease 1)

treatment_protocol: A total of five children with obesity and five normal-weight children undergoing abdominal elective surgery were selected. RNA was extracted from muscle tissue biopsies.

value: rectus femoris

value: female

tag: age

tag: phenotype

value: healthy children


title: C57BL/6J_Y5

value: heart


title: C57BL/6J_Y7


title: Mock Treg cells rep2

value: PBS  for 4 days


title: ANCA4_002

value: ANCA


title: ANCA4_014


title: volunteer 29

value: male


title: cervical lymph node CD8 transferred rep4

city: Toulouse

first: Leila

last: Khajavi

address: TOULOUSE

country: France

institute: INSERM

data_processing:
Library preparation and RNA-sequencing were performed by the Genomics Facility Basel in Zurich using an Illumina HiSeq 2500, generating 75-bp single-end reads.
Sequences were quality checked using FastQC (V0.11.2) and FastqScreen (V0.11.4)
alignment with STAR (V2.4.0i)
featureCounts (V1.4.5-p1) and PicardTools (V2.17.3) were used to assess the mapping quality
RSEM (V1.3.0) was used to generate the expression matrix
analysis performed in Rstudio (R V3.4.4, BioConductor V3.6)
DESeq2 (V1.24.0) was used  to identify the differentially expressed genes (DEGs).
contrast for differential expression: Hypothalamus CD4 transferred vs Spleen CD4 transferred
contrast for differential expression: Hypothalamus CD8 transferred vs Spleen CD8 transferred
Genome_build: Mus musculus primary genome sequence (Gencode: GRCm38.p5, release M16)
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample generated using RSEM
Supplementary_files_format_and_content: Tab-delimited text files including raw values per sample
Supplementary_files_format_and_content: differential expression matrix for Hypothalamus vs Spleen CD4 transferred
Supplementary_files_format_and_content: differential expression matrix for Hypothalamus vs Spleen CD8 transferred

source_name: cervical lymph node

extract_protocol:
Orex-HA mice were immunized intramuscularly with Pandemrix® vaccine 1 day after the adoptive transfer of naïve (CD45.1+CD62L+CD25-) HA-specific CD4+ and CD8+ T cells. At day 14 post-vaccination, endogenous (CD45.1-) and transferred HA-specific (CD45.1+) populations of CD44highCD62LlowCD4+ and CD44highCD62LlowCD8+ T cells were isolated from spleens, cervical lymph nodes and hypothalami by FACS sorting in 4 independent experiments involving 20 to 30 mice each.   Total RNA was extracted from the sorted cells using RNeasy Micro Kit (Quiagen). RNA quality and quantity was checked by Eukaryote Total RNA Pico assay (Agilent) and validated with a RIN > 7. Library preparation and RNA-sequencing were performed by the Genomics Facility Basel in Zurich using an Illumina HiSeq 2500, generating 75-bp single-end reads.   Sequences were quality checked using FastQC (version V0.11.2) and FastqScreen (version V0.11.4) prior to aligning to the Mus musculus primary genome sequence (Gencode: GRCm38.p5, release M16) using STAR (version V2.4.0i). FastQC, featureCounts (V1.4.5-p1) and PicardTools (version V2.17.3) were used to assess the mapping quality. RSEM (V1.3.0) was used to generate the expression matrix that was then analyzed with DESeq2 (R version V3.4.4, BioConductor version V3.6) to identify the differentially expressed genes (DEGs).
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Orex-HA

value: cervical lymph node

tag: sample type

value: transferred


title: C57BL/6J_Y3

value: M


title: C57BL/6J_Y6


title: Mock Treg cells rep1


title: volunteer 15


title: ANCA4_001


title: volunteer 14


title: volunteer 33


title: cervical lymph node CD8 transferred rep3

tag: cell type


title: cervical lymph node CD8 transferred rep1


title: S21N

city: Shen Zhen

first: Kang

last: Wu

state: Guang Dong

address: 47 Youyi Road, Luohu District

department: Urology

institute: The Third Affiliated Hospital of Shenzhen University (LuoHu Hospital Group)

data_processing:
Basecalls performed using CASAVA version 1.8
Umi-tools was utilized to calculate the raw counts and cell whitelist by default parameter
1. We applied the Seurat [https://satijalab.org/seurat/] package for cell normalization and cell filtering considering the MT percentage, minimum and maximum gene numbers under following criteria:
 MT% < 20%;
 Cell Gene Number < 5000;
 Cell Gene Number > 200.
PCA and tSNE analysis was used for the single cell to cell relation description. The fastMNN function  (k = 5, d = 50, approximate = TRUE, auto.order = TRUE) from R package scran (v1.10.2) was used to apply mutual nearest neighbor method to correct for batch effect among samples.  Graphcluster was utilized for cell clustering and based on the marker gene achieved some cluster was combined. Wilcox rank sum test was then used for marker gene analysis.
Genome_build: GRCh38
Supplementary_files_format_and_content: whitelist.list file and counts.tsv.gz file contain counts for each barcode and gene

source_name: healthy bladder tissue

extract_protocol:
Cells from each sample were used for single-cell isolation using BD Rhapsody Single-Cell Analysis System (BD Biosciences). Before single-cell isolation, all cells were labeled using a BD Single-Cell Multiplexing Kit.
Sequencing libraries were conducted using the BD Rhapsody Single-Cell Analysis System (BD Biosciences), following the manufacture's protocol.

treatment_protocol: Collagenase digestion in DMEM medium with 2% BSA

value: bladder

value: healthy bladder


title: cervical lymph node CD8 transferred rep2


title: S21T

source_name: bladder cancer tissue

value: bladder cancer


title: C57BL/6J_Y2


title: S13N


title: S13T


title: C57BL/6J_Y1


title: cervical lymph node CD8 endogenous rep4

value: endogenous


title: volunteer 24

value: children with obesity


title: Cd34+ isolated cells [sample_51]

city: Lund

first: Kenichi

last: Miharada

address: Klinikgatan 17

country: Sweden

institute: Lund University

data_processing:
Demultiplexing: organizing the FASTQ files based on the sample index information, and generating the statistics and reporting files. This task was performed using the bcl2fastq2 software with default settings.
Read Mapping: alignment of reads to a specified reference genome. This task was performed using the STAR software, and the reference genome sequence was from the Ensemble database, the Human GRCh38 primary assemply, and the annotation (GTF) from gencode version 33. Data is sorted by genomic coordinate.
Expression counts: assembly of the alignments into full transcripts and quantification of the expression levels of each gene and transcript. This task was performed using the featureCounts software.
FPKM calculation: Raw gene counts were transformed to FPKM using in-house python scrip
MultiQC: Summarizing statistics from demultiplexing, raw QC, read mapping, and expression counts
Differential expression analysis: Exploratory analysis was done in R, using the DESeq2 library.
Genome_build: GRCh38
Supplementary_files_format_and_content: Tab delimited DESeq2 result file comparing donor grouped on erythroid differentiation potential

source_name: Cord blood

extract_protocol:
RNeasy kit (QIAGEN)
Protocol: SMARTer® Stranded Total RNA-Seq Kit v2 – Pico Input Mammalian User Manual (063017). RNA Fragmentation time is 4 minutes and PCR2-Final RNA-Seq Library Amplification is 15-16 PCR cycles depends on RNA input.  Reagent/kit: SMARTer® Stranded Total RNA-Seq Kit v2 – Pico Input Mammalian Components (634418, Takara Bio USA, Inc.) Index: SMARTer® RNA Unique Dual Index Kit – 96U Set A (634452, Takara Bio USA, Inc.) Sequencing: NovaSeq 6000 System (20012850, Illumina)

value: Cd34+ isolated cells

value: Cord blood

tag: treatment

value: Healthy donor

tag: group based on erythroid potential

value: GroupA

value: Male


title: volunteer 26

tag: tissue

value: rectus femoris


title: cervical lymph node CD8 endogenous rep3

tag: strain


title: volunteer 13

tag: Sex


title: 12-ZBP1_pIC

city: Boston

first: Alexander

last: Poltorak

state: Massachusetts

address: 150 Harrison avenue

institute: Tufts University

description: mRNA

data_processing:
The resulted data were demultiplexed using CASAVA version 1.4.
Tophat2 alignment of raw paired reads to mm10 genome.
Cuffdiff
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: genes.fpkm_tracking: Tab-delimited text file includes FPKM values.

source_name: mouse macrophages

extract_protocol:
RNA was prepared according to manufacturer's instructions.
Libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit (Part# 0801-0303). Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (32 to 52 exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation DNA was PCR amplified with Illumina primers for 15 cycles and library fragments of ~250 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Genome Analyzer following the manufacturer's protocols.
Paired mRNA library.

tag: genotype

value: macrophages

value: poly I:C, 10 ng/ml, 4 hours


title: volunteer 11

value: male


title: Cd34+ isolated cells [sample_48]

tag: gender


title: C57BL/6J_YF7

value: F

value: heart

value: Control diet


title: 10-ZBP1_unst

description: mRNA

value: Unstimulated


title: Cd34+ isolated cells [sample_40]


title: 11-ZBP1_LPS

description: mRNA

value: LPS, 10 ng/ml, 4 hours


title: Cd34+ isolated cells [sample_31]

value: Female


title: C57BL/6J_YF6


title: cervical lymph node CD8 endogenous rep2

value: Orex-HA

value: cervical lymph node

value: endogenous


title: C57BL/6J_Y4

value: M


title: C57BL/6J_YF5


title: cervical lymph node CD8 endogenous rep1


title: cervical lymph node CD4 transferred rep4

value: transferred


title: 8-Myd88_LPS

description: mRNA


title: Cd34+ isolated cells [sample_27]

value: Cd34+ isolated cells

value: Cord blood

value: Healthy donor

value: GroupB


title: C57BL/6J_YF4


title: 7-MyD88_unst

description: mRNA

value: macrophages


title: volunteer 23

value: rectus femoris

value: male

value: children with obesity


title: Cd34+ isolated cells [sample_19]

value: Male


title: Cd34+ isolated cells [sample_18]


title: C57BL/6J_YF8

value: F

value: heart

value: Control diet


title: C57BL/6J_YF3


title: cervical lymph node CD4 transferred rep2

value: Orex-HA


title: 6-TRIF_pIC

description: mRNA

value: TRIF-KO

value: poly I:C, 10 ng/ml, 4 hours


title: 4-TRIF_unst

description: mRNA

value: Unstimulated


title: cervical lymph node CD4 transferred rep1

value: cervical lymph node

value: transferred


title: cervical lymph node CD4 endogenous rep4

value: endogenous


title: 9-MyD88_pIC

description: mRNA


title: cervical lymph node CD4 endogenous rep3


title: Cd34+ isolated cells [sample_13]

value: Cd34+ isolated cells

value: Cord blood

value: Healthy donor

value: GroupA


title: Cd34+ isolated cells [sample_14]

value: GroupB


title: 3-B6_pIC

description: mRNA

value: WT

value: macrophages


title: cervical lymph node CD4 endogenous rep2


title: Cd34+ isolated cells [sample_9]

value: Male


title: Cd34+ isolated cells [sample_8]


title: 2-B6_LPS

description: mRNA

value: LPS, 10 ng/ml, 4 hours


title: cervical lymph node CD4 transferred rep3


title: C57BL/6J_YF2

value: F

value: heart

value: Control diet


title: Cd34+ isolated cells [sample_16]


title: 5-TRIF_LPS

description: mRNA

value: TRIF-KO


title: Isotype_3

city: Indianapolis

first: Rakshin

last: Kharwadkar

state: Indiana

address: 635 Branhill Dr., 418 MS building

department: Microbiology and Immunology

institute: Indiana University School of Medicine

description:
Single cell
A single cell suspension of total lung cells was generated from mouse that was treated with isotype (100 μg/ml, i.n.) anitody during the recall challenge in Aspergillus fumigatus induced recall model. Cells were then loaded onto the 10X Genomics Chromium platform.

data_processing:
CellRanger 3.0.2 (http://support.10xgenomics.com/) was utilized to process the raw sequence data generated. Briefly, CellRanger used bcl2fastq (https://support.illumina.com/) to demultiplex raw base sequence calls generated from the sequencer into sample-specific FASTQ files. The FASTQ files were then aligned to the mouse reference genome mm10 with RNAseq aligner STAR. The aligned reads were traced back to individual cells and the gene expression level of individual genes were quantified based on the number of UMIs (unique molecular indices) detected in each cell. The filtered feature-cell barcode matrices generated by CellRanger were used for further analysis.
The R package Seurat development version 3.1.0 (Satija et al. 2015; Butler et al. 2018; Stuart et al. 2018) is used for the follwoing analyses. This includes cell type/state discovery with graph-based clustering, cell cluster marker gene identification, and various visualization.
A QC metrics of library size, nuber of features/genes, and mitochondrial reads (based on median-absolute-deviation (MAD), 3 MAD used here) is calculated with scater (McCarthy et al. 2017). This together with the QC analysis in Seurat are used to determine the parameters used for excluding low quality cells.
Genome_build: mm10

source_name: Total Lung cells_Isotype_3

extract_protocol:
Lung total cells were used.
Chromium™ Single Cell 3’ Library & Gel Bead Kit V3, 4 rxns PN-120267, Chromium™ Single Cell A Chip Kit, 16 rxns PN-1000009, Chromium™ i7 Multiplex Kit, 96 rxns PN-120262
28 bp of cell barcode and UMI sequences and 91 bp RNA reads were generated with Illumina NovaSeq 6000 at CMG of Indiana University School of Medicine.

treatment_protocol: Cells are from Aspergillus fumigatas induced allergic lung inflammation mice in recall model, that received intranasal treatment of isotype or anti-IL-9 antibody during the recall challenge.

value: Lung

value: total lung cells


title: Anti-IL-9_2

description:
Single cell
A single cell suspension of total lung cells was generated from mouse that was treated with anti-IL-9 (100 μg/ml, i.n.) anitody during the recall challenge in Aspergillus fumigatus induced recall model. Cells were then loaded onto the 10X Genomics Chromium platform.

source_name: Total Lung cells_anti-IL-9_2


title: cervical lymph node CD4 endogenous rep1

value: Orex-HA

value: cervical lymph node


title: Anti-IL-9_1

source_name: Total Lung cells_anti-IL-9_1


title: Spleen CD8 transferred rep1

source_name: spleen

value: spleen

value: transferred


title: Isotype_2

source_name: Total Lung cells_Isotype_2


title: ST2_neg_1_snATAC-seq

description:
Single nuclei
ST2- CD4+ total lung cells were sorted from Aspergillus fumigatus challenged mice in the recall model. Lung ST2+ CDt+ cells were pooled and then loaded onto the 10X Gennomics Chromium platform

data_processing:
cellranger-atac v1.1.0 (http://support.10xgenomics.com/) was utilized to process the raw sequence data generated. The filtered barcode-peak matrices and fragment file generated by CellRanger were used for further analysis.
The R package Seurat version 3.1.0 (Satija et al. 2015; Butler et al. 2018; Stuart et al. 2019) and Signac 0.1.6 are used for further analyses.
Genome_build: mm10

source_name: Lung ST2- CD4+ T cells

extract_protocol:
Lung total ST2 positive and ST2 negative CD4 T cells were isolated by FACS sorting.
Single cell ATAC-seq experiment is conducted using the Chromium single cell system (10x Genomics, Inc) and the NovaSeq 6000 sequencer (Illumina, Inc). (Chromium single cell ATAC Kit., 16 rxns. PC100110)
16 bp of cell barcode, and 49 bp paired-end reads were generated with Illumina NovaSeq 6000 at CMG of Indiana University School of Medicine

treatment_protocol: Cells are from Aspergillus fumigatas induced allergic lung inflammation mice in recall model.

value: ST2- CD4 T cells


title: 1-B6_unst

description: mRNA

value: Unstimulated


title: ST2_pos_2_snATAC-seq

description:
Single nuclei
ST2+ CD4+ total lung cells were sorted from Aspergillus fumigatus challenged mice in the recall model. Lung ST2+ CDt+ cells were pooled and then loaded onto the 10X Gennomics Chromium platform

source_name: Lung ST2+ CD4+ T cells

value: ST2+ CD4 T cells


title: ST2_pos_1_snATAC-seq


title: ST2_neg_2_scRNA-seq

description:
Single cell
ST2- CD4+ total lung cells were sorted from Aspergillus fumigatus challenged mice in the recall model. Lung ST2+ CDt+ cells were pooled and then loaded onto the 10X Gennomics Chromium platform

extract_protocol:
Lung total ST2 positive and ST2 negative CD4 T cells were isolated by FACS sorting.
Chromium™ Single Cell 3’ Library & Gel Bead Kit V3, 4 rxns PN-120267, Chromium™ Single Cell A Chip Kit, 16 rxns PN-1000009, Chromium™ i7 Multiplex Kit, 96 rxns PN-120262
28 bp of cell barcode and UMI sequences and 91 bp RNA reads were generated with Illumina NovaSeq 6000 at CMG of Indiana University School of Medicine.


title: Spleen CD8 transferred rep2


title: Spleen CD8 endogenous rep2

value: endogenous


title: Spleen CD8 endogenous rep3


title: Isotype_1

source_name: Total Lung cells_Isotype_1


title: Spleen CD8 transferred rep3


title: ST2_neg_2_snATAC-seq


title: Spleen CD8 transferred rep4


title: Spleen CD8 endogenous rep4


title: ST2_neg_1_scRNA-seq


title: Anti-IL-9_3

source_name: Total Lung cells_anti-IL-9_3


title: Cd34+ isolated cells [sample_3]

value: Cd34+ isolated cells

value: Cord blood

value: Healthy donor

value: GroupB


title: ST2_pos_2_scRNA-seq

description:
Single cell
ST2+ CD4+ total lung cells were sorted from Aspergillus fumigatus challenged mice in the recall model. Lung ST2+ CDt+ cells were pooled and then loaded onto the 10X Gennomics Chromium platform


title: Spleen CD8 endogenous rep1


title: Spleen CD4 transferred rep4


title: Spleen CD4 transferred rep3


title: ST2_pos_1_scRNA-seq


title: Spleen CD4 transferred rep2


title: Spleen CD4 endogenous rep4


title: Spleen CD4 transferred rep1


title: wild-type_treated_4 [WT_TCPOBOP_rep4]

city: Odense

first: Lars

last: Grøntved

address: Campusvej 55

department: Biochemistry and Molecular Biology

country: Denmark

institute: University of Southern Denmark

data_processing:
Aligned to mouse genome (mm10) using STAR and differential expression analyzed by DESeq2.
Genome_build: mm10
Supplementary_files_format_and_content: RNAseq count matrix

extract_protocol:
Livers were snap-frozen and RNA was later isolated using Trizol reagent.
1 µg of total RNA was used for sequencing. mRNA was isolated using polydT enrichment according to the manufacturer’s instructions (Illumina), followed by cDNA library preparation using the NEBNext RNA library prep kit for Illumina.

treatment_protocol: 48 hours TCPOBOP treatment (2 afministrations after 24 hour, 3mg/kg, n=4)

value: C57BL/6 Ntac

value: TCPOBOP 3mg/kg

value: liver


title: wild-type_treated_1 [WT_TCPOBOP_rep1]


title: wild-type_control_4 [WT_veh_rep4]

value: vehicle (2% DMSO in corn oil)


title: wild-type_treated_3 [WT_TCPOBOP_rep3]


title: wild-type_treated_2 [WT_TCPOBOP_rep2]


title: Spleen CD4 endogenous rep3


title: Spleen CD4 endogenous rep2


title: wild-type_control_3 [WT_veh_rep3]


title: Spleen CD4 endogenous rep1


title: Rhesus endometrium, Day 2 Post-Ovulation (Group 2a)_4

city: New Delhi

first: Debabrata

middle: Government

last: Ghosh

state: DELHI

address: Ansari Nagar, New Delhi

department: Physiology

country: India

institute: All India Institute of Medical Sciences-Delhi

description: Rhesus monkey whole genome expression microarray of endometrium obtained on day 2 after ovulation in  non-mated normo-ovulatory cycles in rhesus monkeys

hyb_protocol: 1.5 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 250 ml containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 250 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Human Genome Oligo Microarrays for 17 hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 1x44k array slides (Scan Area 61x21.6 mm, Scan resolution 5 um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 10.7.3.1 (Agilent) using default parameters (protocol GE1-v1_91) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

organism: Macaca mulatta

source_name: Endometrium, day 2, after ovulation, replicate 4

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 200 ng total RNA using the One-Color Low TOTAL RNA Input Linear Amplification kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification.  Dye incorporation and cRNA yield were checked with the NanoDrop ND-2000 Spectrophotometer.

extract_protocol: RNA was prepared using Trizol reagent.  The protocol includes brief homogenisation using polytron homogeniser, followed by phase seperation by chloroform and precipitation using iso-propanol. This was followed by washing by 75% ethanol and elution in nuclease-free waster. Total RNA was quantified using a NanoDrop-2000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer.

value: Endometrium

value: Female

tag: group

value: post-ovulation

tag: day


title: Rhesus endometrium, Day 2 Post-Ovulation (Group 2b)_1

description: Rhesus monkey whole genome expression microarray of endometrium obtained on day 4 after ovulation in  non-mated normo-ovulatory cycles in rhesus monkeys

source_name: Endometrium, day 4, after ovulation, replicate 1


title: Rhesus endometrium, Day 2 Post-Ovulation (Group 2c)_2

description: Rhesus monkey whole genome expression microarray of endometrium obtained on day 6 after ovulation in  non-mated normo-ovulatory cycles in rhesus monkeys

source_name: Endometrium, day 6, after ovulation, replicate 2


title: Rhesus endometrium, Day 2 Post-Ovulation (Group 2c)_4

source_name: Endometrium, day 6, after ovulation, replicate 4


title: Rhesus endometrium, Day 2 Post-Ovulation (Group 2b)_2

source_name: Endometrium, day 4, after ovulation, replicate 2


title: Rhesus endometrium, Day 2 Post-Ovulation (Group 2c)_3

source_name: Endometrium, day 6, after ovulation, replicate 3


title: Rhesus endometrium, Day 6 Post-Fertilization (Group 1c)_3

description: Rhesus monkey whole genome expression microarray of endometrium obtained on day 6 after ovulation in mated, proven conception cycles in rhesus monkeys

source_name: Endometrium, day 6, post fertilization, replicate 3

value: post-fertilization


title: Rhesus endometrium, Day 2 Post-Ovulation (Group 2b)_3

source_name: Endometrium, day 4, after ovulation, replicate 3


title: Rhesus endometrium, Day 2 Post-Ovulation (Group 2a)_2

source_name: Endometrium, day 2, after ovulation, replicate 2


title: Rhesus endometrium, Day 2 Post-Ovulation (Group 2a)_3

source_name: Endometrium, day 2, after ovulation, replicate 3


title: Rhesus endometrium, Day 2 Post-Ovulation (Group 2a)_1

source_name: Endometrium, day 2, after ovulation, replicate 1


title: Rhesus endometrium, Day 2 Post-Ovulation (Group 2c)_1

source_name: Endometrium, day 6, after ovulation, replicate 1


title: Rhesus endometrium, Day 2 Post-Ovulation (Group 2b)_4

source_name: Endometrium, day 4, after ovulation, replicate 4


title: Hypothalamus CD8 transferred rep4

source_name: hypothalamus

value: Orex-HA

value: hypothalamus

value: transferred


title: Rhesus endometrium, Day 6 Post-Fertilization (Group 1c)_4

source_name: Endometrium, day 6, post fertilization, replicate 4


title: Rhesus endometrium, Day 6 Post-Fertilization (Group 1c)_1

source_name: Endometrium, day 6, post fertilization, replicate 1


title: Hypothalamus CD8 transferred rep2


title: Rhesus endometrium, Day 6 Post-Fertilization (Group 1c)_2

source_name: Endometrium, day 6, post fertilization, replicate 2


title: Hypothalamus CD8 transferred rep1


title: wild-type_control_1 [WT_veh_rep1]


title: humanized_treated_2 [hCAR_TCPOBOP_rep2]

value: humanized PXR-CAR-CYP3A4/3A7


title: Hypothalamus CD8 transferred rep3


title: humanized_treated_4 [hCAR_TCPOBOP_rep4]


title: humanized_treated_3 [hCAR_TCPOBOP_rep3]


title: Hypothalamus CD8 endogenous rep4

value: endogenous


title: Rhesus endometrium, Day 4 Post-Fertilization (Group 1b)_3

description: Rhesus monkey whole genome expression microarray of endometrium obtained on day 4 after ovulation in mated, proven conception cycles in rhesus monkeys

source_name: Endometrium, day 4, post fertilization, replicate 3


title: humanized_treated_1 [hCAR_TCPOBOP_rep1]


title: Rhesus endometrium, Day 4 Post-Fertilization (Group 1b)_1

source_name: Endometrium, day 4, post fertilization, replicate 1


title: Rhesus endometrium, Day 4 Post-Fertilization (Group 1b)_2

source_name: Endometrium, day 4,post fertilization, replicate 2


title: Hypothalamus CD8 endogenous rep3


title: humanized_control_4 [hCAR_veh_rep4]


title: Rhesus endometrium, Day 4 Post-Fertilization (Group 1b)_4

source_name: Endometrium, day 4, post fertilization, replicate 4


title: humanized_control_3 [hCAR_veh_rep3]


title: wild-type_control_2 [WT_veh_rep2]


title: humanized_control_2 [hCAR_veh_rep2]


title: Hypothalamus CD4 transferred rep4


title: BCL2L11_rep2_Experiment_11 [LIB6_12]

city: Milano

first: Francesco

last: Nicassio

address: Via Adamello 16

department: Center for genomic science

institute: Istituto Italiano di Tecnologia

description: processed data file: Library_6.xlsx

data_processing:
FASTQ data were trimmed using cutadapt-1.9.1; then trimmed data was aligned to custom sequence libraries listing all isoforms of small RNA molecules by using Bowtie with --best and -v 0 switches and saved in .map output format.
Isomirage software was used to count the number of occurrences in the .map file of each isoform listed in the .genome file
Genome_build: hg19
Supplementary_files_format_and_content: Excel Spreadsheet containing raw counts for miRNA, including isoforms

source_name: HeLa Cells_72 hrs after transfection of TDMD constuct_BCL2L11

growth_protocol: DMEM + 10% FBS

extract_protocol:
Total RNA, including microRNAs, was isolated through the miRNeasy mini kit (Qiagen).
1000 nanograms of total RNA were used to prepare Small RNA libraries following the Illumina TruSeqTM Small RNA kit instructions

treatment_protocol: Transfection by Lipofectamine 3000 of PCDNA 3.1 vectors containing indicated MDEs

tag: cell line

value: HeLa

tag: library

tag: experiment

tag: tdmd construct

tag: miRNA family

tag: time point

value: 72 hours after transfection of TDMD constuct

tag: molecule subtype

value: small RNA


title: C22_AQRKD2_rep3

city: Providence

first: William

last: Fairbrother

state: RI

address: 70 Ship St, Box G

department: Molecular Biology, Cell Biology and Biochemistry

institute: Brown University

data_processing:
Reads originating from lariats were identified in the sequenced reads using an implementation of the branchpoint detection algorithm described in Pineda and Bradley (2018)
Genome_build: hg19
Supplementary_files_format_and_content: BED - each mapped lariat read is listed with the start and end coordinates being the 5' splice site and branchpoint (or vice versa if the the lariat maps to the negative strand); additionally, the read ID, inferred branchpoint nucleotide, and nearest 3' splice site are listed in the name field

source_name: HEK293T cells

growth_protocol: DMEM media +10% FBS with 1% pen-strep, 5% CO2, 37 deg. C

extract_protocol:
Trizol
Illumina with rRNA depletion

value: transfection of AQR-targeting siRNA Thermo s18726


title: C22_AQRKD2_rep1


title: Hypothalamus CD8 endogenous rep1

tag: cell type

tag: sample type


title: Hypothalamus CD4 transferred rep3


title: BCL2L11_rep1_Experiment_11 [LIB6_11]

description: processed data file: Library_6.xlsx


title: 321XYF

city: Oklahoma City

first: Michael

last: Stout

state: OK

address: 825 N.E. 13th Street

department: Aging and Metabolism

institute: Oklahoma Medical Research Foundation

description: whole genome oxidative bisulfite sequncing

data_processing:
Before aligning, paired-end reads were adaptor-trimmed and filtered using Trimmomatic 0.35. End-trimming removed leading and trailing bases with Q-score<25, cropped 4 bases from the start of the read, dropped reads less than 25 bases long, and dropped reads with average Q-score<25. Unpaired reads after trimming were not considered for alignment.
Alignment of trimmed OxBS-converted sequences was carried out using Bismark 0.16.3 with Bowtie 2 against the mouse reference genome (GRCm38/mm10). Bams were de-duplicated using Bismark.
Methylation call percentages for each CpG and non-CpG (CH) site within the genome were calculated by dividing the methylated counts over the total counts for that site in the oxidative bisulfite - converted libraries (OXBS). Genome-wide CpG and CH methylation levels were calculated separately.
BAM files generated during alignment were run through MethylKit in R to generate context-specific (CpG/CH) coverage text files.
Genome_build: mm10
Supplementary_files_format_and_content: CpG/CHG/CHH coverage txt files

source_name: hippocampus

growth_protocol: All animal procedures were approved by the Institutional Animal Care and Use Committee at the University of Alabama at Birmingham (UAB) under protocol 21506. Four Core Genotypes mice on a C57Bl/6J background were obtained from the Jackson Laboratory where they were revitalized from frozen embryo stocks. Breeder pairs were set up with a XX female and a XY male. Pups were weaned into sex specific cages of 4-5 animals based on visual inspection of genitalia. Animals were maintained in an AAALAC approved UAB animal facility at 21°C on a 12/12 light/dark cycle (lights on at 6:00am). Animals were provided ad libitum water and standard mouse chow (NIH31) until time of tissue collection, ~12 months of age for both males and females. Euthanasia prior to tissue harvesting was carried out by cervical dislocation followed by rapid decapitation.

extract_protocol:
Hippocampi were dissected from XXF, XXM, XYF, and XYM FCG mice (n=3/group), snap frozen in microfuge tubes with liquid nitrogen, and stored at -80ºC prior to DNA isolation. Nucleic acids (DNA/RNA) were isolated from flash-frozen tissues using the All Prep DNA/RNA Mini Kit (Qiagen, Germantown, MD).
Whole genome oxidative bisulfite sequencing libraries were prepared according to manufacturers guidelines (Ovation Ultralow Methyl-Seq Library System, Tecan Genomics, Inc., Redwood City, CA).
Whole Genome Oxidative Bisulfite Sequencing (WGoxBS-Seq)

tag: animal number

tag: sex chromosome

value: XY

tag: gonad

value: ovaries


title: C22_AQRKD2_rep2

tag: treatment


title: humanized_control_1 [hCAR_veh_rep1]

tag: strain

tag: tissue

value: liver


title: 325XXF

value: XX


title: Rhesus endometrium, Day 2 Post-Fertilization (Group 1a)_4

description: Rhesus monkey whole genome expression microarray of endometrium obtained on day 2 after ovulation in mated, proven conception cycles in rhesus monkeys

source_name: Endometrium, day 2, post fertilization, replicate 4

value: Endometrium

tag: gender

tag: group


title: Hypothalamus CD4 endogenous rep4


title: Hypothalamus CD4 transferred rep2


title: Mutated_CRKL_Control_rep2_Experiment_11 [LIB6_10]

description: processed data file: Library_6.xlsx

source_name: HeLa Cells_72 hrs after transfection of TDMD constuct_Mutated_CRKL_Control

tag: cell line

value: negative control


title: HEK293T_AQRKD2_rep3

tag: genotype

value: wild type


title: Rhesus endometrium, Day 2 Post-Fertilization (Group 1a)_2

source_name: Endometrium, day 2, post fertilization, replicate 2

value: Female

value: post-fertilization

tag: day


title: Rhesus endometrium, Day 2 Post-Fertilization (Group 1a)_1

source_name: Endometrium, day 2, post fertilization, replicate 1


title: 320XYF


title: Hypothalamus CD8 endogenous rep2

value: Orex-HA

value: hypothalamus


title: Hypothalamus CD4 endogenous rep3


title: Mutated_CRKL_Control_rep1_Experiment_11 [LIB6_9]

description: processed data file: Library_6.xlsx

tag: library

tag: experiment

tag: tdmd construct


title: 319XYM

value: testes


title: HEK293T_AQRKD2_rep1


title: Scrambled_Control_rep2_Experiment_11 [LIB6_8]

description: processed data file: Library_6.xlsx

source_name: HeLa Cells_72 hrs after transfection of TDMD constuct_Scrambled_CRKL_Control

tag: miRNA family

tag: time point

tag: molecule subtype


title: Hypothalamus CD4 endogenous rep2

tag: cell type

tag: sample type

value: endogenous


title: Hypothalamus CD4 endogenous rep1


title: 318XYM

tag: animal number

tag: sex chromosome

tag: gonad


title: Rhesus endometrium, Day 2 Post-Fertilization (Group 1a)_3

source_name: Endometrium, day 2, post fertilization, replicate 3

tag: tissue


title: Scrambled_Control_rep1_Experiment_11 [LIB6_7]

description: processed data file: Library_6.xlsx

value: HeLa


title: C22_AQRKD1_rep2

tag: treatment

value: transfection of AQR-targeting siRNA Thermo s18725


title: 312XXM


title: 311XXM


title: C22_AQRKD1_rep3


title: CRKL_rep2_Experiment_11 [LIB6_6]

description: processed data file: Library_6.xlsx

source_name: HeLa Cells_72 hrs after transfection of TDMD constuct_CRKL

value: CRKL

value: 72 hours after transfection of TDMD constuct

value: small RNA


title: CRKL_rep1_Experiment_11 [LIB6_5]

description: processed data file: Library_6.xlsx


title: 310XYM

value: XY


title: C22_AQRKD1_rep1


title: 306XYF

value: ovaries


title: Mutated_GATA6_Control_rep2_Experiment_10 [LIB6_4]

description: processed data file: Library_6.xlsx

source_name: HeLa Cells_72 hrs after transfection of TDMD constuct_Mutated_GATA6_Control


title: HEK293T_AQRKD1_rep3


title: HEK293T_AQRKD1_rep2


title: CD49a+ ILC3 - CRACR #1

city: Paris

first: Rachel

last: Legendre

address: 28, rue du docteur Roux

department: Research and Resource Center for Scientific Informatics

institute: Institut Pasteur

data_processing:
Reads were cleaned of adapter sequences and low-quality sequences using cutadapt version 1.11. Only sequences at least 25 nt in length were considered for further analysis.
STAR version 2.5.0a, with default parameters, was used for alignment on the reference genome (GRCm38 from Ensembl database)
Genes were counted using featureCounts version 1.4.6-p3 from Subreads package (parameters: -t gene -s 1)
Count data were analyzed using R version 3.3.2  and the Bioconductor package DESeq2 version 1.12.4. The normalization and dispersion estimation were performed with DESeq2 using the default parameters and statistical tests for differential expression were performed applying the independent filtering algorithm. A generalized linear model was set in order to test for the differential expression. For each pairwise comparison, raw p-values were adjusted for multiple testing according to the Benjamini and Hochberg (BH) procedure  and genes with an adjusted p-value lower than 0.05 were considered differentially expressed.
Genome_build: GRCm38 from Ensembl database version 74
Supplementary_files_format_and_content: DESeq2 output

source_name: Small intestine

extract_protocol:
Cells from each population were FACS Aria sorted directly in RNA lysis buffer. mRNA were purified using Rneasy microkit (Giagen). Qalitly and integrity were checked on Bioanalyser system (Agilent)
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Small intestines were collected from euthanized mice. Peyer’s patches were removed and intestinal epithelial cells were eliminated by shaking incubation in 0.5 mM EDTA and 1 mM Hepes (Sigma Aldrich) for 20 min at 37°C. Subsequently, the intestinal tissue was minced and incubated two times in a digestion solution containing 0.5 mg/ml collagenase VII (Sigma-Aldrich) for 20 min at 37°C in a shaking incubator to isolate the lamina propria lymphocytes (LPL). LPLs were further purified using a 40% Percoll, filtered through a 70μm nylon mesh and kept in 10% FCS RPMI

value: Small intestine

tag: reporter mouse

value: RorcGFP x Il22TdT

value: CR + Abx + CR

value: CD49a+ ILC3


title: CD49a+ ILC3 - CRACR #2


title: CD49a+ ILC3 - CRA #3

value: CR + Abx


title: Mutated_GATA6_Control_rep1_Experiment_10 [LIB6_3]

description: processed data file: Library_6.xlsx

tag: cell line

value: negative control


title: CD49a+ ILC3 - CRA #2


title: 303XXF

value: XX


title: HEK293T_AQRKD1_rep1

tag: genotype

value: wild type


title: HEK293T_AQRKD2_rep2

value: transfection of AQR-targeting siRNA Thermo s18726


title: CD49a+ ILC3 - CRA #1


title: C22_negcontrol_rep3

value: transfection of non-targeting siRNA Thermo 4390843


title: GATA6_rep1_Experiment_10 [LIB6_1]

description: processed data file: Library_6.xlsx

source_name: HeLa Cells_72 hrs after transfection of TDMD constuct_GATA6

value: HeLa


title: 296XXF


title: ACPL2_rep2_Experiment_9 [LIB5_12]

description: processed data file: Library_5.xlsx

source_name: HeLa Cells_72 hrs after transfection of TDMD constuct_ACPL2


title: CD49a+ ILC3 - CR #3

value: Citrobacter rodentium (CR)


title: CD49a+ ILC3 - CRACR #3


title: C22_negcontrol_rep2


title: Main olfactory bulb replicate 2 slide 20

city: Worcester

first: I-Hao

last: Wang

state: MA

address: 370 Sunderland Rd, Unit D24

department: PMM

institute: UMMS

data_processing:
Library strategy: Slide-seq V2
The data processing were performed as previously described (PMID: 33288904)
All the downstring analysis were processed with Seurat, the scripts can be found at https://github.com/Greerlab/OSN_2021_paper
Genome_build: mm10
Supplementary_files_format_and_content: Seruat object containing the raw and normalized count, PCA, UMAP, spatial coordinates

source_name: Main olfactory bulb

extract_protocol: The extraction and library protocol were performed as previously described (PMID: 33288904)

treatment_protocol: Male mice were euthanized according to our IACUC protocol. The anterior part of the brain containing the olfactory bulb was dissected and placed in a plastic mold filled with OCT (Sakura Finetek from VWR), The molds were then frozen with dry ice pre-chilled 2-methylbutane (Fisher Scientific). The samples were incubated in -80°C overnight prior to cryosectioning. 20 OB sections were obtained with equal spacing (130 μm) along the anterior-posterior axis. In total, two sets of 20 slides were obtained from different animals.

value: Main olfactory bulb

tag: gender

value: male


title: ACPL2_rep1_Experiment_9 [LIB5_11]

description: processed data file: Library_5.xlsx

tag: library

value: 72 hours after transfection of TDMD constuct

value: small RNA


title: Main olfactory bulb replicate 2 slide 19


title: CD49a+ ILC3 - CR #1


title: HEK293T_negcontrol_rep3


title: DIP2A_rep1_Experiment_9 [LIB5_9]

description: processed data file: Library_5.xlsx

source_name: HeLa Cells_72 hrs after transfection of TDMD constuct_DIP2A

tag: experiment


title: CD49a+ ILC3 - Control #3

value: w/o


title: CD49a+ ILC3 - Control #2

value: Small intestine


title: VEGFA_rep2_Experiment_9 [LIB5_8]

description: processed data file: Library_5.xlsx

source_name: HeLa Cells_72 hrs after transfection of TDMD constuct_VEGFA

tag: tdmd construct

value: VEGFA


title: DIP2A_rep2_Experiment_9 [LIB5_10]

description: processed data file: Library_5.xlsx

tag: miRNA family


title: Main olfactory bulb replicate 2 slide 18


title: HEK293T_negcontrol_rep2


title: GATA6_rep2_Experiment_10 [LIB6_2]

description: processed data file: Library_6.xlsx

tag: time point


title: Main olfactory bulb replicate 2 slide 16


title: CD49a+ ILC3 - Control #1

value: RorcGFP x Il22TdT


title: VEGFA_rep1_Experiment_9 [LIB5_7]

description: processed data file: Library_5.xlsx

tag: molecule subtype


title: Main olfactory bulb replicate 2 slide 17


title: 301XXM

value: testes


title: C22_untreated_rep3

value: untreated


title: HEK293T_negcontrol_rep1


title: CCR6+ ILC3 - CRACR #3

value: CR + Abx + CR

tag: cell type

value: CCR6+ ILC3


title: Main olfactory bulb replicate 2 slide 15

value: wild type


title: C22_untreated_rep2


title: CCR6+ ILC3 - CRACR #2


title: Main olfactory bulb replicate 2 slide 14


title: IQSEC_rep2_Experiment_9 [LIB5_6]

description: processed data file: Library_5.xlsx

source_name: HeLa Cells_72 hrs after transfection of TDMD constuct_IQSEC1


title: IQSEC1_rep1_Experiment_9 [LIB5_5]

description: processed data file: Library_5.xlsx


title: C22_untreated_rep1

source_name: HEK293T cells


title: CD49a+ ILC3 - CR #2

value: CD49a+ ILC3


title: CCR6+ ILC3 - CRACR #1


title: Main olfactory bulb replicate 2 slide 13


title: HEK293T_untreated_rep3


title: Perfect_TDMD_miR-106b_rep1_Experiment_9 [LIB5_4]

description: processed data file: Library_5.xlsx

source_name: HeLa Cells_72 hrs after transfection of TDMD constuct_Perfect_TDMD_miR-106b


title: C22_negcontrol_rep1

value: transfection of non-targeting siRNA Thermo 4390843


title: Scrambled_Control_rep1_Experiment_9 [LIB5_3]

description: processed data file: Library_5.xlsx

source_name: HeLa Cells_72 hrs after transfection of TDMD constuct_Scrambled_MAP3K9_Control

value: HeLa

value: negative control


title: Main olfactory bulb replicate 2 slide 12

value: Main olfactory bulb


title: CCR6+ ILC3 - CRA #3

value: CR + Abx


title: GFP_Control_rep2_Experiment_9 [LIB5_2]

description: processed data file: Library_5.xlsx

source_name: HeLa Cells_72 hrs after transfection of TDMD constuct_GFP_empty

value: 72 hours after transfection of TDMD constuct


title: CCR6+ ILC3 - CRA #2


title: CCR6+ ILC3 - CRA #1


title: HEK293T_untreated_rep1


title: Main olfactory bulb replicate 2 slide 10

value: male


title: Sample 22 RNA-seq

city: Kashiwa

first: Shogo

last: Kumagai

state: Chiba

address: 6-5-1 Kashiwanoha

country: Japan

institute: National Cancer Center

data_processing:
The prepared RNA-seq libraries underwent next-generation sequencing of 120 bp from both ends (paired-end reads) with a HiSeq2500 platform.
For expression profiling with the RNA-seq data, paired-end reads were aligned to the hg38 human genome assembly using TopHat2 (https://ccb.jhu.edu/software/tophat/index.shtml).
Genome_build: hg38
Supplementary_files_format_and_content: The expression level of each RefSeq gene was calculated from the mapped read counts using Cufflinks (http://cufflinks.cbcb.umd.edu).

source_name: gastric adenocarcinoma

extract_protocol:
Illumina TruSeq RNA Sample Prep Kit was used  for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: gastric adenocarcinoma

tag: age

value: Male

tag: histology

value: Intestinal

tag: pathological stage

value: IIB

tag: ebv infection

value: negative


title: CCR6+ ILC3 - CR #3

tag: tissue

value: Small intestine

value: RorcGFP x Il22TdT

value: Citrobacter rodentium (CR)


title: Mutated_MAP3K9_rep2_Experiment_8 [LIB4_8]

description: processed data file: Library_4.xlsx

source_name: HeLa Cells_72 hrs after transfection of TDMD constuct_Mutated_MAP3K9_Control

value: small RNA


title: GFP_Control_rep1_Experiment_9 [LIB5_1]

description: processed data file: Library_5.xlsx


title: Main olfactory bulb replicate 2 slide 11

value: wild type


title: Sample 23 RNA-seq

value: Female

value: IIIC


title: Main olfactory bulb replicate 2 slide 8


title: CCR6+ ILC3 -CR #2

tag: treatment

value: CCR6+ ILC3


title: Mutated_MAP3K9_rep1_Experiment_8 [LIB4_7]

description: processed data file: Library_4.xlsx

value: HeLa

value: negative control


title: Sample 21 RNA-seq

value: IIA


title: Main olfactory bulb replicate 2 slide 9

value: Main olfactory bulb

value: male


title: Main olfactory bulb replicate 2 slide 7


title: MAP3K9_rep2_Experiment_8 [LIB4_6]

description: processed data file: Library_4.xlsx

source_name: HeLa Cells_72 hrs after transfection of TDMD constuct_MAP3K9

value: 72 hours after transfection of TDMD constuct


title: Main olfactory bulb replicate 2 slide 6


title: Sample 19 RNA-seq

value: gastric adenocarcinoma

value: Diffuse


title: CCR6+ ILC3 - Control #3

tag: reporter mouse

value: w/o


title: Main olfactory bulb replicate 2 slide 5


title: CCR6+ ILC3 - Control #2

value: Small intestine


title: MAP3K9_rep1_Experiment_8 [LIB4_5]

description: processed data file: Library_4.xlsx

tag: cell line


title: HEK293T_untreated_rep2

value: untreated

tag: genotype


title: Sample 18 RNA-seq

tag: gender

value: Male

value: Intestinal

value: positive


title: Sample 17 RNA-seq

value: negative


title: Main olfactory bulb replicate 2 slide 4

value: wild type


title: Main olfactory bulb replicate 2 slide 3


title: C8orf58_rep1_Experiment_8 [LIB4_3]

description: processed data file: Library_4.xlsx

source_name: HeLa Cells_72 hrs after transfection of TDMD constuct_C8orf58

tag: library

value: small RNA


title: GFP_Control_rep2_Experiment_8 [LIB4_2]

description: processed data file: Library_4.xlsx

value: HeLa

tag: experiment


title: Sample 16 RNA-seq

value: IB


title: Sample 15 RNA-seq

value: Female

value: IIA


title: Main olfactory bulb replicate 2 slide 1

value: Main olfactory bulb

value: male


title: Main olfactory bulb replicate 2 slide 2


title: Perfect_TDMD_miR-26a_rep1_Experiment_7 [LIB3_12]

description: processed data file: Library_3.xlsx

source_name: HeLa Cells_72 hrs after transfection of TDMD constuct_Perfect_TDMD_miR-26a

tag: tdmd construct

value: 72 hours after transfection of TDMD constuct


title: Sample 14 RNA-seq

value: gastric adenocarcinoma

value: IIB


title: Main olfactory bulb replicate 1 slide 20


title: 323XXM

description: rRNA depleted

data_processing:
Following sequencing, reads were trimmed, aligned, differential expression statistics and correlation analyses were performed in Strand NGS software package (Agilent).
Alignment and filtering criteria included: adapter trimming, fixed 2bp trim from 5’ and 6bp from 3’ ends, a maximum number of one novel splice allowed per read, a minimum of 90% identity with the reference sequence, a maximum of 5% gap, trimming of 3’ end with Q<30.
Alignment was performed directionally with Read 1 aligned in reverse and Read 2 in forward orientation. Reads were filtered based on the mapping status and only those reads that aligned normally (in the appropriate direction) were retained. Normalization was performed with the DESeq algorithm.
Transcripts with an average read count value >20 in at least 100% of the samples in at least one group were considered expressed at a level sufficient for quantitation per tissue. Those transcripts below this level were considered not detected/not expressed and excluded, as these low levels of reads are close to background and are highly variable.
Genome_build: mm10 (RefSeq Genes and Transcripts (2013.04.01))
Supplementary_files_format_and_content: matrix of all expressed genes (txt)

source_name: hippocampus

extract_protocol:
Hippocampi were dissected from XXF, XXM, XYF, and XYM FCG mice (n=5-6/group), snap frozen in microfuge tubes with liquid nitrogen, and stored at -80ºC prior to DNA isolation. Nucleic acids (DNA/RNA) were isolated from flash-frozen tissues using the All Prep DNA/RNA Mini Kit (Qiagen, Germantown, MD).
Illumina’s TruSeq Stranded mRNA Library Prep Kit (#20020594, Illumina) was used on 500 ng of total RNA for the preparation of strand-specific sequencing libraries according to manufacturer’s guidelines. As previously described, rRNA depletion was performed prior to library construction.

tag: animal number

tag: sex chromosome

value: XX

tag: gonad

value: testes

value: hippocampus


title: 326XYM

description: rRNA depleted

value: XY


title: GFP_Control_rep1_Experiment_8 [LIB4_1]

description: processed data file: Library_4.xlsx

tag: miRNA family

value: negative control

tag: time point

tag: molecule subtype


title: CCR6+ ILC3 - CR #1

source_name: Small intestine

value: Small intestine

value: RorcGFP x Il22TdT

value: Citrobacter rodentium (CR)

tag: cell type

value: CCR6+ ILC3


title: Mutated_REEP4_Control_rep1_Experiment_7 [LIB3_11]

description: processed data file: Library_3.xlsx

source_name: HeLa Cells_72 hrs after transfection of TDMD constuct_Mutated_REEP4_Control

value: HeLa

value: small RNA


title: 321XYF

description: rRNA depleted

value: ovaries


title: Sample 20 RNA-seq

tag: age

value: Male

tag: histology

value: Intestinal

tag: pathological stage

value: IB

tag: ebv infection

value: negative


title: Sample 13 RNA-seq

tag: tissue

value: gastric adenocarcinoma

value: IIB


title: Sample 12 RNA-seq

value: Diffuse

value: IIIA


title: Scrambled_Control_rep2_Experiment_7 [LIB3_10]

description: processed data file: Library_3.xlsx

source_name: HeLa Cells_72 hrs after transfection of TDMD constuct_Scrambled_REEP4_Control

tag: cell line

value: 72 hours after transfection of TDMD constuct


title: 320XYF

description: rRNA depleted

value: XY

value: hippocampus


title: Main olfactory bulb replicate 1 slide 18

source_name: Main olfactory bulb

value: Main olfactory bulb

tag: genotype

value: wild type

tag: gender

value: male


title: Main olfactory bulb replicate 1 slide 19


title: 319XYM

description: rRNA depleted

value: testes


title: C8orf58_rep2_Experiment_8 [LIB4_4]

description: processed data file: Library_4.xlsx

value: HeLa

tag: library

tag: experiment

value: small RNA


title: YIPF4_rep2_Experiment_7 [LIB3_8]

description: processed data file: Library_3.xlsx

source_name: HeLa Cells_72 hrs after transfection of TDMD constuct_YIPF4

tag: tdmd construct


title: 318XYM

description: rRNA depleted

tag: animal number

tag: sex chromosome


title: Sample 11 RNA-seq

value: Female


title: Main olfactory bulb replicate 1 slide 17


title: CCR6+ ILC3 - Control #1

value: Small intestine

tag: reporter mouse

value: RorcGFP x Il22TdT

tag: treatment

value: w/o

value: CCR6+ ILC3


title: Scrambled_Control_rep1_Experiment_7 [LIB3_9]

description: processed data file: Library_3.xlsx

tag: miRNA family

value: negative control

tag: time point

tag: molecule subtype


title: 316XYM

description: rRNA depleted

tag: gonad


title: Main olfactory bulb replicate 1 slide 16


title: Main olfactory bulb replicate 1 slide 15


title: HGF_rep3_Experiment_7 [LIB3_6]

description: processed data file: Library_3.xlsx

source_name: HeLa Cells_72 hrs after transfection of TDMD constuct_HGF

value: HGF


title: YIPF4_rep1_Experiment_7 [LIB3_7]

description: processed data file: Library_3.xlsx


title: 322XXM

description: rRNA depleted

value: XX


title: Sample 09 RNA-seq

value: gastric adenocarcinoma

tag: age

tag: histology

value: Diffuse

tag: pathological stage

value: IV

value: negative


title: Main olfactory bulb replicate 1 slide 14

tag: tissue

value: Main olfactory bulb

value: wild type


title: 313XXF

description: rRNA depleted

value: ovaries

value: hippocampus


title: HGF_rep2_Experiment_7 [LIB3_5]

description: processed data file: Library_3.xlsx

tag: cell line

value: HeLa

value: 72 hours after transfection of TDMD constuct

value: small RNA


title: 312XXM

description: rRNA depleted

value: testes


title: Sample 07 RNA-seq

tag: gender

value: Female

tag: ebv infection


title: Main olfactory bulb replicate 1 slide 13

tag: genotype

value: male


title: 311XXM

description: rRNA depleted


title: HGF_rep1_Experiment_7 [LIB3_4]

description: processed data file: Library_3.xlsx

tag: library

tag: experiment

tag: tdmd construct


title: Sample 06 RNA-seq

value: Male

value: Intestinal

value: IIIA


title: 310XYM

description: rRNA depleted

tag: animal number

tag: sex chromosome

value: XY


title: Main olfactory bulb replicate 1 slide 12


title: Sample 05 RNA-seq

value: gastric adenocarcinoma


title: 306XYF

description: rRNA depleted


title: Main olfactory bulb replicate 1 slide 11


title: REEP4_rep2_Experiment_7 [LIB3_2]

description: processed data file: Library_3.xlsx

source_name: HeLa Cells_72 hrs after transfection of TDMD constuct_REEP4

tag: miRNA family


title: REEP4_rep1_Experiment_7 [LIB3_1]

description: processed data file: Library_3.xlsx

tag: time point


title: Sample 03 RNA-seq

value: IA


title: Main olfactory bulb replicate 1 slide 10


title: Sample 10 RNA-seq

value: IIB

value: negative


title: Main olfactory bulb replicate 1 slide 9

value: Main olfactory bulb

value: wild type


title: SERPINE1_rep1_Experiment_3 [LIB2_12]

description: processed data file: Library_2.xlsx

source_name: HeLa Cells_72 hrs after transfection of TDMD constuct_SERPINE1

tag: molecule subtype


title: Sample 02 RNA-seq

value: IIA


title: Sample 08 RNA-seq

value: Diffuse


title: 303XXF

description: rRNA depleted

value: XX

tag: gonad

value: ovaries

value: hippocampus


title: 305XYF

description: rRNA depleted


title: Mutated_PTEN_Control_rep1_Experiment_6 [LIB2_11]

description: processed data file: Library_2.xlsx

source_name: HeLa Cells_72 hrs after transfection of TDMD constuct_Mutated_PTEN_Control

value: HeLa

value: negative control

value: 72 hours after transfection of TDMD constuct

value: small RNA


title: Sample 01 RNA-seq

tag: age

value: Male

value: Intestinal


title: Main olfactory bulb replicate 1 slide 8

value: male


title: 301XXM

description: rRNA depleted

value: testes


title: Main olfactory bulb replicate 1 slide 6


title: 304XXF

description: rRNA depleted


title: Scrambled_Control_rep1_Experiment_4 [LIB2_10]

description: processed data file: Library_2.xlsx

source_name: HeLa Cells_72 hrs after transfection of TDMD constuct_Scrambled_CNKSR2_Control


title: TMEM_rep2_Experiment_6 [LIB2_9]

description: processed data file: Library_2.xlsx

source_name: HeLa Cells_72 hrs after transfection of TDMD constuct_TMEM196


title: REEP4_rep3_Experiment_7 [LIB3_3]

description: processed data file: Library_3.xlsx


title: 302XXM

description: rRNA depleted


title: Main olfactory bulb replicate 1 slide 7


title: Main olfactory bulb replicate 1 slide 5


title: Sample 04 RNA-seq

source_name: gastric adenocarcinoma

value: gastric adenocarcinoma

tag: histology

value: IA


title: RAB21_rep2_Experiment_6 [LIB2_7]

description: processed data file: Library_2.xlsx

source_name: HeLa Cells_72 hrs after transfection of TDMD constuct_RAB21


title: 298XXF

description: rRNA depleted


title: 297XYF

description: rRNA depleted

value: XY


title: Dd2_WT

city: Braga

first: Nuno

middle: S.

last: Osório

address: Campus de Gualtar

country: Portugal

institute: ICVS

data_processing:
Transcriptome datasets for both 3D7 and Dd2 were mapped against the 3D7 v3 (Böhme, U. et al., Wellcome Open Res., 2019) reference sequence using HISAT2 2-2.0.0-beta (Kim, D. et al., Nat.Biotechnol, 2019) (--rna-strandness RF --max-intronlen 5000).
Read counts were determined using HTSEQ v0.6.0 (Anders, S. et al., Oxf. Engl., 2015) (-r pos -s no). Deconvolution analysis was performed as described previously in Aunin, E. et al., PLOS Pathogens, 2020.
Differentially expressed genes were determined using edgeR (Robinson, M.D. et al.,  Bioinforma, 2010), with genes expressed at <=3 counts per million (cpm) excluded.
Because there were no biological replicates for any condition, we used the exact test with dispersion set to 0.01, as suggested for data concerning genetically identical model organisms (https://www.bioconductor.org/packages/release/bioc/vignettes/edgeR/inst/doc/edgeRUsersGuide.pdf).
We used a false discovery rate (FDR) cut off of 0.01 and a fold change cut off of 2 to call differentially expressed genes.
Genome_build: 3D7 v3 reference sequence (Böhme, U. et al., Wellcome Open Res., 2019)
Supplementary_files_format_and_content: Table with genes up or down in KO relative to WT  with FDR <= 0.01 and fold change > 2. Direction of up or downregulation, gene ID, false discovery rate (FDR), log counts per million (logCPM), log fold change (logFC), and gene description (Desc).

organism: Plasmodium falciparum Dd2

source_name: Red blood cells infected P. falciparum

growth_protocol: P. falciparum 3D7 and Dd2 strains (MRA-120 and MRA-156, MR4-Malaria Resources) were maintained at 4% hematocrit in RBCs with RPMI-1640 (Gibco) supplemented with 2 g/L sodium bicarbonate, 2 mM L-glutamine, 25 mM HEPES (Gibco), 25 µg/mL gentamycin (Gibco), 100 µM hypoxanthine (Sigma-Aldrich) and 0.25% (w/v) AlbuMAXII (Gibco) with daily medium changes. Parasites were maintained at 37 °C in an airtight environment with 3% O2, 5% CO2 and 92% of N2.

extract_protocol:
RNA was extracted from trophozoite stages, estimated between 28 to 32 hours old, using a RNeasy Mini Kit (Qiagen)
Libraries and sequencing were outsourced (Macrogen Inc), using TruSeq RNA Illumina Library v2 construction (nonstranded polyA enrichment) and HiSeq2500 Illumina 2x100bp 2Gb (20M pair-end reads) throughput-based sequencing.

treatment_protocol: Parasites were tightly synchronized with 5% sorbitol in intervals of 20 hours for 3 consecutive life cycles.

tag: strain

value: 28-32h after cycle initiation

value: wild-type


title: RAB21_rep1_Experiment_6 [LIB2_6]

description: processed data file: Library_2.xlsx


title: Main olfactory bulb replicate 1 slide 3

tag: tissue

value: Main olfactory bulb

value: wild type


title: Main olfactory bulb replicate 1 slide 2


title: PTEN_rep2_Experiment_6 [LIB2_5]

description: processed data file: Library_2.xlsx

source_name: HeLa Cells_72 hrs after transfection of TDMD constuct_PTEN

tag: cell line

value: PTEN


title: Main olfactory bulb replicate 1 slide 1

tag: gender


title: PTEN_rep1_Experiment_6 [LIB2_4]

description: processed data file: Library_2.xlsx