title: JC2590_Xenograft_MCF7_PR_E2 r13

description: ChIP for PR in xenograft (MCF7 cells grown in mouse) after E2 treatment [Tumour #3]

data_processing:
Single-end reads were aligned against the Human Reference Genome (assembly hg19, NCBI GRCH37) using BWA version 0.5.5. Reads were filtered by removing those with a BWA alignment quality score less than 15. A further filtration was carried out by removing reads falling into the 'blacklist' regions identified by ENCODE.
Quality was confirmed using Biocnoductor package ChIPQC. Peaks we called using MACS v 1.4.1.
The Bioconductor package DiffBind was used to determine clustering, formulate consensus peaksets, and identify differentially bound sites.
Genome_build: hg19, Genome Reference Consortium GRCh37
Supplementary_files_format_and_content: MACS peaks in .csv file format (named as .txt as per MACS software)

growth_protocol: Age matched female NOD/SCID/IL2Rg-/- (NSG) mice were injected subcutaneously into the No 4 inguinal mammary fat pad with a suspension of 10^5 MCF7-Luc2/YFP cells in 50% growth factor reduced MatrigelTM (BD Biosciences).

extract_protocol: immunoprecipitated DNA was end-repaired, A-tailed, ligated to the sequencing adapters, amplified by 18 cycles of PCR and size selected (200-300 bp) followed by single end 4 sequencing on an Illumina HiSeq 2000 according to the manufacturer’s recommendationas described in Chandra, T. et al. Independence of Repressive Histone Marks and ChromatinCompaction during Senescent Heterochromatic Layer Formation. Mol Cell 47, 203–214 (2012)

treatment_protocol: 90 day slow-release 17b-estradiol (0.72 mg/pellet) and/or progesterone (10 mg/pellet) and/or placebo hormone pellets (Innovative Research of America) were implanted subcutaneously in recipient mice. Concomitantly, ovariectomisation was performed.

tag: implated cell line/type

value: MCF7; MCF7-Luc2/YFP cells

tag: host strain

value: age-matched female NOD/SCID/IL2Rg-/- (NSG)

value: xenografts tumors in vivo

tag: treatment groupd

value: PR Antibody (H-190)

tag: chip antibody vendor

value: Santa Cruz

tag: chip antibody cat. #

tag: chip antibody lot #


title: MCF7_E2_Rep3

status: Public on May 22 2015

type: SRA

city: Cambridge

first: Chandra

last: Chilamakuri

address: Robinson Way

country: United Kingdom

institute: Cancer Research UK Cambridge Institute

description: RNA-seq from MCF7 cells treated with E2 (Replicate 3)

library_source: transcriptomic

data_processing:
Single-end 40 bp reads generated on Illumina HiSeq were aligned to the human genome version GRCh37.64 using TopHat v2.0.4 (Trapnell et al., 2009). Read counts were obtained using HTSeq-count v0.5.3p9 (Anders et al., 2014).
Read counts were normalised and tested for differential gene expression using the DESeq5 workflow. Multiple testing correction was applied using the Benjamini-Hochberg method. Genes were selected as differentially expressed such that FDR <0.01.
Genome_build: GRCh37.64
Supplementary_files_format_and_content: HTSeq-count gene counts

molecule: polyA RNA

organism: Homo sapiens

growth_protocol: Cells grown in DMEM, supplemented with 10% FBS

extract_protocol:
Total RNA (miRNeasy kit, Qiagen) from the flow sorted cells was used to prepare libraries using the TruSeq RNA sample preparation kit (Illumina).
as per instructions from the TruSeq RNA sample preparation kit

treatment_protocol: Cells were treated with progesterone (100nM) or R5020 (10nM) for 3hr and RNA extracted

tag: cell line

tag: cell type

value: ER+ breast cancer cell line

tag: treated with


title: JC2589_Xenograft_MCF7_PR_E2 r12

description: ChIP for PR in xenograft (MCF7 cells grown in mouse) after E2 treatment [Tumour #2]

library_source: genomic

molecule: genomic DNA

tag: tissue

tag: chip antibody


title: JC2588_Xenograft_MCF7_PR_E2 r11

description: ChIP for PR in xenograft (MCF7 cells grown in mouse) after E2 treatment [Tumour #1]


title: JC2587_Xenograft_MCF7_PR_E2 r10

description: ChIP for PR in xenograft (MCF7 cells grown in mouse) after E2 treatment [Tumour #10]


title: JC2583_Xenograft_MCF7_PR_E2+PG r6

description: ChIP for PR in xenograft (MCF7 cells grown in mouse) after E2+PG treatment [Tumour #6]


title: JC2582_Xenograft_MCF7_PR_E2+PG r5

description: ChIP for PR in xenograft (MCF7 cells grown in mouse) after E2+PG treatment [Tumour #5]


title: JC2585_Xenograft_MCF7_PR_E2+PG r8

description: ChIP for PR in xenograft (MCF7 cells grown in mouse) after E2+PG treatment [Tumour #8]


title: JC2580_Xenograft_MCF7_PR_E2+PG r3

description: ChIP for PR in xenograft (MCF7 cells grown in mouse) after E2+PG treatment [Tumour #3]


title: JC2579_Xenograft_MCF7_PR_Vehicle r2

description: ChIP for PR in xenograft (MCF7 cells grown in mouse) after Vehicle treatment [Tumour #2]

value: Vehicle


title: Input H1

city: La Jolla, San Diego

first: conchi

last: estaras

state: CA

address: 10010 N Torrey Pines Rd

department: Regulatory Biology

country: USA

institute: The Salk Institute

description: ChIpseq

data_processing:
Peak calling was performed using Homer software
Genome_build: hg19
Supplementary_files_format_and_content: wig

source_name: H1 human ESCs

growth_protocol: H1 hESCs grown in mTeSR media

extract_protocol:
For ChIPseq, DNA was extracted Qiaquick PCR extraction kit (cat 28106, Qiagen). For GROseq, nascent RNA purification was done using Trizol LS (Invitrogene).
For ChIPseq, libraries were done with Illumina reagents. For GROseq, libraries were prepared with NEBnext kit (E7300S)

treatment_protocol: H1 hESCs were left untreated, or treated with Wnt3a (200ng/ml), Activin (100ng/ml), or both cytokines together for 4h (ChIPseq) or 6h (GRO-seq). For siRNA-GROseq experiments, hESCs were transfected with specific siRNAs (using RNAimax) 48h before adding cytokine treatments.

value: embryonic stem cells

tag: passages/media

tag: treatment

value: untreated


title: JC2578_Xenograft_MCF7_PR_Vehicle r1

description: ChIP for PR in xenograft (MCF7 cells grown in mouse) after Vehicle treatment [Tumour #1]


title: JC2577_Xenograft_MCF7_ER_E2 r14

description: ChIP for ER in xenograft (MCF7 cells grown in mouse) after E2 treatment [Tumour #4]

value: ERα Antibody (HC-20)


title: JC2591_Xenograft_MCF7_PR_E2 r14

description: ChIP for PR in xenograft (MCF7 cells grown in mouse) after E2 treatment [Tumour #4]


title: JC2581_Xenograft_MCF7_PR_E2+PG r4

description: ChIP for PR in xenograft (MCF7 cells grown in mouse) after E2+PG treatment [Tumour #4]


title: JC2576_Xenograft_MCF7_ER_E2 r13

description: ChIP for ER in xenograft (MCF7 cells grown in mouse) after E2 treatment [Tumour #3]


title: JC2586_Xenograft_MCF7_PR_E2 r9

description: ChIP for PR in xenograft (MCF7 cells grown in mouse) after E2 treatment [Tumour #9]


title: JC2584_Xenograft_MCF7_PR_E2+PG r7

description: ChIP for PR in xenograft (MCF7 cells grown in mouse) after E2+PG treatment [Tumour #7]


title: JC2575_Xenograft_MCF7_ER_E2 r12

description: ChIP for ER in xenograft (MCF7 cells grown in mouse) after E2 treatment [Tumour #2]


title: JC2573_Xenograft_MCF7_ER_E2 r10

description: ChIP for ER in xenograft (MCF7 cells grown in mouse) after E2 treatment [Tumour #10]


title: JC2572_Xenograft_MCF7_ER_E2 r9

description: ChIP for ER in xenograft (MCF7 cells grown in mouse) after E2 treatment [Tumour #9]


title: JC2574_Xenograft_MCF7_ER_E2 r11

description: ChIP for ER in xenograft (MCF7 cells grown in mouse) after E2 treatment [Tumour #1]


title: JC2570_Xenograft_MCF7_ER_E2+PG r7

description: ChIP for ER in xenograft (MCF7 cells grown in mouse) after E2+PG treatment [Tumour #7]


title: JC2569_Xenograft_MCF7_ER_E2+PG r6

description: ChIP for ER in xenograft (MCF7 cells grown in mouse) after E2+PG treatment [Tumour #6]


title: JC2565_Xenograft_MCF7_ER_Vehicle r2

description: ChIP for ER in xenograft (MCF7 cells grown in mouse) after Vehicle treatment [Tumour #2]


title: JC2566_Xenograft_MCF7_ER_E2+PG r3

description: ChIP for ER in xenograft (MCF7 cells grown in mouse) after E2+PG treatment [Tumour #3]


title: JC2568_Xenograft_MCF7_ER_E2+PG r5

description: ChIP for ER in xenograft (MCF7 cells grown in mouse) after E2+PG treatment [Tumour #5]


title: JC2567_Xenograft_MCF7_ER_E2+PG r4

description: ChIP for ER in xenograft (MCF7 cells grown in mouse) after E2+PG treatment [Tumour #4]


title: JC2593_Xenograft_MCF7_Input_Vehicle r2

description: Input control for xenograft (MCF7 cells grown in mouse) after Vehicle treatment [Tumour #2]

value: none (Input)


title: JC2594_Xenograft_MCF7_Input_E2+PG r1

description: Input control for xenograft (MCF7 cells grown in mouse) after E2+PG treatment [Tumour #1]


title: JC2596_Xenograft_MCF7_Input_E2 r1

description: Input control for xenograft (MCF7 cells grown in mouse) after E2 treatment [Tumour #1]


title: JC2592_Xenograft_MCF7_Input_Vehicle r1

description: Input control for xenograft (MCF7 cells grown in mouse) after Vehicle treatment [Tumour #1]


title: JC2595_Xenograft_MCF7_Input_E2+PG r2

description: Input control for xenograft (MCF7 cells grown in mouse) after E2+PG treatment [Tumour #2]


title: JC2380_T47D_PR_3hr_PG r3

description: ChIP for PR in T47D cell line after 3 hours treatment with PG [Replicate 3]

extract_protocol: Immunoprecipitated DNA was end-repaired, A-tailed, ligated to the sequencing adapters, amplified by 18 cycles of PCR and size selected (200-300 bp) followed by single end 50bp sequencing on an Illumina HiSeq 2000 according to the manufacturer’s recommendations

treatment_protocol: Cells were treated with progesterone (100nM) or R5020 (10nM) for 3hr and immunoprecipitated, and DNA extracted.

tag: condition

value: PG


title: JC2378_T47D_PR_3hr_Vehicle r3

description: ChIP for PR in T47D cell line after 3 hours treatment with Vehicle [Replicate 3]


title: JC2377_T47D_PR_3hr_E2+PG r2

description: ChIP for PR in T47D cell line after 3 hours treatment with E2+PG [Replicate 2]


title: JC2379_T47D_PR_3hr_E2 r3

description: ChIP for PR in T47D cell line after 3 hours treatment with E2 [Replicate 3]


title: JC2376_T47D_PR_3hr_PG r2

description: ChIP for PR in T47D cell line after 3 hours treatment with PG [Replicate 2]


title: JC2375_T47D_PR_3hr_E2 r2

description: ChIP for PR in T47D cell line after 3 hours treatment with E2 [Replicate 2]


title: JC2373_T47D_PR_3hr_E2+PG r1

description: ChIP for PR in T47D cell line after 3 hours treatment with E2+PG [Replicate 1]


title: JC2571_Xenograft_MCF7_ER_E2+PG r8

description: ChIP for ER in xenograft (MCF7 cells grown in mouse) after E2+PG treatment [Tumour #8]


title: JC2369_T47D_ER_3hr_E2+PG r3

description: ChIP for ER in T47D cell line after 3 hours treatment with E2+PG [Replicate 3]


title: JC2370_T47D_PR_3hr_Vehicle r1

description: ChIP for PR in T47D cell line after 3 hours treatment with Vehicle [Replicate 1]


title: JC2371_T47D_PR_3hr_E2 r1

description: ChIP for PR in T47D cell line after 3 hours treatment with E2 [Replicate 1]


title: JC2372_T47D_PR_3hr_PG r1

description: ChIP for PR in T47D cell line after 3 hours treatment with PG [Replicate 1]


title: JC2368_T47D_ER_3hr_PG r3

description: ChIP for ER in T47D cell line after 3 hours treatment with PG [Replicate 3]


title: JC2366_T47D_ER_3hr_Vehicle r3

description: ChIP for ER in T47D cell line after 3 hours treatment with Vehicle [Replicate 3]


title: JC2564_Xenograft_MCF7_ER_Vehicle r1

description: ChIP for ER in xenograft (MCF7 cells grown in mouse) after Vehicle treatment [Tumour #1]


title: JC2365_T47D_ER_3hr_E2+PG r2

description: ChIP for ER in T47D cell line after 3 hours treatment with E2+PG [Replicate 2]


title: JC2374_T47D_PR_3hr_Vehicle r2

description: ChIP for PR in T47D cell line after 3 hours treatment with Vehicle [Replicate 2]


title: JC2363_T47D_ER_3hr_E2 r2

description: ChIP for ER in T47D cell line after 3 hours treatment with E2 [Replicate 2]


title: JC2597_Xenograft_MCF7_Input_E2 r2

description: Input control for xenograft (MCF7 cells grown in mouse) after E2 treatment [Tumour #2]


title: JC2361_T47D_ER_3hr_E2+PG r1

description: ChIP for ER in T47D cell line after 3 hours treatment with E2+PG [Replicate 1]


title: JC2364_T47D_ER_3hr_PG r2

description: ChIP for ER in T47D cell line after 3 hours treatment with PG [Replicate 2]


title: JC2367_T47D_ER_3hr_E2 r3

description: ChIP for ER in T47D cell line after 3 hours treatment with E2 [Replicate 3]


title: JC2362_T47D_ER_3hr_Vehicle r2

description: ChIP for ER in T47D cell line after 3 hours treatment with Vehicle [Replicate 2]


title: JC2356_MCF7_PR_3hr_PG r3

description: ChIP for PR in MCF7 cell line after 3 hours treatment with PG [Replicate 3]


title: JC2357_MCF7_PR_3hr_E2+PG r3

description: ChIP for PR in MCF7 cell line after 3 hours treatment with E2+PG [Replicate 3]


title: JC2358_T47D_ER_3hr_Vehicle r1

description: ChIP for ER in T47D cell line after 3 hours treatment with Vehicle [Replicate 1]


title: JC2355_MCF7_PR_3hr_E2 r3

description: ChIP for PR in MCF7 cell line after 3 hours treatment with E2 [Replicate 3]


title: JC2353_MCF7_PR_3hr_E2+PG r2

description: ChIP for PR in MCF7 cell line after 3 hours treatment with E2+PG [Replicate 2]


title: JC2348_MCF7_PR_3hr_PG r1

description: ChIP for PR in MCF7 cell line after 3 hours treatment with PG [Replicate 1]


title: JC2354_MCF7_PR_3hr_Vehicle r3

description: ChIP for PR in MCF7 cell line after 3 hours treatment with Vehicle [Replicate 3]


title: JC2351_MCF7_PR_3hr_E2 r2

description: ChIP for PR in MCF7 cell line after 3 hours treatment with E2 [Replicate 2]


title: JC2381_T47D_PR_3hr_E2+PG r3

description: ChIP for PR in T47D cell line after 3 hours treatment with E2+PG [Replicate 3]


title: JC2352_MCF7_PR_3hr_PG r2

description: ChIP for PR in MCF7 cell line after 3 hours treatment with PG [Replicate 2]


title: JC2349_MCF7_PR_3hr_E2+PG r1

description: ChIP for PR in MCF7 cell line after 3 hours treatment with E2+PG [Replicate 1]


title: JC2350_MCF7_PR_3hr_Vehicle r2

description: ChIP for PR in MCF7 cell line after 3 hours treatment with Vehicle [Replicate 2]


title: JC2347_MCF7_PR_3hr_E2 r1

description: ChIP for PR in MCF7 cell line after 3 hours treatment with E2 [Replicate 1]


title: JC2342_MCF7_ER_3hr_Vehicle r3

description: ChIP for ER in MCF7 cell line after 3 hours treatment with Vehicle [Replicate 3]


title: JC2346_MCF7_PR_3hr_Vehicle r1

description: ChIP for PR in MCF7 cell line after 3 hours treatment with Vehicle [Replicate 1]


title: JC2344_MCF7_ER_3hr_PG r3

description: ChIP for ER in MCF7 cell line after 3 hours treatment with PG [Replicate 3]


title: JC2343_MCF7_ER_3hr_E2 r3

description: ChIP for ER in MCF7 cell line after 3 hours treatment with E2 [Replicate 3]


title: JC2341_MCF7_ER_3hr_E2+PG r2

description: ChIP for ER in MCF7 cell line after 3 hours treatment with E2+PG [Replicate 2]


title: JC2345_MCF7_ER_3hr_E2+PG r3

description: ChIP for ER in MCF7 cell line after 3 hours treatment with E2+PG [Replicate 3]


title: JC2340_MCF7_ER_3hr_PG r2

description: ChIP for ER in MCF7 cell line after 3 hours treatment with PG [Replicate 2]


title: JC2339_MCF7_ER_3hr_E2 r2

description: ChIP for ER in MCF7 cell line after 3 hours treatment with E2 [Replicate 2]


title: JC2360_T47D_ER_3hr_PG r1

description: ChIP for ER in T47D cell line after 3 hours treatment with PG [Replicate 1]


title: JC2338_MCF7_ER_3hr_Vehicle r2

description: ChIP for ER in MCF7 cell line after 3 hours treatment with Vehicle [Replicate 2]


title: JC2337_MCF7_ER_3hr_E2+PG r1

description: ChIP for ER in MCF7 cell line after 3 hours treatment with E2+PG [Replicate 1]


title: JC2336_MCF7_ER_3hr_PG r1

description: ChIP for ER in MCF7 cell line after 3 hours treatment with PG [Replicate 1]


title: JC1548_MCF7_PR_R5020_3hr r3

description: ChIP for PR in MCF7 cell line after 3hr treatment with R5020 [Replicate 3]

data_processing:
Single-end reads were aligned against the Human Reference Genome (assembly hg19, NCBI GRCH37) using BWA version 0.5.5. Reads were filtered by removing those with a BWA alignment quality score less than 15. A further filtration was carried out by removing reads falling into the 'blacklist' regions identified by ENCODE.
Quality was confirmed using Biocnoductor package ChIPQC. Peaks we called using MACS v 1.4.1.
The Bioconductor package DiffBind was used to determine clustering, formulate consensus peaksets, and identify differentially bound sites.
Genome_build: hg19, Genome Reference Consortium GRCh37
Supplementary_files_format_and_content: MACS peaks in .csv file format (named as .xls as per MACS software)


title: JC2335_MCF7_ER_3hr_E2 r1

description: ChIP for ER in MCF7 cell line after 3 hours treatment with E2 [Replicate 1]


title: JC1538_MCF7_PR_R5020_3hr r2

description: ChIP for PR in MCF7 cell line after 3hr treatment with R5020 [Replicate 2]


title: JC2359_T47D_ER_3hr_E2 r1

description: ChIP for ER in T47D cell line after 3 hours treatment with E2 [Replicate 1]


title: JC1528_MCF7_PR_R5020_3hr r1

description: ChIP for PR in MCF7 cell line after 3hr treatment with R5020 [Replicate 1]


title: JC1376_MCF7_PR_R5020_24hr r0

description: ChIP for PR in MCF7 cell line after 24hr treatment with R5020 [Replicate 0]


title: JC1547_MCF7_PR_Progesterone_3hr r3

description: ChIP for PR in MCF7 cell line after 3hr treatment with Progesterone [Replicate 3]

value: Progesterone


title: JC1375_MCF7_PR_R5020_3hr r0

description: ChIP for PR in MCF7 cell line after 3hr treatment with R5020 [Replicate 0]


title: JC1536_MCF7_PR_Full_Media_3hr r2

description: ChIP for PR in MCF7 cell line after 3hr treatment with Full_Media [Replicate 2]


title: JC1541_MCF7_p300_R5020_3hr r2

description: ChIP for p300 in MCF7 cell line after 3hr treatment with R5020 [Replicate 2]

value: p300 Antibody (C-20)


title: JC1546_MCF7_PR_Full_Media_3hr r3

description: ChIP for PR in MCF7 cell line after 3hr treatment with Full_Media [Replicate 3]


title: JC1527_MCF7_PR_Progesterone_3hr r1

description: ChIP for PR in MCF7 cell line after 3hr treatment with Progesterone [Replicate 1]


title: JC1537_MCF7_PR_Progesterone_3hr r2

description: ChIP for PR in MCF7 cell line after 3hr treatment with Progesterone [Replicate 2]


title: JC1526_MCF7_PR_Full_Media_3hr r1

description: ChIP for PR in MCF7 cell line after 3hr treatment with Full_Media [Replicate 1]


title: JC1530_MCF7_p300_Progesterone_3hr r1

description: ChIP for p300 in MCF7 cell line after 3hr treatment with Progesterone [Replicate 1]


title: JC1540_MCF7_p300_Progesterone_3hr r2

description: ChIP for p300 in MCF7 cell line after 3hr treatment with Progesterone [Replicate 2]


title: JC1381_MCF7_p300_R5020_24hr r0

description: ChIP for p300 in MCF7 cell line after 24hr treatment with R5020 [Replicate 0]


title: JC1551_MCF7_p300_R5020_3hr r3

description: ChIP for p300 in MCF7 cell line after 3hr treatment with R5020 [Replicate 3]


title: JC1379_MCF7_p300_Progesterone_24hr r0

description: ChIP for p300 in MCF7 cell line after 24hr treatment with Progesterone [Replicate 0]


title: JC1380_MCF7_p300_R5020_3hr r0

description: ChIP for p300 in MCF7 cell line after 3hr treatment with R5020 [Replicate 0]


title: JC1377_MCF7_p300_Full_Media_3hr r0

description: ChIP for p300 in MCF7 cell line after 3hr treatment with Full_Media [Replicate 0]


title: JC1539_MCF7_p300_Full_Media_3hr r2

description: ChIP for p300 in MCF7 cell line after 3hr treatment with Full_Media [Replicate 2]


title: JC1550_MCF7_p300_Progesterone_3hr r3

description: ChIP for p300 in MCF7 cell line after 3hr treatment with Progesterone [Replicate 3]


title: JC2334_MCF7_ER_3hr_Vehicle r1

description: ChIP for ER in MCF7 cell line after 3 hours treatment with Vehicle [Replicate 1]


title: JC1545_MCF7_ER_R5020_3hr r3

description: ChIP for ER in MCF7 cell line after 3hr treatment with R5020 [Replicate 3]


title: JC1532_MCF7_Input_Full_Media_3hr r1

description: Input control for MCF7 cell line after 3hr treatment with Full_Media [Replicate 1]

value: none (input)


title: JC1535_MCF7_ER_R5020_3hr r2

description: ChIP for ER in MCF7 cell line after 3hr treatment with R5020 [Replicate 2]


title: JC1552_MCF7_Input_Full_Media_3hr r3

description: Input control for MCF7 cell line after 3hr treatment with Full_Media [Replicate 3]


title: JC1525_MCF7_ER_R5020_3hr r1

description: ChIP for ER in MCF7 cell line after 3hr treatment with R5020 [Replicate 1]


title: JC1542_MCF7_Input_Full_Media_3hr r2

description: Input control for MCF7 cell line after 3hr treatment with Full_Media [Replicate 2]


title: JC1544_MCF7_ER_Progesterone_3hr r3

description: ChIP for ER in MCF7 cell line after 3hr treatment with Progesterone [Replicate 3]


title: JC1543_MCF7_ER_Full_Media_3hr r3

description: ChIP for ER in MCF7 cell line after 3hr treatment with Full_Media [Replicate 3]


title: JC1531_MCF7_p300_R5020_3hr r1

description: ChIP for p300 in MCF7 cell line after 3hr treatment with R5020 [Replicate 1]


title: JC1523_MCF7_ER_Full_Media_3hr r1

description: ChIP for ER in MCF7 cell line after 3hr treatment with Full_Media [Replicate 1]


title: JC1549_MCF7_p300_Full_Media_3hr r3

description: ChIP for p300 in MCF7 cell line after 3hr treatment with Full_Media [Replicate 3]


title: JC1378_NA_p300_Progesterone_3hr r0

description: ChIP for p300 in MCF7 cell line after 3hr treatment with Progesterone [Replicate 0]


title: JC1578_T47D_PR_R5020_3hr r3

description: ChIP for PR in T47D cell line after 3hr treatment with R5020 [Replicate 3]


title: JC1533_MCF7_ER_Full_Media_3hr r2

description: ChIP for ER in MCF7 cell line after 3hr treatment with Full_Media [Replicate 2]


title: JC1529_MCF7_p300_Full_Media_3hr r1

description: ChIP for p300 in MCF7 cell line after 3hr treatment with Full_Media [Replicate 1]


title: JC1577_T47D_PR_Progesterone_3hr r3

description: ChIP for PR in T47D cell line after 3hr treatment with Progesterone [Replicate 3]


title: JC1571_T47D_p300_R5020_3hr r2

description: ChIP for p300 in T47D cell line after 3hr treatment with R5020 [Replicate 2]


title: JC1557_T47D_PR_Progesterone_3hr r1

description: ChIP for PR in T47D cell line after 3hr treatment with Progesterone [Replicate 1]


title: JC1561_T47D_p300_R5020_3hr r1

description: ChIP for p300 in T47D cell line after 3hr treatment with R5020 [Replicate 1]


title: JC1566_T47D_PR_Full_Media_3hr r2

description: ChIP for PR in T47D cell line after 3hr treatment with Full_Media [Replicate 2]


title: JC1558_T47D_PR_R5020_3hr r1

description: ChIP for PR in T47D cell line after 3hr treatment with R5020 [Replicate 1]


title: JC1568_T47D_PR_R5020_3hr r2

description: ChIP for PR in T47D cell line after 3hr treatment with R5020 [Replicate 2]


title: JC1576_T47D_PR_Full_Media_3hr r3

description: ChIP for PR in T47D cell line after 3hr treatment with Full_Media [Replicate 3]


title: JC1579_T47D_p300_Full_Media_3hr r3

description: ChIP for p300 in T47D cell line after 3hr treatment with Full_Media [Replicate 3]


title: JC1580_T47D_p300_Progesterone_3hr r3

description: ChIP for p300 in T47D cell line after 3hr treatment with Progesterone [Replicate 3]


title: JC1567_T47D_PR_Progesterone_3hr r2

description: ChIP for PR in T47D cell line after 3hr treatment with Progesterone [Replicate 2]


title: JC1559_T47D_p300_Full_Media_3hr r1

description: ChIP for p300 in T47D cell line after 3hr treatment with Full_Media [Replicate 1]


title: JC1570_T47D_p300_Progesterone_3hr r2

description: ChIP for p300 in T47D cell line after 3hr treatment with Progesterone [Replicate 2]


title: JC1569_T47D_p300_Full_Media_3hr r2

description: ChIP for p300 in T47D cell line after 3hr treatment with Full_Media [Replicate 2]


title: JC1581_T47D_p300_R5020_3hr r3

description: ChIP for p300 in T47D cell line after 3hr treatment with R5020 [Replicate 3]


title: JC1582_T47D_Input_Full_Media_3hr r3

description: Input control for T47D cell line after 3hr treatment with Full_Media [Replicate 3]


title: JC1556_T47D_PR_Full_Media_3hr r1

description: ChIP for PR in T47D cell line after 3hr treatment with Full_Media [Replicate 1]


title: JC1562_T47D_Input_Full_Media_3hr r1

description: Input control for T47D cell line after 3hr treatment with Full_Media [Replicate 1]


title: JC1524_MCF7_ER_Progesterone_3hr r1

description: ChIP for ER in MCF7 cell line after 3hr treatment with Progesterone [Replicate 1]


title: JC1575_T47D_ER_R5020_3hr r3

description: ChIP for ER in T47D cell line after 3hr treatment with R5020 [Replicate 3]


title: JC1565_T47D_ER_R5020_3hr r2

description: ChIP for ER in T47D cell line after 3hr treatment with R5020 [Replicate 2]


title: JC1564_T47D_ER_Progesterone_3hr r2

description: ChIP for ER in T47D cell line after 3hr treatment with Progesterone [Replicate 2]


title: JC1574_T47D_ER_Progesterone_3hr r3

description: ChIP for ER in T47D cell line after 3hr treatment with Progesterone [Replicate 3]


title: JC1554_T47D_ER_Progesterone_3hr r1

description: ChIP for ER in T47D cell line after 3hr treatment with Progesterone [Replicate 1]


title: JC1555_T47D_ER_R5020_3hr r1

description: ChIP for ER in T47D cell line after 3hr treatment with R5020 [Replicate 1]


title: JC1573_T47D_ER_Full_Media_3hr r3

description: ChIP for ER in T47D cell line after 3hr treatment with Full_Media [Replicate 3]


title: JC1563_T47D_ER_Full_Media_3hr r2

description: ChIP for ER in T47D cell line after 3hr treatment with Full_Media [Replicate 2]


title: JC1553_T47D_ER_Full_Media_3hr r1

description: ChIP for ER in T47D cell line after 3hr treatment with Full_Media [Replicate 1]


title: KIsmallRNA_undetermined

city: New York

first: Doron

last: Betel

state: NY

address: 1305 York Avenue (Box 140)

department: Medicine

institute: Weill Cornell Medical College

description: All reads that could not be assigned to any of the genotypes

data_processing:
Basecalling by RTA 1.17.21.3
Trimmed adapter sequence TCGTATGCCGTCTTCTGCTTG using Flexbar
Demux samples by custom python script
Align to mm9 using STAR v.2.2.0 with .--outFilterMismatchNmax 1
BAM files generated by samtools (v0.1.19)
Transcripts reads by featureCounts (subread-1.4.2) using GTF file miRBase version 18
Genome_build: mm9
Supplementary_files_format_and_content: R data file of miRNA un-normalized counts matrix

molecule: total RNA

organism: Mus musculus

source_name: Whole embryo E9.5

growth_protocol: MiR-17~92 mutant animals were subjected to timed-mating. At E9.5, females were euthanized and embryos were harvested.

extract_protocol:
RNA was extracted using Trizol (Invitrogen) according to manufacturer's instructions.
Libraries were prepared using a published protocol (Hafner et al., Methods 2012).

treatment_protocol: Embryos were microdissected to isolate the heart and tail bud. The remaining embryo was  collected in Trizol and used for this analysis.

tag: gender

value: female

value: whole embryo

tag: developmental stage

tag: genotype

value: Undetermined reads


title: KIsmallRNA_Delta-17,18

description: miR-17,18 KO from whole embryo sample

value: miR-17,18 deleted


title: JC1560_T47D_p300_Progesterone_3hr r1

description: ChIP for p300 in T47D cell line after 3hr treatment with Progesterone [Replicate 1]


title: KIsmallRNA_19-only

description: miR-17,18,92 KO from whole embryo sample

value: miR-17,18,92 deleted


title: JC1534_MCF7_ER_Progesterone_3hr r2

description: ChIP for ER in MCF7 cell line after 3hr treatment with Progesterone [Replicate 2]


title: KIsmallRNA_Delta-18

description: miR-18 KO from whole embryo sample

value: miR-18 deleted


title: KIsmallRNA_Delta-92

description: miR-92 KO from whole embryo sample

value: miR-92 deleted


title: JC1572_T47D_Input_Full_Media_3hr r2

description: Input control for T47D cell line after 3hr treatment with Full_Media [Replicate 2]

value: ER+ breast cancer cell line


title: KIsmallRNA_Wild-type

description: Wild type from whole embryo sample

value: Wild type:full miR-17-92 cluster


title: KIsmallRNA_Delta-17

description: miR-17 KO from whole embryo sample

value: miR-17 deleted


title: PS041-2_R2_4_877

status: Public on May 21 2015

first: Peter

middle: A

last: Sims

address: 3960 Broadway, Lasker 203AC

institute: Columbia University

description:
PS041_4
3'-end RNA-Seq
processed data file: PS041-2_R2_4.txt

data_processing:
Read 1 of our single cell RNA-Seq data contains a cell-identifying barcode sequence followed by poly(dT), and read 2 contains a 8-base UMI followed by a 6-base lane-identifying barcode and a transcript sequence. We first demultiplex the reads based on the lane-identifying barcode while recording the corresponding UMI using a custom Python script. We then map the remainder of read 2 to the human genome and transcriptome (hg19, Ensembl annotation from Illumina iGenomes) using the STAR aligner.  Mapped reads for each lane are then demultiplexed based on the cell-identifying barcodes in read 1 and assigned to a gene using HTSeq.  Both the lane- and cell-identifying barcodes were allowed to have a single-base mismatch during demultiplexing. We note that >30% of reads map to the PhiX spike-in genome from the Illumina sequencing kit.
We collected the set of reads that uniquely mapped to the transcriptome and assigned an address comprised of its cell-identifying barcode, gene, UMI, and mapping position.  We then filtered the reads to identify unique molecules. Reads with identical addresses were collapsed to a single molecule.  In addition, reads with identical cell-identifying barcodes, genes, mapping positions, and with UMIs having a Hamming distance less than or equal to two were collapsed to a single molecule. Finally, because the mapping positions produced by STAR do not necessarily correspond to the beginning of a read, we further considered reads to originate from identical molecules if they had identical genes, cell-identifying barcodes, UMIs with a Hamming distance less than or equal to two, and a mapping position within five bases.
To identify barcodes that correspond to actual individual cells in our device, we filtered the observed cell-identifying barcodes by progressively downsampling the corresponding gene profiles to the same number of total reads and assessing the number of unique molecules detected from each cell-identifying barcode. After excluding cell-identifying barcodes having zero associated molecules, we found the distribution of associated unique molecules to be bimodal, with one small subpopulation having nearly as many unique molecules as reads at low read totals. We found the size of this subpopulation to be in excellent agreement with our device imaging data. We took these 598 profiles to represent the actual individual cells captured in our device with a barcoded bead.
We conducted more detailed analysis on 396 single-cell profiles with the highest coverage in our data set across all five lanes of the microfluidic device for PS034 and 247 single-cell profiles from PS041. Raw fastq data from read 2 of those 396 cells from PS034 and 247 cells from PS041 are provided here. Note that the UMI for each read appears in the comment line of each fastq entry.
The processed data files contain the number of molecules counted for each gene based on counting reads with HTSeq and filtering the UMIs to identify unique molecules. If two UMIs had a Hamming distance less than three, they were considered to be the same UMI.  If two reads with identical UMIs mapped to the transcriptome to within 6 bases of each other, they were considered identical molecules.  In addition, any molecules considered to be identical by the above defintion, but that appeared in two different cells were eliminated to mitigate any sources of cross-talk resulting from PCR recombination
Genome_build: hg19
Supplementary_files_format_and_content: The processed data files contain the number of molecules counted for each gene based on counting reads with HTSeq and filtering the UMIs to identify unique molecules.

source_name: mixture of U87 human glioma cells and WI-38 human lung fibroblast cells

growth_protocol: Cells were cultured in DMEM supplemented with 10% FBS.

extract_protocol:
RNA was extracted from individual cells in individual microfluidic chambers following cell lysis by Triton X-100 and freeze-thaw.
mRNA from individual cells was reverse transcribed with a primer containing a cell-identifying barcode followed by oligo(dT). Following second strand synthesis using DNA Polymerase I and reagents from the MessageAmp II kit (Ambion), ds-cDNA from all barcoded individual cells was pre-amplified by in vitro transcription using T7 RNA polymerase in a pool. The pools of amplified RNA from each lane of the microfluidic device were individually reverse transcribed using barcoded random hexamers containing both a unique molecular identifier (random 8-base barcode) followed by a lane-identifying barcode (6-base barcode). Illumina adapters were inserted on either end of the library during the two previous reverse transcription steps and were used to then enrich the library by PCR. The pooled library was sequenced on an Illumina NextSeq 500.


title: PS041-2_R2_4_79

value: mixture of U87 human glioma cells and WI-38 human lung fibroblast cells


title: KIsmallRNA_Full-KO

description: Full cluster KO from whole embryo sample

value: miR-17~92 Knockout


title: PS041-2_R2_4_776


title: PS041-2_R2_4_828


title: PS041-2_R2_4_824


title: PS041-2_R2_4_734


title: PS041-2_R2_4_96


title: PS041-2_R2_4_747


title: PS041-2_R2_4_71


title: PS041-2_R2_4_686


title: PS041-2_R2_4_7


title: PS041-2_R2_4_647


title: PS041-2_R2_4_67


title: PS041-2_R2_4_673


title: PS041-2_R2_4_602


title: PS041-2_R2_4_575


title: KIsmallRNA_Delta-19

description: miR-19 KO from whole embryo sample

value: miR-19 deleted


title: PS041-2_R2_4_571


title: PS041-2_R2_4_372


title: PS041-2_R2_4_47


title: PS041-2_R2_4_360


title: PS041-2_R2_4_337


title: PS041-2_R2_4_266


title: PS041-2_R2_4_243


title: PS041-2_R2_4_239


title: PS041-2_R2_4_282


title: PS041-2_R2_4_268


title: PS041-2_R2_4_13


title: PS041-2_R2_3_828

description:
PS041_3
3'-end RNA-Seq
processed data file: PS041-2_R2_3.txt


title: PS041-2_R2_3_903


title: PS041-2_R2_3_893


title: PS041-2_R2_3_807


title: PS041-2_R2_3_80


title: PS041-2_R2_3_822


title: PS041-2_R2_3_789


title: PS041-2_R2_3_757


title: PS041-2_R2_3_597


title: PS041-2_R2_3_618


title: PS041-2_R2_4_519


title: PS041-2_R2_3_678


title: PS041-2_R2_3_885


title: PS041-2_R2_3_441


title: PS041-2_R2_3_502


title: PS041-2_R2_3_667


title: PS041-2_R2_3_436


title: PS041-2_R2_3_435


title: PS041-2_R2_3_481


title: PS041-2_R2_3_563


title: PS041-2_R2_3_567


title: PS041-2_R2_3_467


title: PS041-2_R2_3_400


title: PS041-2_R2_3_397


title: PS041-2_R2_3_273


title: PS041-2_R2_3_239


title: PS041-2_R2_3_3


title: PS041-2_R2_3_351


title: PS041-2_R2_3_109


title: PS041-2_R2_2_950

description:
PS041_2
3'-end RNA-Seq
processed data file: PS041-2_R2_2.txt


title: PS041-2_R2_2_951


title: PS041-2_R2_2_934


title: PS041-2_R2_3_108


title: PS041-2_R2_2_920


title: PS041-2_R2_3_525


title: PS041-2_R2_2_92


title: PS041-2_R2_2_879


title: PS041-2_R2_2_906


title: PS041-2_R2_2_855


title: PS041-2_R2_2_864


title: PS041-2_R2_3_339


title: PS041-2_R2_2_845


title: PS041-2_R2_2_84


title: PS041-2_R2_2_803


title: PS041-2_R2_3_220


title: PS041-2_R2_2_828


title: PS041-2_R2_2_797


title: PS041-2_R2_3_122


title: PS041-2_R2_2_820


title: PS041-2_R2_2_761


title: PS041-2_R2_2_783


title: PS041-2_R2_2_768


title: PS041-2_R2_2_81


title: PS041-2_R2_2_752


title: PS041-2_R2_2_746


title: PS041-2_R2_2_73


title: PS041-2_R2_2_67


title: PS041-2_R2_2_617


title: PS041-2_R2_2_757


title: PS041-2_R2_2_628


title: PS041-2_R2_2_684


title: PS041-2_R2_2_607


title: PS041-2_R2_2_598


title: PS041-2_R2_2_592


title: PS041-2_R2_2_559


title: PS041-2_R2_2_842


title: PS041-2_R2_2_547


title: PS041-2_R2_2_567


title: PS041-2_R2_2_526


title: PS041-2_R2_2_518


title: PS041-2_R2_2_511


title: PS041-2_R2_2_512


title: PS041-2_R2_2_754


title: PS041-2_R2_2_461


title: PS041-2_R2_2_489


title: PS041-2_R2_2_483


title: PS041-2_R2_2_414


title: PS041-2_R2_2_377


title: PS041-2_R2_2_347


title: PS041-2_R2_2_457


title: PS041-2_R2_2_379


title: PS041-2_R2_2_359


title: PS041-2_R2_2_328


title: PS041-2_R2_2_402


title: PS041-2_R2_2_300


title: PS041-2_R2_2_314


title: PS041-2_R2_2_299


title: PS041-2_R2_2_237


title: PS041-2_R2_2_240


title: PS041-2_R2_2_502


title: PS041-2_R2_2_201


title: PS041-2_R2_2_14


title: PS041-2_R2_2_177


title: PS041-2_R2_2_188


title: PS041-2_R2_2_11


title: PS041-2_R2_2_135


title: PS041-2_R2_2_208


title: PS041-2_R2_1_96

description:
PS041_1
3'-end RNA-Seq
processed data file: PS041-2_R2_1.txt

source_name: WI-38 human lung fibroblast cells

value: WI-38 human lung fibroblast cells


title: PS041-2_R2_2_367


title: PS041-2_R2_2_409


title: PS041-2_R2_1_931


title: PS041-2_R2_2_105


title: PS041-2_R2_1_829


title: PS041-2_R2_1_928


title: PS041-2_R2_2_327


title: PS041-2_R2_1_927


title: PS041-2_R2_1_813


title: PS041-2_R2_2_23


title: PS041-2_R2_1_787


title: PS041-2_R2_1_77


title: PS041-2_R2_1_786


title: PS041-2_R2_1_726


title: PS041-2_R2_1_725


title: PS041-2_R2_1_67


title: PS041-2_R2_1_654


title: PS041-2_R2_1_632


title: PS041-2_R2_1_628


title: PS041-2_R2_1_589


title: PS041-2_R2_1_511


title: PS041-2_R2_1_57


title: PS041-2_R2_1_805


title: PS041-2_R2_1_500


title: PS041-2_R2_1_495


title: PS041-2_R2_1_817


title: PS041-2_R2_1_527


title: PS041-2_R2_1_490


title: PS041-2_R2_1_472


title: PS041-2_R2_1_449


title: PS041-2_R2_1_398


title: PS041-2_R2_1_762


title: PS041-2_R2_1_47


title: PS041-2_R2_1_350


title: PS041-2_R2_1_387


title: PS041-2_R2_1_35


title: PS041-2_R2_1_319


title: PS041-2_R2_1_306


title: PS041-2_R2_1_217


title: PS041-2_R2_1_296


title: PS041-2_R2_1_27


title: PS041-2_R2_1_297


title: PS041-2_R2_1_299


title: PS041-2_R2_1_66


title: PS041-2_R2_2_231


title: PS041-2_R2_1_200


title: PS041-2_R2_1_17


title: PS041-2_R2_1_189


title: PS041-2_R2_1_163


title: PS041-2_R2_1_150


title: PS041-2_R2_0_934

description:
PS041_0
3'-end RNA-Seq
processed data file: PS041-2_R2_0.txt

source_name: U87 human glioma cells

value: U87 human glioma cells


title: PS041-2_R2_0_940


title: PS041-2_R2_0_95


title: PS041-2_R2_0_868


title: PS041-2_R2_0_800


title: PS041-2_R2_0_909


title: PS041-2_R2_0_944


title: PS041-2_R2_0_952


title: PS041-2_R2_0_798


title: PS041-2_R2_0_857


title: PS041-2_R2_0_776


title: PS041-2_R2_0_881


title: PS041-2_R2_0_815


title: PS041-2_R2_0_803


title: PS041-2_R2_0_772


title: PS041-2_R2_0_779


title: PS041-2_R2_0_737


title: PS041-2_R2_0_764


title: PS041-2_R2_0_639


title: PS041-2_R2_0_646


title: PS041-2_R2_0_664


title: PS041-2_R2_0_732


title: PS041-2_R2_0_887


title: PS041-2_R2_0_630


title: PS041-2_R2_0_638


title: PS041-2_R2_0_610


title: PS041-2_R2_0_599


title: PS041-2_R2_0_59


title: PS041-2_R2_0_571


title: PS041-2_R2_0_644


title: PS041-2_R2_0_726


title: PS041-2_R2_0_570


title: PS041-2_R2_0_511


title: PS041-2_R2_0_460


title: PS041-2_R2_0_448


title: PS041-2_R2_0_437


title: PS041-2_R2_0_443


title: PS041-2_R2_0_409


title: PS041-2_R2_0_569


title: PS041-2_R2_0_518


title: PS041-2_R2_0_558


title: PS041-2_R2_0_483


title: PS041-2_R2_0_537


title: PS041-2_R2_0_473


title: PS041-2_R2_0_631


title: PS041-2_R2_0_327


title: PS041-2_R2_0_379


title: PS041-2_R2_0_326


title: PS041-2_R2_0_239


title: PS041-2_R2_0_397


title: PS041-2_R2_0_249


title: PS041-2_R2_0_242


title: PS041-2_R2_0_387


title: PS041-2_R2_0_366


title: PS041-2_R2_0_189


title: PS041-2_R2_0_289


title: PS041-2_R2_0_179


title: PS041-2_R2_0_338


title: PS041-2_R2_0_278


title: PS041-2_R2_0_267


title: PS041-2_R2_0_405


title: PS041-2_R2_0_145


title: PS041-2_R2_0_132


title: PS041-2_R2_0_178


title: PS041-2_R2_0_116


title: PS041-2_R2_0_105


title: PS041-2_R2_0_148


title: PS041-2_R2_0_10


title: PS041-2_R2_0_15


title: PS034_R2_4_85

description:
PS034_4
3'-end RNA-Seq
processed data file: PS034_R2_4.txt

source_name: MCF10a human breast cancer cells

value: MCF10a human breast cancer cells


title: PS041-2_R2_0_333


title: PS041-2_R2_0_147


title: PS034_R2_4_27


title: PS034_R2_4_261


title: PS034_R2_4_254


title: PS034_R2_3_37

description:
PS034_3
3'-end RNA-Seq
processed data file: PS034_R2_3.txt

source_name: mixture of U87 human glioma cells and MCF10a human breast cancer cells


title: PS034_R2_4_119


title: PS034_R2_3_781

value: mixture of U87 human glioma cells and MCF10a human breast cancer cells


title: PS034_R2_2_895

description:
PS034_2
3'-end RNA-Seq
processed data file: PS034_R2_2.txt


title: PS034_R2_2_88


title: PS034_R2_2_813


title: PS034_R2_2_740


title: PS034_R2_2_656


title: PS034_R2_2_44


title: PS034_R2_1_846

description:
PS034_1
3'-end RNA-Seq
processed data file: PS034_R2_1.txt


title: PS034_R2_2_287


title: PS034_R2_2_260


title: PS034_R2_1_809


title: PS034_R2_2_776


title: PS034_R2_1_441


title: PS034_R2_1_165


title: PS034_R2_0_388

description:
PS034_0
3'-end RNA-Seq
processed data file: PS034_R2_0.txt


title: PS034_R2_0_16


title: PS034_R2_4_959

data_processing:
We collected the set of reads that uniquely mapped to the transcriptome and assigned an address comprised of its cell-identifying barcode, gene, UMI, and mapping position.  We then filtered the reads to identify unique molecules. Reads with identical addresses were collapsed to a single molecule.  In addition, reads with identical cell-identifying barcodes, genes, mapping positions, and with UMIs having a Hamming distance less than or equal to two were collapsed to a single molecule. Finally, because the mapping positions produced by STAR do not necessarily correspond to the beginning of a read, we further considered reads to originate from identical molecules if they had identical genes, cell-identifying barcodes, UMIs with a Hamming distance less than or equal to two, and a mapping position within five bases.
To identify barcodes that correspond to actual individual cells in our device, we filtered the observed cell-identifying barcodes by progressively downsampling the corresponding gene profiles to the same number of total reads and assessing the number of unique molecules detected from each cell-identifying barcode. After excluding cell-identifying barcodes having zero associated molecules, we found the distribution of associated unique molecules to be bimodal, with one small subpopulation having nearly as many unique molecules as reads at low read totals. We found the size of this subpopulation to be in excellent agreement with our device imaging data. We took these 598 profiles to represent the actual individual cells captured in our device with a barcoded bead.
We conducted more detailed analysis on 370 single-cell profiles with the highest coverage in our data set across all five lanes of the microfluidic device. Raw fastq data from read 2 of those 370 cells is provided here. Note that the UMI for each read appears in the comment line of each fastq entry.
The processed data files contain the number of molecules counted for each gene based on counting reads with HTSeq and filtering the UMIs to identify unique molecules. If two UMIs had a Hamming distance less than three, they were considered to be the same UMI.  If two reads with identical UMIs mapped to the transcriptome to within 6 bases of each other, they were considered identical molecules.
Genome_build: hg19
Supplementary_files_format_and_content: The processed data files contain the number of molecules counted for each gene based on counting reads with HTSeq and filtering the UMIs to identify unique molecules.


title: PS034_R2_4_932


title: PS034_R2_4_97


title: PS034_R2_4_955


title: PS034_R2_0_891


title: PS034_R2_4_956


title: PS034_R2_4_930


title: PS034_R2_2_939


title: PS034_R2_2_950


title: PS041-2_R2_0_16


title: PS034_R2_4_914


title: PS034_R2_4_9


title: PS034_R2_4_894


title: PS034_R2_4_909


title: PS034_R2_4_881


title: PS034_R2_4_88


title: PS034_R2_4_818


title: PS034_R2_4_839


title: PS034_R2_4_884


title: PS034_R2_4_814


title: PS034_R2_4_81


title: PS034_R2_4_779


title: PS034_R2_1_253


title: PS034_R2_4_793


title: PS034_R2_4_784


title: PS034_R2_4_761


title: PS034_R2_4_750


title: PS034_R2_4_764


title: PS034_R2_4_75


title: PS034_R2_4_724


title: PS034_R2_4_720


title: PS034_R2_4_765


title: PS034_R2_4_763


title: PS034_R2_4_76


title: PS034_R2_4_725


title: PS034_R2_4_700


title: PS034_R2_4_718


title: PS034_R2_4_815


title: PS034_R2_4_715


title: PS034_R2_4_801


title: PS034_R2_4_671


title: PS034_R2_4_701


title: PS034_R2_4_684


title: PS034_R2_4_662


title: PS034_R2_4_63


title: PS034_R2_4_620


title: PS034_R2_4_589


title: PS034_R2_4_538


title: PS034_R2_4_544


title: PS034_R2_4_624


title: PS034_R2_4_595


title: PS034_R2_4_616


title: PS034_R2_4_587


title: PS034_R2_4_559


title: PS034_R2_4_518


title: PS034_R2_4_535


title: PS034_R2_4_483


title: PS034_R2_4_493


title: PS034_R2_4_486


title: PS034_R2_4_515


title: PS034_R2_4_464


title: PS034_R2_4_481


title: PS034_R2_4_436


title: PS034_R2_4_425


title: PS034_R2_4_43


title: PS034_R2_4_629


title: PS034_R2_4_407


title: PS034_R2_4_384


title: PS034_R2_4_404


title: PS034_R2_4_396


title: PS034_R2_4_379


title: PS034_R2_4_363


title: PS034_R2_4_352


title: PS034_R2_4_328


title: PS034_R2_4_285


title: PS034_R2_4_284


title: PS034_R2_4_305


title: PS034_R2_4_35


title: PS034_R2_4_374


title: PS034_R2_4_495


title: PS034_R2_4_347


title: PS034_R2_4_276


title: PS034_R2_4_28


title: PS034_R2_4_262


title: PS034_R2_4_258


title: PS034_R2_4_246


title: PS034_R2_4_234


title: PS034_R2_4_23


title: PS034_R2_4_253


title: PS034_R2_4_205


title: PS034_R2_4_203


title: PS034_R2_4_197


title: PS034_R2_4_381


title: PS034_R2_4_180


title: PS034_R2_4_190


title: PS034_R2_4_198


title: PS034_R2_4_161


title: PS034_R2_4_143


title: PS034_R2_4_151


title: PS034_R2_4_308


title: PS034_R2_4_128


title: PS034_R2_4_115


title: PS034_R2_3_956


title: PS034_R2_3_938


title: PS034_R2_3_921


title: PS034_R2_3_863


title: PS034_R2_3_875


title: PS034_R2_3_861


title: PS034_R2_3_838


title: PS034_R2_3_803


title: PS034_R2_3_854


title: PS034_R2_3_84


title: PS034_R2_3_744


title: PS034_R2_3_71


title: PS034_R2_3_723


title: PS034_R2_3_693


title: PS034_R2_3_694


title: PS034_R2_3_607


title: PS034_R2_3_638


title: PS034_R2_3_679


title: PS034_R2_3_576


title: PS034_R2_3_590


title: PS034_R2_3_541


title: PS034_R2_3_958


title: PS034_R2_3_573


title: PS034_R2_3_556


title: PS034_R2_3_957


title: PS034_R2_3_527


title: PS034_R2_3_491


title: PS034_R2_3_494


title: PS034_R2_3_511


title: PS034_R2_3_878


title: PS034_R2_3_51


title: PS034_R2_3_454


title: PS034_R2_3_349


title: PS034_R2_3_319


title: PS034_R2_3_379


title: PS034_R2_3_394


title: PS034_R2_3_435


title: PS034_R2_3_341


title: PS034_R2_3_682


title: PS034_R2_3_235


title: PS034_R2_3_283


title: PS034_R2_3_253


title: PS034_R2_3_232


title: PS034_R2_3_224


title: PS034_R2_3_257


title: PS034_R2_3_200


title: PS034_R2_3_201


title: PS034_R2_3_504


title: PS034_R2_3_168


title: PS034_R2_3_163


title: PS034_R2_3_145


title: PS034_R2_3_109


title: PS034_R2_3_113


title: PS034_R2_3_104


title: PS034_R2_3_274


title: PS034_R2_2_828


title: PS034_R2_2_923


title: PS034_R2_3_0


title: PS034_R2_2_925


title: PS034_R2_2_822


title: PS034_R2_2_806


title: PS034_R2_2_898


title: PS034_R2_2_809


title: PS034_R2_2_824


title: PS034_R2_2_783


title: PS034_R2_2_767


title: PS034_R2_2_734


title: PS034_R2_2_754


title: PS034_R2_2_700


title: PS034_R2_2_687


title: PS034_R2_2_753


title: PS034_R2_2_763


title: PS034_R2_3_161


title: PS034_R2_2_688


title: PS034_R2_2_60


title: PS034_R2_2_592


title: PS034_R2_2_627


title: PS034_R2_3_1


title: PS034_R2_2_602


title: PS034_R2_2_582


title: PS034_R2_2_571


title: PS034_R2_2_794


title: PS034_R2_2_568


title: PS034_R2_2_519


title: PS034_R2_2_443


title: PS034_R2_2_453


title: PS034_R2_2_465


title: PS034_R2_2_760


title: PS034_R2_2_387


title: PS034_R2_2_403


title: PS034_R2_2_366


title: PS034_R2_2_374


title: PS034_R2_2_405


title: PS034_R2_2_505


title: PS034_R2_2_276


title: PS034_R2_2_297


title: PS034_R2_2_264


title: PS034_R2_2_295


title: PS034_R2_2_254


title: PS034_R2_2_285


title: PS034_R2_2_237


title: PS034_R2_2_241


title: PS034_R2_2_223


title: PS034_R2_2_542


title: PS034_R2_2_214


title: PS034_R2_2_469


title: PS034_R2_2_530


title: PS034_R2_3_188


title: PS034_R2_2_207


title: PS034_R2_2_201


title: PS034_R2_2_134


title: PS034_R2_2_177


title: PS034_R2_2_376


title: PS034_R2_2_170


title: PS034_R2_2_13


title: PS034_R2_1_98


title: PS034_R2_1_97


title: PS034_R2_1_941


title: PS034_R2_1_955


title: PS034_R2_1_947


title: PS034_R2_1_953


title: PS034_R2_1_93


title: PS034_R2_1_927


title: PS034_R2_1_928


title: PS034_R2_1_922


title: PS034_R2_1_907


title: PS034_R2_1_908


title: PS034_R2_1_871


title: PS034_R2_1_853


title: PS034_R2_1_877


title: PS034_R2_1_851


title: PS034_R2_1_85


title: PS034_R2_1_841


title: PS034_R2_1_829


title: PS034_R2_2_169


title: PS034_R2_1_804


title: PS034_R2_1_790


title: PS034_R2_1_835


title: PS034_R2_1_99


title: PS034_R2_1_726


title: PS034_R2_1_721


title: PS034_R2_1_746


title: PS034_R2_1_716


title: PS034_R2_1_717


title: PS034_R2_1_925


title: PS034_R2_1_713


title: PS034_R2_1_68


title: PS034_R2_1_703


title: PS034_R2_1_712


title: PS034_R2_1_694


title: PS034_R2_1_674


title: PS034_R2_1_686


title: PS034_R2_1_673


title: PS034_R2_1_656


title: PS034_R2_1_664


title: PS034_R2_1_614


title: PS034_R2_1_65


title: PS034_R2_1_601


title: PS034_R2_1_549


title: PS034_R2_1_592


title: PS034_R2_1_776


title: PS034_R2_1_526


title: PS034_R2_1_531


title: PS034_R2_1_498


title: PS034_R2_1_603


title: PS034_R2_1_505


title: PS034_R2_1_485


title: PS034_R2_1_572


title: PS034_R2_1_480


title: PS034_R2_1_473


title: PS034_R2_1_451


title: PS034_R2_1_513


title: PS034_R2_1_515


title: PS034_R2_1_660


title: PS034_R2_1_446


title: PS034_R2_1_411


title: PS034_R2_1_433


title: PS034_R2_1_426


title: PS034_R2_1_434


title: PS034_R2_1_389


title: PS034_R2_1_388


title: PS034_R2_1_386


title: PS034_R2_1_363


title: PS034_R2_1_525


title: PS034_R2_1_340


title: PS034_R2_1_366


title: PS034_R2_1_32


title: PS034_R2_1_341


title: PS034_R2_1_319


title: PS034_R2_1_289


title: PS034_R2_1_300


title: PS034_R2_1_28


title: PS034_R2_1_284


title: PS034_R2_1_450


title: PS034_R2_1_238


title: PS034_R2_1_25


title: PS034_R2_1_254


title: PS034_R2_1_24


title: PS034_R2_1_23


title: PS034_R2_1_241


title: PS034_R2_1_260


title: PS034_R2_1_193


title: PS034_R2_1_16


title: PS034_R2_1_207


title: PS034_R2_1_222


title: PS034_R2_1_157


title: PS034_R2_1_21


title: PS034_R2_1_133


title: PS034_R2_1_130


title: PS034_R2_0_99


title: PS034_R2_0_927


title: PS034_R2_0_942


title: PS034_R2_0_835


title: PS034_R2_0_863


title: PS034_R2_0_885


title: PS034_R2_0_924


title: PS034_R2_0_796


title: PS034_R2_0_821


title: PS034_R2_0_772


title: PS034_R2_0_78


title: PS034_R2_0_817


title: PS034_R2_0_763


title: PS034_R2_0_776


title: PS034_R2_0_762


title: PS034_R2_0_753


title: PS034_R2_0_760


title: PS034_R2_0_737


title: PS034_R2_0_721


title: PS034_R2_0_736


title: PS034_R2_0_664


title: PS034_R2_0_656


title: PS034_R2_0_661


title: PS034_R2_0_652


title: PS034_R2_0_629


title: PS034_R2_1_13


title: PS034_R2_0_611


title: PS034_R2_0_585


title: PS034_R2_0_597


title: PS034_R2_0_554


title: PS034_R2_0_541


title: input (no Ab)

city: Padova

first: Silvio

last: Bicciato

address: via U. Bassi 59/b

department: Molecular Medicine

country: Italy

institute: University of Padova

data_processing:
Reads from each sample were mapped in three consecutive steps taking into account from 0 to a maximum of 2 mismatches. After each mapping step the unmapped reads were filtered out and remapped by increasing of one. The results of each mapping step were then pooled together into a single bam file.
sample resulted in a merged BAM file that was then processed by using SAMtools, and converted into a bed file using BEDTools
ChIP-seq peak calling was performed using SICER (Chongzhi Zang et al., 2009) and using  INPUT data (control DNA) to model the background noise.
Genome_build: Hg19
Supplementary_files_format_and_content: The bed files contains the genomic regions of the peaks identified after peak calling with SICER

source_name: NESCs

growth_protocol: NESCs were grown in DMEM/F12 with 20 μg/mL insulin (Sigma–Aldrich), 1.6 g/L glucose, 10 ng/mL FGF2 (R&D Systems), 10 ng/mL EGF (R&D Systems), and 1 μl/ml B27 supplement (Invitrogen)

extract_protocol:
Chromatin preparation and processing was performed starting from pellets of 5 106 NESCs and following the truChIP Chromatin Shering Kit standard protocol (PN520076, Covaris Inc.).
Libraries were prepared according to Illumina's instructions accompanying  the standard protocol of Illumina ChIP-seq DNA sample preparation kit (IP-102-1001, Illumina Inc.).

tag: sample type

value: ESC-derived neural precursors

value: human neuroepithelial-like stem cells (NESCs)

value: none (chromatin processed without incubation with the antibody)


title: ChIP-Seq analysis of H3K4me3 in human neuroepithelial-like stem cells (NESCs)

value: Abcam


title: PS034_R2_0_529


title: PS034_R2_0_514


title: Level 2 promoters in human ESCs and NESCs

description: ESCs (H9 NIH code WA09, ISL1 Ds-Red) were kindly provided by the group of K.R. Chien.

data_processing:
After the sequencing, sequence raw data were generated with processing by GenomeAnalyzer Iix. For CAGE tags mapping to multiple genome locations, a weighting strategy based on the number of CAGE tags within a 200 bp neighbourhood around each candidate mapping location was applied. (Faulkner GJ, et al 2008).
Level-1 promoters (TSSs) were created by summing the weighted number of CAGE tags at each genome position. We required at least one CAGE tag in at least one experimental condition; other mapping positions were discarded. The level-1 promoters were clustered into Level-2 promoters (CAGE-promoters) if they were within 20 bp of each other on the same chromosomal strand. We required that the expression of each level-2 promoter was at least 10 tpm in at least one experimental condition; other promoters were dropped.
Tpm were calculated for each level-1 and level-2 promoter by dividing the number of CAGE tags of each promoter in each experimental condition by the total number of mapped CAGE tags in that condition, and multiplying by 106.
Genome_build: Hg19
Supplementary_files_format_and_content: The bed.txt file contains the genomic regions of the level-2 promoters and the TPM levels.

source_name: ESCs and NESCs

growth_protocol: ESCs were maintained on irradiated mouse embryonic fibroblasts (MEFs) at 5% CO2 in Knockout-DMEM (Invitrogen), containing 20% FCS, 1% non-essential amino acids, 1 mM glutamine, 0.1mM ß-mercaptoethanol and 10 ng/mL FGF2 (Invitrogen). NESCs were grown in DMEM/F12 with 20 μg/mL insulin (Sigma–Aldrich), 1.6 g/L glucose, 10 ng/mL FGF2 (R&D Systems), 10 ng/mL EGF (R&D Systems), and 1 μl/ml B27 supplement (Invitrogen)

extract_protocol:
CAGE-seq was performed by DNAFORM Inc. at RIKEN Omics Science Center. The samples were prepared according to the OP-SOLEXA-96CAGE-v.3.0.
The sequencing run and the base call analysis were performed according to the manufacturer's protocol Illumina Sequencing Kit v4.

value: ESCs (H9 NIH code WA09, ISL1 Ds-Red); ESC-derived neural precursors


title: PS034_R2_0_495


title: ChIP-Seq analysis of H3K4me1 in human neuroepithelial-like stem cells (NESCs)


title: PS034_R2_0_485


title: PS034_R2_0_672


title: PS034_R2_0_638


title: PS034_R2_0_492


title: PS034_R2_0_478


title: CTRL_10p_10

city: Philadelphia

first: Junhyong

last: Kim

state: PA

address: 433 S University Avenue

department: Biology

institute: University of Pennsylvania

data_processing:
Illumina Casava 1.8.1 and 1.8.2 software used for basecalling.
We trimmed reads for adapter and poly-A contamination using in-house software before aligning to the mouse genome and transcriptome using RNA-Seq Unified Mapper (versions 2.0.2_06 and 2.0.3_04) and mouse genome build mm9 (mouse) or to the rat genome using STAR and rat genome build rn5. We required three or less mismatches per 100 bases.
Using uniquely aligned reads to RefSeq annotations downloaded from UCSC genome browser, we assigned read counts to genes using HTSeq and htseq-count. Only exonic reads were counted, with overlap assigned using the intersection non-empty method.
genome_build: mm9
genome_build: rn5
Supplementary_files_format_and_content: tab-delimited text files include raw counts for each gene

source_name: Heart; Population

extract_protocol:
Starting from bulk heart tissue total RNA from a C57/BL6 adult male mouse (Zyagen), five replicates were begun with 10 pg. of total RNA. Each sample was individually amplified using three rounds of a linear in vitro-transcription-based method.
Samples were prepared for multiplexed paired-end sequencing using the Illumina Truseq stranded system according to manufacturer instructions.

tag: strain

value: Adult

value: Heart

value: Population


title: CTRL_10p_12


title: PS034_R2_0_465


title: CTRL_10p_11


title: PS034_R2_0_446


title: CTRL_10p_9


title: CTRL_10p_7


title: PS034_R2_0_627


title: PS034_R2_0_434


title: CTRL_10p_8


title: CTRL_10p_6


title: PS034_R2_0_367


title: CTRL_10p_5


title: CTRL_10p_4


title: PS034_R2_0_572


title: PS034_R2_0_363


title: PS034_R2_0_360


title: PS034_R2_0_36


title: PS034_R2_0_319


title: PS034_R2_0_31


title: PS034_R2_0_321


title: CTRL_10p_3


title: CTRL_10p_1


title: S28

city: Shanghai

first: Kunshan

last: Zhang

address: 389 Xincun Road

department: Stem cell Translational Research center

country: China

institute: Tongji Hospital, Tongji University

data_processing:
Tophat(v1.41) used to mapping reads with default parameter.
Cufflinks(v2.02) used to estimate gene expression level (Fragment Per Kilobase per Million mapped reads, FPKM) with Ensembl Genes.
In all expression profile analysis, genes with FPKM < 0.1 were removed.
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

source_name: forebrain neurogenic zone

extract_protocol: RNA libraries were prepared for sequencing using single cell protocols

value: Subventricular Zone

tag: age

value: post natal day 21

tag: cell number

value: single cell


title: CTRL_10p_2


title: S27


title: PS034_R2_0_306


title: PS034_R2_0_3


title: S25


title: S22


title: S24


title: PS034_R2_0_258


title: PS034_R2_0_28


title: PS034_R2_0_254


title: PS034_R2_0_251


title: PS034_R2_0_237


title: S19


title: Sample_HD_2012_02_27_09

organism: Rattus norvegicus

source_name: Hippocampus; Pyramidal neuron

growth_protocol: Primary cultures of hippocampal and cortical neurons were plated at 100,000 per ml in neurobasal medium (Invitrogen) with B-27 supplement (Sigma) on 12-mm round German Spiegelglas coverslips (Bellco Glass) and grown for 14 days.

extract_protocol:
We identified pyramidal neurons by cell morphology, isolated single cells by aspiration using a wide-bore pipette, deposited collected material into an eppendorf tube and froze immediately at -20C until storage at -80C. Collected samples were individually amplified using three rounds of a linear in vitro-transcription-based method.
Samples were prepared for multiplexed paired-end sequencing using the Illumina TruSeq system according to manufacturer instructions.

value: Sprague-Dawley

value: embryonic day 18

value: Hippocampus

value: Pyramidal neuron


title: S26


title: PS034_R2_0_188

value: U87 human glioma cells


title: S20


title: Sample_HD_2012_02_27_07


title: S21


title: PS034_R2_0_187


title: S18


title: PS034_R2_0_155


title: Sample_HD_2012_02_27_05


title: Sample_HD_2012_02_06_04


title: Sample_HD_2012_01_30_24


title: PS034_R2_0_140


title: S23


title: HIP_7

data_processing:
genome_build: mm9
genome_build: rn5
Illumina Casava 1.8.1 and 1.8.2 software used for basecalling.
We trimmed reads for adapter and poly-A contamination using in-house software before aligning to the mouse genome and transcriptome using RNA-Seq Unified Mapper (versions 2.0.2_06 and 2.0.3_04) and mouse genome build mm9 (mouse) or to the rat genome using STAR and rat genome build rn5. We required three or less mismatches per 100 bases.
Using uniquely aligned reads to RefSeq annotations downloaded from UCSC genome browser, we assigned read counts to genes using HTSeq and htseq-count. Only exonic reads were counted, with overlap assigned using the intersection non-empty method.
Supplementary_files_format_and_content: tab-delimited text files include raw counts for each gene

extract_protocol:
We identified pyramidal neurons by cell morphology, isolated single cells by aspiration using a wide-bore pipette, deposited collected material into an eppendorf tube and froze immediately at -20C until storage at -80C. Collected samples were individually amplified using three rounds of a linear in vitro-transcription-based method.
Samples were prepared for multiplexed paired-end sequencing using the Illumina TruSeq v2 system according to manufacturer instructions.


title: Sample_HD_2012_01_30_15


title: DR_22

description: 5HT 5

source_name: Dorsal Raphe; 5-HT neuron

extract_protocol:
Serotonergic neurons, identified with YFP expression, were isolated by pipette directly from acute slices of the dorsal raphe. Collected samples were individually amplified using three rounds of a linear in vitro-transcription-based method.
Samples were prepared for multiplexed paired-end sequencing using the Illumina TruSeq system according to manufacturer instructions.

value: e-PET-YFP

value: post natal day 60

value: Dorsal Raphe

value: 5-HT neuron


title: DR_19

description: 5HT 8


title: DR_21

extract_protocol:
Serotonergic neurons, identified with YFP expression, were isolated by pipette directly from acute slices of the dorsal raphe. Collected samples were individually amplified using three rounds of a linear in vitro-transcription-based method.
Samples were prepared for multiplexed paired-end sequencing using the Illumina TruSeq v1 system according to manufacturer instructions.


title: DR_18


title: DR_20


title: PS034_R2_0_102


title: Sample_HD_2012_01_30_21


title: DR_17


title: DR_16

description: 5HT 4


title: Rn_CTX_6

source_name: Cortex; Pyramidal neuron

value: Cortex


title: Rn_CTX_8


title: Rn_CTX_5


title: Sample_HD_2012_01_30_13


title: HIP_16


title: Rn_CTX_7


title: Rn_CTX_4


title: Meis1f/f_vehicle

city: Cincinnati

first: Ashish

last: Kumar

state: Ohio

address: 3333 Burnet Avenue. Cincinnati. Ohio 45229

department: Bone Marrow Transplanation

institute: Cincinnati Children's Hospital & Medical Center

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm8 whole genome using bowtie
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: mm8
Supplementary_files_format_and_content: xlsx files containing RPKM values for each Sample.

growth_protocol: MLL-AF9 fusion leukemic cells were grown in were cultured in Iscove’s modified Dulbecco’s medium (IMDM) supplemented with 20% fetal calf serum (FCS), 100 U/ml penicillin, 100 mg/ml streptomycin, 10ng/ml of SCF, IL-3, GM-CSF, IL-6.

extract_protocol:
RNA was isolated with QIAGEN RNAeasy mini kit in accordance with the prescribed protocol with the kit. Quaity control was analysed by Agilent Bioanalyser.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: MLL-AF9 fusion leukemic cells were treated with vehicle-control or 4-hydroxy tamoxifen.

value: Meis1f/fCreER+/- MLL-AF9-/+

value: vehicle

value: bone marrow leukemic cells


title: Meis1f/f_4-OHT

value: 1000 nM of 4-hydroxy tamoxifen for 24 hrs


title: DR_14

description: 5HT 16


title: PS034_R2_0_142


title: DR_15

description: 5HT 20


title: DR_13

description: 5HT 15


title: DR_12

description: 5HT 13


title: control_4-OHT


title: DR_11

description: 5HT 2


title: control_vehicle


title: Rn_CTX_2


title: CTRL_50p_9

description: 50 F

extract_protocol:
Starting from bulk heart tissue total RNA from a C57/BL6 adult male mouse (Zyagen), five replicates were begun with 50 pg. of total RNA. All diluted replicates shared the same original mother tube. Each sample was individually amplified using three rounds of a linear in vitro-transcription-based method.
Samples were prepared for multiplexed paired-end sequencing using the Illumina Truseq stranded system according to manufacturer instructions.

value: Adult

value: Heart

value: Population


title: DR_9

description: 5HT 18


title: CTRL_50p_8


title: oocytes_smallRNA_Dvir_rep1

city: Pasadena

first: Maria

last: Ninova

address: 1200 E California Blvd

department: Division of Biology and Biological Engineering

institute: Calfironia Institute of Technology

description: small RNA

data_processing:
Illumina small RNA adaptor sequences were removed using the cutadapt tool. Small RNA sequencing reads were mapped to the D. melanogaster or D. virilis genomes, respectively, using Bowtie v1.0 allowing one mismatch; raw read counts per microRNA gene were calculated by a custom script accounting for multiple mapping positions
Genome_build: D. melanogaster r5.45;  D. Virilis dvir_r1.2  (flyBase)
Supplementary_files_format_and_content: tab-delimited file of genes/microRNAs and read counts

organism: Drosophila virilis

source_name: unfertilized eggs

growth_protocol: virgin females (for oocytes) were allowed to lay on apple juica agar plates at 25°C and oocytes were collected at 4-hour intervals

extract_protocol:
Standard Trizol RNA extraction
Illumina TruSeq small RNA sample prep kit

value: unfertilized eggs


title: oocytes_smallRNA_Dvir_rep2

description: small RNA


title: CTRL_50p_7


title: CTRL_50p_6


title: DR_8

description: 5HT 14


title: P4

value: Subventricular Zone

value: post natal day 21

value: 10 cells


title: DR_5

extract_protocol:
Serotonergic neurons, identified with YFP expression, were isolated by pipette directly from acute slices of the dorsal raphe. Collected samples were individually amplified using three rounds of a linear in vitro-transcription-based method.
Samples were prepared for multiplexed paired-end sequencing using the Illumina mRNA-Seq system according to manufacturer instructions.


title: CTRL_100p_8

extract_protocol:
Starting from bulk heart tissue total RNA from a C57/BL6 adult male mouse (Zyagen), five replicates were begun with 100 pg. of total RNA. All diluted replicates shared the same original mother tube. Each sample was individually amplified using three rounds of a linear in vitro-transcription-based method.
Samples were prepared for multiplexed paired-end sequencing using the Illumina Truseq stranded system according to manufacturer instructions.


title: P3


title: DR_6

description: 5HT 17


title: oocytes_smallRNA_Dmel_rep1

description: small RNA

organism: Drosophila melanogaster


title: DR_4


title: Rn_CTX_3

value: Sprague-Dawley

value: embryonic day 18

value: Pyramidal neuron


title: CTRL_100p_9


title: P2


title: CTRL_100p_6


title: DR_3

value: e-PET-YFP

value: post natal day 60

value: Dorsal Raphe


title: P1


title: CTRL_100p_5


title: Rn_CTX_1

value: Cortex


title: DR_2

value: 5-HT neuron


title: DR_10

description: 5HT 19


title: S17

value: single cell


title: CTRL_50p_5


title: oocytes_smallRNA_Dmel_rep2

description: small RNA


title: DR_1


title: S16


title: DR_7

description: 5HT 6


title: CTX_19


title: S15


title: CTRL_50p_3


title: CTRL_50p_4


title: CTRL_100p_7


title: CTRL_50p_2


title: S13


title: S12


title: CTX_18


title: CTX_15


title: CTX_14


title: CTX_17


title: S11


title: S10


title: CTRL_100p_2


title: CTX_13


title: CTX_12


title: CTRL_100p_3


title: S9


title: CTX_11


title: S8


title: CTRL_100p_1


title: HIP_18

value: Hippocampus


title: CTX_10


title: S7


title: S14


title: HIP_15


title: S5


title: CTX_9


title: CTRL_50p_1

value: Adult


title: CTRL_100p_4

value: Heart


title: CTX_8


title: HIP_13


title: HIP_12


title: S4


title: S3


title: CTX_6


title: S2


title: HIP_14


title: S1


title: CTX_5


title: CTX_7


title: HIP_10


title: CTX_3


title: HIP_11


title: HIP_9


title: CTX_2


title: S6


title: CTX_1


title: HIP_8


title: HIP_6


title: HIP_17


title: RNA-seq of oriPtL overexpressing Mutu cells_2

city: New Orleans

first: Erik

middle: K

last: Flemington

state: Louisiana

address: 1430 Tulane Avenue, SL-79

department: Tulane Cancer Center/Pathology and Laboratory Medicine

institute: Tulane University

data_processing:
FASTQ files were aligned to human reference genome hg19 and Akata EBV genome using the sequence and junction aligner, TopHat
Strand specific gene expression was quantified by SAMMate
Genome_build: hg19 and Akata EBV genome
Supplementary_files_format_and_content: Excel file include RPKM values of EBV genes for each sample

organism: human gammaherpesvirus 4

source_name: EBV-infected B cells

extract_protocol:
Total RNA was isolated using TRIzol® Reagent (Life technologies, Cat. #15596-018) or a miRNeasy Mini Kit (Qiagen, Cat. #217004) following the respective vendor’s protocols.
Truseq strand specific protocol

tag: host organism

value: homo sapiens

tag: host cell line

value: Mutu


title: RNA-seq of oriPtL overexpressing Mutu cells_1


title: RNA-seq of control Mutu cells_1


title: CRD_19

source_name: Heart; Cardiomyocyte

extract_protocol:
Ventricular cardiomyocytes were isolated from E14.5 transgenic mice expressing the green S/G2/M fluorescent ubiquitination-based cell cycle indicator, “Fucci” (A. Sakaue-Sawano et al., Visualizing spatiotemporal dynamics of multicellular cell-cycle progression. Cell 132, 487–498 (2008)), using a modified protocol of the neomyts cardiomyocyte isolation kit (Cellutron Life Technologies).  The dissociated cell suspensions were resuspended in 500μl of PBS supplemented with 5% FBS solution and sorted by flow cytometryon a FACSAria instrument operating at low pressure (20 psi) using a 100μm nozzle. Samples were sorted individually into 96-well plates containing RT buffer for linear in vitro-transcription T7-based antisense RNA (aRNA) amplification. Collected samples were individually amplified using three rounds of a linear in vitro-transcription-based method.
Samples were prepared for multiplexed paired-end sequencing using the Illumina TruSeq system according to manufacturer instructions.

value: AG-Geminin

value: embryonic day 14.5

value: Cardiomyocyte


title: HIP_5


title: CRD_18


title: RNA-seq of induced oriPtL knockdown Akata cells (using GapmeR 2 for knockdown)_3

value: Akata


title: CRD_17


title: CRD_16


title: RNA-seq of induced oriPtL knockdown Akata cells (using GapmeR 2 for knockdown)_2


title: CTX_4

value: embryonic day 18


title: HIP_3

value: Pyramidal neuron


title: RNA-seq of induced oriPtL knockdown Akata cells (using GapmeR 2 for knockdown)_1


title: RNA-seq of induced oriPtL knockdown Akata cells (using GapmeR 1 for knockdown)_3


title: CRD_14


title: CTX_16


title: CRD_15


title: CRD_13


title: RNA-seq of induced oriPtL knockdown Akata cells (using GapmeR 1 for knockdown)_2


title: HIP_1


title: RNA-seq of induced oriPtL knockdown Akata cells (using GapmeR 1 for knockdown)_1


title: RNA-seq of control Mutu cells_2


title: d_red_ZF_sample_0012

city: Haifa

first: Naftalie

last: Senderovich

state: International

address: Technion city, Faculty of biology

country: Israel

institute: Technion - Israel Institute of Technology

data_processing:
Libraries were sequenced on the Illumina HiSeq2500 according to standard, paired-end sequencing, protocols. Primary analysis done in RTA 1.17.20,1.13.48
Conversion from BCL to FASTQ and deumltiplexing using CASAVA-1.8 (configureBclToFastq.pl--fastq-cluster-count 1234567890 --mismatches 0 --use-bases-mask Y15n,I6n,Y35n)
Filter and read trimming (barcode minimum quality of 20. trimming of read2 to 35 bases - not required).
CEL-Seq (Hashimshony, et al. 2012) demultiplexing of second mate, using first mate barcode, allowing no mismatches in barcode.
bowtie2, version 2.1.0, against Zv9 genome
Read counting with htseq-count version 0.5.4p3. Using on Ensemble Zv9 annotations. Reads with the same unique molecular identifiers (UMIs) were colapsed for transcript counting.
Genome_build: Zv9
Supplementary_files_format_and_content: Tabular expression matrix includes number of transcript molecules.

organism: Danio rerio

source_name: Dorsal endothelial cells

growth_protocol: The vPCV vs dPCV endothelial cells were analyzed at 24hpf

extract_protocol:
RNA was isolated using TRIzol with addition of ERCC spike-ins and GenElute LPA (Sigma)
The CEL-Seq protocol (Hashimshony, et al. 2012) was used to amplify and sequence. CEL-Seq multiplexing barocdes with slite modification were used. Each CEL-Seq primer cointained a barcode and a unique moleculare identifier (Teemu, et al. 2011)

value: 24hours post fertilization


title: d_red_ZF_sample_0008


title: RNA-seq of induced control Akata cells (using CNTL GapmeR)_3


title: RNA-seq of induced control Akata cells (using CNTL GapmeR)_2


title: MCF10A Clone D

city: Leuven

first: Anna

last: Sablina

state: Vlaams Brabant

address: O&N4, Herestraat 49, bus 602

department: Center for the Biology of Disease

country: Belgium

institute: VIB/KU Leuven

data_processing:
Illumina Casava software used for basecalling, Quality of sequencing was checked with FastQC (Version-0.10.1), Adapter sequences were trimmed using CutAdapt (Version 1.4.1)
Reads were aligned to Hg19 transcriptome suing TopHat2 (Version- 2.0.11) fr-unstranded read-realign-edit-dist 0 --no-coverage-search
Samtools sorted and convert BAM to Sam
Sam file was provided to HTSeq (Version - 0.6.1)
Genome_build: Hg19
Supplementary_files_format_and_content: Count files were generated using HTSeq; The numbers represent the count of reads per exonic feature

source_name: Epithelial Breast Cell Line

extract_protocol: RNA libraries were prepared for sequencing using standard Illumina protocols

tag: phenotype

value: 8p Wild-type

tag: cell line


title: CRD_12

tag: cell type


title: HIP_4

tag: tissue


title: MCF10A Clone ED7

value: 8p LOH


title: CRD_10


title: CRD_11


title: MCF10A Clone AH4


title: RNA-seq of induced control Akata cells (using CNTL GapmeR)_1


title: CRD_9

extract_protocol: Ventricular cardiomyocytes were isolated from E14.5 transgenic mice expressing the green S/G2/M fluorescent ubiquitination-based cell cycle indicator, “Fucci” (A. Sakaue-Sawano et al., Visualizing spatiotemporal dynamics of multicellular cell-cycle progression. Cell 132, 487–498 (2008)), using a modified protocol of the neomyts cardiomyocyte isolation kit (Cellutron Life Technologies).  The dissociated cell suspensions were resuspended in 500μl of PBS supplemented with 5% FBS solution and sorted by flow cytometryon a FACSAria instrument operating at low pressure (20 psi) using a 100μm nozzle. Samples were sorted individually into 96-well plates containing RT buffer for linear in vitro-transcription T7-based antisense RNA (aRNA) amplification. Collected samples were individually amplified using three rounds of a linear in vitro-transcription-based method.


title: HIP_2


title: V_red_ZF_sample_0007

source_name: Ventral endothelial cells


title: CRD_8


title: V_red_ZF_sample_0011


title: CRD_7


title: CRD_6


title: RNA-seq of uninduced Akata cells_1


title: MCF10A Clone E


title: CRD_4


title: Leydig repC

city: Melbourne

first: Katrina

middle: M

last: Bell

state: Victoria

address: RCH, Flemington Rd, Parkville

country: Australia

institute: MCRI

data_processing:
Illumina base calls
Reads mapped with Tophat2 (v2.0.6), using default parameters with additional options of -G ensemble.gft  --library-type=fr-firststrand   --max-multihits 1
Read counts were summarized to gene features using HTSeq-count, with Ensembl mm10 gene annotation
No lane effects were observed, so the four lane files per sample were merged for differential expression analysis
Only genes with at least 1 count per million in three or more samples were retained for differential expression analysis
Differential analyisis within R statisitcal computing enviroment (v3.0.1), normalisation with TMM and Voom, and differential analysis with Limma
Genome_build: mm10
Supplementary_files_format_and_content: counts_per_Lane_per_Sample.txt: Raw counts of sequencing reads for the gene features, per lane per sample.
Supplementary_files_format_and_content: Interstitial_vs_Sertoli.txt, Leydig_vs_Sertoli.txt, Leydig_vs_Sertoli.txt: Differential analysis results extracted from the limma analysis.

source_name: Enriched Leydig cells

growth_protocol: Embryos were collected from timed matings of Sf1-eGFP strain mice (Beverdam, A. (2006)). Sf1-eGFP litters (12.5 dpc) gonads and the mesonephros were dissected in cold PBS and gonads sexed by presence of Testis cords

extract_protocol:
Total RNA was extracted (Micro RNeasy kit without carrier RNA, Qiagen) from CD31-treated FACS-sorted cells. Each sample represented approximately 10 sorting experiments conducted on different days with 4-10 litters of Sf1-eGFP embryos in each experiment. We prepared sample A, sample B and Sample A+B (a mix of samples A and B), with 100ng of total RNA in each sample.
Libraries were prepared using TruSeq Stranded Total RNA Libraries  (Illumina protocol 15031048 Rev C, Sep 2012), with multiplexing, Ribosomal depletion,with all sample run over the 4 rapid lanes

treatment_protocol: Gonads were enzymatically dissociated using 0.25% Trypsin EDTA (Gibco) or TryplE (Gibco) with 5 U/ml DNase1 (Sigma) for 20min at 37 °C and then mechanically dissociated using 18- and 23-gauge syringes. 1 mL of PBS was added to the cells which were then pelleted by centrifugation (3000 rpm at 4 °C for 10 min); after supernatant was removed the cells were resuspended in 400 μL of ice-cold PBS and stored on ice. Cells were then incubated with anti-SSEA1-PE (#FAB2155P, R&D Systems, specific for germ cells) or anti-CD31-APC (#551262, Becton Dickinson, specific for germ and endothelial cells) antibody for 20 min.  The former was used in characterization of cell population studies whilst the later was used to remove germ and endothelial cells prior to RNA-Seq.  Cells were fractionated using a BD FACSAria Cell Sorter. Cell populations were collected in PBS and kept on ice before further processing

value: gonad


title: Leydig repB


title: Interstitial repC

source_name: Enriched Interstitial cells


title: Interstitial repA


title: Interstitial repB


title: CRD_2


title: Leydig repA


title: Sertoli repB

source_name: Enriched Sertoli cells


title: CRD_3


title: Sertoli repA


title: BAT_13

description: BAT 3-1

source_name: Interscapular brown adipose; Adipocyte

growth_protocol: Samples were extracted from mouse and cultured for one day.

extract_protocol:
Individual cells identified by morphology as brown adipocytes were collected by patch pipette.  Collected samples were individually amplified using three rounds of a linear in vitro-transcription-based method.
Samples were prepared for multiplexed paired-end sequencing using the Illumina TruSeq system according to manufacturer instructions.

value: embryonic day 17.5

value: Interscapular brown adipose

value: Adipocyte


title: BAT_12

description: BAT 3-3


title: BAT_11

description: BAT 3-5


title: CRD_1


title: Sertoli repC


title: BAT_10

description: BAT 2-2


title: RNA-seq of uninduced Akata cells_2


title: RNA-seq of uninduced Akata cells_3


title: BAT_7


title: BAT_9

description: BAT 2-1


title: BAT_5

description: BAT 2-4


title: BAT_4

description: BAT 3-4


title: CRD_5


title: BAT_3


title: BAT_6


title: BAT_2


title: BAT_1


title: P14 mouse retina 4

status: Public on May 20 2015

city: Boston

first: Evan

last: Macosko

state: MA

address: 77 Avenue Louis Pasteur, NRB 260

department: Genetics

institute: Harvard Medical School

description: Drop-Seq

data_processing:
Base calls performed with bcl2fastq2.15.
Read 2 was aligned with Star v2.4.0.
Each aligned read was tagged with its mate-pair UMI and cell barcode.
For replicates 4-6, human reads from spiked-in HEK cells (0.5%) were removed from BAMs and digital expression files.
Each aligned exonic read was tagged with a gene name.
A digital expression matrix was built by counting the number of unique UMIs per gene within each cell; columns are cells, and rows are genes.
The first inflection point was estimated on a cumulative sum plot of the digital expression matrix to determine the number of cells in the sample.
Samples 1-7 -- prepared from P14 mouse retinas on four separate days -- were merged together into a single matrix.
Genome_build: mm10 (GRCm38) Supplementary_files_format_and_content: Digital expression matrices. Compressed, flat text files with tab delimiters.

source_name: Mus musculus retina, P14

extract_protocol:
Single-cell suspensions were processed through Drop-Seq to generate single-cell cDNA libraries attached to microbeads.  For replicates 4-6, 0.5% human HEK cells were included.
Microbeads were counted, and amplified by PCR, and the 3' end of the cDNA prepared for sequencing using a modified Nextera XT protocol.

tag: strain/background

tag: genotype/variation

value: wild-type

value: retina


title: P14 mouse retina 2

description: Drop-Seq

data_processing:
Base calls performed with bcl2fastq2.15.
Read 2 was aligned with Star v2.4.0.
Each aligned read was tagged with its mate-pair UMI and cell barcode.
Each aligned exonic read was tagged with a gene name.
A digital expression matrix was built by counting the number of unique UMIs per gene within each cell; columns are cells, and rows are genes.
The first inflection point was estimated on a cumulative sum plot of the digital expression matrix to determine the number of cells in the sample.
Samples 1-7 -- prepared from P14 mouse retinas on multiple separate days -- were merged together into a single matrix. Merged DGE file from all 7 samples generated.  log(1+10,000*(DGE normalized to total transcripts per cell)) calculated on DGE.
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: Digital expression matrices. Compressed, flat text files with tab delimiters.

extract_protocol:
Single-cell suspensions were processed through Drop-Seq to generate single-cell cDNA libraries attached to microbeads.
Microbeads were counted, and amplified by PCR, and the 3' end of the cDNA prepared for sequencing using a modified Nextera XT protocol.


title: P14 mouse retina 6

description: Drop-Seq

data_processing:
Base calls performed with bcl2fastq2.15.
Read 2 was aligned with Star v2.4.0. Each aligned read was tagged with its mate-pair UMI and cell barcode.
For replicates 4-6, human reads from spiked-in HEK cells (0.5%) were removed from BAMs and digital expression files.
Each aligned exonic read was tagged with a gene name.
A digital expression matrix was built by counting the number of unique UMIs per gene within each cell; columns are cells, and rows are genes. The first inflection point was estimated on a cumulative sum plot of the digital expression matrix to determine the number of cells in the sample.
Samples 1-7 -- prepared from P14 mouse retinas on four separate days -- were merged together into a single matrix.
Genome_build: mm10 (GRCm38) Supplementary_files_format_and_content: Digital expression matrices.
Compressed, flat text files with tab delimiters.

extract_protocol:
Single-cell suspensions were processed through Drop-Seq to generate single-cell cDNA libraries attached to microbeads.
For replicates 4-6, 0.5% human HEK cells were included.
Microbeads were counted, and amplified by PCR, and the 3' end of the cDNA prepared for sequencing using a modified Nextera XT protocol.


title: P14 mouse retina 5

description: Drop-Seq

data_processing: Base calls performed with bcl2fastq2.15. Read 2 was aligned with Star v2.4.0. Each aligned read was tagged with its mate-pair UMI and cell barcode. For replicates 4-6, human reads from spiked-in HEK cells (0.5%) were removed from BAMs and digital expression files. Each aligned exonic read was tagged with a gene name. A digital expression matrix was built by counting the number of unique UMIs per gene within each cell; columns are cells, and rows are genes. The first inflection point was estimated on a cumulative sum plot of the digital expression matrix to determine the number of cells in the sample. Samples 1-7 -- prepared from P14 mouse retinas on four separate days -- were merged together into a single matrix. Genome_build: mm10 (GRCm38) Supplementary_files_format_and_content: Digital expression matrices. Compressed, flat text files with tab delimiters.


title: P14 mouse retina 3

description: Drop-Seq

data_processing:
Base calls performed with bcl2fastq2.15.
Read 2 was aligned with Star v2.4.0.
Each aligned read was tagged with its mate-pair UMI and cell barcode.
Each aligned exonic read was tagged with a gene name.
A digital expression matrix was built by counting the number of unique UMIs per gene within each cell; columns are cells, and rows are genes.
The first inflection point was estimated on a cumulative sum plot of the digital expression matrix to determine the number of cells in the sample.
Samples 1-7 -- prepared from P14 mouse retinas on multiple separate days -- were merged together into a single matrix.  Merged DGE file from all 7 samples generated.  log(1+10,000*(DGE normalized to total transcripts per cell)) calculated on DGE.
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: Digital expression matrices. Compressed, flat text files with tab delimiters.


title: BAT_8

description: BAT 3-2


title: P14 mouse retina 1

description: Drop-Seq


title: shAFF4 rep1

city: Berkeley

first: Qiang

last: Zhou

address: 575 LKS, UC Berkeley

department: MCB

institute: UC Berkeley

data_processing:
Standard FASTQ files were outputed by CASAVA_v1.8.0
All sequencing reads were aligned to the Homo sapiens reference genome (UCSC hg19 release) and RefSeq reference transcriptiome (ftp://ftp.ncbi.nih.gov/refseq) using Tophat version 2.0.11
Cufflinks version 2.2.1 were used to quantify the mRNA abundance of each gene. The following non-default options were used with cufflinks: --frag-bias-correct --multi-read-correct
We used RankProd to perform differential expression analysis between AFF1/4 knockdown and GFP knockdown samples
Genome_build: hg19
Supplementary_files_format_and_content: mRNA abundance are represented by Fragments Per Kilobase of exon model per Million mapped fragments, referred to as FPKM

growth_protocol: HeLa cells were cultured in DMEM supplemented with 10% FBS. Cells were maintained at 37 °C under 5% CO2

extract_protocol:
Total RNA was extracted from each KD cells and depleted of rRNA with Ribo-zero (Illumina)
rRNA depleted samples were converted into multiplexed libraries using mRNA-seq Trueseq Kit following the manufacturer’s instructions (Illumina)

treatment_protocol: HeLa cells were infected with lentivirus expressing shRNA against GDP, AFF1 or AFF4. Total RNA was extracted with the RNeasy kit from Qiagen and residual DNA was digested with RNase-free DNase I

value: HeLa

tag: shRNA expression

value: shRNA against AFF4


title: shAFF1 rep2

value: shRNA against AFF1


title: mouse ES cells, sample 2, tech Rep 2 (3.5k cells)

first: Allon

last: Klein

address: 200 Longwood Avenue

department: Systems Biology

description: mouse ES cells biological replicate (different passage) - technical replicate 2

data_processing:
Reads were first filtered based on presence in read 1 of two sample barcode components separated by the W1 adaptor sequence (GAGTGATTGCTTGTGACGCCTT)
Read 2 was then trimmed using Trimomatic (5) (version 0.30; parameters: LEADING:28 SLIDINGWINDOW:4:20  MINLEN:19).
Barcodes for each read were matched against a list of the 3842 pre-determined barcodes, and errors of up to two nucleotides mismatch were corrected. Reads with a barcode separated by more than two nucleotides from the reference list were discarded. The reads were then split into barcode-specific files for mapping and UMI filtering.
The trimmed reads were aligned using Bowtie (version 0.12.0, parameters: -n 1 -l 15 -e 300 -m 200 -best -strata -a) to the mouse transcriptome. The reference transcriptome was built using all annotated transcripts (extended with a 125bp poly-A tail) from the UCSC mm10 genome assembly.
We used a custom Python and PySAM script to process mapped reads into counts of UMI-filtered transcripts per gene.
Genome_build: mm10 for ES cells; hg19 for K562 cells.
Supplementary_files_format_and_content: Columns = cells; rows = genes. Column 1 contains gene symbols. Values show unique molecular identifier (UMI)-filtered counts per cell detected in the raw data. No normalization is performed.

source_name: mouse 129/Ola strain called IB10 (subcloned from E14)

growth_protocol: The ES cells were maintained in ESC base media inside culture flasks pre-coated with gelatin at 37°C in 5% CO2 and 60-80% humidity at density ~3 × 10^5 cells ml–1. The ESC media contained phenol red free DMEM (Gibco), supplemented with 15% (v/v) fetal bovine serum (Gibco), 2 mM L-glutamine, 1x MEM non-essential amino acids (Gibco), 1% (v/v) penicillin-streptomycin antibiotics, 110 µM b-mercaptoethanol, 100 µM sodium pyruvate.

extract_protocol:
Cells were encapsulated into droplets on ice and lysed  in the 4nL microfluidic droplets using a final concentration of 0.4% NP-40. Single cell lysates were subject to reverse transcription at 50°C without purification of RNA.
Cells were barcoded using the db-Seq platform, which makes use of the CEL-Seq protocol for library construction (Hashimshony et al., Cell Reports 2011).

treatment_protocol: In the undifferentiated state the ESC base media was supplemented with Leukemia Inhibitory Factor (LIF) at final concentration 1000 U/mL and for unguided mES differentiation the media was without LIF. Within 2 days of LIF withdrawal the culture experienced significant morphological changes indicating the differentiation of mES cells.

value: embryonic stem cell (ES)

tag: days post-lif

tag: number cells in sample


title: mouse ES cells, sample 2, tech Rep 1 (2.5k cells)

description: mouse ES cells biological replicate (different passage) - technical replicate 1


title: P14 mouse retina 7

description: Drop-Seq


title: shGFP rep2

value: shRNA against GFP


title: mouse ES cells LIF-, 7 days (799 cells)


title: shGFP rep1


title: K0519Sr

city: Houston

first: Horatiu

last: Voicu

address: One Baylor Plaza

institute: Baylor College of Medicine

data_processing:
Basecalls performed using CASAVA version 1.8.2
RNA-Seq reads were trimmed for adaptor sequence, and  aligned to hg19 using TopHat v2.0.8b
HTSeq-0.5.3p9 was used to generate counts for each gene and edgeR Bioconductor package was used for analysis
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text file include gene counts for all samples

source_name: Renal Cell Carcinoma

extract_protocol:
Total cellular RNA was isolated from core punches using the Epicentre  MasterPure™ Complete DNA and RNA Purification Kit (Illumina Inc., San Diego, CA) according to the manufacturer’s protocol following de-paraffinization and proteinase K treatment. RNA was quantified using the  Picogreen assay.
cDNA was made from total RNA using the NuGEN Ovation RNA-Seq FFPE System (Part # 7150-08). Libraries were prepared for sequencing using cDNA into the Illumina TruSeq DNA-seq protocol (Part #: FC-121-2001). Both parts followed the standard NuGEN and Illumina protocols.

value: S

tag: pretreatment

tag: grade

value: Sarcomatoid

tag: Stage

value: IV


title: K0517S

tag: sample type

value: III


title: K0516E

value: E

value: Epithelioid


title: K0523E


title: K0521Er


title: K0518E


title: K0520R

value: R

value: Rhabdoid


title: K0514Er


title: K0515S


title: K0507S


title: K0513R


title: K0508E


title: shAFF4 rep2


title: K0505R

value: Sutent


title: K0503Er


title: shAFF1 rep1


title: K0504Sr


title: K0502R


title: K0501Sr


title: K0506Er


title: K06-P04

value: E*


title: K06-P03


title: K06-P02


title: mouse ES cells LIF-,4 days (682 cells)


title: mouse ES cells LIF-, 2 days (301 cells)


title: K06-P01


title: K06-P05


title: second_pregnancy

city: Guangzhou

first: Ji-Long

last: Liu

address: 483 Wushan Rd

institute: South China Agricultural University

data_processing:
A computational pipeline was used to process the sequencing data. Raw sequence data in fastq format were filtered to remove reads with more than 10% unknown nucleotides. Clean reads were mapped to mouse reference genome mm9 with Tophat v1.4.0 allowing no more than two mismatches. The expected fragment length was set at 200 ± 50 bp. The mapped reads were assembled into genes and transcripts by Cufflinks v1.3.0. Gene models were downloaded from the UCSC RefSeq annotation, which was used to generate a Cufflinks-compatible GTF format file by an in-house PERL script. Gene expression levels were calculated using fragments per kilobase of transcript per million mapped fragments (FPKM) in Cufflinks.
Genome_build: mm9
Supplementary_files_format_and_content: Tab-delimited text files include RPKM values for each sample. The first column is gene name and the second column is RPKM value.

source_name: uterus collected on day 8 of second pregnancy

growth_protocol: CD-1 mice were caged in a controlled environment with a 14 h light and 10 h dark cycle. A total of 30 age- and weight-matched adult virgin females were recruited for this study. The experiment started with mating these females with fertile males. Successful mating was confirmed by the observation of a vaginal plug. Subsequently, pregnant mice were allowed to give birth and raise their litters to weaning, while non-pregnant ones served as controls. Finally, mice during first pregnancy and second pregnancy were obtained at the same time by mating with fertile males. The mating partners were fixed throughout the experiment. Decidual samples were collected on day 8 of pregnancy (day 1=day of vaginal plug). Fetal tissues were dissected out and discarded under a stereomicroscope.

extract_protocol: Total RNA was isolated using TRIZOL reagent (Invitrogen). RNA purity was assessed using the ND-1000 spectrophotometer (Nanodrop Technologies). For each total RNA sample, the A260/A280 ratio was greater than 1.8 and A260/A230 ratio greater than 2.0. RNA integrity was evaluated using the Agilent 2200 TapeStation. All total RNA samples had a RINe value above 7.0. Oligo-(dT) magnetic beads were used to isolate poly-(A)+ mRNA from total RNA. The resulting mRNA was fragmented to approximately 200 bp in fragmentation buffer. Subsequently, these short fragments were used as templates for first strand and second strand cDNA synthesis. The double-stranded cDNA fragments were purified, end-repaired and then ligated to sequencing adapters. After purification, suitable fragments were enriched by PCR amplification according to instructions of TruSeq® RNA LT/HT Sample Prep Kit (Illumina).

value: uterus

tag: group

tag: strain


title: first_pregnancy

source_name: uterus collected on day 8 of first pregnancy


title: mouse ES cells, sample 1 (935 cells)

description:
mouse ES cells
Illumina HiSeq 2500 + NextSeq (merged)