title: C1_G9_F_R2

description:
Control population 1, Generation 9, Female, Replicate 2
STH_397

data_processing:
Base calls and quality were assessed  using RTA version 1.18.64 and CASAVA 1.8.2.
We used fastqc to evaluate the quality of each sequence (Babraham Institute, Cambridge, UK).
We used STAR to align reads to the genome (Dobin et al., 2013, PMID: 23104886) with the default parameters except that minimum and maximum intron sizes were coded as 2 and 268,107 based on the Flybase FB2015_04 release 6 version 07 genome.
We used HTSeq to count only the uniquely mapped reads (Anders et al., 2015, PMID: 25260700).
Read counts were normalized using the method described by Love et al., 2014 (PMID: 25516281)
Assembly: FlyBase FB2015_04 release 6 version 07
Supplementary files format and content: There are two supplemental tables. The first, 'Raw_read_counts.csv', contains the raw read counts per gene as evaluated using HTSeq. The second file, 'Normalized_read_counts.csv', are the DESeq-normalized read counts for each gene. Both files are comma-separated values.

extract_protocol:
Total RNA was extracted using Qiazol (Qiagen, Hilden, Germany), followed with phenol-chloroform extraction, isopropanol precipitation, and DNase digestion (Qiagen, Hilden, Germany).  Qiagen RNeasy MinElute Cleanup kits (Qiagen, Hilden, Germany) were used to purify RNA according to the manufacturer’s instructions.  Total RNA yield was measured using a Nanodrop 8000 (Thermo Scientific, Waltham, MA).  We used Agilent Bioanalyzer RNA chips on the 2100 Bioanalyzer system (Agilent, Santa Clara, CA) according to the manufacturer instructions to visually inspect electrophoregrams for RNA degradation.
PolyA-selected stranded mRNA libraries were constructed from 1 µg total RNA using Illumina TruSeq Stranded mRNA Sample Prep Kits (Illumina, San Diego, CA).  We followed the manufacturer’s protocol with the exception of the PCR amplification. The PCR amplification was performed for 10 cycles rather than 15 in order to reduce potential over-amplification.  We applied unique barcode adapters to each library. Libraries were pooled for sequencing.  To achieve a minimum of 38 million 126-base read pairs, the pooled libraries were sequenced on multiple lanes of an Illumina HiSeq2500 (Illumina, San Diego, CA) using version 4 chemistry.

value: Female

value: control


title: C1_G9_F_R1

status: Public on Jul 29 2023

type: SRA

city: Bethesda

first: Susan

middle: T

last: Harbison

state: MD

address: 10 Center Drive, Bldg. 10, Rm. 7D13

department: Center for Systems Biology

country: USA

institute: National Heart Lung and Blood Institute

description:
Control population 1, Generation 9, Female, Replicate 1
STH_376

library_source: transcriptomic

molecule: polyA RNA

organism: Drosophila melanogaster

source_name: Whole body

growth_protocol: All flies were kept in the following controlled environmental conditions.  They were reared in an incubator on standard Drosophila food (http://flystocks.bio.indiana.edu/Fly_Work/media-recipes/bloomfood.htm) at 25°C, 60% humidity, and a 12:12-hour light:dark  cycle.  Prior to making sleep measurements, we collected and maintained male and female virgins at 20 flies to a same-sex vial for four days to control for social exposure.  We assayed night sleep duration as well as other sleep and activity measures using the Drosophila Activity Monitoring System (DAMS) (Trikinetics, Waltham, MA).  Night and day sleep duration, average sleep bout length, and bout number as well as sleep latency and waking activity were computed from the DAMS activity data using an in-house C# program (R. Sean Barnes, personal communication).

treatment_protocol: We created four populations selected for long and short night sleep and two control populations in two stages.  In the first stage, we created an outbred population (the Sleep Advanced Intercross Population, SAIP) using the five longest- and five shortest-sleeping lines of the Drosophila Genetic Reference Panel (DGRP) (Mackay et al., Nature, 2012, PMID 22318601; Huang et al., Genome Res, 2014, PMID 24714809).  We crossed the following DGRP lines in a full diallel cross: DGRP_38, DGRP_235, DGRP_310, DGRP_313, DGRP_335, DGRP_338, DGRP_365, DGRP_379, DGRP_808, and DGRP_832.  Two virgin males and two virgin females from each of the 100 F1 crosses were mixed together, and 10 males and 10 females were placed into 20 bottles.  The progeny from the bottles were mixed for 21 generations, with 20 males and 20 females placed in each bottle for the subsequent generations.  After generation 21, the bottles were maintained by bottle-to-bottle tipping.  In the second stage, we established six populations at generation 47 of the outbred population by randomly choosing 25 males and 25 virgin females from the SAIP for each bottle.  We assayed night sleep duration as well as other sleep and activity measures in 100 males and 100 females in each population.   In two of the populations, the 25 longest-sleeping males and females were chosen from each bottle as parents to establish replicate long-sleeping populations.  We followed a similar procedure to establish two replicate short-sleeper populations, choosing the 25 shortest-sleeping males and 25 shortest-sleeping females in each population as parents for the next generation.  The remaining two populations served as replicated unselected controls; the parents for these populations were chosen by randomly selecting 25 males and 25 females from each of these populations.  We repeated this procedure for 13 generations, and flies were not mixed across replicate populations.  For generation 0 and generations 2-13, we randomly froze virgin male and virgin female flies from the sleep assays for RNA extraction.  Ten males and ten females were frozen in two same-sex replicates from each of the six populations to generate 24 RNA sequence profiles per generation.  All flies were frozen for RNA extraction at the same circadian time (12:00 pm).

tag: developmental stage

value: Adult

tag: Sex

tag: selection treatment

tag: selection generation

tag: population replicate

tag: sample replicate


title: Aortic Endothelial Cells (AoECs) from stressed (S) mice rep3

city: Munich

first: Hendrik

last: Sager

address: Lazarettstr. 36

department: Klinik für Herz- und Kreislauferkrankungen

country: Germany

institute: Deutsches Herzzentrum München

data_processing:
Raw data was generated and processed using the Real Time Analysis 2.4.11 Software (RTA) and Illumina Sequence Analysis Viewer (SVA) 2.4.7.
Raw reads were quality and adapter trimmed with Trimmomatic, mapped to mm10 using the STAR aligner and de-convoluted into gene abundances using featureCounts.
Genome_build: mm10
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

molecule: total RNA

organism: Mus musculus

source_name: Aortic Endothelial Cells (AoECs)

extract_protocol:
Messenger RNA (mRNA) was extracted from FACS-sorted endothelial cells using the Arcturus PicoPure RNA Isolation Kit (KIT0204, Applied Biosystems) according to the manufacturer’s protocol.
Sequencing libraries were constructed using the TruSeq Stranded kit (Illumina).

tag: cell type

value: Aortic Endothelial Cells (AoECs)

tag: treatment

value: acute mental stress (S)

tag: strain

value: ApoE


title: RNA-seq from Silc1{+/+} hippocampus in novel environment, replicate 1

city: Rehovot

first: Igor

last: Ulitsky

address: Hertzl St.

country: Israel

institute: Weizmann Institute of Science

data_processing:
RNA-seq: RNA-seq reads were mapped to the mouse genome (mm10 assembly) using STAR (Dobin et al., 2013) to generate read coverage tracks visualized using the UCSC genome browser. RSEM (Li and Dewey, 2011) with RefSeq annotations was used to call differential expression between samples
ATAC-seq: ATAC-seq reads were mapped to the mouse genome using Bowtie2 (Langmead and Salzberg, 2012) and peaks were called using all the samples together using MACS2 (Zhang et al., 2008).
Assembly: mm10
Supplementary files format and content: bigWig read coverage files are provided for all samples. RSEM quantification is provided for the RNA-seq samples, and MACS2-called peaks are provided for the ATAC-seq data.

source_name: hippocampus

extract_protocol:
Total RNA was extracted from the hippocampus using the TRIREAGENT (MRC) according to the manufacturer’s protocol.
Strand-specific mRNA-seq libraries were prepared from 1 ug total RNA using the SENSE-mRNA-Seq-V2 (Lexogen), according to the manufacturers’ protocol

tag: tissue

value: hippocampus

tag: genetic background

value: WT

tag: aav

tag: environment

value: Novel environment


title: BCG_Cystitis_Case5

city: Tokyo

first: Yoshiyuki

last: AKIYAMA

state: Please select...

department: Urology

country: Japan

institute: The University of Tokyo

data_processing:
Adaptor and low-quality portions, defined as sequences with an average Phred score < 10 in a 10-bp window, were removed from the raw reads. All remaining reads ≥ 36 bp in length were regarded as high-quality, clean data and used in downstream analyses.
The clean PE reads were aligned to the University of California Santa Cruz (UCSC) human reference genome (hg19) using Genedata Profiler Genome ver. 11.0.8 (Genedata, Basel, Switzerland).
To quantify gene expression, fragments per kilobase of exon per million mapped fragments (FPKM) values for each gene model were calculated using the Genedata Profiler Genome.
Assembly: Mapped reads were assembled using STAR ver. 2.5.3a by referring to gene structures described in the National Center for Biotechnology Information RefSeq.
Supplementary files format and content: tab-delimited text file includes FPKM value for each sample.

organism: Homo sapiens

source_name: Bladder

extract_protocol:
Total RNA was extracted from frozen samples using NucleoSpin RNA (Macherey-Nagel, Düren, Germany). RNA was quantified on a NanoDrop 2000c Spectrophotometer (Thermo Fisher Scientific, San Jose, CA, USA), and the purity was measured using an RNA ScreenTape assay on a 2200 TapeStation (Agilent Technologies, Santa Clara, CA, USA). Quality assessment was performed using 2200 TapeStation Software (Agilent Technologies).
Purified total RNA (10 ng) was resuspended in Clontech buffers for mRNA amplification using 5′ template switching PCR with a Clontech SMART-Seq v4 Ultra Low Input RNA kit (Clontech, Palo Alto, CA, USA) according to the manufacturer’s instructions. Amplified cDNA was fragmented and appended with dual-indexed barcodes using Illumina Nextera XT DNA Library Prep kits (Illumina, San Diego, CA, USA).

value: Bladder

tag: disease

value: Mycobacterium bovis bacillus Calmette–Guérin (BCG)-related cystitis

tag: biopsied site

value: reddened mucosal flat lesion

tag: gender

value: M

tag: age


title: Aortic Endothelial Cells (AoECs) from stressed (S) mice rep2


title: BCG_Cystitis_Case4


title: RNA-seq from Silc1{+/+} hippocampus in home cage, replicate 3

value: Home cage


title: C1_G8_M_R2

description:
Control population 1, Generation 8, Male, Replicate 2
STH_355

tag: developmental stage

value: Male


title: BCG_Cystitis_Case3


title: Aortic Endothelial Cells (AoECs) from stressed (S) mice rep1


title: KD 6

city: Wuhan

first: xinhe

last: XinheHuang

state: Hubei

address: Hust

country: Singapore

institute: Huazhong University of Science and Technology

data_processing:
Use fastp v 0.19.3 to filter the original data, mainly to remove reads with adapters;
Download the reference genome and its annotation files from the designated website, use HISAT v2.1.0 to construct the index, and compare clean reads to the reference genome
Use StringTie v1.3.4d for new gene prediction. StringTie applies network streaming algorithms and optional de novo to splice transcripts. Compared with Cufflinks and other software, StringTie can splice a more complete and accurate transcript, and the splicing speed is faster.
Supplementary files format and content: xlsx file includes raw counts for each Sample

source_name: mouse liver

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen). 1 μg of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using NEBNext®UltraTM RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer's protocols.

value: mouse liver

value: ketogenic diet


title: C1_G8_M_R1

description:
Control population 1, Generation 8, Male, Replicate 1
STH_354

tag: Sex


title: RNA-seq from Silc1{+/+} hippocampus in home cage, replicate 2


title: RNA-seq from Silc1{+/+} hippocampus in home cage, replicate 1


title: BCG_Cystitis_Case2


title: BCG_Cystitis_Case1


title: C1_G8_F_R2

description:
Control population 1, Generation 8, Female, Replicate 2
STH_353

value: Female

tag: selection treatment


title: Aortic Endothelial Cells (AoECs) from non-stressed (NS) mice rep5

value: non-stressed (NS)


title: Aortic Endothelial Cells (AoECs) from stressed (S) mice rep4


title: Hunner_Type_Interstitial_Cystitis_Case25_Non_Hunner_Lesion

value: F


title: RNA-seq from Silc1{-/-} hippocampus in novel environment, replicate 2


title: Aortic Endothelial Cells (AoECs) from non-stressed (NS) mice rep3

value: Aortic Endothelial Cells (AoECs)


title: Aortic Endothelial Cells (AoECs) from non-stressed (NS) mice rep4


title: Aortic Endothelial Cells (AoECs) from non-stressed (NS) mice rep2


title: RNA-seq from Silc1{-/-} hippocampus in novel environment, replicate 1


title: Hunner_Type_Interstitial_Cystitis_Case24_Non_Hunner_Lesion


title: RNA-seq from Silc1{-/-} hippocampus in home cage, replicate 3


title: C1_G7_M_R1

description:
Control population 1, Generation 7, Male, Replicate 1
STH_330

value: Adult

value: control

tag: selection generation


title: Aortic Endothelial Cells (AoECs) from non-stressed (NS) mice rep1

value: ApoE


title: Hunner_Type_Interstitial_Cystitis_Case23_Non_Hunner_Lesion


title: C1_G7_F_R2

description:
Control population 1, Generation 7, Female, Replicate 2
STH_329

tag: population replicate


title: Hunner_Type_Interstitial_Cystitis_Case22_Non_Hunner_Lesion


title: RNA-seq from Silc1{-/-} hippocampus in home cage, replicate 1

value: hippocampus


title: C1_G6_M_R2

description:
Control population 1, Generation 6, Male, Replicate 2
STH_307

tag: sample replicate


title: C1_G7_F_R1

description:
Control population 1, Generation 7, Female, Replicate 1
STH_328


title: C1_G8_F_R1

description:
Control population 1, Generation 8, Female, Replicate 1
STH_352


title: Hunner_Type_Interstitial_Cystitis_Case21_Non_Hunner_Lesion


title: WTspiderB

city: Iowa City

first: Damian

middle: Joseph

last: Krysan

state: IA

address: 200 Hawkins Drive

institute: University of Iowa Department of Pediatrics

data_processing:
Sequence reads were cleaned and adapter trimmed using trimmomatic-0.36
Each sample was mapped individually to the C. Albicans reference genome (SC5314 from NCBI) with STAR2.5.2b
Raw read counts were obtained using featurecounts from the subread1.5.0p3 package and SC5314 gene annotations using only uniquely aligned reads
DESeq2-1.14.1 within R-3.3.2 was used to perform data normalization and differential expression analysis with an adjusted p-value threshold of 0.05 on each set of raw expression measures.
Assembly: SC5314 from NCBI
Supplementary files format and content: tab-delimited text file containing raw counts for each sample

organism: Candida albicans

growth_protocol: The reference strain SN250 and the corresponding rob1ΔΔ mutant were subjected to hyphal induction conditions using either Spider medium or RPMI at 37oC for 4 hr.

extract_protocol:
Total RNA was isolated with the MasterPure yeast RNA purification kit.
RNA TruSeq Kit was used for library construction

treatment_protocol: Samples were normalized to expression from cells grown in YPD at 30 degrees C

tag: cell line

tag: genotype

value: WT

value: Spider 37 degrees


title: RNA-seq from Silc1{+/+} hippocampus, replicate 2


title: C1_G7_M_R2

description:
Control population 1, Generation 7, Male, Replicate 2
STH_331


title: C1_G6_M_R1

description:
Control population 1, Generation 6, Male, Replicate 1
STH_306


title: WTspiderA

tag: treatment


title: Hunner_Type_Interstitial_Cystitis_Case20_Non_Hunner_Lesion

tag: tissue

value: Bladder


title: C1_G6_F_R2

description:
Control population 1, Generation 6, Female, Replicate 2
STH_305


title: RNA-seq from Silc1{+/+} hippocampus, replicate 1

tag: genetic background


title: WTrpmiB

value: RPMI 37 degrees


title: C1_G6_F_R1

description:
Control population 1, Generation 6, Female, Replicate 1
STH_304


title: RNA-seq from Silc1{polyA/polyA} hippocampus, replicate 2

tag: aav


title: WTrpmiA


title: WT30_degrees_YPD_B

value: YPD 30 degrees


title: RNA-seq from Silc1{polyA/polyA} hippocampus, replicate 1

tag: environment

value: Home cage


title: Hunner_Type_Interstitial_Cystitis_Case19_Non_Hunner_Lesion

tag: disease

value: M


title: Hunner_Type_Interstitial_Cystitis_Case18_Non_Hunner_Lesion

tag: biopsied site


title: WT30_degrees_YPD_A


title: RNA-seq from Silc1{-/-} hippocampus in home cage, replicate 2


title: Hunner_Type_Interstitial_Cystitis_Case17_Non_Hunner_Lesion

tag: gender


title: C1_G5_M_R2

description:
Control population 1, Generation 5, Male, Replicate 2
STH_283

value: Male


title: RNA-seq from WT hippocampal neurons cultured for 2 weeks

source_name: cultured adult hippocampal neurons

value: cultured adult hippocampal neurons


title: C1_G5_M_R1

description:
Control population 1, Generation 5, Male, Replicate 1
STH_282


title: Hunner_Type_Interstitial_Cystitis_Case16_Non_Hunner_Lesion

tag: age


title: ROB1NULLspiderB


title: Hunner_Type_Interstitial_Cystitis_Case15_Non_Hunner_Lesion


title: RNA-seq from WT hippocampal neurons cultured for 1 week


title: RNA-seq from Silc1-/- hippocampal neurons cultured for 2 weeks


title: C1_G5_F_R1

description:
Control population 1, Generation 5, Female, Replicate 1
STH_280

tag: developmental stage

value: Female


title: Hunner_Type_Interstitial_Cystitis_Case14_Non_Hunner_Lesion


title: C1_G4_M_R2

description:
Control population 1, Generation 4, Male, Replicate 2
STH_259

tag: Sex


title: ROB1NULLrpmiB


title: Hunner_Type_Interstitial_Cystitis_Case13_Non_Hunner_Lesion


title: ROB1NULLrpmiA


title: RNA-seq from Silc1-/- hippocampal neurons cultured for 1 week


title: C1_G4_M_R1

description:
Control population 1, Generation 4, Male, Replicate 1
STH_258

tag: selection treatment


title: Hunner_Type_Interstitial_Cystitis_Case12_Non_Hunner_Lesion


title: RNA-seq from the hippocampus of mice injected with GFP-Sox11 AAV, replicate 3


title: ROB1NULL30_degrees_YPD_B


title: ROB1NULL30_degrees_YPD_A


title: RNA-seq from the hippocampus of mice injected with GFP-Sox11 AAV, replicate 2


title: RNA-seq from the hippocampus of mice injected with GFP-Sox11 AAV, replicate 1


title: RNA-seq from the hippocampus of mice injected with GFP-Silc1 AAV, replicate 3


title: Hunner_Type_Interstitial_Cystitis_Case10_Non_Hunner_Lesion


title: Hunner_Type_Interstitial_Cystitis_Case9_Non_Hunner_Lesion


title: C1_G4_F_R1

description:
Control population 1, Generation 4, Female, Replicate 1
STH_256

tag: selection generation


title: RNA-seq from the hippocampus of mice injected with GFP-Silc1 AAV, replicate 2


title: ROB1NULLspiderA


title: C1_G3_M_R1

description:
Control population 1, Generation 3, Male, Replicate 1
STH_233

tag: population replicate


title: C1_G3_M_R2

description:
Control population 1, Generation 3, Male, Replicate 2
STH_234

tag: sample replicate


title: Hunner_Type_Interstitial_Cystitis_Case11_Non_Hunner_Lesion


title: C1_G4_F_R2

description:
Control population 1, Generation 4, Female, Replicate 2
STH_257


title: C1_G5_F_R2

description:
Control population 1, Generation 5, Female, Replicate 2
STH_281


title: Hunner_Type_Interstitial_Cystitis_Case8_Non_Hunner_Lesion


title: Large8

city: Hamilton

first: Yonghong

last: Wan

state: Ontario

address: 1280 Main St W

department: Medicine

country: Canada

institute: McMaster University

data_processing:
Samples were sequenced on an Illumina HiSeq 2500 with an Illumina HiSeq Rapid v2 kit using a single-read 1 × 50 bp configuration.
Gene counts were normalized using trimmed means of M-values (TMM) and converted to log2 counts per million using the Limma-Voom package. Normalized counts were used for subsequent analyses.
Supplementary files format and content: tab-delimited files includes raw counts for each sample
Supplementary files format and content: tab-delimited files includes RPKM values for each sample

source_name: Intradermal tumor

growth_protocol: All the cells were maintained at 37°C in a humidified atmosphere containing 5% CO2. CMS5 cells were cultured in DMEM supplemented with 10% FBS, penicillin/streptomycin (100 U/mL and 100 ng/mL, respectively), and 2 mM l-glutamine.

extract_protocol:
For RNA extraction, tumors were excised, snap-frozen in liquid nitrogen, and homogenized in TRIzol. RNA was extracted and purified using an RNeasy Mini Kit. mRNA was enriched using the NEBNext Poly(A) mRNA Isolation Module where each sample had an RNA integrity number (RIN) score of >7.
A NEBNext Ultra II Directional RNA Library kit was used for RNA-seq library construction.

value: Intradermal tumor

tag: strain

value: balb/c

tag: cell line

tag: cell type

value: fibrosarcoma


title: Large9

tag: tissue

tag: genotype

tag: treatment


title: C1_G3_F_R2

description:
Control population 1, Generation 3, Female, Replicate 2
STH_232

value: Adult


title: RNA-seq from the hippocampus of mice injected with GFP-Silc1 AAV, replicate 1

tag: genetic background

tag: aav

tag: environment


title: Large7


title: SmallS1


title: C1_G3_F_R1

description:
Control population 1, Generation 3, Female, Replicate 1
STH_231

value: control


title: RNA-seq from the hippocampus of mice injected with GFP AAV (control for Silc1 OE), replicate 6


title: C1_G2_M_R2

description:
Control population 1, Generation 2, Male, Replicate 2
STH_223


title: RNA-seq from the hippocampus of mice injected with GFP AAV (control for Silc1 OE), replicate 5


title: Hunner_Type_Interstitial_Cystitis_Case6_Non_Hunner_Lesion

tag: disease

tag: biopsied site

tag: gender

value: F


title: Small2


title: Small1


title: RNA-seq from the hippocampus of mice injected with GFP AAV (control for Silc1 OE), replicate 4

value: hippocampus


title: C1_G2_M_R1

description:
Control population 1, Generation 2, Male, Replicate 1
STH_203

tag: developmental stage

tag: Sex


title: C1_G2_F_R2

description:
Control population 1, Generation 2, Female, Replicate 2
STH_202

tag: selection treatment

tag: selection generation


title: RNA-seq from the hippocampus of mice injected with GFP AAV (control for Sox11 OE), replicate 3

value: WT


title: Hunner_Type_Interstitial_Cystitis_Case4_Non_Hunner_Lesion

tag: age


title: Large11_MS275

tag: strain


title: Large10_MS275

tag: cell line


title: RNA-seq from the hippocampus of mice injected with GFP AAV (control for Sox11 OE), replicate 2


title: C1_G2_F_R1

description:
Control population 1, Generation 2, Female, Replicate 1
STH_201

tag: population replicate

tag: sample replicate


title: C1_G0_M_R2

description:
Control population 1, Generation 0, Male, Replicate 2
STH_130


title: RNA-seq from the hippocampus of mice injected with GFP AAV (control for Sox11 OE), replicate 1

tag: tissue


title: RNA-seq from Sox11{loxP/loxP} mice injected with Cre, replicate 3


title: NightWT-3

city: Shanghai

first: Youwen

last: Si

address: North Zhongshan Road Campus: 3663 N. Zhongshan Rd., Shanghai

country: China

institute: East China Normal University

data_processing:
CLC Genomics Workbench v 11.0.1
Sequence reads were trimmed for adaptor sequence/low-quality sequence using CLC genomic benchwork (parameter- Quality limit: 0.05)
Trimmed sequence reads were mapped to GRCm38.p6 using CLC genomic benchwork (parameters- mismath cost: 2 insertion cost: 3 deletion cost: 3 length fraction: 0.8 similarity fraction: 0.8)
Read count extraction and normalization were performed using CLC genomic benchwork
Assembly: GRCm38.p6
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

source_name: brain

extract_protocol:
RNA was harvested using mirVana™ miRNA ISOlation Kit (Ambion). 1 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using TruSeq Stranded Total RNA with Ribo-Zero Gold following manufacturer's protocols.

value: brain

tag: genotype

tag: timepoint

value: Night


title: C1_G0_M_R1

description:
Control population 1, Generation 0, Male, Replicate 1
STH_129


title: Hunner_Type_Interstitial_Cystitis_Case1_Non_Hunner_Lesion

value: Bladder


title: RNA-seq from Sox11{loxP/loxP} mice injected with Cre, replicate 2

tag: genetic background

tag: aav


title: Hunner_Type_Interstitial_Cystitis_Case5_Non_Hunner_Lesion

tag: disease


title: Hunner_Type_Interstitial_Cystitis_Case25_Hunner_Lesion

tag: biopsied site


title: NightWT-1


title: Hunner_Type_Interstitial_Cystitis_Case23_Hunner_Lesion

tag: gender


title: RNA-seq from Sox11{loxP/loxP} mice injected with Cre, replicate 1

tag: environment


title: Hunner_Type_Interstitial_Cystitis_Case2_Non_Hunner_Lesion


title: C1_G0_F_R1

description:
Control population 1, Generation 0, Female, Replicate 1
STH_127

tag: developmental stage

tag: Sex


title: NightDKO-3

value: Presenilin-1/2 conditional knockout (DKO)


title: Hunner_Type_Interstitial_Cystitis_Case3_Non_Hunner_Lesion


title: RNA-seq from mice injected with GFP (negative control for Cre), replicate 3

value: Home cage


title: RNA-seq from mice injected with GFP (negative control for Cre), replicate 2


title: NightDKO-2


title: NightDKO-1


title: TSeL+L2

city: Tianjin

first: Chunqiu

last: Zhang

address: NO 94 Weijin Road

institute: Nankai University

data_processing:
Basecalls performed usingMGISEQ-2000
SOAPnuke was used to get the "clean reads".
Bowtie2 was used to get the mapping ratio.
Fragments Per Kilobase Million (FPKM) was calculated based on the RSEM.
Supplementary files format and content: tab-delimited text files include fpkm values for each Sample …

source_name: skin

extract_protocol:
Skins were removed, flash frozen on dry ice, and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction
RNA libraries were prepared for sequencing using  oligo -dT beads

value: skin

value: BALB/C

tag: treatment

value: TSeL+L


title: TSeL+L1


title: Hunner_Type_Interstitial_Cystitis_Case21_Hunner_Lesion

tag: age


title: TSeL+L3


title: NightWT-2


title: ATAC-seq in hippocampus from WT mice, replicate 6

library_source: genomic

molecule: genomic DNA

extract_protocol:
Hippocampus tissue was extracted in 500 µl Nuclear extraction buffer (10mM Tris, 10mM NaCl, 3mM MgCl2, 0.1% Igepal, 0.1% Tween, protease inhibitor cocktail) for 5 minutes on ice, then a 21g needle on a 1 mL syringe was used to shear the tissue through the needle 5 times. NeuN-positive nuclei were separated by fluorescence-activated cell sorting.
ATAC-seq was performed as previously described by Buenrostro et al., 2013

value: Novel environment


title: LargeS6_MS275

value: Intradermal tumor

tag: strain

tag: cell type


title: C1_G0_F_R2

description:
Control population 1, Generation 0, Female, Replicate 2
STH_128

value: Female

tag: selection treatment

tag: selection generation

tag: population replicate


title: DayDKO-3

tag: tissue

tag: genotype

value: Day


title: TSeL3

value: TSeL


title: Hunner_Type_Interstitial_Cystitis_Case24_Hunner_Lesion


title: Hunner_Type_Interstitial_Cystitis_Case22_Hunner_Lesion


title: Hunner_Type_Interstitial_Cystitis_Case20_Hunner_Lesion


title: ATAC-seq in hippocampus from WT mice, replicate 5

tag: genetic background


title: TSeL2


title: Hunner_Type_Interstitial_Cystitis_Case18_Hunner_Lesion


title: DayDKO-1

tag: timepoint


title: ATAC-seq in hippocampus from WT mice, replicate 4

tag: aav


title: DayWT-3


title: Hunner_Type_Interstitial_Cystitis_Case17_Hunner_Lesion

tag: disease

tag: biopsied site


title: ATAC-seq in hippocampus from WT mice, replicate 3

tag: environment


title: TL+L3

value: TL+L


title: RNA-seq from mice injected with GFP (negative control for Cre), replicate 1


title: DayWT-2


title: ATAC-seq in hippocampus from WT mice, replicate 2


title: Hunner_Type_Interstitial_Cystitis_Case15_Hunner_Lesion

tag: gender

value: M


title: Hunner_Type_Interstitial_Cystitis_Case16_Hunner_Lesion

value: F


title: TL+L2


title: Hunner_Type_Interstitial_Cystitis_Case19_Hunner_Lesion


title: DayWT-1

value: WT


title: DayDKO-2

value: brain


title: ATAC-seq in hippocampus from WT mice, replicate 1

value: hippocampus


title: Hunner_Type_Interstitial_Cystitis_Case13_Hunner_Lesion

value: Bladder


title: TL+L1


title: sgSETD1Aex8_2

city: Chiba

first: Masaki

last: Fukuyo

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

department: Department of Molecular Oncology

institute: Chiba University

description: SETD1A-BuGZ_RNAseq_sgBuGZ_FPKM_Hoshii20230609edited.txt

data_processing:
Illumina Casava1.8.2 software used for basecalling.
Reads from sample no.1-16 were aligned with HISAT2.
Fragments per kilobase of exon model per million mapped fragments (FPKM) were calculated using Cufflinks v2.0.2.
Assembly: mm10 or hg19
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample.

growth_protocol: Mouse leukemai cells were cultured in RPMI-1640 containing penicillin-streptomycin, supplemented with 10% fetal bovine serum and 10 ng/mL rmIL-3. MOLM-13 cells were cultured in RPMI-1640 containing penicillin-streptomycin, supplemented with 10% fetal bovine serum.

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

treatment_protocol: Setd1afl/fl;CreER;MLL-AF9 leukemia cells were infected with retrovirus vector containing GFP or hSETD1A-GFP-CDT expression construct and then treated with tamoxifen (or EtOH as control) for 72h. Doxycycline-inducible Cas9 expression vector was introduced with lentivirus and stable expressing single cell clone was established. sgRNA vector was introduced with lentivirus and GFP-positive cells were collected by cell sorter. 1 µg / mL of Doxycycline was treated for 6 days.

tag: stimulation

value: Dox

tag: time

tag: cell line


title: ATAC-seq in hippocampus from Silc1-/- mice, replicate 5


title: sgSETD1Aex8_3


title: ATAC-seq in hippocampus from Silc1-/- mice, replicate 6


title: PBS3

tag: treatment

value: PBS


title: PBS2

value: skin


title: sgSETD1Aex8_1


title: ATAC-seq in hippocampus from Silc1-/- mice, replicate 4


title: Hunner_Type_Interstitial_Cystitis_Case12_Hunner_Lesion

tag: age


title: PBS1

value: BALB/C


title: Hunner_Type_Interstitial_Cystitis_Case11_Hunner_Lesion


title: TSeL1


title: ATAC-seq in hippocampus from Silc1-/- mice, replicate 3


title: sgBuGZ_2-2

value: sgBuGZ


title: Hunner_Type_Interstitial_Cystitis_Case10_Hunner_Lesion


title: MPhage_Female_CXCL4_3h_Rep3

city: New York

first: David

last: Oliver

state: New York

address: 535 E 70th St

department: Research

institute: Hospital for Special Surgery

data_processing:
fastp -q 15 -n 10 -l 20 –detect_adapter_for_pe  -i target_R1.fastq -I target_R2.fastq (fastp v0.19.10)
STAR --readFilesIn target_R1.fastq target_R2.fastq --outSAMtype BAM Unsorted --outFilterMultimapNmax 4 --outFilterType BySJout --outSAMmultNmax 1 --outFilterMismatchNoverReadLmax 0.1 --outSAMstrandField intronMotif --sjdbGTFfile gencode_v33.gtf --outReadsUnmapped Fastx (STAR v2.7.3a)
samtools sort -n target_STAR.Aligned.out.bam | samtools fixmate -rm - - | samtools sort - | samtools markdup -l 800 -rs – target_STAR.Aligned.sortedByCoord.out.bam (samtools v1.9)
featureCounts -p -a gencode_v33.gtf -s 2 -o reverse_stranded.txt target_STAR.Aligned.sortedByCoord.out.bam (featureCounts v2.0.1)
Assembly: hg38 or mm10
Supplementary files format and content: Tab Separated File containg gene level counts per sample

source_name: blood

growth_protocol: Monocytes were cultured overnight at 37oC, 5% CO2 in RPMI-1640 medium (Invitrogen) supplemented with 10% heat-inactivated defined FBS (HyClone Fisher), penicillin-streptomycin (Invitrogen), L-glutamine (Invitrogen) and 20 ng/ml human M-CSF. after at least 12 hr culture,

extract_protocol:
cell were harvested and total RNA were extreacted using Rneasy Mini Kit from QIAGEN
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: In vitro experiment,  the cells were then stimulated with 10 ug/ml CXCL4 for 1 h and 3 h. In vivo experiment, full-thickness wounds were created by excision of 4-mm punches on either side of midline, 4 wounds were generated in the upper and lower back of mice for 2 days before cell sorting.

value: blood

tag: cell type

value: primary macrophages

value: healthy donor

value: CXCL4 3 h


title: sgBuGZ_2-1


title: MPhage_Female_CXCL4_3h_Rep2


title: ATAC-seq in hippocampus from Silc1-/- mice, replicate 2

value: Novel environment


title: Hunner_Type_Interstitial_Cystitis_Case14_Hunner_Lesion


title: ATAC-seq in hippocampus from Silc1-/- mice, replicate 1


title: Hunner_Type_Interstitial_Cystitis_Case9_Hunner_Lesion


title: sgBuGZ_1-2


title: sgBuGZ_1-1


title: MPhage_Male_CXCL4_3h_Rep1


title: Hunner_Type_Interstitial_Cystitis_Case8_Hunner_Lesion


title: WT.Ly6ChiF4_80dim_Male_rep3

value: sorted from Wounded skin


title: Hunner_Type_Interstitial_Cystitis_Case7_Hunner_Lesion


title: MPhage_Female_CXCL4_1h_Rep3

value: CXCL4 1 h


title: WT.Ly6ChiF4_80dim_Male_rep2


title: MPhage_Female_CXCL4_1h_Rep2


title: WT.Ly6ChiF4_80dim_Male_rep4


title: Hunner_Type_Interstitial_Cystitis_Case5_Hunner_Lesion

value: F


title: sgEmpty_3

value: sgEmpty


title: MPhage_Female_CTRL_0h_Rep3

value: unstimulated


title: WT.Ly6ChiF4_80dim_Male_rep1

value: WT


title: MPhage_Male_CXCL4_1h_Rep1


title: sgEmpty_1


title: sgEmpty_2


title: LCW62-smallRNA

city: Indianapolis

first: Shannon

middle: M.

last: Hawkins

state: IN

address: 550 N University Blvd UH2440

institute: Indiana University School of Medicine

description:
mirDeepCounts.tsv
Eoma_4

data_processing:
Demultiplexing of the reads was performed with bcl2fastq version unknown pipeline
NextSeq reads were trimmed using fastp (version 0.23.2) with parameters “-l 17 -g -p”
PolyA reads were mapped against GRCh38 using HISAT2 version 2.2.1 with parameters “--rna-strandness R“
PolyA read counts for each gene were created using featureCounts from the Subread package (version 2.0.3) and Gencode v42 as the annotation.
smallRNA reads were mapped against GRCh38 and also miRbase version 22 as reference using miRDeep2 version 2.0.1.3 to identify and quantify known microRNA’s.
Differential expression analysis was performed using the DESeq2 package (version 1.36.0) in R/Bioconductor (R version 4.2.0)
Assembly: GRCh38
Supplementary files format and content: tab-delimited text file of raw gene count values for each Sample
Supplementary files format and content: tab-delimited text file of raw miRNA count values for each Sample

source_name: Ovary

extract_protocol:
The RNA was extracted according the the manufacturer's (mirVana) protocol. Summary of protocol: 50-100ng of fresh frozen ttissue samples were lysed, purified with cholorform/ethanol, and Dnase I digest (Turbo DNA-free kit.
Poly-A RNA libraries were constructed using mRNA Stranded TruSeq protocol (Illumina, San Diego, CA). Small RNA library construction was performed using the TruSeq Small RNA kit (Illumina). Purified libraries were visualized and quantified using a TapeStation HSD1000 (Agilent, Santa Clara, CA).

value: Ovary

tag: histology

value: Ovarian endometrioma

value: 25 years

tag: Stage


title: MPhage_Female_CTRL_0h_Rep2

tag: tissue


title: G741-smallRNA

description:
mirDeepCounts.tsv
CCOC_4

value: Ovarian Clear cell carcinoma with concurrent endometriosis

value: 51 years

value: IIB


title: Hunner_Type_Interstitial_Cystitis_Case4_Hunner_Lesion

value: Bladder


title: Hunner_Type_Interstitial_Cystitis_Case3_Hunner_Lesion


title: MPhage_Male_CTRL_0h_Rep1

value: blood

value: primary macrophages

tag: genotype


title: WT.Ly6CdimF4_80hi_Male_rep3

value: skin


title: Hunner_Type_Interstitial_Cystitis_Case2_Hunner_Lesion


title: Hunner_Type_Interstitial_Cystitis_Case1_Hunner_Lesion


title: G506-smallRNA

description:
mirDeepCounts.tsv
CCOC_2

value: 50 years

value: IIIC


title: WT.Ly6CdimF4_80hi_Male_rep2

value: sorted from Wounded skin


title: Isotype + Isotype µg/ml [0.01+0.01]

city: South San Fransisco

first: Shree

last: Bhagwat

address: 213 E Grand Ave

institute: Merck & Co., Inc., Kenilworth, NJ, USA

description:
isotype
16

data_processing:
Sequence reads were trimmed to remove possible adapter sequences and nucleotides with poor quality using Trimmomatic v.0.36. The trimmed reads were mapped to the Homo sapiens GRCh38 reference genome available on ENSEMBL using the STAR aligner v.2.5.2b.
Unique gene hit counts were calculated by using featureCounts from the Subread package v.1.5.2. Only unique reads that fell within exon regions were counted. After extraction of gene hit counts, the gene hit counts table was used for downstream differential expression analysis. Using DESeq2, a comparison of gene expression between the treatment and isotype controls  was performed. The Wald test was used to generate p-values and log2 fold changes.
Assembly: Homo sapiens GRCh38
Supplementary files format and content: CSV file containing unique gene hit counts for each sample.
Supplementary files format and content: Differential gene expression .csv files with log2 fold changes and adjusted p-values for each group comparison.

source_name: JurkatLAG3+PD1+ and Raji-PDL1

growth_protocol: Cells were maintained in complete media with 10 % Fetal bovine serum (Hyclone) with the appropriate selection reagent of  0.25 µg/ml puromycin for Raji-PDL1 and 0.2µg/ml Puromycin + 500 µg/ml of Geneticin (Gibco) for JurkatLag3+PD1+.

extract_protocol:
Cells from multiple wells were  washed with PBS  and pooled to generate a pellet of  0.8x10^6 cells per treatment condition.Total RNA extracted according to the manufacturer's instructions . QC was performed for RNA integrity by Agilent Tapestation and concentration by Qubit assay.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: JurkatLag3+PD1+ cells [1X10^5 cells/well] were incubated with a serial dilution of antibodies either single or combination (starting at 10 µg/ml) and then co-cultured with SED (100 ng/ml) loaded Raji-PDL1 cells [1X10^5 cells/well] for 24hours.

value: Isotype + Isotype µg/ml [0.01+0.01]

tag: replicate group

value: Co-culture Assay

value: JurkatLAG3+PD1+ and Raji-PDL1

tag: time point

value: 24 hr


title: WT.Ly6CdimF4_80hi_Male_rep1

value: WT


title: Isotype + Isotype µg/ml [1+1]

description:
isotype
14

value: Isotype + Isotype µg/ml [1+1]


title: Isotype + Isotype µg/ml [0.1+0.1]

description:
isotype
15

value: Isotype + Isotype µg/ml [0.1+0.1]


title: CW9-smallRNA

description:
mirDeepCounts.tsv
Eoma_3

value: Ovary

value: Ovarian endometrioma

value: 43 years


title: Cxcl4KO.Ly6ChiF4_80dim_Male_rep1

value: CXCL4 KO


title: WT.Ly6CdimF4_80hi_Male_rep4


title: Anti PD1 + Anti LAG3 µg/ml [0.01+0.01]

description:
Treatment
12

value: Anti PD1 + Anti LAG3 µg/ml [0.01+0.01]


title: Anti PD1 + Anti LAG3 µg/ml [0.1+0.1]

description:
Treatment
11

value: Anti PD1 + Anti LAG3 µg/ml [0.1+0.1]


title: Hunner_Type_Interstitial_Cystitis_Case6_Hunner_Lesion

value: Bladder

value: F


title: CW44-smallRNA

description:
mirDeepCounts.tsv
Eoma_1

value: 30 years


title: CRC tissure 2

first: da

last: song

address: Jiefang Avenue 1095

department: tongji hospital

institute: huazhong university of science and technology

description: Colume-K

data_processing:
The raw  paired end reads were trimmed and quality controlled by fastp with default parameters
Clean reads were separately aligned to reference genome with orientation mode using HISAT2 software
The mapped reads of each sample were assembled by StringTie in a reference-based approach
To identify DEGs between two different samples, the expression level of each transcript was calculated according to the transcripts per million reads method
Differential expression analysis was performed using the DESeq2. DEGs with |log2Fc|>=1 and FDR <=0.05 were considered to be significantly expressed genes
Assembly: hg18
Supplementary files format and content: Excel includede raw counts for all samples

source_name: CRC

growth_protocol: SW620 and SW630L1 cells were maintained in DMEM supplemented with 10% FBS and antibiotics in humidified atmosphere with 5% CO2 at 37℃

extract_protocol:
Total RNA was extracted from the cells using TRIzol Reagent according to the mamufacture's instructions (Invitrogen) and genomic DNA was removed using Dnase I (Takara)
The RNA-seq transcriptome library was prepared following Illumina NovaSeq Reagent Kit

treatment_protocol: normally

value: CRC


title: CRC liver metastase tissue 2

description: Colume-I

source_name: CRC liver metastase

value: CRC liver metastase


title: Cxcl4KO.Ly6ChiF4_80dim_Male_rep2

value: skin

value: primary macrophages

value: sorted from Wounded skin


title: CRC liver metastase tissue 1

description: Colume-H


title: Cxcl4KO.Ly6CdimF4_80hi_Male_rep2


title: CW195-smallRNA

description:
mirDeepCounts.tsv
Eoma_5

value: 36 years


title: G618-smallRNA

description:
mirDeepCounts.tsv
CCOC_1

value: Ovarian Clear cell carcinoma with concurrent endometriosis

value: 52 years

value: IA


title: Anti PD1 + Anti LAG3 µg/ml [1+1]

description:
Treatment
10

value: Anti PD1 + Anti LAG3 µg/ml [1+1]

value: Co-culture Assay

value: JurkatLAG3+PD1+ and Raji-PDL1

value: 24 hr


title: SW620L1 cells, biol rep 3

description: Colume-D

value: CRC cells

value: WT


title: Cxcl4KO.Ly6CdimF4_80hi_Male_rep1

value: CXCL4 KO


title: LCW62

description:
geneCounts.tsv
Eoma_4

value: Ovary

value: Ovarian endometrioma

value: 25 years


title: WT.Ly6ChiF4_80dim_Female_rep6

value: skin


title: Anti PD1 + Isotype µg/ml [0.01+0.01]

description:
Treatment
8

value: Anti PD1 + Isotype µg/ml [0.01+0.01]


title: G741

description:
geneCounts.tsv
CCOC_4

value: 51 years

value: IIB


title: SW620 cells, biol rep 3

description: Colume-G


title: G002-smallRNA

description:
mirDeepCounts.tsv
CCOC_5

value: Ovarian Clear cell carcinoma with concurrent endometriosis

value: 48 years


title: WT.Ly6ChiF4_80dim_Female_rep5

value: primary macrophages

value: sorted from Wounded skin


title: WT.Ly6CdimF4_80hi_Female_rep6


title: SW620 cells, biol rep 2

description: Colume-F


title: Anti PD1 + Isotype µg/ml [1+1]

description:
Treatment
6

value: Anti PD1 + Isotype µg/ml [1+1]

value: Co-culture Assay


title: G506

description:
geneCounts.tsv
CCOC_2

value: 50 years

value: IIIC


title: SW620L1 cells, biol rep 1

description: Colume-B

value: CRC cells

value: WT


title: Anti LAG3 + Isotype µg/ml [0.01+0.01]

description:
Treatment
4

value: Anti LAG3 + Isotype µg/ml [0.01+0.01]

value: JurkatLAG3+PD1+ and Raji-PDL1

value: 24 hr


title: SW620 cells, biol rep 1

description: Colume-E


title: CRC tissure 1

description: Colume-J

value: CRC


title: CW9

description:
geneCounts.tsv
Eoma_3

value: Ovary

value: Ovarian endometrioma

value: 43 years


title: Cxcl4KO.Ly6ChiF4_80dim_Female_rep3

value: skin

value: CXCL4 KO


title: G002

description:
geneCounts.tsv
CCOC_5

value: Ovarian Clear cell carcinoma with concurrent endometriosis

value: 48 years

value: IA


title: Anti LAG3 + Isotype µg/ml [0.1+0.1]

description:
Treatment
3

value: Anti LAG3 + Isotype µg/ml [0.1+0.1]

value: Co-culture Assay


title: Cxcl4KO.Ly6CdimF4_80hi_Female_rep4

value: primary macrophages

value: sorted from Wounded skin


title: sgBuGZ-1_SETD1A

description: CUT&Tag

data_processing:
library strategy: CUT&Tag
CUT&Tag library were sequenced with paired-end, but analyzed from read R1 fastq files.
BCL2FASTQ version1.8.4 software was used for basecalling.
ChIP-seq reads were aligned to hg19 reference human genome, using bowtie. CUT&Tag reads were aligned to hg19 and mm10.
The mapped sequence reads were extended to 500 bp and converted to the continuous signal data in wig format or converted to bigwig format using HOMER software. Wig files were converted to bigwig files using UCSC wigToBigWig program.
Assembly: hg19, mm10

growth_protocol: MOLM-13 cells were cultured in RPMI-1640 containing penicillin-streptomycin, supplemented with 10% fetal bovine serum.

extract_protocol:
For ChIP-seq, cells were fixed with 2mM DSG and 1% formaldehyde, and samples from sonicated nuclear fraction were incubated with each antibody and histone-DNA complexes were isolated. For CUT&Tag, human MOLM-13 cells were mixed with 1/10 number of mouse MLL-AF9 transduced cells for spike-in control, and fixed with 0.1% formaldehyde. Cells were mixed with conA beads, and then incubated with SETD1A antibody.
ChIP-seq libraries were prepared using NEBNext ChIP-Seq Library Preparation Set for Illumina (New England Biolabs) following the manufacturer’s protocol. For CUT&Tag, tagmentation was performed using pA-Tn5 with adaptor complex.

treatment_protocol: HA-FKBP-hSETD1A expression vector were introduced with lentivirus and stable expressing cell was established. Doxycycline-inducible Cas9 expression vector was introduced with lentivirus and stable expressing single cell clone was established. sgRNA-GFP vector was introduced with lentivirus and GFP-positive cells were sorted. GFP sorted cells were treated with doxycycline for 4 days.

tag: vector

tag: chip antibody

value: SETD1A (#61702 Cell Signaling)

value: Doxycycline


title: Cxcl4KO.Ly6ChiF4_80dim_Female_rep4


title: CW44

description:
geneCounts.tsv
Eoma_1

value: 30 years


title: CW195

description:
geneCounts.tsv
Eoma_5

value: 36 years


title: Hunner_Type_Interstitial_Cystitis_Case7_Non_Hunner_Lesion

value: Bladder

tag: disease

tag: biopsied site

value: F


title: Cxcl4KO.Ly6CdimF4_80hi_Female_rep3


title: SW620L1 cells, biol rep 2

description: Colume-C

value: CRC cells

value: WT


title: G618

description:
geneCounts.tsv
CCOC_1

value: Ovary

value: 52 years


title: Anti PD1 + Isotype µg/ml [0.1+0.1]

description:
Treatment
7

value: Anti PD1 + Isotype µg/ml [0.1+0.1]

value: JurkatLAG3+PD1+ and Raji-PDL1

value: 24 hr


title: WT_Virgin_rep2

status: Public on Jul 28 2023

first: Hye Kyung

last: Lee

address: 8 CENTER DR RM 107

department: National Institute of Diabetes and Digestive and Kidney (NIDDK)

institute: National Institutes of Health (NIH)

data_processing:
RNA-seq data were trimmed using trimmomatic (Bolger et al., Bioinformatics, 2014) and subsequently aligned to the reference genome mm10 applying STAR RNA-seq aligner (Dobin et al., Bioinformatics, 2013). Rsubread (Liao et al., Nucleic Acids Research, 2013) was was applied to calculate raw read counts.
Assembly: mm10
Supplementary files format and content: raw read counts from RNA-seq samples

source_name: Mammary gland

growth_protocol: RNA-seq was done for the mammary tissues at virgin, day one and ten of lactation (L1, L10) and the salivary tissues of male mice at 2-month-old age.

extract_protocol:
Total RNA was extracted from frozen mammary tissue from wild type mice at day one and ten of lactation and purified with RNeasy Plus Mini Kit (Qiagen, 74134). Ribosomal RNA was removed from 1ug of total RNAs and cDNA was synthesized using SuperScript III (Invitrogen). Libraries for sequencing were prepared according to the manufacturer’s instructions with TruSeq Stranded Total RNA Library Prep Kit with Ribo-Zero Gold (Illumina, RS-122-2301) and paired-end sequencing was done with a HiSeq 2500 instrument (Illumina).
Libraries for sequencing were prepared using standard Illumina protocols.

value: Mammary gland

tag: strain

tag: developmental stage

value: Virgin

value: wild-type


title: WT_Virgin_rep3


title: WT.Ly6CdimF4_80hi_Female_rep5

value: skin

value: primary macrophages

value: sorted from Wounded skin


title: WT_Virgin_rep1


title: WT_SG_rep3

source_name: Salivary gland

value: Salivary gland


title: WT_SG_rep2


title: delOdam_SG_rep2

value: delOdam


title: delOdam_SG_rep1


title: delOdam_SG_rep3


title: Anti LAG3 + Isotype µg/ml [1+1]

description:
Treatment
2

value: Anti LAG3 + Isotype µg/ml [1+1]

value: Co-culture Assay


title: delCsn2-P-E123_Virgin_rep3


title: delCsn2-P-E123_L10_rep2

value: Lactation day 10


title: delCsn2-P-E123_L10_rep3


title: delCsn2-P-E123_Virgin_rep1


title: sgEmpty_SETD1A

description: CUT&Tag

value: SETD1A (#61702 Cell Signaling)

tag: stimulation

value: Doxycycline

tag: time


title: delCsn2-P-E123_L1_rep4

value: Lactation day 1


title: delCsn2-P-E123_L1_rep3


title: delCsn2-P-E123_L10_rep1


title: delCsn2-P-E123_Virgin_rep2


title: delCsn2-P-E123_L1_rep1


title: delCsn2-P_Virgin_rep3


title: delCsn2-P_Virgin_rep1


title: delCsn2-P_Virgin_rep2


title: delCsn2-P_L10_rep3


title: delCsn2-P_L10_rep4


title: ChIP_Input

city: New Delhi

first: Shashank

last: Shekhar

state: New Delhi

address: JNU Campus

department: Special Centre for Molecular Medicine

country: India

institute: Jawaharlal Nehru University

description: Sample

data_processing:
PfMCM6 ChIP-seq high quality paired end reads were mapped with the reference genome downloaded from PlasmoDB database (version=2015-06-18 of P. falciparum 3D7) using Bowtie2 v2.3.4.1 this was followed by sorting (Samtools v1.7) and removal of duplicate reads (Picard). Peak calling was done by MACS2 v2.2.7.1 with 0.05 p-value cutoff.
Assembly: PlasmoDB database (version=2015-06-18 of P. falciparum 3D7)
Supplementary files format and content: broadPeak

organism: Plasmodium falciparum

source_name: Plasmodium falciparum 3D7

growth_protocol: Parasites were cultivated in O+ human erythrocytes at 3% haematocrit in RPMI 1640 medium supplemented with 0.5% Albumax II, 0.2% sodium bicarbonate, 27.2 mg/litre hypoxanthine and 50 mg/litre Gentamycin. The parasites were grown at 37°C in an atmosphere of 5% CO2, 5% O2 and 90% nitrogen. Synchronization of parasites was carried out using 5% sorbitol treatment.

extract_protocol:
Parasites were resuspended in ice cold SDS lysis buffer (1% SDS, 10mM EDTA, 50mM Tris-HCl, pH 8.1) supplemented with PMSF (100μM/ml) and protease inhibitor cocktail for 10 minutes on ice. Parasite lysate was then sonicated to generate the sheared chromatin of ~500bp and centrifuged at 1000g for 15 minutes. After the removal of debris from the lysate, the lysate was further diluted 10 times in ChIP dilution buffer (0.01% SDS, 0.1% Triton-X 100, 1.2mM EDTA, 16.7mM Tris, pH 8.1, and 150mM NaCl). Subsequently, the parasite lysates were precleared using protein A sepharose beads at 4°C for 1 hour. Cleared chromatins were incubated with pre-immune sera and immune MCM6 sera for overnight at 4°C on rotating wheel.
ChIP and Control DNA libraries were generated using NEBNext® Ultra™ II DNA Library Prep Kit for Illumina (#E7645S). The method involves the end repair and A tailing and adapter ligation. The adapter-ligated DNA was enriched by PCR amplification by using Illumina index primers. The final amplified product were purified using Ampure beads to remove unused primers. The library was quantitated using Qubit DNA High Sensitivity quantitation assay and library quality was checked on Bioanalyzer 2100 using Agilent High Sensitivity DNA Kit. The librares were sequenced to generate 150 bases paired end reads using the use of HiSeq.

treatment_protocol: Trophozoite stage parasites with 10% parasitemia were harvested and fixed with 1% formaldehyde at 37°C for 10 minutes. To prevent the over crosslinking, excess formaldehyde was quenched by addition of glycine to a final concentration of 150 mM. After that, the parasitized RBC’s were washed twice with 1x PBS followed by saponin lysis to remove the RBCs.

value: Plasmodium falciparum 3D7

value: Trophozoite

value: none (input)


title: ChIP_PfMCM6

description: Sample

value: Polyclonal antibodies against PfMCM6 (generated in-house)


title: WT_SG_rep1


title: delCsn2-P_L10_rep1

value: Mammary gland


title: delCsn2-P_L1_rep3


title: delCsn2-P_L10_rep2


title: delCsn2-P_L1_rep2


title: delCsn2-P_L1_rep1


title: delCsn2-E123_L1_rep3


title: delCsn2-P-E123_L1_rep2


title: delCsn2-E123_L1_rep4


title: delCsn2-E123_L1_rep2


title: delCsn-SE_SG_rep2

value: delCsn-SE


title: delCsn-SE_SG_rep3


title: delCsn2-E123_L1_rep1


title: delCsn2-E123_L10_rep1


title: WT_virMEC_NFIB

data_processing:
The fastq files were subjected to QC analyses using the FastQC tool (version 0.11.9). Quality filtering and alignment of the raw reads was done using Trimmomatic (version 0.36) and Bowtie (version 1.2.2) and Samtools (version 1.8), with the parameter ‘-m 1’ to keep only uniquely mapped reads, using the reference genome mm10. Homer30 (version 4.9.1) software was applied to generate bedGraph files, seperately. Integrative Genomics Viewer (version 2.3.98) was used for visualization with the parameter of -m 1 to retrieve only uniquely mapped reads, and Picard Tools to remove duplicates. Homer software was applied  for the generation of bedGraph files.
Assembly: mm10
Supplementary files format and content: bedgraph of ChIP-seq

source_name: Mammary epithelial cells

growth_protocol: Mouse mammary gland tissues were harvested at virgin, day six of pregnancy (p6) and day one of lactation (L1). Mouse salivary gland tissues were harvested from male mice of 2-month-old age.

extract_protocol:
Chromatin was fixed with formaldehyde (1% final concentration) for 15 min at room temperature, and then quenched with glycine (0.125 M final concentration). Samples were processed as previously described. The following antibodies were used for ChIP-seq: H3K27ac (Abcam, ab4729), RNA polymerase II (Abcam, ab5408), H3K4me1 (Active Motif, 39297) and H3K4me3 (Millipore, 07-473). Libraries for next-generation sequencing were prepared and sequenced with a HiSeq 3000 instrument (Illumina). Libraries for sequencing were prepared using standard Illumina protocols.
Libraries for sequencing were prepared using standard Illumina protocols.

value: Mammary epithelial cells

value: Virgin

value: wild-type

tag: antibody

value: NFIB (Sigma-Aldrich, HPA003956)


title: WT_SG_PolII_rep2

value: Salivary gland

value: RNA polymerase II (Abcam, ab5408)


title: WT_SG_H3K27ac_rep2

value: H3K27ac (Abcam, ab4729)


title: WT_virMEC_H3K27ac


title: delCsn-SE_SG_rep1


title: WT_virMEC_PolII


title: WT_SG_H3K27ac_rep1


title: WT_p6_PolII_rep2

value: Pregnancy day 6


title: delOdam_SG_PolII_rep2

value: delOdam


title: WT_p6_PolII_rep1


title: WT_SG_PolII_rep1


title: delOdam_SG_H3K27ac_rep2


title: delOdam_SG_PolII_rep1


title: delOdam_SG_H3K27ac_rep1


title: delOdam_L1_STAT5_rep1

value: STAT5A (Santa Cruz Biotechnology, sc-271542)


title: delOdam_L1_STAT5_rep2

value: Lactation day 1


title: delOdam_L1_NFIB_rep1


title: delOdam_L1_PolII_rep2


title: delOdam_L1_PolII_rep1


title: delOdam_L1_H3K27ac_rep2


title: delCsn3-E2-SN_L1_STAT5_rep2


title: delCsn2-E123_L10_rep2

value: Lactation day 10


title: delOdam_L1_H3K27ac_rep1


title: delOdam_L1_GR_rep2

value: GR (Thermo Fisher Scientific, PA1-511A)


title: delCsn3-E2-S_L1_PolII_rep2


title: delCsn3-E2-SN_L1_H3K27ac_rep1


title: delCsn3-E2-SN_L1_STAT5_rep1


title: delCsn3-E2-S_L1_NFIB_rep1


title: delCsn3-E2-S_L1_NFIB_rep2


title: delCsn3-E2-SN_L1_NFIB_rep2


title: delCsn3-E2-SN_L1_H3K27ac_rep2


title: delOdam_L1_GR_rep1


title: delCsn3-E2-SN_L1_NFIB_rep1


title: delCsn3-E2-SN_L1_GR_rep1


title: delCsn3-E2-S_L1_H3K27ac_rep2


title: delCsn3-E1_L1_NFIB_rep1


title: delCsn3-E2-S_L1_STAT5_rep2


title: delCsn3-E2-SN_L1_GR_rep2


title: delCsn3-E2-S_L1_H3K27ac_rep1


title: delCsn3-E2-SN_L1_PolII_rep2


title: delCsn2-P-E123-B_L1_PolII_rep2


title: delCsn2-P-E123-B_L1_STAT5_rep1


title: delCsn2-P-E123-B_L1_PolII_rep1


title: delCsn3-E2-S_L1_GR_rep2


title: delCsn3-E2-S_L1_PolII_rep1


title: delCsn3-E2-S_L1_STAT5_rep1


title: delCsn2-P-E123-B_L1_H3K27ac_rep1


title: delCsn2-P-E123-B_L1_H3K27ac_rep2


title: delCsn2-P-E123-B_L1_STAT5_rep2


title: delCsn3-E1_L1_PolII_rep1


title: delCsn3-E1_L1_PolII_rep2


title: delCsn3-E2-S_L1_GR_rep1


title: delCsn3-E2-SN_L1_PolII_rep1


title: delCsn2-P-E123-A_L1_STAT5_rep2


title: delCsn2-P-E123-A_L1_PolII_rep1


title: delCsn2-P-E123-A_L1_H3K27ac_rep2


title: delCsn2-P-E123-B_L1_GR_rep1


title: delCsn2-P-E123-A_L1_H3K27ac_rep1


title: delCsn2-P-E123-A_L1_STAT5_rep1


title: delCsn2-P-E123-A_L1_GR_rep2


title: delCsn2-P-E123-A_L1_PolII_rep2


title: delCsn2-P-E123_L1_STAT5_rep1


title: delCsn2-P-E123-A_L1_GR_rep1


title: delCsn2-P-E123_L1_STAT5_rep2


title: delCsn2-P-E123_L1_PolII_rep2


title: delCsn2-P-E123_L1_PolII_rep1


title: delCsn2-P-E123_L1_H3K27ac_rep2


title: delCsn2-P-E123_L1_GR_rep1


title: delCsn2-P_L1_STAT5_rep2


title: delCsn2-P_L1_PolII_rep2


title: delCsn2-P_L1_H3K27ac_rep1


title: delCsn2-P_L1_PolII_rep1


title: delCsn2-P_L1_STAT5_rep1


title: delCsn2-P-E123-B_L1_GR_rep2


title: delCsn2-E123_L1_STAT5_rep2


title: delCsn2-E123_L1_H3K27ac_rep2


title: delCsn2-E123_L1_PolII_rep2


title: delCsn2-E123_L1_H3K27ac_rep1


title: delCsn2-P_L1_GR_rep1


title: delCsn2-E123_L1_STAT5_rep1


title: delCsn2-E123_L1_PolII_rep1


title: delCsn2-E23_L1_STAT5_rep2


title: delCsn2-E123_L1_GR_rep1


title: delCsn2-E123_L1_GR_rep2


title: delCsn2-E23_L1_STAT5_rep1


title: delCsn2-E23_L1_PolII_rep1


title: delCsn2-E23_L1_PolII_rep2


title: delCsn2-E23_L1_H3K27ac_rep1


title: delCsn2-E23_L1_H3K27ac_rep2


title: delCsn2-P_L1_H3K27ac_rep2


title: delCsn2-E1_L1_STAT5_rep1


title: delCsn2-E23_L1_GR_rep2


title: delCsn2-E23_L1_GR_rep1


title: delCsn2-E1_L1_STAT5_rep2


title: delCsn2-E1_L1_PolII_rep2


title: delCsn2-E1_L1_PolII_rep1


title: delCsn2-E1_L1_H3K27ac_rep1


title: delCsn2-E1_L1_H3K27ac_rep2


title: delCsn1s1-E2_L1_STAT5_rep1


title: delCsn2-P_L1_GR_rep2


title: delCsn2-E1_L1_GR_rep2


title: delCsn2-P-E123_L1_H3K27ac_rep1


title: delCsn1s1-E2_L1_STAT5_rep2


title: delCsn2-E1_L1_GR_rep1


title: delCsn1s1-E2_L1_NFIB_rep2


title: delCsn1s1-E2_L1_PolII_rep1


title: delCsn1s1-E2_L1_GR_rep2


title: delCsn1s1-E2_L1_H3K27ac_rep1


title: delCsn1s1-E2_L1_H3K27ac_rep2


title: delCsn1s1-E2_L1_NFIB_rep1


title: delCsn1s1-E2_L1_GR_rep1


title: delCsn1s1-E1_L1_STAT5_rep2


title: delCsn1s1-E2_L1_PolII_rep2


title: delCsn1s1-E1_L1_H3K27ac_rep1


title: delCsn1s1-E1_L1_H3K27ac_rep2


title: delCsn1s1-E1_L1_NFIB_rep2


title: delCsn-SE_SG_H3K27ac_rep2


title: delCsn-SE_SG_PolII_rep1


title: wholeblood-ALS-mat-124 [124_WB]

type: other

city: Ulm

first: Karin

last: Danzer

address: Albert-Einstein-Allee 11

institute: DZNE

description: whole blood was used for DNA isolation

hyb_protocol: GeneChip® CustomSeq® Resquencing Array Protocol Version 2.1 ; 270ng of fragmented mtDNA were hybridized to GeneChip™ Human Mitochondrial Resequencing Arrays 2.0 (MitoChip v2.0, Zhou et al., 2006 ).

scan_protocol: GeneChip® CustomSeq® Resquencing Array Protocol Version 2.1; The Arrays were washed using Affymetrix fluidics station FS450, and scanned using the Gene Chip Scanner 3000 7G.

data_processing: GSEQ Version 4.1.1

label: biotin

molecule: other

source_name: whole blood (EDTA, frozen) of fALS patient with maternal inheritance

extract_protocol: QiaAmp Blood Kit for DNA isolation; REPLI-g mitochondrial DNA kit (Qiagen, Hilden, Germany)  for amplification of mtDNA; Purification using Agencourt® AMPure® XP magnetic beads (QIAGEN Supplementary Protocol, REPLI-g mitochondrial DNA kit)

tag: mat vs non-mat

value: maternal

tag: disease state

value: ALS

tag: age

tag: gender

value: m

tag: mutation

value: whole blood


title: wholeblood-ALS-mat-120 [120_WB]

description: whole blood was used for DNA isolation

label_protocol: GeneChip® CustomSeq® Resquencing Array Protocol Version 2.1

value: f

tag: cell type


title: wholeblood-ALS-mat-122 [122_WB]

description: whole blood was used for DNA isolation

value: FUS


title: delCsn1s1-E1_L1_PolII_rep1

tag: tissue

value: Mammary gland

tag: genotype


title: delCsn1s1-E1_L1_NFIB_rep1

value: NFIB (Sigma-Aldrich, HPA003956)


title: delCsn1s1-E1_L1_GR_rep1


title: wholeblood-ALS-nonmat-125 [125_WB]

description: whole blood was used for DNA isolation

source_name: whole blood (EDTA, frozen) of fALS patient with non-maternal inheritance

value: non-maternal


title: delCsn-SE_SG_H3K27ac_rep1

value: Salivary gland

value: delCsn-SE


title: wholeblood-ALS-nonmat-119 [119_WB]

description: whole blood was used for DNA isolation


title: wholeblood-contr-116 [116_WB]

description: whole blood was used for DNA isolation

source_name: whole blood (EDTA, frozen) of control person

value: Control

value: control


title: wholeblood-ALS-mat-121 [121_WB]

description: whole blood was used for DNA isolation


title: wholeblood-ALS-nonmat-118 [118_WB]

description: whole blood was used for DNA isolation


title: wholeblood-contr-114 [114_WB]

description: whole blood was used for DNA isolation


title: wholeblood-contr-113 [113_WB]

description: whole blood was used for DNA isolation


title: wholeblood-ALS-nonmat-112 [112_WB]

description: whole blood was used for DNA isolation


title: wholeblood-contr-111 [111_WB]

description: whole blood was used for DNA isolation


title: wholeblood-contr-107 [107_WB]

description: whole blood was used for DNA isolation


title: delCsn1s1-E1_L1_STAT5_rep1

value: STAT5A (Santa Cruz Biotechnology, sc-271542)


title: wholeblood-contr-110 [110_WB]

description: whole blood was used for DNA isolation


title: wholelbood-contr-104 [104_WB]

description: whole blood was used for DNA isolation


title: wholelbood-contr-106 [106_WB]

description: whole blood was used for DNA isolation


title: delCsn1s1-E1_L1_GR_rep2

value: Lactation day 1


title: delCsn1s1-E1_L1_PolII_rep2

value: RNA polymerase II (Abcam, ab5408)


title: delCsn-SE_SG_PolII_rep2


title: wholeblood-contr-103 [103_WB]

description: whole blood was used for DNA isolation


title: wholeblood-contr-98 [98_WB]

description: whole blood was used for DNA isolation


title: wholeblood-ALS-mat-97 [97_WB]

description: whole blood was used for DNA isolation


title: wholeblood-contr-99 [99_WB]

description: whole blood was used for DNA isolation


title: whitebloodcells-contr-86 [86_WBC]

description: isolation of white blood cells by differential centrifugation and subsequent clean up of the sample by depletion of CD61 positive cells using magnetic beads (MACS miltenyi)

source_name: White blood cells isolated from fresh EDTA blood of a control person

value: white blood cells


title: wholeblood-ALS-mat-87 [87_WB]

description: whole blood was used for DNA isolation

value: maternal


title: wholeblood-contr-96 [96_WB]

description: whole blood was used for DNA isolation


title: wholeblood-contr-94 [94_WB]

description: whole blood was used for DNA isolation


title: whitebloodcells-contr-87 [87_WBC]


title: wholeblood-ALS-mat-93 [93_WB]

description: whole blood was used for DNA isolation

value: ALS


title: wholeblood-contr-95 [95_WB]

description: whole blood was used for DNA isolation


title: wholeblood-contr-88 [88_WB]

description: whole blood was used for DNA isolation


title: wholeblood-contr-102 [102_WB]

description: whole blood was used for DNA isolation


title: whitebloodcells-ALS-nonmat-83 [83_WBC]

source_name: White blood cells isolated from fresh EDTA blood of a fALS patient with non-maternal inheritance


title: whitebloodcells-ALS-nonmat-84 [84_WBC]


title: wholeblood-contr-84 [84_WB]

description: whole blood was used for DNA isolation

value: m


title: whitebloodcells-contr-85 [85_WBC]


title: wholeblood-contr-92 [92_WB]

description: whole blood was used for DNA isolation

value: whole blood


title: whitebloodcells-contr-79 [79_WBC]


title: whitebloodcells-ALS-nonmat-82 [82_WBC]


title: whitebloodcells-ALS-mat-81 [81_WBC]

source_name: White blood cells isolated from fresh EDTA blood of a fALS patient with maternal inheritance


title: wholeblood-contr-83 [83_WB]

description: whole blood was used for DNA isolation


title: whitebloodcells-contr-80 [80_WBC]


title: wholeblood-contr-79 [79_WB]

description: whole blood was used for DNA isolation

value: f


title: wholeblood-contr-91 [91_WB]

description: whole blood was used for DNA isolation


title: wholeblood-ALS-mat-90 [90_WB]

description: whole blood was used for DNA isolation

value: FUS


title: whitebloodcells-contr-88 [88_WBC]


title: wholeblood-contr-86 [86_WB]

description: whole blood was used for DNA isolation


title: whitebloodcells-contr-78 [78_WBC]


title: whitebloodcells-contr-77 [77_WBC]


title: wholeblood-contr-77 [77_WB]

description: whole blood was used for DNA isolation


title: whitebloodcells-contr-76 [76_WBC]


title: wholeblood-contr-80 [80_WB]

description: whole blood was used for DNA isolation


title: wholeblood-contr-76 [76_WB]

description: whole blood was used for DNA isolation


title: whitebloodcells-ALS-nonmat-74 [74_WBC]


title: wholeblood-contr-74 [74_WB]

description: whole blood was used for DNA isolation


title: whitebloodcells-contr-75 [75_WBC]


title: whitebloodcells-ALS-mat-71 [71_WBC]


title: whitebloodcells-ALS-nonmat-73 [73_WBC]


title: whitebloodcells-ALS-nonmat-72 [72_WBC]


title: MRSA monoculture in TSB, replicate 4

city: Philadelphia

first: Monica

middle: H

last: Wei

state: PA

address: 421 Curie Blvd, BRB II/III 1046

department: Department of Dermatology

institute: University of Pennsylvania

data_processing:
Kallisto v 0.48.0 against cds from NC_010079.1 (USA300 representative genome)
edgeR v 3.40.2 TMM normalization after filtering (genes with mean count <1 per sample per group removed)
Assembly: NC_010079.1
Supplementary files format and content: abundance.tsv files from Kallisto
Supplementary files format and content: edgeR output as matrix table with log2 transformed counts

organism: Staphylococcus aureus

source_name: cell culture

growth_protocol: 1 mL S. aureus (OD = 0.05) was growtn in TSB in the bottom well of a Corning transwell .4uM 12 well culture dish.  500uL TSB (ctrl) or D. incerta (OD = 2.0) was grown in the top well

extract_protocol:
ZymoResearch DirectZol RNA-Purification Kit
Stranded Total RNA Prep Ligation with Ribo-Zero Plus kit and 10bp IDT for Illumina indices (SeqCenter)

value: cell culture

tag: cell line

value: ATCC cat.# BAA-1717

tag: treatment

value: monoculture in TSB


title: MRSA coculture with D. incerta, replicate 3

value: coculture with D. incerta


title: MRSA monoculture in TSB, replicate 1


title: MRSA coculture with D. incerta, replicate 1


title: whitebloodcells-ALS-mat-70 [70_WBC]


title: MRSA coculture with D. incerta, replicate 2


title: Gpr44 homozygous knockout AML3

city: University Park,

first: Sandeep

last: Prabhu

state: Pennsylvania

address: 108 K Animal & Veterinary and Biomedical Sciences (AVBS) Building

department: Veterinary and Biomedical Science

institute: the Pennsylvania State University

data_processing:
After sequencing, sequence quality per based was checked by FastQC (v0.11.2).
The filtered reads were aligned to the GRCm38.p6 (mm10) from EMBL-EBI with Burrows-Wheeler Aligner (BWA, v 0.7.17-r1188). The large nucleotide sequence alignments were sorted and indexed, and the alignment reports were generated by using SAMtools (v1.10).
The raw count matrix for genes was obtained from featureCounts (v2.0.0).
Genes were annotated against the GENCODE vM18 from EMBL-EBI while generating the count matrix.
Assembly: GRCm38.p6 (mm10)
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample

source_name: bone marrow

growth_protocol: Bone marrow cells isolated from CD45.1 wild type and CD45.2 gpr44 knockout female C57BL/6 mice were selected by lineage negative selection kit and stained with sca-1 and ckit fluorescent antibodies. Hematopoietic stem cellls were sorted as Lin-Sca-1+c-Kit+ population and transduced with MLL-AF9-oncogene virus; then cells were transplanted into CD45.2 and RFP+ mice for CD45.1 WT and CD45.2 gpr44 knockout donors, respectively. When recipient mice showed signs of leukemia, mice were euthanized and spleens were isolated to acquire luekemia cells for secondary transplantation. Secondary transplantation was done on CD45.2 male mice and RFP+ male mice for CD45.1 WT and gpr44 knockout AML donor cells. When secondary recipient mice showed full-blown AML, bone marrow cells were isolated. Wild type and gpr44 knockout leukemia-initiating cells were sorted as CD45.1+Lin-sca-1-c-Kit+ and RFP-Lin-Sca-1-c-Kit+ populations, respectively. In the meantime, Lin-sca-1-c-Kit+ cells were also isolated from wild type, gpr44 heterozygous knockout, and gpr44 homozygous knockout female mice. Each group has three mice

extract_protocol:
Total RNA was extracted from sorted cells with TRIzol reagent (Thermo Fisher Scientific) and the quality of extracted RNA (concentration, total mass, RNA integrity and 28S/18S ratio) was validated by an RNA 6000 Nano kit on an Agilent 2100 Bioanalyzer system.
Library preparation for next generation sequencing was performed by using MGIEasy RNA Library Prep Kit according to the manufacturer’s instructions. RNA sequencing was performed for each sample by using DNA nanoball sequencing technology on a DNBSEQ-T7 sequencer with 40 million 100 bp paired-end reads.

treatment_protocol: no special treatments on the sorted cells

tag: Sex

value: female

value: AML

value: Gpr44 honozygous knockout

tag: cell marker


title: wholeblood-contr-70 [70_WB]

description: whole blood was used for DNA isolation

value: Control

value: control


title: Gpr44 homozygous knockout AML1

tag: strain


title: whitebloodcells-ALS-nonmat-69 [69_WBC]

value: non-maternal


title: Gpr44 homozygous knockout AML2


title: wholeblood-contr-71 [71_WB]

description: whole blood was used for DNA isolation


title: wholeblood-contr-69 [69_WB]

description: whole blood was used for DNA isolation


title: whiteblood-contr-68 [68_WBC]

value: white blood cells


title: WT AML3

value: wild type


title: WT AML2


title: WT AML1


title: MRSA coculture with D. incerta, replicate 4


title: wholeblood-ALS-mat-68 [68_WB]

description: whole blood was used for DNA isolation

value: maternal

value: ALS


title: normal Gpr44 homozygous knockout3

value: healthy

value: Gpr44 homozygous knockout


title: MRSA monoculture in TSB, replicate 3


title: MRSA monoculture in TSB, replicate 2


title: whitebloodcells-contr-67 [67_WBC]

value: m


title: wholeblood-contr-67 [67_WB]

description: whole blood was used for DNA isolation

value: whole blood


title: normal Gpr44 homozygous knockout2


title: normal Gpr44 homozygous knockout1


title: whitebloodcells-contr-66 [66_WBC]


title: wholeblood-ALS-mat66 [66_WB]

description: whole blood was used for DNA isolation


title: normal Gpr44 heterozygous knockout3

value: Gpr44 heterozygous knockout


title: normal Gpr44 heterozygous knockout2


title: whitebloodcells-contr-65 [65_WBC]


title: normal WT3


title: normal WT1


title: H3K27ac_ChIP_NPC2_MLL34dCD_MLL2dTAG_rep2

city: La Jolla

first: Bing

last: Ren

state: CA

address: 9500 Gilman Dr., CMM-East, Admin Area/Rm 2071

institute: University of California, San Diego School of Medicine

data_processing:
The processed files (bigWig) were created using deepTools (Ramírez et al., 2016).
Supplementary files format and content: bigWig

source_name: E14 mouse neural precursor cell

growth_protocol: Cells were grown in DMEM supplemented with 100 U/mL penicillin, 100 mg/mL streptomycin, 15% KnockOut Serum Replacement (ThermoFisher, 10828028), Glutamax (Gibco, 35050), 0.1 mM non-essential amino acid, 0.1mM beta-mercaptoethanol, and 500 U/ml LIF at 37°C and 5% CO2

extract_protocol: ChIP and input library preparation were carried out as described in ENCODE experiments (“Ren Lab ENCODE Chromatin Immunoprecipitation Protocol” in https://www.encodeproject.org/documents/)

treatment_protocol: For the dTAG treatment, 2uM ofdTAG-13 (Tocris Bioscience) was added from day 1 of NPC differentiation and cells were harvested on day 4.

value: E14 mouse neural precursor cell

tag: chip antibody

value: MLL3/4 dCD+MLL2 dTAG

value: dTAG-13 + RA


title: normal WT2

value: female


title: normal Gpr44 heterozygous knockout1


title: H3K27ac_ChIP_NPC2_MLL34dCD_MLL2dTAG_rep1


title: whitebloodcells-contr-64 [64_WBC]

value: f


title: whitebloodcells-contr-63 [63_WBC]


title: wholeblood-ALS-mat-65 [65_WB]

description: whole blood was used for DNA isolation


title: wholeblood-contr-63 [63_WB]

description: whole blood was used for DNA isolation

value: Control


title: whitebloodcells-ALS-nonmat-61 [61_WBC]


title: wholeblood-contr-62 [62_WB]

description: whole blood was used for DNA isolation

value: control


title: H3K27ac_ChIP_NPC2_MLL34dCD_rep1

value: MLL3/4 dCD


title: wholeblood-ALS-mat-61 [61_WB]

description: whole blood was used for DNA isolation


title: H3K27ac_ChIP_NPC2_WT-MLL2dTAG_rep2

value: MLL2 dTAG


title: H3K27ac_ChIP_NPC2_WT_rep2

value: wild type


title: H3K27ac_ChIP_NPC2_WT-MLL2dTAG_rep1


title: whitebloodcells-ALS-nonmat-59 [59_WBC]

value: non-maternal

value: white blood cells


title: wholeblood-contr-60 [60_WB]

description: whole blood was used for DNA isolation


title: H3K27ac_ChIP_NPC2_WT_rep1


title: wholeblood-ALS-nonmat-59 [59_WB]

description: whole blood was used for DNA isolation

value: ALS


title: H3K27ac_ChIP_ESC2_MLL34dCD_MLL2dTAG_rep2

source_name: E14 mouse embryonic stem cell

value: E14 mouse embryonic stem cell


title: whitebloodcells-ALS-nonmat-58 [58_WBC]

value: m


title: whitebloodcells-ALS-nonmat-62 [62_WBC]


title: wholeblood-ALS-mat-58 [58_WB]

description: whole blood was used for DNA isolation

value: maternal

value: whole blood


title: whitebloodcells-ALS-nonmat-57 [57_WBC]


title: H3K27ac_ChIP_ESC2_MLL34dCD_rep1


title: H3K27ac_ChIP_ESC2_MLL34dCD_MLL2dTAG_rep1


title: H3K27ac_ChIP_ESC2_WT_rep2


title: H3K27ac_ChIP_ESC2_WT-MLL2dTAG_rep2


title: H3K4me3_ChIP_NPC2_MLL34dCD_MLL2dTAG_rep2

value: E14 mouse neural precursor cell


title: H3K27ac_ChIP_NPC2_MLL34dCD_rep2


title: wholeblood-ALS-mat-56 [56_WB]

description: whole blood was used for DNA isolation


title: whitebloodcells-contr-55 [55_WBC]


title: H3K4me3_ChIP_NPC2_MLL34dCD_MLL2dTAG_rep1

value: MLL3/4 dCD+MLL2 dTAG


title: whitebloodcells-contr-56 [56_WBC]


title: H3K27ac_ChIP_ESC2_WT_rep1


title: wholeblood-ALS-nonmat-57 [57_WB]

description: whole blood was used for DNA isolation

value: FUS


title: wholeblood-ALS-mat-55 [55_WB]

description: whole blood was used for DNA isolation


title: H3K27ac_ChIP_ESC2_WT-MLL2dTAG_rep1


title: whitebloodcells-contr-54 [54_WBC]


title: whiteblood-ALS-nonmat-60 [60_WBC]


title: H3K4me3_ChIP_NPC2_MLL34dCD_rep2

value: dTAG-13 + RA


title: H3K4me3_ChIP_NPC2_MLL34dCD_rep1


title: whitebloodcells-contr-53 [53_WBC]

value: f


title: wholeblood-ALS-mat-53 [53_WB]

description: whole blood was used for DNA isolation


title: whitebloodcells-contr-52 [52_WBC]


title: H3K4me3_ChIP_NPC2_WT-MLL2dTAG_rep1


title: H3K4me3_ChIP_NPC2_WT_rep2


title: whitebloodcells-contr-51 [51_WBC]


title: H3K4me3_ChIP_ESC2_MLL34dCD_MLL2dTAG_rep2


title: wholeblood-ALS-nonmat-51 [51_WB]

description: whole blood was used for DNA isolation


title: whitebloodcells-ALS-nonmat-50 [50_WBC]


title: H3K4me3_ChIP_ESC2_MLL34dCD_MLL2dTAG_rep1


title: whitebloodcells-ALS-nonmat-49 [49_WBC]


title: H3K4me3_ChIP_ESC2_MLL34dCD_rep1


title: wholeblood-ALS-mat-54 [54_WB]

description: whole blood was used for DNA isolation


title: whitebloodcells-ALS-mat-47 [47_WBC]


title: wholeblood-ALS-nonmat-47 [47_WB]

description: whole blood was used for DNA isolation


title: H3K4me3_ChIP_ESC2_WT_rep2


title: whitebloodcells-ALS-nonmat-48 [48_WBC]


title: wholeblood-ALS-mat-46 [46_WB]

description: whole blood was used for DNA isolation


title: H3K4me3_ChIP_ESC2_WT-MLL2dTAG_rep2


title: H3K4me3_ChIP_ESC2_WT-MLL2dTAG_rep1


title: H3K4me1_ChIP_NPC2_MLL34dCD_MLL2dTAG_rep1


title: H3K4me3_ChIP_ESC2_WT_rep1


title: H3K4me3_ChIP_NPC2_WT-MLL2dTAG_rep2


title: H3K4me1_ChIP_NPC2_MLL34dCD_MLL2dTAG_rep2


title: whitebloodcells-ALS-mat-45 [45_WBC]


title: wholeblood-ALS-nonmat-45 [45_WB]

description: whole blood was used for DNA isolation


title: H3K4me1_ChIP_NPC2_MLL34dCD_rep2


title: wholeblood-ALS-nonmat-44 [44_WB]

description: whole blood was used for DNA isolation


title: wholeblood-ALS-nonmat-52 [52_WB]

description: whole blood was used for DNA isolation


title: H3K4me3_ChIP_NPC2_WT_rep1


title: H3K4me1_ChIP_NPC2_WT-MLL2dTAG_rep2


title: platelets-contr-44 [44_PLT]

description: isolation of platelets by differential centrifugation and subsequent clean up of the sample by depletion of CD45 positive cells using magnetic beads (MACS miltenyi)

source_name: Platelets isolated from fresh EDTA blood of a control person

value: platelets


title: platelets-contr-43 [43_PLT]

value: control


title: platelets-contr-42 [42_PLT]


title: H3K4me1_ChIP_NPC2_WT_rep2


title: H3K4me3_ChIP_ESC2_MLL34dCD_rep2

value: MLL3/4 dCD


title: whitebloodcells-ALS-mat-46 [46_WBC]


title: H3K4me1_ChIP_NPC2_WT_rep1


title: H3K4me1_ChIP_ESC2_MLL34dCD_MLL2dTAG_rep2


title: platelets-contr-41 [41_PLT]


title: platelets-contr-40 [40_PLT]


title: wholeblood-ALS-nonmat-39 [39_WB]

description: whole blood was used for DNA isolation


title: H3K4me1_ChIP_ESC2_MLL34dCD_rep2


title: H3K4me1_ChIP_ESC2_MLL34dCD_rep1


title: H3K4me1_ChIP_ESC2_WT-MLL2dTAG_rep1

value: MLL2 dTAG


title: wholeblood-ALS-nonmat-38 [38_WB]

description: whole blood was used for DNA isolation


title: H3K4me1_ChIP_ESC2_WT_rep2

value: wild type


title: platelets-ALS-nonmat-36 [36_PLT]

source_name: Platelets isolated from fresh EDTA blood of a fALS patient with non-maternal inheritance

value: non-maternal


title: platelets-ALS-nonmat-35 [35_PLT]


title: H3K4me1_ChIP_ESC2_MLL34dCD_MLL2dTAG_rep1


title: platelets-ALS-mat-37 [37_PLT]

source_name: Platelets isolated from fresh EDTA blood of a fALS patient with maternal inheritance


title: H3K4me1_ChIP_ESC2_WT-MLL2dTAG_rep2


title: platelets-ALS-nonmat-39 [39_PLT]


title: H3K4me1_ChIP_NPC2_MLL34dCD_rep1


title: H3K4me1_ChIP_ESC2_WT_rep1


title: C57BL/6, morphine, rep 4

city: Haikou

first: Feifan

last: Zhou

address: 58 Renmin Avenue

institute: Hainan University

data_processing:
Reads obtained from the sequencing machines includes raw reads containing adapters or low quality bases which will affect the following assembly and analysis. Thus, to get high quality clean reads, reads were further filtered by fastp (version 0.18.0).
Short reads alignment tool Bowtie2 (version 2.2.8) was used for mapping reads to ribosome RNA (rRNA) database. The rRNA mapped reads then will be removed. The remaining clean reads were further used in assembly and gene abundance calculation.
An index of the reference genome was built, and paired-end clean reads were mapped to the reference genome using HISAT2. 2.4 with “-rna-strandness RF” and other parameters set as a default.
The mapped reads of each sample were assembled by using StringTie v1.3.1 in a reference-based approach. For each transcription region, a FPKM (fragment per kilobase of transcript per million mapped reads) value was calculated to quantify its expression abundance and variations, using RSEM software.
Given FPKM(A) to be the expression of gene A, C to be number of fragments mapped to gene A, N to be total number of fragments that mapped to reference genes, and L to be number of bases on gene A. The FPKM method is able to eliminate the influence of different gene lengths and sequencing data amount on the calculation of gene expression. Therefore, the calculated gene expression can be directly used for comparing the difference of gene expression among samples.
Assembly: mm10
Supplementary files format and content: FPKM values for each sample

source_name: nucleus accumbens

extract_protocol:
Total RNA was extracted using Trizol reagent (Invitrogen,15596018)
The cell lysis or the extracted total RNA was mixed with 1 μl of 10 μM Oligo-dT primer and 1 μl of 10 μM dNTP reagent and then incubated at 72℃ for 3 min. The reverse transcription reaction was performed in 1X Super Script II first-strand buffer system with 200 U of Super Script II reverse transcriptase, 0.1 μl of TSO (100 μM), 20 U RNAse Inhibitor, 0.75ul of DTT (100 mM), 3 μl of Betaine (5 M) and 0.09 μl of MgCl2 (1 M). The full length cDNA was synthesized at 42℃ for 90 min and then with 10 cycles of 50℃ for 2 min and 42℃ for 2 min. Finally, the product was incubated at 70℃ for 15 min to inactive the enzyme activation. After amplified the synthesized cDNA with 10 to 15 cycles of PCR amplification, the product was purified and used for library construction. After analyzed by Agilent Bioanalyzer and quantified by real time PCR, the library was sequenced with Illumina Novaseq platform.

value: nucleus accumbens

value: morphine


title: C57BL/6, morphine, rep 3


title: wholeblood-ALS-nonmat-34 [34_WB]

description: whole blood was used for DNA isolation

value: ALS


title: platelets-contr-34 [34_PLT]

value: m


title: H3K4me1_ChIP_NPC2_WT-MLL2dTAG_rep1


title: wholeblood-contr-33 [33_WB]

description: whole blood was used for DNA isolation

value: Control


title: C57BL/6, morphine, rep 1


title: platelets-contr-33 [33_PLT]


title: C57BL/6, morphine, rep 2


title: C57BL/6, saline, rep 4

value: saline


title: whoelblood-contr-32 [32_WB]

description: whole blood was used for DNA isolation

value: whole blood


title: platelets-ALS-nonmat-38 [38_PLT]


title: platelets-contr-32 [32_PLT]


title: C57BL/6, saline, rep 2


title: C57BL/6, saline, rep 1


title: platelets-contr-31 [31_PLT]


title: whoelblood-ALS-mat-40 [40_WB]

description: whole blood was used for DNA isolation

value: maternal


title: wholeblood-contr-30 [30_WB]

description: whole blood was used for DNA isolation


title: C57BL/6, saline, rep 3


title: platelets-contr-30 [30_PLT]


title: wholeblood-contr-28 [28_WB]

description: whole blood was used for DNA isolation


title: platelets-contr-29 [29_PLT]


title: wholeblood-ALS-nonmat-29 [29_WB]

description: whole blood was used for DNA isolation


title: platelets-ALS-nonmat-28 [28_PLT]


title: platelets-ALS-mat-27 [27_PLT]


title: wholeblood-ALS-nonmat-27 [27_WB]

description: whole blood was used for DNA isolation


title: platelets-ALS-nonmat-26 [26_PLT]


title: platelets-ALS-nonmat-25 [25_PLT]


title: Il12rb2fl_naive_2

city: Zurich

first: Genome

last: Informatics

address: Winterthurerstrasse 190

department: Functional Genomics Center Zurich (FGCZ)

country: Switzerland

institute: ETH ZURICH / University of Zurich

library_source: transcriptomic single cell

data_processing:
CellRanger software (v6.0.2) was implemented for library demultiplexing, barcode processing, fastq file generation, gene alignment to the mouse genome (GENCODE reference build GRCm39), and unique molecular identifier (UMI) counts. We implemented the 'include-introns' option for counting intronic reads, as the snRNA-seq assay captures unspliced pre-mRNA as well as mature mRNA. For each sample, a CellRanger report was obtained with all the available information regarding sequencing and mapping parameters. All samples were merged into a matrix using CellRanger (cellranger -aggr function).
Assembly: GRCm39
Supplementary files format and content: 10x Genomics output files: barcodes.tsv.gz, features.tsv.gz, matrix.mtx.gz

source_name: CNS

extract_protocol:
Mouse cerebellum and brainstem (of one brain hemisphere) and cervical spinal cord (C1-C2) were harvested from adult male mice (8-12 weeks old) and immediately snap-frozen in liquid nitrogen and stored at -80oC until further processing. Nuclei were isolated with the EZ PREP lysis buffer (#NUC-101, Sigma). Tissue samples were homogenized using a glass dounce tissue grinder (#D8938, Sigma) (25 strokes with pastel A, 25 strokes with pastel B) in 2 ml of ice-cold EZ prep lysis buffer and incubated on ice with an additional 2 ml of ice-cold EZ PREP lysis buffer. During incubation, 1 μΜ of Hoechst (#H3570, Thermo Fisher Scientific) dye and 40 U/μl of RiboLock inhibitors (#EO0382, Thermo Fisher Scientific) were added to the homogenate. Following incubation, the homogenate was filtered through a 30 μM FACS tube filter. Nuclei were sorted based on the fluorescent Hoechst signal using a BD FACS Aria sorter III with an 85 μm nozzle configuration at 4oC, directly into PBS + 4% BSA + RiboLock inhibitors (40 U/μl) (Cat # EO0382). As CNS nuclei vary strongly in size, no doublet exclusion was performed based on FSC or SSC to avoid bias against nucleus size. Nuclei were then counted based on brightfield image and Trypan Blue staining (Cat # 15250061) using a Neubauer counting chamber and a Keyence BZX-710 microscope.
Library was performed according to the manufacter’s instructions (single cell 3’ v2 protocol, 10x Genomics). Briefly, GCs were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead-in-emulsion (GEM). The poly-A RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA, which contains an Ilumina R1 primer sequence, Unique Molecular Identifier (UMI) and the 10x Barcode. The pooled barcoded cDNA was then cleaned up with Silane DynaBeads, amplified by PCR and the apropiated sized fragments were selected with SPRIselect reagent for subsequent library construction. During the library construction Ilumina R2 primer sequence, paired-end constructs with P5 and P7 sequences and a sample index were added.

treatment_protocol: EAE was induced by injection of 200 μg of myelin oligodendrocyte glycoprotein epitope MOG35-55 (#RP10245, Genscript) emulsified in complete Freund’s adjuvant (CFA) (#231131, BD). All mice received two subcutaneous (s.c.) injections into the flank, each of 100 μl of the freshly prepared MOG-CFA mixture and a single intraperitoneal injection (i.p.) of 50-100 ng pertussis toxin (PT) (List Biological Laboratories, #179A).

value: CNS

value: male

value: nuclei

value: non-immunized

tag: sequencing batch

value: Run 2


title: NestinCre_Il12rb2fl_EAE_2

value: Experimental Autoimmune Encephalomyelitis- day 10

value: Run 1


title: NestinCre_Il12rb2fl_EAE


title: NestinCre_Il12rb2fl_EAE_3


title: Il12rb2fl_naive_3

value: Run 3


title: NestinCre_Il12rb2fl_EAE_1


title: wholeblood-ALS-nonmat-31 [31_WB]

description: whole blood was used for DNA isolation

value: non-maternal


title: NestinCre_Il12rb2fl_naive_2


title: Il12rb2fl_EAE


title: Il12rb2fl_EAE_2


title: Il12rb2fl_EAE_1


title: platelets-ALS-nonmat-24 [24_PLT]

value: platelets


title: platelets-ALS-nonmat-23 [23_PLT]

value: f


title: platelets-contr-22 [22_PLT]

value: control


title: wholeblood-contr-22 [22_WB]

description: whole blood was used for DNA isolation


title: platelets-contr-21 [21_PLT]


title: wholeblood-contr-20 [20_WB]

description: whole blood was used for DNA isolation


title: Il12rb2fl_EAE_3


title: platelets-contr-19 [19_PLT]


title: platelets-contr-18 [18_PLT]


title: wholeblood-ALS-nonmat-19 [19_WB]

description: whole blood was used for DNA isolation

value: ALS

value: m


title: platelts-contr-17 [17_PLT]


title: wholeblood-contr-17 [17_WB]

description: whole blood was used for DNA isolation


title: platelets-contr-20 [20_PLT]


title: wholeblood-contr-16 [16_WB]

description: whole blood was used for DNA isolation


title: Trim33 KO HU rep2

city: Tübingen

first: Nikita

last: Popov

address: Otfried-Müller-Str 14

department: Clinical Tumor Biology

institute: University Hospital Tübingen

data_processing:
Sequencing was performed on the Illumina NovaSeq 6000, SP flow cell, 2 x 51 bp
Demultiplexing of the sequencing reads was performed with Illumina bcl2fastq (2.20). Adapters were trimmed with Skewer (version 0.2.2); the quality of the FASTQ files was analyzed with FastQC (version 0.11.5-cegat).
Reads were aligned to mouse genome (mm19) with STAR (2.5.4) and differentially expressed genes were determined using EdgeR (3.26.8).
Assembly: mm9
Supplementary files format and content: Tab-delimited text files (EdgeR output) include differential expression (log2FC) and average logCPM values for Trim33-KO vs Trim33-Ctrl  or HU-treated vs Ctrl samples.
Supplementary files format and content: Tab-delimited text file with normalized counts for all libraries

source_name: liver

growth_protocol: p19Nras cells were cultured in DMEM supplemented with 10% fetal bovine serum (FBS) and 1% Pen-Strep in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
Total RNA was extracted using TRIzol reagent (Sigma). 1 ug of total RNA was used for the construction of sequencing libraries.
RNA-seq libraries were prepared using NEBNext® Ultra™ II RNA Library Prep Kit for Illumina® following manufacturer's protocol.

treatment_protocol: 1mM HU or control for 4 hours

value: liver

value: HCC

value: HU


title: Trim33 WT HU rep2

value: sgCtrl


title: platelets-ALS-nonmat-15 [15_PLT]


title: platelts-ALS-nonmat-16 [16_PLT]


title: Trim33 KO rep2

value: Vehicle


title: wholeblood-ALS-nonmat-14 [14_WB]

description: whole blood was used for DNA isolation

value: whole blood


title: wholeblood-contr-15 [15_WB]

description: whole blood was used for DNA isolation


title: wholeblood-ALS-nonmat-23 [23_WB]

description: whole blood was used for DNA isolation


title: plateltes-ALS-nonmat-14 [14_PLT]


title: Trim33 KO HU rep1


title: Trim33 WT rep 2


title: wholeblood-ALS-nonmat-21 [21_WB]

description: whole blood was used for DNA isolation


title: Trim33 KO rep1


title: Trim33 WT HU rep1


title: wholeblood-ALS-nonmat-13 [13_WB]

description: whole blood was used for DNA isolation


title: Trim33 WT rep 1


title: wholeblood-contr-18 [18_WB]

description: whole blood was used for DNA isolation


title: platelets-ALS-nonmat-13 [13_PLT]


title: irCLIP_cap_1

city: Wako

first: tomoya

last: fujita

state: Saitama

address: 2-1, Hirosawa

department: Cluster for Pioneering Research

institute: RIKEN

description: irCLIP-seq

data_processing:
Basecalling with Illumina Casava 1.8 software
3' adapter trimming with FastX-toolkit
Library sorting based on sample barcode sequence with custom script
Random barcode triming with custom script
rRNA and other non-coding RNA alignment with bowtie2 v2.1.0
Alignment with bowtie2 v2.1.0
Read quantitation using custom scripts
Genome_build: NC_000913.2
Supplementary_files_format_and_content: text files contain three columns: 1. transcript name;2. CDS region (nt) used for read counting;3. read counts

organism: Escherichia coli str. K-12 substr. MG1655

extract_protocol: MNase footprinting, ribosome pelleting, RNA extraction, preadenylated linker ligation, rRNA depeletion, reverse transcription, cDNA circularization, PCR amplification  (for ribosome profiling) or deacylation reaction, preadenylated linker ligation, rRNA depeletion, reverse transcription, cDNA circularization, PCR amplification  (for tRNA-seq) or ultraviolet crosslinking, ribosome pelleting, on beads MNase treatment, preadenylated linker ligation, RNA extraction, rRNA depeletion, reverse transcription, cDNA circularization, PCR amplification (for irCLIP-seq)

tag: agent

value: capreomycin 2000 microg/ml


title: irCLIP_cm_1

description: irCLIP-seq

value: chloramphenicol


title: irCLIP_cm_2

description: irCLIP-seq


title: irCLIP_cap_2

description: irCLIP-seq


title: wholeblood-ALS-nonmat-12 [12_WB]

description: whole blood was used for DNA isolation


title: tRNA_input

description: tRNA-seq


title: tRNA_RNC1

description: tRNA-seq


title: tRNA_RNC2

description: tRNA-seq


title: Trim33WT_HU NP7

data_processing:
Demultiplexing of the sequencing reads was performed with Illumina bcl2fastq (version 2.20). Adapters were trimmed with Skewer (version 0.2.2).
Reads were aligned to mouse genome (mm9) with STAR (version 2.5.4) and tag directories were generated using Homer (version 4.10.3)
Bedgraph files were generated using Homer makeUCSCfile script
Sequencing tag coverage was calculated using Homer annotatePeaks script
Assembly: mm9
Supplementary files format and content: Bedgraph

extract_protocol:
Cells were fixed with 0.2% formaldehyde and Cut&Run assay was performed using the  anti-E2f4 antibody (Proteintech, 10923-1-AP) and the NEB CUT&RUN kit (#86652P)
Sequencing libraries were prepared using NEBNext Ultra II DNA Library Prep Kit for Illumina according to manufacturer's protocol

treatment_protocol: Hydrohyurea at 1 mM (or vehicle - water) was added to cell culture medium for 4 hours


title: Trim33WT_Ctrl NP5


title: platelets-ALS-mat-12 [12_PLT]

value: maternal


title: Trim33KO_HA_E2f4-dDB rep2

extract_protocol:
Cells were fixed with 0.2% formaldehyde and Cut&Run assay was performed using the anti-HA tag antibody (Cell Signaling #2367S) or anti-Recql antibody (Abcam ab151501) and the NEB CUT&RUN kit (#86652P).
Sequencing libraries were prepared using NEBNext Ultra II DNA Library Prep Kit for Illumina according to manufacturer's protocol

value: Recql antibody


title: delta6_cap_high

description: Ribosome Profiling

data_processing:
Library strategy: Ribo-Seq
Basecalling with Illumina Casava 1.8 software
3' adapter trimming with FastX-toolkit
Library sorting based on sample barcode sequence with custom script
Random barcode triming with custom script
rRNA and other non-coding RNA alignment with bowtie2 v2.1.0
Alignment with bowtie2 v2.1.0
Read quantitation using custom scripts
Genome_build: NC_000913.2
Supplementary_files_format_and_content: text files contain three columns: 1. transcript name;2. CDS region (nt) used for read counting;3. read counts

tag: genetic background


title: Trim33KO_HA_E2f4-dC rep2


title: platelets-ALS-mat-11 [11_PLT]

tag: mat vs non-mat


title: WT_cap2_high

description: Ribosome Profiling


title: wholeblood-contr-10 [10_WB]

description: whole blood was used for DNA isolation

tag: disease state

value: Control


title: delta56_cm

description: Ribosome Profiling


title: WT_cap1_high

description: Ribosome Profiling


title: rpsa1_cap_high

description: Ribosome Profiling


title: Trim33KO_HA_E2f4-FL rep2


title: Trim33KO_HA_E2f4-dDB rep1

value: HA-tag antibody


title: delta6_cm

description: Ribosome Profiling


title: plateltes-ALS-mat-10 [10_PLT]

tag: age

value: platelets


title: Trim33KO_HA_E2f4-dC rep1


title: rpsa1_cm

description: Ribosome Profiling


title: wholeblood-contr-9 [09_WB]

description: whole blood was used for DNA isolation

tag: gender


title: WT_cm2

description: Ribosome Profiling


title: Trim33KO_HA_E2f4-FL rep1


title: platelets-contr-9 [09_PLT]

tag: mutation


title: WT_line

description: Ribosome Profiling

value: linezolid


title: WT_spec_high

description: Ribosome Profiling

value: spectinomycin 2000 microg/ml


title: WT_vio_high

description: Ribosome Profiling

value: viomycin 2000 microg/ml


title: Zswim8 KO Lung scRNA-seq Rep 3

city: Cambridge

first: Charlie

middle: Y.

last: Shi

state: MA

address: 455 Main St.

department: Biology

institute: Whitehead Institute / MIT

description: 150 x 150 bp reads

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were performed using the Cell Ranger software v4.0.0 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger).
Assembly: mm10
Supplementary files format and content: Tab-separated tables of features
Supplementary files format and content: Tab-separated tables of barcodes
Supplementary files format and content: Tab-separated tables of count matrices

source_name: Lung

extract_protocol:
scRNA-seq data were generated from dissociated whole lungs dissected from two Zswim8+/– and three Zswim8–/– E18.5 embryos. For dissociation, each set of lungs was minced on ice with scissors and incubated in 500 μL digestion solution composed of 100 μL collagenase (2000U/mL; Thermo Fisher Scientific), 16.5 uL DNAse I (0.33U/mL; Roche), and 383.5 μL DMEM/F-12 media (Life Technologies), and rotated end-over-end for 45 minutes at 37ºC. Following dissociation, 500 μL DMEM/F-12 + 10% fetal bovine serum (FBS) was added to the reaction, and the suspension was filtered through a 70 μm strainer. The filtrate was pelleted at 400g for 5 min at 4°C, resuspended in 500 μL red blood cell lysis buffer (StemCell Technologies) with a wide-bore P1000 tip, incubated for one minute at room temperature, and again pelleted at 400g for 5 min at 4°C. The pellet was resuspended in 200 μL DMEM/F12 + 10% FBS with a wide-bore P1000 tip, and cells were counted and assessed for viability by trypan blue staining. For the five samples, viabilities ranged from 64–81%.
Dissociated cells were loaded onto a Chromium controller for library preparation using the Chromium Next GEM Single Cell 3′ GEM, Library & Gel Bead Kit v3.1 (10X Genomics), targeting 10,000 cells per library, following the manufacturer's instructions.

value: Lung

tag: cell type

value: Dissociated lung cells


title: WT_cm1

description: Ribosome Profiling


title: delta56_cap_high

description: Ribosome Profiling


title: WT_blast

description: Ribosome Profiling

value: blasticidin


title: wholeblood-ALS-nonmat-11 [11_WB]

description: whole blood was used for DNA isolation

value: non-maternal

value: ALS

value: f


title: WT_spec_low

description: Ribosome Profiling

value: spectinomycin 200 microg/ml


title: wholeblood-contr-8 [08_WB]

description: whole blood was used for DNA isolation

value: m

value: control

value: whole blood


title: Zswim8 KO Lung scRNA-seq Rep 2

description: 150 x 150 bp reads

tag: tissue


title: platelets-contr-8 [08_PLT]


title: WT_vio_low

description: Ribosome Profiling

value: viomycin 200 microg/ml


title: Zswim8 Het Lung scRNA-seq Rep 2

description: 150 x 150 bp reads

tag: genotype


title: wholeblood-contr-7 [07_WB]

description: whole blood was used for DNA isolation

value: Control


title: WT_cap_low

description: Ribosome Profiling

value: capreomycin 200 microg/ml


title: Zswim8 KO Lung scRNA-seq Rep 1

description: 150 x 150 bp reads


title: platelets-ALS-nonmat-7 [07_PLT]

value: platelets


title: Zswim8 Het Lung scRNA-seq Rep 1

description: 150 x 150 bp reads


title: WT_no_drug

description: Ribosome Profiling

value: no drug treatment